algal_mat_microbiome_east_antarctica

Versão mais recente published by SCAR - Microbial Antarctic Resource System on jun 10, 2021 SCAR - Microbial Antarctic Resource System
Publication date:
10 de Junho de 2021
Licença:
CC-BY 4.0

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Descrição

Amplicon sequencing dataset (Illumina MiSeq) targeting Bacteria (16S ssu rRNA) and Eukaryotes (18S ssu rRNA) in microbial mat samples (n=13) from in and around lakes in East Antarctica (Langhovde and Skarvness regions).

Versões

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Como citar

Pesquisadores deveriam citar esta obra da seguinte maneira:

Hirose Y, Shiozaki T, Otani M, Kudoh S, Imura S, Eki T, Harada N (2021): algal_mat_microbiome_east_antarctica. v1.0. SCAR - Microbial Antarctic Resource System. Dataset/Metadata. https://ipt.biodiversity.aq/resource?r=algal_mat_microbiome_east_antarctica&v=1.0

Direitos

Pesquisadores devem respeitar a seguinte declaração de direitos:

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

GBIF Registration

Este recurso foi registrado no GBIF e atribuído ao seguinte GBIF UUID: 5d7ab0cf-4c60-4b8d-bea4-04632af68fc9.  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.

Palavras-chave

Metadata

Contatos

Yuu Hirose
  • Originador
  • Usuário
  • Ponto De Contato
Toyohashi University of Technology
Aichi
JP
Takuhei Shiozaki
  • Originador
JP
Masahiro Otani
  • Originador
JP
Sakae Kudoh
  • Originador
JP
Satoshi Imura
  • Originador
JP
Toshihiko Eki
  • Originador
JP
Naomi Harada
  • Originador
JP
Maxime Sweetlove
  • Provedor Dos Metadados
Royal Belgian Institute of Natural Sciences
Brussels
BE

Cobertura Geográfica

East Antarctica, Langhovde and Skarvnes region

Coordenadas delimitadoras Sul Oeste [-69,484, 39,571], Norte Leste [-69,241, 39,756]

Cobertura Temporal

Data Inicial / Data final 2018-12-24 / 2019-01-13

Dados Sobre o Projeto

Nenhuma descrição disponível

Título Algal Communities in Lacustrine and Hydro-Terrestrial Environments of East Antarctica
Financiamento This research was supported by Grant-in-Aid for Scientific Research (S) (Grant number 15H05712) to N.H. from Japan Society for the Promotion of Science (JSPS).

O pessoal envolvido no projeto:

Yuu Hirose

Métodos de Amostragem

Microbial mat samples were collected from 1–2 cm of the surface using a scoop. Water samples were collected using a disposable plastic syringe. Samples were transferred to the icebreaker SHIRASE and then frozen until DNA extraction was performed. Sample S1 was a brown mat isolated from Lake Mitsu Ike; S2 was a red colored bloom observed in a puddle of thawing snow in the coastal area; S3 was a green and brown mat that was collected in Lake Yukidori Ike; S4 was a black microbial mat in Lake Bosatsu Ike; S5 was a small white filamentous aggregate floating on the surface of Lake Bosatsu Ike; S6 was a brown microbial mat in Lake Bosatsu Ike; S7 was a green colored aggregate found in a small stream near Lake Suribati Ike; S8 was a brown mat found near the stream; S9 was a white aggregate floating on the surface of Lake Suribati Ike; S10 was a black and brown mat collected from Lake Neko Ike; S11 was a floating brown mat that originated from the benthic algal mat in Lake Kobachi Ike; S12 was a dark yellow mat collected from thawed soil near Lake Tokkuri Ike; and S13 was a orange mat, found at the bottom of the shallows in Lake Kumogata Ike.

Área de Estudo Lacustrine and hydro-terrestrial environments in East Antarctica were sampled from December 2018 to January 2019, by the Japanese Antarctic Research Expedition.

Descrição dos passos do método:

  1. The samples were mixed with 10 mL of 10 mM Tris-HCl pH 8.0, 5 mL of phenol pH 8.0, and 2 g of zirconia/glass beads (diameter 0.1 mm), and vortexed vigorously for three minutes at room temperature. After heat treatment at 65 ◦C for 10 min, the debris and beads were removed by centrifugation for five minutes at 16,000× g. The upper water phase was transferred to a new tube and an equal volume of chloroform/isoamylalchol (24:1) was added, vortexed vigorously, and centrifuged for five minutes at 16,000× g. The upper water phase was precipitated with 2.5 volumes of 99.5% ethanol and 0.1 volumes of sodium acetate pH 5.2, and precipitated with centrifugation for 10 min at 21,600× g. The white pellets containing genomic DNA were washed with 70% ethanol, dried for five minutes at room temperature, and dissolved with 300 μl of 10 mM Tris-HCl pH 8.5. DNA was further purified using a DNeasy Blood and Tissue kit (Qiagen, Hilden, Germany), in accordance with the manufacturer’s instructions, and eluted with water.
  2. The V3–V4 region of the 16S rRNA and the V7–V8 region of the 18 rRNA genes were amplified using KOD FX Neo (Toyobo, Osaka, Japan). Primer sets 341F and 805R were used for 16S rRNA analysis and F1183 and R1631 for 18S rRNA. PCR thermal cycle was an initial denaturing step at 94 ◦C for two minutes, 35 cycles of denaturation at 98 ◦C for 10 s, annealing at 55 ◦C for 30 s, and extension at 68 ◦C for 30 s, with the final extension step at 68 ◦C for five minutes. The PCR product was purified with 0.8 volumes of AMPure XP beads, in accordance with the manufacturer’s instructions, and eluted with 10 mM Tris-HCl pH 8.5. Index PCR was performed in eight cycles using a Nextera XT Index Kit v2 (Illumina, San Diego, California, USA), in accordance with the manufacturer’s instructions. The same index was used for the 16S and 18S rRNA amplicons that were obtained from the same sample. The amplified libraries were purified by the addition of 1.12 volumes of AMPure XP beads, in accordance with the manufacturer’s instructions, and eluted with 10 mM Tris-HCl pH 8.5. The concentration of each library was quantified using a spectrophotometer, and equal amounts of each library were pooled and quantified using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, Massachusetts, USA).
  3. Each 300 bp end of the pooled library was sequenced using an MiSeq Reagent Kit v3 (600 cycles; Illumina) on the MiSeq instrument (Illumina).

Citações bibliográficas

  1. Hirose, Y., Shiozaki, T., Otani, M., Kudoh, S., Imura, S., Eki, T., & Harada, N. (2020). Investigating algal communities in lacustrine and hydro-terrestrial environments of east Antarctica using deep amplicon sequencing. Microorganisms, 8(4), 497.

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