Bacteria-Oil Microaggregates Are an Important Mechanism for Hydrocarbon Degradation in the Marine Water Column

Abstract

Following oil spills in aquatic environments, oil-associated flocculants observed within contaminated waters ultimately lead to the sedimentation of oil as marine oil snow (MOS). To better understand the role of aggregates in hydrocarbon degradation and transport, we experimentally produced a MOS sedimentation event using Gulf of Mexico coastal waters amended with oil or oil plus dispersant. In addition to the formation of MOS, smaller micrometer-scale (10- to 150-μm) microbial aggregates were observed. Visual inspection of these microaggregates revealed that they were most abundant in the oil-amended treatments and frequently associated with oil droplets, linking their formation to the presence of oil. The peak abundance of the microaggregates coincided with the maximum rates of biological hydrocarbon oxidation estimated by the mineralization of ¹⁴C-labeled hexadecane and naphthalene. To elucidate the potential of microaggregates to serve as hot spots for hydrocarbon degradation, we characterized the free-living and aggregate-associated microbial assemblages using 16S rRNA gene sequencing. The microaggregate population was found to be bacterially dominated and enriched with putative hydrocarbon-degrading taxa. Direct observation of some of these taxa using catalyzed reporter deposition fluorescence in situ hybridization confirmed their greater abundance within microaggregates relative to the surrounding seawater. Metagenomic sequencing of these bacteria-oil microaggregates (BOMAs) further supported their community's capacity to utilize a wide variety of hydrocarbon compounds. Taken together, these data highlight that BOMAs are inherent features in the biological response to oil spills and likely important hot spots for hydrocarbon oxidation in the ocean. IMPORTANCE Vast quantities of oil-associated marine snow (MOS) formed in the water column as part of the natural biological response to the Deepwater Horizon drilling accident. Despite the scale of the event, uncertainty remains about the mechanisms controlling MOS formation and its impact on the environment. In addition to MOS, we observed micrometer-scale (10- to 150-μm) aggregates whose abundance coincided with maximum rates of hydrocarbon degradation and whose composition was dominated by hydrocarbon-degrading bacteria with the genetic potential to metabolize a range of these compounds. This targeted study examining the role of these bacteria-oil microaggregates in hydrocarbon degradation reveals details of this fundamental component of the biological response to oil spills, and with it, alterations to biogeochemical cycling in the ocean.

Keywords: hydrocarbon degradation; marine oil snow; microbial aggregate.

FIG 1

Hydrocarbon degradation over time. (A) Oil concentration expressed as estimated oil equivalents (previously reported by reference 24). (B) Microaggregate abundance is shown as microaggregates per milliliter (left axis). Oxidation rates of [¹⁴C]hexadecane and [¹⁴C]naphthalene (right axis), respectively, are shown for each treatment group as a percentage of total available substrate oxidized per hour.

FIG 2

Microbial community composition as assessed via PCR amplicon analysis of the V4 region of the 16S rRNA gene. The community’s taxonomic distribution is described at the family level. Only the 20 most abundant families are shown.

FIG 3

Comparison of the microbial communities between aggregated and free-living groups for each treatment. Differential abundance analysis shows certain phylogenetic groups and ASVs are more abundant in either the >3.0-μm (relative abundance on y axis) or 0.2- to 3.0-μm (relative abundance on x axis) filter size fraction. The 20 most abundant genera are highlighted with all other less abundant genera as well as groups of unresolved phylogenetic affiliation denoted as other. ASVs of interest discussed in the main text are denoted with numbers within the graphs. A 1:1 ratio between the abundance of ASVs on the >3.0- and 0.2- to 3.0-μm size fractions is depicted as a gray diagonal line within the graphs.

FIG 4

Abundance of metagenome-assembled genomes (MAGs) in microaggregates expressed as reads per kilobase per million (RPKM). Statistics for individual MAGs are provided in Table S1.

FIG 5

Hydrocarbon degradation potential in metagenome-assembled genomes (MAGs) from taxa more abundant in microaggregates. Abundance of genes involved in the degradation of n-alkanes, PAHs, and fatty acids in MAGs.