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

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Latest version published by SCAR - Microbial Antarctic Resource System on Mar 19, 2019 SCAR - Microbial Antarctic Resource System
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19 March 2019
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Description

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.

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How to cite

Researchers should cite this work as follows:

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

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 2cc6227c-a416-4928-bd1f-8458741b8377.  SCAR - Microbial Antarctic Resource System publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Scientific Committee on Antarctic Research.

Keywords

Bacterioplankton; Antarctic Peninsula; 16S rRNA; metagenome; marine; archaea; bacteria; summer; winter; Other

Contacts

Alison Murray
  • Metadata Provider ●
  • Originator ●
  • Point Of Contact ●
  • Principal Investigator
  • Associate Research Professor
DRI
  • 2215 Raggio Parkway
89512 Reno
NV
US
  • 775 673 7361
Joseph Grzymski
  • Principal Investigator
  • Assistant Research Professor
DRI
  • 2215 Raggio Parkway
89512 Reno
NV
US
  • 775 673 7478

Geographic Coverage

Samples were collected in the nearshore region of Anvers Island, near Palmer Station.

Bounding Coordinates South West [-64.78, -64.07], North East [-64.77, -64.05]

Taxonomic Coverage

Plankton surveys of community structure were conducted of those organisms passing through a 1.6 micron glass fiber filter.

Domain Archaea, Bacteria

Temporal Coverage

Start Date 2002-08-20
Start Date 2006-02-28
Start Date 2002-01-17
Start Date 2002-07-17

Project Data

No Description available

Title IPY Antarctic Peninsula Bacterioplankton
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 Description 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.

The personnel involved in the project:

Alison Murray
  • Principal Investigator

Sampling Methods

Seawater was collected by submersible pump and filtered at the Station, see Grzymski et al. 2012 for details.

Study Extent See Geographic coverage
Quality Control 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).

Method step description:

  1. A MICROBIAL_SEQUENCE_SET Description file describing 9 data sets was uploaded to the IPT. 9 MIMARKS data files were uploaded to the IPT.

Bibliographic Citations

  1. 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
  2. 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
  3. 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