The data reports the pigment concentrations and results of CHEMTAX analysis for 2 summer seasons in Antarctic. In 2008/09 three experiments in which 6 x 650 l minicosms (polythene tanks) were used to incubate natural microbial communities (less than 200 um diameter) at a range of CO2 concentrations while maintained at constant light, temperature and mixing. The communities were pumped from ice-free water ~60 m offshore on 30/12/08, 20/01/09 and 09/02/09. These experiments received no acclimation to CO2 treatment. A further experiment was performed in 2014/15 using water helicoptered from ~ 1 km offshore amongst decomposing fast ice on 19/11/14. This experiment included a 5 day period during which the community was exposed top low light and the CO2 was gradually raised to the target value for each tank, followed by a two day period when the light was raised to an irradiance that was saturating but not inhibitory for photosynthesis. A range of coincident measurements were performed to quantify the structure and function of the microbial community (see Davidson et al. 2016 Mar Ecol Prog Ser 552: 93–113, doi: 10.3354/meps11742 and Thomson et al 2016 Mar Ecol Prog Ser 554: 51–69, 2016, doi: 10.3354/meps11803). The data provides a matrix of samples against component pigment concentration and the output from CHEMTAX that best explained the phytoplankton composition of the community based on the ratios of the component pigments. For the 2008/09 experiments, samples were obtained every 2 days for 10, 12 and 10 days in experiments 1, 2 and 3 respectively. In 2014/15 samples were obtained from each incubation tank on days 1,3, 5, and 8 during th acclimation period and every 2 days until day 18 thereafter. For each sample a measured volume was filtered through 13 mm Whatman GF/F filters for 20 mins. Filters were folded in half, blotted dry, and immediately frozen in liquid nitrogen for analysis in Australia. Pigments were extracted, analysed by HPLC, and quantified following the methods of Wright et al. (2010). Pigments (including Chl a) were extracted from filters with 300 micro l dimethylformamide plus 50 micro l methanol, containing 140 ng apo-8'-carotenal (Fluka) internal standard, followed by bead beating and centrifugation to separate the extract from particulate matter. Extracts (125 micro l) were diluted to 80% with water and analysed on a Waters HPLC using a Waters Symmetry C8 column and a Waters 996 photodiode array detector. Pigments were identified by comparing retention times and spectra to a mixed standard sample from known cultures (Jeffrey and Wright, 1997), run daily before samples. Peak integrations were performed using Waters Empower software, checked manually for corrections, and quantified using the internal standard method (Mantoura and Repeta, 1997).

Size fractionated chlorophyll a data (total and less than 20 µm) analysed using high performance liquid chromatography (HPLC). Underway samples were taken using a seawater line in the oceanographic lab on RSV Aurora Australis (approx. depth 4 m). CTD samples were taken using Niskin bottles attached to a CTD rosette. Six depths were sampled per station, based on fluorescence profiles from the CTD. Two of the two of six samples always included both near-surface (approximately 10 m) and the depth of the chlorophyll maximum where applicable. HPLC analyses were conducted according to the method of Wright et al. (2010). Column chlorophylls (µg L-1) and integrated chlorophylls (mg m-2) are shown in two separate tabs within the Excel spreadsheet.

Metadata record for data from ASAC Project 1101 See the link below for public details on this project. ---- Public Summary from Project ---- Most of our knowledge of the Antarctic marine ecosystems comes from summer surveys. There are very few observations of this ecosystem in winter and there is a fundamental lack of knowledge of understanding of even basic questions such as 'what is there?' and 'what's it doing?'. The proposed visit to the sea ice zone in winter is a rare opportunity to conduct observations on phytoplankton, krill, birds, seals and whales, so that we can begin to understand the biological processes that go on in winter. Data for this project were intended to be collected on a 1998 winter voyage of the Aurora Australis, but a fire on board meant that the voyage had to return to port before work could be carried out. Data were then collected the following year during a 1999 winter voyage of the Aurora Australis (IDIOTS), which ran from July to September. Data attached to this metadata record, include protist, bacteria and virus data collected from the Mertz Glacier region. The purpose of this research was to quantify and identify the different assemblages of phytoplankton, change in virus populations and the number of live/dead bacteria between Tasmania and the polynya, within the polynya and sea ice. A variety of methods were used including HPLC, light and fluorescent microscopy and the collection of samples for subsequent analysis upon return to the Antarctic Division. More information is available in the download file. The samples were collected by Rick van den Enden.

Field-based sampling: As part of Australian Antarctic Science project # 4298, a total number of 44 sea ice sites were sampled for bio-optical measurements along 4 transects on land-fast sea ice off Davis Station (Antarctica) during November – December 2015. Measurements included simultaneous hyperspectral down-welling (ice surface) irradiance (triplicate) and under-ice radiance (triplicate) measurements (320 – 900 nm, 3.3 nm resolution) with a TriOS ACC and Trios ARC radiometer, respectively. The radiance measurements were conducted with the TriOS ARC radiometer mounted onto an L-shaped arm (for deployment details see Melbourne-Thomas et al. 2015). Subsequently, snow thickness was measured with a ruler and an ice core was collected directly above the radiometer location. Sea-ice freeboard (tape measure) and ice thickness (ice core length) were also recorded. Ice cores (9 cm internal diameter) were cut into sections, and these were melted in the dark at +4 degrees C, filtered onto GFF filters and then used to measure ice algal pigment content (using High Performance Liquid Chromatography (HPLC) and spectral ice algal absorption coefficients (ap, ad, aph) for entire vertical profiles or for the lower-most 0.1 m of ice cores. The location of the sampling grid had its origin (x=0, y=0) at GPS position: -68.568904, 77.945439. Transects (128m – 512 m in length) started at x=60, x=70, x=80 and x=90 m and were sampled at y-positions of 0m, 0.5m, 1m, 2m, 4m, 8m, 16m, 32m, 64m, 128m, (256m, and 512m) on 19/11/2015, 23/11/2015, 29/11/2015 and 02/12/2015, respectively. Analysis of ice algal chlorophyll a concentration: For pigment analysis, 0.25 to 1.0 litres of melted ice core subsamples were passed through 25 mm diameter glass-fiber (Whatman GF/F) filters. The filters were then frozen and stored below −80 degrees C prior to analysis using HPLC. Samples were extracted over 15 to 18 hours in acetone before analysis by HPLC using a modified C8 column and binary gradient system with an elevated column temperature [Van Heukelem and Thomas, 2001]. Pigments were identified by retention time and absorption spectra from a photo-diode array (PDA) detector, and concentrations were determined from commercial and international standards (Sigma; DHI, Denmark). Analysis of particulate (algal and non-algal) absorption: The optical density (OD) spectra of the particulate material on these filters (see section above) were measured over the 350 to 750 nm spectral range in 0.9 nm increments, using a Cintra 404 UV/VIS dual-beam spectrophotometer equipped with an integrating sphere. The pigments on the sample filter were then extracted using the method of Kishino et al. [1985]'s method to determine the OD of the non-algal particles in a second scan. The OD due to ice algae was then obtained by calculating the difference between the optical density of the total particulate and non-algal fractions. The OD measurements were converted to absorption spectra using blank filter measurements, and by first normalizing the scans to zero at 750 nm and then correcting for the path length amplification using the coefficients of Mitchell [1990]. A detailed description of the method is given in Clementson et al. [2001], and followed SeaWiFS protocols [Muller et al., 2003]. An exponential function was fitted to all spectra of non-algal particulate material: ad(λ) = ad(350 nm) exp[−S(λ − 350 nm)] + b, (1) where ad(λ) is the residual absorption coefficient over the wavelength (λ) range 350 to 750 nm of the particles after methanol extraction, also referred to as absorption of detritus [m−1] although this may include absorption of non-extractable pigments and heterotrophic protists. A non-linear least-squares technique was used to fit Equation 1 to the untransformed data, where S and b are empirically-determined constants. The inclusion of an offset b allows for any baseline correction. In some samples, pigment extraction was incomplete, leaving small residual peaks in detritus spectra at the principal chlorophyll absorption bands. To avoid distorting the fitted detritus spectra, data at these wavelengths were omitted when all spectra were fitted. Total particulate spectra were smoothed using a running box-car filter with 10 nm width, and the fitted detritus spectra were subtracted to yield the ice algae spectra. Subtracting fitted detritus spectra minimized any artifacts due to incomplete extraction of pigments. The resulting ice algae spectra were base-corrected by subtracting absorption at 750 nm to obtain aph(λ). The following parameters were then determined: ap(λ) = absorption coefficient of particles [m−1]; aph(λ) = absorption coefficient of ice algae [m−1] calculated as the difference between ap(λ) and ad(λ). Literature cited: Clementson, L. A., J. S. Parslow, A. R. Turnbull, D. C. McKenzie, and C. E. Rathbone (2001), Optical properties of waters in the Australasian sector of the Southern Ocean, Journal of Geophysical Research: Oceans, 106(C12), 31,611–31,625, doi:10.1029/2000jc000359. Kishino, M., M. Takahashi, N. Okami, and S. Ichimura (1985), Estimation of the spectral absorption-coefficients of phytoplankton in the sea, Bulletin of Marine Science, 37(2), 634–642.Melbourne-Thomas, J., K. Meiners, C. Mundy, C. Schallenberg, K. Tattersall, and
G. Dieckmann (2015), Algorithms to estimate Antarctic sea ice algal biomass from under-ice irradiance spectra at regional scales, Marine Ecology Progress Series, 536, 107–121, doi:10.3354/meps11396. Mitchell, B. G. (1990), Algorithms for determining the absorption coefficient for aquatic particulates using the quantitative filter technique, Orlando’90, 1302, 137–148, doi:10.1117/12.21440. Müller, J. L., R. R. Bidigare, C. Trees, W. M. Balch, and J. Dore (2003), Ocean Optics Protocols for Satellite Ocean Colour Sensor Validation, Revision 5, Volume V: Biogeochemical and Bio-Optical Measurements and Data, NASA Tech. Memo. Van Heukelem, L., and C. S. Thomas (2001), Computer-assisted high-performance liquid chromatography method development with applications to the isolation and analysis of phytoplankton pigments, Journal of Chromatography A, 910(1), 31–49, doi:10.1016/s0378-4347(00)00603-4.

This data set was collected from a ocean acidification minicosm experiment performed at Davis Station, Antarctica during the 2014/15 summer season. It includes: - description of methods for all data collection and analyses. - marine microbial community data; Chlorophyll a concentration, particulate organic matter concentration (carbon and nitrogen), bacterial cell abundance. - phytoplankton primary productivity data; 14C-sodium bicarbonate incorporation raw data (decays per minute: DPM) and modelled productivity from photosynthesis versus irradiance (PE) curves, O2-evolution derived net community productivity, respiration, and gross primary productivity. - phytoplankton photophysiology data; community photosynthetic efficiency from PAM measurements (maximum quantum yield of PSII: Fv/Fm), PAM steady state light curve data and derived non-photochemical quenching of Chl a fluorescence (NPQ), relative electron transport rates (rETR), and effective quantum yield of PSII (delta F/Fm'). - phytoplankton carbon concentrating mechanism (CCM) data; maximum quantum yield of PSII (Fv/Fm) and effective quantum yield of PSII (∆F/Fm') from PAM measurements on size-fractionated phytoplankton samples (less than 10 microns and greater than 10 microns cells) exposed to; ethoxzolamide (EZA) which inhibits both intracellular carbonic anhydrase (iCA) and extracellular carbonic anhydrase (eCA), acetazolamide (AZA), which blocks eCA only, and a control (no inhibitor) sample. - bacterial productivity data; 14C-Leucine incorporation raw data (decays per minute: DPM) and calculated productivity.

---- Public Summary from Project ---- The lakes and fjords of the Vestfold Hills region of Antarctica provide unique ecosystems for studying environmental changes in Antarctica over the past 8000 years. Studies of the changes in organic matter composition in sediment cores provide information how the microbial and plankton communities have changed over time in response to varying chemical and physical conditions. Our study will provide new information about how the cycles of the biologically-important elements carbon and sulfur are linked and why some sediments can preserve large amounts of organic carbon. This information will be useful for studies of palaeoclimate and will also provide valuable insights into the processes that produce petroleum source rocks. From the abstracts of the referenced papers: Preserved ribosomal DNA of planktonic phototrophic algae was recovered from Holocene anoxic sediments of Ace Lake (Antarctica), and the ancient community members were identified based on comparative sequence analysis. The similar concentration profiles of DNA of haptophytes and their traditional lipid biomarkers (alkenones and alkenoates) revealed that fossil rDNA also served as quantitative biomarkers in this environment. The DNA data clearly revealed the presence of six novel phylotypes related to known alkenone and alkenoate-biosynthesising haptophytes with Isochrysis galbana UIO 102 as their closest relative. The relative abundance of these phylotypes changed as the lake chemistry, particularly salinity, evolved over time. Changes in the alkenone distributions reflect these population changes rather than a physiological response to salinity by a single halophyte. Using this novel palaeo-ecological approach of combining data from lipid biomarkers and preserved DNA, we showed that the post-glacial development of Ace Lake from freshwater basin to marine inlet and the present-day lacustrine saline system caused major qualitative and quantitative changes in the biodiversity of the planktonic populations over time. Post-glacial Ace Lake (Vestfold Hills, Antarctica), which was initially a freshwater lake and then an open marine system, is currently a meromictic basin with anoxic, sulfidic and methane-saturated bottom waters. Lipid and 16S ribosomal RNA gene stratigraphy of up to 10,400-year-old sediment core samples from the lake revealed that these environmentally induced chemical and physical changes caused clear shifts in the species composition of archaea and aerobic methanotrophic bacteria. The combined presence of lipids specific for methanogenic archaea and molecular remains of aerobic methanotrophic bacteria (13C-depleted delta8(14)-sterols and 16S rRNA genes) revealed that an active methane cycle occurred in Ace Lake during the last 3000 calendar years and that the extant methanotrophs were most likely introduced when it became a marine inlet (9400 y BP); rDNA sequences showed 100% sequence similarity with Methanosarcinales species from freshwater environments and were the source of sn-2- and sn3-hydroxyarchaeols. Archaeal phylotypes related to uncultivated Archaea associated with various marine environments were recovered from the present-day anoxic water column and sediments deposited during the meromictic and marine period.

Locations of sampling sites for ASAC project 40 on voyage 3 of the Aurora Australis in the 2005/2006 season (the BROKE-West voyage). Samples were collected between January and March of 2008. Three datasets are currently included in this download - an excel spreadsheet and a draft publication providing details on the methodology, etc employed, as well as two copies of corrected fluoro data for BROKE-West (BW_UwayFLuChla - in excel and csv formats). Public Summary from the project: This program aims to determine the role of single celled plants, animals, bacteria and viruses in Antarctic waters. We quantify their vital role as food for other organisms, their potential influence in moderating global climate change through absorption of CO2 and production of DMS, and determine their response to effect of climate change. For more information, see the other metadata records related to ASAC project 40 (ASAC_40). ###### Taken from the abstract of the draft paper: The geographic distribution, stocks and vertical profiles of phytoplankton of the seasonal ice zone off east Antarctica were determined during the 2005-2006 austral summer as part of the Baseline Research on Oceanography, Krill and the Environment-West (BROKE-West) survey. CHEMTAX analysis of HPLC pigment samples, coupled with microscopy, permitted a detailed survey along eight transects covering an extensive area between 30 degrees E and 80 degrees E, from 62 degrees S to the fast ice. Significant differences were found in the composition and stocks of populations separated by the Southern Boundary of the Antarctic Circumpolar Current (SB), as well as a small influence of the Weddell Gyre in the western sector of the zone south of the SB (SACCZ). Within the SACCZ, we identified a primary bloom under the ice, a secondary bloom near the ice edge, and an open ocean deep population. The similarity of distribution patterns across all transects allowed us to generalise a hypothesized sequence for the season. The primary bloom was initiated by release of cells and detritus from melting sea ice, some 35 days before ice melting, with stocks of Chl a ranging from 115-239 mg.m-2, apart one leg (41 mg.m-2), which was sampled late in the season. The bloom was dominated by haptophytes (in particular, colonies and gametes of Phaeocystis antarctica), diatoms and cryptophytes (or Myrionecta rubrum). The detrital material quickly sank from the upper water column, but the bloom of diatoms and, to a lesser extent cryptophytes, continued until 20 days after ice melt. Average Chl a stocks during this bloom ranged from 56-92 mg.m-2 between transects. A bloom of Phaeocystis gametes immediately after ice melt lasted for about 10 days. Grazing activity, as indicated by phaeophytin a, also increased at the same time. The diatom bloom became senescent, probably as a result of iron exhaustion, as indicated by chlorophyllides, which reached 45% of total Chl a. The bloom then rapidly declined, apparently due to grazing krill. Well-defined 'holes' in the chlorophyll distribution of most suggested that the krill were moving southward following the retreating sea ice and clearing the ice edge bloom. There was no evidence that blooms had been terminated by sinking or by vertical mixing. It appears that grazing of the bloom and export of cellular material as faecal pellets stripped the upper water column of iron, preventing its normal recycling via the microbial network. Thus, export of iron by grazing, and possibly sedimentation, created a southward migrating iron front, limiting growth in the upper water column. North of the iron front, a recycling nanoflagellate community developed at depth, sustained by residual iron, as indicated by a close correspondence between distributions of Chl a and profiles of Fv/Fm. Its depth was independent of the mixed layer and the pycnoclines. This community consisted of haptophytes (chiefly Phaeocystis gametes), dinoflagellates, prasinophytes, cryptophytes, and some small diatoms. The community may have derived from, and was possibly sustained by, selective grazing by krill. Average stocks of Chl a ranged from 36-49 mg.m-2 between transects. North of the SB, communities were found in the mixed layer, although they still had low Fv/Fm ratios. Populations were dominated by Phaeocystis gametes (with colonies north of the southern ACC front), diatoms such as Pseudonitzschia sp., Fragilariopsis pseudonana, F. kerguelensis, F. curta, and Gymnodinium sp. Average stocks of Chl a ranged from 40-67 mg.m-2 between transects.These appeared to be recycling communities that had been advected into the BROKE-West study region. These interpretations provide a cogent explanation for the composition and structure of microbial populations in the marginal ice zone during the latter half of the summer. ###### The fields in this dataset are: Peak Pigment name Retention times Visible maxima Comments Leg Zone Latitude Longitude CTD Julian Day Date Ice free days Pigment concentrations Protists

During the K-Axis marine voyage from mid Jan-late Feb 2016, a diverse range of sampling techniques were employed to collect specimens and data. Each sampling event was recorded by scientists and technical support staff in a logbook that was kept in the operations room on board the Aurora Australis. This is a direct digital copy/transcription of the paper logbook. event_number: A unique event identifier in the log, in the order that the events were written down (usually but not always chronologically) event_type: The code defined and used by each research project to identify the types of equipment deployed or samples collected for an event. event_type_prefix: A non-mandatory prefix field used by some research projects to identify the type of an event event_type_number: A sequential number or alphanumeric-number combination defined and used by each research project to identify unique equipment deployment or sample collection events station_number: A universal (voyage-wide) station number used across all projects to identify a nominal lat/lon position defined during voyage planning leg: A nominally straight-line section of the voyage track defined during voyage planning. The voyage track was planned as a series of roughly N-S and E-W transects that intersected in some locations. Legs start at a station and continue through more stations to a vertex-station which is the start of the next leg. Legs are numbered consecutively. waypoint: A GPS waypoint used by Aurora Australis crew, AAD science technical support and researchers to identify target lat/lon positions in the voyage. Some waypoints correspond with station numbers. start_date_utc: The start date of the event in UTC start_time_utc: The start time of the event in UTC start_lat_deg: The latitude (whole degrees) of the vessel at the beginning of the event start_lat_min: The latitude (minutes) of the vessel at the beginning of the event start_lat_dec_deg: The latitude (decimal degrees) of the vessel at the beginning of the event start_lon_deg: The longitude (whole degrees) of the vessel at the beginning of the event start_lon_min: The longitude (minutes) of the vessel at the beginning of the event start_lon_dec_deg: The longitude (decimal degrees) of the vessel at the beginning of the event end_date_utc: The end date of the event in UTC end_time_utc: The end time of the event in UTC end_lat_deg: The latitude (whole degrees) of the vessel at the end of the event end_lat_min: The latitude (minutes) of the vessel at the end of the event end_lat_dec_deg: The latitude (decimal degrees) of the vessel at the end of the event end_lon_deg: The longitude (whole degrees) of the vessel at the end of the event end_lon_min: The longitude (minutes) of the vessel at the end of the event end_lon_dec_deg: The longitude (decimal degrees) of the vessel at the end of the event remarks: Comments/remarks written by researchers when completing the paper log transcribe_comments: Comments/remarks made by the transcriber when the log was digitised

The Kerguelen Axis voyage was planned to collect data to enhance the realism of end-to-end ecosystem models being developed in the Antarctic Climate and Ecosystems Cooperative Research Centre, to investigate the effects of climate change and ocean acidification on Southern Ocean ecosystems in the Indian Sector (particularly in relation to factors affecting the northern distribution of Antarctic krill) and to contribute to assessment of the spatial relationship of mesopelagic mid-trophic level species, in particular zooplanktivores, to foraging strategies by marine mammals and birds on the Kerguelen Plateau. Nine projects were undertaken aboard the Aurora Australis. Each project had individual objectives and outputs, and there are metadata records for each data set collected. They were designed to be complementary in order that the whole data set and project analyses could be used to address the objectives of the Kerguelen Axis program. Observations will be contributed to the Southern Ocean Observing System (SOOS) and will facilitate the design of future ecosystem observing in the region.

This dataset contains results from the Second International BIOMASS Experiment II (SIBEX II) cruise of the Nella Dan, taken in January 1985. This cruise was the fourth cruise in a series of six. Phytoplankton samples were taken off Antarctica in the Australian sector (Mawson to Davis region) and Prydz Bay in January 1985. Taxonomic identity, distribution and abundance data were obtained, together with an extensive range of pigment analysis, using high performance liquid chromatography (HPLC). Over 60 pigments were analysed (only the major ones are listed here). The major phytoplankton investigated were diatoms, dinoflagellates and flagellates. This dataset is a subset of the full cruise. An excel spreadsheet containing the full pigment analysis obtained from the cruise is available for download from the URL given below. The spreadsheet is a digital version of the data presented in ANARE Research Notes 58, which was a report written based on this dataset. There are three worksheets to the spreadsheet: 1) Abbrev. - details the abbreviations used in worksheets 2 and 3. 2) Table 3 - Table 3 data entered from ANARE Research Notes 58. 3) Transposed Table 3 - The same data as worksheet 2, but arranged differently. A pdf copy of ANARE Research Notes 58 is also available for download at the URL given below. A paper written in 2006 about pigments in microalgae, which provides some up-to-date explanations about pigmentation, is also available for download, but owing to copyright restrictions, is only available for download by Australian Antarctic Division personnel. The fields in this dataset are: Date Time (GMT) Latitude Longitude Depth (metres) Pigment concentration (nanograms per litre) chlorophyllide a chlorophyll c methyl chlorophyllide a phaeophorbide a peridinin 19'-butanoyloxyfucoxanthin fucoxanthin 19'-hexanoyloxyfucoxanthin Neoxanthin Prasinoxanthin Violaxanthin Diadinoxanthin Alloxanthin diatoxanthin Zeaxanthin Canthaxanthin Unknown Chlorophyll b Chlorophyll a allomer Chlorophyll a Chlorophyll a epimer Phaeophytin a derivative Phaeophytin b Phaeophytin a Chlorophyll a total % Degradation Pigment total This work was completed as part of ASAC project 40 (ASAC_40).