Integrating omics approaches to provide a systems-level view of microbial community responses in benthic ecosystems affected by the Deepwater Horizon oil spill
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The Deepwater Horizon (DWH) oil spill in 2010, one of the largest environmental accidents in history, had pronounced impacts affecting vast areas of the open ocean, deep sea, and coastal ecosystems. Biodegradation mediated by a complex network of microorganisms and their interaction with their physicochemical environment ultimately dictates the fate of these hydrocarbons. Most of these interactions remain elusive due to the limitations of traditional, culture-based approaches, but the advent of next generation sequencing has enabled new opportunities to mine the “microbial dark matter”, and thus provide new insights into these issues. The impacts on coastal ecosystems, in particular, remain comparatively less understood due to the stochasticity and complexity of ecosystem processes and lack of appropriate model microorganisms. To close these knowledge gaps, this thesis integrated taxonomic, genetic and oil degradation rate data from laboratory advective flow chambers that simulated the temporal oxic-anoxic cycles observed in the natural beach sand environment. Hydrocarbon quantification and metatranscriptomics analyses showed that oil biodegradation was not severely limited in the absence of oxygen, with sulfate and to a lesser extent, nitrate, serving as alternative electron acceptors in the anoxic phases. Interestingly, microbial activities during the oxic phases further promoted the anaerobic biodegradation by re-oxidizing (and/or detoxifying) the (reduced) alternative electron acceptors and providing nitrogen, a limiting nutrient, through biological nitrogen fixation. The thesis also generated reliable biomarkers to screen for oil degradation potential in marine ecosystems which are essential in determining if an ecosystem is more “primed” for oil biodegradation. Using genome-resolved metagenomic approaches, the key hydrocarbon degrading and nitrogen-fixing microorganism in these laboratory incubations, which made up ~30% of the total microbial community, was isolated and characterized. This organism, provisionally named Candidatus Macondimonas diazotrophica, represents a previously overlooked family of hydrocarbon degraders that are major responders to oil spills in coastal environments worldwide. A new, divergent clade of alkane monooxygenase (alkB) specialized to crude oil, as opposed to algae-derived, hydrocarbons was also discovered. Therefore, this thesis provided reliable biomarkers of the different phases of oil biodegradation (e.g., oxic/anoxic and early/late) and novel organisms for bioaugmentation that should be useful for managing future oil spills. All underlying genomic, metagenomic and associated metadata were organized into an interactive and searchable webserver, called “Genome repository of oiled systems” or GROS (http://microbial-genomes.org/projects/GROS). GROS should facilitate future studies to further understand the interactions among microbial community members and their chemical environment that ultimately control the fate of oil spills.