Somente metadatos

Bacterial in the Amundsen Sea Polynya (Southern Ocean): community composition in environmental samples and mesocosm experiment

Versão mais recente publicado por SCAR - Microbial Antarctic Resource System em 19 de Março de 2019 SCAR - Microbial Antarctic Resource System
Publication date:
19 de Março de 2019
License:
CC-BY-NC 4.0

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Descrição

Amplicon sequencing dataset (454 pyrosequencing) of microbial diversity (Bacteria, based on the 16S ssu rRNA gene) in the Amundsen Sea Polynya. This dataset was used in a study where the Amundsen Sea Polynya (Southern Ocean) was used as a model system to investigate important environmental factors that shape the coastal Southern Ocean microbiota. Population dynamics of abundant taxa was studied in both environmental samples and microcosm experiments.

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Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

Richert I, Dinasquet J, Logares R, Riemann L, Yager P, Wendeberg A, Bertilsson S (2019): Bacterial in the Amundsen Sea Polynya (Southern Ocean): community composition in environmental samples and mesocosm experiment. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=bacterial_diversity_admunsen_sea_southern_ocean&v=1.1

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O editor e o detentor dos direitos deste trabalho é SCAR - Microbial Antarctic Resource System. This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC) 4.0 License.

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: fe6e1a81-7a45-45b2-8faa-f164647b8684.  SCAR - Microbial Antarctic Resource System publica este recurso, e está registrado no GBIF como um publicador de dados aprovado por Scientific Committee on Antarctic Research.

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Metadata

Contatos

Quem criou esse recurso:
-

Inga Richert
Uppsala University
Uppsala
SE
Julie Dinasquet
University of Copenhagen
Helsingør
DK
Ramiro Logares
Institute of Marine Sciences
Barcelona
ES
Lasse Riemann
University of Copenhagen
Helsingør
DK
Patricia Yager
University of Georgia
Athens
US
Annelie Wendeberg
Microbial Ecosystem Services Group
Leipzig
DE
Stefan Bertilsson
Uppsala University
Uppsala
SE

Quem pode responder a perguntas sobre o recurso:

Inga Richert
Uppsala University
Uppsala
SE
Stefan Bertilsson
Uppsala University
Uppsala
SE

Quem preencher os metadados:
-

Maxime Sweetlove
Research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
1000 Brussels
BE

Quem mais foi associado com o recurso:

Usuário

Cobertura Geográfica

Amundsen Sea Polynya, Southern Ocean, Antarctica

Coordenadas delimitadoras Sul Oeste [-74,22, -118,47], Norte Leste [-71,86, -112]

Cobertura Taxonômica

Bacteria 16S ssu rRNA gene

Domínio Bacteria (Bacteria)

Cobertura Temporal

Período de Formação 2010-11 to 2011-01

Dados Sobre o Projeto

Nenhuma descrição disponível

Título ASPIRE Microbiome
Financiamento The creation of this dataset was made possible with funding of the Swedish Research Council and by the US National Science Foundation Office of Polar Programs (ANT-0839069). Sequencing was made possible by an instrument grant from the K&A Wallenberg foundation.

O pessoal envolvido no projeto:

Inga Richert

Métodos de Amostragem

Seawater was collected in 12 L Niskin bottles attached to a 24-bottle SBE 32 rosette; coupled to the rosette was a system of sensors reading depth-resolved pro les of temperature [° C], conductivity [S m−1], oxygen [mg L−1], photosynthetically active radiation (PAR) [μmol photons s−1 m−2 ] and uorescence [mg m−3 chl-a] for each cast (SBE 911, Sea-Bird Electronics, Bellevue, Washington, USA). Water samples for incubation experiments were processed immediately at 2°C in a temperature-controlled room.

Área de Estudo Sampling was conducted during the austral summer (November 2010 to January 2011) from the icebreaker Nathaniel B. Palmer. Samples from 15 stations were obtained to include samples from the three major water masses of the Amundsen Sea Polynya and its margins (71–75°S, 110–120°W) during the summer season.

Descrição dos passos do método:

  1. Processing of the samples used in the mesocosm experiments: To assess bacterioplankton responses to light and dark conditions in the absence of larger predators and eukaryotic phytoplankton, 0.2 μm filtered seawater in 1 L acid washed polycarbonate bottles was inoculated with 5% [v/v] 0.6 μm filltered seawater from the same depth using a vacuum pump to a total volume of 1 L. The experimental design by station included two factors (water mass source of inoculum: epipelagic and mesopelagic) with two treatments (dark and light) for each inoculum. Triplicate incubations were conducted under the dark and light conditions using water from each of three stations: 35 (73°27′95′′S, 112°10′41′′W ), 50 (73° 41′60′′S, 115°25′03′′W ) and 57.2 (73°70′73′′S, 113°26′5′′W ). Each experiment included one inoculum from the light-exposed AASW, and one from the mesopelagic zone from either WW or mCDW. Each 0.2-μm ltered seawater medium came from the same depth and station as its inoculum. The light source imitated light levels at approximately 20–50 m below the surface (Philips TLD-18W/18 blue, 1.5–1.99 *10−2 μmol photons s−1 m−2) in a PAR range of 400–500 nm (according to manufacturer), excluding the short-wavelength UV. After a 7-day incubation at near in situ temperature (0.5°C), bacteria from the full sample volume were collected by vacuum filtration onto 0.2-μm, 47-mm Supor filters (Pall, Lund, Sweden) and stored at −80°C in sucrose lysis buffer (20% sucrose, 50 mM EDTA, 50 mM TrisHCl, pH = 8). Darkness was achieved by covering the bottles with black and lightproof foil.
  2. The DNA was extracted using a phenol-chloroform extraction approach as previously described (Riemann et al., 2000). Prior to extraction, microorganisms were enzymatically digested for 30 min with lysozyme at 37°C followed by an overnight digestion with Proteinase K (both 20 mg ml−1, Sigma Aldrich) at 55°C (Boström et al., 2004). The 16S rRNA genes were amplified using the bacterial primers Bakt_341F (CCTACGGGNGGCWGCAG) and Bakt_805R (GACTACHVGGGTATCTAATCC) with 454-Lib-L adapters and sample-specific barcodes on the reverse primer (Herlemann et al., 2011). Each set consisted of up to 72 samples with individual barcodes pooled for sequencing.Triplicate PCR reactions for each sample were carried out with 10 to 70 ng extracted environmental DNA as template. Each 20-μl reaction also contained Phusion Hot Start high- delity DNA polymerase ( thermo Scientific). Ampli cation was carried out by initial denaturation at 98°C for 30 seconds followed by 25 cycles of an initial 98°C denaturation for 30 seconds, subsequent annealing at 50°C for 30 seconds and 30-second extension at 72°C. ese 25 cycles were followed by a final 7-min extension at 72°C. Triplicate reactions for each sample were pooled and PCR products were purified using the Agencourt AMPure XP kit according to manufacturer instructions (Beckman Coulter) and quantified with a Picogreen quantification essay (Invitrogen). Equimolar amounts of amplicon from each sample were pooled and sequenced by 454 pyrosequencing using Titanium chemistry at the SNP/SEQ SciLifeLab platform hosted by Uppsala University (Sweden).

Citações bibliográficas

  1. Richert, I., Dinasquet, J., Logares, R., Riemann, L., Yager, P. L., Wendeberg, A., & Bertilsson, S. (2015). The influence of light and water mass on bacterial population dynamics in the Amundsen Sea Polynya.

Metadados Adicionais

Identificadores alternativos fe6e1a81-7a45-45b2-8faa-f164647b8684
https://ipt.biodiversity.aq/resource?r=bacterial_diversity_admunsen_sea_southern_ocean