Degradation of Deepwater Horizon oil buried in a Florida beach influenced by tidal pumping

Exploring the bacterial genetic diversity and community structure of crude oil contaminated soils using microbiomics

The impact of environmental pollution in air and water is reflected mainly in the soil ecosystem as it impairs soil functions. Also, since the soil is the habitat for billions of organisms, the biodiversity is in turn altered. Microbes are precise sensors of ecological contamination, and bacteria have a key and important function in terms of bioremediation of the contaminated soil. Hence in the current work, we aimed at assessing the unidentified bacterial population through Illumina MiSeq sequencing technology and their community structural changes in different levels of petroleum-contaminated soil and sludge samples (aged, sludge, and leakage soil) to identify unique bacteria for their potential application in remediation. The studies showed that major bacterial consortiums namely, Proteobacteria (57%), Alphaproteobacteria (31%), and Moraxellaceae (23%) were present in aged soil, whereas Proteobacteria (52%), Alphaproteobacteria (33%), and Rhodobacteraceae (28%) were dominantly found in sludge soil. In leakage soil, Proteobacteria (59%), Alphaproteobacteria (33%), and Rhodobacteraceae (29%) were abundantly present. The Venn diagrams are used to analyze the distribution of abundances in individual operational taxonomic units (OTUs) within three soil samples. After data filtering, they were grouped into OTU clusters and 329 OTUs were identified from the three soil samples. Among the 329, 160 OTUs were common in the three soil samples. The bacterial diversity is estimated using alpha diversity indices and Shanon index and was found to be 4.490, 4.073 and 4.631 in aged soil, sludge soil and leakage soil, respectively and similarly richness was found to be 618, 417 and 418. The heat map was generated by QIIME software and from the top 50 enriched genera few microbes such as Pseudomonas, Bacillus, Mycobacterium, Sphingomonas and Paracoccus, were shown across all the samples. In addition, we also analyzed various physicochemical properties of soil including pH, temperature, salinity, electrical conductivity, alkalinity, total carbon, total organic matter, nitrogen, phosphorus and potassium to calculate the soil quality index (SQI). The SQI of aged, sludge and leakage soil samples were 0.73, 0.64, and 0.89, respectively. These findings show the presence of unexplored bacterial species which could be applied for hydrocarbon remediation and further they can be exploited for the same.

Temporal variability of microbial response to crude oil exposure in the northern Gulf of Mexico

Oil spills are common occurrences in the United States and can result in extensive ecological damage. The 2010 Deepwater Horizon oil spill in the Gulf of Mexico was the largest accidental spill recorded. Many studies were performed in deep water habitats to understand the microbial response to the released crude oil. However, much less is known about how planktonic coastal communities respond to oil spills and whether that response might vary over the course of the year. Understanding this temporal variability would lend additional insight into how coastal Florida habitats may have responded to the Deepwater Horizon oil spill. To assess this, the temporal response of planktonic coastal microbial communities to acute crude oil exposure was examined from September 2015 to September 2016 using seawater samples collected from Pensacola Beach, Florida, at 2-week intervals. A standard oil exposure protocol was performed using water accommodated fractions made from MC252 surrogate oil under photo-oxidizing conditions. Dose response curves for bacterial production and primary production were constructed from 3H-leucine incorporation and 14C-bicarbonate fixation, respectively. To assess drivers of temporal patterns in inhibition, a suite of biological and environmental parameters was measured including bacterial counts, chlorophyll a, temperature, salinity, and nutrients. Additionally, 16S rRNA sequencing was performed on unamended seawater to determine if temporal variation in the in situ bacterial community contributed to differences in inhibition. We observed that there is temporal variation in the inhibition of primary and bacterial production due to acute crude oil exposure. We also identified significant relationships of inhibition with environmental and biological parameters that quantitatively demonstrated that exposure to water-soluble crude oil constituents was most detrimental to planktonic microbial communities when temperature was high, when there were low inputs of total Kjeldahl nitrogen, and when there was low bacterial diversity or low phytoplankton biomass.

Beach sand oil spills select for generalist microbial populations

The specialization-disturbance hypothesis predicts that, in the event of a disturbance, generalists are favored, while specialists are selected against. This hypothesis has not been rigorously tested in microbial systems and it remains unclear to what extent it could explain microbial community succession patterns following perturbations. Previous field observations of Pensacola Beach sands that were impacted by the Deepwater Horizon (DWH) oil spill provided evidence in support of the specialization-disturbance hypothesis. However, ecological drift as well as uncounted environmental fluctuations (e.g., storms) could not be ruled out as confounding factors driving these field results. In this study, the specialization-disturbance hypothesis was tested on beach sands, disturbed by DWH crude oil, ex situ in closed laboratory advective-flow chambers that mimic in situ conditions in saturated beach sediments. The chambers were inoculated with weathered DWH oil and unamended chambers served as controls. The time series of shotgun metagenomic and 16S rRNA gene amplicon sequence data from a two-month long incubation showed that functional diversity significantly increased while taxonomic diversity significantly declined, indicating a decrease in specialist taxa. Thus, results from this laboratory study corroborate field observations, providing verification that the specialization-disturbance hypothesis can explain microbial succession patterns in crude oil impacted beach sands.

Hypersaline Pore Water in Gulf of Mexico Beaches Prevented Efficient Biodegradation of Deepwater Horizon Beached Oil

The 2010 Deepwater Horizon (DWH) blowout released 3.19 million barrels (435 000 tons) of crude oil into the Gulf of Mexico. Driven by currents and wind, an estimated 22 000 tons of spilled oil were deposited onto the northeastern Gulf shorelines, adversely impacting the ecosystems and economies of the Gulf coast regions. In this work we present field work conducted at the Gulf beaches in three U.S. States during 2010-2011: Louisiana, Alabama, and Florida, to explore endogenous mechanisms that control persistence and biodegradation of the MC252-oil deposited within beach sediments as deep as 50 cm. The work involved over 1500 measurements incorporating oil chemistry, hydrocarbon-degrading microbial populations, nutrient and DO concentrations, and intrinsic beach properties. We found that intrinsic beach capillarity along with groundwater depth provides primary controls on aeration and infiltration of near-surface sediments, thereby modulating moisture and redox conditions within the oil-contaminated zone. In addition, atmosphere-ocean-groundwater interactions created hypersaline sediment environments near the beach surface at all the studied sites. The fact that the oil-contaminated sediments retained near or above 20% moisture content and were also eutrophic and aerobic suggests that the limiting factor for oil biodegradation is the hypersaline environment due to evaporation, a fact not reported in prior studies. These results highlight the importance of beach porewater hydrodynamics in generating unique hypersaline sediment environments that inhibited oil decomposition along the Gulf shorelines following DWH.

Integrated Omics Elucidate the Mechanisms Driving the Rapid Biodegradation of Deepwater Horizon Oil in Intertidal Sediments Undergoing Oxic-Anoxic Cycles

Crude oil buried in intertidal sands may be exposed to alternating oxic and anoxic conditions but the effect of this tidally induced biogeochemical oscillation remains poorly understood, limiting the effectiveness of remediation and managing efforts after oil spills. Here, we used a combination of metatranscriptomics and genome-resolved metagenomics to study microbial activities in oil-contaminated sediments during oxic-anoxic cycles in laboratory chambers that closely emulated in situ conditions. Approximately 5-fold higher reductions in the total petroleum hydrocarbons were observed in the oxic as compared to the anoxic phases with a relatively constant ratio between aerobic and anaerobic oil decomposition rates even after prolonged anoxic conditions. Metatranscriptomics analysis indicated that the oxic phases promoted oil biodegradation in subsequent anoxic phases by microbially mediated reoxidation of alternative electron acceptors like sulfide and by providing degradation-limiting nitrogen through biological nitrogen fixation. Most population genomes reconstructed from the mesocosm samples represented uncultured taxa and were present typically as members of the rare biosphere in metagenomic data from uncontaminated field samples, implying that the intertidal communities are adapted to changes in redox conditions. Collectively, these results have important implications for enhancing oil spill remediation efforts in beach sands and coastal sediments and underscore the role of uncultured taxa in such efforts.

Bacterial Community Legacy Effects Following the Agia Zoni II Oil-Spill, Greece

In September 2017 the Agia Zoni II sank in the Saronic Gulf, Greece, releasing approximately 500 tonnes of heavy fuel oil, contaminating the Salamina and Athens coastlines. Effects of the spill, and remediation efforts, on sediment microbial communities were quantified over the following 7 months. Five days post-spill, the concentration of measured hydrocarbons within surface sediments of contaminated beaches was 1,093-3,773 μg g-1 dry sediment (91% alkanes and 9% polycyclic aromatic hydrocarbons), but measured hydrocarbons decreased rapidly after extensive clean-up operations. Bacterial genera known to contain oil-degrading species increased in abundance, including Alcanivorax, Cycloclasticus, Oleibacter, Oleiphilus, and Thalassolituus, and the species Marinobacter hydrocarbonoclasticus from approximately 0.02 to >32% (collectively) of the total bacterial community. Abundance of genera with known hydrocarbon-degraders then decreased 1 month after clean-up. However, a legacy effect was observed within the bacterial community, whereby Alcanivorax and Cycloclasticus persisted for several months after the oil spill in formerly contaminated sites. This study is the first to evaluate the effect of the Agia Zoni II oil-spill on microbial communities in an oligotrophic sea, where in situ oil-spill studies are rare. The results aid the advancement of post-spill monitoring models, which can predict the capability of environments to naturally attenuate oil.

Occurrence and weathering of petroleum hydrocarbons deposited on the shoreline of the North Saskatchewan River from the 2016 Husky oil spill

Following the 16TAN Husky oil spill along the North Saskatchewan River (NSR), the occurrence and natural attenuation of the petroleum hydrocarbons were assessed by analyzing the littoral zone sediments/oil debris collected from July 2016 to October 2017. Husky oil-free, mixed sediment-Husky oil, and Husky oil debris samples were identified for all the collected samples. Shoreline sediments were contaminated by mixed biogenic, pyrogenic and petrogenic inputs prior to the spill. Oil stranded on the shoreline of NSR was moved or buried due to the very dynamic conditions of the shoreline, or cleaned through a series of cleanup activities after the spill. Most normal alkanes were naturally weathered, whereas most of the branched alkanes and all of the saturated petroleum biomarkers remained. Some lighter molecular weight (e.g., 2 to 3-ring) polycyclic aromatic hydrocarbons (PAHs) were lost rapidly after the spill, whereas sulfur containing components, e.g., dibenzothiophenes and benzonaphthothiiophenes, and those having a heavier molecular weight did not change markedly even 15 months post-spill. Similarly, some light hydrocarbons (e.g., <C₁₀) were lost over the first kilometers from the point of entry (POE), while heavier hydrocarbons did not show any major differences away from the POE. Very large inter-site and inter-survey discrepancies were found for samples. Evaporation into the air and dissolution into water, combined with biodegradation, were together or independently the main contributors to the loss of the light molecular hydrocarbons.

Succession of microbial populations and nitrogen-fixation associated with the biodegradation of sediment-oil-agglomerates buried in a Florida sandy beach

The Deepwater Horizon (DWH) oil spill contaminated coastlines from Louisiana to Florida, burying oil up to 70 cm depth in sandy beaches, posing a potential threat to environmental and human health. The dry and nutrient-poor beach sand presents a taxing environment for microbial growth, raising the question how the biodegradation of the buried oil would proceed. Here we report the results of an in-situ experiment that (i) characterized the dominant microbial communities contained in sediment oil agglomerates (SOAs) of DWH oil buried in a North Florida sandy beach, (ii) elucidated the long-term succession of the microbial populations that developed in the SOAs, and (iii) revealed the coupling of SOA degradation to nitrogen fixation. Orders of magnitude higher bacterial abundances in SOAs compared to surrounding sands distinguished SOAs as hotspots of microbial growth. Blooms of bacterial taxa with a demonstrated potential for hydrocarbon degradation (Gammaproteobacteria, Alphaproteobacteria, Actinobacteria) developed in the SOAs, initiating a succession of microbial populations that mirrored the evolution of the petroleum hydrocarbons. Growth of nitrogen-fixing prokaryotes or diazotrophs (Rhizobiales and Frankiales), reflected in increased abundances of nitrogenase genes (nifH), catalyzed biodegradation of the nitrogen-poor petroleum hydrocarbons, emphasizing nitrogen fixation as a central mechanism facilitating the recovery of sandy beaches after oil contamination.

Oil Spills and Human Health: Contributions of the Gulf of Mexico Research Initiative

The Gulf of Mexico Research Initiative (GoMRI) was established in 2010 with $500 million in funding provided by British Petroleum over a 10-year period to support research on the impacts of the Deepwater Horizon oil spill and recovery. Contributions of the GoMRI program to date focused on human health are presented in more than 32 peer-reviewed papers published between 2011 and May 2019. Primary findings from review of these papers are (i) the large quantity of dispersants used in the oil cleanup have been associated with human health concerns, including through obesogenicity, toxicity, and illnesses from aerosolization of the agents; (ii) oil contamination has been associated with potential for increases in harmful algal blooms and numbers of pathogenic Vibrio bacteria in oil-impacted waters; and (iii) members of Gulf communities who are heavily reliant upon natural resources for their livelihoods were found to be vulnerable to high levels of life disruptions and institutional distrust. Positive correlations include a finding that a high level of community attachment was beneficial for recovery. Actions taken to improve disaster response and reduce stress-associated health effects could lessen negative impacts of similar disasters in the future. Furthermore, GoMRI has supported annual conferences beginning in 2013 at which informative human health-related presentations have been made. Based on this review, it is recommended that the Oil Pollution Act of 1990 be updated to include enhanced funding for oil spill impacts to human health.

Decomposition of sediment-oil-agglomerates in a Gulf of Mexico sandy beach

Sediment-oil-agglomerates (SOA) are one of the most common forms of contamination impacting shores after a major oil spill; and following the Deepwater Horizon (DWH) accident, large numbers of SOAs were buried in the sandy beaches of the northeastern Gulf of Mexico. SOAs provide a source of toxic oil compounds, and although SOAs can persist for many years, their long-term fate was unknown. Here we report the results of a 3-year in-situ experiment that quantified the degradation of standardized SOAs buried in the upper 50 cm of a North Florida sandy beach. Time series of hydrocarbon mass, carbon content, n-alkanes, PAHs, and fluorescence indicate that the decomposition of golf-ball-size DWH-SOAs embedded in beach sand takes at least 32 years, while SOA degradation without sediment contact would require more than 100 years. SOA alkane and PAH decay rates within the sediment were similar to those at the beach surface. The porous structure of the SOAs kept their cores oxygen-replete. The results reveal that SOAs buried deep in beach sands can be decomposed through relatively rapid aerobic microbial oil degradation in the tidally ventilated permeable beach sand, emphasizing the role of the sandy beach as an aerobic biocatalytical reactor at the land-ocean interface.

"Candidatus Macondimonas diazotrophica", a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments

Modeling crude-oil biodegradation in sediments remains a challenge due in part to the lack of appropriate model organisms. Here we report the metagenome-guided isolation of a novel organism that represents a phylogenetically narrow (>97% 16S rRNA gene identity) group of previously uncharacterized, crude-oil degraders. Analysis of available sequence data showed that these organisms are highly abundant in oiled sediments of coastal marine ecosystems across the world, often comprising ~30% of the total community, and virtually absent in pristine sediments or seawater. The isolate genome encodes functional nitrogen fixation and hydrocarbon degradation genes together with putative genes for biosurfactant production that apparently facilitate growth in the typically nitrogen-limited, oiled environment. Comparisons to available genomes revealed that this isolate represents a novel genus within the Gammaproteobacteria, for which we propose the provisional name "Candidatus Macondimonas diazotrophica" gen. nov., sp. nov. "Ca. M. diazotrophica" appears to play a key ecological role in the response to oil spills around the globe and could be a promising model organism for studying ecophysiological responses to oil spills.

Anaerobic degradation of hexadecane and phenanthrene coupled to sulfate reduction by enriched consortia from northern Gulf of Mexico seafloor sediment

To advance understanding of the fate of hydrocarbons released from the Deepwater Horizon oil spill and deposited in marine sediments, this study characterized the microbial populations capable of anaerobic hydrocarbon degradation coupled with sulfate reduction in non-seep sediments of the northern Gulf of Mexico. Anaerobic, sediment-free enrichment cultures were obtained with either hexadecane or phenanthrene as sole carbon source and sulfate as a terminal electron acceptor. Phylogenetic analysis revealed that enriched microbial populations differed by hydrocarbon substrate, with abundant SSU rRNA gene amplicon sequences from hexadecane cultures showing high sequence identity (up to 98%) to Desulfatibacillum alkenivorans (family Desulfobacteraceae), while phenanthrene-enriched populations were most closely related to Desulfatiglans spp. (up to 95% sequence identity; family Desulfarculaceae). Assuming complete oxidation to CO₂, observed stoichiometric ratios closely resembled the theoretical ratios of 12.25:1 for hexadecane and 8.25:1 for phenanthrene degradation coupled to sulfate reduction. Phenanthrene carboxylic acid was detected in the phenanthrene-degrading enrichment cultures, providing evidence to indicate carboxylation as an activation mechanism for phenanthrene degradation. Metagenome-assembled genomes (MAGs) revealed that phenanthrene degradation is likely mediated by novel genera or families of sulfate-reducing bacteria along with their fermentative syntrophic partners, and candidate genes linked to the degradation of aromatic hydrocarbons were detected for future study.

Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline

The dinitrogenase reductase gene (nifH) is the most widely established molecular marker for the study of nitrogen-fixing prokaryotes in nature. A large number of PCR primer sets have been developed for nifH amplification, and the effective deployment of these approaches should be guided by a rapid, easy-to-use analysis protocol. Bioinformatic analysis of marker gene sequences also requires considerable expertise. In this study, we advance the state of the art for nifH analysis by evaluating nifH primer set performance, developing an improved amplicon sequencing workflow, and implementing a user-friendly bioinformatics pipeline. The developed amplicon sequencing workflow is a three-stage PCR-based approach that uses established technologies for incorporating sample-specific barcode sequences and sequencing adapters. Based on our primer evaluation, we recommend the Ando primer set be used with a modified annealing temperature of 58°C, as this approach captured the largest diversity of nifH templates, including paralog cluster IV/V sequences. To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences. In addition, we employed an empirical model to derive optimal operational taxonomic unit (OTU) cutoffs for the nifH gene at the species, genus, and family levels. A comprehensive workflow script named TaxADivA (TAXonomy Assignment and DIVersity Assessment) is provided to ease processing and analysis of nifH amplicons. Our approach is then validated through characterization of diazotroph communities across environmental gradients in beach sands impacted by the Deepwater Horizon oil spill in the Gulf of Mexico, in a peat moss-dominated wetland, and in various plant compartments of a sugarcane field.IMPORTANCE Nitrogen availability often limits ecosystem productivity, and nitrogen fixation, exclusive to prokaryotes, comprises a major source of nitrogen input that sustains food webs. The nifH gene, which codes for the iron protein of the nitrogenase enzyme, is the most widely established molecular marker for the study of nitrogen-fixing microorganisms (diazotrophs) in nature. In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering, and produces output in formats that may be used by programs that facilitate data exploration and analysis. Diazotroph diversity and community composition are linked to ecosystem functioning, and our results advance the phylogenetic characterization of diazotroph communities by providing empirically derived nifH similarity cutoffs for species, genus, and family levels. The utility of our pipeline is validated for diazotroph communities in a variety of ecosystems, including contaminated beach sands, peatland ecosystems, living plant tissues, and rhizosphere soil.