Project Overview

Summary:

     In January 2016, Dr. Markus Huettel at Florida State University was awarded an RFP-V grant of $1,098,974 to lead the GoMRI project entitled, “A Systems Approach to Improve Predictions of Biodegradation and Ecosystem Recovery in Coastal Marine Sediments Impacted by Oil Spill” consisted of 1 collaborative institution and approximately 14 research team members (including students).

     After coastal oil spills, petroleum hydrocarbons accumulate in submerged nearshore sediments and on beaches, poisoning these ecosystems and creating health risks for coastal organisms and humans. Erosion and deposition cycles lead to burial of weathered crude oil in submerged shelf beds, intertidal sediments, and dry beach sands. Prediction of the effects and fate of these buried petroleum hydrocarbons remains hampered by our limited understanding of the controls of the biodegradation and functioning of sedimentary microbial communities that break down petroleum hydrocarbons. Transport of oxygen and nutrients to the buried oil is expected to control the rates of hydrocarbon biodegradation. While the flow of air through dry beach sands can rapidly transport oxygen to buried oil, it cannot carry nutrients that are limiting the degradation of the oil. Transport via pore water flows in submerged sand beds is slower than the gas transport in dry sand, but water can transport dissolved nutrients to buried hydrocarbons. It is therefore hypothesized that microbial oil degradation in dry, temporally wet and water-saturated sediments differ. A quantitative understanding of the mechanisms controlling these differences is a central prerequisite for the modeling of oil decomposition in these coastal ecosystems. The main goals of this project therefore are to link microbial degradation of buried oil and associated transport processes, and to integrate these data in a model that allows predictions of pathways and rates of oil degradation, and thus, forecasting recovery pathways in future oil spills.

     This project contributes to GoMRI RFP-V research theme (2) and couples cutting-edge microbiological and geochemical approaches in the field with targeted laboratory experiments, genomic analyses and predictive mathematical modeling. The field research focused on the degradation of oil buried in beach sands and the inter- and subtidal environment. In the laboratory experiments, biodegradation rates of specific hydrocarbon compounds were linked to the metabolic potential of microbial groups using a combination of metagenomic and metatranscriptomic sequencing and culture-based physiological and genetic manipulations. A distinguishing aspect of this research was that it integrated taxonomic, genetic and functional data from complex, multivariate experiments into advanced dynamic models that represent responses of whole microbial communities and allow predictions of their activities under different levels of oxygen and nutrients. The broader impact of this research is related to the potential environmental and health risks associated with petroleum hydrocarbons still persisting in the coastal environment. The project produced tools (e.g., models and microbial indicators of oil degradation) for environmental managers and decision makers that can help planning responses to future oil spills.

Research Highlights

     As of December 31, 2019, this project’s research resulted in 7 peer-reviewed publications, 2 Book Chapters, and 25 scientific presentations and 21 datasets being submitted to the GoMRI Information and Data Cooperative (GRIIDC), which are/will be made available to the public. The project also engaged 1 Master’s level and 6 PhD level students over its award period. Significant outcomes of this project’s research according to GoMRI Research Theme are highlighted below.

            GoMRI Research Theme Two:

Chemical evolution and biological degradation of the petroleum

     Degradation of Deepwater Horizon oil buried in a Florida beach influenced by tidal pumping. The field research of this project conducted at Penscola Beach/Florida revealed deep burial of the stranded oil and relatively rapid degradation in the permeable beach sand. After Deepwater Horizon oil reached the Florida coast, oil was buried in Pensacola Beach (PB) sands to ~70 cm depth, resulting in Total Petroleum Hydrocarbon (TPH) concentrations up to ~2 kg per meter of beach. The study followed the decomposition of the buried oil and the factors influencing its degradation. The abundance of bacteria in oiled sand increased by 2 orders of magnitude within one week after oil burial, while diversity decreased by ~50%. Half-lives of aliphatic and aromatic hydrocarbons reached 25 and 22 days, respectively. Aerobic microbial oil decomposition, promoted by tidal pumping, and human cleaning activities effectively removed oil from the beach. After one year, concentrations of GC-amenable hydrocarbons at PB were similar to those in the uncontaminated reference beach at St. George Island/FL, and microbial populations that disappeared after the oil contamination had reestablished. Yet, oxihydrocarbons can be found at PB to the present day (Huettel et al., 2018).

     Decomposition of sediment-oil-agglomerates in a Gulf of Mexico sandy beach. To determine the rates at which larger sediment-oil-agglomerates (SOA) are degraded after burial in Florida beaches, a long-term in-situ experiment was initiated. SOAs 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. The 3-year in-situ experiment 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 revealed that the decomposition of golfball- 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 indicate 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 (Bociu et al., 2019).

     Succession of microbial populations linked to sediment oil agglomerate (SOA) degradation in Pensacola Beach sands impacted by the Deepwater Horizon oil spill. 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. This study of the microbial community associated with the SOAs buried in Pensacola Beach sands during the insitu experiment (i) characterized the dominant microbial communities contained in sediment oil agglomerates (SOAs), (ii) determined the long-term succession of the microbial populations that developed in the SOAs, and (iii) assessed 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. (Shin et al., 2019)

     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. This study achieved 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 the provisional name “Candidatus  Macondimonas diazotrophica”  gen. nov., sp. nov was proposed. “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 (Karthikeyan et al., 2019).

     Genome Repository of Oiled Systems (GROS): an interactive and searchable database that expands the catalogued diversity of oil-associated microbes. Our research supports that microbial communities ultimately control the fate of petroleum hydrocarbons (PHCs) that enter the natural environment, but the interactions of microbes with PHCs and the environment are highly complex and poorly understood. Genome-resolved metagenomics can help unravel these complex interactions. However, the lack of a comprehensive database that integrates existing genomic/metagenomic data from oil environments with physicochemical parameters known to regulate the fate of PHCs currently limits data analysis and interpretations. This study developed a comprehensive, searchable database that documents microbial populations in natural oil ecosystems and oil spills, along with available underlying physicochemical data, geocoded via geographic information system to reveal their geographic distribution patterns. Analysis of the ~2000 metagenome-assembled genomes (MAGs) available in the database revealed strong ecological niche specialization within habitats. Over 95% of the recovered MAGs represented novel taxa underscoring the limited representation of cultured organisms from oil-contaminated and oil reservoir ecosystems. The majority of MAGs linked to oil-contaminated ecosystems were detectable in non-oiled samples from the Gulf of Mexico but not in comparable samples from elsewhere, indicating that the Gulf is primed for oil biodegradation. The repository should facilitate future work toward a predictive understanding of the microbial taxa and their activities that control the fate of oil spills (Karthikeyan et al., 2020).

     Toward a Predictive Understanding of the Benthic Microbial Community Response to Oiling on the Northern Gulf of Mexico Coast. Through the field investigations, in-situ experiment, laboratory experiments and detailed analyses of the microbial communities associated with oil-contaminated sediment, this GoMRI RFP V project produced a comprehensive answer to the central question of this study addressing the fate of the Deepwater Horizon (DWH) oil that washed onto Florida beaches. Sedimentary microorganisms mediate central ecosystem services on the coast, such as carbon and nutrient cycling, and these services may be adversely impacted by oil perturbation. During the response to the DWH oil discharge in the Gulf of Mexico, the project put focued on characterizing the response of benthic microbial communities to oil deposition on shorelines of the Northern Gulf where oil came ashore. Oil perturbation elicited a pronounced microbial response in coastal ecosystems, altering the abundance, diversity, and community composition of sedimentary microorganisms. Next-generation gene sequencing and metagenomic approaches, which were not available during previous large oil spills, provided new insights into the microbial response after the DWH discharge. By directly linking oil degradation in the coastal sands to microbial community structure and oil-decomposition activities, this project established mechanistic and quantitative links between the benthic microbial community dynamics and petroleum hydrocarbon degradation in Florida beaches. These links can now be used in possible future oil spills for predicting the response of the sedimentary system to the hydrocarbon input and the duration of beach pollution. This information was integrated in a searchable global data base that now can be used to investigate responses of microbial communities to petroleum hydrocarbon contamination (Kostka et al., 2020).

References

Bociu, I., Shin, B., Wells, W. B., Kostka, J. E., Konstantinidis, K. T. & Huettel, M. (2019). Decomposition of sediment-oil-agglomerates in a Gulf of Mexico sandy beach. Scientific Reports 9, 10071.

Huettel, M., Overholt, W. A., Kostka, J. E., Hagan, C., Kaba, J., Wells, W. B. & Dudley, S. (2018). Degradation of Deepwater Horizon oil buried in a Florida beach influenced by tidal pumping. Marine Pollution Bulletin 126, 488-500.

Karthikeyan, S., Rodriguez-R, L. M., Heritier-Robbins, P., Hatt, J. K., Huettel, M., Kostka, J. E. & Konstantinidis, K. T. (2020). Genome repository of oil systems: An interactive and searchable database that expands the catalogued diversity of crude oil-associated microbes. Environmental Microbiology.

Karthikeyan, S., Rodriguez-R, L. M., Heritier-Robbins, P., Kim, M., Overholt, W. A., Gaby, J. C., Hatt, J. K., Spain, J. C., Rossello-Mora, R., Huettel, M., Kostka, J. E. & Konstantinidis, K. T. (2019). "Candidatus Macondimonas diazotrophica", a novel gammaproteobacterial genus dominating crude-oil-contaminated coastal sediments. Isme Journal 13, 2129-2134.

Kostka, J. E., Overholt, W. A., Rodriguez-R, L. M., Huettel, M. & Konstantinidis, K. (2020). Toward a Predictive Understanding of the Benthic Microbial Community Response to Oiling on the Northern Gulf of Mexico Coast. In: (eds), M. S. e. a. (ed.) Scenarios and Responses to Future Deep Oil Spills. . First Online 05 July 2019 Springer.

Shin, B., Bociu, I., Kolton, M., Huettel, M. & Kostka, J. E. (2019). Succession of microbial populations and nitrogen-fixation associated with the biodegradation of sediment-oil-agglomerates buried in a Florida sandy beach. Scientific Reports 9, 19401.

  Proposal Abstract - RFP-V PI Markus Huettel