Influence of oil, dispersant, and pressure on microbial communities from the Gulf of Mexico

Atlas, R. M. & Hazen, T. C. Oil biodegradation and bioremediation: A tale of the two worst spills in u.s. history. Environmental Science & Technology 45, 6709–6715, https://doi.org/10.1021/es2013227 (2011).

McNutt, M. K. et al. Applications of science and engineering to quantify and control the Deepwater Horizon oil spill. Proceedings of the National Academy of Sciences 109, 20222–20228, https://doi.org/10.1073/pnas.1214389109 (2012).

Camilli, R. et al. Tracking hydrocarbon plume transport and biodegradation at Deepwater Horizon. Science 330, 201–204, https://doi.org/10.1126/science.1195223 (2010).

Ryerson, T. B. et al. Chemical data quantifyDeepwater Horizon hydrocarbon flow rate and environmental distribution. Proceedings of the National Academy of Sciences 109, 20246–20253, https://doi.org/10.1073/pnas.1110564109 (2012).

Joye, S. B. Deepwater Horizon, 5 years on. Science 349, 592–593, https://doi.org/10.1126/science.aab4133 (2015).

Romero, I. C. et al. Hydrocarbons in deep-sea sediments following the 2010 Deepwater Horizon blowout in the northeast gulf of mexico. PLoS ONE 10, e0128371, https://doi.org/10.1371/journal.pone.0128371 (2015).

Daly, K. L., Passow, U., Chanton, J. & Hollander, D. Assessing the impacts of oil-associated marine snow formation and sedimentation during and after theDeepwater Horizon oil spill. Anthropocene 13, 18–33, https://doi.org/10.1016/j.ancene.2016.01.006 (2016).

• Article
• Google Scholar

Redmond, M. C. & Valentine, D. L. Natural gas and temperature structured a microbial community response to the Deepwater Horizon oil spill. Proceedings of the National Academy of Sciences 109, 20292–20297, https://doi.org/10.1073/pnas.1108756108 (2012).

Hazen, T. C., Prince, R. C. & Mahmoudi, N. Marine oil biodegradation. Environmental Science & Technology 50, 2121–2129, https://doi.org/10.1021/acs.est.5b03333 (2016).

Dubinsky, E. A. et al. Succession of hydrocarbon-degrading bacteria in the aftermath of the Deepwater Horizon oil spill in the gulf of mexico. Environmental Science & Technology 47, 10860–10867, https://doi.org/10.1021/es401676y (2013).

Kostka, J. E. et al. Hydrocarbon-degrading bacteria and the bacterial community response in gulf of mexico beach sands impacted by the Deepwater Horizon oil spill. Applied and Environmental Microbiology 77, 7962–7974, https://doi.org/10.1128/aem.05402-11 (2011).

Liu, Z. & Liu, J. Evaluating bacterial community structures in oil collected from the sea surface and sediment in the northern gulf of mexico after the Deepwater Horizon oil spill. MicrobiologyOpen 2, 492–504, https://doi.org/10.1002/mbo3.89 (2013).

Crespo-Medina, M. et al. The rise and fall of methanotrophy following a deepwater oil-well blowout. Nature Geoscience 7, 423–427, https://doi.org/10.1038/ngeo2156 (2014).

Kimes, N. E. et al. Metagenomic analysis and metabolite profiling of deep-sea sediments from the gulf of mexico following theDeepwater Horizon oil spill. Frontiers in Microbiology 4, https://doi.org/10.3389/fmicb.2013.00050 (2013).

Techtmann, S. M. et al. Corexit 9500 enhances oil biodegradation and changes active bacterial community structure of oil-enriched microcosms. Applied and Environmental Microbiology 83, https://doi.org/10.1128/aem.03462-16 (2017).

Kleindienst, S. et al. Chemical dispersants can suppress the activity of natural oil-degrading microorganisms. Proceedings of the National Academy of Sciences 112, https://doi.org/10.1073/pnas.1507380112 (2015).

Margesin, R. & Schinner, F. Biodegradation and bioremediation of hydrocarbons in extreme environments. Applied Microbiology and Biotechnology 56, 650–663, https://doi.org/10.1007/s002530100701 (2001).

Scoma, A., Barbato, M., Borin, S., Daffonchio, D. & Boon, N. An impaired metabolic response to hydrostatic pressure explains alcanivorax borkumensis recorded distribution in the deep marine water column. Scientific Reports 6, 31316, https://doi.org/10.1038/srep31316 (2016).

Marietou, A. et al. The effect of hydrostatic pressure on enrichments of hydrocarbon degrading microbes from the gulf of mexico following the Deepwater Horizon oil spill. Frontiers in Microbiology 9, https://doi.org/10.3389/fmicb.2018.00808 (2018).

Prince, R. C., Nash, G. W. & Hill, S. J. The biodegradation of crude oil in the deep ocean. Marine Pollution Bulletin 111, 354–357, https://doi.org/10.1016/j.marpolbul.2016.06.087 (2016).

Schedler, M., Hiessl, R., Valladares Juarez, A., Gust, G. & Muller, R. Effect of high pressure on hydrocarbon-degrading bacteria. AMB Express 4, 77 (2014).

• Article
• Google Scholar

Nguyen, U. T. et al. The influence of pressure on crude oil biodegradation in shallow and deep gulf of mexico sediments. PLOS ONE 13, e0199784, https://doi.org/10.1371/journal.pone.0199784 (2018).

Overholt, W. A. et al. Hydrocarbon degrading bacteria exhibit a species specific response to dispersed oil while moderating ecotoxicity. Applied and Environmental Microbiology https://doi.org/10.1128/aem.02379-15 (2015).

Bælum, J. et al. Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environmental Microbiology 14, 2405–2416, https://doi.org/10.1111/j.1462-2920.2012.02780.x (2012).

Chakraborty, R., Borglin, S. E., Dubinsky, E. A., Andersen, G. L. &Hazen, T. C. Microbial response to the mc252 oil and corexit 9500 in the gulf of mexico. Frontiers in Microbiology 3, https://doi.org/10.3389/fmicb.2012.00357 (2012).

Perez Calderon, L. J. et al. Bacterial community response in deep faroe-shetland channel sediments following hydrocarbon entrainment with and without dispersant addition. Frontiers in Marine Science 5, https://doi.org/10.3389/fmars.2018.00159 (2018).

Bacosa, H. P. et al. Hydrocarbon degradation and response of seafloor sediment bacterial community in the northern gulf of mexico to light louisiana sweet crude oil. The ISME journal 12, 2532–2543, https://doi.org/10.1038/s41396-018-0190-1 (2018).

Hackbusch, S. et al. Influence of pressure and dispersant on oil biodegradation by a newly isolated Rhodococcus strain from deep-sea sediments of the gulf of mexico. Marine Pollution Bulletin 110683, https://doi.org/10.1016/j.marpolbul.2019.110683 (2019).

Peoples, L. M. et al. Microbial community diversity within sediments from two geographically separated hadal trenches. Frontiers in Microbiology 10, https://doi.org/10.3389/fmicb.2019.00347 (2019).

Underwood, G. J. C. et al. Organic matter from arctic sea-ice loss alters bacterial community structure and function. Nature Climate Change 9, 170–176, https://doi.org/10.1038/s41558-018-0391-7 (2019).

Valentine, D. L. et al. Propane respiration jump-starts microbial response to a deep oil spill. Science 330, 208–211, https://doi.org/10.1126/science.1196830 (2010).

Mason, O. U. et al. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. The ISME journal 8, 1464–1475, https://doi.org/10.1038/ismej.2013.254 (2014).

Yang, T. et al. Distinct bacterial communities in surficial seafloor sediments following the 2010 Deepwater Horizon blowout. Frontiers in Microbiology 7, https://doi.org/10.3389/fmicb.2016.01384 (2016).

Satomi, M. The Family Shewanellaceae, 597–625 (Springer Berlin Heidelberg, Berlin, Heidelberg, 2014).

Gentile, G., Bonasera, V., Amico, C., Giuliano, L. & Yakimov, M. Shewanella sp. ga-22, a psychrophilic hydrocarbonoclastic antarctic bacterium producing polyunsaturated fatty acids. Journal of Applied Microbiology 95, 1124–1133, https://doi.org/10.1046/j.1365-2672.2003.02077.x (2003).

Bagi, A., Pampanin, D. M., Lanzén, A., Bilstad, T. & Kommedal, R. Naphthalene biodegradation in temperate and arctic marine microcosms. Biodegradation 25, 111–125, https://doi.org/10.1007/s10532-013-9644-3 (2014).

Ferguson, R. M. W., Gontikaki, E., Anderson, J. A. & Witte, U. The variable influence of dispersant on degradation of oil hydrocarbons in subarctic deep-sea sediments at low temperatures (0–5°c). Scientific Reports 7, 2253, https://doi.org/10.1038/s41598-017-02475-9 (2017).

Bartlett, D. H. Pressure effects on in vivo microbial processes. Biochimica et Biophysica Acta (BBA) – Protein Structure and Molecular Enzymology 1595, 367–381, https://doi.org/10.1016/S0167-4838(01)00357-0 (2002).

Xu, Y. et al. Moritella profunda sp. nov. and Moritella abyssi sp. nov., two psychropiezophilic organisms isolated from deep atlantic sediments. International Journal of Systematic and Evolutionary Microbiology 53, 533–538, https://doi.org/10.1099/ijs.0.02228-0 (2003).

Kujawinski, E. B. et al. Fate of dispersants associated with the Deepwater Horizon oil spill. Environmental Science & Technology 45, 1298–1306, https://doi.org/10.1021/es103838p (2011).

Liu, J., Sun, Y.-W., Li, S.-N. & Zhang, D.-C. Thalassotalea profundi sp. nov. isolated from a deep-sea seamount. International Journal of Systematic and Evolutionary Microbiology 67, 3739–3743, https://doi.org/10.1099/ijsem.0.002180 (2017).

Stelling, S. C. et al. Draft genome sequence ofThalassotalea sp. strain nd16a isolated from eastern mediterranean sea water collected from a depth of 1,055 meters. Genome announcements 2, e01231–14, https://doi.org/10.1128/genomeA.01231-14 (2014).

Lindstrom, J. E. & Braddock, J. F. Biodegradation of petroleum hydrocarbons at low temperature in the presence of the dispersant corexit 9500. Marine Pollution Bulletin 44, 739–747, https://doi.org/10.1016/S0025-326X(02)00050-4 (2002).

Geiselbrecht, A. D. Cycloclasticus, 1–6 (John Wiley & Sons, Ltd, 2015).

White, H. K. et al. Long-term persistence of dispersants following the Deepwater Horizon oil spill. Environmental Science & Technology Letters 1, 295–299, https://doi.org/10.1021/ez500168r (2014).

Muyzer, G., de Waal, E. C. & Uitterlinden, A. G. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16s rrna. Applied and Environmental Microbiology 59, 695–700 (1993).

Klindworth, A. et al. Evaluation of general 16s ribosomal rna gene pcr primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Research 41, e1–e1, https://doi.org/10.1093/nar/gks808 (2013).

Callahan, B. J. et al. Dada2: High-resolution sample inference from illumina amplicon data. Nature Methods 13, 581–583, https://doi.org/10.1038/nmeth.3869 (2016).

Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome data science using quime 2. Nature Biotechnology 37, 852–7, https://doi.org/10.1038/s41587-019-0209-9 (2019).

Pedregosa, F. et al. Scikit-learn: Machine learning in python. Journal of Machine Learning Research 12, 2825–2830 (2011).

Quast, C. et al. The silva ribosomal rna gene database project: improved data processing and web-based tools. Nucleic Acids Research 41, D590–D596, https://doi.org/10.1093/nar/gks1219 (2013).

Bokulich, N. A. et al. Optimizing taxonomic classification of marker-gene amplicon sequences with qiime 2’s q2-feature-classifier plugin. Microbiome 6, 90, https://doi.org/10.1186/s40168-018-0470-z (2018).

Werner, J. J. et al. Impact of training sets on classification of high-throughput bacterial 16s rrna gene surveys. The ISME journal 6, 94–103, https://doi.org/10.1038/ismej.2011.82 (2012). 

McMurdie, P. J. & Holmes, S. phyloseq: An r package for reproducible interactive analysis and graphics of microbiome census data. PLOS ONE 8, e61217, https://doi.org/10.1371/journal.pone.0061217 (2013).

R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria (2013).

Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer Publishing Company, Incorporated, 2009).

Oksanen, J. et al. vegan: Community Ecology Package. R package version 2, 4–6 (2018).

• Google Scholar

Jiang, L. et al. Discrete false-discovery rate improves identification of differentially abundant microbes. mSystems 2, https://doi.org/10.1128/mSystems.00092-17 (2017).

Heberle, H., Meirelles, G. V., da Silva, F. R., Telles, G. P. & Minghim, R. Interactivenn: a web-based tool for the analysis of sets through venn diagrams. BMC Bioinformatics 16, 169, https://doi.org/10.1186/s12859-015-0611-3 (2015).