Microbial Community Successional Patterns in Beach Sands Impacted by the Deepwater Horizon Oil Spill
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The ISME Journal (2015) 9, 1928–1940 & 2015 International Society for Microbial Ecology All rights reserved 1751-7362/15 www.nature.com/ismej ORIGINAL ARTICLE Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill Luis M Rodriguez-R1, Will A Overholt1, Christopher Hagan2, Markus Huettel2, Joel E Kostka1,3 and Konstantinos T Konstantinidis1,4 1School of Biology, Georgia Institute of Technology, Atlanta, GA, USA; 2Department of Earth, Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA; 3School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA and 4School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA 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. The ISME Journal (2015) 9, 1928–1940; doi:10.1038/ismej.2015.5; published online 17 February 2015 Introduction Gulf of Mexico including an increase in the relative abundance of members of the Gammaproteobacteria,a The oil spill caused by the blowout of the Deepwater prevalence of known hydrocarbon-degrading popula- Horizon (DWH). Drilling rig in April 2010 constitu- tions, and the enriched abundance and expression of tes the largest accidental release of oil into the genes related to hydrocarbon degradation (Joye et al., marine environment in recorded history. Oil con- 2014; Kostka et al., 2014; King et al., 2015). These tamination from the DWH spill had a profound patterns and microbial responses are also in accor- impact on indigenous microbial communities, and dance with observations from laboratory studies and all available studies recognize shifts in the composi- previous accidental releases of oil in marine environ- tion of microbial communities in direct contact with ments (Ro¨ling et al., 2002; Head et al.,2006;Yakimov oiled seawater and sediments in comparison with et al., 2007; Berthe-Corti and Nachtkamp, 2010; Greer, pristine environments (Atlas and Hazen, 2011; Joye 2010; McGenity et al., 2012). et al., 2014; Kostka et al., 2014; King et al., 2015). The Unified Area Command estimated that Moreover, consistent patterns were observed in approximately one-half of the B4.9 million barrels microbial communities exposed to DWH oil in the of oil released from the DWH blowout reached the ocean surface (Lubchenco et al., 2010), and a portion of this surfaced oil transported to nearshore and Correspondence: KT Konstantinidis, Civil and Environmental coastal ecosystems was buried in the sediments Engineering, Georgia Institute of Technology, 311 Ferst Dr, Ford (Hayworth et al., 2011; Wang and Roberts, 2013), ES&T Building, Suite 3224, Atlanta, GA 30332, USA. E-mail: [email protected] impacting approximately 850 km of beaches from Received 12 September 2014; revised 16 December 2014; accepted east Texas to west Florida (Michel et al., 2013). Oil 23 December 2014; published online 17 February 2015 started depositing on the Pensacola Beach sands Response of benthic microbes to oiling LM Rodriguez-R et al 1929 studied here on 22 June 2010. The input of large in plant and animal communities that generalist amounts of crude oil, including an array of poten- populations better withstand disturbances, whereas tially toxic compounds, posed a potential distur- specialist populations tend to be favored in stable bance for benthic microbial communities (Valentine environments (specialization-disturbance hypo- et al., 2012). Available studies to date were primarily thesis; Va´zquez and Simberloff, 2002). According focused on the water column and/or deep sea to the disturbance-specialization hypothesis, most ecosystems, and less is known about the response specialist taxa are selected against when commu- or adaptation of sedimentary communities to oiling nities experience a severe disturbance, as they are (Huettel et al., 2014). Studies characterizing the adapted to relatively narrow niches in their natural taxonomic shifts between contaminated and non- ecosystem. In contrast, generalists are more resilient contaminated beach sediments recognized that the to disturbances altering the niches. In turn, the oil input strongly affected the beach sand microbial taxonomic diversity of the community is negatively communities, which responded with increased impacted by a disturbance, but the functional bacterial cell densities (Kostka et al., 2011), reduced diversity can increase as an effect of the disturbance. taxonomic diversity, and a succession of microbial Although some previous studies applied ecological populations that paralleled the changes in abun- theory to describe the response and recovery of dance and composition of deposited hydrocarbons community dynamics to disturbance (cf. Prosser (Kostka et al., 2011; Bik et al., 2012; Lamendella et al., 2007; Shade et al., 2012), the relationship of et al., 2014). Consistent responses have been disturbance and specialization remains largely observed across study sites, although other factors unexplored in microbial communities. Disturbed such as site heterogeneity and seasonal fluctuations communities are typically observed to encompass in environmental parameters have been shown to reduced taxonomic and/or phylogenetic diversity somewhat confound assessments of the oil impact in compared with undisturbed controls, but whether certain beaches (Newton et al., 2013), sometimes this pattern translates to reduced functional diver- making them undetectable (Ro¨ling et al., 2004). In sity or increased specialization remains largely general, an initial increase in the relative represen- unknown. In this study, we aimed to characterize tation of known oil degraders, mostly of the the response of sedimentary microbial communities Gammaproteobacteria class (most notably Alcani- from Pensacola Beach to the DWH oil spill, as an vorax), was observed together with a temporal in-situ experiment of the effects of disturbance on succession characterized by an increase in relative functional and taxonomic diversity. abundance of Bacillus, Microbacterium and mem- bers of the Alphaproteobacteria class at later stages, when recalcitrant oil hydrocarbons predominate Materials and methods (Kostka et al., 2011). Moreover, the increase in oil degraders was concomitant with an increased Beach sands were collected at Pensacola Municipal expression of polycyclic aromatic hydrocarbons, Beach, FL, USA (30119.57 N, 087110.47 W) on 6, 10, n-alkane and toluene degradation genes as assessed 20 and 24 May 2010 (before arrival of the oil plume by metatranscriptomics (Lamendella et al., 2014). to the shoreline; hereafter, termed pre-oil commu- Although these findings provided important nities/samples), 30 July 2010 (one month after the insights into the effects of oil on benthic microbial oil reached the beach; oiled), 20 October 2010 (when community composition, the gene functions oil constituents were still present in the sand; selected for and the genomic adaptations in weathered oiled), and 14 June 2011 (when oil was response to the presence of oil remained mostly not visually detectable; recovered; Table 1 and uncharacterized in the Gulf coast. Supporting methods). Samples were collected from Previously identified shifts in microbial commu- aerobic beach sediments (oxygen concentrations nities in response to DWH oil, both in the water between 210 and 230 mmol l À 1 down to 55 cm depth, column and sediments, indicated significant sus- which represents 450% of air saturation level) ceptibility of these communities; susceptibility above groundwater level. defined as the degree to which community composi- 16S rRNA gene amplicons were sequenced, and tion changes in response to disturbance (Shade the resulting sequences were analyzed as described et al., 2012). These observations are in accordance recently (Poretsky et al., 2014). Trimmed sequences with