Bacterial community during Phaeocystis antarctica blooms (Amundsen Sea polynya)

最新版本 published by SCAR - Microbial Antarctic Resource System on 三月 19, 2019 SCAR - Microbial Antarctic Resource System
發布日期:
2019年3月19日
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CC-BY 4.0

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說明

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

版本

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如何引用

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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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此資料的發布者及權利單位為 SCAR - Microbial Antarctic Resource System。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF 註冊

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關鍵字

Metadata

聯絡資訊

Tom Delmont
  • 出處
  • 連絡人
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Woods Hole
US
Katherine Hammar
  • 出處
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Woods Hole
US
Hugh Ducklow
  • 出處
Columbia University
Palisades
US
Patricia Yager
  • 出處
University of Georgia
Athens
US
Anton Post
  • 出處
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Woods Hole
US
Maxime Sweetlove
  • 元數據提供者
Research assistant
Royal Belgian Institute for Natural Sciences
Rue Vautier 29
1000 Brussels
Anton post
  • 連絡人
Josephine Bay Paul Center for Comparative Molecular Biology and Evolution
Woods Hole
US

地理涵蓋範圍

Amundsen Sea polynya, Antarctica/Southern Ocean

界定座標範圍 緯度南界 經度西界 [-73.94, -115.68], 緯度北界 經度東界 [-73.94, -115.68]

分類群涵蓋範圍

Bacteria, 16S ssu rRNA gene, v6 region

Domain Bacteria (Bacteria)

時間涵蓋範圍

彙整期間 2007-2011

計畫資料

無相關描述

計畫名稱 International Census of Marine Microbes
辨識碼 ICoMM
經費來源 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).
研究區域描述 Amundsen Sea, Antarctica

參與計畫的人員:

Tom Delmont

取樣方法

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.

研究範圍 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).

方法步驟描述:

  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.

引用文獻

  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.

額外的詮釋資料