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Metatranscriptome from microbial mats in Arctic and Antarctic polar tundra environments

Citation

Rippin M, Williams L, Colesie C, Borchardt N, Jung P, Budel B, Karsten U, Becker B, Sweetlove M (2019). Metatranscriptome from microbial mats in Arctic and Antarctic polar tundra environments. Version 1.1. SCAR - Microbial Antarctic Resource System. Metadata dataset https://doi.org/10.15468/e2zhxj accessed via GBIF.org on 2023-03-31.

Description

Metatranscriptome dataset (Illumina HiSeq) of RNA from soil microbial mat samples in Arctic (Svalbard) and Antarctic (Livingston Island) polar tundra environments

Sampling Description

Study Extent

Soil crust samples were collected during expeditions to the Arctic and Antarctica in August 2014 and February 2015, respectively. Arctic samples were taken near the station Ny-Ålesund. The Antarctic samples were collected close by the Spanish Juan Carlos I Antarctic Base at Livingston Island, South Shetland Islands.

Sampling

Samples (1 g) were taken aseptically, and were preserved using the LifeGuard™ Soil Preservation Solution (MO BIO Laboratories, Carlsbad, CA, USA).

Method steps

  1. The Arctic samples (NA) were processed according to Rippin et al. (2016) using the CTAB protocol, DNase I (Thermo Fisher Scientific, Waltham, MA, USA) and the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). Due to low RNA yields, a total of six biological replicates were extracted and combined to obtain three pooled replicates. RNA from three biological replicates, collected at Livingston Island (Gr1), was isolated using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich, St. Louis, MO, USA), treated with DNase I (Thermo Fisher Scientific, Waltham, MA, USA) and purified using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany) as described by Rippin et al. (2016). Single samples yielded sufficient amounts of RNA.
  2. All RNA samples were further processed by Eurofins Genomics (Ebersberg, Germany). The processing included quality control utilizing the BioAnalyzer (Agilent Technologies, Santa Clara, CA, USA) and library preparation for both triplicates. Eukaryotic mRNA was enriched using oligo-(dT) beads, fragmented and, subsequently, cDNA was synthesized using random hexamers. Finally, Illumina compatible adapters were ligated. The libraries of the individual samples NÅ and Gr1 were applied to an Illumina HiSeq 2500, all triplicates multiplexed on one lane, using 125 bp paired-end and single-end mode, respectively. For sample NÅ, the HiSeq Control Software 2.2.58, RTA 1.18.64 and bcl2fastq-1.8.4 were used while the detected signals from sample Gr1 were processed by operating the HiSeq Control Software 2.2.38, RTA 1.18.61 and bcl2fastq-1.8.4 (Illumina, San Diego, CA, USA).

Taxonomic Coverages

microbial meta transcriptome
  1. Eukaryote
    common name: Eukaryota rank: domain
  2. Bacteria
    common name: Bacteria rank: domain
  3. Archaea
    common name: Archaea rank: domain

Geographic Coverages

Livinston Island, near the Juan Carlos I base (Antarctica); and Ny-Alsesund on Svalbard (Arctic)

Bibliographic Citations

  1. Rippin, M., Borchhardt, N., Williams, L., Colesie, C., Jung, P., Büdel, B., ... & Becker, B. (2018). Genus richness of microalgae and Cyanobacteria in biological soil crusts from Svalbard and Livingston Island: morphological versus molecular approaches. Polar Biology, 41(5), 909-923. - https://doi.org/10.1007/s00300-018-2252-2
  2. Williams, L., Borchhardt, N., Colesie, C., Baum, C., Komsic-Buchmann, K., Rippin, M., ... & Büdel, B. (2017). Biological soil crusts of Arctic Svalbard and of Livingston Island, Antarctica. Polar Biology, 40(2), 399-411. -

Contacts

Martin Rippin
originator
University of Cologne
Cologne
DE
Laura Williams
originator
University of Kaiserslautern
Kaiserslautern
DE
Claudia Colesie
originator
Swedish University of Agricultural Sciences
Umea
SE
Nadine Borchardt
originator
University of Rostock
Rostock
DE
Patrick Jung
originator
University of Kaiserslautern
Kaiserslautern
DE
Burkhard Budel
originator
University of Kaiserslautern
Kaiserslautern
DE
Ulf Karsten
originator
University of Rostock
Rostoc
DE
Burkhard Becker
originator
University of Cologne
Cologne
DE
Maxime Sweetlove
metadata author
position: Research assistent
Royal Belgian Institute of Natural Sciences
Rue Vautier 29
Brussels
1000
BE
email: msweetlove@naturalsciences.be
Martin Rippin
administrative point of contact
University of Cologne
Cologne
DE
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