Quantification of microbial cells and virus-like particles in sediments from Kermadec Trench


Sediment cores from sites K3, K4, K5, and K7 were recovered by subsampling a box corer (50 × 50 cm), while sediment cores from sites K4 and K6 were collected using an autonomous lander system. Microbes and virus-like particles were extracted from sediments in a 3°C room using a modified version of the washing protocol of Danovaro and Middelboe, 2010 (see Schauberger et al., 2021). After the washing procedure, the extracted microbial cells and virus-like particles were fixed with 25% glutaraldehyde (1% final concentration) and stored at −80°C prior to flow cytometry. These samples were measured in triplicates using a BD FACSCanto™ II flow cytometer, after staining with SYBR Green I. Sediment extracts were diluted 1 : 10 in 0.02 μm-filtered TE Buffer prior to all measurements. The flow rate was 5–7 μl/min, as determined by BD Trucount™ Beads. The laser settings and gating examples can be found in the Supporting Information of Schauberger et al. (2021).

DOI https://doi.org/10.1594/PANGAEA.965926
Related Identifier https://doi.org/10.1002/lno.11711
Metadata Access https://ws.pangaea.de/oai/provider?verb=GetRecord&metadataPrefix=datacite4&identifier=oai:pangaea.de:doi:10.1594/PANGAEA.965926
Creator Schauberger, Clemens ORCID logo; Middelboe, Mathias ORCID logo; Glud, Ronnie N (ORCID: 0000-0002-7069-893X)
Publisher PANGAEA
Publication Year 2024
Funding Reference Danish National Research Foundation https://doi.org/10.13039/501100001732 Crossref Funder ID DNRF145 Danish Center for Hadal Research, HADAL
Rights Creative Commons Attribution 4.0 International; https://creativecommons.org/licenses/by/4.0/
OpenAccess true
Resource Type Dataset
Format text/tab-separated-values
Size 914 data points
Discipline Earth System Research
Spatial Coverage (-177.399W, -32.187S, -176.561E, -30.381N); Kermadec Trench
Temporal Coverage Begin 2017-11-30T00:00:00Z
Temporal Coverage End 2017-12-10T11:01:02Z