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

  • Environmental Microbiology
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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.

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Acknowledgments

M.L. and H.M.D. are staff members from The Argentinean National Research Council (CONICET), and F.E. is a doctoral fellow from CONICET. The amplicon dataset was generated by the Earth Microbiome Project (www.earthmicrobiome.org/). The metagenomic dataset was generated at the Department of Energy-Joint Genome Institute (DOE-JGI) under the Community Sequencing Program (CSP proposal ID 328, project IDs 403959, 404206, 404777–404782, 404786, 404788–404801). Sampling was funded by grants from CONICET (No. 112-200801-01736) and The National Agency for the Promotion of Science and Technology of Argentina (ANPCyT PICT2008 No. 0468), the Argentinean Antarctic Institute, the Universidad de Buenos Aires (UBA 20020100100378), ANPCyT (PICT-O 0124), and the Research Council of Norway (grant no. 228107). This research was also partly funded under the Laboratory Directed Research and Development Program at PNNL, a multi-program national laboratory operated by Battelle for the U.S. Department of Energy under Contract DE-AC05-76RL01830. We would like to thank Ricardo Vera, Horacio Ocariz, and Alejandro Ulrich for their help in sample collection.

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Authors and Affiliations

  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

    Fernando Espínola, Hebe M. Dionisi & Mariana Lozada

  2. Energy Geosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Sharon Borglin

  3. Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA

    Colin J. Brislawn & Janet K. Jansson

  4. Instituto Nanobiotec, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, CONICET, Buenos Aires, Argentina

    Walter P. Mac Cormack

  5. Instituto Antártico Argentino, Buenos Aires, Argentina

    Walter P. Mac Cormack

  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

    JoLynn Carroll

  7. School of Natural Sciences and Environmental Studies, Södertörn University, Huddinge, Sweden

    Sara Sjöling

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  1. Fernando Espínola
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  2. Hebe M. Dionisi
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  9. Mariana Lozada
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Correspondence to Mariana Lozada.

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Espínola, F., Dionisi, H.M., Borglin, S. et al. Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. Microb Ecol 75, 123–139 (2018). https://doi.org/10.1007/s00248-017-1028-5

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  • DOI: https://doi.org/10.1007/s00248-017-1028-5

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