Protocol detail

Metagenomic analysis of coastal sediments

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A dataset including six metagenomes from coastal sediments of Ushuaia Bay (Tierra del Fuego Island, Argentina) and six from Potter Cove (25 de Mayo/King George Island, South Shetland Islands, Antarctica) was used for this study (S1 Table). In each of these enclosed environments, triplicate samples of superficial (0–5 cm) subtidal sediments were obtained using cores from two sampling sites distanced approximately 500 m (Fig 1). The sediments collected in Ushuaia Bay and Potter Cove contained moderate and low levels of hydrocarbon pollution, respectively [30 (link)]. DNA extraction, sequencing (Illumina HiSeq 2000 platform) and functional annotation (Integrated Microbial Genomes & Microbiomes (IMG/M) pipeline, [31 (link)]) were similar for the six metagenomes, and were described in previous works [30 (link), 32 (link)]. A second metagenomic dataset was obtained by sequencing the fosmids of a metagenomic library (Illumina HiSeq 1500 platform) constructed from intertidal sediments located near the OR sampling sites within Ushuaia Bay, as previously described [33 (link)–35 (link)].

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Galván V., Pascutti F., Sandoval N.E., Lanfranconi M.P., Lozada M., Arabolaza A.L., Mac Cormack W.P., Alvarez H.M., Gramajo H.C, & Dionisi H.M. (2023). High wax ester and triacylglycerol biosynthesis potential in coastal sediments of Antarctic and Subantarctic environments. PLOS ONE, 18(7), e0288509.

Publication 2023

HiSeq 2000 platform HiSeq 1500 platform

Hydrocarbon Library Metagenomic Microbial genomes Microbiomes

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Variable analysis

independent variables

Geographical location (Ushuaia Bay vs. Potter Cove)

dependent variables

Metagenomic profiles (functional annotation)

control variables

Sampling depth (0-5 cm subtidal sediments)
Sampling method (cores from two sites approximately 500 m apart)

Annotations

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