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

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Dernière version Publié par SCAR - Microbial Antarctic Resource System le mars 19, 2019 SCAR - Microbial Antarctic Resource System
Accueil:
http://genex2.dri.edu/index.php
Date de publication:
19 mars 2019
Licence:
CC-BY 4.0

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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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Comment citer

Les chercheurs doivent citer cette ressource comme suit:

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

Droits

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L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. Ce travail est sous licence Creative Commons Attribution (CC-BY) 4.0.

Enregistrement GBIF

Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : 2cc6227c-a416-4928-bd1f-8458741b8377.  SCAR - Microbial Antarctic Resource System publie cette ressource, et est enregistré dans le GBIF comme éditeur de données avec l'approbation du Scientific Committee on Antarctic Research.

Mots-clé

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

Contacts

Alison Murray
  • Fournisseur Des Métadonnées ●
  • Créateur ●
  • Personne De Contact ●
  • Chercheur Principal
  • Associate Research Professor
DRI
  • 2215 Raggio Parkway
89512 Reno
NV
US
  • 775 673 7361
Joseph Grzymski
  • Chercheur Principal
  • Assistant Research Professor
DRI
  • 2215 Raggio Parkway
89512 Reno
NV
US
  • 775 673 7478

Couverture géographique

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

Enveloppe géographique Sud Ouest [-64,78, -64,07], Nord Est [-64,77, -64,05]

Couverture taxonomique

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

Domain Archaea, Bacteria

Couverture temporelle

Date de début 2002-08-20
Date de début 2006-02-28
Date de début 2002-01-17
Date de début 2002-07-17

Données sur le projet

Pas de description disponible

Titre IPY Antarctic Peninsula Bacterioplankton
Financement 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.
Description du domaine d'étude / de recherche Seawater (1.6 - 0.2 micron fraction) sampled off of Anvers Island, Antarctic Peninsula.
Description du design 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.

Les personnes impliquées dans le projet:

Alison Murray
  • Chercheur Principal

Méthodes d'échantillonnage

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

Etendue de l'étude See Geographic coverage
Contrôle qualité 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).

Description des étapes de la méthode:

  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.

Citations bibliographiques

  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