Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes
- 970 Downloads
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.
KeywordsCold environments Subtidal sediments Hydrocarbons Anaerobic biodegradation Community structure Metagenomics Biomarker genes
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.
Compliance with Ethical Standards
Conflict of Interest
The authors declare no conflict of interest.
- 2.Atlas RM (2010) Microbial bioremediation in polar environments: current status and future directions. In: Bej AK, Aislabie J, Atlas RM (eds) Polar microbiology: the ecology, biodiversity and bioremediation potential of microorganisms in extremely cold environments. CRC Press, Boca Raton, pp. 373–391Google Scholar
- 11.Acosta-González A, Marqués S (2016) Bacterial diversity in oil-polluted marine coastal sediments Energy Biotechnol. Environ. Biotechnol 38:24–32Google Scholar
- 14.Kappell AD, Wei Y, Newton RJ, Van Nostrand JD, Zhou J, McLellan SL, Hristova KR (2014) The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill Front. Microbiol. 5:205CrossRefPubMedPubMedCentralGoogle Scholar
- 15.Kostka JE, Prakash O, Overholt WA, Green SJ, Freyer G, Canion A, et al. (2011) Hydrocarbon-degrading bacteria and the bacterial community response in Gulf of Mexico beach sands impacted by the Deepwater Horizon oil spill Appl. Environ. Microbiol. 77:7962–7974CrossRefPubMedPubMedCentralGoogle Scholar
- 39.Legendre P, Legendre LFJ (2012) Numerical ecology. ElsevierGoogle Scholar
- 40.Kuntze K, Shinoda Y, Moutakki H, McInerney MJ, Vogt C, Richnow H-H, Boll M (2008) 6-Oxocyclohex-1-ene-1-carbonyl-coenzyme a hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes Environ. Microbiol. 10:1547–1556CrossRefPubMedGoogle Scholar
- 64.Ivanova EP, Flavier S, Christen R (2004) Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov Int. J. Syst. Evol. Microbiol. 54:1773–1788CrossRefPubMedGoogle Scholar
- 79.Loviso C l, Lozada M, Guibert L m, Musumeci M a, Sarango Cardenas S, Kuin RV, et al. (2015) Metagenomics reveals the high polycyclic aromatic hydrocarbon-degradation potential of abundant uncultured bacteria from chronically polluted subantarctic and temperate coastal marine environments J. Appl. Microbiol. 119:411–424CrossRefPubMedGoogle Scholar