CRUISE REPORT: P15S
(Updated MAY 2017)





Highlights

 

                          Cruise Summary Information

 
               Section Designation  P15S
Expedition designation (ExpoCodes)  096U20160426
                  Chief Scientists  Bernadette Sloyan (leg 1), 
                                    Susan Wijffles (leg 2)
                             Dates  2016 APR 26 - 2016 JUN 22
                              Ship  R/V Investigator
                     Ports of call  Hobart - Wellington (NZ) - Lautoka (Fiji)

                                                45° 29' 49"S
             Geographic Boundaries  149°25'41"E              168°36'57"W
                                                66° 19' 55"S

                          Stations  140
      Floats and drifters deployed  Argo: 25, Deep Argo: 2, bio-geochemical: 13, 
                                    shear and BGC: 3
    Moorings deployed or recovered  0

                             Contact Information:

                 Bernadette Sloyan             Susan Wijffles
            Bernadette.Sloyan@cisro.au    Susan.Wijffels@cisro.au

 
 
















RV Investigator Voyage Summary

Voyage #:              IN2016_V03
Voyage title:          Monitoring Ocean Change and Variability along 170°W 
                       from the ice edge to the equator
Mobilisation:          Hobart,  Tuesday 26 April, 2016
Depart Leg 1:          Hobart, 2000 Tuesday 26 April, 2016
Arrive Leg 1:          Wellington (NZ): 1100 Thursday 26 May
Depart Leg 2:          Wellington (NZ): 1230, Friday 27 May, 2016
Arrive Leg 2:          Lautoka (Fiji), 0800 Wednesday, 30 June, 2016
Demobilisation:        Hobart, Thursday July 14th, Friday July 15th & Monday 
                       July 18th, 2016
Voyage Manager Leg 1:  Don McKenzie     Contact details: Don.Mckenzie@csiro.au
Voyage Manager Leg 2:  Stephen Thomas   Contact details: Stephen.Thomas@csiro.au
Chief Scientist Leg 1: Bernadette Sloyan
Affiliation:           CSIRO Oceans     Contact details: Bernadette.Sloyan@csiro.au
                       and Atmosphere
Chief Scientist Leg 2: Susan Wijffels
Affiliation:           CSIRO Oceans     Contact details: Susan.Wijffels@csiro.au
                       and Atmosphere
Principal              Bernadette Sloyan, Susan Wijffels, Bronte Tilbrook, Lev
Investigators:         Bodrossy, Bec Cowley
Project name:          As above
Affiliation:           CSIRO Oceans     Contact details: Susan.Wijffels@csiro.au
                       and Atmosphere                    Bronte.tilbrook@csiro.au 
                                                         Lev.Bodrossy@csiro.au 
                                                         Rebecca.Cowley@csiro.au
Principal              Mark Warner, John Bullister
Investigators:
Project name:          As above         Contact details: warner@u.washington.edu
Affiliation:           U. Washington, 
                       Seattle, WA USA
                       NOAA-PMEL
Supplementary Project
Principal              Alex Forrest, University of Tasmania
Investigator:
Project name:          Working from the other side: facing the challenges of 
                       under-ice for autonomous navigation in Antarctica
Affiliation:           AMC,             Contact details:	Email: Alex.Forrest@amc.edu.au
                       University of 
                       Tasmania 

 

Scientific objectives

Sloyan, Wijffels, Cowley, Tilbrook, Bullister, Warner, Bodrossy:

The full suite of key ocean parameters and the deep ocean heat and carbon reservoirs 
remain poorly measured. This proposal will complete full-depth, high-precision 
hydrographic, carbon, and tracer measurements, along 170°W from the sea-ice edge to 
the equator, to monitor and detect ocean variability and change including changes in 
the carbonate chemistry associated with acidification. The line comprises the line 
P15S that is part of the international GO-SHIP repeat global survey network (www.go-
ship.org).

These data, together with other observational data and numerical models, will allow 
for the detection and attribution of ocean change and variability and to assess the 
impact of the ocean on climate variability.

This hydrographic section will monitor ocean change and variability by:

1. Directly measuring the full suite of ocean water properties (temperature, 
   salinity, velocity, nutrients, tracers and ocean mixing) at high vertical 
   and spatial resolution throughout the entire water column and in the deep 
   boundary currents, contributing to the international GO-SHIP program.
2. Providing high precision biogeochemical measurements to monitor changes in 
   ocean carbon storage and oxygen concentrations, contributing to the IOCCP 
   international program to monitor the global carbon budget.
3. Directly measure ocean mixing to improve our knowledge of the ocean 
   Meridional Overturning Circulation.
4. Provide high precision baseline data to calibrate the Argo array, XBT 
   program, and other autonomous observations (ocean gliders, moorings and 
   satellites) in the vicinity of the section.
5. Deploy Argo floats for the core mission and contributions to the 
   international SOCCOM project.
6. Obtain side-by-side CTD/XBT data for the assessment of bias errors in XBT 
   measurements.


Voyage objectives

Sloyan, Wijffels, Cowley, Tilbrook, Warner, Bullister, Bodrossy:

The primary voyage objective is to obtain a repeat occupation of the 155 full-depth 
CTD and Niskin casts that comprise the GO-SHIP P15S section, with chemistry 
performed on water collected at 36 bottle levels. We measured temperature, salinity, 
pressure, oxygen, fluorometry, shear and micro-scale temperature continuously, and 
the major nutrients, oxygen, salinity, CFC and carbon components discretely via 
chemical analysis on board. Small amounts of material will be filtered and stored 
for genomic analyses back on land. CSIRO has completed this line twice before and 
international groups have completed similar work along lines further east. The work 
plan and timings are based on these past voyages.

Argo float deployments will also be carried out – usually when just leaving a CTD 
station (SOCCOM floats) or during transit (we may slow the ship speed slightly). 
These will be over the ship’s stern (preferred).

 
Results

2016 occupation of the P15S Hydrographic section: Overall delivery against the 
original plan was around 90%.

Of the 155 stations originally planned, before leaving port, the plan was scaled 
back to 150 stations due to emerging information about the time required for the 
Wellington port call and a recommended reduction in the planned transit speeds from 
12 to 11 knots. However, two extra ship days were provided later to compensate for 
time lost due to winch/wire issues. Ultimately of the original 155, we achieved 
occupation of 140 stations. Ten stations were abandoned on Leg 1, most due to wire 
or termination damage, one to weather and one to sea ice. One station was abandoned 
on Leg 2 due to a winch brake failure, ongoing winch alarm and wrap laying issues. 
Besides the CTD sensor traces, most casts provided Niskin bottle water samples for 
on board analyses. A few stations did not collect samples due to electrical damage 
to the CTD cable and subsequent loss of communication to the rosette.

The heave compensation system (only used during Leg 2) on the CTD winches appears to 
be a key factor which enabled the completion of the section without further wire 
damage. It also has a profound and beneficial impact on the raw sensor streams, 
almost entirely removing package flow contamination in these data. The other key 
event was the near-loss of the entire frame, instruments and our main CTD wire due 
to a winch break failure at station 83. The safe recovery of both the wire and 
instrument package by the ship’s crew was nothing short of a miracle. The winch was 
rebuilt, the cable trimmed, spooled out and de- torqued, and the system was put back 
into service. This was voyage saving, as we later learned that our spare CTD (#22) 
had an unrepairable leak and there were no other spare CTD buses on board.

CTD traces: The performance of the CTD system was mixed, but the issues are largely 
recoverable through post-calibration. While the sensors were generally stable 
throughout the voyage, large and uncharacteristic offsets were found between the 
sensor behaviour at sea (compared to excellent bottle salts) and in the calibration 
laboratory. This issue remains unexplained. Two secondary C-cells were somehow 
damaged and not working within specifications. Despite this, due to the sensor 
stability, having dual sensor lines, and the high quality of the bottle salts and 
through assistance from SeaBird, the final calibrated data will be excellent. See 
Appendix 1 for details on C-cell troubleshooting. Table 2 has the full list of CTD 
stations occupied.

Optics: On leg 1 (stations 1-50), and in support of SOCCOM (see below), a University 
of Maine Wetlabs FLBBRTD (SN3698) was installed onto the 9plus analogue channels, 
measuring the optical parameters fluorescence, backscatter, Photosynthetically 
Active Radiance (PAR) and light transmission. This was removed in Wellington. From 
stations 56-140, the MNF’s Chelsea Aquatracker was fitted onto the frame, returning 
fluorescence, backscatter, and light transmission.

Hydrochemical Data: Laboratory results for the major nutrients, oxygen and salinity, 
from the CSIRO hydrochemistry team are excellent and will meet GO-SHIP standards. 
This is the best deep section data set this team has ever delivered and it is an 
outstanding effort. The team kept up with the intense throughput associated with 
processing 36 bottle samples per cast. The good instrumentation, standards used and 
very stable laboratory temperatures were also vital ingredients, along with the 
teams’ dedication and thorough preparation.

Anthropogenic trace gases: The measurements of the chlorofluorocarbon-11 (CFC-11), 
CFC-12 and sulphur hexafluoride (SF6) by the University of Washington/NOAA-PMEL team 
are of high quality -2187 samples were collected in coordination with the carbon 
chemistry team. See Appendix 2 for details and highlights.

Carbon chemistry: A total of 2625 water samples were analysed for total dissolved 
inorganic carbon from a subset of the Niskin water samples, with an additional 269 
duplicate samples analysed. Also, 2628 seawater samples were analysed for total 
alkalinity, plus 224 duplicate samples. The data are deemed of very high quality.  
See Appendix 3 for details and highlights from the carbon team.

Helium Data: Seawater was collected from some of the Niskin bottles at 20 stations 
to produce 219 duplicate 10-inch long sealed (crimped) copper tubes for future 
analysis of helium isotopes onshore. Originally we had planned to sample 22 
stations, however the sea ice edge did not permit sampling as far as 68°S. At CTD 
station 2 the helium crimping equipment froze. We relocated the crimper to the dry-
clean laboratory and helium sampling was completed out of the normal water sampling 
order. See Appendix 9 for an overview of the helium sampling.

Velocity Shear: Data was collected via a two unit Lowered Acoustic Doppler Current 
profiler system on nearly all casts. On some casts, data download delays meant we 
had to abandon those data in order to avoid a schedule slip. The data are also 
somewhat compromised by two factors:

• Heading on the master (150kHz) instrument was bad
• One beam on this instrument also failed.

However, we believe these data will be still very useful after processing for mixing 
and flow studies. See Appendix 10 for further details.

Temperature microstructure: On nearly all casts, fast (100Hz) temperature and 
package motion were measured via Chi-pods. This data can be used to determine ocean 
mixing and dissipation rates. Typically, 2 instruments sampled the waters at the 
leading edge of the frame (above and below). Data were downloaded every second day 
or as needed.  See Appendix 4 for more detail.

Underway velocity: Both RDI Ocean Surveyors (150kHz and 75kHz) acoustic Doppler 
profilers (ADCPs) were run continuously for the voyage. The raw data looks good, and 
will likely underpin an excellent final velocity data set. The OS150 alignment error 
used on acquisition was wrong and the correct value is currently unknown since the 
instrument was refit in October 2015. This requires a new bottom tracking data set 
to be collected for calibration. There is a heading error in the processing for the 
Leg 1 data that also remains unresolved. The acquisition system appeared to drop 
navigation data intermittently, possibly due to buffer limits. We believe these can 
all be recovered in post processing. Both ringing and bubble contamination afflict 
the upper bins, but their impact was partially reduced by extending the drop keel to 
its medium setting.

eXpendable BathyThermograph side-by-side data: At several groups of station, two 
teams would drop eXpendable BathyThermograph (XBT) probes during the upper 1000db of 
the downcast. The purpose is to diagnose and quantify depth and temperature biases 
in XBT types and ages to help improve their use for climate studies. Several probe 
types and temperature regimes were covered. In total 295 probes were deployed. See 
Appendix 5 for details.

Nitrogen processes, budgets, plankton and bacterial phylogeny: The data arising from 
this study will be a major source of new information on N2 fixation rates and the 
controls of the N-cycle contributing to regional primary productivity in the 
different water masses along the P15 GO-SHIP line. They will fill in a major 
knowledge gap in regards to N and C cycling in the world open oceans. Most of these 
data require substation shore-based analyses.
Samples that were taken for:

• Picoplankton analysis, using flowcytometry back on land
• Chlorophyll a and phytoplankton pigment analysis, using HPLC back on land
• DNA analyses using targeted functional gene expression analyses and high-
  throughput sequencing back on land
• Primary productivity, following isotopic tracer incorporation into the 
  particulated matter, using stable isotopes 13C, aboard using incubation bins
• Dissolved inorganic nitrogen uptake measurements, using standard 15N 
  protocols, aboard using incubation bins
• N2-fixation rates, using 15N gas as an injected tracer to measure fixation 
  rates, aboard using incubation bins
• Nitrification rates

See Appendix 6 for details.

Profiling Float deployments: The Argo community joined together to take full 
advantage of the relatively rare chance to deploy profiling floats into the far 
Southern Ocean with a shipped-based high quality GO-SHIP deployment profile with 
full chemistry for calibration. The aft laboratory was literally filled with floats 
of various types when it left Hobart. In total we deployed 43 profilers – 25 floats 
for the core Argo mission, 2 prototype deep Argo floats, 13 bio-geochemical floats 
for the Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) 
experiment. In addition, 3 non- Argo shear and BGC floats were deployed for the 
University of Tasmania. Floats were deployed on leaving a completed station or 
during transit. At each SOCCOM float deployment CTD, samples were collected for pH 
sample for depths to 2000m, up to 24 per cast plus 2 duplicates at any of those 
depths (0.8 litres each). High Pressure Liquid Chromatograph samples at surface and 
chlorophyll max, plus a duplicate at one of those depths (1-2 litres each). 
Particulate Organic Carbon sample at surface and chlorophyll max, plus a duplicate 
at one of those depths (2-3 litres each). These samples were sent back to the US for 
shore-based analysis.

The details of the float deployments can be found in Table 1.

Deep Argo CTD testing: Two prototype SBE-61 internally recording CTDs were attached 
to the frame above the SBE 9plus intakes. The SBE-61 is being developed for use in 
the deep Argo program and is still being tested and refined. The SBE’s were on for 
all 140 CTD casts, and survived the sea floor impact on station 83. The data will be 
returned for analysis by SeaBird Electronics, Seattle.

Inertial Navigation System test (U. Tasmania piggy back project): The PHINS 
(PHotonic Inertial Navigation System) is a device capable of measuring all 
navigational parameters associated with the motion of a vehicle (e.g. heading, 
speed, position, and attitude), and is to be used in Autonomous Underwater Vehicle 
navigation and control. This cruise provided the perfect opportunity to test the 
behaviour of the PHINS technology at a range of different latitudes, with the aim of 
quantifying the effect of latitude on the accuracy of heading and position. To this 
end, the PHINS was operated continuously, with a repeating 12 hour testing regime, 
for the duration of the voyage. See Appendix 7 for details.

Atmospheric Chemistry and Aerosols: During the voyage, instrumentation was run 
continuously to investigate the chemical composition, size distribution, optical 
properties and cloud nucleating properties of marine aerosol over the southern 
hemisphere. These parameters are important in the quantification of regional 
contributions of aerosols to radiative forcing, and will help to improve 
meteorological and climate change models. With a few exceptions, the instrumentation 
has operated with only minor issues and a wealth of data has been successfully 
collected. See Appendix 8

Graduate student training: In addition to the science objectives, we were able to 
offer a seagoing observational experience to several graduate students in marine 
science from Australia and New Zealand. As well as assisting with the CTD and water 
sampling, the students undertook small projects in data analysis, and helped trouble 
shoot the systems on the ship. We believe this was a terrific and successful 
learning experience for these students, in the challenges of observational science 
and physical oceanography.

 

VOYAGE NARRATIVE

Leg 1- Narrative by Bernadette Sloyan

Tuesday 26 April – Tuesday 3 May 2016

We departed Hobart on Tuesday 26 April at 2000 and began our transit to our first 
plan CTD stations of the P15S hydrographic section (170W, 68S). On the transit we 
stopped to completed a test CTD station (149 25.704’E, 45 29.813’S) and all CTD 
volunteers were shown how to run the CTD console and instructed on water sampling 
method for carbon, oxygen, helium, nutrients and salt. The CTD watches were 
established and everyone settled into their respective watches.

We provided a link to the Master of the sea ice images that were being update daily 
by Benoit Legrassy (CSIRO). The Master found these images very useful for navigation 
during the last few days of the transit, determining the position of the northern 
edge of the sea-ice and likely location of our most southern station.

The weather during the transit was relatively calm and we averaged 11-12 knots. 

On the transit 12 Argo floats were deployed (see Table 1).

Wednesday 4 May – Sunday 8 May 2016

As Investigator approached the ice edge the outside air temperature decreased to 
sub-zero temperatures. We consulted with Steve Rintoul, Nathan Bindoff and Mark 
Rosenberg regarding strategies to mitigate freezing of CTD sensors and Niskin 
bottles. Following their advice, we will dried the conductivity sensors prior to 
deployment and opened the CTD door at the last possible moment.

We started CTD operation on CTD Winch 2 (outboard) and using CTD 20. We arrived at 
our first CTD (CTD 002) location (169 59.97 W, 66 20.08 S) at 8pm. Air temperature 
was -17.0C and decreasing. Condition were calm with less than 10 knots of wind. The 
CTD was deployed smoothly and the station completed successfully. The CTD upon 
removal from the water snapped froze – frozen sensor, tubing, and spigots. In the 
CTD room pipes (freshwater and salt) and the Helium crimping equipment froze during 
the duration of the door being open. We had to use a hair dryer to defrost the 
niskin spigots. Once the pipes and taps defrosted water leaked from cracks and all 
water valves to the CTD room were isolated. The CTD water samplers were very cold by 
the end of sampling. No damage was done to the CTD sensors, Niskins, or rosette.

The current configuration of the CTD room is not suitable for sub-zero CTD 
operations. A heater needs to added to ensure we raise the room above 0°C.
After CTD 002, we continued south in anticipation of a CTD station further south. 
During the transit the wind increased to 40 knots and spray froze when hitting the 
ships superstructure. Sea-ice was seen on the surface. At 5am Thursday morning we 
decided with sea-ice in the area and strong winds it was unlikely we would be able 
to complete a CTD station further south. Therefore, we turned north and CTD 002 
became our most southern CTD station.

CTD stations, 003, 004, 005 and 006 were completed without incident, although CTD 
005 was undertaken in a confused sea. We completed our first mechanical re-
termination at the end of station 005.

On Saturday (7 May) as we prepared to deploy CTD 007 the CTD winch wire jumped the 
pulley and was jammed between the winch cheeks. The wire required an electrical re-
termination. We moved to CTD Winch 1 in an attempt to continue CTD operations.

At 350 m the CTD deck box sounded an alarm indicating loss of communication with the 
CTD. The deck box was turned off and the rosette was returned to the deck. Upon 
recovery the wire was tested and found to be damaged. We now need to re-terminate 
both CTD wires. With both CTD wires requiring re-termination we were unable to 
undertake CTDs for 24 hours. Given the delay we abandoned CTD 007 and made a slow 
transit to CTD 008. During the transit, we tested the deck box using the spare CTD; 
It tested okay. The fuses were examined and they had not blown. Water was found in 
both cables and over 500m was cut from each cable.

On Sunday as we prepared the CTD (CTD 008) ready for deployment the deck unit failed 
and was turned off. On inspection the transformer on the deck unit had failed and 
CTD instrument (CTD 20) was now faulty. The problem was sourced to an incorrect fuse 
in the unit which was corrected.

Working on CTD winch 2 and the spare CTD (CTD 22) we completed CTD 008 and 009.

CTD 010 was deployed but at 2000 m the deck box alarmed and blew a fuse. The broken 
fuse was replaced but blew immediately. The CTD/rosette package was recovered. Upon 
recovery we found that the electrical termination failed. We now have to re- 
terminate CTD winch 2.

For CTD 011 we moved to the CTD winch 1 and completed the abandoned station 10. No 
LADCP data were taken as the connecting cable was broken. The MNF electronic 
technicians repaired the CTD 20 unit. We now have 2 working CTD units.

At the end of most of these stations either an Argo or SOCCOM float was deployed.

Monday 9 May – Sunday 15 May 2016

CTD 012 and 013 were completed. On CTD 014 at 3300 dbar on the up-cast we lost 
communication to CTD. The station was aborted and we hauled the CTD/rosette back to 
the surface. Another broken electrical termination. Only bottom water samples were 
collected.

We now have another 24-hour delay as both CTD winch wires require an electrical re-
termination.

By Wednesday we were back in the water and completed CTD 015. On CTD 016 we again 
lost communication to the CTD package at 7 dbar on the downcast. We abandoned the 
station.

We switched to CTD winch 2 (outboard) and deployed the wire with a 35 Kg weight. The 
electrical termination had failed on return. Now have two winch cables that need re-
termination. We moved to cold terminations. These take 2-3 hours to be completed.

CTD 017 was further delayed due to weather (12 hours). The station was eventually 
completed. Niskin bottles 2-7 failed to close. Signal to close was sent but no reply 
received. Alarm sounded as CTD/rosette was returned to deck when a cable distortion 
went over a sieve. Electrical termination had failed on deck.

For CTD 018 we moved to CTD winch 2 (cold mould) and completed the station, however 
the bottles failed to fire; No bottle samples were collected. A CTD cable was 
changed and the carousel tested, bottle non- firing issue was fixed.

Moving to cold mould electrical termination increased the success rate of CTD 
stations. During Saturday we completed CTD stations 019 through to 022.

We had further issues at CTD 023. We had two attempts at starting the station. On 
the first the CTD deck unit alarmed just as the rosette entered the water. The 
rosette was recovered and all electrical connections were tested; these were all 
working. We then tested all connections by spraying water on the CTD rosette with 
tension on the wire. Everything seemed fine. We then re-deployed the package and it 
again failed on entry to the water, just as the mechanical termination entered the 
water. We recovered the CTD, went to breakfast to decide what to do next. It was 
decided to move the distorted wire past the mechanical termination and coil this 
excess wire within the rosette frame. Thus the new mechanical termination was on an 
undamaged section of wire. We also found that we had lost a nut that holds the 
package to the wire, on inspection a few other bolts were hanging on by one thread. 
The crew then checked and tightened all nuts and bolts on the rosette frame. We re-
deployed the CTD with the damaged wire past the mechanical termination. The CTD deck 
box did not alarm and we proceeded with the stations.  The wire had no kinks on 
return, but the deck box did alarm as we came back on board. The cable tested 
positive, so a new mechanical termination was completed with more damaged wire 
coiled inside the CTD frame.

Continuing to take these mitigation steps – moving wire through the mechanical 
termination and re- terminating using cold mould - we were able to complete CTD 023 
-025. We lost approximately 93 hours due to wire issues.

Monday 16 May – Sunday 22 May 2016

This was our most successful week, with the mitigation steps, we averaged 4 CTD 
stations a day. We completed 18 CTD stations – CTD 026 - 043. We added to our 
mitigation steps, rotating the CTD anti-clockwise, some times 3-4 times, at the end 
of a station before landing the rosette on the deck. This action was implemented 
given that LACDP initial processing showed that the CTD was rotating during the 
cast.

With the CTD situation somewhat under control, we had a chance to begin to look at 
the data. The nutrient data was compared to the previous occupations of this 
section. The LADCP was processed using the CTD and SADCP data. This showed that 
there was a significant difference between the headings of the downward and upward 
ADCPs. Using software developed for ADCP processing (moorings) we determined that 
the lower ADCP unit heading was noisy and “wanders” significantly during a cast. We 
have implemented a LADCP processing that uses only the up-ward ADCP heading data.

Saturday and Sunday saw our first significant weather delays. Our planned CTD 
station at 45 56.41 S, 171 49.84 W was not attempted as the wind was 35-40 knots and 
we are running out of time. We decide to move to the next station. We expect the 
front to slide southeast and have improved weather conditions at the next station. 
We continued to transit to 45 33.52 S, 172 16.71. We arrived at this location at 
midnight and the wind was still 45-50 knots. We decided to heave-to and wait out the 
weather. At 5am the wind was still averaging 40 knots. We had a look at the weather 
forecast and the strong winds were predicted to continue for the next 6-10 hours. We 
decided to move to the next station at 45 10.57 S, 172 43.92 W.

We arrived at the station location and waited 1.5 hours for the wind to decrease. We 
started CTD 044 at 12:30. The station was completed and the wind speed had decreased 
to 15 knots. After completion of station 044 we decided to back-track south to pick 
up the CTD station at 45 33.52 S, 172 16.71 W. We examined the GRIB charts and 
decided that although the wind would increase as we moved south there was the chance 
of completing a station at the base of the Chatham Plateau. 1.5 hours into the 
transit the wind had increased to a mean of 35 knots and gusts over 40 knots. It was 
decided that we would be unable to complete a station further south. Thus we turned 
around and headed north. Unfortunately, we have missed stations at the based of the 
Chatham Plateau.

Station 045 was completed successfully.

Processing of CTD 040 LADCP data showed that the 150 kHz downward unit had a broken 
beam – beam 4. We have now implemented a 3-beam solution method

Monday 23 May – Tuesday 24 May

At CTD 046, the deck unit alarm sounded on deployment. The CTD was brought back on 
board. The cabling was checked and everything tested positive. The CTD was 
redeployed, alarm sounded again. The alarm is the bottom depth alarm. The property 
traces looked fine. It was decided to continue the station and move to CTD 20 at the 
next station. Large wire kinks were found on recovery of the CTD. We decided move to 
CTD winch 1 and re-terminate the wire (CTD winch 2).

At CTD 047, now using CTD 20, the pumps switched off at approximately 1200 dbar on 
the down-cast. Given the time constraints, we decided to continue the station. Pumps 
came on at approximately 1600 dbar, however the pump again turned off on the upcast. 
There were large kinks in the wire. A new CTD cable fixed the pump issue, however we 
required another cold mould re-termination.

Deployment of CTD 048 was delayed due to the short distance between stations and 
having to fault find the issues of pumps turning off and on, and re-terminate the 
wire. We were further delayed due to CAP computing issues.

These delays required constant re-planning of CTD stations. The delays resulted in 
the dropping of three planned station on the Chatham Rise (shallower than 1200 m) 
and two station on the northern slope of the Plateau. We hope leg 2, that has been 
provided with an extra 24 hours, will be able to complete the stations on the 
northern slope.

CTD 049 and 050 were successfully completed. Our final CTD station (050) was 
completed at 0830 on Tuesday morning. We then began our transit to Wellington.
In total we lost a total of 10 planned CTD stations on leg 1, of which two were due 
to the northward extent of sea-ice.

Investigator arrived in Wellington at 10am on May 27. Handovers began around midday 
and went until late afternoon. SOCCOM samples were removed from the vessel and 
shipped to Scripps for analysis.

 

Leg 2- Narrative by Susan Wijffels

Friday May 27

We left around 1230pm with a largely new science party and new marine crew. All of 
our 63 day’ers returned after a night ashore. Every one settled in, we ran the 
safety induction, muster and held a brief science/life-aboard briefing.  Most 
started to move into watches.

Saturday May 28

We made quick headway downwind and swell towards our first station, making up some 
time. We trained the watches on water sampling techniques and the underway systems. 
We also had many discussions on managing or mitigating against the wire damage 
experienced on leg. These centred around:

1. Preventing zero tension events that might lead to a snap and high-load 
   sequence – this means only lowering slowly in the upper few 100ms on the 
   downcast. We discussed this with the bosun (Graham) and winch drivers and 
   need to manage these low tension events in big sea states.
2. Measuring the rotation of the package via a newly installed Motion 
   Reference Unit (MRU) and attempting to compensate the observed rotation on 
   retrieval by spinning the package.
3. In cases where the ship is rolling on station, reduce the CTD-boom 
   extension to reduce the swell effect on the tensions
4. Trying heave compensation during a down cast to see if that helps reduce 
   tension shocks. 

Sunday May 29

CTD 51 was started around 4am and proceeded smoothly in a fairly mild sea state. The 
acquisition went smoothly. Sampling took a while as the watches are still being 
trained, and many were down with sea sickness. CTD 52, 53 and 54 went relatively 
smoothly- though we noticed a few snap and load events in the building sea state.  
Many volunteers are out of action due to seas sickness and the DAP and SIT team, 
Bernie Heaney and I are assisting the watches.

Monday May 30

CTD 55 resulted in some kinks forming just above the frame. These were pulled 
through the mechanical termination and stowed inside the frame to avoid an 
electrical re-termination. We are firing the near surface bottle on the fly to 
reduce exposure to the surface waves. We realized the Boss Flourometer had been 
offloaded in New Zealand. We worked on finding the MNF flourometer to prepare it to 
be added to the frame.

CTD 56 After discussion and with the strong support of the ship’s bosun, we decided 
to employ heave compensation on the downcast and lowered the speed to 50m/min. This 
will reduce exposure to a snap/load event during the downcast where drag is opposing 
gravity. Upcast was slowed to 50m/min until 2500db and then increased to 60m/min. 
Heave compensation was not used on upcast due to the danger of a bad wrap at the lay 
turnarounds at the drum ends. CTD station 57 we used HC at 60m/min, but with slow 
uphaul speeds out of HC. A SOCCOM float was deployed in dirty conditions over the 
aft port corner. MNF’s Chelsea Aquatracker was fitted to the 9plus on channel 6.

CTD 58 revealed new kinks developing. As the station was delayed as a squall came 
through we pulled the wire through the mechanical termination again. The cast 
proceeded fine but again with slower wire speeds, which is driving an unsustainable 
schedule slip.

Tuesday May 31

CTD 59 Tried increasing downcast wire speeds with HC on, and successfully used HC 
during the bottom approach. Upcast speeds were kept to 50m/min until 2500db and then 
increased to 60m/min.

CTD 60 Used HC during the upcast but with a switch off during the drum end wraps. 
The deck team worked this well, diligently working with the CTD watch to monitor the 
wraps on the drum. CTD61 – Successful and operated as above. SOCCOM float deployed.

Wednesday June 1

CTD 62 completed as above.

During CTD 63 after firing eight bottles, the deckbox fuse blew at 2900db and we 
lost communication with the 9plus. We retrieved the CTD and frame without 
communication. When the frame came aboard and the wire de-tensioned, many spools 
sprung loose on the drum indicating the cable was under high torque, which agreed 
with the MRU readings showing the package was continuously rotating clockwise (3-10) 
times per upcast. Subsequent diagnosis on the wire shows that it has a short 4km 
from the termination. This essentially makes this winch/wire unusable for the rest 
of our voyage. I sent out a call to international colleagues to ask for advice on 
managing wire damage. The response was excellent from our GO-SHIP collaborators. 
Suggestions included minimizing snap/shock load events, putting on a vane to reduce 
rotation and thus increased torqueing of the wire, and streaming out the wire with a 
swivel and weight to de-torque the cable.

The mechanical termination was moved to CTD Winch 1. The system tests all looked OK.

CTD 64. As we spooled out this new cable we came across many messy wraps and gaps on 
the drum near the end plates. During the upcast this required careful spooling to 
ensure the cable lays went on properly, reducing the effective wire speeds 
considerably. HC was used on both the up and down casts (but switched off when the 
cable lay is at the drum ends). SIT team and ship’s engineers start work on 
manufacturing a vane from material we sourced from NIWA in New Zealand.

Thursday June 2

CTD 65 - 67. Went smoothly except for stops for minor wrap adjustments – we are now 
in HC and doing up and down casts at 60m/min. Both CTD watch and deck crew are 
monitoring the winch drum. Frame continues to rotate.

Friday June 3

CTD 68 – completed without incident though the frame continues to rotate. A vane 
constructed by SIT staff and the ship's engineers was fitted to the package. As a 
test we deployed down to 500db and back up, to confirm that it worked as hoped. On 
the full cast the vane very effectively prevented any rotation of the frame. CTD 70 
– 71 were completed. Several CAP crashes occurred and there were several incidents 
of having to spool back out and in again on the upcasts to prevent a bad lay on the 
drum.

 
Saturday June 4

CTD 72-74 – we attempted to upgrade the software on Winch 1 to the same version as 
Winch 2, but this has failed. There is a continuing need to stop and adjust spooling 
during these casts, costing between 5-20 minutes per cast.

Sunday June 5

CTDs 75-78 completed. Around three spool adjustments per cast with both deck team 
and CTD watch monitoring the cable wraps carefully.

Monday June 6

CTDs 79-81 completed as above. Schedule slowly sliding behind. Tuesday June 7
CTD 82 was completed as above. CTD 83 proceeded smoothly. At 1103am, just after 
firing the second bottle on, the winch brake failed completely and the cable started 
to spool out violently at over 200m/min. In a few minutes our CTD frame was on the 
sea floor. By the time the Chief Engineer had managed to manually screw down the 
break band at least a further 1000m of cable was also payed out. The ship’s crew 
then put in a mammoth effort over the next 36 hours to retrieve the cable and 
rosette.

Tuesday June 8

Ongoing activities to prepare for the retrieval of the frame. This included 
stoppering off the cable with 3 Chicago clamps, keeping the ship hovering over the 
package, stripping and rebuilding the CTD winch break, testing its efficacy and then 
checking the winch gearbox, motor and controls.

Once the winch was tested and ready, tension was transferred back to the winch drum, 
and uphaul began slowly at 10- 20m/min. There were some moments with large tension 
spikes just before we lofted the wire off a rough bottom, and then the tension 
returned to what we would normally expect for the frame on uphaul. Once we were 
certain the frame had been lifted off the sea floor, we powered on the deckbox, and 
the CTD started sending data as usual. This turned out to be remarkable given the 
wire damage.

A slow agonizing retrieval near 20-30m/min ensued, with the frame rotating very 
rapidly. A few hundred meters above the termination, there were knots in the 
conducting cable (which took hours to unsnarl and feed through the blocks) and the 
wire was wrapped around the package on retrieval. The frame was back on deck around 
410am

Once on deck we could see the top guard rail of the frame was snapped, but amazingly 
no Niskins were smashed. Even the upper LADCP, which was pushed over, remained 
functional. As far as we can tell nearly all our sensors had no calibration shift. 
The ships engineers and deck crew rebuilt and tested the winch break, checked the 
system and readied it for use. If this had failed we would have had to move to the 
24 bottle frame and coring boom out of the shelter deck. Just in case, this backup 
system was set up in the shelter deck area.

The kinked and knotted cable was cut away and then we spooled out the cable with a 
small weight and swivel to help de-torque it. This took another 11.5 hours to 
complete, with the uphaul very slow due to frequent winch alarms constantly shutting 
down power and interrupting the operation. An entire 1.5 hours was lost trying to 
diagnose the source of these somewhat random winch alarms. Rather than continue to 
lose time, once the wire was fully on board, we moved the ship 15nm, which merged 
two stations and resulted a 45nm spacing. The transfer of the newly terminated cable 
to the CTD and frame, and the set up for the next station by the science team was 
fast. The LADCP was mounted on a bracket from the 24 bottle frame, and as a result 
it blocked lanyards from two Niskins, so these were left off.

Tuesday June 9

CTD 85 was a merger of two stations resulting in 45’ separation at this part of the 
section. The rebuilt winch seemed to work reasonably well, though many stops and 
rewinds were needed. The upward looking LADCP was remounted on its old frame which 
had been repaired by the ship’s engineers. CTDs 86-87 proceeded well, with 2-3 
spooling adjustments. Upcast speeds are slowed to keep tensions below 2.1-2.2T at 
depth but were sped up to 70m/min above ~3000db to make up time. This seems to work 
well. A request to the MNF for additional ship time to help compensate for the time 
lost to date due to the winch break failure was successful with the granting of an 
additional 24 hours to this leg.

Wednesday June 10 – Saturday June 11

CTD 88-95 proceeded smoothly with 2-3 spooling adjustments. The secondary 
conductivity sensor continued to develop an anomalous salty bias in the upper 1000m 
(both compared to the bottle salts and the primary channel). Swapped in SBE C4 SN 
4718 and checked the line plumbing. A deep SOLO was deployed gently in its box after 
station 88.

Sunday June 12

CTDs 94-95 were completed. The new C cell did not fix the anomalous behaviour of the 
secondary channel. SIT fitted a new pump to that line. We continue to require close 
attention to cable lays on the drum by both the deck crew and the CTD watch. Each 
station has several stops to adjust the spool or to backwind to correct a bad lay. 
Random winch alarms also slowed down the stations. We realigned the flow path on 
both 9plus channels to go from deep to shallow.

Monday June 13 - Hump Day

CTDs 96-100 proceeded as above. Further delays occurred due to the CTD door opening. 
A Hump Day meeting was held. We could see the lights of Nuie from the bridge.

Tuesday June 14

We continue to search for the causes of the bad conductivity in the secondary 
channel. After CTD 101, we pulled the 9plus forward to give greater clearance of the 
rosette frame struts. This did not solve it in the data from CTD 102.

Wednesday June 15

CTD 103. We decided to try the other 9plus (CTD #22 SN 1324) to ensure we had a 
useable secondary C trace. However at 300db the oxygen values corrupted and then the 
deckbox alarmed. Power was shut down and the frame was retrieved. On inspection it 
was found that the 9plus had leaked. We had to switch back to CTD #22 (SN 552). The 
aborted cast data was parked and a new station 103 was completed. It is likely that 
we have no spare 9plus on board at this point.

CTDs 104-105 completed. The old square vane was put back on as the new version was 
not preventing rotation as well.

Thursday June 16

CTD 106-111 completed as normal (2-3 spooling adjustments).  As we are passing 
across a deep ridge we have close station spacing. The station turnarounds are fast 
and this is tough on the chemistry laboratories. After CTD 110 we changed out the 
oxygen sensor (SN 3195).on the secondary line, based on a suggestion by Dave Murphy 
at SeaBird.

Friday June 17

CTDs 112-114 completed. Before 113, Ben Baldwin suggested trying yet another C cell 
in the secondary line. This fixed the problem! We had, in fact, two bad C-cells, one 
after the other! It is a relief to have a backup channel as there is more sea snot 
and other fouling turning up on the frame and in the bottles.

Saturday June 18 – Sunday June 24

CTDs 115 – 141 were completed without incident in hot steamy conditions. The deck 
crew became very efficient at minimizing spooling stops while still closely 
monitoring the cable and winch drum, and the deployments and retrievals were honed 
down to an efficient operation between the deck, bridge and science crews. Faster 
upcast speeds above ~3500db also helped us bank time. In this way we were able to 
occupy nearly all of the planned stations. A great achievement given the challenges 
we faced at the start and the near loss of our primary cable and instrument package.

Summary

Despite the challenges we were able to overcome most problems and complete the bulk 
of our planned work. The quality of the data collected is very high, particularly 
from the chemistry teams who have delivered an excellent and very high resolution 
(due to the 36 bottle sampling) data set. We are confident that this occupation of 
P15S has uncovered clear and ongoing changes to the deep ocean heat and carbon 
content, and chemistry. The novel genomic and production sampling coordinated by 
Eric Raes will likely deliver some ground-breaking insights. The mixing information 
taken via the shear measured by the LADCP, sADCP and fine and microscale properties 
via the chi-pods and CTD will also be very insightful and unprecedented along this 
line.

 
Voyage Track (see pdf)


 
Marsden Squares (see pdf)

Move a red “x” into squares in which data was collected




 
Moorings, bottom mounted gear and drifting systems

Table 1: Float details in order of deployment. All deployments have code: D06 
         Institutions/PIs are as follows:
         SIO = Scripps Institution of Oceanography -PI – Dean Roemmich
         SOCCOM = Southern Ocean Carbon and Climate Observation and Modelling 
         experiment – PI Lynne Talley UTAS – University of Tasmania, PI - 
         Helen Phillips and Pete Strutton
         CSIRO PI – Susan Wijffels.

Deploy Order  Hull      Date/time      Longitude     Latitude      Type     Owner
              No.
------------  -----  ---------------  ------------  -----------  ---------  ------
 1            8390   27/4/2016 22:04  151 27.29' E  47 57.20' S  Solo II    SIO 
 2            8447   28/4/2016 04:33  152 21.20' E  49 59.90' S  Solo II    SIO 
 3            7741   29/4/2016 12:50  156 33.97' E  54  0.03' S  APEX       CSIRO
 4            7738   30/4/2016 04:04  159 28.82' E  56 14.40' S  APEX       CSIRO
 5            7742    1/5/2016 01:50  164 59.00' E  59 14.90' S  APEX       CSIRO
 6            8352    1/5/2016 07:09  166 16.19' E  60  0.06' S  Solo II    SIO
 7            8448    1/5/2016 17:37  169 10.20' E  61 31.00' S  Solo II    SIO
 8            7743    1/5/2016 21:14  170 14.04' E  62 00.07' S  APEX       CSIRO
 9            8454    2/5/2016 04:48  172 33.76' E  63  0.36' S  Solo II    SIO
10            8455    3/5/2016 06:47  178 30.22' W  64 45.00' S  Solo II    SIO
11            8456    4/5/2016 01:30  172 29.70' W  65 47.20' S  Solo II    SIO
12            7740    4/5/2016  5:47  170 43.41' W  66 11.79' S  APEX       CSIRO
13            8457    4/5/2016 17:20  169 58.60' W  66 39.30' S  Solo II    SIO
14            F0568   5/5/2016 06:25  170 03.95' W  65 39.84' S  NAVIS      SOCCOM 
15            7739    4/5/2016 21:23  169 49.30' W  66 20.50' S  APEX       CSIRO
16            F0570   4/5/2016 12:10  170  0.10' W  66 20.51' S  NAVIS      SOCCOM
17            8462    5/5/2016 06:20  170 03.95' W  65 39.84' S  Solo II    SIO     
18            8463    6/5/2016 12:56  169 58.50' W  63 59.70' S  Solo II    SIO
19 – CTD 6    F0565   6/5/2016 07:42  170 04.30' W  64  0.00' S  NAVIS      SOCCOM
20 – CTD 9    8464    8/5/2016 09:22  169 59.82' W  62 29.71' S  Solo II    SIO
21 – CTD 11   9761    8/5/2016 18:35  169 59.30' W  61 59.90' S  APEX       SOCCOM
22 – CTD 15   F0571  11/5/2016 15:37  170 01.10' W  59 59.70' S  NAVIS      SOCCOM
23            8460   10/5/2016 02:46  169 59.20' W  60 30.40' S  Solo II    SIO
24 – CTD 19   9265   13/5/2016 16:10  170  0.50' W  57 59.80' S  APEX       SOCCOM
25 – CTD 25   F0566  15/5/2016 15:18  170  0.70' W  55  0.70' S  NAVIS      SOCCOM
26 – CTD 27   7718   16/5/2016 07:10  169 56.04' W  53 59.15' S  APEX       UTAS
27 – CTD 29   7719   16/5/2016 21:31  170  0.92' W  52 59.92' S  APEX       UTAS
28 – CTD 29   7789   16/5/2016 21:27  170  0.87' W  53 00.06' S  APEX       UTAS
29 – CTD 31   9660   17/5/2016 11:57  170 04.20' W  57 59.70' S  APEX       SOCCOM
30 – CTD 30   7612   17/5/2016 04:51  169 59.30' W  52 29.70' S  APEX       CSIRO
31 – CTD 35   9632   18/5/2016 16:27  169 59.50' W  50  0.50' S  APEX       SOCCOM
32            8453   18/5/2016 06:32  170  0.00' W  49  0.00' S  Solo II    SIO
33 – CTD 39   9634   19/5/2016 20:11  169 59.30' W  47 59.16' S  APEX       SOCCOM
34 – CTD 40   7611   20/5/2016 03:56  169 58.90' W  47 29.03' S  APEX       CSIRO
35 – CTD 42   8465   20/5/2016 18:14  170 54.60' W  46 42.80' S  Solo II    SIO
36 - CTD 43   9762   21/5/2016 05:23  171 22.20' W  46 19.80' S  APEX       SOCCOM
37 – CTD 44   7610   22/5/2016 04:11  172 43.90' W  45 10.50' S  APEX       CSIRO
38 – CTD 57   9630   30/5/2016 09:17  172 41.70' W  39 58.00' S  APEX       SOCCOM
39 – CTD 59   F0634  31/5/2016 00:43  172 07.55' W  39 04.13' S  NAVIS      CSIRO     
40 – CTD 61   9752   31/5/2016 15:03  171 30.98' W  38 11.09' S  APEX       SOCCOM
41 – CTD 88   6012    9/6/2016 22:46  170  0.13' W  24 57.53' S  DEEP SOLO  SIO
42 – CTD 92   6013   11/6/2016 05:16  169 99.38' W  22 98.93' S  DEEP SOLO  SIO
43 – CTD 120  F0632  18/6/2016 18:29  169 37.59' W   9 55.35' S  NAVIS      CSIRO     
 


Summary of Measurements and samples taken

                                         DATA 
      PI                NO     UNITS     TYPE

Item  see page above    see    see       Enter 
No.                     above  above     code(s)
                                         from     DESCRIPTION
                                         list 
                                         on 
                                         last 
                                         page
----  ----------------  -----  --------  -------  -----------------------------
      Sloyan/Wijffels   140    CTD                Full depth continuous profiles of 
                                                  temperature, conductivity, pressure, 
                                                  oxygen, flourescence, PAR, light 
                                                  transmission, scattering, temperature 
                                                  microstructure, velocity, and 
                                                  additional prototype measurements of 
                                                  temperature, pressure and 
                                                  conductivity.
       Sloyan/Wijffels   140   Niskin             With the above, discrete water 
                               casts              samples were capture by 36 Niskin 
                                                  bottles per cast, and analysed by 
                                                  onboard laboratories for: nitrate, 
                                                  nitrite, phosphate, oxygen, silicate, 
                                                  and salinity.
       Tilbrook          140   Niskin             From a subset of the Niskins above, 
                                                  alkalinity, total dissolved inorganic 
                                                  carbon.
       Raes/Bodrossy     140   Niskin             From a subset of the Niskins above, 
                                                  microbial material was filtered and 
                                                  stored for later genomic analysis
       Warner/Bullister  140   Niskin             From a subset of the Niskins above, 
                                                  concentrations of CFC-11, CFC-12 and 
                                                  SF-6.
       Cowley/Wijffels   295   XBT                At some CTD stations, XBTs were 
                               drops              dropped simultaneous with the 
                                                  downcast from 0-1000db.
       Sloyan/Downes      20   Niskins            From a subset of the Niskins between 
                                                  66S and 42.73S
       Alroe/Brown             underway           Atmospheric Chemistry and Aerosols

 
Table 2. List of all CTDs completed.

Stn         Start Time                End Time            Longitude  Latitude  Depth (m)
---  ------------------------  ------------------------  ----------  --------  ---------
  1  2016-04-27T04:00:32.472Z  2016-04-27T06:59:57.909Z    149.428    -45.497     4299
  2  2016-05-04T08:44:01.018Z  2016-05-04T11:46:03.271Z    189.992    -66.332     3277
  3  2016-05-05T03:20:41.153Z  2016-05-05T06:00:56.633Z    189.968    -65.662     3297
  4  2016-05-05T13:20:24.907Z  2016-05-05T16:12:14.822Z    189.984    -64.995     2836
  5  2016-05-05T21:45:09.215Z  2016-05-06T00:44:24.863Z   -170.003    -64.502     2348
  6  2016-05-06T05:01:56.231Z  2016-05-06T07:28:53.065Z    189.958    -63.990     2807
  8  2016-05-08T01:41:57.338Z  2016-05-08T03:16:23.764Z    189.968    -63.001     3046
  9  2016-05-08T06:50:03.329Z  2016-05-08T09:11:46.453Z    190.008    -62.499     2539
 10  2016-05-08T12:21:19.393Z                              189.998    -62.001     3302
 11  2016-05-08T15:35:30.046Z  2016-05-08T18:19:30.052Z   -170.004    -62.003     3360
 12  2016-05-08T21:46:21.480Z  2016-05-09T00:50:36.208Z    189.998    -61.491     3470
 13  2016-05-09T16:31:07.920Z  2016-05-09T20:32:56.941Z    189.988    -61.001     4483
 14  2016-05-09T23:35:04.451Z                              190.002    -60.500     3951
 15  2016-05-11T11:51:23.283Z  2016-05-11T15:25:39.232Z    189.996    -60.000     3905
 16  2016-05-11T18:40:15.773Z                             -169.997    -59.498     4672
 17  2016-05-12T20:00:04.319Z  2016-05-13T00:57:54.416Z    190.002    -58.994     4763
 18  2016-05-13T04:41:15.570Z  2016-05-13T08:56:24.213Z    189.986    -58.491     5190
 19  2016-05-13T12:19:34.718Z  2016-05-13T16:02:55.979Z   -170.010    -58.001     4432
 20  2016-05-13T19:10:57.839Z  2016-05-13T23:12:03.895Z    189.994    -57.503     5019
 21  2016-05-14T02:14:19.014Z  2016-05-14T06:32:38.209Z    190.003    -57.002     5078
 22  2016-05-14T09:26:16.442Z  2016-05-14T13:52:34.294Z    189.991    -56.498     5090
 23  2016-05-14T21:22:12.759Z  2016-05-15T01:56:39.672Z   -170.008    -56.002     5121
 24  2016-05-15T04:41:21.185Z  2016-05-15T08:21:22.581Z    189.989    -55.514     4833
 25  2016-05-15T11:08:33.772Z  2016-05-15T15:04:08.054Z   -170.002    -54.996     4843
 26  2016-05-15T20:00:12.895Z  2016-05-15T23:57:17.125Z    189.997    -54.500     4831
 27  2016-05-16T02:49:06.749Z  2016-05-16T06:58:44.984Z   -169.985    -53.996     5142
 28  2016-05-16T09:54:08.128Z  2016-05-16T13:49:43.812Z    190.009    -53.501     5226
 29  2016-05-16T16:37:36.199Z  2016-05-16T21:18:15.385Z    189.989    -53.004     5220
 30  2016-05-17T00:16:45.970Z  2016-05-17T04:29:21.431Z    189.990    -52.505     5161
 31  2016-05-17T07:55:27.336Z  2016-05-17T11:47:36.463Z    189.922    -52.002     4913
 32  2016-05-17T14:36:45.966Z  2016-05-17T18:37:59.133Z    189.984    -51.492     4732
 33  2016-05-17T21:41:11.848Z  2016-05-18T01:43:26.543Z    189.990    -51.002     5248
 34  2016-05-18T04:20:50.075Z  2016-05-18T08:27:37.658Z    190.004    -50.497     5052
 35  2016-05-18T11:37:36.343Z  2016-05-18T16:13:53.136Z    190.007    -50.006     5384
 36  2016-05-18T19:15:06.047Z  2016-05-18T23:30:41.690Z    189.983    -49.504     5220
 37  2016-05-19T02:15:29.121Z  2016-05-19T06:14:07.361Z    189.996    -48.995     5262
 38  2016-05-19T09:15:42.998Z  2016-05-19T13:13:36.267Z    190.000    -48.502     5298
 39  2016-05-19T15:59:05.698Z  2016-05-19T19:58:50.793Z    190.007    -47.995     5310
 40  2016-05-19T23:38:42.257Z  2016-05-20T03:49:04.376Z    190.009    -47.503     5379
 41  2016-05-20T06:49:55.735Z  2016-05-20T10:51:27.177Z   -170.466    -47.109     5412
 42  2016-05-20T13:48:55.354Z  2016-05-20T18:06:13.182Z    189.089    -46.719     5296
 43  2016-05-21T01:16:15.147Z  2016-05-21T05:18:16.866Z    188.624    -46.326     5100
 44  2016-05-22T00:21:11.875Z  2016-05-22T04:06:09.426Z   -172.736    -45.176     4665
 45  2016-05-22T10:03:02.223Z  2016-05-22T13:20:54.416Z   -173.141    -44.835     3830
 46  2016-05-22T16:39:56.631Z  2016-05-22T19:39:03.940Z    186.498    -44.525     3414
 47  2016-05-22T23:35:42.231Z  2016-05-23T02:40:24.000Z   -173.746    -44.328     3102
 48  2016-05-23T06:20:59.593Z  2016-05-23T08:21:23.577Z    186.063    -44.156     1892
 49  2016-05-23T15:42:28.390Z  2016-05-23T17:01:48.390Z    185.215    -42.931     1057
 50  2016-05-23T18:19:40.160Z  2016-05-23T19:55:49.608Z    185.347    -42.746     1584
 51  2016-05-28T16:14:20.306Z  2016-05-28T18:54:54.994Z   -174.410    -42.400     2666
 52  2016-05-28T21:29:48.241Z  2016-05-29T00:04:10.766Z   -174.250    -42.167     2866
 53  2016-05-29T03:10:55.467Z  2016-05-29T06:24:11.017Z    186.052    -41.717     3116
 54  2016-05-29T09:20:12.256Z  2016-05-29T12:48:15.813Z    186.363    -41.273     3292
 55  2016-05-29T16:03:03.069Z  2016-05-29T19:21:51.563Z    186.668    -40.832     4178
 56  2016-05-29T22:03:34.309Z  2016-05-30T02:04:33.488Z    186.976    -40.392     4592
 57  2016-05-30T04:47:48.414Z  2016-05-30T09:01:22.620Z    187.294    -39.958     4739
 58  2016-05-30T12:14:08.948Z  2016-05-30T16:12:59.901Z   -172.414    -39.511     4776
 59  2016-05-30T20:33:42.659Z  2016-05-31T00:29:43.153Z    187.883    -39.068     4861
 60  2016-05-31T03:40:12.877Z  2016-05-31T08:05:21.954Z   -171.808    -38.628     4929
 61  2016-05-31T10:54:53.015Z  2016-05-31T14:55:29.261Z    188.499    -38.187     4945
 62  2016-05-31T17:39:55.439Z  2016-05-31T21:49:35.251Z   -171.201    -37.757     5028
 63  2016-06-01T00:46:26.310Z                              189.107    -37.307     5146 
 64  2016-06-01T07:45:39.848Z  2016-06-01T12:21:23.997Z    189.394    -36.871     5303
 65  2016-06-01T15:00:17.591Z  2016-06-01T18:57:40.511Z    189.706    -36.450     5087
 66  2016-06-01T21:52:55.429Z  2016-06-02T02:10:17.334Z    189.998    -36.002     5084
 67  2016-06-02T07:11:03.580Z  2016-06-02T08:09:51.319Z    189.993    -35.680     4372
 68  2016-06-02T10:05:44.979Z  2016-06-02T14:11:33.883Z    190.000    -35.337     4909
 69  2016-06-02T17:14:37.276Z  2016-06-02T21:02:31.630Z   -169.995    -35.014     5264
 70  2016-06-02T23:56:59.914Z  2016-06-03T04:17:59.232Z   -170.006    -34.505     5505
 71  2016-06-03T06:55:55.109Z  2016-06-03T11:30:53.771Z    190.001    -34.012     5547
 72  2016-06-03T14:09:08.789Z  2016-06-03T18:18:02.498Z    190.000    -33.501     5446
 73  2016-06-03T21:12:13.104Z  2016-06-04T01:32:03.632Z    189.994    -33.000     5591
 74  2016-06-04T04:25:07.081Z  2016-06-04T09:44:26.841Z    190.003    -32.500     5572
 75  2016-06-04T12:27:50.130Z  2016-06-04T16:51:53.619Z    190.005    -32.002     5700
 76  2016-06-04T19:44:17.163Z  2016-06-04T23:48:47.511Z    190.006    -31.499     5553
 77  2016-06-05T02:23:03.598Z  2016-06-05T06:52:03.414Z    190.002    -31.023     5630
 78  2016-06-05T09:36:11.341Z  2016-06-05T13:56:01.685Z    190.004    -30.512     5556
 79  2016-06-05T16:40:46.912Z  2016-06-05T21:25:47.606Z   -169.993    -29.999     5437
 80  2016-06-05T23:53:43.091Z  2016-06-06T04:03:12.410Z    190.000    -29.501     5226
 81  2016-06-06T06:53:23.015Z  2016-06-06T11:36:55.821Z   -169.995    -29.006     5605
 82  2016-06-06T14:09:24.425Z  2016-06-06T18:28:26.073Z    190.001    -28.503     5454
 83  2016-06-07T15:26:50.239Z  2016-06-07T15:53:02.758Z   -169.991    -27.984     5264
 84  2016-06-08T10:24:16.518Z  2016-06-08T15:05:51.923Z    190.002    -27.272     5464
 85  2016-06-08T19:10:59.700Z  2016-06-09T00:17:28.530Z    190.004    -26.495     5637
 86  2016-06-09T02:51:15.437Z  2016-06-09T07:54:44.048Z    190.007    -26.000     5607
 87  2016-06-09T10:31:19.445Z  2016-06-09T15:11:53.560Z    190.002    -25.509     5836
 88  2016-06-09T18:06:23.701Z  2016-06-09T22:29:28.525Z    189.998    -24.999     5653
 89  2016-06-10T01:42:23.191Z  2016-06-10T06:08:34.689Z    189.999    -24.501     5670
 90  2016-06-10T09:20:24.195Z  2016-06-10T13:53:06.924Z    189.999    -24.000     5689
 91  2016-06-10T16:52:43.422Z  2016-06-10T21:20:17.826Z    190.004    -23.505     5676
 92  2016-06-11T00:26:01.170Z  2016-06-11T04:56:47.183Z    190.004    -22.999     5701
 93  2016-06-11T08:02:25.191Z  2016-06-11T12:32:10.517Z    190.000    -22.501     5663
 94  2016-06-11T15:30:50.404Z  2016-06-11T20:06:09.433Z    190.000    -22.002     5636
 95  2016-06-11T22:53:18.177Z  2016-06-12T03:03:14.292Z    190.001    -21.503     5430
 96  2016-06-12T05:52:54.391Z  2016-06-12T10:06:28.855Z    190.001    -20.998     5482
 97  2016-06-12T12:47:03.016Z  2016-06-12T17:32:12.377Z    190.001    -20.503     5675
 98  2016-06-12T20:14:10.806Z  2016-06-13T00:23:47.764Z   -170.002    -20.000     5341
 99  2016-06-13T03:03:07.613Z  2016-06-13T06:49:42.210Z    189.997    -19.498     4915
100  2016-06-13T09:33:26.523Z  2016-06-13T12:14:50.468Z    189.942    -19.004     2989
101  2016-06-13T15:03:29.146Z  2016-06-13T18:54:55.035Z    189.998    -18.503     5269
102  2016-06-13T21:39:46.446Z  2016-06-14T01:15:19.931Z    190.000    -18.001     4919
103  2016-06-14T06:52:34.183Z  2016-06-14T10:30:37.926Z    189.999    -17.499     5037
104  2016-06-14T13:19:40.044Z  2016-06-14T16:51:38.553Z    189.998    -17.003     5005
105  2016-06-14T19:49:13.424Z  2016-06-14T23:24:11.140Z   -170.000    -16.504     5140
106  2016-06-15T02:10:16.869Z  2016-06-15T06:06:31.818Z    189.999    -16.003     5150
107  2016-06-15T08:54:05.975Z  2016-06-15T12:53:20.966Z    189.999    -15.498     5095
108  2016-06-15T15:32:26.391Z  2016-06-15T18:56:06.305Z    190.000    -15.005     4826
109  2016-06-15T20:52:44.028Z  2016-06-15T23:30:52.379Z    190.001    -14.666     3330
110  2016-06-16T01:40:00.371Z  2016-06-16T04:49:52.408Z    190.002    -14.282     3546
111  2016-06-16T06:43:49.711Z  2016-06-16T09:24:24.872Z   -169.999    -13.972     2972
112  2016-06-16T11:14:01.550Z  2016-06-16T14:26:37.400Z   -169.999    -13.819     4338
113  2016-06-16T16:18:09.474Z  2016-06-16T19:47:25.972Z    189.998    -13.504     4888
114  2016-06-16T22:54:35.623Z  2016-06-17T02:30:24.514Z    190.001    -13.000     4980
115  2016-06-17T05:22:04.447Z  2016-06-17T09:01:31.046Z   -169.999    -12.499     5012
116  2016-06-17T11:45:19.226Z  2016-06-17T15:35:37.121Z    189.997    -11.998     5097
117  2016-06-17T18:25:04.949Z  2016-06-17T21:58:04.975Z   -169.999    -11.496     5069
118  2016-06-18T00:37:17.771Z  2016-06-18T04:30:02.323Z    190.000    -11.001     5135
119  2016-06-18T07:22:02.899Z  2016-06-18T10:47:57.099Z    190.001    -10.500     4878
120  2016-06-18T14:33:07.577Z  2016-06-18T18:21:06.416Z    190.371     -9.925     5227
121  2016-06-18T22:41:57.912Z  2016-06-19T02:48:28.206Z    191.002     -9.499     5357
122  2016-06-19T05:43:59.835Z  2016-06-19T09:22:06.274Z    191.125     -8.997     4891
123  2016-06-19T12:09:30.173Z  2016-06-19T16:06:03.387Z    191.251     -8.495     5182
124  2016-06-19T18:58:14.874Z  2016-06-19T22:39:57.802Z    191.384     -8.001     5212
125  2016-06-20T01:21:14.743Z  2016-06-20T05:22:17.796Z    191.249     -7.501     5287
126  2016-06-20T08:06:41.515Z  2016-06-20T12:15:06.408Z    191.249     -7.000     5676
127  2016-06-20T14:56:28.342Z  2016-06-20T18:58:25.358Z    191.251     -6.502     5553
128  2016-06-20T21:39:59.661Z  2016-06-21T01:50:54.802Z    191.249     -6.000     5679
129  2016-06-21T04:34:11.165Z  2016-06-21T08:39:59.859Z    191.250     -5.502     5476
130  2016-06-21T11:17:38.778Z  2016-06-21T15:18:39.517Z   -168.750     -5.000     5583
131  2016-06-21T17:50:18.275Z  2016-06-21T21:47:59.558Z    191.250     -4.501     5555
132  2016-06-22T00:21:47.029Z  2016-06-22T04:27:36.064Z    191.249     -4.001     5178
133  2016-06-22T07:06:59.058Z  2016-06-22T10:53:32.647Z    191.250     -3.502     5023
134  2016-06-22T13:38:31.916Z  2016-06-22T17:25:35.631Z    191.249     -3.000     5388
135  2016-06-22T20:10:50.573Z  2016-06-22T23:53:22.984Z    191.250     -2.499     5346
136  2016-06-23T02:35:31.797Z  2016-06-23T05:19:52.127Z    191.250     -2.001     3413
137  2016-06-23T08:09:26.337Z  2016-06-23T12:30:51.322Z    191.251     -1.501     5926
138  2016-06-23T15:14:59.409Z  2016-06-23T19:24:07.539Z    191.250     -1.001     5803
139  2016-06-23T22:08:54.069Z  2016-06-24T02:01:32.511Z    191.250     -0.501     5513
140  2016-06-24T04:55:31.999Z  2016-06-24T09:09:54.961Z    191.250     -0.002     5628

 
Personnel List
Leg 1

     Name                    Organisation  Role
---  ----------------------  ------------  --------------------------
 1.  Don McKenzie            CSIRO MNF     Voyage Manager
 2.  Lloyd Fletcher          Doctor        Aspen Medical
 3.  Bernadette Sloyan       CSIRO         Chief Scientist
 4.  Kate Berry              CSIRO         Carbon Team
 5.  Abe Passmore            CSIRO         Carbon Team
 6.  Christine Rees          CSIRO MNF     Hydrochemist
 7.  Erik Van Ooijen         CSIRO         Carbon Team
 8.  Eric Raes               U. WA         Bacteria/Genomics
 9.  Craig Neill             CSIRO         Carbon Team
10.  Kelly Brown             CSIRO         Hydrochemist
11.  John Church             CSIRO         CTD Watch Leader
12.  Ian McRobert            CSIRO         MNF  Electronics
13.  Rod Palmer              CSIRO         MNF  Electronics
14.  Bonnie Chang            U. WA         CFC
15.  Dave Wisegarver         NOAA PMEL     CFC
16.  Stephen Tibben          CSIRO MNF     Hydrochemist
17.  Anoosh Sarraf           CSIRO MNF     Data Processing
18.  Steven Van Graas        CSIRO MNF     Data Processing
19.  Matt Boyd               CSIRO MNF     GSM
20.  Peter Hughes            CSIRO MNF     Hydrochemist
21.  Taha Cowen              U. Tasmania   CTD watch
22.  Madi Rosevear           U. Tasmania   CTD watch
23.  Tobias Aldridge         U. Tasmania   CTD watch/iXblue PHINS INS
24.  Hayden Martin           ANU           Carbon Team
25.  Paul Sandery            U. Tasmania   CTD watch
26.  Rodrigo Gurdec          JCU           CTD watch
27.  Nicole Hellessey        U. Tasmania   Bacteria/Genomics
28.  Swan Sow                CSIRO         Bacteria/Genomics
29.  Nic Pittman             U. Tasmania   CTD watch
30.  Joel Alroe              QUT           Atmospherics

 
Leg 2

     Name                    Organisation  Role
---  ----------------------  ------------  --------------------------
 1.  Steve Thomas            CSIRO MNF     Voyage Manager
 2.  Susan Wijffels          CSIRO         Chief Scientist
 3.  Ben Baldwinson          CSIRO         MNF  Electronics
 4.  Will Ponsonby           CSIRO         MNF  Electronics
 5.  Hugh Barker             CSIRO         MNF  Data Processing
 6.  Stew Wilde              CSIRO         MNF  Data Processing
 7.  Bernie Heaney           CSIRO         MNF  GSM
 8.  Ann Thresher            CSIRO         CTD Watch Leader
 9.  Mark Rosenberg          U. Tasmania   CTD Watch Leader
10.  Esmee Van Wijk          CSIRO         CTD watch
11.  Yue Hau Li              U. Tasmania   CTD watch
12.  Asha Vijayeta           Monash U.     CTD watch
13.  Maija Kaipio            U. Auckland   CTD watch
14.  Edward King             CSIRO         CTD watch
15.  Mainak Mondal           ANU           CTD watch
16.  Luwei Yang              U. Tasmania   CTD watch
17.  Tobias Aldridge         U. Tasmania   CTD watch/iXblue PHINS INS
18.  Christine Rees          CSIRO MNF     Hydrochemist
19.  Cassie Schwanger        CSIRO         Hydrochemist
20.  Kelly Brown             CSIRO         Hydrochemist
21.  Stephen Tibben          CSIRO MNF     Hydrochemist
22.  Bronte Tilbrook         CSIRO         Carbon Team/co-PI
23.  Kate Berry              CSIRO         Carbon Team
24.  Abe Passmore            CSIRO         Carbon Team
25.  Erik Van Ooijen         CSIRO         Carbon Team
26.  Craig Neill             CSIRO         Carbon Team
27.  Hayden Martin           ANU           Carbon Team
28.  Jessica Ericson         U. Tasmania   Carbon Team
29.  Charles Maxson          U. Auckland   Carbon Team
30.  Eric Raes               U. WA         Bacteria/Genomics
31.  Gaby Paniagua Cabarrus  U. Tasmania   Bacteria/Genomics
32.  Bernhard Tschitschko    UNSW          Bacteria/Genomics
33.  Reece Brown             QUT           Atmospherics
34.  Bonnie Chang            U. WA, USA    CFC
35.  Rolf Sonnerup           U. WA, USA    CFC

 
Marine Crew

Leg 1

Name                Role
------------------  -----------------------
Mike Watson         Master
Roderick Quinn      Chief Mate
Brendan Eakin       Second Mate
Thomas Watson       Third Mate
Gennadiy Gervasiev  Chief Engineer
Sam Benson          First Engineer
Ian McDonald        Second Engineer
Damian Wright       Third Engineer
John Curran         Electrical Engineer
Alan Martin         Chief Caterer
Emma Lade           Caterer
Rebecca Lee         Chief Cook
Matt Gardiner       Cook
Jonathan Lumb       Chief Integrated Rating
Dean Hingston       Integrated Rating
Darren Capon        Integrated Rating
Murray Lord         Integrated Rating
Matthew McNeill     Integrated Rating
Kel Lewis           Integrated Rating
Ryan Drennan        Integrated Rating

Leg 2

Name                Role
------------------  -----------------------
John Highton        Master
Gurmukh Nagra       Chief Mate
Adrian Koolhof      Second Mate
James Hokin         Third Mate
Chris Minness       Chief Engineer
Mark Elliot         First Engineer
Michael Sinclair    Second Engineer
Ryan Agnew          Third Engineer
Shan Kromkamp       Electrical Engineer
Cassy Rowse         Chief Caterer
Emma Lade           Caterer
Keith Shepherd      Chief Cook
Matt Gardiner       Cook
Graham McDougall    Chief Integrated Rating
Chris Dorling       Integrated Rating
Matt McNeill        Integrated Rating
Paul Langford       Integrated Rating
Peter Taylor        Integrated Rating
Dennis Bassi        Integrated Rating
Rod Langham         Integrated Rating

 

Acknowledgements

We thank the Masters and crew of the Investigator, and the MNF electronic and 
computing support teams. Their willingness to help work through some of the major 
issues we encountered was essential to our success. Don McKenzie and Steve Thomas, 
our Voyage Managers, were a joy to work with. Their thorough knowledge of the vessel 
and equipment was invaluable, their calm personalities and strong support for our 
goals and care for our team made our jobs very easy and kept all safe and happy. We 
thank the MNF management team for their support in organizing the large team, and 
for making extra time available to help reach our goals. We thank Mark Rayner and 
the CSIRO hydrochemistry team for their outstanding preparation for this challenging 
voyage. Mike Jackson was invaluable in assisting us upgrade the laboratories HVAC 
for the challenges of the tropics.

This voyage is the last one to be supported by the Australian Climate Change Science 
Program (Department of Environment). We thank our international GO-SHIP colleagues 
(Brian King, Greg Johnson, Toste Tanhua, Kats Katsumata, Jim Swift) for sending 
their advice on winches, wire torsion, tension and cable management to help us 
improve operation of the new systems on Investigator. We also thank Norge Larson and 
David Murphy from Seabird Electronics for their prompt and helpful advice with 
troubleshooting our conductivity cell issues.

Lastly, we are grateful to our Leg 2 Bosun, Graham McDougall, and Chief Engineer, 
Chris Minness, for their outstanding work in assisting with the winch brake failure 
incident and restoring a workable system to us. This enabled the successful 
completion of our work and their actions were truly voyage saving.

Signature


Your name     Bernadette Sloyan          Susan Wijffels
Title         Chief Scientist (Leg 1)    Chief Scientist (Leg 2)
Signature(s)	
Date          14 July 2016	

 
List of additional figures and documents

Appendix 1  CTD Calibrations Issues 
Appendix 2  Anthropogenic Trace Gases
Appendix 3  Total Dissolved Inorganic Carbon and Total Alkalinity 
Appendix 4  Temperature Microstructure
Appendix 5  XBT Calibration Projects
Appendix 6  Nitrogen processes, budgets, plankton and bacterial phylogeny 
Appendix 7  Inertial Navigation System tests
Appendix 8  Atmospheric Chemistry and Aerosols 
Appendix 9  Helium isotopes
Appendix 10 Lowered ADCP Issues

 

Appendix 1  CTD calibration issues
S.E. Wijffels, June 2016

Issue 1 – Large Conductivity Offsets


Uncalibrated CTD – bottle conductivity differences are large ~ 0.01 - 0.02, for both 
channels and both CTDs. Stations 1-47 were done with sensors calibrated in March 
2016. Note, after station 7, due to damage, the CTD was changed from # 20 to #22 but 
sensors from 20 were moved to 22 and operated out to station 46. Then we changed 
back to CTD 20 but with sensors with much older calibrations.

This is a large and surprising conductivity offset error - out of tolerance for both 
the instrument (SBE C4 and T3 and 9plus) and the calibration laboratories (SeaBird 
and CSIRO).

Steps taken to track this down at sea include:

1) Checking all SNs and calibration coefficients used on acquisition (multiple 
   times)– while we found some errors, none explained this problem
2) Checking bottle salts against historical P15S occupations. These agreed to 
   within tolerance (0.001) where they should, in the well mixed and ancient 
   North Pacific Deep Waters.
3) Analysed all past CTD calibrations on CTD data from Investigator. These all 
   showed similar sized offsets, with cells remaining stable between 
   calibrations and across buses. Most disturbingly, the primary set used on 
   our stations 1-46 had a lower offset (salty by 0.01) before it went through 
   the CSIRO calibration lab in March (now salty by 0.025). In fact, for all 
   Investigator data, a clear pattern emerged showing that all CSIRO 
   calibrations resulted in a salty offset (0.01-0.025) compared to at sea 
   bottle salts, while all SBE calibrations were fresh (0.007-0.01). This 
   pattern remains regardless of the 9plus bus used. See below.
4) Tested the raw hex data recorded by the CAP acquisition system against the 
   SBE SeaSoft processing suite, and demonstrated that the resulting data are 
   identical to within numerical precision. Thus we do not believe it to be 
   due to CAP.
5) Engaged Norge Larsen and Dave Murphy at SBE, who kindly sent suggestions on 
   what to test. At the end of process, they are equally mystified.

We suggest that the MNF work with the CSIRO calibration laboratory to try to 
understand where these offsets arise.

Issue 2 - Pressure dependent error in our secondary C-cells.

We found two types of depth dependence of CTD-bottle salt offsets in our data. Most 
T/C cell combinations give an offset that is downward increasing (or upward 
decreasing). This error is relatively small and in spec (~0.002). More concerning, 
the T/C secondary channel on CTD 20 had an offset that swings salty towards the 
surface. This persisted even when the C cell was changed! This behaviour could be 
seen on acquisition.

Below are example of the offsets, with the bottom right showing the large swing to 
salty on the secondary channels. (see pdf)

After discussions by email with Norge Larson, the linear shift with pressure is well 
known as explained here from Norge: “The linear pressure effect in salinity is a 
common feature of the SBE-4 conductivity cell. There is a pressure correction 
coefficient on the conductivity calibration sheet (CPCOR) which is the theoretical 
compression coefficient for pure borosilicate glass. In reality the conductivity 
cell exhibits a composite compression coefficient due to its hard epoxy coating. 
This expresses itself as a residual linear pressure effect of typical magnitude (0.7 
- 1) * (+0.001 psu / 1000 dbar). The physical mechanism is well studied and is 
properly corrected by adjusting the value of CPCOR to a smaller magnitude number 
(coefficient remains a negative value).”

This advice has been used in the calibration model we will use to adjust the data to 
the bottle salts.

The strong swing to salty values was not explained. However, after swapping out the 
secondary thermistor, oxygen sensor, checking the flow lines, moving the CTD to 
change the flow dynamics, we finally swapped in a THIRD C-cell. This last change 
fixed the problem. The two damaged cells (SBE 4C SNs 2312 and 2235) will be sent 
back to SeaBird for careful diagnosis. Norge was skeptical it could be a crack in 
the ceramic of the cell.

An example on this cell error can be seen in the secondary-primary differences 
below. This pattern was seen on acquisition.

Issue 3 – Calibration Model to apply to the Conductivity Data

The depth-dependent calibration changes noted above will not be removed by the 
current cell constant and offset used by CAPpro. Thus we need to include more terms. 
I tested 4 calibration models – a 7 term model used by Scripps ODF (constant plus 
quadratic in T,C and P), a fit where the SBE coefficients CTcorr and CPcorr are 
varied as well as the cell constant and offset (SBE model), and the current one used 
in CAPpro (conductivity offset and slope).

These models, were run across burst samples from both the primary and secondary 
channels for all sensor combinations, and the residuals compared. The upshot is that 
a SBE model that keeps CTcorr at the nominal value and allows CPcorr to be varied is 
the most physically sensible (based on advice from SBE) and fits as much of the 
variance as the more complex ODF model. The resulting residuals are largely 
unstructured, except for small time drifts and shifts (due to cell rinses or 
cleans). The bad C-cells in the secondary channels for stations 51-113 did not yield 
well to calibration (as expected) and this data should not be used.


Figure 1.1


Residuals in primary CTD-bottle conductivities for stations 1-46. Red is the ODF 
model, blue is the current model used in CAPpro (offset by 1e-3 S/m) and green is 
the SBE –P model (offset by 2e-3). Below (offset by -1e-3) are the variance 
accounted for by the non-standard model terms. The SBE model does as well as the 
more complex ODF model.

 
Figure 1.2: As for Figure 1.1, but for the second set of primary sensors used 
            in stations 47-140.

 
Sensor combinations and calibration dates: blue shows changes made

Sensor/   1-46   47-50  51-87  88-93  94-110  111-113   114 -
 Station  (Leg1)        (Leg2) 
--------  -----  -----  -----  -----  ------  -------  ------
T1        4722   6022   6022   6022   6022     6022     6022
          CSIRO  SBE    SBE    SBE    SBE      SBE      SBE 
          3/16   7/15   7/15   7/15   7/15     7/15     7/15

C1        3868   44425  4425   4425   4425     4425     4425
          CSIRO  SSBE   SBE    SBE    SBE      SBE      SBE 
          3/16   77/15  7/15   7/15   7/15     7/15     7/15

Pump 1    2492   8344   8344   8344   8344     8344     8344

T2        4522   6024   6024   6024   4718     4718     4718
          CSIRO  SBE    SBE    SBE    CSIRO    CSIRO    CSIRO
          3/16   7/15   7/15   7/15   10/15    10/15    10/15

C2        4426   2312   2312   2235   2235     2235     4426
          SBE    bad    bad    bad    bad      bad      SBE 
          7/15                                          7/15

Pump 2    2494   8345   8345   8345   5105     5105     5105

DO1       3154   1794   1794   1794   1794     1794     1794

DO2       3198   3199   3199   3199   3199     3198     3198

9plus     552    552    552    552    552      552      552
          (1-7)
          1243
          (8-46)




Analysis of past voyage conductivity offsets

Based on raw scan files and bottle salts

IN2016_V02
Voyage title:      SOTS: Southern Ocean Time Series automated moorings for 
                   climate and carbon cycle studies southwest of Tasmania
Mobilisation:      Hobart, Friday-Monday, 11-14 March 2016
Depart:            Monday 14th March 1000
Return:            Hobart, 0930 Saturday 16 April 2016




Table 1: Lowered CTD configuration

CTD Configuration 

UNIT                           MODEL     SERIAL NUMBER 
-----------------------------  --------  ------------------------------
CTD#20                         SBE9+ V2  552 
Primary Temperature            SBE 3T    4722 
Primary Conductivity           SBE4C     3868 
Secondary Temperature          SBE3T     4522 
Secondary Conductivity         SBE4C     Castl 3168 | casts2-39 2235 
                                         | Cast 40 4426 
Primary Pump                   SBE5      2492 
Secondary Pump                 SBE5      2494 
Primary Oxygen (AO)            SBE43     castl-1794 | From cast2-3154 
Secondary Oxygen (Al)          SBE43     casts 1-39 3159 | Cast 40-3198 
PAR (A2)                       QCP2300   70111 
Altimeter (A3)                 PA500     5301 
Transmissometer (A4)           C-Star    CST-1421DR 
Spare (A5) 
Wetlabs ECO-Chlorophyll (A6)   FLBBNTU   3698 (User supplied) 
Wetlabs ECO - Scattering (A7)  FLBBNTU   3698 (User supplied) 
LADCP Downward looking         WHM150    16710 
LADCP Upward looking           WHM300    16673 


 
Same CTD and sensors as on our voyage and large S offsets are the same. Last cast 
changed to same C sensor as our voyage 1-46 and offsets agree. This suggests it is 
not the bus but is due to the calibrations.

 
Bottle/CTD offsets on voyages leading up to V03:

IN2016_V01	
Voyage title:           HEOBI: Heard Earth-Ocean- Biosphere Interactions
Mobilisation:           Fremantle, 6th-7th January 2016
Depart:                 Fremantle, 1430 Friday 8th January 2016
Return:                 Hobart, 0800 Saturday 27th February 2016



Table 1: CTD configuration

CTD Configuration 
The CTD configuration used throughout the voyage is shown in Table 1

UNIT                          MODEL         SERIAL NUMBER 
----------------------------  ------------  ----------------------------
CTD#20 V2                     SBE9+          552 
Primary Temperature           SBE 3T         4722 
Primary Conductivity          SBE4C          3868 
Secondary Temperature         SBE3T          4522 
Secondary Conductivity        SBE4C          3168/2312 (cast 19 onwards) 
Primary Pump                  SBE5           2492 
Secondary Pump                SBE5           2494 
(AO) Primary Oxygen           SBE43          1794  
(Al) Secondary Oxygen         SBE43          3159  
(A2) PAR                      Biospherical   70111 
(A3) Altimeter                PA500          5301 
(A4) Transmissometer          C-Star         CST-1421DR 
(A5) ORP                      ORP4CTD        ORP4CTD-09/ORP4CTD-03
(A6) Fluorometer-Chlorophyll  FLBBRTD        3698 (User supplied) 
(A7) Fluorometer-Scattering   FLBBRTD        3698 (User supplied) 




 







 
Appendix 2  Anthropogenic Trace Gases
Rolf Sonnerup, U. Washington, USA 

Introduction

Oceanic distributions of the anthropogenic trace gases, chlorofluorocarbon-11 (CFC-
11), CFC-12 and sulfur hexafluoride (SF6) reveal pathways and time-scales for waters 
to move from the surface mixed layer into the interior ocean. The 1990s World Ocean 
Circulation Experiment (WOCE) global survey provided a snapshot of the oceanic 
uptake of CFCs into the thermoclines of the subtropical gyres, and into 
intermediate, deep, and abyssal waters. These tracers provide critical measures of 
how quickly the ocean interacts with the atmosphere, and its anthropogenic changes. 
This project was part of the international CLIVAR Repeat Hydrography CO2/Tracer 
Program (RH) effort to measure CFC and SF6 on all of the CLIVAR RH (now GO-SHIP) 
lines.

An important finding of the RH program thus far has been warming of bottom waters 
throughout the world ocean over the past 20 years. The P15S section is vital to the 
RH program goals because it crosses the deep western boundary current (DWBC) of the 
Southwest Pacific, an important abyssal pathway for anthropogenic change, in four 
separate locations. In 1996 and 2009, P15S measurements sampled the leading edge of 
the CFCs’ arrival in the abyssal Pacific as far north as 9ºS, in the Samoan Passage. 
The tracer observations provide an opportunity to use the CFCs to estimate the more 
difficult to quantify anthropogenic CO2 and heat burdens in the abyssal Southwest 
Pacific.

Measurements

2187 samples were collected and analyzed following Bullister and Wisegarver, 2008. 

Findings

In comparison with the most recent occupation of the P15 line for tracers (2009), we 
found

• Decreases CFCs in the upper 500m reflecting the recent (since 1994) decline 
  in atmospheric CFC levels
• At low latitudes (north of 35°S) deeper penetration of CFCs by ~ 200m
• Significant increases in the abyss, reflecting the arrival of and increases 
  in the anthropogenic influence on the abyssal Southwest Pacific. For example 
  CFC-12 increased
  o from 0.075 to 0.12 and 0.075 to 0.14 pmol kg-1 at DWBC crossings to the 
    North and South of Chatham rise
  o from 0.019 to 0.030 pmol kg-1 in the DWBC’s transit through the Samoan 
    Passage (9°S)

The abyssal CFC plume (defined as detectable values in excess of 0.005 pmol kg-1) 
had shoaled from 4000m in 1996 to 3400m in 2009 to 3000 m in 2016 at 30°S. Farther 
to the North, the abyssal plume had not shoaled significantly since 2009. Both CFCs 
were easily detectable at the seafloor over the full extent of the section from 66°S 
to the equator.

The mid-depth (1000-3000m) location where CFC-free waters are found had not moved 
significantly since 2009. However, as a consequence of the shoaling abyssal plume, 
and deepening penetration through the thermocline, the total volume of CFC free 
waters in this region was decreasing. In the locations where CFC12 was not 
detectable (North of 35S, 1500-35000m typically) we detected a bottle blank on order 
(preliminarily) of 0.005 pmol kg-1 for CFC-11. The reported CFC-11 values were not 
corrected for this possible offset. Bottle blanks of zero for SF6, CFC-12, and CCl4 
were estimated from niskin samples in this region.

 


Appendix 3  Total Dissolved Inorganic Carbon and Total Alkalinity
PI: Dr Bronte Tilbrook, CSIRO Oceans and Atmosphere, and Antarctic Climate and 
Ecosystems Co- operative Research Centre, Hobart, Tasmania

Samples were analysed for total dissolved inorganic carbon dioxide and total 
alkalinity following techniques developed for measurements in ocean waters on 
WOCE/CLIVAR sections. Certified reference materials from the Scripps Institution of 
Oceanography are analysed to determine the accuracy and precision of the 
measurements. Detailed analytical procedures are provided in Dickson et al (2007).

Water sampling

Stations sampled for total dissolved inorganic carbon and total alkalinity are shown 
in Figure 1 and listed in Table 1. For each sample, water was siphoned from a 10L 
Niskin bottle into 250 ml glass bottles using silicone tubing. The bottles were 
rinsed three times with water from the Niskin bottle and the seawater sample was 
then overflowed by about one half of the bottle volume. Each bottle had about a 5ml 
head space, and 100 microlitres of a saturated solution of mercuric chloride was 
added prior to sealing the samples using air-tight screw caps. Samples were sealed 
within one minute of collection. An additional 100 samples were collected using the 
same method from the ships underway seawater line while the ship was in transit to 
and from the P15S section. Samples were analysed onboard within 1- 3 days of 
collection.


Figure 1: Carbon water sampling sites (blue dots) for section P15S with some 
          CTD station numbers shown.

 
Total dissolved inorganic carbon:

Total dissolved carbon dioxide (TCO2) was analysed using a SOMMA system and 5011 UIC 
coulometer (Johnson et al., 1993 and Dickson et al.,2007). The SOMMA loads seawater 
from a sample bottle into a calibrated pipette (21.8ml) that is thermostated to 
20°C. The sample in the pipette is dispensed into a stripping chamber to which 1 ml 
of a 10% (v/v) solution of phosphoric acid has been added. High purity nitrogen 
carrier gas (>99.995%) is bubbled through the water to extract the CO2 from the 
sample. The CO2 in the carrier gas stream flows into the cathode compartment of a 
coulometer cell where it is quantitatively trapped in an ethanolamine solution. The 
absorbed CO2 reacts to form hydroxyethylcarbamic acid, causing a change in the 
colour of the cell solution due to the presence of a thymolphthalein pH indicator in 
the solution. Base is generated at the cell cathode, until the solution colour 
returns to its starting point.

About 36 samples are analysed before a new coulometer cell and solution are 
required. This provides enough capacity for a whole station with duplicates, and 
certified reference material. The efficiency of the coulometric method is determined 
by injecting known amounts of pure CO2 (>99.99%) at the beginning of each new cell. 
After the calibration of the SOMMA is complete, test seawater samples are analysed 
followed by certified reference material from the Scripps Institution of 
Oceanography. The SOMMA system also loads sample into a Seabird conductivity cell, 
which is used along with a temperature to determine the salinity of the sample. 
Concentrations are in units of micromol kg-1.

For legs 1 and 2, a total of 2625 water samples were analysed for TCO2 (Figure 2), 
with an additional 269 duplicate samples analysed from shallow, mid-depth and deep 
samples to cover the range of TCO2 values through the water column. Certified 
Reference Material from Scripps Institution of Oceanography (Batch 363) was analysed 
at the beginning and end of the coulometer cells. Over a typical cell, the 
measurements of reference material drifted by 1-2 micromol kg-1. The average offset 
for each cell was used to correct the final TCO2 values of the samples. The initial 
analysis of duplicate samples gave an average absolute difference of 1.71 +- 1.24 
micromol kg-1 (s.d., n=269) indicating a precision of better than 2 micromol kg-1.


Total alkalinity:

Automated open-cell potentiometric titrations were used to measure total alkalinity 
(TA) (Dickson et al, 2007). Two systems were operated side by side, with Tiamo 
software used to control the titrations. Each titration was performed on a 100ml 
seawater sample measured using an Metrohm Dosino 800 burette and a 5ml burette on a 
Metrohm Titrando 904 was used to deliver acid titrant. The delivery volumes for the 
Titrando and Dosino burettes were calibrated in the laboratory prior to cruise. 
Metrohm combination pH electrodes were used to track the progress of the titrations. 
Refrigerated water baths were used to keep the acid titrant and sample at a constant 
temperature of 20.5C for each analysis.

For a titration, the sample is first acidified to a pH of about 3.6 using 0.1N HCl 
titrant, which contains 0.6 mol Kg-1 sodium chloride to match the ionic strength of 
seawater. After the initial addition of acid, the acidified seawater is stirred for 
10 minutes to remove dissolved CO2 from the sample. Smaller aliquots of titrant are 
then added and acid volume and electrode millivolt readings is recorded by the Tiamo 
software until a pH of about 2.9 is reached. A non-linear fitting routine similar to 
Johansson and Wedborg (1982) and Dickson et al. (2007) was used to calculate TA. The 
routine used was compared to a calculated result for data published in Dickson et al 
(2007) and both methods agree within 0.01%.

The performance of the titration systems was monitored using certified seawater 
reference material from the Scripps Institution of Oceanography (Batch 363), and by 
using duplicate water samples collected from the CTD casts. The duplicate water 
samples were collected from surface, mid-depth and deep water samples to cover the 
range of total alkalinity values for the water column.  There was about a 6 micromol 
kg-1 offset between the measured and certified reference material values for TA due 
to the acid titrant having a slightly different concentration than originally 
assigned. Evaporation of acid titrant was also a source of a small drift, and the 
titrant was regularly replaced with new titrant that prepared prior to the cruise 
and stored in sealed borosilicate glass bottles. The average offset between the 
measured and certified reference material values were used to correct the TA for 
samples from each station.

For the section, 2628 seawater samples were analysed (Figure 3), plus 224 duplicate 
samples. The analysis of duplicate samples for both titration systems showed average 
absolute differences of 0.90 +- 0.90 micromol kg-1 (s.d., n=119) and 0.97 +- 1.17 
mircomol kg-1 (s.d. n=106), indicating a precision of better than +-1 micromol kg-1.


Figure 2: Preliminary total dissolved inorganic carbon (micromole kg-1) 
          measurements along the P15S section, Apr-Jun 2016.

Figure 3: Preliminary total alkalinity (micromole kg-1) measurements along the 
          P15S section, Apr-Jun 2016.

 

Table 1: Station/CTD numbers (STNNBR), locations and numbers of TCO2 and TA 
         samples.

STN      DATE      TIME                           DEPTH  SAMPLE 
NBR    yyyymmdd    hhmm    LATITUDE   LONGITUDE    db    NUMBER
---    --------    ----    --------   ---------   -----  ------
  2    20160504    0844    -66.332    -170.008    3277    36
  3    20160505    0320    -65.662    -170.032    3297    32
  4    20160505    1320    -64.995    -170.016    2836    31
  5    20160505    2145    -64.502    -170.004    2348    2
  6    20160506    0501    -63.990    -170.042    2807    31
  8    20160508    0141    -63.001    -170.032    3046    33
  9    20160508    0650    -62.499    -169.992    2539    2
 11    20160508    1535    -62.003    -170.004    3360    33
 12    20160508    2149    -61.492    -169.997    3470    2
 13    20160509    1631    -61.005    -170.004    4483    33
 14    20160509    2335    -60.502    -169.991    3951    5
 15    20160511    1151    -60.000    -170.005    3905    35
 17    20160512    2000    -58.994    -169.998    4763    30
 19    20160513    1219    -58.001    -170.010    4432    34
 20    20160513    1911    -57.504    -170.006    5019    36
 21    20160514    1414    -57.002    -169.998    5078    33
 22    20160514    0926    -56.498    -170.009    5090    2
 23    20160514    2122    -56.002    -169.008    5121    36
 24    20160515    0441    -55.514    -170.011    4833    2
 25    20160515    1108    -54.996    -170.002    4843    30
 26    20160515    2000    -54.500    -170.003    4831    10
 27    20160516    0249    -53.996    -169.985    5142    30
 28    20160516    0954    -53.501    -169.991    5226    10
 29    20160516    1637    -53.004    -170.011    5220    30
 30    20160517    0016    -52.505    -170.010    5161    10
 31    20160517    0755    -52.002    -170.078    4913    30
 32    20160517    1436    -51.492    -170.016    4732    10
 33    20160517    2141    -51.002    -170.010    5248    32
 34    20160518    0420    -51.497    -169.996    5052    10
 35    20160518    1137    -50.006    -169.993    5384    33
 36    20160518    1915    -49.504    -170.017    5220    10
 37    20160519    0215    -48.995    -170.004    5262    30
 38    20160519    0915    -48.502    -170.000    5298    10
 39    20160519    1559    -47.995    -169.993    5310    32
 40    20160519    2338    -47.503    -169.989    5379    10
 41    20160520    0649    -47.109    -170.466    5412    32
 42    20160520    1348    -46.719    -170.911    5296    10
 43    20160521    0116    -46.326    -171.376    5100    32
 44    20160522    0021    -45.176    -172.736    4665    32
 45    20160522    1003    -44.835    -173.141    3830    31
 46    20160522    1639    -44.525    -173.502    3414    28
 47    20160522    2335    -44.328    -173.746    3102    15
 48    20160523    0620    -44.156    -173.938    1892    26
 49    20160523    1542    -42.931    -174.785    1057    16
 50    20160523    1819    -42.746    -174.653    1584    23

STN      DATE      TIME                           DEPTH  SAMPLE 
NBR    yyyymmdd    hhmm    LATITUDE   LONGITUDE    db    NUMBER
---    --------    ----    --------   ---------   -----  ------
 51    20160528    1614    -42.400    -174.410    2666    21
 52    20160528    2129    -42.167    -174.250    2866    11
 53    20160529    0310    -41.717    -173.949    3116    24
 54    20160529    0920    -41.273    -173.637    3292    8
 55    20160529    1603    -40.832    -173.332    4178    29
 56    20160529    2203    -40.392    -173.024    4592    9
 57    20160530    0447    -39.958    -173.706    4739    30
 58    20160530    1214    -39.511    -172.414    4776    8
 59    20160530    2033    -39.068    -172.117    4861    30
 60    20160531    0340    -38.628    -171.808    4929    8
 61    20160531    1054    -38.187    -171.501    4945    32
 62    20160531    1739    -37.757    -171.201    5028    8
 63    20160531    0046    -37.307    -170.893    5146    8
 64    20160601    0745    -36.871    -170.606    5303    30
 65    20160601    1500    -36.450    -170.294    5087    9
 66    20160601    2152    -36.002    -170.002    5084    31
 67    20160602    0711    -35.680    -170.007    4372    8
 68    20160602    1005    -35.337    -170.000    4909    30
 69    20160602    1714    -35.014    -169.995    5264    8
 70    20160602    2356    -34.505    -170.006    5505    29
 71    20160603    0655    -34.012    -169.999    5547    4
 72    20160603    1409    -33.501    -170.000    5446    28
 73    20160603    2112    -33.000    -170.006    5591    4
 74    20160604    0425    -32.500    -169.997    5572    28
 75    20160604    1227    -32.002    -169.995    5700    4
 76    20160604    1944    -31.499    -169.994    5553    28
 77    20160605    0223    -31.023    -169.998    5630    4
 78    20160605    0936    -30.512    -169.996    5556    32
 79    20160605    1640    -29.999    -169.993    5437    4
 80    20160605    2353    -29.501    -170.000    5226    29
 81    20160606    0653    -29.006    -169.995    5605    4
 82    20160606    1409    -28.503    -169.999    5454    28
 83    20160607    1526    -27.984    -169.991    5264    2
 84    20160608    1024    -27.272    -169.998    5464    30
 85    20160608    1910    -26.495    -169.996    5637    8
 86    20160609    0251    -26.000    -169.993    5607    30
 87    20160609    1031    -25.509    -169.998    5836    5
 88    20160609    1806    -24.999    -170.002    5653    30
 89    20160610    0142    -24.501    -170.001    5670    7
 90    20160610    0920    -24.000    -170.001    5689    30
 91    20160610    1652    -23.505    -169.996    5676    8
 92    20160611    0026    -22.999    -169.996    5701    29
 93    20160611    0802    -22.501    -170.000    5663    7
 94    20160611    1530    -22.002    -170.000    5636    32
 95    20160611    2253    -21.503    -169.999    5430    7
 96    20160612    0552    -20.998    -169.999    5482    30
 97    20160612    1247    -20.503    -169.999    5675    8
 98    20160612    2014    -20.000    -170.002    5341    30
 99    20160613    0303    -19.498    -170.003    4915    7
100    20160613    0933    -19.004    -170.058    2989    24
101    20160613    1503    -18.503    -170.002    5269    12

STN      DATE      TIME                           DEPTH  SAMPLE 
NBR    yyyymmdd    hhmm    LATITUDE   LONGITUDE    db    NUMBER
---    --------    ----    --------   ---------   -----  ------
102    20160613    2139    -18.001    -170.000    4919    30
103    20160614    0652    -17.499    -170.001    5037    9
104    20160614    1319    -17.003    -170.002    5005    30
105    20160614    1949    -16.504    -170.000    5226    8
106    20160615    0210    -16.003    -170.001    5150    28
107    20160615    0854    -15.498    -170.001    5095    7
108    20160615    1532    -15.005    -170.000    4826    30
109    20160615    2052    -14.666    -169.999    3330    7
110    20160616    0140    -14.282    -169.998    3546    23
111    20160616    0643    -13.972    -169.999    2972    6
112    20160616    1114    -13.819    -169.999    4338    23
113    20160616    1618    -13.504    -170.002    4888    7
114    20160616    2254    -13.000    -169.999    4980    29
115    20160616    0522    -12.499    -169.999    5012    7
116    20160617    1145    -11.998    -170.003    5097    25
117    20160617    1825    -11.496    -169.999    5069    7
118    20160618    0037    -11.001    -170.000    5135    24
119    20160618    0722    -10.500    -169.999    4878    7
120    20160618    1433     -9.925    -169.629    5227    24
121    20160618    2241     -9.499    -168.998    5357    18
122    20160619    0543     -8.997    -168.875    4891    19
123    20160619    1209     -8.495    -168.749    5182    18
124    20160619    1858     -8.001    -168.616    5212    24
125    20160620    0121     -7.501    -168.751    5287    20
126    20160620    0806     -7.000    -168.751    5676    23
127    20160620    1456     -6.502    -168.749    5553    8
128    20160620    2139     -6.000    -168.751    5679    29
129    20160621    0434     -5.502    -168.750    5476    8
130    20160621    1117     -5.000    -168.750    5583    28
131    20160621    1750     -4.501    -168.750    5555    8
132    20160622    0021     -4.001    -168.751    5178    28
133    20160622    0706     -3.502    -168.750    5023    8
134    20160622    1338     -3.000    -168.751    5388    30
135    20160622    2010     -2.499    -168.750    5346    8
136    20160623    0235     -2.001    -168.750    3413    24
137    20160623    0809     -1.501    -168.749    5926    12
138    20160623    1514     -1.001    -168.750    5803    28
139    20160623    2208     -0.501    -168.750    5512    8
140    20160624    0455     -0.002    -168.750    5628    29

 


Radiocarbon in total dissolved inorganic carbon:
PIs: Dr Ann McNichol, Woods Hole Oceanographic Institution, Massachusetts, USA 
     Dr Robert Key, Princeton University, New Jersey, USA

A total of 600 samples were collected for analysis of 14C. Seawater samples were 
collected about every 4 to 8 CTD stations (Table 2) using a combination of shallow 
sampling (upper 2000m) and sampling through the entire water column. The samples 
were collected in cleaned one liter ground- glass stoppered, borosilicate glass 
bottles. Silicon tubing attached to Niskin bottle spigots was used to fill the 
bottles. Each bottle was first filled about 30% as a rinse, followed by filling and 
overflowing the bottle by about 50%. Samples were preserved by adding 100 
microlitres of a saturated mercuric chloride solution. The ground glass necks of the 
sample bottles were dried and Apiezon grease applied to the stopper before sealing. 
Samples will be analysed using an accelerator mass spectrometer at Woods Hole 
Oceanographic Institution.


Table 2: Station/CTD numbers (STNNBR), locations and numbers of radiocarbon 
         samples.

         STNNBR  DATE      TIME  LATITUDE  LONGITUDE  DEPTH    14C
                 yyyymmdd  hhmm                         db   samples
         ------  --------  ----  --------  ---------  -----  -------
             3   20160505  0320  -65.662   -170.032    3297    32
             6   20160506  0501  -63.990   -170.042    2807    32
            13   20160509  1631  -61.005   -170.004    4483    32
            21   20160514  1414  -57.002   -169.998    5078    32
            29   20160516  1637  -53.004   -170.011    5220    32
            35   20160518  1137  -50.006   -169.993    5384    32
            41   20160520  0649  -47.109   -170.466    5412    32
            45   20160522  1003  -44.835   -173.141    3830    31
            51   20160528  1614  -42.400   -174.410    2666    16
            55   20160529  1603  -40.832   -173.332    4178    16
            61   20160531  1054  -38.187   -171.501    4945    32
            66   20160601  2152  -36.002   -170.002    5084    16
            72   20160603  1409  -33.501   -170.000    5446    16
            78   20160605  0936  -30.512   -169.996    5556    32
            86   20160609  0251  -26.000   -169.993    5607    16
            94   20160611  1530  -22.002   -170.000    5636    32
           100   20160613  0933  -19.004   -170.058    2989    16
           106   20160615  0210  -16.003   -170.001    5150    16
           112   20160616  1114  -13.819   -169.999    4338    23
           118   20160618  0037  -11.001   -170.000    5135    16
           121   20160618  2241   -9.499   -168.998    5357    18
           124   20160619  1858   -8.001   -168.616    5212    23
           130   20160621  1117   -5.000   -168.750    5583    16
           134   20160622  1338   -3.000   -168.751    5388    16
           140   20160624  0455   -0.002   -168.750    5628    25



pH and total alkalinity
PI: Professor Andrew Dickson, Scripps Institution of Oceanography

Samples for calibration of sensors on SOCCOM floats were collected from Niskin 
bottles in the upper 2000m of the water column. Floats were deployed as the ship was 
leaving the CTD station and just after completion of the CTD cast. The water samples 
were collected in pre-cleaned glass-stoppered borosilicate bottles, the same as for 
radiocarbon samples. Each bottle was first filled about 30% as a rinse, followed by 
filling and overflowing the bottle by about 50%. Samples were preserved by adding 
100 microlitres of a saturated mercuric chloride solution. Apiezon grease was 
applied to the ground glass stoppers and the bottles sealed. Samples will be 
analysed at Scripps Institution of Oceanography using spectrophotometry (pH) and 
open cell potentiometric titration (total alkalinity), as described in Dickson et al 
(2007).

 
Table 3: Station/CTD numbers (STNNBR), locations and numbers of samples for pH 
         and TA analyses.

         STNNBR  DATE      TIME  LATITUDE  LONGITUDE  DEPTH  NUMBER
                 yyyymmdd  hhmm                         db   SAMPLES
         ------  --------  ----  --------  ---------  -----  -------
             3   20160505  0320  -65.662   -170.032    3297    28
             6   20160506  0501  -63.990   -170.042    2807    29
            11   20160508  1535  -62.003   -170.004    3360    27
            15   20160511  1151  -60.000   -170.005    3905    27
            19   20160513  1219  -58.001   -170.010    4432    23
            25   20160515  1108  -54.996   -170.002    4843    24
            31   20160517  0755  -52.002   -170.078    4913    24
            35   20160518  1137  -50.006   -169.993    5384    24
            39   20160519  1559  -47.995   -169.993    5310    24
            43   20160521  0116  -46.326   -171.376    5100    23
            57   20160530  0447  -39.958   -173.706    4739    25
            61   20160531  1054  -38.187   -171.501    4945    24

 

Dissolved Calcium and Magnesium
PI: Professor Stephen Eggins, Australian National University, Canberra, ACT

Duplicate samples were collected from 10 depths (approx. 20, 50, 100, 150, 200, 300, 
500, 750, 1000 and 2000m) at each of the stations listed in Table 3. Seawater was 
collected into 30m plastic luer-lok syringes. The syringes were rinsed three times 
with sample, filled, and a 0.22 micron PES membrane filter attached to the syringe. 
The filter was flushed with about 10ml of seawater and 5ml polypropylene vials were 
rinsed three times with filtered water. The vials were then filled and capped and 
stored at room temperature in sealed plastic bags and returned to Australia for 
analysis by isotope dilution using a multi collector inductively couple plasma mass 
spectrometer.

Table 4: Station/CTD numbers (STNNBR), locations and numbers of of calcium and 
         magnesium water column samples.


         STNNBR  DATE      TIME  LATITUDE  LONGITUDE  DEPTH  NUMBER
                 yyyymmdd  hhmm                         db   SAMPLES
         ------  --------  ----  --------  ---------  -----  -------
             5   20160505  2145  -64.502   -170.004    2348    10
            12   20160508  2149  -61.492   -169.997    3470    10
            17   20160512  2000  -58.994   -169.998    4763    10
            23   20160514  2122  -56.002   -169.008    5121    10
            30   20160517  0016  -52.505   -170.010    5161    10
            37   20160519  0215  -48.995   -170.004    5262    10
            40   20160519  2338  -47.503   -169.989    5379    10
            43   20160521  0116  -46.326   -171.376    5100    10
            45   20160522  1003  -44.835   -173.141    3830    10
            53   20160529  0310  -41.717   -173.949    3116    10
            59   20160530  2033  -39.068   -172.117    4861    10
            64   20160601  0745  -36.871   -170.606    5303    10
            72   20160603  1409  -33.501   -170.000    5446    10
            78   20160605  0936  -30.512   -169.996    5556    10
            82   20160606  1409  -28.503   -169.999    5454    10
            86   20160609  0251  -26.000   -169.993    5607    10
            92   20160611  0026  -22.999   -169.996    5701    10
            98   20160612  2014  -20.000   -170.002    5341    10
           104   20160614  1319  -17.003   -170.002    5005    10
           110   20160616  0140  -14.282   -169.998    3546    10
           116   20160617  1145  -11.998   -170.003    5097    10
           122   20160619  0543   -8.997   -168.875    4891    9
           128   20160620  2139   -6.000   -168.751    5679    10
           134   20160622  1338   -3.000   -168.751    5388    10
           140   20160624  0455   -0.002   -168.750    5628    9


References

Dickson, A.G., Sabine, C.L and Christian, J.R. (Eds) (2007). Guide to Best 
    Practices for Ocean CO2 Measurements. PICES Special Publication 3.

Johansson, O. and Wedborg, M. (1982) Oceanologica Acta, 5, pp 209–210.

Johnson, K.M., Wills, K.D., Butler, D.B., Johnson, W.K., and Wong, C.S. 
    (1993). Coulometric total carbon dioxide analysis for marine studies: 
    Maximizing the performance of an automated continuous gas extraction 
    system and coulometric detector. Marine Chemistry, 44, pp 167–189.

 


APPENDIX 4  TEMPERATURE MICROSTRUCTURE

PI Jonathon Nash, U. Oregon 
Report by Esmee Van Wijk, CSIRO

Chipods are instruments that measure high frequency temperature and instrument 
motion at 100 Hz. The data is used to estimate mixing rates; the dissipation rate of 
small-scale temperature variance and the turbulent diffusivity of heat.

There were 4 instrument packages installed on the 36 bottle rosette; 2 upward 
looking and 2 downward looking chipods.  These were configured so that the upward 
thermistors were raised above the rosette frame near the outer rim, and on a stalk 
to ensure a clear view of the water passing over the package. The downward 
thermistors are more subject to contamination by deflection of the fluid around the 
instrument as they are located above the bottom limit of the rosette frame but with 
as clear a view of the water column as possible. The instruments are powered by 2 
Lithium D-cell batteries, are internally recording and are pressure rated to 6000db.

Even though the chipods record all data internally onto memory cards, the data was 
downloaded every two days. It would take 25-40 mins to download each instrument (if 
everything was working perfectly) and there was only just enough time to do this in 
the time we needed to turn around the rosette and get it back into the water. It 
required one person to download the chipods, which was a significant diversion of 
time away from the core work of the sampling team. It was also necessary to then 
back up the data from the mixing computer onto a hard drive and then onto the 
server.
Generating check plots to make sure that the instruments were working correctly took 
additional time. All of this was only possible because we had one extra volunteer 
from another program who was able to assist with the CTD sampling. For future 
cruises, the chipod team should send their own technician or ensure that these are 
internally recording with no downloading required as this extra work had not been 
considered when planning the staffing for this voyage.

Problems:

1. Often the downloading would hang on a particular file and the mini host 
   logger would not respond. You would then need to work out which file was 
   causing the problem and then download all of the other files around this 
   one individually. No matter how many times you would try to download the 
   affected file, it would continually crash.
2. Occasionally one of the instruments would get stuck in a loop where it 
   would run strange characters across the data screen. The only way to fix 
   this would be to disconnect the USB cable and the sensor cable (difficult 
   with a rosette that is being sampled and with the pressure case right 
   inside the internals the only way this be done was by taking bottles off 
   the CTD after sampling had been completed, which then delayed the CTD for 
   the next station.
3. Once when having the above problem I was not able to communicate with the 
   instrument after three separate tries of disconnecting and reconnecting. I 
   left this instrument and downloaded the others and then disconnected and 
   reconnected once again and it worked on the fourth time. This kind of 
   troubleshooting can take up a lot of extra time.
4. I needed to replace four thermistors during Leg 2 of the voyage, plus two 
   pressure cases and loggers, as well as a sensor cable due.
5. After cast 83 where the CTD hit bottom, the two upward thermistors were 
   sheared off and the upward stalk had collapsed. I replaced the thermistors 
   and re-attached the upward stalk to the frame - this was not exactly at the 
   same height as it had been before.
6. Something to emphasise (and that would have been handy to know from the 
   start) is that if you are having problems it is worth forcing the 
   instrument to start logging by typing in the ‘sl’ (start logging) command, 
   waiting for a few seconds and then hitting the space bar to see if bytes 
   are being written to file. If this is the last thing you do before 
   disconnecting the USB it would often work.


 



 
APPENDIX 5  XBT CALIBRATION PROJECTS

Ann Thresher and Rebecca Cowley

XBTs measure upper ocean temperatures using a thermistor, and a calculated depth 
based on an assumed fall rate and time. It has been shown that this fall rate has 
changed over the history of the XBT resulting in a bias of the data in the archives.

In order to compute the real fall rate for XBTs of various vintages, it is necessary 
to drop them coincident with a CTD. An approximation of the correct fall rate is 
then calculated using the upper ocean thermal structure, matching features and 
generating new fall-rate coefficients. CSIRO has led this effort with Rebecca Cowley 
conducting these experiments whenever possible in order to completely characterize 
these changes through time.

XBTs of various ages were loaded onto Investigator with the aim of dropping them 
with CTDs during IN2016-V03. Because of the latitude range covered, this also gives 
us information about fall rates in water of different temperatures (which is also 
suspected of affecting XBT speed).

Two systems, the Ship’s and the CSIRO Wireless systems, were used to simultaneously 
drop XBTs as a CTD was deployed. The goal was to complete as many XBTs as possible 
before the CTD dropped below their maximum depth. In most cases, we managed to drop 
4-6 XBTs per system before the CTD reached 700-800db, providing good data for the 
comparison. More were dropped if they were shorter range XBTs or failed early.

During leg1, we dropped a total of 112 XBTs (62 on the CSIRO wireless system and 59 
on the ship’s system). During leg 2, we dropped a total of 88 XBTS using the Ship’s 
system and 86 using the CSIRO Wireless system. A few of these were dropped for 
training purposes and will not be useful for analysis. For the entire voyage, 32 
CTDs were used at latitudes ranging from 66o S to 6o 30 S. The table below shows the 
CTD stations vs XBT deployments.

Problems encountered were, for the most part, minor. Some boxes of XBTs had more 
failures (early wire break, no traces) than others. T-5 XBTs (rated to 1800db) were 
found to be useless and so were abandoned though we may try to collect some data 
when over shallower water. Given that these were manufactured in 1990, their failure 
is not surprising.

The wireless system sometimes had communication problems with the computer and both 
the box and the computer had to be rebooted several times during the tests. The Ship 
system had no issues, though it appeared to renumber at least one drop.

Some XBTs were misidentified early in the trip and these can hopefully be corrected. 
Others were dropped from the wrong system and so the serial numbers, batch dates, 
etc will need to be adjusted.  All notes are in the log sheets.

All data and the summary log sheets can be found on the science drive in the XBT 
folder.

 

Latitude        CTD #       Ship System       CSIRO Wireless System
--------------  ----------  ----------------  ------------------------
43°32’S to      NA.         12 – T5 for hit   T5 for hit 
43°41’S         26/04/2016  bottom testing    12 – bottom testing
55°30’S to      NA.         12 – T5 for hit   12 – T5 for hit
55°36’S         29/04/2016  bottom testing    bottom testing
66°30’S         2           3 – DB            4 – DB
62°30’S         9           4 – DB            4 – DB
62°S            10          3 – DB            3 – DB
62°S            11          3 – DB            3 – DB
61°30’S         12          3 – DB            1 – DB
60°S            15          3 – DB            2 – DB
59°S            17          3 – DB            3 – DB
58°30’S         18          3 – DB            3 – DB
58°S            19          3 – DB            3 – DB
57°S            21          3 – DB            3 – DB
56°30’S         22          3 – DB            3 – DB
55°30’S         24          4 – DB            3 – DB
----------------------------------------------------------------------
Totals Leg 1:   12          62                59
      
36°S            66          3 – T-5 –         3 – T-5 –
                            training/testing  training/testing
35°40’S         67          3 – DB            3 – DB  mis-id’d as T-5s
35°20’S         68          4 – DB            4 – DB
35°S            69          4 – DB            4 – DB
34°30’S         70          4 – DB            4 – DB
34°S            71          4 – DB            4 – DB
13°30’S         113         4 – T-4           4 – T-4
13°S            114         4 – T-4           4 – T-4
12°30’S         115         6 – T-4           5 – T-4
12°S            116         5 – T-4           5 – T-4
11°30’S         117         5 – T-4 serial    5 – T-4 serial
                            #s switched       #s switched
                            with wireless     with ship
11°S            118         5 – T-4           5 – T-4
10°30’S         119         6 – T-4           5 – T-4 Bad box
9°55’S          120         7 – T-4           7 – T-4
9°S             122         4 – DB batch      4 – DB batch
                            date wrong        date wrong
8°30’S          123         4 – DB            4 – DB
8°S             124         4 – DB            4 – DB
7°30’S          125         4 – DB            4 – DB
7°S             126         4 – DB            4 – DB
6°30’S          127         4 – DB            4 – DB
----------------------------------------------------------------------
Totals Leg 2:   20          88                86
======================================================================
Overall totals  32          150               145

 


APPENDIX 6  NITROGEN PROCESSES, BUDGETS, PLANKTON AND BACTERIAL PHYLOGENY 
            ALONG THE P15 GO-SHIP LINE: FROM THE ICE EDGE UP TO THE EQUATOR.

by Eric Raes, U.W.A 

Introduction

The supply of biologically-available nitrogen (N) can be a bottleneck in the 
efficiency of the biological oceanic carbon pump. Reactive nitrogen (Nr) in the open 
ocean regulates primary productivity and a cascade of associated carbon-nitrogen 
coupled transformations mediated by both eukaryotic and prokaryotic microorganisms 
(Ward et al., 2013). An understanding of potential alterations at the base of the 
food chain particulary reductions in planktonic biomass is essential, as a decline 
(Boyce et al., 2010) or communty shift (Montes-Hugo et al., 2009) in primary 
productivity will impact ecosystem services, such as O2 production, carbon 
sequestration, biogeochemical cycling and fisheries (Lehodey et al., 2010, Hollowed 
et al., 2013, Séférian et al., 2014).

Rationale

While we are getting better insights in the microbial community and their taxonomy, 
uptake and rate measurements of N and C are still very sparse throughout the world 
oceans and are a high priority to accurately quantify C, N cycles and the associated 
primary productivity. Our research is motivated by the need to further enhance our 
fundamental knowledge of the N-cycle and the different biogeochemical and physical 
parameters that control primary productivity.

Aims

The main aim of this study was to contribute knowledge of important fluxes of key 
elements (nitrogen and carbon) in this largely unstudied region (from a biological 
oceanography point of view). In order to tackle this aim we investigated the 
relationships between dissolved inorganic nutrients, phytoplankton pigment 
composition, microbial community structures, dinitrogen fixation rates, NO3- and 
NH4+ assimilation rates, and nitrification rates along the p15 GO-SHIP line from 
66˚S to 0˚S.

Specifically our objectives were:

1. To test whether N2 fixation is a process facilitating planktonic CO2 
   fixation along the whole p15 line.
2. To unravel the biogeochemical components of the N-cycle that control 
   primary productivity and N regeneration.
3. To link primary productivity and N transformation processes to functional 
   phylogenetic groups of marine protists and microbes (archaea and bacteria) 
   involved in the C and N cycle through targeted molecular approaches which 
   elucidate community structure and activity (functional gene expression).

 
Outcomes and benefits

The data arising from this study will be a major source of new information on N2 
fixation rates and the controls of the N-cycle contributing to regional primary 
productivity in the different water masses along the p15 GO-SHIP line. A basic 
understanding of the biological and physical oceanographic parameters that control 
primary productivity in the world’s oceans is crucial to maintain clear conservation 
strategies of the natural marine ecology (Burrows et al., 2011). These data will 
provide new insights that will hopefully allow us to better understand, predict and 
manage the impacts of human induced climate changes.

Methods

Samples were taken for

• Picoplankton analysis, using flowcytometry back on land
  a. collaborations with University of Technology Sydney (UTS) and Macquarie 
     University
• Chlorophyll a and phytoplankton pigment analysis, using HPLC back on land
  a. collaborations with CSIRO, University of Tasmania (UTAS) and Alfred 
     Wegner Institute (AWI)
• DNA analyses using targeted functional gene expression analyses and high-
  throughput sequencing back on land
  a. collaborations with CSIRO and AWI
• Primary productivity, following isotopic tracer incorporation into the 
  particulated matter, using stable isotopes 13C, aboard using incubation bins
  a. collaborations with AWI
• Dissolved inorganic nitrogen uptake measurements, using standard 15N 
  protocols, aboard using incubation bins
  a. collaborations with AWI
• N2-fixation rates, using 15N gas as an injected tracer to measure fixation 
  rates, aboard using incubation bins
  a. collaborations with Southern Cross University and AWI
• Nitrification rates
  a. collaborations with AWI 

Note:

a. We have collected the first dissolved inorganic nitrogen assimilation and 
   fixation rates along the entire p15 Line. These data will fill in a major 
   knowledge gap in regards to N and C cycling in the world open oceans.
b. We have collected the first high resolution (every half a degree and depth 
   stratified) data set for DNA analysis stretching from the ice edge up to 
   the equator.
c. All these samples will be analysed back on land so unfortunately we don’t 
   have any preliminary results.

 
IN2016_V03 Genomics team: Nicole Hellessey, Swan Sow, Gaby Paniagua Cabarrus, 
Bernhard Tschitschko and Eric Raes


References:

Boyce, D. G., Lewis, M. R. & Worm, B. 2010. Global phytoplankton decline over 
    the past century. Nature, 466, 591-596.

Burrows, M. T., Schoeman, D. S., Buckley, L. B., Moore, P., Poloczanska, E. 
    S., Brander, K. M., Brown, C., Bruno, J. F., Duarte, C. M., Halpern, B. 
    S., Holding, J., Kappel, C. V., Kiessling, W., O’Connor, M. I., Pandolfi, 
    J. M., Parmesan, C., Schwing, F. B., Sydeman, W. J. & Richardson, A. J. 
    2011. The Pace of Shifting Climate in Marine and Terrestrial Ecosystems. 
    Science, 334, 652-655.

Hollowed, A. B., Barange, M., Beamish, R. J., Brander, K., Cochrane, K., 
    Drinkwater, K., Foreman, M. G., Hare, J. A., Holt, J. & Ito, S.-i. 2013. 
    Projected impacts of climate change on marine fish and fisheries. ICES 
    Journal of Marine Science: Journal du Conseil, 70, 1023-1037.

Lehodey, P., Senina, I., Sibert, J., Bopp, L., Calmettes, B., Hampton, J. & 
    Murtugudde, R. 2010. Preliminary forecasts of Pacific bigeye tuna 
    population trends under the A2 IPCC scenario. Progress in Oceanography, 
    86, 302-315.

Montes-Hugo, M., Doney, S. C., Ducklow, H. W., Fraser, W., Martinson, D., 
    Stammerjohn, S. E. & Schofield, O. 2009. Recent changes in phytoplankton 
    communities associated with rapid regional climate change along the 
    western Antarctic Peninsula. Science, 323, 1470-1473.

Séférian, R., Bopp, L., Gehlen, M., Swingedouw, D., Mignot, J., Guilyardi, E. 
    & Servonnat, J. 2014. Multiyear predictability of tropical marine 
    productivity. Proceedings of the National Academy of Sciences, 201315855.

Ward, B., Voss, M., Bange, H. W., Dippner, J. W., Middelburg, J. J. & Montoya, 
    J. P. 2013. The marine nitrogen cycle: recent discoveries, uncertainties.

 


APPENDIX 7  INERTIAL NAVIGATION SYSTEM TESTS

By Tobias Aldridge 
Device Description:

The PHINS (PHotonic Inertial Navigation System) is a device capable of measuring all 
navigational parameters associated with the motion of a vehicle (e.g. heading, 
speed, position, and attitude). Designed to be used for applications such as AUV 
navigation, the PHINS can accept many forms of navigational aiding (e.g. GPS, 
acoustic, pressure, etc.); however, the unit is also capable of operating in the 
absence of external aids. The challenge is that the navigational accuracy of PHINS 
units degrades the longer they operate without said aiding. As the navigational 
accuracy depends heavily on the initial alignment, which in turn is a function of 
the forcing around the z-axis, the rate of degradation will also increase as a 
function of latitude.

What measurements, and where?

This cruise provided the perfect opportunity to test the behaviour of the PHINS 
technology at a range of different latitudes, with the aim of quantifying the effect 
of latitude on the accuracy of heading and position. To this end, the PHINS was 
operated continuously, with a repeating 12 hour testing regime, for the duration of 
the voyage. This testing regime included 2 hours of operation with GPS aiding for 
the calibration phase of the testing, and then 10 hours operation with no aiding, to 
measure the quality of the positioning.

Preliminary findings:

A very clear trend of increasing heading accuracy was found with a decreasing 
latitude, shown in Figure 1. This was expected, as the ability of an INS device to 
align with North is reduced with increasing latitude.


Figure 1: Preliminary results for PHINS standard deviation on heading. One 
          data point per test. The device is considered aligned when the 
          heading standard deviation is below 0.1 degrees


In the general operations on board an AUV, the PHINS will be supplemented with a 
feed from the on board Doppler velocity log (DVL), tracking the velocity of motion 
over the sea floor. For this configuration, the primary cause of INS position 
degradation is the difference between PHINS estimated heading and true heading. This 
will result in a position error of 0.05 – 0.1% of distance travelled. For example, 
200 – 400m off after a distance of 400km travelled. As this is a function of heading 
accuracy, the potential for position error will increase with increasing latitude.

For a PHINS without any navigational aiding, the specified position accuracy is 0.6 
nautical miles per hour error. It was expected that the position accuracy of the INS 
would improve with increasing latitude, as the heading uncertainty is reduced; 
however, preliminary results are showing no clear trend of improving position 
accuracy. These results are shown in Figure 2. Preliminary results are showing that 
the primary cause of position error for an unaided PHINS is an incorrect velocity 
estimation; this source of error is orders of magnitude higher than would be caused 
by heading uncertainty.


Figure 2: Preliminary results for PHINS rate of position 'drift'. One data 
          point per test. PHINS specification for unaided operation is 0.6 
          nm/hr


How will these results be used?

These results will inform both AUV deployments at high latitudes in general and 
future ARC SRI Gateway AUV deployments specifically. This is particularly true for 
deployments under Antarctic ice sheets, as it is often not possible to employ bottom 
tracking while exploring the underside of an ice sheet.

 


APPENDIX 8  ATMOSPHERIC CHEMISTRY AND AEROSOLS

By Reece Brown

This voyage has seen the deployment of several pieces of aerosol instrumentation to 
investigate the chemical composition, size distribution, optical properties and 
cloud nucleating properties of marine aerosol over the southern hemisphere. These 
parameters are important in the quantification of regional contributions of aerosols 
to radiative forcing, and will help to improve meteorological and climate change 
models. With a few exceptions, the instrumentation has operated with only minor 
issues and a wealth of data has been successfully collected.

Two mass spectrometer systems were used to investigate the chemical composition of 
aerosols. Particle composition was analysed through the use of an ACSM, which 
provides online, high resolution chemical analysis of particles. Early data analysis 
shows mass concentrations of sulphate, with lower levels of organics, chlorine and 
ammonium. These results are consistent with the sea spray generated aerosol which 
are expected to be the primary source of aerosols in the open ocean. There were some 
periods of very high organic mass concentrations due to non-optimum wind conditions 
causing the diesel exhaust to blow over the sampling inlet. However, this effect was 
kept to a minimum due to careful ship directions placement during CTD deployments. A 
PTRMS system was used to perform analysis on water soluble species including DMS, 
however further data analysis is required before this data will be understood. 
Offline PM1 filter and VOC collections systems were also employed to allow for 
further chemical analysis at a later date.

Particle sizing measurements were performed utilizing two scanning mobility particle 
sizer (SMPS) systems, a NAIS, and an aerodynamic particle sizer (APS). The 
combination of equipment allowed for real time particle size measurements 
continuously from 0.5 nanometers up to 20 micrometres. The NAIS was also used to 
track potential particle formation events, however early analysis has not yielded 
any conclusive results. Particle concentrations were measured through a condensation 
particle counter (CPC) and were typically in the range of 200 – 300 particles per 
cubic centimetre of air when sampling clean ocean air. As a comparison a relatively 
clean city such as Brisbane will see concentrations ten times this value.

Aerosol cloud condensation properties were measured through the use of a cloud 
condensation nuclei counter (CCNC) and a volatility hygroscopicity tandem 
differential mobility analyser (VHTDMA). The CCNC concentrations were generally only 
slightly lower than the CPC readings, indicating that the vast majority of particles 
measured are potential cloud condensation nuclei. This result is expected as sea 
salt is very hygroscopic and will readily form cloud droplets given suitable 
circumstances. The VHTDMA system analysed the volatility and hygroscopicity of 
particles, which are important parameters in determining if a particle can become a 
cloud condensation nuclei.

The primary issues encountered during the first leg of IN2016_V03 were caused 
through sea spray entering into the inlet due to high sea swells. During leg two a 
similar issue was encountered due to the high humidity in the tropical regions 
causing condensation in the sampling lines. In both cases careful management of 
instrument setup and water traps, regular dryer maintenance, and clearing of 
condensation from the lines allowed for meaningful data to be collected despite 
these setbacks.

 


APPENDIX 9 - HELIUM SAMPLING

Stephanie Downes, Antarctic Climate and Ecosystems Co-operative Research Centre, 
Hobart, Tasmania

John Lupton, NOAA/Pacific Marine Environmental Laboratory, Newport, OR, USA

Helium is a passive tracer ideal for identifying hydrothermal activity and for 
tracing deep ocean circulation. However, helium has been sparsely sampled across 
Southern Ocean voyage transects and never before has it been sampled along the P15S 
line. On this voyage, 219 duplicate seawater samples were collected along 20 
stations (Figure 1, Table 1). At each of the 20 stations, between 8 and 13 depths 
were sampled, paying particular attention to topographical features in the region to 
hopefully capture interesting hydrothermal activity close to mid-ocean ridges.

Water sampling

For each sample, a 24-inch copper tubing (5/8 inch in diameter) was filled with 
seawater drawn from the 10L Niskin bottles within two hours of the CTD arriving back 
on the ship. The copper tube was hermetically sealed (crimped) in three places using 
a hydraulic crimper to produce two 10-inch sealed duplicate samples. Directly after 
all samples for the station were crimped, the copper tubes were rinsed with fresh 
water, dried thoroughly, and stored in foam-lined cardboard boxes in fibreglass 
crates. Other than freezing of the crimper at the first few stations and a 
productive sea ice season eliminating the first proposed sampling station, all 
planned helium sampling stations and depths were accounted for.

Analysis

The helium isotopes will be processed and quality controlled onshore at the 
NOAA/Pacific Marine Environmental Laboratory (John Lupton). The samples will be 
processed to separate the dissolve gases from the water, followed by analysis of 3He 
concentrations, 4He concentrations and 3He/4He ratios using the extracted dissolved 
gases on a special mass spectrometer. Samples will be made publically available once 
onshore processing is completed.


Figure 1: Helium stations (green) sampled. Also shown are major ocean currents 
          (the Antarctic Circumpolar Current and Ross Gyre to the south), as 
          well as previously inferred and identified hydrothermal activity 
          (blue and yellow) within the vicinity of the P15S transect.

 
Table 1. Station/CTD numbers (STNNBR), locations and numbers of He samples.

         STNNBR  DATE      TIME  LATITUDE  LONGITUDE  DEPTH  NUMBER
                 yyyymmdd  hhmm                         db   SAMPLES
         ------  --------  ----  --------  ---------  -----  -------
            2    20160504  0844  -66.332   -170.008    3277    10
            5    20160505  2145  -64.502   -170.004    2348     9
            9    20160508  0650  -62.499   -169.992    2539    10
           12    20160508  2149  -61.492   -169.997    3470    10
           14    20160509  2335  -60.502   -169.991    3951    11
           19    20160513  1219  -58.001   -170.010    4432    11
           20    20160513  1911  -57.504   -170.006    5019    12
           21    20160514  1414  -57.002   -169.998    5078    12
           22    20160514  0926  -56.498   -170.009    5090    12
           24    20160515  0441  -55.514   -170.011    4833    13
           26    20160515  2000  -54.500   -170.003    4831    13
           29    20160516  1637  -53.004   -170.011    5220    13
           33    20160517  2141  -51.002   -170.010    5248    13
           37    20160519  0215  -48.995   -170.004    5262    13
           41    20160520  0649  -47.109   -170.466    5412    13
           46    20160522  1639  -44.525   -173.502    3414    10
           47    20160522  2335  -44.328   -173.746    3102     8
           48    20160523  0620  -44.156   -173.938    1892     8
           49    20160523  1542  -42.931   -174.785    1057    16
           50    20160523  1819  -42.746   -174.653    1584     8

 


APPENDIX 10  LOWERED ADCP ISSUES

Bec Cowley and Bernadette Sloyan, 20 May, 2016

The slave (upward, 300 kHz) and master (downward, 150 kHz ) ADCPs on the CTD package 
were processed on-board. The processing software (LDEO LADCP) produced a warning 
error of a large offset in the heading between the upward and downward looking ADCP 
units. This error will result in incorrect velocity vectors when the data is 
processed.

The raw data files were loaded into RDI propriety software to investigate further 
the heading error. The tilt, pitch and roll of the instruments was reviewed. During 
the review there was found to be a time offset between the instruments where one 
lagged the other in tilt. The time stamps were further investigated and an offset 
was found between the slave and master time stamps (Figure 1).


Figure 1: Difference in time stamps (Slave-Master) for each deployment 
          (numbered).


We investigated applying a simple time offset to the raw data and re-processing, but 
this did not make any difference. A closer look at the heading values from the 
instruments gave a clear indication of the problem. The Master instrument has a poor 
heading record that is not consistent in its behaviour. A single example from Cast 7 
is shown in figure 2.

 
Figure 2: The upper panel shows the raw heading values for the master and 
          slave, the lower panel the absolute difference between the two.


The tilt, pitch and roll for the master look comparable to the slave, but with an 
offset (Figure 3 and 4). This is the case for most of the stations. We processed the 
LADCP from the previous section and found the same heading error. Thus we suspect 
the unit was faulty prior to our voyage.

For this voyage we will process the LACDP data using only the slave heading data. 
Finally, during the voyage beam-4 of the downward looking unit failed.

 
Figure 3. Master and slave pitch and roll from Station 7.

Figure 4. Master and slave tilt from station 7.

 










RV INVESTIGATOR
HYDROCHEMISTRY DATA PROCESS REPORT




Voyage:                                IN2016_v03 Leg 1/Leg2
Chief Scientist:                  Bernadette Sloyan/Susan Wijffels
Voyage title:         Monitoring Ocean Change and Variability along 170°W from 
                                    the ice edge to the equator
Report compiled by:      Christine Rees, Peter Hughes, Stephen Tibben, Kelly 
                              Brown, Cassie Schwanger & Melissa Miller

 


















Contents

1 Itinerary                                                                  50
2 Key personnel list                                                         50
3 Summary                                                                    51
  3.1 Hydrochemistry                                                         51
  3.2 Rosette and CTD                                                        51
  3.3 Procedure Summary                                                      51
4 Salinity Data Processing                                                   52
  4.1 Salinity Parameter Summary                                             52
  4.2 CTD vs Hydro Salinities Plot                                           53
  4.3 Missing or Suspect Salinity Data and Actions taken                     53
5 Dissolved Oxygen Data Processing                                           54
  5.1 Dissolved Oxygen Parameter Summary                                     54
  5.2 CTD vs Hydro DO Plot                                                   55
  5.3 Dissolved Oxygen thiosulphate normality across voyage                  55
  5.4 Dissolved Oxygen blank concentration across voyage                     55
  5.5 Missing or Suspect Dissolved Oxygen Data and Actions taken             55
6 Nutrient Data Processing                                                   56
  6.1 Nutrient Parameter Summary                                             56
  6.2 Nutrient calibration and data parameter summary                        57
  6.3 Accuracy - Reference Material for Nutrient in Seawater (RMNS) Plots    58
      6.3.1 Silicate RMNS Plot                                               59
      6.3.2 Phosphate RMNS Plot                                              59
      6.3.3 Nitrate + Nitrite (NOx) RMNS Plot                                59
      6.3.4 Nitrite RMNS Plot                                                59
  6.4 Analytical Precision                                                   59
  6.5 Sampling Precision                                                     60
      6.5.1 Silicate Duplicate Plot                                          60
      6.5.2 Phosphate Duplicate Plot                                         60
      6.5.3 Nitrate + Nitrite (NOx) Duplicate Plot                           60
      6.5.4 Nitrite Duplicate Plot                                           60
      6.5.5 Redfield Ratio Plot (14.0)                                       60
  6.6 Calibration and QC edited data                                         60
  6.7 Investigation of Missing or Flagged Nutrient Data and Actions taken    61
  6.8 Temperature & Humidity Change over Nutrient Analyses                   63
7 Appendix                                                                   63
  7.1 Salinity Reference Material                                            63
  7.2 Hypro Flag Key for CSV & NetCDF file                                   63
  7.3 GO-SHIP Specifications                                                 64
  7.4 RMNS Values for each CTD                                               64
  7.5 Nutrient Methods                                                       68
8 References                                                                 69

 









1  ITINERARY

Depart Leg 1      Date          Time
Hobart            26 April      0800
Arrive            Date          Time
Wellington (NZ)   26 May        1100
Depart Leg 2      Date          Time
Wellington (NZ)   27 May        1100
Arrive            Date          Time
Lautoka (Fiji)    30 June       0800




2  KEY PERSONNEL LIST

Name                   Role                    Organisation
---------------------  ----------------------  ------------
Dr. Bernadette Sloyan  Chief Scientist Leg 1   CSIRO 
Dr. Susan Wijffels     Chief Scientist Leg 2   CSIRO
Don McKenzie           Voyage Manager Leg 1    CSIRO 
Stephen Thomas         Voyage Manager Leg 2    CSIRO
Peter Hughes           Hydrochemist Leg 1      CSIRO
Christine Rees         Hydrochemist Leg 1 & 2  CSIRO
Stephen Tibben         Hydrochemist Leg 1 & 2  CSIRO
Kelly Brown            Hydrochemist Leg 1 & 2  CSIRO
Melissa Miller         Hydrochemist Leg 1      SCRIPPS
Cassie Schwanger       Hydrochemist Leg 2      CSIRO




3  SUMMARY

All finalized data can be obtained from the CSIRO data centre. RMNS corrected 
nutrient data will be provided at a later date to the data centre.

Dissolved Oxygen data has been corrected for Thiosulfate and blank concentration 
variation across the voyage (see section 5).

Nutrient experimental samples for ammonium were frozen and measured during transit 
at the end of each voyage leg.


3.1  Hydrochemistry

Analysis                                Sampled
Salinity (Guildline Salinometer)        5740

Dissolved Oxygen (automated titration)  4690 CTD
                                        94 UWY

Nutrients (AA3)                         4705 CTD
                                        94 UWY
                                        245 EXP (NH4)
Note: CTD-samples collected from NISKIN bottles on CTD rosette, UWY-underway samples 
collected from underway seawater intake and EXP-experimental samples.


3.2  Rosette and CTD

• 140 CTD stations were sampled with a 36 bottle rosette (12 L), Dep 1 was the 
  test cast to train samplers.  However, salinities were analysed from this 
  deployment.
• The following deployments failed either due to CTD malfunction or bottles 
  not firing; deployment 7, 10, 14 (only 5 Niskin bottles closed), 16, 18, and 
  83.
• See in2016_v03_HydrochemistryReport.pdf (voyage report) for more details on 
  sample collection.

 
3.3  Procedure Summary

The procedure for data processing is outline in Figure 1.

Figure 1: The process above shows the data trail procedure from the initial data 
generated to output via HyPro for reporting.

Nutrients:
Data collected in Seal AACE 6.10 software
            HyPro: .csv & .CHD files (raw data) imported
            for peak analysis, calculationsand QC
                         HyPro: waterfall and sensor plots compared 
                         for anamolies and outlier identification

Salinity: 
Data collected in Osil software
            Excel file exported from Osil and deployment 
            numbers added to Sample ID field
                         HyPro: Excel file is imported for reporting; water-
                         fall and sensor plots examined for outliers

Dissolved Oxygen: 
Data is collected in SCRIPPS software
            Oxygen .LST files were directly imported into Hypro
                         HyPro: .LST file is imported for reporting; water-
                         fall and sensor plots examined for outliers
 










4  SALINITY DATA PROCESSING

4.1  Salinity Parameter Summary

Details
HyPro Version             4.12
Instrument                Guildline Autosal Laboratory Salinometer 8400(B) – 
                          SN 71613        
Software                  Osil
Methods                   Hydrochemistry Operations Manual + Quick Reference 
                          Manual      
Accuracy                  ± 0.001 salinity units
Analyst(s)                Stephen Tibben
Lab Temperature (±0.5°C)  21.0 -24.0°C during analysis.
Bath Temperature          24°C
Reference Material        Osil IAPSO - Batch P157
Sampling Container type   200 ml volume OSIL bottles made of type II glass 
                          (clear) with disposable plastic insert and plastic 
                          screw cap.
Sample Storage            Samples held in Salt Room for 7-8 hrs to reach 
                          22°C before analysis. A duplicate sample from 
                          rosette position 2 was used to monitor the 
                          temperature of the samples to ensure temperature 
                          equilibration had occurred before analysis.
Comments                  Principle investigators chose to use a smaller 
                          headspace within the salinity bottles (8 ml, 
                          compared with 25 ml recommended by Hydrochemistry 
                          team) from deployment 62 onwards. Experimental 
                          work during voyage showed no significant 
                          difference between salinity bottles with an 8 ml 
                          headspace compared to that of a 25 ml headspace.

 
4.2  CTD vs Hydro Salinities Plot (see pdf)

 
4.3  Missing or Suspect Salinity Data and Actions taken

Data is flagged based on notes from CTD sampling log sheet, observations during 
analysis, and examination of depth profile and waterfall plots.

CTD      RP     Bottle  Analysis  Flag  Reason for Flag or Action
---  ---------  ------  --------  ----  -----------------------------------
  1      26      C26     Salt      69   Sampling error? Training 
                                        samplers/changed O-rings
  1       5      C05     Salt     141   Niskin lid did not close, no sample
  1      10      C10     Salt      69   Sampling error? Training
  2      31      J32     Salt      69   Very high Niskin frozen
  6      31      B31     Salt      69   Very high Niskin frozen
 15      17      J17     Salt     133   Waterfall profile out
 19    17, 23            Salt     141   Niskin bottles did not fire.
 24       7      E07     Salt     141   Niskin bottles did not fire.
 24      13      E13     Salt      69   Waterfall profile out
 38     all      all     Salt       0   All samples had less than 
                                        recommended headspace.
 44      20      E21     Salt     141   Niskin Lanyard caught in lid 
                                        bottle leaking.
 47      36              Salt     141   Niskin fired in air.
 49   2, 3, 6,           Salt     141   Niskins not sampled
       8, 10,
      12, 14,
      16, 18,
      20, 22,
      24, 26,
      28, 30,
 50  3, 7, 10,           Salt     141   Niskins not sampled
      12, 14,
      16, 18,
      20, 22,
      24, 26,
      29, 32 
 52      20      H20     Salt     133   Outlier – lanyard was caught 
                                        on bottle so possible leak
 53      17              Salt     141   Niskin end cap didn’t close
 55      32              Salt     141   No data

  67     25       K25     Salt     133   Waterfall profile out
 72   10, 9    H10, H09  Salt      69   Waterfall profile out and also in
                                        error plot.
 74     09               Salt     141   Niskin leaking did not sample
 84    1, 2              Salt     141   Niskins not sampled
 90     13       A13     Salt       0   Waterfall profile out
102  15,16,17  A15,A16,  Salt      69   Waterfall profile out
        A17                             RP15 was leaking
103      5       J05     Salt     133   Waterfall profile out, noted in
                                        sample log niskin rp 5 was warmer
                                        temperature than other bottles.
112     33-36            Salt     141   Niskins not sampled
113      10              Salt     141   Niskin not sampled
119      13              Salt     141   Niskin not sampled
124    10, 26            Salt     141   Niskin not sampled
134      11              Salt     141   Niskin not sampled
137       3      J03     Salt       0   Waterfall plot out
138      14              Salt     141   Niskin not sampled
139      14      C14     Salt       0   Waterfall plot out – niskin had 
                                        just been majorly serviced
140      27      A27     Salt     133   Vertical profile plot out. Niskin
                                        Lanyard caught in lid - bottle
                                        leaking.  Also bad for nutrients.

 







5  DISSOLVED OXYGEN DATA PROCESSING


5.1  Dissolved Oxygen Parameter Summary

Details
----------------------------------------------------------------------------
HyPro Version           4.12
Instrument              Automated Photometric Oxygen system
Software                SCRIPPS
Methods                 SCRIPPS
Accuracy                0.01 ml/L + 0.5%
Analyst(s)              Kelly Brown
Lab Temperature (±1°C)  Variable, 20.0  - 23.0°C
Sample Container type   Pre-numbered glass 140 mL glass vial w/stopper, 
                        sorted into 18 per box and boxes labelled A to S.
Sample Storage          Samples were stored within Hydrochemistry lab under 
                        the forward starboard side bench until analysis. All 
                        samples were analysed within ~18 hrs
Comments                Duplicate samples were collected randomly during 
                        every deployment to monitor sampling consistency. 
                        The duplicate sample was analysed as a test sample.

                        There was some concern about the integrity of the 
                        tropical surface samples stored in the 21°C 
                        Hydrochemistry lab. An experiment was conducted to 
                        compare dissolved oxygen samples stored at 21°C and 
                        30°C, no statistical difference was found between 
                        the dissolved oxygen concentrations. The samples 
                        continued to be stored in the hydrochemistry lab 
                        until analysis.


An extra calculation for the final dissolved oxygen concentration was implemented 
during the voyage. This calculation smoothed the data due to the day-to-day 
variation in the thiosulphate titrant concentration and blank values. Kelly Brown 
performed the calculation according to the Oxygen Titration Manual SIO/STS version: 
Jun-2015 section 7.1 Thiosulfate Smoothing Procedure. Steve vanGraas wrote a script 
that pulled the corrected data into the existing LST files which was then be re-read 
by HyPro.

 
5.2  CTD vs Hydro DO Plot (see pdf)

 
5.3  Dissolved Oxygen thiosulphate normality across voyage(see pdf)


5.4  Dissolved Oxygen blank concentration across voyage(see pdf)

 
5.5  Missing or Suspect Dissolved Oxygen Data and Actions taken

Data is flagged as Good, Suspect or Bad in Hypro based on notes from CTD sampling 
log sheet, observations during analysis, and examination of depth profile and 
waterfall plots.

CTD    RP    Bottle  Analysis  Flag        Reason for Flag or Action
---  ------  ------  --------  ----  --------------------------------------
2      31     187     D.O.      69   High Niskin bottle froze
uwy   017     647     D.O.      69   pCO2 system blowing air
4      11     252     D.O.     133   Incorrect volume possibly? Profile 
                                     suspect
6      12     252     D.O.     133   Incorrect volume possibly? Profile 
                                     suspect- flask pulled from box.
13     23     440     D.O.     141   Flask broke,  lost sample, removed 
                                     from file
15     17     430     D.O.     133   Profile is suspect, is also 
                                     suspect for nuts, salt, cfc’s.
19   17, 23           D.O.     141   Bottles did not fire.
22     08     143     D.O.     141   Abort, titrator malfunc-tion, lost 
                                     sample removed from file
30     20     407     D.O.     141   Abort, titrator malfunc-tion, lost 
                                     sample removed from file
31     19     161     D.O.     141   Abort, titrator malfunc-tion, lost 
                                     sample removed from file
32     21     261     D.O.     141   Abort, titrator malfunc-tion, lost 
                                     sample removed from file
32     27     267     D.O.     141   Abort, titrator malfunc-tion, lost 
                                     sample removed from file
38     11     147     D.O.     141   Flask smashed while sampling
uwy   045     638     D.O.      69   NaOH/I bubble
39     01     232     D.O.     133   Draw Temp maybe incorrect, tempera-
                                     ture probe was malfunctioning.
39     03     235     D.O.     141   Also sample 03 Abort, titrator 
                                     malfunction, lost sample.
41     04     136     D.O.     133   2 magnets in flask bad endpoint
42     04     200     D.O.      69   Profile suspect in waterfall plot.
44     20             D.O.     141   Niskin Lanyard caught in lid 
                                     bottle leaking.
47     36             D.O.     141   Niskin fired in air.
53     36     653     D.O.     141   Abort, not enough NaOH/I in sample 
                                     to titrate.
56     01     728     D.O.     133   black particles in flask
59     01     161     D.O.     141   Abort, titrator malfunction, lost 
                                     sample removed from file
60     01             D.O.     141   Stopper put in bottle upside down
74     09             D.O.     141   Niskin leaking did not sample
100    11     322     D.O.     141   Abort, titrator malfunction, lost 
                                     sample removed from file
103    05     566     D.O.     133   Waterfall profile out noted in 
                                     sample log niskin rp 5 warmer 
                                     temperature than other niskins.
110    04     582     D.O.     133   Waterfall profile out.
112    02     279     D.O.     141   Abort, titrator malfunction, lost 
                                     sample removed from file
128    13     687     D.O.     141   Abort, titrator malfunction, lost 
                                     sample removed from file
134    11             D.O.     141   NISKIN leaking not sampled for D.O.
136  14, 15           D.O.     141   NISKINS leaking not sampled for D.O.
138    14             D.O.     141   NISKIN leaking not sampled for D.O.
139    31             D.O.     141   NISKIN leaking not sampled for D.O.
140  19, 22,          D.O.     141   NISKINS leaking not sampled for D.O.
       27   

 


6  NUTRIENT DATA PROCESSING


6.1  Nutrient Parameter Summary

Details
HyPro Version              4.12
Instrument                 AA3
Software                   Seal AACE 6.10
Methods                    AA3 Analysis Methods internal manual
Nutrients analysed         Silicate  Phosphate  Nitrate +  Nitrite   Ammonia
                                                Nitrite  
                           --------  ---------  ---------  --------  ---------
Concentration range        140       3          42.0       1.4       2.0
                           µmol l-1  µmol l-1   µmol l-1   µmol l-1  µmol l-1
Method Detection Limit*    0.2       0.02       0.02       0.02      0.02
(MDL)                      µmol l-1  µmol l-1   µmol l-1   µmol l-1  µmol l-1
Matrix Corrections         N         N          N          N         N
Analyst(s)                 Peter Hughes, Melissa Miller, Christine Rees and 
                           Cassie Schwanger
Lab Temperature (±1°C)     Variable, 20.0 – 23.0°C
Reference Material         RMNS – CA, BV, BW
Sampling Container type    10 mL polypropylene
Sample Storage             < 2 hrs at room temperature or ≤ 12 hrs @ 4°C
Pre-processing of Samples  None
Comments                   Non-CTD related samples were analysed and 
                           processed with the prefix- uwy and exp. Exp 
                           samples were collected and frozen for ammonia 
                           analysis. Ammonia was measured at the end of 
                           Leg 1 and again at the end of Leg 2. Surface 
                           ammonia samples were collected from the CTD as 
                           well as a MDL that varied in depth. Underway 
                           samples were measured within a 24 hour period 
                           of sample collection.


6.2  Nutrient calibration and data parameter summary

During the course of the voyage all run information was logged - LNSW batch, new 
cadmium column, new stock standard, daily standard information, fresh reagent 
information, instrumentation settings, pump tube changes and pump tube hours. This 
information along with calibration summary data and calibration plots for each 
analysis run are available in the following zip folder consisting of files 
containing; mdl, drift, baseline, carry-over, calibration & RMNS results: 
http://www.cmar.csiro.au/datacentre/process/data_files/Investigator_NF/in2016_v03/da
ta/in2016_v03Hydro_nc.zip

All NUT### file numbers with each ctd deployment analysed per analysis run can be 
viewed in the pdf file “AA3FileLog.pdf” in the above location. The latitude, 
longitude and time (UTC) that matches the UWY samples is located in file “IN2016 V03 
UWY.pdf”. All runs have a corresponding AA3_Run_Analysis_sheet and 
AA3_Processing_Worksheet file to assist in characterizing data and note questionable 
peaks. This information is contained in the voyage documentation and available upon 
request.

The raw data is imported into Hypro for peak determination. For each analysis run 
(indicated by a NUT###), HyPro fits the best calibration curve to the standards by 
performing several passes over each standard point. If the measured value is 
different from the calculated value it will allocate less weighting to the point in 
the calibration curve. HyPro will mark these points as suspect or bad within the 
calibration curve. Following standard procedures, the operator may choose to remove 
bad calibration points by placing a # in front of the peak start column within the 
data file (see section 6.6 for edited data). Below are the standard corrections and 
settings that Hypro applies to the raw data.


Result Details        Silicate  Phosphate  Nitrate +  Nitrite    Ammonia
                                            Nitrite      
--------------------  --------  ---------  ---------  ---------  ---------
Data Reported as      µmol l-1  µmol l-1   µmol l-1   µmol l-1   µmol l-1
Calibration Curve     Linear    Linear     Quadratic  Quadratic  Quadratic
  degree    
Forced through zero?     N         N          N           N         N
# of points in           7         6          7           6         6
  Calibration      
Matrix Correction        N         N          N           N         N
Blank Correction         N         N          N           N         N
Carryover Correction     Y         Y          Y           Y         Y
  (Hypro)
Baseline Correction      Y         Y          Y           Y         Y
  (Hypro)
Drift Correction         Y         Y          Y           Y         Y
  (Hypro)
Data Adj for RMNS        N         N          N           N         N
Window Defined*       HyPro      HyPro      HyPro       HyPro     HyPro
Medium of Standards   LNSW (bulk on deck of Investigator) collected 
                      17/5/2015 off shore from Brisbane (-27.1S, 155.2E) 
                      using the clean instrument seawater supply inlet. 
                      Twenty five carboys were filtered through 1µM by 
                      Stephen Tibben and Kendall Sherrin on the 21st and 
                      22nd of April 2016 and stored in the constant 
                      temperature room at 21°C.
Medium of Baseline    18.2 Ω MQ
Proportion of         1 duplicate for each CTD from NISKIN bottle 1
  samples in 
  duplicate?      
Comments              Calibration and QC data that was edited or removed 
                      is located in the table in section 3.6.6. The 
                      reported data is not corrected to the RMNS. Per run 
                      RMNS data can be found in Appendix 5.4.


6.3  Accuracy - Reference Material for Nutrient in Seawater (RMNS) Plots

The certified reference materials (CRM) for silicate, phosphate, nitrate and nitrite 
in seawater produced by KANSO – Japan was used in each nutrient analysis to ensure 
the accuracy of results. The RMNS was run 4 times after the calibration standards. 
No QC data is supplied for the experimental ammonia samples as there is not a CRM. 
Accuracy is determined by comparing the new standard batch with the old and tracking 
to ensure the concentration is within 1% accuracy between batches.

The RMNS Lot CA (produced 22/02/2013) was measured 4 times in every CTD analysis. 
The RMNS Lot BV (produced 15/09/2011) was analysed every few days alongside the CA. 
The RMNS Lot BW was only measured once in 4 replicates during the voyage. RMNS 
results were converted from µ mol/kg to µ mol l-1 at 21°C in the following table.


Table 1: RMNS CA, BV and BW concentrations (µM) at 21°C

               RMNS   NO3    NOX    NO2   PO4   SiO4
               ----  -----  -----  -----  ----  -----
               CA    20.13  20.20  0.065  1.44  37.46
               BV    36.21  36.26  0.048  2.56  104.6
               BW    25.18  25.25  0.069  1.58  61.45

The submitted nutrient results do NOT have RMNS corrections applied.

During the voyage principal researchers corrected the data within each nutrient 
analysis using the CA RMNS.  The following calculation was performed:


RMNS Correction 
% error = (RMNS measured – RMNS Published)/RMNS Published 
Corrected Nutrient Concentration = Nutrient measured – (nutrient measured x error) 
Note: NOx data should be corrected as NO3 and NO2. 


The following plots show RMNS values within 1% (green lines), 2% (pink lines) and 3% 
(red lines) of the published RMNS value except for nitrite. The nitrite limit is set 
to ±0.020 µM (MDL) as 1% is below the method MDL. The GO-SHIP criteria (Hyde et al., 
2010), reference section 5.3, specifies using 1-3 % of full scale (depending on the 
nutrient) as acceptable limits of accuracy. The calculated RMNS values per CTD are 
reported in the table in section 5.4.


6.3.1  Silicate RMNS Plot

6.3.2  Phosphate RMNS Plot

6.3.3  Nitrate + Nitrite (NOx) RMNS Plot

6.3.4  Nitrite RMNS Plot

 
6.4  Analytical Precision

The CSIRO Hydrochemistry method measurement uncertainty (MU) has been calculated for 
each nutrient based on variation in the calibration curve, calibration standards, 
pipette and glassware calibration, and precision of the CRM over time (Armishaw 
2003).

                  Silicate  Phosphate    Nitrate +    Nitrite  Ammonia
                                       Nitrite (NOx)
----------------  --------  ---------  -------------  -------  -------
Calculated MU* @   ±0.017    ±0.020       ±0.017      ±0.108   ±0.066¥
   1 µmol l-1   

*The reported uncertainty is an expanded uncertainty using a coverage factor of 2 
giving a 95% level of confidence.

¥The ammonia MU precision component does not include data on the CRM.

Method detection limits (MDL) achieved during the voyage were much lower than the 
nominal detection limits, indicating high analytical precision at lower 
concentrations. Results are µmol l-1. The precision of the RMNS is was also 
determined.

      MDL         Silicate  Phosphate    Nitrate +    Nitrite  Ammonia
                                       Nitrite (NOx)
----------------  --------  ---------  -------------  -------  -------
Nominal MDL*       0.20       0.02         0.02        0.02     0.02
Min                0.002      0.001        0.002       0.001    0.009
Max                0.227      0.015        0.032       0.011    0.009
Mean               0.057      0.004        0.007       0.003    0.009
Median             0.039      0.003        0.006       0.003    0.009
Precision of       0.050      0.003        0.005       0.002    NA
  MDL (stdev)

*MDL is based on 3 times the standard deviation of Low Nutrient Seawater (LNSW) 
analysed in each nutrient run.  

Published RMNS    37.46      1.441        20.20        0.065      -
  (µmol l-1) 
w/uncertainty    ± 0.22    ± 0.014       ± 0.16      ± 0.010  
RMNS Min          36.03      1.413        19.96        0.062      -
RMNS Max          38.51      1.488        20.54        0.087      -
RMNS Mean         37.26      1.447        20.29        0.074      -
RMNS Median       37.26      1.445        20.31        0.073      -
RMNS Std Dev       0.43      0.017         0.12        0.005      -

 

6.5  Sampling Precision

Duplicates samples were collected from NISKIN bottle 1 to measure the precision of 
nutrient sampling (this is not a measurement of analytical precision). The duplicate 
measurements are reported in the data as an average when the duplicates are flagged 
GOOD. The sampling precision is deemed good if difference between duplicate 
concentrations is below the MDL for silicate, phosphate and nitrite and within 0.05 
µM for nitrate.

6.5.1  Silicate Duplicate Plot(see pdf)

6.5.2  Phosphate Duplicate Plot(see pdf)

6.5.3  Nitrate + Nitrite (NOx) Duplicate Plot(see pdf)

6.5.4  Nitrite Duplicate Plot

6.5.5 Redfield Ratio Plot (14.0)(see pdf)

Plots consists of phosphate versus NOx, best fit ratio = 14.37.


6.6  Calibration and QC edited data

CTD      Peak         Analysis                   Action
---  ---------------  --------  -------------------------------------------
 29      Cal 5          NO2     Cal 5 was removed from curve, no carry over 
                                corrections were applied
 30      Cal 5          NO2     Cal 5 was removed from curve, no carry over 
                                corrections were applied
108    Recovery         NOx     No cadmium column recovery determined
113      Cal 2          NOx     2nd Cal 2 removed due to spike on the peak
122      Cal 2          SiO4    Removed – outlier on curve
123      Cal 2          SiO4    Removed – outlier on curve
128      Cal 2          NOx     Removed – outlier on curve
128      Cal 4          SiO4    Removed – outlier on curve
129      Cal 1          NOx     Removed – outlier on curve
134      Cal 3          SiO4    Removed – outlier on curve
135      Cal 3          SiO4    Removed – outlier on curve
136      Cal 3          SiO4    Removed – outlier on curve
139  Cal 1, 2, 3, 4, 5  SiO4    Removed – outlier on curve
140   Cal 1, 2, 3, 4    SiO4    Removed – outlier on curve
140      Cal 1          NOx     Removed – outlier on curve


6.7  Investigation of Missing or Flagged Nutrient Data and Actions taken.

The table below identifies all flagged data and data that was repeated. Data that 
falls below the detection limit, Flag 63, is not captured in this table. All GOOD 
data is flagged 0 in the .csv and .netcdf files. Refer to Appendix 7.2 for flag 
explanations.

CTD    RP       Run      Analysis   Flag   Reason for Flag or Action
---  ---------  -------  ---------  ----  ---------------------------------------------
  2    20       Nut017    NOx        65   Data good, hypro flag due to peak shape
  3    11       Nut018    SiO4       65   Data good, hypro flag due to peak shape
  4    03       Nut019    SiO4       65   Data good, hypro flag due to peak shape
  9    07       Nut024    NOx         0   Outlier in waterfall profile for the first , 
                                          analysis repeated and reported result from 
                                          run nut025
 11    04       Nut025    NOx         0   Outlier in waterfall profile, repeated in  
                                          nut026, use result from nut026
 11    28       Nut025    PO4         0   Outlier in waterfall profile, repeated in  
                                          nut026, use result from nut026.
 12    15       Nut026    NOx         0   Outlier in waterfall profile, repeated in 
                                          nut027, use result from nut027.
 15    17       Nut029    All Nuts  133   Does not follow water fall plot, flagged as 
                                          bad. Niskin mistrip.
 19    01       Nut032    NOx         0   Outlier in waterfall profile, repeated in 
                                          nut033, use result from nut033
 19    17,23    Nut032    All Nuts  141   Bottles did not fire, no samples collected
 21    01,02    Nut034    Silicate    0   Odd Peak Shapes repeated in nut035 use 
                                          results from nut035.
 23    01       Nut036    NOx,NO2     0   2nd duplicate Flagged as Bad in HyPro – 
                                          waterfall plot shows bad data. Duplicate
                                          >0.02.
 24    21       Nut037    NOx         0   Suspect peak shape repeated in nut038 for 
                                          final reported value.
 27    22       Nut040    SiO4       65   Data good, hypro flag due to peak shape
 41    11       All nuts            141   Emptied NISKIN before collecting nutrient samples.
 48    01       Nut063    NOx         0   Difference between duplicates > 0.02µM (MDL), 
                                          repeated in nut064 and use 2nd result.
 49  2, 3, 6,   Nut064    All Nuts  141   Niskins not sampled
      8, 10,
     12, 14,
     16, 18,
     20, 22,
     24, 26,
     28, 30  
 50  3, 7, 10,  Nut064    All Nuts  141   Niskins not sampled
     12, 14,
     16, 18,
     20, 22,
     24, 26,
     29, 32     
EXP    MLD      Nut065    NH4         0   Suspect peak shape; repeated in nut066 for final 
 24                                       reported value.
 52    20       Nut071    All Nuts  133   Outlier in waterfall profile, lanyard caught in 
                                          top of NISKIN –lanyard pulled out. Repeated the 
                                          analysis gave same result.
 53    17       Nut072    All Nuts  141   Niskin end cap didn’t close
 56    26       Nut075    NOx         0   Suspect peak shape; repeated in nut076 for final 
                                          reported value
 64    01       Nut083    NOx         0   Difference between duplicates > 0.02µM (MDL), 
                                          repeated in nut084 and use 2nd result.
 68    01       Nut087    NOx         0   Difference between duplicates > 0.02µM (MDL), 
                                          repeated in nut088 use this 2nd result.
 70    10       Nut089    All Nuts  133   Outlier in waterfall plot, noted that vent popped 
                                          off NISKIN.
 70    01       Nut089    SiO4        0   Difference between duplicates > 0.20µM (MDL), 
                                          repeated in nut090 use this 2nd result.
 79    all      Nut098    NOx         0   Cd column blocked shifted peak windows and decreased 
                                          NO3 conversion to NO2. Repeated samples in Nut099 
                                          for reported results.
 81    03       Nut101    NOx         0   Blip on plateau, outlier in waterfall profile. 
                                          Repeated in Nut102 for final result.
 83  01, 02     Nut103    NOx        69   Bad duplicates >0.02, these NISKIN bottles were down 
                                          at bottom of ocean floor. Crash Samples.
 84  01, 02     Nut104    All Nuts  141   No samples collected
 98    All      Nut118    NOx         0   BAD calibration curve causing RMNS to be above 3%. 
                                          Data removed from slk file and re- ran in nut120 for 
                                          reported results.
103     5       Nut124    All Nuts  133   The depth profile show an anomaly in this RP sample 
                                          and a bottle temperature note was recorded on the 
                                          sampling sheet. Salt and oxygen data also show an anomaly.
106    All      Nut127    NOx         0   RMNS low and results in profile much lower than previous 
                                          runs. Repeated in nut 130.
CTD    RP       Run       Analysis  Flag  Reason for Flag or Action
111    All      Nut132    NOx         0   Results in profile much lower than all other runs. 
                                          Repeated in nut135.
112   33-36     Nut133    All Nuts  141   Air valves not closed on niskins, no samples collected
113     10      Nut134    All Nuts  141   Niskin leaked, no samples collected
117     10      Nut138    SiO4        0   Large air spike on top of peak, repeated in nut139 for 
                                          reported final results.
119    all      Nut140    NOx         0   RMNS 3% high, repeated run in nut142.
119     13      Nut142    All Nuts  141   No sample collected
121     30      Nut143    NOx         0   Bump in peak window –peak shape. Repeated in nut144 for 
                                          reported result.
122     01      Nut144    NOx        69   Difference between duplicates 0.07µM (MDL = 0.02 µM), 
                                          repeated in nut145 result not any better leave as is.
124  10, 26     Nut146    All Nuts  141   Niskins leaked, no samples collected
125     32      Nut149    NO2       129   The peak was off scale in AACE. Sample repeated with 
                                          dilution 3mL sample + 6mL LNSW in run nut150
                                          =(0.591-0.001)x3=1.77 µM updated csv file not netcdf
134     11      Nut157    All  Nuts  141  Niskin leaked, no sample collected
138     14      Nut161    All  Nuts  141  Niskin leaked, no sample collected
140     27      Nut163    All  nuts  141  Lanyard caught in top cap-leaked.













6.8  Temperature & Humidity Change over Nutrient Analyses

The temperature and humidity within the AA3 chemistry module was logged using a 
temperature/humidity logger QP6013 (Jaycar) placed on the deck of the chemistry 
module.

Refer to “in2016_v03_hyd_voyagereport.docx” for room temperature graphs, nutrient 
samples were placed on XY3 auto sampler at the average room temperature of 21.5ºC.

 

 



7  Appendix


7.1  Salinity Reference Material

Osil IAPSO Standard Seawater
----------------------------
    K15          0.99985
    Use by date  15/04/17
    Batch        P157

 
7.2  Hypro Flag Key for CSV & NetCDF file

Flag  Meaning      
  0   Data is GOOD – nothing detected.      
192   Data not processed.      
 63   Below nominal detection limit.      
 69   Data flagged suspect by operator. Set suspect by software if Calibration 
      or Duplicate data is outside of set limits but not so far out as to be 
      flagged bad.      
 65   Peak shape is suspect.      

133   Error flagged by operator. Data is bad – operator identified by # in slk 
      file or by clicking on point.      
129   Peak exceeds maximum A/D value.  Data is bad.      
134   Error flagged by software. Peak shape is bad - Median Absolute Deviation 
      (MAD) analysis used. Standards, MDL’s and Duplicates deviate from the 
      median, Calibration data falls outside set limits.      
141   Missing data, no result for sample ID. Used in netcdf file as an array 
      compiles results. Not used in csv file.      
 79   Method Detection Limit (MDL) during run was equal to or greater than 
      nominal MDL. Data flagged as suspect.      

 



7.3  GO-SHIP Specifications

Salinity  Accuracy of 0.001 is possible with Autosal™ salinometers and 
          concomitant attention to methodology, e.g., monitoring Standard Sea 
          Water. Accuracy with respect to one particular batch of Standard Sea 
          Water can be achieved at better than 0.001 PSS-78. Autosal precision 
          is better than 0.001 PSS-78. High precision of approximately 0.0002 
          PSS-78 is possible following the methods of Kawano (this manual) 
          with great care and experience. Air temperature stability of ± 1°C 
          is very important and should be recorded.1
O2        Target accuracy is that 2 sigma should be less than 0.5% of the 
          highest concentration found in the ocean. Precision or 
          reproducibility (2 sigma) is 0.08% of the highest concentration 
          found in the ocean.
SiO2      Approximately 1-3% accuracy†, 2 and 0.2% precision, full-scale.
PO4       Approximately 1-2% accuracy†, 2 and 0.4% precision, full scale.
NO3       Approximately 1% accuracy†, 2 and 0.2% precision, full scale.

Notes:    † If no absolute standards are available for a measurement then 
            accuracy should be taken to mean the reproducibility presently 
            obtainable in the better laboratories.

          1 Keeping constant temperature in the room where salinities are 
            determined greatly increases their quality. Also, room temperature 
            during the salinity measurement should be noted for later 
            interpretation, if queries occur. Additionally, monitoring and 
            recording the bath temperature is also recommended. The frequent 
            use of IAPSO Standard Seawater is endorsed. To avoid the changes 
            that occur in Standard Seawater, the use of the most recent 
            batches is recommended. The bottles should also be used in an 
            interleaving fashion as a consistency check within a batch and 
            between batches.

          2 Developments of reference materials for nutrients are underway 
            that will enable improvements in the relative accuracy of 
            measurements and clearer definition of the performance of 
            laboratories when used appropriately and the results are reported 
            with the appropriate meta data.

 
7.4  RMNS Values for each CTD

CTD      SiO4    SiO4   PO4     PO4    NO2     NO2     NOx     NOx
         mea-    ex-    mea-    ex-    mea-    ex-     mea-    ex-  
         sured   pect-  sured   pect-  sured   pect-   sured   pect-  
                 ed             ed             ed              ed    
-------  -----   -----   ----   ----   -----   -----   -----   -----
  2       37.9    37.5   1.48   1.44   0.082   0.065   20.37   20.20
  3       38.5    37.5   1.48   1.44   0.081   0.065   20.31   20.20
  3      106.1   104.7   2.62   2.56   0.066   0.048   36.53   36.26
  4       38.2    37.5   1.48   1.44   0.080   0.065   20.31   20.20
  4      105.7   104.7   2.61   2.56   0.063   0.048   36.48   36.26
  5       38.1    37.5   1.47   1.44   0.074   0.065   20.41   20.20
  6       38.1    37.5   1.48   1.44   0.085   0.065   20.50   20.20
  8       38.2    37.5   1.46   1.44   0.074   0.065   20.41   20.20
  9       38.1    37.5   1.47   1.44   0.074   0.065   20.39   20.20
 11       38.1    37.5   1.46   1.44   0.072   0.065   20.45   20.20
 11      105.1   104.7   2.58   2.56   0.055   0.048   36.55   36.26
 12       38.0    37.5   1.46   1.44   0.078   0.065   20.47   20.20
 12      105.1   104.7   2.58   2.56   0.059   0.048   36.42   36.26
 13       37.7    37.5   1.48   1.44   0.076   0.065   20.40   20.20
 14       37.6    37.5   1.47   1.44   0.084   0.065   20.43   20.20
 15       37.7    37.5   1.47   1.44   0.072   0.065   20.38   20.20
 17       37.5    37.5   1.46   1.44   0.074   0.065   20.42   20.20
 19       37.6    37.5   1.46   1.44   0.076   0.065   20.54   20.20
 20       37.6    37.5   1.47   1.44   0.067   0.065   20.29   20.20
 21       37.4    37.5   1.46   1.44   0.075   0.065   20.31   20.20
 21      104.3   104.7   2.57   2.56   0.055   0.048   36.30   36.26
 22       37.4    37.5   1.46   1.44   0.076   0.065   20.29   20.20
 23       37.7    37.5   1.48   1.44   0.073   0.065   20.28   20.20
 24       37.8    37.5   1.48   1.44   0.072   0.065   20.36   20.20
 25       37.8    37.5   1.47   1.44   0.075   0.065   20.35   20.20
 26       37.8    37.5   1.47   1.44   0.075   0.065   20.35   20.20
 27       37.4    37.5   1.46   1.44   0.078   0.065   20.38   20.20
 28       37.4    37.5   1.47   1.44   0.076   0.065   20.28   20.20
 29       37.6    37.5   1.46   1.44   0.075   0.065   20.40   20.20
 30       37.5    37.5   1.47   1.44   0.076   0.065   20.44   20.20
 31       37.5    37.5   1.47   1.44   0.070   0.065   20.37   20.20
 32       37.6    37.5   1.45   1.44   0.066   0.065   20.38   20.20
 
  
 
CTD      SiO4    SiO4   PO4     PO4    NO2     NO2     NOx     NOx
         mea-    ex-    mea-    ex-    mea-    ex-     mea-    ex-  
         sured   pect-  sured   pect-  sured   pect-   sured   pect-  
                 ed             ed             ed              ed    
-------  -----   -----   ----   ----   -----   -----   -----   -----
 33       37.4    37.5   1.46   1.44   0.066   0.065   20.45   20.20
 34       37.5    37.5   1.47   1.44   0.074   0.065   20.30   20.20
 34      104.6   104.7   2.59   2.56   0.054   0.048   36.37   36.26
 35       37.6    37.5   1.45   1.44   0.120   0.065   20.51   20.20
 36       37.3    37.5   1.47   1.44   0.071   0.065   20.34   20.20
 37       37.4    37.5   1.48   1.44   0.078   0.065   20.44   20.20
 38       37.5    37.5   1.47   1.44   0.072   0.065   20.40   20.20
 39       37.3    37.5   1.45   1.44   0.072   0.065   20.31   20.20
 40       37.4    37.5   1.46   1.44   0.075   0.065   20.33   20.20
 41       37.4    37.5   1.46   1.44   0.073   0.065   20.26   20.20
 42       37.3    37.5   1.45   1.44   0.079   0.065   20.35   20.20
 43       37.4    37.5   1.45   1.44   0.076   0.065   20.27   20.20
 44       37.3    37.5   1.46   1.44   0.077   0.065   20.28   20.20
 45       37.3    37.5   1.44   1.44   0.076   0.065   20.19   20.20
 46       37.0    37.5   1.43   1.44   0.076   0.065   20.26   20.20
 46      103.7   104.7   2.54   2.56   0.057   0.048   36.42   36.26
 47       37.3    37.5   1.44   1.44   0.077   0.065   20.36   20.20
 48       37.2    37.5   1.43   1.44   0.078   0.065   20.30   20.20
 49       37.1    37.5   1.42   1.44   0.075   0.065   20.32   20.20
 50       37.1    37.5   1.42   1.44   0.075   0.065   20.32   20.20
 51       37.1    37.5   1.44   1.44   0.069   0.065   20.31   20.20
 52       37.0    37.5   1.46   1.44   0.068   0.065   20.31   20.20
 52      103.9   104.7   2.58   2.56   0.055   0.048   36.47   36.26
 53       37.1    37.5   1.46   1.44   0.073   0.065   20.31   20.20
 54       37.1    37.5   1.47   1.44   0.069   0.065   20.30   20.20
 55       37.3    37.5   1.46   1.44   0.070   0.065   20.31   20.20
 56       37.3    37.5   1.47   1.44   0.080   0.065   20.30   20.20
 57       37.4    37.5   1.45   1.44   0.080   0.065   20.29   20.20
 58       36.6    37.5   1.44   1.44   0.080   0.065   20.22   20.20
 59       36.6    37.5   1.45   1.44   0.071   0.065   20.19   20.20
 60       36.9    37.5   1.42   1.44   0.074   0.065   20.15   20.20
 61       36.9    37.5   1.42   1.44   0.073   0.065   20.19   20.20
 61       36.8    37.5   1.44   1.44   0.067   0.065   20.16   20.20
 62       36.8    37.5   1.43   1.44   0.073   0.065   20.14   20.20
 62      102.9   104.7   2.53   2.56   0.055   0.048   36.08   36.26
 63       36.8    37.5   1.43   1.44   0.073   0.065   20.14   20.20

 
CTD      SiO4    SiO4   PO4     PO4    NO2     NO2     NOx     NOx
         mea-    ex-    mea-    ex-    mea-    ex-     mea-    ex-  
         sured   pect-  sured   pect-  sured   pect-   sured   pect-
                 ed             ed             ed              ed   
-------  -----   -----   ----   ----   -----   -----   -----   -----
 64       36.6    37.5   1.43   1.44   0.076   0.065   20.12   20.20
 65       36.6    37.5   1.45   1.44   0.071   0.065   20.11   20.20
 66       36.8    37.5   1.44   1.44   0.069   0.065   20.12   20.20
 67       36.8    37.5   1.45   1.44   0.071   0.065   20.12   20.20
 68       36.6    37.5   1.44   1.44   0.070   0.065   20.09   20.20
 69       36.6    37.5   1.43   1.44   0.070   0.065   20.09   20.20
 70       36.6    37.5   1.44   1.44   0.066   0.065   20.03   20.20
 70      102.7   104.7   2.55   2.56   0.051   0.048   36.00   36.26
 71       36.7    37.5   1.45   1.44   0.072   0.065   20.19   20.20
 72       36.6    37.5   1.46   1.44   0.072   0.065   20.18   20.20
 73       36.7    37.5   1.45   1.44   0.070   0.065   20.21   20.20
 74       36.7    37.5   1.44   1.44   0.072   0.065   20.27   20.20
 75       36.7    37.5   1.43   1.44   0.062   0.065   20.30   20.20
 76       36.7    37.5   1.44   1.44   0.072   0.065   20.25   20.20
 77       36.7    37.5   1.46   1.44   0.073   0.065   20.24   20.20
 78       36.9    37.5   1.44   1.44   0.071   0.065   20.16   20.20
 79       37.2    37.5   1.45   1.44   0.079   0.065   20.14   20.20
 80       37.2    37.5   1.46   1.44   0.080   0.065   20.18   20.20
 80      103.7   104.7   2.56   2.56   0.064   0.048   36.09   36.26
 81       37.9    37.5   1.43   1.44   0.076   0.065   20.07   20.20
 82       37.4    37.5   1.44   1.44   0.072   0.065   20.13   20.20
 83       38.0    37.5   1.43   1.44   0.074   0.065   20.14   20.20
 84       37.4    37.5   1.42   1.44   0.072   0.065   20.07   20.20
 85       37.1    37.5   1.44   1.44   0.007   0.065   20.20   20.20
 85      103.9   104.7   2.54   2.56   0.053   0.048   36.04   36.26
 86       37.2    37.5   1.45   1.44   0.073   0.065   19.96   20.20
 87       37.2    37.5   1.44   1.44   0.076   0.065   20.18   20.20
 88       37.0    37.5   1.44   1.44   0.078   0.065   20.22   20.20
 89       37.3    37.5   1.43   1.44   0.068   0.065   20.20   20.20
 90       37.4    37.5   1.45   1.44   0.069   0.065   20.22   20.20
 91       37.1    37.5   1.44   1.44   0.070   0.065   20.23   20.20
 92       37.2    37.5   1.45   1.44   0.076   0.065   20.28   20.20
 93       37.0    37.5   1.43   1.44   0.072   0.065   20.09   20.20
 94       36.8    37.5   1.43   1.44   0.071   0.065   20.01   20.20
 95       36.9    37.5   1.42   1.44   0.075   0.065   20.11   20.20
 96       36.9    37.5   1.44   1.44   0.076   0.065   20.15   20.20

 
CTD      SiO4    SiO4   PO4     PO4    NO2     NO2     NOx     NOx
         mea-    ex-    mea-    ex-    mea-    ex-     mea-    ex-  
         sured   pect-  sured   pect-  sured   pect-   sured   pect-
                 ed             ed             ed              ed   
-------  -----   -----   ----   ----   -----   -----   -----   -----
 97       37.0    37.5   1.44   1.44   0.075   0.065   20.06   20.20
 98       36.9    37.5   1.42   1.44   0.074   0.065   20.06   20.20
 99       37.0    37.5   1.43   1.44   0.073   0.065   20.08   20.20
100       36.8    37.5   1.44   1.44   0.080   0.065   20.13   20.20
101       36.8    37.5   1.43   1.44   0.090   0.065   20.18   20.20
102       36.8    37.5   1.43   1.44   0.069   0.065   20.21   20.20
103       37.1    37.5   1.43   1.44   0.071   0.065   20.04   20.20
104       37.1    37.5   1.44   1.44   0.078   0.065   20.07   20.20
105       37.0    37.5   1.43   1.44   0.080   0.065   20.16   20.20
106       37.0    37.5   1.42   1.44   0.069   0.065   20.01   20.20
107       36.7    37.5   1.44   1.44   0.075   0.065   19.89   20.20
108       36.9    37.5   1.44   1.44   0.073   0.065   20.09   20.20
109       36.8    37.5   1.44   1.44   0.068   0.065   20.01   20.20
110       36.8    37.5   1.45   1.44   0.073   0.065   20.04   20.20
110      103.2   104.7   2.55   2.56   0.058   0.048   35.92   36.26
111       36.8    37.5   1.43   1.44   0.069   0.065   20.03   20.20
112       36.8    37.5   1.42   1.44   0.074   0.065   20.09   20.20
113       36.8    37.5   1.42   1.44   0.083   0.065   20.18   20.20
114       36.8    37.5   1.42   1.44   0.070   0.065   20.03   20.20
115       37.2    37.5   1.44   1.44   0.079   0.065   20.06   20.20
116       37.2    37.5   1.44   1.44   0.078   0.065   20.15   20.20
117       37.1    37.5   1.43   1.44   0.079   0.065   19.96   20.20
118       37.2    37.5   1.45   1.44   0.080   0.065   20.09   20.20
118      104.5   104.7   2.55   2.56   0.065   0.048   36.08   36.26
119       37.0    37.5   1.44   1.44   0.080   0.065   20.10   20.20
120       36.8    37.5   1.43   1.44   0.079   0.065   20.14   20.20
120       36.8    37.5   1.43   1.44   0.079   0.065   20.14   20.20
121       36.9    37.5   1.45   1.44   0.076   0.065   20.09   20.20
122       36.7    37.5   1.42   1.44   0.072   0.065   20.05   20.20
123       36.3    37.5   1.43   1.44   0.069   0.065   20.01   20.20
124, 125  37.4    37.5   1.44   1.44   0.072   0.065   20.04   20.20
126, 127  37.4    37.5   1.44   1.44   0.067   0.065   20.07   20.20
128       37.2    37.5   1.44   1.44   0.070   0.065   20.33   20.20
128      103.6   104.7   2.54   2.56   0.054   0.048   35.63   36.26
129       37.3    37.5   1.44   1.44   0.072   0.065   20.01   20.20
130       37.7    37.5   1.45   1.44   0.068   0.065   20.17   20.20

 
CTD      SiO4    SiO4   PO4     PO4    NO2     NO2     NOx     NOx
         mea-    ex-    mea-    ex-    mea-    ex-     mea-    ex-  
         sured   pect-  sured   pect-  sured   pect-   sured   pect-
                 ed             ed             ed              ed   
-------  -----   -----   ----   ----   -----   -----   -----   -----
131       37.7    37.5   1.44   1.44   0.065   0.065   20.13   20.20
132       37.6    37.5   1.45   1.44   0.070   0.065   20.16   20.20
133       37.8    37.5   1.45   1.44   0.069   0.065   20.39   20.20
134       37.8    37.5   1.43   1.44   0.068   0.065   20.04   20.20
134       37.8    37.5   1.43   1.44   0.068   0.065   20.04   20.20
135       37.4    37.5   1.42   1.44   0.067   0.065   20.04   20.20
136       37.7    37.5   1.43   1.44   0.072   0.065   20.10   20.20
137       37.2    37.5   1.43   1.44   0.069   0.065   20.09   20.20
138       37.3    37.5   1.43   1.44   0.068   0.065   20.01   20.20
139       37.8    37.5   1.44   1.44   0.071   0.065   20.00   20.20
139      104.2   104.7   2.54   2.56   0.055   0.048   36.01   36.26
140       37.3    37.5   1.42   1.44   0.070   0.065   20.02   20.20
uwy088-   37.8    37.5   1.41   1.44   0.057   0.065   20.00   20.20
090
uwy091-   37.1    37.5   1.42   1.44   0.057   0.065   20.13   20.20
094



7.5  Nutrient Methods

CSIRO Oceans and Atmosphere Hydrochemistry nutrient analysis is performed with a 
segmented flow auto-analyser – Seal AA3 – to measure silicate, phosphate, nitrite, 
nitrate plus nitrite, and ammonia.


Table 2: Calibration range and detection limits of nutrient analysis

Details
Instrument          AA3
Software            Seal AACE 6.10
Methods             AA3 Analysis Methods internal manual
Nutrient         Silicate     Phosphate       Nitrate +       Nitrite        Ammonia
                                               Nitrite
               ------------  -------------  -------------  -------------  -------------
Concentration  140 µmol l-1     3 µmol l-1    42 µmol l-1   1.4 µmol l-1   2.0 µmol l-1
  range  
Method         0.2 µmol l-1  0.02 µmol l-1  0.02 µmol l-1  0.02 µmol l-1  0.02 µmol l-1
  Detection     
  Limit (MDL)


Silicate analysis is based on a modified Armstrong et al. (1967) method. Silicate in 
seawater reacts with acidified ammonium molybdate to produce silicomolybdic acid.  
This solution will also react with phosphate producing a phosphomolybdic acid. 
Tartaric acid is introduced to remove this interference. Finally, Stannous Chloride 
(Tin II Chloride) is added to reduce silicomolybdic acid to the blue compound 
silicomolybdous acid which can be detected at 660 nm or 820 nm.

Phosphate measurement is based on the original Murphy and Riley (1962) method with 
some modifications developed at the NIOZ-SGNOS Practical Workshop 2012 optimizing 
antimony catalyst/phosphate ratio and reduction of silicate interferences by pH. 
Phosphate in seawater forms a phosphomolybdenum blue complex with acidified ammonium 
molybdate reduced by ascorbic acid which can be detected at 880 nm.

Nitrate is determined by first reducing to nitrite via a basic buffered copperized 
cadmium column before the colour reaction (Wood et al., 1967). Nitrite in seawater 
will react with sulphanilamide under acidic conditions to form a diazo compound. 
This compound couples with 1-N-naphthly- ethylenediamine di-hydrochloride to produce 
a reddish purple azo complex which can be detected at 520 nm.

The ammonia method, developed by Roger Kérouel and Alain Aminot, IFREMER (1997 
Mar.Chem.57), is based on the reaction of ammonium with orthophtaldialdehyde and 
sulfite at a pH of 9.0-9.5 producing an intensely fluorescent product; excitation 
370 nm, emission 460 nm.

Detailed SOPs can be obtained from the CSIRO Oceans and Atmosphere Hydrochemistry 
Group on request.



8  REFERENCES

Armishaw, Paul, “Estimating measurement uncertainty in an afternoon. A case 
    study in the practical application of measurement uncertainty.” Accred 
    Qual Assur, 8, pp. 218-224 (2003).

Armstrong, F.A.J., Stearns, C.A., and Strickland, J.D.H., “The measurement of 
    upwelling and subsequent biological processes by means of the Technicon 
    Autoanalyzer and associated equipment,” Deep-Sea Research, 14, pp.381-389 
    (1967).

Hood, E.M. (2010). “Introduction to the collection of expert reports and 
    guidelines.” The GO-SHIP Repeat Hydrography Manual: A Collection of Expert 
    Reports and Guidelines. IOCCP Report No 14, ICPO Publication Series No. 
    134, Version 1, 2010.

Hydes, D., Aoyama, M., Aminot, A., Bakker, K., Becker, S., Coverly, S., 
    Daniel, A.G., Dickson, O., Grosso, R., Kerouel, R., van Ooijen, J., Sato, 
    K., Tanhua, T., Woodward, E.M.S., and Zhang, J.Z. (2010). "Determination 
    of dissolved nutrients (N, P, Si) in seawater with high precision and 
    inter-comparability using gas-segmented continuous flow analysers." The 
    GO-SHIP Repeat Hydrography Manual: A Collection of Expert Reports and 
    Guidelines. IOCCP Report No 14, ICPO Publication Series No. 134, Version 
    1, 2010.

Kérouel, Roger and Alain Aminot, “Fluorometric determination of ammonia in sea 
    and estuarine waters by direct segmented flow analysis”. Journal of Marine 
    Chemistry 57 (1997) pp. 265- 275.

Murphy, J. And Riley, J.P.,”A Modified Single Solution Method for the 
    Determination of Phosphate in Natural Waters”, Anal.Chim.Acta, 27, p.30, 
    (1962)

Wood, E.D., F.A.J. Armstrong, and F.A. Richards. (1967) “Determination of 
    nitrate in seawater by cadmium-copper reduction to nitrite.” Journal of 
    the Marine Biological Association of U.K. 47: pp. 23-31.

 
RV INVESTIGATOR
CTD PROCESSING REPORT


Voyage #:            IN2016_V03
Voyage title:        Monitoring Ocean Change and Variability along 170°W 
                     from the ice edge to the equator.
Depart:              Hobart, 0900 Tuesday, 26 April 2016
Return:              Hobart, 0800 Thursday, 30 June 2016
Report compiled by:  Steven Van Graas

 

Contents

1  Summary                                                          70
2  Voyage Details                                                   71
   2.1  Title                                                       71
   2.2  Principal Investigators                                     71
   2.3  Voyage Objectives                                           71
   2.4  Area of operation                                           71
3  Processing Notes                                                 71
   3.1  Background Information                                      71
   3.2  Pressure and temperature calibration                        73
   3.3  Conductivity Calibration                                    73
   3.4  Dissolved Oxygen Sensor Calibration                         74
   3.5  Other sensors                                               75
   3.6  Bad data detection                                          75
   3.7  Averaging                                                   76
4  References                                                       76

 

1  SUMMARY

These notes relate to the production of quality controlled, calibrated CTD data from 
RV Investigator voyage in2016_v03, from 26 Apr 2016 – 30 Jun 2016.

Data for 141 deployments were acquired using the Seabird SBE911 CTD 20, fitted with 
36 ten litre bottles on the rosette sampler. CSIRO supplied calibrations were 
applied to the temperature, conductivity, oxygen, and pressure data. The data were 
subjected to automated QC to remove spikes and out-of-range values.

The final conductivity calibration is based on multiple deployment groupings, due to 
sensor and deck box changes. Processing was performed on each unique sensor 
configuration in order to best account for the individual characteristics of each 
sensor. The final calibration from the primary sensor for casts 1-7 had a standard 
deviation (S.D) of 0.00088 PSU, a S.D of 0.00117 for casts 8-46, and S.D of 0.00114 
for casts 47-141, well within our target of ‘better than 0.002 PSU’. The standard 
product of 1 dbar binned averaged were produced using data from the primary 
temperature and conductivity sensors, and the secondary Oxygen sensor.

Similarly, the dissolved oxygen data were calibrated in groups of deployments due to 
sensor changes. The dissolved oxygen data calibration fit had a S.D. of 0.865uM for 
casts 1-7, S.D. of 0.906uM for casts 8-46, S.D. of 1.05uM for casts 47-63, 0.739uM 
for casts 64-83, S.D. of 0.874uM for casts 84-110, and a S.D. of 1.0479 for casts 
111-141. The agreement between the CTD and bottle data was good.

A Fluorometer, Transmissometer, and altimeter were also installed and logged on the 
auxiliary A/D channels of the CTD.



2  VOYAGE DETAILS


2.1  Title

Monitoring Ocean Change and Variability along 170o W from the ice edge to the 
equator.


2.2  Principal Investigators

Bernadette Sloyan – Leg 1, Susan Wijffels – Leg 2


2.3  Voyage Objectives

The scientific objectives for in2016_v03 were outlined in the Voyage Plan.

For further details, refer to the Voyage Plan and/or summary which can be viewed on 
the CSIRO Marine and Atmospheric Research web site.


2.4  Area of operation

FIGURE 1. Area of operation for in2016_v03



3  PROCESSING NOTES

3.1 Background Information
The data for this voyage were acquired with the CSIRO CTD unit #20 and #22, Seabird 
SBE911 with dual conductivity and temperature sensors.

The CTD was additionally fitted with SBE43 dissolved oxygen sensors, an altimeter, 
Transmissometer and Fluorometer. Additionally the CTD unit provided power only for 
two SBE61 units. The sensors that were equipped are described in Table 1 below.




TABLE 1: CTD Sensor configuration on in2016_v03

Description      Sensor            Casts    Serial  A/D  Calibration  Calibration 
                                            No.             Date         Source
---------------  ----------------  -------  ------  ---  -----------  -------------
Pressure         Digiquartz SBE9+  1-7,     552      P   2016-03-09   CSIRO Cal Lab
                                   47-141
Pressure         Digiquartz SBE9+  8-46     1243     P   2016-03-09   CSIRO Cal Lab
Primary Seabird  SBE3plus          1-46     4722     T0  2016-03-01   CSIRO Cal Lab
  Temperature      
Primary          Seabird SBE3plus  47-141   6022     T0  2015-07-15   CSIRO Cal Lab
  Temperature
Secondary        Seabird SBE3plus  1-46     4522     T1  2016-03-01   CSIRO Cal Lab
  Temperature
Secondary        Seabird SBE3plus  47-93    6024     T1  2015-07-24   CSIRO Cal Lab
  Temperature
Secondary        Seabird SBE3plus  94-141   4718     T1  2015-10-29   CSIRO Cal Lab
  Temperature
Primary          Seabird SBE4C     1-46     3868     C0  2016-03-02   CSIRO Cal Lab
  Conductivity
Primary          Seabird SBE4C     47-141   4425     C0  2015-07-08   CSIRO Cal Lab
  Conductivity
Secondary        Seabird SBE4C     1-46,    4426     C1  2015-07-08   CSIRO Cal Lab
  Conductivity                     114-141
Secondary        Seabird SBE4C     47-88    2312     C1  2015-11-24   CSIRO Cal Lab
  Conductivity
Secondary        Seabird SBE4C     89-113   2235     C1  2015-11-24   CSIRO Cal Lab
  Conductivity
Primary          SBE43             1-46     3154     A0  2016-03-10   CSIRO Cal Lab
  Dissolved 
  Oxygen
Primary          SBE43             47-141   1794     A0  2016-03-10   CSIRO Cal Lab
  Dissolved 
  Oxygen
Secondary        SBE43             1-46,    3198     A1  2015-08-12   CSIRO Cal Lab
  Dissolved                        111-141
  Oxygen
Secondary        SBE43             47-111   3199     A1  2015-08-12   CSIRO Cal Lab
  Dissolved 
  Oxygen
Transmissometer  C-Star            1-141    CST-     A2  2015-08-14   Manufacturer
                                            1421DR
Altimeter        PA500             1-141    5301.    A3  2015-05-22   Manufacturer
                                            228403
Fluorometer      Chelsea           57-141   0088-    A6  2014-02-06   Manufacturer
                 Aquatracka III             3598C



Water samples were collected using a Seabird SBE32, 24-bottle rosette sampler. 
Sampling was from 36 ten litre bottles which were fitted to the frame. There were 
141 deployments.

The raw CTD data were converted to scientific units and written to netCDF format 
files for processing using the Matlab-based, CapPro package.

The CapPro software was used to apply automated QC and preliminary processing to the 
data. This included spike removal, identification of water entry and exit times, 
conductivity sensor lag corrections and the determination of the pressure offsets. 
The automatically determined pressure offsets and in-water points were inspected and 
adjusted where necessary. It also loaded the hydrology data and computed the 
matching CTD sample burst data. Filtering for bad data caused by ship heave 
affecting the velocity of the package was also applied to the binned average data.

The bottle sample data were used to compute final conductivity and dissolved oxygen 
calibrations. These were applied to the data, after which files of binned 1dB 
averaged data were produced.


3.2  Pressure and temperature calibration

The pressure offsets are plotted in Figure 2 below. The blue circles refer to 
initial out-of-water values and the red circles the final out-of-water values. The 
jump in the plot that is evident at cast 47 is due to changing the pressure sensor.

 
FIGURE 2: CTD pressure offsets


3.3  Conductivity Calibration

Discrepancies and possible sampling problems between bottle and CTD salinities for 
the primary conductivity sensor would show in Figure 4, the plot of calibrated (CTD 
- Bottle) salinity below, for all groups of deployments processed. The calibration 
was based upon the sample data for an overall total of 3654 of the total of 4720 
samples taken during deployments (the outliers marked in Figure 4 below with the 
magenta diamonds are excluded from the calibration).

 
FIGURE 4: CTD - bottle salinity plot.

 
The final result for the primary conductivity sensor for casts 1 - 7 was –

Scale Factor (a1)       0.99943         wrt. CSIRO calibration
Offset (a0)            -8.6338e-05              ditto
Calibration S.D. (Sal)  0.00087776 PSU


The final result for the primary conductivity sensor for casts 8 - 46 was –

Scale Factor (a1)       0.99941         wrt. CSIRO calibration
Offset (a0)            -2.4759e-05              ditto
Calibration S.D. (Sal)	0.0011708 PSU


The final result for the primary conductivity sensor for casts 47 - 141 was –

Scale Factor (a1)       1.0005          wrt. CSIRO calibration
Offset (a0)            -0.00069281              ditto
Calibration S.D. (Sal)  0.0011492 PSU




This is a good calibration. We normally aim for a S.D. of 0.002 psu for ‘typical’ 
oceanographic voyages. The above calibration factors were applied to all deployments 
in their respective calibration groups.

Data from the primary conductivity and temperature sensors were used to produce the 
averaged salinities.

The calibration using the secondary conductivity sensor was well beyond our 
acceptable standard deviation range, and as such was not applied.


3.4  Dissolved Oxygen Sensor Calibration


3.4.1 SBE calibration procedure

Sea-Bird (2010a) describes the SBE43 as “a polarographic membrane oxygen sensor 
having a single output signal of 0 to +5 volts, which is proportional to the 
temperature-compensated current flow occurring when oxygen is reacted inside the 
membrane. A Sea-Bird CTD that is equipped with an SBE43 oxygen sensor records this 
voltage for later conversion to oxygen concentration, using a modified version of 
the algorithm by Owens and Millard (1985)”.

Calibration involves performing a linear regression, as per Sea-Bird (2010b) to 
produce new estimates of the calibration coefficients Soc and Voffset. These new 
coefficients are used, along with the other, manufacturer-supplied coefficients, to 
derive oxygen concentrations from the sensor voltages.

 
Results

Deeper casts (>1000m) are known to be affected by pressure-induced hysteresis with 
this sensor. This is corrected automatically within CapPro using the method 
discussed by Sea-Bird (2010c).

There is a small mismatch between downcast and upcast dissolved oxygen due to the 
response time of the sensor. No correction for the sensor lag effect has been 
applied.

Multiple deployment calibration groups were used with the associated SBE43 up-cast 
data to compute the new Soc and Voffset coefficients, due to changes of sensors 
throughout the voyage.

The old and new Soc and Voffset values for DO sensors are listed in Table 2 below. 
The Soc value is a linear slope scaling coefficient; Voffset is the fixed sensor 
voltage at zero oxygen. As expected, over time, the increasing Soc scale factors 
show the SBE43 sensor is losing sensitivity.

The calibrations were applied for each sensor and the averaged files were created 
using the result from the primary sensor for casts 1-7, and the secondary sensor for 
casts 8 – 141. These groups were divided further due to changing the CTD unit. The 
primary oxygen sensor for casts 47-141 calibrated extremely poorly.


TABLE 2: Dissolved oxygen calibrations

        Casts               CSIRO calibration  sensor       Primary/
                            of sensor          calibration  Secondary
        -------  ---------  -----------------  -----------  ---------
        1-7      Voffset    -0.50133997        -0.47032     Primary
                 Soc         0.47520554         0.49124     
                 Fit SD (uM)                    0.86539     

        8-46     Voffset    -0.4982            -0.45105     Secondary
                 Soc         0.4241             0.42153     
                 Fit SD (uM)    --              0.9063    

        47-63    Voffset    -0.4873            -0.45033     Secondary
                 Soc         0.5318             0.53553     
                 Fit SD (uM)    --              1.0502    

        64-83    Voffset    -0.4873            -0.45744     Secondary
                 Soc         0.5318             0.5505    
                 Fit SD (uM)    --              0.7398    

        84-110   Voffset    -0.4873            -0.44407     Secondary
                 Soc         0.5318             0.54158     
                 Fit SD (uM)    --              0.87393     

        111-141  Voffset    -0.4982            -0.41699     Secondary
                 Soc         0.4241             0.40081    
                 Fit SD (uM)    --              1.0479    


3.5  Other sensors

The Chelsea fluorometer was used for deployments 57 onwards. The fluorometer has 
been calibrated to give nominal outputs of 0-100 fsd (full scale deflection).


3.6  Bad data detection

The limits for each sensor are configured in the CAP the CTD acquisition software 
and are written to the netCDF scan file. Typical limits used for the sensor range 
and maximum second difference are in Table 3 below. The rejection rate is recorded 
in the CapPro processing log file.








TABLE 3: Sensor limits for bad data detection

              Sensor        Range min  Range max  Max Second Diff
              ------------  ---------  ---------  ---------------
              temperature       -2         40          0.05
              conductivity      -0.01       7          0.01
              oxygen            -1        500          0.5
              fluorometer        0        100          0.5


3.7  Averaging

The calibrated data were ‘filtered’ to remove pressure reversals and binned into the 
standard product of 1dbar averaged NetCDF files. The binned values were calculated 
by applying a linear, least-squares fit as a function of pressure to the sensor data 
for each bin, using this to interpolate the value for the bin mid-point. This method 
is used to avoid possible biases which would result from averaging with respect to 
time.

Each binned parameter is assigned a QC flag. Our quality control flagging scheme is 
described in Pender (2000).

The QC Flag for each bin is estimated from the values for the bin components. The QC 
Flag for derived quantities, such as Salinity and Dissolved Oxygen are taken to be 
the worst of the estimates for the parameters from which they are derived.

 

4  REFERENCES

Sloyan, Wijffels., 2016: The RV Investigator. Voyage Plan IN2016_V03 - 
    http://mnf.csiro.au/~/media/Files/Voyage-plans-and- 
    summaries/Investigator/Voyage%20Plans%20summaries/2016/IN2016_V03%20Voy 
    age%20Plan%2020160427%20FINAL.ashx

Pender, L., 2000: Data Quality Control Flags.
    http://www.cmar.csiro.au/datacentre/ext_docs/DataQualityControlFlags.pdf

Sea-Bird Electronics Inc., 2010a: Application Note No 64: SBE 43 Dissolved 
    Oxygen Sensor -- Background Information, Deployment Recommendations, and 
    Cleaning and Storage. 
    http://www.seabird.com/pdf_documents/ApplicationNotes/appnote64Feb10.pdf

Sea-Bird Electronics Inc., 2010b: Application Note No 64-2: SBE 43 Dissolved 
    Oxygen Sen- sor Calibration and data Corrections using Winkler Titrations. 
    http://www.seabird.com/pdf_documents/ApplicationNotes/Appnote64-2Feb10.pdf

Sea-Bird Electronics Inc., 2010c: Application Note No 64-3: SBE 43 Dissolved 
    Oxygen (DO) Sensor - Hysteresis Corrections. 
    http://www.seabird.com/pdf_documents/ApplicationNotes/Appnote64-3Feb10.pdf

 

CCHDO DATA PROCESSING NOTES

• File Online Carolina  Berys

IN2016_V03 Voyage Summary.pdf (download) #78dd5
Date: 2017-04-11
Current Status: unprocessed




• File Online Carolina  Berys

in2016_v03_HYD_ProcessingReport.pdf (download) #5b51f
Date: 2017-04-11
Current Status: unprocessed




• File Online Carolina  Berys

IN2016_V03CTD.pdf (download) #cc14c
Date: 2017-04-11
Current Status: unprocessed




• File Submission Bernadette  Sloyan

IN2016_V03CTD.pdf (download) #cc14c
Date: 2017-04-11
Current Status: unprocessed
Notes
Voyage report for P15S.

These include:
Summary
Hydrochemistry report. Flags used by the CSIRO hydrochemistry group have been 
converted to standard flags in the data submission. Please note I am working with 
Bob Key to get this completed, hopefully the data will be submitted by the end of 
the week
CSIRO CTD processing report.

Voyage report for P15S.

These include:
Summary
Hydrochemistry report. Flags used by the CSIRO hydrochemistry group have been 
converted to standard flags in the data submission. Please note I am working with 
Bob Key to get this completed, hopefully the data will be submitted by the end of 
the week
CSIRO CTD processing report.




• File Submission Bernadette  Sloyan

IN2016_V03 Voyage Summary.pdf (download) #78dd5
Date: 2017-04-11
Current Status: unprocessed
Notes
Voyage report for P15S.

These include:
Summary
Hydrochemistry report. Flags used by the CSIRO hydrochemistry group have been 
converted to standard flags in the data submission. Please note I am working with 
Bob Key to get this completed, hopefully the data will be submitted by the end of 
the week
CSIRO CTD processing report.




• File Online Carolina  Berys

P15S_ct.tar (download) #6b8ea
Date: 2017-01-19
Current Status: unprocessed

Dear CCHDO,

Attached are the CTD and Hydro exchange files for the Australian occupation of the 
GO-SHIP P15S section (EXPOCODE = 096U20160426).

The CTD oxygen data is flagged questionable as I am still working through 
calibration issues. The oxygen bottle data is of high quality and appropriately 
flagged.

I am still working on the section report. I'll send this when completed. Please 
contact me if you have any question.
Regards Bernadette




