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.     

Role of methylotrophs in the degradation of hydrocarbons during the Deepwater Horizon oil spill

The role of methylotrophic bacteria in the fate of the oil and gas released into theGulf of Mexico during the Deepwater Horizon oil spill has been controversial,particularly in relation to whether organisms such as Methylophaga hadcontributed to the consumption of methane. Whereas methanotrophy remains unqualifiedin these organisms, recent work by our group using DNA-based stable-isotope probingcoupled with cultivation-based methods has uncovered hydrocarbon-degradingMethylophaga. Recent findings have also shown that methylotrophs,including Methylophaga, were in a heightened state of metabolic activitywithin oil plume waters during the active phase of the spill. Taken collectively,these findings suggest that members of this group may have participated in thedegradation of high-molecular-weight hydrocarbons in plume waters. The discovery ofhydrocarbon-degrading Methylophaga also highlights the importance ofconsidering these organisms in playing a role to the fate of oil hydrocarbons atoil-impacted sites.     

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.     

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.     

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.     

Benthic taxa as potential indicators of a deep-sea oil spill

The effect of the Deepwater Horizon oil spill on benthic macrofauna in the deep-sea Gulf of Mexico was measured in September–October 2010. Macrofauna community diversity and abundance were lowest closest to the wellhead and increased with distance from the wellhead up to 10 km. The macrofauna loss was primarily in surface sediments, which could be due to the deposition of oil and other toxic chemicals. Crustacean taxa appeared to be sensitive to the deep-sea blowout. Polychaete taxa varied in their sensitivity, but Dorvilleidae which is often associated with organic enrichment, was responsible for the largest amount of dissimilarity between stations close and far from the wellhead. Several other taxa were classified as sensitive or tolerant to the deep-sea blowout by comparing their distributions among impacted and non-impacted zones. The macrobenthic communities in the deep Gulf of Mexico exhibit a toxic response to the blowout on the Deepwater Horizon well, and this is correlated with barium and petroleum hydrocarbons.     

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.     

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.     

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.     

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.     

Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California

Crude oils can be major contaminants of the marine ecosystem and microorganisms play a significant role in the degradation of its main constituents. To increase our understanding of the microbial hydrocarbon degradation process in the marine ecosystem, we collected crude oil from an active seep area located in the Santa Barbara Channel (SBC) and generated a total of about 52 Gb of raw metagenomic sequence data. The assembled data comprised ~500 Mb, representing ~1.1 million genes derived primarily from chemolithoautotrophic bacteria. Members of Oceanospirillales, a bacterial order belonging to the Deltaproteobacteria, recruited less than 2% of the assembled genes within the SBC metagenome. In contrast, the microbial community associated with the oil plume that developed in the aftermath of the Deepwater Horizon (DWH) blowout in 2010, was dominated by Oceanospirillales, which comprised more than 60% of the metagenomic data generated from the DWH oil plume. This suggests that Oceanospirillales might play a less significant role in the microbially mediated hydrocarbon conversion within the SBC seep oil compared to the DWH plume oil. We hypothesize that this difference results from the SBC oil seep being mostly anaerobic, while the DWH oil plume is aerobic. Within the Archaea, the phylum Euryarchaeota, recruited more than 95% of the assembled archaeal sequences from the SBC oil seep metagenome, with more than 50% of the sequences assigned to members of the orders Methanomicrobiales and Methanosarcinales. These orders contain organisms capable of anaerobic methanogenesis and methane oxidation (AOM) and we hypothesize that these orders – and their metabolic capabilities – may be fundamental to the ecology of the SBC oil seep.     

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.     

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.     

Detangling spaghetti: Tracking deep ocean currents in the Gulf of Mexico

Creation of physical models can help students learn science by enabling them to be more involved in the scientific process of discovery and to use multiple senses during investigations. This activity achieves these goals by having students model ocean currents in the Gulf of Mexico. In general, oceans play a key role in influencing weather patterns and climate. Water movement also affects fisheries through transport of various fish and invertebrate species as well as their predators and prey. Currents also impact the dispersion of pollutants, as in after an oil spill such as the catastrophe of the Deepwater Horizon oil rig in 2010. Currents exist deep in the ocean, and they do not always travel in the same direction as currents at the surface. This concept of the existence of ocean currents below the surface can be hard to explain, but we provide methodology for sharing this information in a way that is accessible to K–12 students, including the visually impaired. In addition to the NGSS standards and Ocean Literacy principles addressed, this activity has larger implications related to socioeconomics and international law.     

Intensity of the Microbiological Processes of the Methane Cycle in Different Types of Baltic Lakes

The intensity of the microbiological processes of methane formation (MF) and methane oxidation (MO) was determined in the sediments and water of different types of Baltic lakes. The emission of methane from the lake sediments and methane distribution in the water column of the lakes were studied as functions of the lake productivity and hydrologic conditions. During summers, the intensity of MF in the lake sediments and waters varied from 0.001 to 106 ml CH₄/(dm³ day) and from 0 to 3.2 ml CH₄/(l day), respectively, and the intensity of MO in the sediments and water varied from 0 to 11.2 ml CH₄/(dm³ day) and from 0 to 1.1 ml CH₄/(l day), respectively. The total methane production (MP) in the lakes varied from 15 to 5000 ml CH₄/(m² day). In anoxic waters, the MP comprised 9–18% of the total PM in the lakes. The consumption of organic carbon for methanogenesis varied from 0.03 to 9.7 g/(m² day). The role of the methane cycle in the degradation of organic matter in the lakes increased with their productivity.     

海洋溢油生态环境损害因果关系判定方法与模型研究

海洋溢油对生态环境造成污染损害,构成了对海洋环境安全和人体健康的重大威胁,科学地评估溢油污染损害可以发挥为损害修复和赔偿仲裁提供依据的重要作用,为成就这一目标,亟待加强有关溢油污染损害的因果关系及其判定方法与准则的相关理论、技术方法和业务化应用的研究。为此,在对不同原油的各馏分占比和分类组分及含量进行统计分析的基础上,构建了溢油成分统计均值指标体系,基于WHO/IARC化学物质引起人类癌症危险性评价,揭示了不同种类溢油所造成的海洋生态环境损害类型和程度有所不同的因果关系,进而研究提出了基于溢油环境归宿和POPs毒性理论的损害机理分析方法,构建了包括事故发生、成分含量、分类后果、时空分布4类判定准则及其相应指标体系的海洋生态环境损害因果关系判定方法,提出了包括因果关系判定模型、多类型辅助评估模型、调查试验诊断评估方法及业务化流程、以及损害基线与程度判定准则及指标体系的海洋生态损害评估模型体系总体架构,设计阐述了多类型辅助评估模型、损害基线与程度判定准则及指标体系的构建方案。针对辅助评估模型中具有代表性的易受损因子--海水水质指标的损害因果关系判定和损害程度量化问题,构建了基于溢油风化缩比仿真试验的溢油风化水质影响评估模型,采用溢油事故引起海水水质超过不同等级水质标准的超标面积,以及事故发生前后实测的相关海域海水水质超过不同等级水质标准的超标面积发生变化以及出现峰值的状况,作为判定损害因果关系存在和评估损害程度的量化指标,通过开展"塔兹曼海"、大连"7.16"等发生于渤海和黄海的溢油及危化品事故案例调查,实施了判定方法与模型的应用研究,对模型参数进行了率定,模型和实测结果均显示,在具有连通性的渤海和黄海海域,不同时段超过不同等级海水水质标准的超标面积增量与该海域实际发生溢油事故的时间存在显著的关联响应关系。综合判断,溢油污染损害与污染事故发生的时间和位置、所处海域的连通性及扩散条件、入海溢油的总量及环境污染持久性呈密切相关的因果关系。     

Populations of heavy fuel oil-degrading marine microbial community in presence of oil sorbent materials

Aims:  To investigate the feasibility of applying sorbent material X-Oil^® in marine oil spill mitigation and to survey the interactions of oil, bacteria and sorbent.
Methods and Results:  In a series of microcosms, 25 different treatments including nutrient amendment, bioaugmentation with Alcanivorax borkumensis and application of sorbent were tested. Microbial community dynamics were analysed by DNA fingerprinting methods, RISA and DGGE. Results of this study showed that the microbial communities in microcosms with highly active biodegradation were strongly selected in favour of A. borkumensis . Oxygen consumption measurements in microcosms and gas chromatography of oil samples indicated the fast and intense depletion of linear alkanes as well as high oxygen consumption within 1 week followed by consequent slower degradation of branched and polyaromatic hydrocarbons.
Conclusion:  Under given conditions, A. borkumensis was an essential organism for biodegradation, dominating the biofilm microbial community formation and was the reason of emulsification.
Significance and Impact of the Study:  This study strongly emphasizes the pivotal importance of A. borkumensis as an essential organism in the initial steps of marine hydrocarbon degradation. Interaction with the sorbent material X-Oil^® proved to be neutral to beneficial for biodegradation and also promoted the growth of yet unknown micro-organisms.