Antarctic Peninsula Bacterioplankton 16S rRNA gene surveys and metagenomes from Winter 2002 and Summer 2006.

Alison Murray1, Joseph Grzymski1

1 DRI, 2215 Raggio Parkway, 89512, Reno, United States

Corresponding author(s): Alison Murray (Alison.Murray@dri.edu)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

Murray, AE and JJ Grzymski. 2007. Diversity and genomics of Antarctic marine microorganisms. Phil. Trans. Roy. Soc. Ser. B. 362:2259-2271. DOI:10.1098/rstb.2006.1944

Abstract

Antarctic surface oceans are well-studied during summer when irradiance levels are high, sea ice is melting and primary productivity is at a maximum. Coincident with this timing, the bacterioplankton respond with significant increases in secondary productivity. Little is known about bacterioplankton in winter when darkness and sea-ice cover inhibit photoautotrophic primary production. We report here an environmental genomic and small subunit ribosomal RNA (SSU rRNA) analysis of winter and summer Antarctic Peninsula coastal seawater bacterioplankton. Intense inter-seasonal differences were reflected through shifts in community composition and functional capacities encoded in winter and summer environmental genomes with significantly higher phylogenetic and functional diversity in winter. In general, inferred metabolisms of summer bacterioplankton were characterized by chemoheterotrophy, photoheterotrophy and aerobic anoxygenic photosynthesis while the winter community included the capacity for bacterial and archaeal chemolithoautotrophy. Chemolithoautotrophic pathways were dominant in winter and were similar to those recently reported in global‘dark ocean’ mesopelagic waters. If chemolithoautotrophy is widespread in the Southern Ocean in winter, this process may be a previously unaccounted carbon sink and may help account for the unexplained anomalies in surface inorganic nitrogen content.

Keywords: Bacterioplankton, Antarctic Peninsula, 16S rRNA, metagenome, marine, archaea, bacteria, summer, winter, Other

Project details

Project title: IPY Antarctic Peninsula Bacterioplankton
Personnel: Alison Murray
Funding: NSF ANT 0632278 supported the researchers and Antarctic expeditions and DOE JGI Community Sequencing Program supported the metagenome and Sanger sequencing of 16S rRNA gene libraries; Pyrosequencing was provided by the International
Census of Marine Microbes (ICoMM) with financial support
from a W. M. Keck foundation award to the Marine Biological
Laboratory in Woods Hole.
Study area descriptions/descriptor: Seawater (1.6 - 0.2 micron fraction) sampled off of Anvers Island, Antarctic Peninsula.
Design description: Samples were collected from surface waters on 12 occasions over the annual cycle in 2002 and in late February in 2006. The samples from 2002 were all analyzed by PCR-DGGE (Murray and Grzymski, 2007) and 3 samples were selected for Roche 454 tag sequencing targeting bacteria. In addition, the sample from 20 August 2002 was selected for (i) 16S rRNA gene clone library sequencing for bacteria and archaea; and (ii) for metagenome sequencing in which a large insert (40 kb) library was prepared and end sequences were determined for ~ 20K clones. Selected clones (~ 96) were then fully sequenced. 

In 2006 samples were collected at the end of February, in which we selected a sample from 28 February 2006 for 16S rRNA gene clone library sequencing for bacteria and archaea; in addition a metagenome sequencing effort was conducted in which a large insert (40 kb) library was prepared and end sequences were determined for ~ 20K clones. Selected clones (~ 96) were then fully sequenced.

Data published through GBIF: http://ipt.biodiversity.aq/resource.do?r=antarctic_peninsula_bacterioplankton_diversity

Taxonomic coverage

General taxonomic coverage description: Plankton surveys of community structure were conducted of those organisms passing through a 1.6 micron glass fiber filter.
Taxonomic ranks
Domain: Archaea, Bacteria

Spatial coverage

General spatial coverage: Samples were collected in the nearshore region of Anvers Island, near Palmer Station.
Coordinates: 64°46'48''S and 64°46'12''S Latitude; 64°4'12''W and 64°2'60''W Longitude 

Temporal coverage: August 20, 2002

Temporal coverage: February 28, 2006

Temporal coverage: January 17, 2002

Temporal coverage: July 17, 2002

Methods

Method step description: A MICROBIAL_SEQUENCE_SET Description file describing 9 data sets was uploaded to the IPT. 

9 MIMARKS data files were uploaded to the IPT.
Study extent description: See Geographic coverage
Sampling description: Seawater was collected by submersible pump and filtered at the Station, see Grzymski et al. 2012 for details.
Quality control description: Sanger sequence data was automatically assembled and chimera checked; metagenome sequence data was automatically annotated at the Joint Genome Institute (see Grzymski et al. 2012).

Metadata language: English
Date of metadata creation: 2012-05-10
Hierarchy level: Dataset

References
Grzymski, JJ, CS Riesenfeld , TJ Williams, AM Dussaq, H Ducklow, M Erickson, R Cavicchioli, & AE Murray. 2012. A metagenomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters. ISME Journal. DOI:10.1038/ismej.2012.31
Ghiglione, JF, and AE Murray. 2012. Pronounced summer to winter differences and higher wintertime richness in coastal Antarctic marine bacterioplankton. Environ. Microbiol. 14(3): 617-629. DOI:10.1111/j.1462-2920.2011.02601.x
Williams, TJ, E Long, F Evans, MZ DeMaere, FM Lauro, MJ Raftery, H Ducklow, JJ Grzymski, AE Murray, R Cavicchioli. 2012. A metaproteomic assessment of summer and winter bacterioplankton from Antarctic Peninsula coastal surface waters. ISME Journal 6:1883-1900. doi: 10.1038/ismej.2012.28