Bacterial community during Phaeocystis antarctica blooms (Amundsen Sea polynya)

Dernière version Publié par SCAR - Microbial Antarctic Resource System le Mar 19, 2019 SCAR - Microbial Antarctic Resource System

Amplicon sequencing dataset of marine microbial Bacteria (16S su rRNA gene, v6) in the Amundsen Sea polynya, during Phaeocystis antarctica blooms

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Delmont T, Hammar K, Ducklow H, Yager P, Post A (2019): Bacterial community during Phaeocystis antarctica blooms (Amundsen Sea polynya). v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacterial_community_during_phaeocystis_antarctica_blooms_in_amundsen_sea_polynya&v=1.1

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L’éditeur et détenteur des droits de cette ressource est SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

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Cette ressource a été enregistrée sur le portail GBIF, et possède l'UUID GBIF suivante : de7916fd-f4ec-496b-9059-f4ae6ba95406.  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

Metadata

Contacts

Personne ayant créé cette ressource:

Tom Delmont
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US
Katherine Hammar
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US
Hugh Ducklow
Columbia University Palisades US
Patricia Yager
University of Georgia Athens US
Anton Post
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US

Personne pouvant répondre aux questions sur la ressource:

Tom Delmont
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US
Anton post
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution Woods Hole US

Personne ayant renseigné les métadonnées:

Maxime Sweetlove
Research assistant
Royal Belgian Institute for Natural Sciences Rue Vautier 29 1000 Brussels

Autres personnes associées à la ressource:

Utilisateur

Couverture géographique

Amundsen Sea polynya, Antarctica/Southern Ocean

Enveloppe géographique Sud Ouest [-73.94, -115.68], Nord Est [-73.94, -115.68]

Couverture taxonomique

Bacteria, 16S ssu rRNA gene, v6 region

Domain  Bacteria (Bacteria)

Couverture temporelle

Epoque de formation 2007-2011

Données sur le projet

Pas de description disponible

Titre International Census of Marine Microbes
Identifiant ICoMM
Financement This dataset was created with financial support from NSF Antarctic Sciences awards ANT-1142095, ANT-0839069 and ANT-0741409, and ANT-0839012. We further acknowledge the support by “Oden Southern Ocean,” SWEDARP 2010/2011, a project organized by the Swedish Polar Research Secretariat and National Science Foundation Office of Polar Programs. The 2007/2008 samples were sequenced as part of the International Census of Marine Microbes (ICOMM).
Description du domaine d'étude / de recherche Amundsen Sea, Antarctica

Les personnes impliquées dans le projet:

Tom Delmont

Méthodes d'échantillonnage

Cruise track, sampling sites and an overview of geochemical and biological properties have been detailed elsewhere (Yager et al., 2012). Additional information can be found in the BCO-DMO database (http://osprey.bco-dmo.org/project.cfm?id=146&flag=view). For the 2010–2011 cruise, water samples (3–10 L) for microbial community sequence analyses were passed over a 20 μm mesh and collected onto 0.2 μm Sterivex membrane filter cartridges by pressure filtration (Whatman Masterflex L/S series). Since high biomass caused rapid clogging of the filters, the sampling volumes varied between stations. Two distinct plankton size classes (0.2–3 μm and 3–200 μm) were fractionated for samples collected during the 2007–2008 cruise. This sampling effort (10–20 L) was done along a depth profile that spanned the full water column and the microbial community analysis was part of the International Consensus for Marine Microbes project. Filters were quickly frozen in the headspace of a LN2 Dewar and stored at −80°C prior to DNA extraction. We note that the 2007–2008 data were determined on samples from a single depth profile inside the ASP. It was decided to incorporate these data in order to derive first hints regarding the reproducibility of bacterial community compositions that accompany Phaeocystis blooms in the ASP and to gain early insights into the bacterial taxa that may associate with Phaeocystis colonies and other particles.

Etendue de l'étude Water samples were collected at various sites across the Amundsen Sea polynya (ASP) during the austral summers of 2007–2008 (aboard the icebreaker R/V “Oden”; depth profiles) and 2010–2011 (ASPIRE cruise aboard the R/V “Nathaniel B Palmer,” horizontal grid of surface samples).

Description des étapes de la méthode:

  1. DNA extraction was performed using the Puregene kit (Gentra®) after disruption of the cells with lytic enzyme coupled to proteinase K (Sinigalliano et al., 2007). DNA concentrations were quantified using a Nanodrop 2000 instrument (Thermo Fisher Scientific, Wilmington, DE).
  2. The V6 hypervariable region of the 16S rRNA gene (typically 60–65 bp in length) was amplified (25 cycles using HiFi buffer 1X, MgSO4 2 mM, dNTPs 0.2 mM, combined primers 0.2 mM and four units of platinum HiFi) in triplicate PCR reaction from 10 ng of environmental DNA templates with reverse primer (1046R) “CGACRRCCATGCANCACCT” and the forward primer mix (967F) “CTAACCGANGAACCTYACC,” “ATACGCGARGAACCTTACC,” “CNACGCGAAGAACCTTANC,” and “CAACGCGMARAACCTTACC.” PCR cycle conditions were defined as follow: 30 s at 94°C followed by 45 s at 60°C and 1 min at 72°C. The PCR started with 3 min at 94°C and ended with 2 min at 72°C followed by a rapid stepdown to 4°C. Negative controls (no template DNA) were run for each of the index primer combinations in the PCR reactions. V6 amplicon sequences from samples collected during the 2007–2008 R/V “Oden” cruise (n = 12) were obtained on a GS-FLX pyrosequencing platform. Sequence reads were subsequently trimmed for low-quality sequences (Huse et al., 2007). For samples collected on the ASPIRE cruise during the 2010–2011 austral summer (n = 23), a paired-end sequencing strategy for Illumina Hiseq platform was employed with custom fusion primers described previously (Eren et al., 2013b) targeting the V6 hypervariable region of the 16S rRNA gene.

Citations bibliographiques

  1. Delmont, T. O., Hammar, K. M., Ducklow, H. W., Yager, P. L., & Post, A. F. (2014). Phaeocystis antarctica blooms strongly influence bacterial community structures in the Amundsen Sea polynya. Frontiers in microbiology, 5, 646.

Métadonnées additionnelles

Identifiants alternatifs de7916fd-f4ec-496b-9059-f4ae6ba95406
https://ipt.biodiversity.aq/resource?r=bacterial_community_during_phaeocystis_antarctica_blooms_in_amundsen_sea_polynya