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  • Metadata record for data from ASAC Project 2547 See the link below for public details on this project. Pue (greater than 90% as determined by SDS-PAGE) samples of nitrate reductase have been isolated from the Antarctic bacterium, Shewanella gelidimarina (ACAM 456T; Accession number U85907 (16S rDNA)). The protein is ~90 kDa (similar to nitrate reductase enzymes characterised from alternate bacteria) and stains positive in an in-situ nitrate reduction (native) assay technique. The protein may be N-terminal blocked, although further sequencing experiments are required to confirm this. This work is based upon phenotyped Antarctic bacteria (S. gelidimarina; S.frigidimarina) that was collected during other ASAC projects. (Refer: Psychrophilic Bacteria from Antarctic Sea-ice and Phospholipids of Antarctic sea ice algal communities new sources of PUFA [ASAC_708] and Biodiversity and ecophysiology of Antarctic sea-ice bacteria [ASAC_1012]). The download file contains 4 scientific papers produced from this work - one of these papers also contains a large set of accession numbers for data stored at GenBank.

  • Oceanographic processes in the subantarctic region contribute crucially to the physical and biogeochemical aspects of the global climate system. To explore and quantify these contributions, the Antarctic Cooperative Research Centre (CRC) organised the SAZ Project, a multidisciplinary, multiship investigation carried out south of Australia in the austral summer of 1997-1998. Taken from the abstracts of the referenced papers: In March 1998 we measured iron in the upper water column and conducted iron- and nutrient-enrichment bottle-incubation experiments in the open-ocean Subantarctic region southwest of Tasmania, Australia. In the Subtropical Convergence Zone (~42 degrees S, 142 degrees E), silicic acid concentrations were low (less than 1.5 micro-M) in the upper water column, whereas pronounced vertical gradients in dissolved iron concentration (0.12-0.84 nM) were observed, presumably reflecting the interleaving of Subtropical and Subantarctic waters, and mineral aerosol input. Results of a bottle-incubation experiment performed at this location indicate that phytoplankton growth rates were limited by iron deficiency within the iron-poor layer of the euphotic zone. In the Subantarctic water mass (-46.8 degrees S, 142 degrees E), low concentrations of dissolved iron (0.05-0.11 nM) and silicic acid (less than 1 micro-M) were measured throughout the upper water column, and our experimental results indicate that algal growth was limited by iron deficiency. These observations suggest that availability of dissolved iron is a primary factor limiting phytoplankton growth over much of the Subantarctic Southern Ocean in the late summer and autumn. The importance of resource limitation in controlling bacterial growth in the high-nutrient, low-chlorophyll (HNLC) region of the Southern Ocean was experimentally determined during February and March 1998. Organic- and inorganic-nutrient enrichment experiments were performed between 42 degrees S and 55 degrees S along 141 degrees E. Bacterial abundance, mean cell volume, and [3H]thymidine and [3H]leucine incorporation were measured during 4- to 5-day incubations. Bacterial biomass, production, and rates of growth all responded to organic enrichments in three of the four experiments. These results indicate that bacterial growth was constrained primarily by the availability of dissolved organic matter. Bacterial growth in the subtropical front, subantarctic zone, and subantarctic front responded most favourably to additions of dissolved free amino acids or glucose plus ammonium. Bacterial growth in these regions may be limited by input of both organic matter and reduced nitrogen. Unlike similar experimental results in other HNLC regions (subarctic and equatorial Pacific), growth stimulation of bacteria in the Southern Ocean resulted in significant biomass accumulation, apparently by stimulating bacterial growth in excess of removal processes. Bacterial growth was relatively unchanged by additions of iron alone; however, additions of glucose plus iron resulted in substantial increases in rates of bacterial growth and biomass accumulation. These results imply that bacterial growth efficiency and nitrogen utilisation may be partly constrained by iron availability in the HNLC Southern Ocean. The download file also contains three excel spreadsheets of iron data from the project. The file Sedwick_A9706_Fe_data contains water-column dissolved Fe and total-dissolvable Fe data from cruise A9706, which is presented in Sedwick et al. (1999) and Sedwick et al. (2008). The files Sedwick_A9706_ProcessStn1_Exp_data and Sedwick_A9706_ProcessStn2_Exp_data present data from shipboard experiments conducted during cruise A9706 at Process Stations 1 and 2, respectively, as reported in Sedwick et al. (1999).

  • Three experiments were performed at Davis Station, East Antarctica, 77 degrees 58' E, 68 degrees 35' S to determine the effects of ocean acidification on natural assemblages of Antarctica marine microbes (bacteria, viruses, phytoplankton and protozoa). Incubation tanks (6 * 650 L minicosms) were filled on the 30/12/08, 20/01/09 and 09/02/09 with sea water that was filtered through 200 microns mesh to remove metazoan grazers. The pH of each tank was adjusted by adding calculated amounts of CO2 saturated sea water. Treatment concentrations were maintained daily and microbial communities incubated for up to 12 days. The three experiments spanned early-, mid- and late-summer, with CO2 treatments ranging from pre-industrial to post-2100. The Excel spreadsheet contains 3 tabs: Experiment 1 - Early Summer Experiment 2 - Mid Summer Experiment 3 - Late Summer Within each tab there are measurements for: pCO2, dissolved inorganic carbon, Pmax, alpha, Ek, chl a, gross primary production (14C), bacterial production (14C), cell-specific bacterial productivity, bacterial abundance, dissolved organic carbon, particulate organic carbon, heterotrophic nanoflagellates, nitrate+nitrite, phosphate, silicate, ammonium, net community production, respiration, gross primary production (O2), photosynthesis:respiration ratios. Units for each measurement supplied within. Please see the following paper for interpretation of this data: Westwood, K.J., Thomson, P.G., van den Enden, R., Maher, L., Wright, S.W., Davidson, A.T. (2018). Ocean acidification impacts primary and bacterial production in Antarctic coastal waters during austral summer. Journal of Experimental Marine Biology and Ecology 498: 46-60, doi: 10.1016/j.jembe.2017.11.003.

  • These data come from a set of experiments conducted on the coastal waters near Davis Station in January 2017. The first set of data are from a transect near the Sorsdal glacier and out to sea, to characterise DMSP-mediated phytoplankton bacteria interactions along a salinity gradient. The second data set are from a series of incubation experiments to gain deeper insight into the role of various infochemicals in Antarctic phytoplankton-bacteria relationships. Specifically, DMSP, VitB12, Tryptophan and Methionine. The last data set is derived from two incubation experiments: a short term DMSP addition experiment to look at its uptake and utilisation by the microbial community; and a longer-term (5 day) stable isotope probing experiment to track DMSP through the lower trophic food web.

  • Two 16S rDNA clone libraries, one from a Brown Bay sample and one from an O'Brien Bay sample were generated. These samples were originally collected as part of ASAC project 868 and the microbiology of the samples is now being investigated as part of ASAC 1228. Two data files are included in the download. Both are in "fasta" format, a text-based format for representing either nucleotide sequences or peptide sequences, in which base pairs or amino acids are represented using single-letter codes. Further information about the dataset can also be found in the referenced paper.

  • Purpose of experiments: Sequence data obtained to determine community structure of pack sea-ice microbial communities and whether it is effected by exposures to elevated CO2 levels. Summary of Methods: Cells in sea-ice brines were filtered onto 0.2 micron filters and material extracted using the MoBio Water DNA extraction kit. The DNA was analysed by Research and Testing Laboratories Inc. (Lubbock, Texas, USA) via 454 pyrosequencing. The bacteria were analysed using primers set 10F-519R, which targets 16S rRNA genes. 16S rRNA genes associated with chloroplast and mitochondria are included in this dataset but represent a minority of sequences in most samples. Eukaryotes were analysed using primers set 550F-1055R, which targets 18S rRNA genes. The 454 pyrosequencing analysis with the Titanium GS FLX+ kit used generates on average 3000 reads incorporating custom pyrotags for later stages of the data analysis. The specific steps used for subsequent data analysis are described in the attached PDF file (Data_Analysis_Methodology.PDF). This output was further refined by first determining consensus sequences at the 98% similarity level using Weizhong Li’s online software site CD-HIT (http://weizhongli-lab.org/cd-hit/) Reference: Niu B, Fu L, Sun S, Li W. 2010. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics 1:187 doi:10.1186/1471-2105-11-187. The consensus sequences were then checked for errors, manually curated, and aligned against closest matching sequences obtained from the NCBI database (www.ncbi.nlm.nih.gov) to finally obtained a list of consensus operational taxonomic entities and the number of reads obtained for each samples analysed. File: SIPEXII_DNA_Sample_information.xlsx provides sampling and analysis information for the detailed results in the other two files File: SCIPEXII__sea_ice_bacteria_OTUs.xlsx contains information on the number of 16S rRNA reads in bacteria Phylum/Class and OTUs File: SCIPEXII_sea_ice_brines_eukaryote_community_OTU_data.xlsx contains information on the number of 16S rRNA reads in eukaryotic microbes: Phylum/Order/Closest taxon and OTUs

  • 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. - flow cytometry counts; autotrophic cells, heterotrophic nanoflagellates, and prokaryotes

  • A meta-analysis was undertaken to examine the vulnerability of Antarctic marine biota occupying waters south of 60 degrees S to ocean acidification. Comprehensive database searches were conducted to compile all English language, peer-reviewed journals articles and literature reviews that investigated the effect of altered seawater carbonate chemistry on Southern Ocean and/or Antarctic marine organisms. A document detailing the methods used to collect these data is included in the download file.

  • 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.

  • Metadata record for data from AAS Project 3127 See the link below for public details on this project. Bacteria in marine environments have been found to be able to partially support growth by using light to generate energy in a non-photosynthetic process. This is possible due to a special protein called proteorhodopsin. It is hypothesised that formation of proteorhodopsin has evolved to cope with extreme lack of nutrients. The goal is to determine the significance of proteorhodopsins in the productivity of Southern Ocean microbial communities. This includes determination of proteorhodopsin distribution, presence in seawater and sea-ice samples using molecular techniques, and determination of how important environmental factors (light, nutrient availability, temperature) may drive its synthesis and activity. Taken from the 2009-2010 Progress Report Project objectives: 1. Determine incidence of proteorhodopsins in Southern Ocean water and sea-ice derived bacteria (Year 1) and other Antarctic aquatic environments (Year 2 and 3). 2. Determine whether proteorhodopsins contribute to food web energy budgets. 3. Determine how proteorhodopsin contributions are influenced by physicochemical features of the environment including light availability, temperature and nutrients. Progress against objectives: Proteorhodopsin is a light harvesting membrane protein that has been found recently to occur in 30-70% of marine bacterial cells. The role of this protein is uncertain but believed to be highly important in energy and nutrient budgets in food webs as it is capable of generating a proton gradient. Amongst a cultured set of Antarctic bacteria we have discovered many PR-producing species. These include many Antarctic lake species. Research is ongoing to determine affect of light on the physiology of these bacteria in particular the genome sequenced species Psychroflexus torquis, an extremely cold-adapted resident of Antarctic sea-ice. 1. Completed screen of Antarctic bacterial collection for proteorhodopsin (PR) genes using PCR-based approaches 2. Proteomic-based analysis of PR-bearing sea-ice species Psychroflexus torquis is currently ongoing 3. Light/dark defined growth-based experiments determining conditions leading to biomass enhancement are ongoing