Microbial community analysis of a coastal salt marsh affected by the Deepwater Horizon oil spill

Coastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf of Mexico coastal salt marsh during and after the influx of petroleum hydrocarbons following the Deepwater Horizon oil spill. Total hydrocarbon concentrations in salt marsh sediments were highest in June and July 2010 and decreased in September 2010. Coupled PhyloChip and GeoChip microarray analyses demonstrated that the microbial community structure and function of the extant salt marsh hydrocarbon-degrading microbial populations changed significantly during the study. The relative richness and abundance of phyla containing previously described hydrocarbon-degrading bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria) increased in hydrocarbon-contaminated sediments and then decreased once hydrocarbons were below detection. Firmicutes, however, continued to increase in relative richness and abundance after hydrocarbon concentrations were below detection. Functional genes involved in hydrocarbon degradation were enriched in hydrocarbon-contaminated sediments then declined significantly (p<0.05) once hydrocarbon concentrations decreased. A greater decrease in hydrocarbon concentrations among marsh grass sediments compared to inlet sediments (lacking marsh grass) suggests that the marsh rhizosphere microbial communities could also be contributing to hydrocarbon degradation. The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems.     

Hydrocarbon-degrading bacteria and the bacterial community response in gulf of Mexico beach sands impacted by the deepwater horizon oil spill

A significant portion of oil from the recent Deepwater Horizon (DH) oil spill in the Gulf of Mexico was transported to the shoreline, where it may have severe ecological and economic consequences. The objectives of this study were (i) to identify and characterize predominant oil-degrading taxa that may be used as model hydrocarbon degraders or as microbial indicators of contamination and (ii) to characterize the in situ response of indigenous bacterial communities to oil contamination in beach ecosystems. This study was conducted at municipal Pensacola Beach, FL, where chemical analysis revealed weathered oil petroleum hydrocarbon (C₈ to C₄₀) concentrations ranging from 3.1 to 4,500 mg kg⁻¹ in beach sands. A total of 24 bacterial strains from 14 genera were isolated from oiled beach sands and confirmed as oil-degrading microorganisms. Isolated bacterial strains were primarily Gammaproteobacteria, including representatives of genera with known oil degraders (Alcanivorax, Marinobacter, Pseudomonas, and Acinetobacter). Sequence libraries generated from oiled sands revealed phylotypes that showed high sequence identity (up to 99%) to rRNA gene sequences from the oil-degrading bacterial isolates. The abundance of bacterial SSU rRNA gene sequences was ∼10-fold higher in oiled (0.44 × 10⁷ to 10.2 × 10⁷ copies g⁻¹) versus clean (0.024 × 10⁷ to 1.4 × 10⁷ copies g⁻¹) sand. Community analysis revealed a distinct response to oil contamination, and SSU rRNA gene abundance derived from the genus Alcanivorax showed the largest increase in relative abundance in contaminated samples. We conclude that oil contamination from the DH spill had a profound impact on the abundance and community composition of indigenous bacteria in Gulf beach sands, and our evidence points to members of the Gammaproteobacteria (Alcanivorax, Marinobacter) and Alphaproteobacteria (Rhodobacteraceae) as key players in oil degradation there.     

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using ¹⁴C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of ¹⁴C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)''s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem.     

Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill

The Deepwater Horizon oil spill resulted in a massive influx of hydrocarbons into the Gulf of Mexico (the Gulf). To better understand the fate of the oil, we enriched and isolated indigenous hydrocarbon-degrading bacteria from deep, uncontaminated waters from the Gulf with oil (Macondo MC252) and dispersant used during the spill (COREXIT 9500). During 20 days of incubation at 5°C, CO(2) evolution, hydrocarbon concentrations and the microbial community composition were determined. Approximately 60% to 25% of the dissolved oil with or without COREXIT, respectively, was degraded, in addition to some hydrocarbons in the COREXIT. FeCl(2) addition initially increased respiration rates, but not the total amount of hydrocarbons degraded. 16S rRNA gene sequencing revealed a succession in the microbial community over time, with an increase in abundance of Colwellia and Oceanospirillales during the incubations. Flocs formed during incubations with oil and/or COREXIT in the absence of FeCl(2) . Synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy revealed that the flocs were comprised of oil, carbohydrates and biomass. Colwellia were the dominant bacteria in the flocs. Colwellia sp. strain RC25 was isolated from one of the enrichments and confirmed to rapidly degrade high amounts (approximately 75%) of the MC252 oil at 5°C. Together these data highlight several features that provide Colwellia with the capacity to degrade oil in cold, deep marine habitats, including aggregation together with oil droplets into flocs and hydrocarbon degradation ability.     

Hydrocarbon-degrading bacteria enriched by the Deepwater Horizon oil spill identified by cultivation and DNA-SIP

The massive influx of crude oil into the Gulf of Mexico during the Deepwater Horizon (DWH) disaster triggered dramatic microbial community shifts in surface oil slick and deep plume waters. Previous work had shown several taxa, notably DWH Oceanospirillales, Cycloclasticus and Colwellia, were found to be enriched in these waters based on their dominance in conventional clone and pyrosequencing libraries and were thought to have had a significant role in the degradation of the oil. However, this type of community analysis data failed to provide direct evidence on the functional properties, such as hydrocarbon degradation of organisms. Using DNA-based stable-isotope probing with uniformly ¹³C-labelled hydrocarbons, we identified several aliphatic (Alcanivorax, Marinobacter)- and polycyclic aromatic hydrocarbon (Alteromonas, Cycloclasticus, Colwellia)-degrading bacteria. We also isolated several strains (Alcanivorax, Alteromonas, Cycloclasticus, Halomonas, Marinobacter and Pseudoalteromonas) with demonstrable hydrocarbon-degrading qualities from surface slick and plume water samples collected during the active phase of the spill. Some of these organisms accounted for the majority of sequence reads representing their respective taxa in a pyrosequencing data set constructed from the same and additional water column samples. Hitherto, Alcanivorax was not identified in any of the previous water column studies analysing the microbial response to the spill and we discuss its failure to respond to the oil. Collectively, our data provide unequivocal evidence on the hydrocarbon-degrading qualities for some of the dominant taxa enriched in surface and plume waters during the DWH oil spill, and a more complete understanding of their role in the fate of the oil.     

Microbial activities and dissolved organic matter dynamics in oil-contaminated surface seawater from the Deepwater Horizon oil spill site

The Deepwater Horizon oil spill triggered a complex cascade of microbial responses that reshaped the dynamics of heterotrophic carbon degradation and the turnover of dissolved organic carbon (DOC) in oil contaminated waters. Our results from 21-day laboratory incubations in rotating glass bottles (roller bottles) demonstrate that microbial dynamics and carbon flux in oil-contaminated surface water sampled near the spill site two weeks after the onset of the blowout were greatly affected by activities of microbes associated with macroscopic oil aggregates. Roller bottles with oil-amended water showed rapid formation of oil aggregates that were similar in size and appearance compared to oil aggregates observed in surface waters near the spill site. Oil aggregates that formed in roller bottles were densely colonized by heterotrophic bacteria, exhibiting high rates of enzymatic activity (lipase hydrolysis) indicative of oil degradation. Ambient waters surrounding aggregates also showed enhanced microbial activities not directly associated with primary oil-degradation (β-glucosidase; peptidase), as well as a twofold increase in DOC. Concurrent changes in fluorescence properties of colored dissolved organic matter (CDOM) suggest an increase in oil-derived, aromatic hydrocarbons in the DOC pool. Thus our data indicate that oil aggregates mediate, by two distinct mechanisms, the transfer of hydrocarbons to the deep sea: a microbially-derived flux of oil-derived DOC from sinking oil aggregates into the ambient water column, and rapid sedimentation of the oil aggregates themselves, serving as vehicles for oily particulate matter as well as oil aggregate-associated microbial communities.     

Deepwater Horizon oil spill impacts on sea turtles could span the Atlantic

We investigated the extent that the 2010 Deepwater Horizon oil spill potentially affected oceanic-stage sea turtles from populations across the Atlantic. Within an ocean-circulation model, particles were backtracked from the Gulf of Mexico spill site to determine the probability of young turtles arriving in this area from major nesting beaches. The abundance of turtles in the vicinity of the oil spill was derived by forward-tracking particles from focal beaches and integrating population size, oceanic-stage duration and stage-specific survival rates. Simulations indicated that 321 401 (66 199–397 864) green (Chelonia mydas), loggerhead (Caretta caretta) and Kemp''s ridley (Lepidochelys kempii) turtles were likely within the spill site. These predictions compared favourably with estimates from in-water observations recently made available to the public (though our initial predictions for Kemp''s ridley were substantially lower than in-water estimates, better agreement was obtained with modifications to mimic behaviour of young Kemp''s ridley turtles in the northern Gulf). Simulations predicted 75.2% (71.9–76.3%) of turtles came from Mexico, 14.8% (11–18%) from Costa Rica, 5.9% (4.8–7.9%) from countries in northern South America, 3.4% (2.4–3.5%) from the United States and 1.6% (0.6–2.0%) from West African countries. Thus, the spill''s impacts may extend far beyond the current focus on the northern Gulf of Mexico.     

Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill

Benthic habitats harbour a significant (yet unexplored) diversity of microscopic eukaryote taxa, including metazoan phyla, protists, algae and fungi. These groups are thought to underpin ecosystem functioning across diverse marine environments. Coastal marine habitats in the Gulf of Mexico experienced visible, heavy impacts following the Deepwater Horizon oil spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity has precluded a thorough assessment of this disturbance. Using a marker gene and morphological approach, we present an intensive evaluation of microbial eukaryote communities prior to and following oiling around heavily impacted shorelines. Our results show significant changes in community structure, with pre-spill assemblages of diverse Metazoa giving way to dominant fungal communities in post-spill sediments. Post-spill fungal taxa exhibit low richness and are characterized by an abundance of known hydrocarbon-degrading genera, compared to prior communities that contained smaller and more diverse fungal assemblages. Comparative taxonomic data from nematodes further suggests drastic impacts; while pre-spill samples exhibit high richness and evenness of genera, post-spill communities contain mainly predatory and scavenger taxa alongside an abundance of juveniles. Based on this community analysis, our data suggest considerable (hidden) initial impacts across Gulf beaches may be ongoing, despite the disappearance of visible surface oil in the region.     

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in the United State history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety of metabolic genes involved in both aerobic and anaerobic hydrocarbon degradation were highly enriched in the plume compared with outside the plume, indicating a great potential for intrinsic bioremediation or natural attenuation in the deep sea. Various other microbial functional genes that are relevant to carbon, nitrogen, phosphorus, sulfur and iron cycling, metal resistance and bacteriophage replication were also enriched in the plume. Together, these results suggest that the indigenous marine microbial communities could have a significant role in biodegradation of oil spills in deep-sea environments.     

Macondo crude oil from the Deepwater Horizon oil spill disrupts specific developmental processes during zebrafish embryogenesis

Background

During nerve growth, cytoplasmic vesicles add new membrane preferentially to the growth cone located at the distal tip of extending axons. Growth cone membrane is also retrieved locally, and asymmetric retrieval facilitates membrane remodeling during growth cone repulsion by a chemorepellent gradient. Moreover, growth inhibitory factors can stimulate bulk membrane retrieval and induce growth cone collapse. Despite these functional insights, the processes mediating local membrane remodeling during axon extension remain poorly defined.

Results

To investigate the spatial and temporal dynamics of membrane retrieval in actively extending growth cones, we have used a transient labeling and optical recording method that can resolve single vesicle events. Live-cell confocal imaging revealed rapid membrane retrieval by distinct endocytic modes based on spatial distribution in Xenopus spinal neuron growth cones. These modes include endocytic "hot-spots" triggered at the base of filopodia, at the lateral margins of lamellipodia, and along dorsal ridges of the growth cone. Additionally, waves of endocytosis were induced when individual filopodia detached from the substrate and fused with the growth cone dorsal surface or with other filopodia. Vesicle formation at sites of membrane remodeling by self-contact required F-actin polymerization. Moreover, bulk membrane retrieval by macroendocytosis correlated positively with the substrate-dependent rate of axon extension and required the function of Rho-family GTPases.

Conclusions

This study provides insight into the dynamic membrane remodeling processes essential for nerve growth by identifying several distinct modes of rapid membrane retrieval in the growth cone during axon extension. We found that endocytic membrane retrieval is intensified at specific subdomains and may drive the dynamic membrane ruffling and re-absorption of filopodia and lamellipodia in actively extending growth cones. The findings offer a platform for determining the molecular mechanisms of distinct endocytic processes that may remodel the surface distribution of receptors, ion channels and other membrane-associated proteins locally to drive growth cone extension and chemotactic guidance.     

Demographic trends of Brown Pelicans in Louisiana before and after the Deepwater Horizon oil spill

Marine oil spills may have extensive and deleterious effects on coastal waterbirds, but pre‐spill data sets are often not available for making comparisons of demographics to the period following a spill. The 2010 Deepwater Horizon oil spill allowed us to compare Brown Pelican (Pelecanus occidentalis) demographics during pre‐ and post‐spill years. We banded 1114 pelicans on Louisiana barrier islands from 2007 to 2009, tracked their distribution via band re‐sighting surveys from 2008 to 2011, and conducted age‐structure surveys. Across Louisiana coastal islands in 2011, we detected 7% of pelicans that had been oiled during the 2010 spill and released following rehabilitation. Similarly, 6% of pelicans (not oiled) banded at the same release site in 2007 were observed across coastal islands 1 yr after banding. We observed variation in proportions of pelicans that were 1, 2, and 3 or more years old among years (2008–2011) and across islands, but little variation could readily be assigned to spill‐related mortality. These Brown Pelican demographic trends one year following the Deepwater Horizon oil spill are contrary to other assessments of the impacts of oil contamination on marine birds. However, additional research is required to evaluate potential long‐term population trends.     

Disturbance and recovery of salt marsh arthropod communities following BP Deepwater Horizon oil spill

Oil spills represent a major environmental threat to coastal wetlands, which provide a variety of critical ecosystem services to humanity. The U.S. Gulf of Mexico is a hub of oil and gas exploration activities that historically have impacted intertidal habitats such as salt marsh. Following the BP Deepwater Horizon oil spill, we sampled the terrestrial arthropod community and marine invertebrates found in stands of Spartina alterniflora, the most abundant plant in coastal salt marshes. Sampling occurred in 2010 as oil was washing ashore and a year later in 2011. In 2010, intertidal crabs and terrestrial arthropods (insects and spiders) were suppressed by oil exposure even in seemingly unaffected stands of plants; however, Littoraria snails were unaffected. One year later, crab and arthropods had largely recovered. Our work is the first attempt that we know of assessing vulnerability of the salt marsh arthropod community to oil exposure, and it suggests that arthropods are both quite vulnerable to oil exposure and quite resilient, able to recover from exposure within a year if host plants remain healthy.     

A suite of citrate-derived siderophores from a marine Vibrio species isolated following the Deepwater Horizon oil spill

Nearly all microbes require iron for growth. The low concentration of iron found in the ocean makes iron acquisition a particularly difficult task. In response to these low iron conditions, many bacteria produce low-molecular-weight iron-binding molecules called siderophores to aid in iron uptake. We report herein the isolation and structural characterization of a suite of amphiphilic siderophores called the ochrobactins-OH, which are produced by a Vibrio species isolated from the Gulf of Mexico after the 2010 Deepwater Horizon oil spill. The citrate-based ochrobactins-OH are derivatives of aerobactin, replacing the acetyl groups with fatty acid appendages ranging in size from C8 to C12, and are distinctly different from the ochrobactins in that the fatty acid appendages are hydroxylated rather than unsaturated. The discovery of the marine amphiphilic ochrobactin-OH suite of siderophores increases the geographic and phylogenetic diversity of siderophore-producing bacteria.     

Interannual patterns of the large free-living nematode assemblages in the Mexican Exclusive Economic Zone,NW Gulf of Mexico after the Deepwater Horizon oil spill

The presence and abundance of particular nematode genera in marine sediments are bioindicators of environmental disturbance. They can even reveal the existence of specific toxicants, such as trace-metals and hydrocarbons derived from fossil fuels. We studied this important infaunal component during a three-year monitoring program in Mexico’s Exclusive Economic Zone (EEZ) in the aftermath of a major oil spill in the northern Gulf of Mexico caused by the sinking of the Deepwater Horizon platform (DWH) in April of 2010. A closer look at the nematode composition and density values throughout and after the DWH oil spill revealed considerable changes. Continental shelf and upper slope sediments sampled in the summer of 2010 included 48 genera and a density of 44.45 ind/10 cm⁻². Eight months later in the winter of 2011, there was a critical decrement in genera number (23) and density (25.22 ind/10 cm⁻²). However, in 2012, the nematode community showed signs of recovery: genus diversity was 58 with a density of 91.45 ind/10 cm⁻². Significant differences were recorded between the first and the last sampling periods, driven by a remarkable turn-over in genera composition, and by an increase in density of the genera Sabatieria, Dorylaimopsis, and Cheironchus. Similarly, significant spatial differences between the nematofauna of the inner-middle shelf and the deepest zone (>2000 m) were detected. Correlation analyses confirmed the tolerant behavior of the above genera to Ni and Co, and their proliferation when hydrocarbon compounds presumably derived from the DWH oil spill increased throughout the study. The Maturity Index (MI) estimated for each survey ranged from 2.35 to 2.6. Environmental Quality Status conditions in the summer of 2010 were good while in the winter of 2011 were poor, and moderate towards the winter of 2012. Index of Trophic Diversity (ITD) values for each survey were high: 0.70, 0.68, and 0.74, respectively. A high predominance of feeding guilds 1B and 2B was recorded throughout the study.The estimated Index of Trophic Diversity (ITD) values resulted high (Table 5). These values apparently indicated that the four feeding types were proportionally distributed in the nematode assemblage. This fact was better reflected during the winter of 2012. Nonetheless, these results are not congruent with the high predominance of feeding guilds 1B and 2B observed throughout the study.     

Oiling rates and condition indices of shorebirds on the northern Gulf of Mexico following the Deepwater Horizon oil spill

The coastline of the Gulf of Mexico in the United States is an important wintering and stopover region for migratory shorebirds. The Deepwater Horizon oil spill (April–August 2010) impacted more than 1700 km of this coastline and could potentially affect shorebirds through long‐term exposure to toxins, degraded habitats, and altered food chains. We investigated the exposure to Deepwater Horizon oil of seven species of shorebirds that winter or stopover along the northern Gulf of Mexico. From October 2010 to May 2012, we captured and banded 691 shorebirds at six sites that experienced varying levels of oil contamination. Of birds sampled, 22 were lightly oiled, with species that forage on the coast having higher rates of oiling than those that forage in more estuarine habitats. Although only 8.6% of birds captured from October 2010 to May 2011 and 0.6% of the birds captured from August 2011 to June 2012 showed signs of oiling, an unknown, but potentially larger, number of shorebirds were likely exposed to indirect effects of the spill, such as decreased foraging time due to oiling of sites or disturbance from cleanup activities. Fuel stores and fattening rates of Dunlins (Calidris alpina) during spring migration, as measured using plasma metabolites, were not influenced by site oiling level. However, the level of disturbance at study sites was a significant predictor of both fuel stores and glycerol levels, suggesting that Dunlins stopping over during spring migration may have had difficulty reaching necessary fuel stores in spring 2011 due to disturbance from cleanup activity on oiled beaches. These effects from disturbance were only observed at sites with high cleanup activity, suggesting that the impact of oil‐spill cleanup on shorebirds may be minimized by limiting cleanup activities to specific areas and times of day.     

Decline in condition of gorgonian octocorals on mesophotic reefs in the northern Gulf of Mexico: before and after the Deepwater Horizon oil spill

Hard-bottom ‘mesophotic’ reefs along the ‘40-fathom’ (73 m) shelf edge in the northern Gulf of Mexico were investigated for potential effects of the Deepwater Horizon (DWH) oil spill from the Macondo well in April 2010. Alabama Alps Reef, Roughtongue Reef, and Yellowtail Reef were near the well, situated 60–88 m below floating oil discharged during the DWH spill for several weeks and subject to dispersant applications. In contrast, Coral Trees Reef and Madison Swanson South Reef were far from the DWH spill site and below the slick for less than a week or not at all, respectively. The reefs were surveyed by ROV in 2010, 2011, and 2014 and compared to similar surveys conducted one and two decades earlier. Large gorgonian octocorals were present at all sites in moderate abundance including Swiftia exserta, Hypnogorgia pendula, Thesea spp., and Placogorgia spp. The gorgonians were assessed for health and condition in a before-after-control-impact (BACI) research design using still images captured from ROV video transects. Injury was modeled as a categorical response to proximity and time using logistic regression. Condition of gorgonians at sites near Macondo well declined significantly post-spill. Before the spill, injury was observed for 4–9 % of large gorgonians. After the spill, injury was observed in 38–50 % of large gorgonians. Odds of injury for sites near Macondo were 10.8 times higher post-spill, but unchanged at far sites. The majority of marked injured colonies in 2011 declined further in condition by 2014. Marked healthy colonies generally remained healthy. Background stresses to corals, including fishing activity, fishing debris, and coral predation, were noted during surveys, but do not appear to account for the decline in condition at study sites near Macondo well.