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Microb Ecol. 2018 Jan;75(1):123-139. doi: 10.1007/s00248-017-1028-5. Epub 2017 Jul 12.

Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes.

Author information

1
Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina.
2
Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
3
Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
4
Instituto Nanobiotec, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina.
5
Instituto Antártico Argentino, Buenos Aires, Argentina.
6
Akvaplan-niva, Fram-High North Research Centre for Climate and the Environment, and ARCEx-Research Centre for Arctic Petroleum Exploration, Department of Geosciences, UiT The Arctic University of Norway, N-9037, Tromsø, Norway.
7
School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden.
8
Laboratorio de Microbiología Ambiental, Centro para el Estudio de Sistemas Marinos (CESIMAR, CONICET), Centro Nacional Patagónico, Blvd. Brown 2915, U9120ACD, Puerto Madryn, Chubut, Argentina. lozada@cenpat-conicet.gob.ar.

Abstract

In this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon's index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.

KEYWORDS:

Anaerobic biodegradation; Biomarker genes; Cold environments; Community structure; Hydrocarbons; Metagenomics; Subtidal sediments

PMID:
28702706
DOI:
10.1007/s00248-017-1028-5

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