Metadata record for data from ASAC Project 2307 See the link below for public details on this project. ---- Public Summary from Project ---- The project investigates microbial life in the Southern Ocean. The studies will investigate two areas - the role of bacteria in the regeneration of the important nutrient silica via decomposition of planktonic biomass and to assess the importance of prokaryotic polyunsaturated fatty acid (PUFA) entering the marine food web from natural communities in Antarctic sea ice and the Southern Ocean. Project objectives: 1. Investigate the role of bacteria in the colonisation and decomposition of phytoplankton and concomitant redispersal of silica from phytoplankton in seawater of the Southern Ocean at various different latitudes. 2. Validate real-time PCR (5-prime nuclease PCR assay) for rapid quantification of key bacterial found in seawater to determine their association with phytoplankton decomposition and silica redispersal. Significance: Recent studies (Bidle and Azam, 1999) demonstrate that much silica regeneration in seawater is due to bacterial enzymatic activity and that diatom decomposition and silica release is highly accelerated in the presence of an active colonising bacterial population. The formation of bacterial biofilms and production of extracellular enzymes on phytoplanktic detritus and aggregates appears to lead to the direct breakdown of proteins and polysaccharides which hold together the diatom frustules. In the Southern Ocean this process could be significant as the foodweb there is sustained by phytoplanktonic (mostly diatom) primary productivity (Bunt 1963) whether it be in sea-ice or in the pelagic zone. If silica redispersal does not occur diatoms would instead eventually become buried in sediment with silica supplies becoming limited, except that supplied by aeolian and terrigenous input. In the marine environment half of primary-produced organic matter is degraded by bacteria (Cole et al., 1988). Thus the bacterial decomposition of diatom biomass and subsequent release of dissolved silica should be an important and relatively rapid process in Southern Ocean waters. At this stage there is still limited data on the role of bacteria in regeneration of silica in the overall marine environment. The study of Bidle and Azam (1999) examined seawater off of California and mostly examined the process itself. Currently, the role of specific bacteria is being examined by Kay Bidle (personal communication) and John Bowman is supplying various marine bacteria to assess this. In the proposed study we wish to examine the role of bacteria in the Southern Ocean in the decomposition of diatom biomass, rate of release of dissolved silica and bacterial groups involved in the process. This research should reveal some fundamental knowledge on a integral role of bacteria in Southern Ocean ecosystems. In order to assess the bacterial role in silica redispersal we wish to use three molecular ecological techniques: fluorescent in situ hybridisation (FISH), denaturing gradient gel electrophoresis (DGGE) and real-time PCR. FISH and DGGE analysis are well established in John Bowmans laboratory and are being used routinely for analysis of Antarctic and Tasmanian natural samples (seawater and sediment). The real-time PCR analysis which can be used as a sensitive quantitative assay for bacterial populations in natural samples is currently in development using a recently purchased Rotorgene (Corbett Research) instrument. The method has been used to great effect in measuring rapidly bacterial populations in seawater (eg., Suzuki et al. 2000). Using these methods will allow us to accurately measure changes in bacterial populations during colonisation and decomposition of the diatom biomass during the silica redispersal experiments. There are two data files associated with this project. Part 1: Total of 9 files: File 1. Seawater sample data - information from two cruises in 2000 and 2001 - includes position of sample, types of sample, temperature and analyses performed subsequently. File 2. 16S rRNA gene sequences derived from Southern ocean seawater bacterial isolates. Sequences are all deposited in the GenBank nucleotide database and are in FASTA format. File 3. 16S rRNA gene sequences derived from denaturing gradient gel electrophoretic gel slices via extraction, PCR and cloning. Sequences are all deposited in the GenBank nucleotide database and are in FASTA format. File 4. Flavobacteria abundance in Southern Ocean samples on the basis of depth. Abundance determined using fluorescent insitu hybridisation using universal bacterial probe EUB338 and flavobacteria specific probe. Details of sites analysed are included in the seawater sample file. File 5. Flavobacteria abundance in Southern Ocean samples on the basis of latitude (transect from 47 S to 63 S). Abundance determined using fluorescent insitu hybridisation using universal bacterial probe EUB338, alphaproteobacteria, gammaproteobacteria and flavobacteria specific probe. Total count of bacteria was determined by epifluorescence using DAPI. Details of sites analysed are included in the seawater sample file. File 6. Nutrient and chlorophyll a data for samples studied (see seawater sample file) including nitrate, phosphate and silica. File 7. Bacterial isolate information including strain designations, site location, and identification to genus level. File 8. . Bacterial isolate fatty acid data for strains designated as novel in bacterial isolate information file. Fatty acids determined using GC-MS analytical methods. File 9. Bacterial isolate phenotypic data for strains designated as novel in bacterial isolate information file. Includes morphological, physicochemical, biochemical and nutritional profile data. Part 2: Total of 4 files: File 1. 16S rRNA gene sequences derived from denaturing gradient gel electrophoretic (DGGE) gel slices via extraction, PCR and cloning. DGGE analysis performed on samples analysed over 30 days from 20 litre microcosms derived from southern seawater to which was added 10 mg sterile diatom detritus derived from axenic Nitszchia closterium. Sequences are all deposited in the GenBank nucleotide database and are in FASTA format. File 2. Flavobacteria abundance in Southern Ocean seawater microcosms over 30 days. Abundance determined using real-time PCR using universal bacterial and flavobacteria specific PCR primers. File 3. Bacterial mediated silica release data from Southern Ocean seawater microcosms over 30 days. Includes non-detritus amended controls that indicate the natural level of of seawater silica. Silica analysis performed by a chemical procedure. File. 4. Seawater sample data obtained during 2001 indicating the sites for seawater used for creating 20 l microcosms and used to assess silica release by bacteria from diatom detritus.

Sediment cores were collected from the East Antarctic margin, aboard the Australian Marine National Facility R/V Investigator from January 14th to March 5th 2017 (IN2017_V01; (Armand et al., 2018). This marine geoscience expedition, named the “Sabrina Sea Floor Survey”, focused notably on studying the interactions of the Totten Glacier with the Southern Ocean through multiple glacial cycles. The cores were collected using a multi-corer (MC), were sliced every centimetre, wrapped up in plastic bags, and stored in the fridge. Sediment samples were dried in an oven at 40°C and ground using a pestle and a mortar. Biogenic silica (or ‘opal’) analysis was carried out following modification of the protocol of Mortlock and Froelich (1989). About 30 mg of sediment was leached with 30 mL of 1M sodium carbonate (Na2CO3) for 5 hours at 80°C. Every hour, 1 mL of sample was removed and centrifuged at 10,000 rpm for 30 sec. A 200 µL aliquot was removed from the supernatant and diluted 50x with Milli-Q water for SiO2 determination by molybdate-blue spectrophotometry. A standard calibration was prepared by dilution of a SiO2 standard solution (sodium hexafluorosilicate, from 0 to 200 µM). The opal concentrations were calculated using the slope of the last three points of the dissolution curve (Demaster, 1981), or the changing slope part of the curve. References - Armand, L. K., O’Brien, P. E., Armbrecht, L., Baker, H., Caburlotto, A., Connell, T., … Young, A. (2018). Interactions of the Totten Glacier with the Southern Ocean through multiple glacial cycles (IN2017-V01): Post-survey report. ANU Research Publications. - Demaster, D. J. (1981). The supply and accumulation of silica in the marine environment. Geochimica et Cosmochimica Acta, 45, 1715–1732. - Mortlock, R. A., and Froelich, P. N. (1989). A simple method for the rapid determination of biogenic opal in pelagic marine sediments. Deep-Sea Research Part I, 36(9), 1415–1426.

These data describe the locations, dates, time, etc where biogeochemistry data were collected on the CEAMARC-CASO cruise in the 2007/2008 Antarctic season. See the CEAMARC-CASO events metadata record for further information. Sample codes are not descriptive. CEMARC/CASO column have underway data (no link to group site) as well as the CEAMARC and CASO sampling locations. Events are recorded by number and the associated type of sample taken. CTD - 0.4 um filtered water sample. Box corer - diatom scrape. Beam Trawl AAD - sponge sample. PHY - phytoplankton sample taken from inline surface seawater system. Van Veen grab - sediment scrape. WAT - surface water sample passed through 0.4 um filter. Description column explains the samples in more detail - eg information on what size fraction the phytoplankton were filtered at. Litres column describes the volume of water that was filtered. Depth is in metres. Time is local time. Temperature is degrees C. Storage location was for shipboard use only. The "other" column details any extra information that may be useful to the sample for example #2153 refers to a sample id code that the French CEAMARC group was using to code for their samples. Our aim for this voyage was to collect surface phytoplankton and water samples across a transect of the Southern Ocean, and to collect benthic sponge and coral samples in Antarctica, to (i) measure the Ge/Si and Si isotope composition to construct a nutrient profile across the Southern Ocean, and to test and calibrate these parameters as proxies for silica utilisation; and (ii) measure the B isotope composition to test the potential of biogenic silica to be used as a seawater pH proxy. We collected phytoplankton, sponges, diatom sediment scrapes and water samples at strategic locations to ensure that the entire water column was surveyed. The data that were collected were used in collaboration with palaeoenvironmental data from sediment cores and experimental culture experiments on diatoms and sponges to gain a better understanding of historical distributions of Silicon and pH in the Southern Ocean.

This is the CTD and Niskin bottle data set from the RV Tangaroa cruise tan0704, 7th Mar 2007 to 29th Mar 2007, along the Macquarie Ridge. This was the deployment cruise for the Macquarie Ridge mooring array. Dissolved oxygen data have been removed from this data set (oxygen bottle data never analysed). There were a total of 75 CTD casts on this cruise.

The absolute abundances (cells per ml) of 22 hard-shelled phytoplankon taxa (comprised of species, genera or higher taxonomic groups) estimated from Scanning Electron Microscope survey of 52 samples collected through 11 austral spring-summers (2002/3 to 2012/13) (part of the L' Astrolabe collection) from the seasonal ice zone of the Southern Ocean (between latitude 62 and 64.4 degrees south, and longitude 135.8 and 150 degrees east) also included are environmental covariables for each sample: three constructed SAM indices, SST, Salinity, NOx, PO4, SiO4, and the sampling date, time, and location. Fifty-two surface-water samples were collected from the seasonal ice zone (SIZ) of the Southern Ocean (SO) across 11 consecutive austral spring-summers from 2002/03 to 2012/13. The samples were collected aboard the French re-supply vessel MV L’Astrolabe during resupply voyages between Hobart, Tasmania, and Dumont d’Urville, Antarctica between the 20th October and the 1st March. Most samples were collected from ice-free water, although some were collected south of the receding ice-edge. The sampled area was in the high latitude SO (Figure 1b) in the south-east corner of the Australian Antarctic Basin, spanning 270 km of latitude between 62°S and 64.5°S, and 625km of longitude between 136°E and 148°E. The area lies greater than 100 km north of the Antarctic continental shelf, in waters greater than 3,000 m depth. Samples were obtained from the clean seawater line of the re-supply ship from around 3 m depth. Each sample represented 250 ml of seawater filtered through a 25 mm diameter polycarbonate-membrane filter with 0.8 µm pores (Poretics). The filter was then rinsed with two additions of approximately 2 ml of MilliQ water to remove salt, then air dried and stored in a sealed container containing silica gel desiccant. Samples were prepared for scanning electron microscope (SEM) survey by mounting each filter onto metal stubs and sputter coating with 15 nm gold or platinum. Only organisms possessing hard siliceous or calcareous shells were sufficiently well preserved through the sample preparation technique that they could be identified by SEM, and included diatoms, coccolithophores, silicoflagellates, Pterosperma, parmales, radiolarians, and armoured dinoflagellates. The composition and abundance the phytoplankton community of each sample was determined using a JEOL JSM 840 Field Emission SEM. Cell numbers for each phytoplankton taxon were counted in randomly selected digital images of SEM fields taken at x400 magnification (Figure 2). Each image represented an area of 301 x 227 µm (0.068 mm2) of each sample filter, which was captured at a resolution 8.5 pixels/µm. A minimum of three SEM fields were assessed for each sample, with more fields assessed when cell densities were lower. On average, 387 cells were counted for each sample. Taxa were classified with the aid of Scott and Marchant (2005), Tomas (1997), and expert opinion. Cell counts per image were converted to volume-specific abundances (cells/ml) by dividing by 0.0348 ml of sea-water represented by each image. A total of 19,943 phytoplankton organisms were identified and counted: 18,872 diatoms, 322 Parmales, 173 coccolithophores, 81 silicoflagellates, and 45 Petasaria. A total of 48 phytoplankton taxa were identified, many to species level. Because the diatoms Fragilariopsis curta (Van Heurck) Hustedt and F. cylindrus (Grunow ex Cleve) Helmcke and Krieger could not be reliably discriminated at the microscope resolution employed, they were pooled into a single taxa-group. Other taxa were also grouped, namely Nitzschia acicularis (Kützing) W.Smith with N. decipiens Hustedt to a single group, and discoid centric diatoms of the genera Thalassiosira, Actinocyclus and Porosira to another. Rare species, with maximum relative abundance less than 2%, were removed from the data prior to analysis as they were not considered to be sufficiently abundant to warrant further analysis (Webb and Bryson 1972, Taylor and Sjunneskog 2002, Swilo et al. 2016). After pooling taxa and deleting rare taxa, twenty-two taxa and taxonomic-groups (species, groups of species and families) remained to describe the composition of the phytoplankton community. Phytoplankton abundances were related to a range of environmental covariates available at the time of sampling. These included the SAM, sea surface temperature (SST), salinity, time since sea ice cover (DaysSinceSeaIce, defined below), minimum latitude of sea ice in the preceding winter, latitude and longitude of sample collection, the days since 1st October that a sample was collected (DaysAfter1Oct), the year of sampling (year, being the year that each spring-summer sampling season began), the time of day that a sample was collected, and macro-nutrient concentrations: phosphate (PO4), silicate (SiO4) and nitrate + nitrite (hereafter nitrate, NOx). Water samples for dissolved macro-nutrients were collected, frozen on ship, and later analysed at CSIRO in Hobart using standard spectrophotometric methods (Hydes et al. 2010). Daily estimates of SAM were obtained from the US NWS Climate Prediction Center's website and are the NOAA Antarctic Oscillation Index values based on 700-hPa geopotential height anomalies (NOAA 2017). The variable DaysSinceSeaIce was defined as the time since sea ice had melted to 20% cover (after Wright et al. 2010) as determined from daily Special Sensor Microwave/Imager (SSM/I) sea ice concentration data distributed by the University of Hamburg (Spreen et al. 2008). To examine the lag in the expression of the SAM on phytoplankton community composition, two response surfaces were constructed relating the variance in phytoplankton community composition explained by the SAM to the temporal positioning of the period over which daily SAM was averaged. These were derived by evaluating separate CAP analyses (described below) based on daily SAM averaged across a range of days {1, 3, 5, … 365} centred on (i) each calendar day individually (1 Jan – 31 Dec) through the year associated with each sample; and (ii) lagged from 1 to 365 days prior to each sample collection date. Empirical identification of the time between variation in the SAM and the manifestation of this variation in the phytoplankton community structure revealed three modes (maxima) in phytoplankton community composition explained by the SAM. The first was an autumn seasonal SAM mode, which was determined to be the average of 57 daily SAM estimates centred on the preceding 11th March (11th Feb – 8th Apr). This mode explained up to 13.3% of the variance in taxonomic composition (SAM autumn). The second was a spring seasonal mode, which was determined to be the average of 75 daily SAM estimates centred on 25th October (20th Sep – 3rd Dec). This mode explained up to 10.3% of variance in taxonomic composition (SAM spring). Unlike the other modes that were related to the time of year, the third mode was timed relative to the date of sample collection for each sample and comprised the average of the 97 daily SAM estimates centred 102 days prior to each sample collection date. It explained 9.9% of the variance in phytoplankton composition (SAM prior). The mean standard error on estimates of SAM were 0.14 SAM index units for SAM autumn and SAM spring, and 0.13 for SAM prior. Note that SAM prior and SAM spring temporally overlapped to varying extents across the 52 samples and so were not entirely independent covariates: for example, a sample collected in the summer had previous days contributing to both SAM prior and SAM spring.

The Sub-Antarctic Zone (SAZ) in the Southern Ocean provides a significant sink for atmospheric CO2 and quantification of this sink is therefore important in models of climate change. During the SAZ-Sense (Sub-Antarctic Sensitivity to Environmental Change) survey conducted during austral summer 2007, we examined CO2 sequestration through measurement of gross primary production rates using 14C. Sampling was conducted in the SAZ to the south-west and south-east of Tasmania, and in the Polar Frontal Zone (PFZ) directly south of Tasmania. Despite higher chlorophyll biomass off the south-east of Tasmania, production measurements were similar to the south-west with rates of 986.2 plus or minus 500.4 and 1304.3 plus or minus 300.1 mg C m-2 d-1, respectively. Assimilation numbers suggested the onset of cell senescence by the time of sampling in the south-east, with healthy phytoplankton populations to the south-west sampled three week earlier. Production in the PFZ (475.4 plus or minus 168.7 mg C m-2 d-1) was lower than the SAZ, though not significantly. The PFZ was characterised by a defined deep chlorophyll maximum near the euphotic depth (75 m) with low production due to significant light limitation. A healthy and less light-limited phytoplankton population occupied the mixed layer of the PFZ, allowing more notable production there despite lower chlorophyll. A hypothesis that iron availability would enhance gross primary production in the SAZ was not supported due to the seasonal effect that masked possible responses. However, highest production (2572.5 mg C m-2 d-1) was measured nearby in the Sub-Tropical Zone off south-east Tasmania in a region where iron was likely to be non-limiting (Bowie et al., 2009). Table 1:Gross primary production at each CTD station and associated data; Mixed layer depth (Zm, m), incoming PAR (mol m-2 d-1), vertical light attenuation (Kd, m-1), euphotic depth (Zeu, m), differences between euphotic depth and mixed layer depth (Zeu-Zm, m), column-integrated chlorophyll a (0 to 150 m, mg m-2), column-integrated production (0 to 150 m, mg C m-2 d-1), production within the mixed layer (mg C m-2 d-1), production below the mixed layer (mg C m-2 d-1), production within the euphotic zone (1% PAR, mg C m-2 d-1), production below the euphotic zone (mg C m-2 d-1). Kd values that were calculated from chlorophyll a v PAR regressions are marked with an asterisk. At some stations there was a surface mixed layer as well as a secondary mixed layer and both depths are indicated. Table 2:Photosynthetic attributes of phytoplankton with depth at each CTD station; Mixed layer depth (m), euphotic depth (Zeu, m), maximum photosynthetic rate [Pmax, mg C (mg chl a)-1 h-1], maximum photosynthetic rate corrected for photoinhibition [Pmaxb, mg C (mg chl a)-1 h-1], initial slope of the light-limited section of the P-I curve [alpha, mg C (mg chl a)-1 h-1 (micro-mol m-2 s-1)-1], rate of photoinhibition [beta, mg C (mg chl a)-1 h-1 (micro-mol m-2 s-1)-1], intercept of the P-I curve with the carbon uptake axis [c, mg C (mg chl a)-1 h-1], light intensity at which carbon-uptake became saturated (Ek, micro-mol m-2 s-1), and chlorophyll a measured using HPLC (mg m-3).

Oceanographic measurements were collected aboard Aurora Australis cruise au1203, voyage 3 2011/2012, from 5th January to 12th February 2012. The cruise commenced with opportunistic CTD's in the region of the Adelie Depression and the former Mertz Glacier ice tongue, followed by a full south to north occupation of the CLIVAR/WOCE meridional section I9S. A total of 95 CTD vertical profile stations were taken on the cruise, most to within 15 metres of the bottom. Over 1500 Niskin bottle water samples were collected for the measurement of salinity, dissolved oxygen, nutrients (phosphate, nitrate+nitrite and silicate), dissolved inorganic carbon (i.e. TCO2), alkalinity, pH, barium (dissolved), and biological parameters, using a 24 bottle rosette sampler. Full depth current profiles were collected by an LADCP attached to the CTD package, while upper water column current profile data were collected by a ship mounted ADCP. Meteorological and water property data were collected by the array of ship's underway sensors. An array of 5 current meter moorings was recovered from the Antarctic continental slope at the south end of the I9S transect.

3 litres of seawater were collected every 2nd CTD (conductivity, temperature and depth) cast on every CTD transect of the BROKE-West voyage. 7 CTD transects were completed on the BROKE-West voyage, all on southwards legs. Samples were collected at 6 depths in the top 200 m of the water column using niskin bottles. 2 litres were filtered through polycarbonate filters and 1 litre was filtered through a fibreglass filter. Chemical digestion of the polycarbonate filter enabled us to determine the particulate silicon concentration for each sample (using the nutrient autoanalyser onboard the Aurora Australis, see hydrochemistry section), fibreglass filters have been dried and stored for CHN analysis back on shore. This work was completed as part of ASAC projects 2655 and 2679 (ASAC_2655, ASAC_2679).

This data set was collected during an ocean acidification mesocosm experiment performed at Davis Station, Antarctica during the 2014/15 summer season. It includes: - description of methods for all data collection and analyses. - diatom cell volume - bulk silicification - species specific silicification via fluorescence microscopy - bulk community Fv/Fm on day 12 - single-cell PAM fluorometry data (maximum quantum yield of PSII: Fv/Fm) A natural community of Antarctic marine microbes from Prydz Bay, East Antarctica were exposed to a range of CO2 concentrations in 650 L minicosms to simulate possible future ocean conditions up to the year ~2200. Diatom silica precipitation rates were examined at CO2 concentrations between 343 to 1641 micro atm, measuring both the total diatom community response and that of individual species, to determine whether ocean acidification may influence future diatom ballast and therefore alter carbon and silica fluxes in the Southern Ocean. Described and analysed in: Antarctic diatom silicification diminishes under ocean acidification (submitted for review) Methods described in: Antarctic diatom silicification diminishes under ocean acidification (submitted for review) Location: Prydz bay, Davis Station, Antarctica (68 degrees 35'S, 77 degrees 58' E) Date: Summer 2014/2015 Worksheet descriptions: Bulk silicification - raw data Measured total and incorporated biogenic silica using spectrophotometer for all tanks on day 12 after 24 h incubation with PDMPO - raw data Bulk Fv/Fm - dark-adapted maximum quantum efficiency of PSII (Fv/Fm) on whole community - raw data Measured Fv/Fm of individual cells from 3 mesocosm tanks. Single-cell silicificiation, Fluorescence microscopy - raw data Measured autofluorescence and PDMPO fluorescence of individual diatoms from 6 mesocosm tanks Single-cell PAM, dark-adapted maximum quantum efficiency of PSII (Fv/Fm) - raw data Measured Fv/Fm of individual cells from 3 mesocosm tanks. Cell volume Calculated cell volume (um3) of 7 species from minicosm tanks 1 and 6 - raw data Abbreviations: Fv/Fm Maximum quantum yield of PSII PDMPO 2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole Tant Thalassiosira antarctica DiscLg Large Discoid centric diatoms Stella Stellarima microtrias Chaeto Chaetoceros spp. Prob Proboscia truncata Pseu Pseudonitzschia turgiduloides FragLg Fragilariopsis cylindrus / curta Centric Large Discoid centric diatoms LargeThalassiosira Large Discoid centric diatoms

From the abstract and introduction of ANARE Research Notes 44 - ADBEX I cruise to the Prydz Bay region, 1982: nutrient data. Nitrate, phosphate and silicate concentrations obtained during the ADBEX I cruise to the Prydz Bay region in November and December 1982 are plotted with depth and the raw data are tabulated. Location of the sampling stations and the average concentration of each nutrient in the top 100 m of the water column is mapped. The ADBEX I (Antarctic Division BIOMASS Experiment) cruise is part of a long-term, national program of field surveys aimed at fulfilling the objectives of the BIOMASS (Biological Investigation of Marine Antarctic Systems and Stocks) program. The ADBEX I cruise on MV Nella Dan to the Prydz Bay region between 19 November and 17 December 1982, is the second Antarctic Division cruise to contribute to BIOMASS, the first being FIBEX (First International Biomass Experiment) in 1981. Nutrient data were collected at twenty-eight of the seventy-nine hydrographic stations to provide information for the interpretation of phytoplankton distribution and abundance. The sampling locations and depths were not selected, therefore, on the basis of nutrient-related considerations. The concentration of nitrate, phosphate and silicate is plotted to 600 m for each station and where casts were much deeper or much shallower, a second plot is shown. To show water column structure at the time of sampling, sigma-t values were also plotted, unless data for a cast were unavailable. In addition to the depth profiles, the average concentration to 100 m of each nutrient species is mapped to give a first-order approximation of the horizontal pattern of nutrient distribution in the upper layers.