Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill

Abstract

Although petroleum hydrocarbons discharged from the Deepwater Horizon (DWH) blowout were shown to have a pronounced impact on indigenous microbial communities in the Gulf of Mexico, effects on nearshore or coastal ecosystems remain understudied. This study investigated the successional patterns of functional and taxonomic diversity for over 1 year after the DWH oil was deposited on Pensacola Beach sands (FL, USA), using metagenomic and 16S rRNA gene amplicon techniques. Gamma- and Alphaproteobacteria were enriched in oiled sediments, in corroboration of previous studies. In contrast to previous studies, we observed an increase in the functional diversity of the community in response to oil contamination and a functional transition from generalist populations within 4 months after oil came ashore to specialists a year later, when oil was undetectable. At the latter time point, a typical beach community had reestablished that showed little to no evidence of oil hydrocarbon degradation potential, was enriched in archaeal taxa known to be sensitive to xenobiotics, but differed significantly from the community before the oil spill. Further, a clear succession pattern was observed, where early responders to oil contamination, likely degrading aliphatic hydrocarbons, were replaced after 3 months by populations capable of aromatic hydrocarbon decomposition. Collectively, our results advance the understanding of how natural benthic microbial communities respond to crude oil perturbation, supporting the specialization-disturbance hypothesis; that is, the expectation that disturbance favors generalists, while providing (microbial) indicator species and genes for the chemical evolution of oil hydrocarbons during degradation and weathering.

Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem

“…Metagenome and genome sequences were trimmed using SolexaQA (59), with a Phred score cutoff (-h) of 20 and a minimum fragment length of 50 bp, as described previously (60). Only paired reads with both sisters longer than 50 bp after trimming were used further (Tables S1 and S2).…”

“…The relative abundances of isolates and genes were calculated as the ratio of the total length of all reads mapping on a reference isolate genome or gene sequence divided by the total length of the reference sequence (ϫ coverage or sequencing depth). To calculate the genome equivalent for each gene/function, i.e., the fraction of total cells containing the gene, an in-house ruby script was used, essentially as described previously (60). Briefly, the script is used to detect and extract reads containing any of 91 essential protein-coding genes (universally conserved single-copy) (75) from the Genome Property database (entry ID, GenProp0799, named "bacterial core gene set, exactly 1 per genome") (76).…”

Biofilms on Hospital Shower Hoses: Characterization and Implications for Nosocomial Infections

“…Hence, metagenome sequencing (i.e., random sequencing of total community DNA extracts) has recently been used to examine the functional network of complex microbial communities (28,29). In spite of the rise of infections by opportunistic premise plumbing pathogens, relatively few studies have assessed the diversity of biofilms growing in DWDS at the metagenome level, especially in health care units (30)(31)(32)(33).…”

Biodegradation of Crude Oil Using Marine <i>Bacillus species</i> from Vadinar Coast, Gujarat, India

“…Similar kinds of studies have been reported for microbial capability exploiting oil and its derivatives as a source of carbon and energy 32,33 . Recently, Rodriguez-R et al 34 reported that the successional patterns of microbial communities respond to crude oil agitation, supporting the specialization disturbance hypothesis during degradation.…”