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Surface and deep marine bacterial communities in the Arctic and Antarctic

Última versión Publicado por SCAR - Microbial Antarctic Resource System en 19 de marzo de 2019 SCAR - Microbial Antarctic Resource System
Fecha de publicación:
19 de marzo de 2019
Licencia:
CC-BY 4.0

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Descripción

Amplicon sequencing dataset (454 pyrosequencing) of Bacteria (16S ssu rRNA gene, v6 region) in surface and deep waters of the Arctic and the Southern oceans. This dataset is part of the International Census of Marine Microbes (ICoMM).

Versiones

La siguiente tabla muestra sólo las versiones publicadas del recurso que son de acceso público.

¿Cómo referenciar?

Los usuarios deben citar este trabajo de la siguiente manera:

Ghiglione J, Galand P, Pommier T, Pedros-Alio C, Maas E, Bakker K, Bertilson S, Kirchman D, Lovejoy C, Yager P, Murray A (2019): Surface and deep marine bacterial communities in the Arctic and Antarctic. v1.1. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=pole_to_pole_marine_bacterial_communities&v=1.1

Derechos

Los usuarios deben respetar los siguientes derechos de uso:

El publicador y propietario de los derechos de este trabajo es SCAR - Microbial Antarctic Resource System. Este trabajo está autorizado bajo una Licencia Creative Commons Atribución/Reconocimiento 4.0 Internacional (CC-BY) 4.0.

Registro GBIF

Este recurso ha sido registrado en GBIF con el siguiente UUID: 8d3fae22-72bd-4e8f-adcd-7f57079c87ce.  SCAR - Microbial Antarctic Resource System publica este recurso y está registrado en GBIF como un publicador de datos avalado por Scientific Committee on Antarctic Research.

Palabras clave

Metadata

Contactos

¿Quién creó el recurso?:
-

Jean-François Ghiglione
University Pierre et Marie Curie
FR
Pierre Galand
University Pierre et Marie Curie
FR
Thomas Pommier
Institut National de la Recherche Agronomique (INRA)
Villeurbanne
FR
Carlos Pedros-Alio
Institut de Ciències del Mar
Barcelona
ES
Elizabeth Maas
National Institute of Water and Atmospheric Research
Wellington
NZ
Kevin Bakker
University of Georgia
Athens
US
Stefan Bertilson
Uppsala University
Uppsala
SE
David Kirchman
University of Delaware
Lewes
US
Connie Lovejoy
Université Laval
Québec
CA
Patricia Yager
University of Georgia
Athens
US
Alison Murray
Desert Research Institute
Reno
US

¿Quién puede resolver dudas acerca del recurso?:

Jean-François Ghiglione
University Pierre et Marie Curie
FR
Alison Murray
Desert Research Institute
Reno
US

¿Quién documentó los metadatos?:
-

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

¿Quién más está asociado con el recurso?:

Usuario

Cobertura geográfica

The Arctic Ocean and the Southern Ocean

Coordenadas límite Latitud Mínima Longitud Mínima [-73,96, -159,34], Latitud Máxima Longitud Máxima [79,99, 126]

Cobertura taxonómica

Bacteria (16S ssu rRNA gene, v6 region)

Dominio Bacteria (Bacteria)

Datos del proyecto

The role of the International Census of Marine Microbes (ICoMM) is to promote an agenda and an environment that will accelerate discovery, understanding, and awareness of the global significance of marine microbes. More details can be found in: Amaral-Zettler, L., Artigas, L.F., Baross, J., Bharathi, L., Boetius, A., Chandramohan, D., Herndl, G., Kogure, K., Neal, P., Pedros-Alio, C., Ramette, A., Schouten, S., Stal, L., Thessen, A., de Leeuw, J. & Sogin, M. 2010. A global census of marine microbes, In: Life in the World's Oceans: Diversity, Distribution and Abundance, Blackwell Publishing Ltd., Oxford, (Ed. McIntyre), pp. 223-45.

Título International Census of Marine Microbes
Identificador ICoMM
Fuentes de Financiación Funding to support sample collection was provided by the Institut Français pour la Recherche et la Technologie Polaires; the Spanish Ministry of Education and Science; the New Zealand International Polar Year-Census of Antarctic Marine Life Project [Phases 1 (So001IPY) and 2 (IPY2007-01)); the Natural Sciences and Engineering Council (NSERC) of Canada; National Science Foundation Grants OPP-0124733, ANT-0632389, and ANT-0741409; and the Swedish Polar Research Secretariat. 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.

Personas asociadas al proyecto:

Linda Amaral-Zettler

Métodos de muestreo

Samples were collected with a 5 l Niskin bottle.

Área de Estudio Water samples were taken from the Southern and the Arctic Oceans

Descripción de la metodología paso a paso:

  1. DNA extraction buffer (0.1 M Tris-HCl [pH 8], 0.1 M Na-EDTA [pH 8], 0.1 M NaH2PO4 [pH 8], 1.5 M NaCl, 5% cetyltri- methylammonium bromide), and proteinase K (1%) was added to each filter. Samples were frozen at -80°C and thawed at 65°C three times and then incubated on a rotating carousel for 30 min at 37°C. Sodium dodecyl sulfate (SDS; 20%) was added to each sample, and the samples were incubated at 65°C on a rotating carousel for 2 h. The liquid was then removed from the filters using a 3-ml syringe and placed in a 2-ml microcentrifuge tube, which was centrifuged at room temperature (6,000 g; 5 min). The supernatant from each microcentrifuge tube was then placed in separate 15-ml Falcon collection tubes. DNA extraction buffer, lysozyme (200 ul; 50 mg ml), SDS, and proteinase K were then added to each filter (1 ml and 75 and 20 ul, respectively) and to each microcentrifuge tube containing spun-down particles (0.37 ml and 75 and 10 ul, respectively). Both the filter samples and the microcentrifuge tubes were incubated on a rotating carousel for 10 min. The microcentrifuge tubes were again centrifuged (6,000 g; 5 min), and the supernatant was added to the appropriate collection tube. Liquid was then removed from the filters, placed in the microcentrifuge tubes, and centrifuged (6,000 g; 5 min), and the supernatant was added to the collection tubes. The extraction buffer, SDS, and proteinase K were added to each filter and the particles again, and the extraction process was repeated. An equal volume of phenol:chloroform:isoamyl alcohol step (25:24:1) was added to each collection tube of supernatant, and the tubes were vortexed and centri- fuged (1,200 g; 10 min). The aqueous (top) layer from each tube was drawn off into a 30-ml acid-washed sterile Corex (Corning) tube, and an equal volume of isopropanol was added to each tube and mixed gently. Often additional aliquots of isopropanol-water (1:1) were added to adequately dissolve the aqueous layer in the isopropanol. After the tubes were incubated for 1 h at room temperature, the precipitated DNA was centrifuged at room temperature (16,000 g; 20 min), and the isopropanol supernatant was removed and replaced with 5 ml of 70% ethanol. After a final centrifugation (16,000 g; 20 min), the ethanol was removed and the DNA was dried down and resuspended in 95 ul of TE buffer (10 mM Tris 1 mM EDTA, pH 8.0). The DNA was purified using Qiaquick PCR purification columns (Qiagen) according to the manufacturer’s instructions and stored at 20°C.
  2. PCR amplicon was done by adding genomic DNA (3–10 ng) to three separate 30 ul amplification mixes. The amplification mix contained 5 units of Pfu Turbo polymerase (Stratagene, La Jolla, CA), 1 Pfu reaction buffer, 200 uM dNTPs (Pierce Nucleic Acid Technologies, Milwaukee, WI), and a 0.2 uM concentration of each primer in a volume of 100 ul. Cycling conditions were an initial denaturation at 94°C for 3 min; 30 cycles of 94°C 30 s, 57°C for 45 s, and 72°C for 1 min; and a final 2-min extension at 72°C. The products were pooled after cycling and cleaned by using the MinElute PCR purification kit (Qiagen, Valencia, CA). The quality of the product was assessed on a Bioanalyzer 2100 (Agilent, Palo Alto, CA) using a DNA1000 LabChip. Only sharp, distinct amplification products with a total yield of 200 ng were used for 454 sequencing. The fragments in the amplicon libraries were bound to beads under conditions that favor one fragment per bead. The beads were emulsified in a PCR mixture in oil, and PCR amplification occurred in each droplet, generating 10 million copies of a unique DNA template. After breaking the emulsion, the DNA strands were denatured, and beads carrying single- stranded DNA clones were deposited into wells on a PicoTiter- Plate (454 Life Sciences) for pyrosequencing on a Genome Sequencer 20 system (Roche, Basel, Switzerland).

Referencias bibliográficas

  1. Amaral-Zettler, L., Artigas, L.F., Baross, J., Bharathi, L., Boetius, A., Chandramohan, D., Herndl, G., Kogure, K., Neal, P., Pedros-Alio, C., Ramette, A., Schouten, S., Stal, L., Thessen, A., de Leeuw, J. & Sogin, M. 2010. A global census of marine microbes, In: Life in the World's Oceans: Diversity, Distribution and Abundance, Blackwell Publishing Ltd., Oxford, (Ed. McIntyre), pp. 223-45.
  2. Ghiglione, J. F., Galand, P. E., Pommier, T., Pedrós-Alió, C., Maas, E. W., Bakker, K., ... & Murray, A. E. (2012). Pole-to-pole biogeography of surface and deep marine bacterial communities. Proceedings of the National Academy of Sciences, 201208160.

Metadatos adicionales

Identificadores alternativos 8d3fae22-72bd-4e8f-adcd-7f57079c87ce
https://ipt.biodiversity.aq/resource?r=pole_to_pole_marine_bacterial_communities