Article

Succession of Hydrocarbon-Degrading Bacteria in the Aftermath of the Deepwater Horizon Oil Spill in the Gulf of Mexico

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Abstract

The Deepwater Horizon oil spill produced large subsurface plumes of dispersed oil and gas in the Gulf of Mexico that stimulated growth of psychrophilic, hydrocarbon degrading bacteria. We tracked succession of plume bacteria before, during and after the 83-day spill to determine the microbial response and biodegradation potential throughout the incident. Dominant bacteria shifted substantially over time and were dependent on relative quantities of different hydrocarbon fractions. Unmitigated flow from the wellhead early in the spill resulted in the highest proportions of n-alkanes and cycloalkanes at depth and corresponded with dominance by Oceanospirillaceae and Pseudomonas. Once partial capture of oil and gas began 43 days into the spill, petroleum hydrocarbons decreased, the fraction of aromatic hydrocarbons increased, and Colwellia, Cycloclasticus and Pseudoalteromonas increased in dominance. Enrichment of Methylomonas coincided with positive shifts in the δ13C values of methane in the plume and indicated significant methane oxidation occurred earlier than previously reported. Anomalous oxygen depressions persisted at plume depths for over six weeks after well shut-in and were likely caused by common marine heterotrophs associated with degradation of high-molecular-weight organic matter, including Methylophaga. Multiple hydrocarbon-degrading bacteria operated simultaneously throughout the spill, but their relative importance was controlled by changes in hydrocarbon supply.

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... However, the use of dispersants as a form of oil-spill remediation remains a source of contention. While several studies suggest that dispersants enhance the growth of hydrocarbon-degrading bacteria (HCB) [11][12][13][14] and increase biodegradation [15,16], other studies show that dispersants do not enhance biodegradation [17,18] or may even inhibit the growth of HCB [19,20]. Ultimately, the environmental impact and fate of an oil spill are among the main considerations of the Spill Impact Mitigation Assessment (SIMA, [21]) process during decision making for incident response. ...
... As with the alkanes, PAHs were biodegraded, but there were no significant differences between any treatments. HCB able to degrade n-alkanes are known to grow more rapidly than those degrading branched alkanes and PAHs [12,85], during which time, in this study, nutrients had been depleted. Had there been a constant supply of inorganic nutrients, as expected during oil dispersed within some marine environment, microcosms containing dispersed oil may have maintained their enhanced biodegradation for longer, which could possibly also translate into significantly enhanced PAH reduction. ...
... This is likely due to the fact Marinomonas and Pseudoalteromonas are known PAH degraders (Supplementary Table S2). Pseudoalteromonas, and genera such as Colwellia and Cycloclasticus (which grew in this study by days 3 and 7, respectively), proliferated in the aromatic hydrocarbon-rich oil plume after the Deepwater Horizon well-blowout [12]. By day 3, ASVs from the genus Oleispira maintained a high relative abundance in the Finasol OSR 52, Slickgone NS, Superdispersant 25, and trehalolipid treatments. ...
Article
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This study evaluated the effects of three commercial dispersants (Finasol OSR 52, Slickgone NS, Superdispersant 25) and three biosurfactants (rhamnolipid, trehalolipid, sophorolipid) in crude-oil seawater microcosms. We analysed the crucial early bacterial response (1 and 3 days). In contrast, most analyses miss this key period and instead focus on later time points after oil and dispersant addition. By focusing on the early stage, we show that dispersants and biosurfactants, which reduce the interfacial surface tension of oil and water, significantly increase the abundance of hydrocarbon-degrading bacteria, and the rate of hydrocarbon biodegradation, within 24 h. A succession of obligate hydrocarbonoclastic bacteria (OHCB), driven by metabolite niche partitioning, is demonstrated. Importantly, this succession has revealed how the OHCB Oleispira, hitherto considered to be a psychrophile, can dominate in the early stages of oil-spill response (1 and 3 days), outcompeting all other OHCB, at the relatively high temperature of 16 °C. Additionally, we demonstrate how some dispersants or biosurfactants can select for specific bacterial genera, especially the biosurfactant rhamnolipid, which appears to provide an advantageous compatibility with Pseudomonas, a genus in which some species synthesize rhamnolipid in the presence of hydrocarbons.
... The availability of nutrients in seawater varies in different seasons, such as when nutrients are scarce in the fall and winter but abundant in the spring and summer [53]. Moreover, nitrate and phosphate are typically enriched in deep water, but depleted in surface water, and may regulate the development of oil-degrading bacterial communities [54][55][56]. ...
... Recent studies have identified bacteria from more than 79 genera that have the capabilities to degrade petroleum hydrocarbons [159]. Several of these bacteria are Oceanospirillales, Rhodobacterales, Altererythrobacter, Neptuniibacter, Colwellia, Cycloclasticus, Pseudoalteromonas, Actinobacteria, Pseudomonas, Bacillus, Burkholderia, Enterobacter, Kocuria, Pandoraea, Corynebacterium [29,40,45,55,126]. Some bacteria including Alcanivorax, Marinobacter, Thallassolituus, Cycloclasticus, Oleispira, and a few other OHCB (obligate Figure 12. ...
... Recent studies have identified bacteria from more than 79 genera that have the capabilities to degrade petroleum hydrocarbons [159]. Several of these bacteria are Oceanospirillales, Rhodobacterales, Altererythrobacter, Neptuniibacter, Colwellia, Cycloclasticus, Pseudoalteromonas, Actinobacteria, Pseudomonas, Bacillus, Burkholderia, Enterobacter, Kocuria, Pandoraea, Corynebacterium [29,40,45,55,126]. Some bacteria including Alcanivorax, Marinobacter, Thallassolituus, Cycloclasticus, Oleispira, and a few other OHCB (obligate hydrocarbonoclastic bacteria), showed a low abundance or undetectable status before pollution but were dominant after petroleum oil contamina-tion [106]. ...
Article
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Over the past century, the demand for petroleum products has increased rapidly, leading to higher oil extraction, processing and transportation, which result in numerous oil spills in coastal-marine environments. As the spilled oil can negatively affect the coastal-marine ecosystems, its transport and fates captured a significant interest of the scientific community and regulatory agencies. Typically, the environment has natural mechanisms (e.g., photooxidation, biodegradation, evaporation) to weather/degrade and remove the spilled oil from the environment. Among various oil weathering mechanisms, biodegradation by naturally occurring bacterial populations removes a majority of spilled oil, thus the focus on bioremediation has increased significantly. Helping in the marginal recognition of this promising technique for oil-spill degradation, this paper reviews recently published articles that will help broaden the understanding of the factors affecting biodegradation of spilled oil in coastal-marine environments. The goal of this review is to examine the effects of various environmental variables that contribute to oil degradation in the coastal-marine environments, as well as the factors that influence these processes. Physico-chemical parameters such as temperature, oxygen level, pressure, shoreline energy, salinity, and pH are taken into account. In general, increase in temperature, exposure to sunlight (photooxidation), dissolved oxygen (DO), nutrients (nitrogen, phosphorous and potassium), shoreline energy (physical advection—waves) and diverse hydrocarbon-degrading microorganisms consortium were found to increase spilled oil degradation in marine environments. In contrast, higher initial oil concentration and seawater pressure can lower oil degradation rates. There is limited information on the influences of seawater pH and salinity on oil degradation, thus warranting additional research. This comprehensive review can be used as a guide for bioremediation modeling and mitigating future oil spill pollution in the marine environment by utilizing the bacteria adapted to certain conditions.
... An evaluation of the hydrocarbon concentrations along the oil spill timeline (from 28 May to Aug 24, 2010) revealed a sharp decrease in aromatic compounds (from 0.574 mg L − 1 to 0 mg L − 1 ) during this period (Table 1). In the beginning, in the oil plume, Colwellia, Cycloclasticus, Methylobacter, Methylococcus, Oceanospirillales, and Pseudomonas were reported as the most abundant groups in the bacterial community (Dubinsky et al., 2013;Hazen et al., 2010;Mason et al., 2012;Redmond and Valentine, 2012;Rivers et al., 2013;Valentine et al., 2010). In the following period, when the partial capture of gas and oil started (reflecting lower petroleum hydrocarbon concentrations and higher aromatic hydrocarbon concentrations), Colwellia, Cycloclasticus, Pseudoalteromonas, and Thalassomonas were the dominant members (Dubinsky et al., 2013). ...
... In the beginning, in the oil plume, Colwellia, Cycloclasticus, Methylobacter, Methylococcus, Oceanospirillales, and Pseudomonas were reported as the most abundant groups in the bacterial community (Dubinsky et al., 2013;Hazen et al., 2010;Mason et al., 2012;Redmond and Valentine, 2012;Rivers et al., 2013;Valentine et al., 2010). In the following period, when the partial capture of gas and oil started (reflecting lower petroleum hydrocarbon concentrations and higher aromatic hydrocarbon concentrations), Colwellia, Cycloclasticus, Pseudoalteromonas, and Thalassomonas were the dominant members (Dubinsky et al., 2013). Afterward, in the blockade, an assessment of the plume revealed the presence of Alteromonadaceae, Rhodobacteraceae, and Flavobacteria (Tenacibaculum and Polaribacter) (Dubinsky et al., 2013). ...
... In the following period, when the partial capture of gas and oil started (reflecting lower petroleum hydrocarbon concentrations and higher aromatic hydrocarbon concentrations), Colwellia, Cycloclasticus, Pseudoalteromonas, and Thalassomonas were the dominant members (Dubinsky et al., 2013). Afterward, in the blockade, an assessment of the plume revealed the presence of Alteromonadaceae, Rhodobacteraceae, and Flavobacteria (Tenacibaculum and Polaribacter) (Dubinsky et al., 2013). According to Liu and Liu (2013), phylogenetic analysis indicates that one year after the oil spill, Stappia, Erythrobacter, Rhodovulum, and Thalassospira (Alphaproteobacteria) were the predominant members in the oil mousses. ...
Article
Over recent decades, hydrocarbon concentrations have been augmented in soil and water, mainly derived from accidents or operations that input crude oil and petroleum into the environment. Different techniques for remediation have been proposed and used to mitigate oil contamination. Among the available environmental recovery approaches, bioremediation stands out since these hydrocarbon compounds can be used as growth substrates for microorganisms. In turn, microorganisms can play an important role with significant contributions to the stabilization of impacted areas. In this review, we present the current knowledge about responses from natural microbial communities (using DNA barcoding, multiomics, and functional gene markers) and bioremediation experiments (microcosm and mesocosm) conducted in the presence of petroleum and chemical dispersants in different samples, including soil, sediment, and water. Additionally, we present metabolic mechanisms for aerobic/anaerobic hydrocarbon degradation and alternative pathways, as well as a summary of studies showing functional genes and other mechanisms involved in petroleum biodegradation processes.
... The availability of nutrients in seawater varies in different seasons, such as when nutrients are scarce in the fall and winter but abundant in the spring and summer [53]. Moreover, nitrate and phosphate are typically enriched in deep water, but depleted in surface water, and may regulate the development of oil-degrading bacterial communities [54][55][56]. ...
... Recent studies have identified bacteria from more than 79 genera that have the capabilities to degrade petroleum hydrocarbons [159]. Several of these bacteria are Oceanospirillales, Rhodobacterales, Altererythrobacter, Neptuniibacter, Colwellia, Cycloclasticus, Pseudoalteromonas, Actinobacteria, Pseudomonas, Bacillus, Burkholderia, Enterobacter, Kocuria, Pandoraea, Corynebacterium [29,40,45,55,126]. Some bacteria including Alcanivorax, Marinobacter, Thallassolituus, Cycloclasticus, Oleispira, and a few other OHCB (obligate Figure 12. ...
... Recent studies have identified bacteria from more than 79 genera that have the capabilities to degrade petroleum hydrocarbons [159]. Several of these bacteria are Oceanospirillales, Rhodobacterales, Altererythrobacter, Neptuniibacter, Colwellia, Cycloclasticus, Pseudoalteromonas, Actinobacteria, Pseudomonas, Bacillus, Burkholderia, Enterobacter, Kocuria, Pandoraea, Corynebacterium [29,40,45,55,126]. Some bacteria including Alcanivorax, Marinobacter, Thallassolituus, Cycloclasticus, Oleispira, and a few other OHCB (obligate hydrocarbonoclastic bacteria), showed a low abundance or undetectable status before pollution but were dominant after petroleum oil contamina-tion [106]. ...
Article
Full-text available
Over the past century, the demand for petroleum products has increased rapidly, leading to higher oil extraction, processing and transportation, which result in numerous oil spills in coastal-marine environments. As the spilled oil can negatively affect the coastal-marine ecosystems, its transport and fates captured a significant interest of the scientific community and regulatory agencies. Typically, the environment has natural mechanisms (e.g., photooxidation, biodegradation, evaporation) to weather/degrade and remove the spilled oil from the environment. Among various oil weathering mechanisms, biodegradation by naturally occurring bacterial populations removes a majority of spilled oil, thus the focus on bioremediation has increased significantly. Helping in the marginal recognition of this promising technique for oil-spill degradation, this paper reviews recently published articles that will help broaden the understanding of the factors affecting biodegradation of spilled oil in coastal-marine environments. The goal of this review is to examine the effects of various environmental variables that contribute to oil degradation in the coastal-marine environments, as well as the factors that influence these processes. Physico-chemical parameters such as temperature, oxygen level, pressure, shoreline energy, salinity, and pH are taken into account. In general, increase in temperature, exposure to sunlight (photooxidation), dissolved oxygen (DO), nutrients (nitrogen, phosphorous and potassium), shoreline energy (physical advection—waves) and diverse hydrocarbon-degrading microorganisms consortium were found to increase spilled oil degradation in marine environments. In contrast, higher initial oil concentration and seawater pressure can lower oil degradation rates. There is limited information on the influences of seawater pH and salinity on oil degradation, thus warranting additional research. This comprehensive review can be used as a guide for bioremediation modeling and mitigating future oil spill pollution in the marine environment by utilizing the bacteria adapted to certain conditions.
... Community shifts have been observed across a variety of oil types, from heavier crudes to lighter distillates [13][14][15]. Chronopoulou et al. [14] found that the dominant bacteria, SAR11 (Pelagibacteracea), was replaced by members of the genus Pseudoalteromonas, which dominated plume samples following the Deepwater Horizon oil spill [16]. Many bacteria, such as Pseudomonas and Colwellia, have been found to degrade BTEX in marine environments and noted as oil-degrading specialists [17,18]. ...
... Several of these include species well known for oil degradation, while others may be opportunistic and take advantage of increased organic matter as phytoplankton abundances decrease. Colwellia has been observed to increase after oil spills, such as after Deepwater Horizon [15,16], and in microcosm experiments using Arabian Light oil [45]. In addition, Sulfitobacter has been associated with early responses in oil spills [46]. ...
Article
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Diesel is frequently encountered in coastal ecosystems due to land runoff from road surfaces. The current study investigates how partially weathered diesel at environmentally relevant concentrations, as may be seen during a runoff event, affect coastal microbial communities. A mesocosm experiment using seawater from the Bedford Basin, Nova Scotia, was followed for 72 h after the addition of partially weathered diesel. Sequencing data suggests partially weathered diesel acts quickly to alter the prokaryotic community, as both opportunistic (Vibrio and Lentibacter) and oil-degrading (Colwellia, Sulfitobacter, and Pseudoalteromonas) bacteria proliferated after 24 h in comparison to the control. In addition, total prokaryotes seemed to recover in abundance after 24 h, where eukaryotes only ceased to decrease slightly at 72 h, likely because of an inability to adapt to the oil-laden conditions, unlike the prokaryotes. Considering there were no highly volatile components (benzene, toluene, ethylbenzene, and xylene) present in the diesel when the communities were exposed, the results indicate that even a relatively small concentration of diesel runoff can cause a drastic change to the microbial community under low energy conditions. Higher energy conditions due to wave action may mitigate the response of the microbial communities by dilution and additional weathering of the diesel.
... Note ordinate axis is displayed in relative abundance known for their quorum sensing ability and it is possible that their metabolic agility [46] allowed them to outcompete Colwellia in the SWD treatment. The observed bloom of the Rhodobacteracaea, mainly Sedimentitalea, Pseudophaeobacter and to a lesser extent Sulfitobacter, may have contributed to oil degradation as members of these genera have hydrocarbon degrading capabilities [39,45,47]. ...
... Cycloclasticus also appeared in BEWAF treatment towards the end of the incubation. Cycloclasticus was not observed in the Finasol-amended treatments, which was surprising since previous studies showed Cycloclasticus domination in the microbial communities in CEWAF amendments of northeast Atlantic seawater [8,38] and in natural deepwater oil plumes during the early phase of the DWH spill [45,47]. However, all of these studies used different types of a synthetic dispersant. ...
Article
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Background Biosurfactants are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 16S rRNA amplicon sequencing and simulation-based approaches, this study investigated the microbial community dynamics, ecological drivers, functional diversity and robustness, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52. Results Psychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment, whereas Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment. Key aromatic hydrocarbon-degrading bacteria, like Cycloclasticus, was not observed in the Finasol treatment but it was abundant in the oil-only and rhamnolipid-amended treatments. Overall, Finasol had a significant negative impact on the community diversity, weakened the taxa-functional robustness of the community, and caused a stronger environmental filtering, more so than oil-only and rhamnolipid-amended oil treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment. Conclusion Overall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants and synthetic dispersant Finasol affect the natural marine microbial community in the FSC, supporting their potential application in oil spills. 43fSDwbdHYX3Ei4X1BHK1YVideo abstract
... Vibrio are known for their quorum sensing ability and it is possible that their metabolic agility [44] allowed them to outcompete Colwellia in the SWD treatment. The observed bloom of the Rhodobacteracaea, mainly Sedimentitalea, Pseudophaeobacter and to a lesser extent Sul tobacter, may have contributed to oil degradation as members of these genera have hydrocarbon degrading capabilities [37,43,45]. ...
... Cycloclasticus also appeared in BEWAF treatment towards the end of the incubation. Cycloclasticus was not observed in the Finasol-amended treatments, which was surprising since previous studies showed Cycloclasticus domination in the microbial communities in CEWAF amendments of northeast Atlantic seawater [8,36] and in natural deepwater oil plumes during the early phase of the DWH spill [43,45]. However, all of these studies used different types of a synthetic dispersant. ...
Preprint
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Background: Biosurfactants, however, are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 16S rRNA amplicon sequencing and simulation-based approaches, this study investigated the microbial community dynamics, ecological drivers, functional diversity and robustness, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52. Results: Psychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment, whereas Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment. The key aromatic hydrocarbon-degrading bacteria like Cycloclasticus was not observed in the Finasol treatment but it was abundant in the oil-only and rhamnolipid-amended treatments. Overall, Finasol had a significant negative impact on the community diversity, weakened the taxa-functional robustness of the community, and caused a stronger environmental filtering, more so than oil-only and rhamnolipid-amended oil treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment. Conclusion: Overall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants and synthetic dispersant Finasol affect the natural marine microbial community in the FSC, supporting their potential application in oil spills.
... Spatial patterns have been 228 used as a proxy for the temporal response of microbial activity before and after the disturbance 229 (21), and to derive hydrocarbon biodegradation rates (20,22). However, heterogeneity in 230 microbial community function or physical transport can result in spatial patterns that do not reflect 231 a simple temporal change in a confined water parcel as demonstrated in decay over time (23). To 232 assess the functional performance of adapted compared with naïve communities, hydrocarbon 233 half-life was computed from a first-order decay model (Fig.4). ...
... The elevated methane concentrations in the two model experiments are at the same level (Fig. S8), which means that the comparison between two experiments is valid, and that the methane biodegradation in the model may be slower than observed. The observed field concentrations (6,22,23) are grouped into the six types of hydrocarbons using the same method as in the model. ...
Preprint
To quantitatively understand the ecological resilience of an ecosystem with specialized habitats, we focused on deep-sea microbial communities and simulated the response of diverse microbes in specialized habitats to a pulse ecosystem disturbance - the Deepwater Horizon Oil Spill in the Gulf of Mexico. Two microbial communities with equivalent metabolic libraries were acclimated to the presence (“seep-adapted community”) or absence (“naïve community”) of natural seeps, then their metabolic and ecological responses following the disturbance were compared on both individual and community scales. Higher variability in functional metabolisms in the naïve community without selection pressure created less predictable response to the disturbance. Although spatially and temporally varying degradation rates resulted from the individual complexity of simulated degraders and their interactions with overall community, seep-adapted communities were more efficient in utilizing substrate when spatially averaged. Seep-adapted communities also had more heterogeneous diversity patterns across space and time and presented lower resistance and higher resilience in returning to baseline conditions following the disturbance. The model suggests that communities exposed to transient pulse disturbance or exchanging species with specialized habitats under selection for the disturbance may have greater sustainability in response to disturbance.
... This contrasts with the primarily lowabundance Rhodobacteraceae OTUs that were selectively found in plastic biofilms, emphasizing their unique role (Fig. 4). Of the plastic-specific, geographically ubiquitous OTUs, one Rhodobacteraceae (OTU13230) and one Flammeovirgaceae (OTU559) showed high levels of sequence similarity to bacterial clones identified in studies of the Deepwater Horizon Oil spill ( Fig. 5; Table S2) (43,44). ...
... Hydrocarbonoclastic bacteria, like Rhodobacteraceae and Flammeovirgaceae, are ubiquitous in marine environments, typically existing in low abundance until a massive influx of hydrocarbons through, e.g., an oil spill leads to a rapid shift in local microbial blooms (43). This is not the first study to identify hydrocarbonoclastic bacteria in plastic biofilms (5,7,9,12,22,23,25). ...
Article
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While it is now appreciated that the millions of tons of plastic pollution travelling through marine systems carry complex communities of microorganisms, it is still unknown to what extent these biofilm communities are specific to the plastic or selected by the surrounding ecosystem. To address this, we characterized and compared the microbial communities of microplastic particles, nonplastic (natural and wax) particles, and the surrounding waters from three marine ecosystems (the Baltic, Sargasso and Mediterranean seas) using high-throughput 16S rRNA gene sequencing. We found that biofilm communities on microplastic and nonplastic particles were highly similar to one another across this broad geographical range. The similar temperature and salinity profiles of the Sargasso and Mediterranean seas, compared to the Baltic Sea, were reflected in the biofilm communities. We identified plastic-specific operational taxonomic units (OTUs) that were not detected on nonplastic particles or in the surrounding waters. Twenty-six of the plastic-specific OTUs were geographically ubiquitous across all sampled locations. These geographically ubiquitous plastic-specific OTUs were mostly low-abundance members of their biofilm communities and often represented uncultured members of marine ecosystems. These results demonstrate the potential for plastics to be a reservoir of rare and understudied microbes, thus warranting further investigations into the dynamics and role of these microbes in marine ecosystems. IMPORTANCE This study represents one of the largest comparisons of biofilms from environmentally sampled plastic and nonplastic particles from aquatic environments. By including particles sampled through three separate campaigns in the Baltic, Sargasso, and Mediterranean seas, we were able to make cross-geographical comparisons and discovered common taxonomical signatures that define the plastic biofilm. For the first time, we identified plastic-specific bacteria that reoccur across marine regions. Our data reveal that plastics have selective properties that repeatedly enrich for similar bacteria regardless of location, potentially shifting aquatic microbial communities in areas with high levels of plastic pollution. Furthermore, we show that bacterial communities on plastic do not appear to be strongly influenced by polymer type, suggesting that other properties, such as the absorption and/or leaching of chemicals from the surface, are likely to be more important in the selection and enrichment of specific microorganisms.
... SSDI, in response to the DwH blowout, created oil-microemulsions that enhanced the solubilization of BTEX and PAHs, leading to enhanced biodegradation of chemically dispersed oil (Kleindienst et al., 2015). Studies indicated that a small fraction of the total hydrocarbons biodegradation was enhanced by SSDI, primarily the soluble and volatile compounds (Gros et al., 2017), as the oil degrading microbes responded effectively to trapped and soluble hydrocarbons, regardless of dispersant application (Dubinsky et al., 2013;Hazen et al., 2010). In the intrusion layer formed in the DwH blowout, a persistent oxygen anomaly was reported, indicating the dominance of aerobic hydrocarbon degradation (Kessler et al., 2011). ...
... In the intrusion layer formed in the DwH blowout, a persistent oxygen anomaly was reported, indicating the dominance of aerobic hydrocarbon degradation (Kessler et al., 2011). Enrichment of methanotrophs and other bacteria such as Flavobacteria, and Alteromonadaceae was reported in the surrounding area, which was fed on the natural gases and soluble BTEX, as well as high-molecular-weight dissolved organic matter in the plume at different periods (Dubinsky et al., 2013). The oxygen limitation on the deep seafloor greatly restricted the microbe activity and oil degradation rates (Kostka et al., 2020b). ...
Article
Growing concerns over the risk of accidental releases of oil into the marine environment have emphasized our need to improve both oil spill preparedness and response strategies. Among the available spill response options, dispersants offer the advantages of breaking oil slicks into small oil droplets and promoting their dilution, dissolution, and biodegradation within the water column. Thus dispersants can reduce the probability of oil slicks at sea from reaching coastal regions and reduce their direct impact on mammals, sea birds and shoreline ecosystems. To facilitate marine oil spill response operations, especially addressing spill incidents in remote/Arctic offshore regions, an in-depth understanding of the transportation, fate and effects of naturally/chemically dispersed oil is of great importance. This review provides a synthesis of recent research results studies related to the application of dispersants at the surface and in the deep sea, the fate and transportation of naturally and chemically dispersed oil, and dispersant application in the Arctic and ice-covered waters. Future perspectives have been provided to identify the research gaps and help industries and spill response organizations develop science-based guidelines and protocols for the application of dispersants application
... The resulting hydrocarbonoclastic community of Ship #1 is reminiscent of the successional patterns observed during the response of open-ocean surface waters to the influx of petroleum from the Deep Water Horizon oil spill 40 . Here too, surface water assemblages underwent shifts within the first week and experienced strong enrichments in hydrocarbonoclastic aerobes 22 . The shift in community proportions encoding hydrocarbon activation genes, as well as the relative abundance of genes from oxygendependent and independent pathways also changed as a function of time (Fig. 5). ...
Article
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Naval vessels regularly mix fuel and seawater as ballast, a practice that might exacerbate fuel biodegradation and metal biocorrosion. To investigate, a metagenomic characterization and metabolite profiling of ballast from U.S. Navy vessels with residence times of 1-, ~20-, and 31 weeks was conducted and compared with the seawater used to fill the tanks. Aerobic Gammaproteobacteria differentially proliferated in the youngest ballast tank and aerobic-specific hydrocarbon degradation genes were quantitatively more important compared to seawater or the other ballast tanks. In contrast, the anaerobic Deltaproteobacteria dominated in the eldest ballast fluid with anaerobic-specific hydrocarbon activation genes being far more prominent. Gene activity was corroborated by detection of diagnostic metabolites and corrosion was evident by elevated levels of Fe, Mn, Ni and Cu in all ballast samples relative to seawater. The findings argue that marine microbial communities rapidly shift from aerobic to anaerobic hydrocarbonoclastic-dominated assemblages that accelerate fuel and infrastructure deterioration.
... At the cold seeps, CH 4 oxidation likely involves communities composed of different functional guilds rather than methanotrophs alone (Dubinsky et al., 2013;Rivers et al., 2013). CH 4 levels at the cold CH 4 seeps vary intermittently from nanomolar to millimolar concentrations (Reeburgh, 2007;Ruff et al., 2013;Grupe et al., 2015). ...
Article
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Methane seeps are chemosynthetic ecosystems in the deep-sea environment. Microbial community structures have been extensively studied in the seepage-affected sediments and investigation in the water column above the seeping sites is still lacking. In this study, prokaryotic communities in the bottom water about 50 cm from the seabed at methane seeps with various seepage intensities in Haima, South China Sea were comparatively studied by using 16S ribosomal RNA gene sequencing. These sites were assigned based on their distinct methane content levels and seafloor landscapes as the non-seepage (NS) site, low-intensity seepage (LIS) site, and high-intensity seepage (HIS) site. The abundances of the dominant phyla Proteobacteria, Bacteroidetes, and Actinobacteria differed significantly between NS and the two seepage sites ( p < 0.05). Alpha diversity differed among the three sites with the HIS site showing the lowest community diversity. Principal component analysis revealed highly divergent bacterial community structures at three sites. Many environmental variables including temperature, alkalinity, pH, methane, dissolved organic carbon (DOC), and inorganic nutrients were measured. Redundancy analysis indicated that methane content is the key environmental factor driving bacterial community variation ( p = 0.001). Linear discriminant analysis effect size analysis identified various differentially enriched genera at the LIS and HIS sites. Phylogenetic analysis revealed close phylogenetic relationship among the operational taxonomic units of these genera with known oil-degrading species, indicating oil seepage may occur at the Haima cold seeps. Co-occurrence networks indicated that the strength of microbial interactions was weakest at the HIS site. This study represents a comprehensive comparison of microbial profiles in the water column of cold seeps in the SCS, revealing that the seepage intensity has a strong impact on bacterial community dynamics.
... Por ejemplo, durante el derrame asociado a la explosión de la plataforma Deepwater Horizon (DWH) que ocurrió en el norte del golfo de México en el 2010, los taxones Oceanospirillales y Pseudomonas dominaron la comunidad microbiana en la fase inicial del derrame cuando la concentración de alcanos fue mayor. Esta población disminuyó y fue sucedida por los géneros Colwellia y Cycloclasticus, que degradan hidrocarburos aromáticos (Dubinsky et al., 2013). ...
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La Zona Económica Exclusiva del golfo de México es un ecosistema poco explorado en cuanto a su diversidad bacteriana. En este Atlas se presenta la primera línea base de bac- terias de dicha zona, basada en la secuenciación del material genético conseguido a partir de muestras de columna de agua y de los sedimentos marinos. El material genético obtenido dio cuenta de la diversidad y abundancia de bacterias del golfo de México desde Tamaulipas hasta Yucatán, poniendo énfasis en la diversidad de bacterias con la capacidad metabólica de degradar hidrocarburos presentes en el petróleo. Adicionalmente, los grupos bacterianos incluídos en este Atlas cuentan con fichas técnicas que describen, de manera resumida, su morfología, fisiología, y su relevancia ecológica, así como su distribución en otros mares del mundo.
... Hydrocarbon oxidation rate. Rates of biological hydrocarbon oxidation were estimated using [1][2][3][4][5][6][7][8][9][10][11][12][13][14] C]hexadecane and [1-14 C]naphthalene (American Radiolabeled Chemicals Inc.). During each time point tested, duplicate 1-ml water samples were collected from each of the triplicate mesocosm tanks for each of the three treatments (seawater control, oil-only, and oil-plus-dispersant). ...
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Vast quantities of oil-associated marine snow (MOS) formed in the water column as part of the natural biological response to the Deepwater Horizon drilling accident. Despite the scale of the event, uncertainty remains about the mechanisms controlling MOS formation and its impact on the environment.
... From day 30, members of the families Rhodobacteraceae and Flavobacteriaceae increased in abundances, both in MI+oil and freshSW+oil. The late increases in abundance of Rhodobacteraceae are in agreement with results from other biodegradation experiments in cold water (Dubinsky et al., 2013;Brakstad et al., 2018a;Ribicic et al., 2018d). It has been proposed that Rhodobacteraceae may be involved in the degradation of recalcitrant hydrocarbons, both larger PAHs and branched alkanes . ...
Article
Oil spilled in the Arctic may drift into ice-covered areas and become trapped until the ice melts. To determine if exposure to oil during freezing may have a priming effect on degradation of the oil, weathered dispersed oil (2-3 mg/L) was frozen into solid ice for 200 days at -10 °C, then melted and incubated for 64 days at 4 °C. No degradation was measured in oil frozen into ice prior to melting. Both total amount of oil and target compounds were biotransformed by the microbial community from the melted ice. However, oil released from melted ice was degraded at a slower rate than oil incubated in fresh seawater at the same temperature (4 °C), and by a different microbial community. These data suggest negligible biodegradation of oil frozen in sea ice, while oil-degrading bacteria surviving in the ice may contribute to biodegradation when the ice melts.
... For instance, oil spills in oceans rapidly induce an increase in specialized hydrocarbondegrading Gammaproteobacteria, such as Alcanivorax, Pseudomonas, Oleispira, and Colwellia, contributing to hydrocarbon biodegradation. Usually, these bacterial communities are present in marine waters and sediments in low abundance (Dubinsky et al. 2013;Godoy-Lozano et al. 2018). Furthermore, plastic wastes in marine environments affect bacterial communities and their function in biogeochemical cycles. ...
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Marine ecosystems are some of the most adverse environments on Earth and contain a considerable portion of the global bacterial population, and some of these bacterial species play pivotal roles in several biogeochemical cycles. Marine bacteria have developed different molecular mechanisms to address fluctuating environmental conditions, such as changes in nutrient availability, salinity, temperature, pH, and pressure, making them attractive for use in diverse biotechnology applications. Although more than 99% of marine bacteria cannot be cultivated with traditional microbiological techniques, several species have been successfully isolated and grown in the laboratory, facilitating investigations of their biotechnological potential. Some of these applications may contribute to addressing some current global problems, such as environmental contamination by hydrocarbons and synthetic plastics. In this review, we first summarize and analyze recently published information about marine bacterial diversity. Then, we discuss new literature regarding the isolation and characterization of marine bacterial strains able to degrade hydrocarbons and petroleum-based plastics, and species able to produce biosurfactants. We also describe some current limitations for the implementation of these biotechnological tools, but also we suggest some strategies that may contribute to overcoming them. Key points • Marine bacteria have a great metabolic capacity to degrade hydrocarbons in harsh conditions. • Marine environments are an important source of new bacterial plastic-degrading enzymes. • Secondary metabolites from marine bacteria have diverse potential applications in biotechnology.
... A method that allows any type of betadiversity measure, whether it is incidence-based (presence-absence) or abundance-based and gives a percentage of stochasticity for samples belonging to a single category Any beta-diversity metric as long as it is normalized to have a range between 0 and 1. Abundance-based Ružička and incidence-based Jaccard metrics were deemed to have a superior performance in view of the simulations done by the author Ning et al. (2019) Hill numbers The effect of deterministic and stochastic factors on explaining the differences between multiple categories Jaccard and Bray-Curtis dissimilarity metrics Modin et al. (2020) β-null deviation Differentiation between niche and neutral community assemblage processes Darcy et al. (2020) and selected for specific taxa responding to hydrocarbons (Doyle et al., 2018;Dubinsky et al., 2013;Gutierrez et al., 2013;Miller et al., 2020;Redmond & Valentine, 2012). Furthermore, chemical dispersants were shown to inhibit oil degradation by suppressing some of the most effective hydrocarbon degraders such as Marinobacter and Rhodococcus (Hackbusch et al., 2020;Hamdan & Fulmer, 2011;Kleindienst et al., 2015;Rahsepar et al., 2016;Rughöft et al., 2020). ...
Article
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Assembly processes in marine microbial communities amended with crude oil and chemical dispersant are poorly understood and even more so when biosurfactants are used. We set up a microcosm experiment in which microbiome structure was analyzed using 16S rRNA gene amplicon sequencing and six null models to better understand and quantify the mechanisms and patterns controlling the assembly of a marine crude oil degrading microbial community in the presence of chemical dispersant or rhamnolipid biosurfactant. Although each null model quantifies different aspects of the community assembly, there was a general agreement that neither purely stochastic nor purely deterministic processes dominated the microbial communities, and their influence was variable over time. Determinism was dominant in the early phase of incubation, while stochasticity was prevalent in the middle and late stages. There was faster recruitment of phylogenetically distant species in the dispersant‐amended community compared to oil‐only or rhamnolipid‐amended communities. This analysis provides important insights of how chemical dispersants and rhamnolipid influence microbial communities' dynamics and identified which groups may be excluded—an important consideration for biodegradation process and oil spill response. Assembly processes in marine microbial communities amended with crude oil and chemical dispersant are poorly understood and even more so when biosurfactants are used. We used a comprehensive set of null models approaches to test traditional macroecological concepts in the context of microbial metagenomics in order to understand and quantify the mechanisms and patterns controlling the complexity of microbial ecology Our results advance the understanding of how chemical and biogenic dispersants affect the ecological processes in marine microbial community response to crude oil.
... Oil exposure is known to induce swift changes in microbial community composition with a transient dominance of obligate hydrocarbondegrading and opportunistic genera including Oleispira, Alcanivorax, Oleibacter, Colwellia, and Cycloclasticus among others. (Brakstad et al., 2015;Catania et al., 2018;Catania et al., 2015;Chakraborty et al., 2012;Dubinsky et al., 2013;Hazen et al., 2010;Krolicka et al., 2017;Mason et al., 2012;Netzer et al., 2018;Ribicic et al., 2018a;Ribicic et al., 2018b;Tremblay et al., 2019). Quantifying these key indicator bacteria could therefore be used as a signal of oil presence in seawater . ...
Article
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Monitoring environmental status through molecular investigation of microorganisms in the marine environment is suggested as a potentially very effective method for biomonitoring, with great potential for automation. There are several hurdles to that approach with regards to primer design, variability across geographical locations, seasons, and type of environmental pollution. Here, qPCR analysis of genes involved in the initial activation of aliphatic and aromatic hydrocarbons were used in a laboratory setup mimicking realistic oil leakage at sea. Seawater incubation experiments were carried out under two different seasons with two different oil types. Degenerate primers targeting initial oxygenases (alkane 1-monooxygenase; alkB and aromatic-ring hydroxylating dioxygenase; ARHD) were employed in qPCR assays to quantify the abundance of genes essential for oil degradation. Shotgun metagenomics was used to map the overall community dynamics and the diversity of alkB and ARHD genes represented in the microbial community. The amplicons generated through the qPCR assays were sequenced to reveal the diversity of oil-degradation related genes captured by the degenerate primers. We identified a major mismatch between the taxonomic diversity of alkB and ARHD genes amplified by the degenerate primers and those identified through shotgun metagenomics. More specifically, the designed primers did not amplify the alkB genes of the two most abundant alkane degraders that bloomed in the experiments, Oceanobacter and Oleispira. The relative abundance of alkB sequences from shotgun metagenomics and 16S rRNA-based Oleispira-specific qPCR assay were better signals for oil in water than the tested qPCR alkB assay. The ARHD assay showed a good agreement with PAHs degradation despite covering only 25% of the top 100 ARHD genes and missing several abundant Cycloclasticus sequences that were present in the metagenome. We conclude that further improvement of the degenerate primer approach is needed to rely on the use of oxygenase-related qPCR assays for oil leakage detection.
... Given the health risks and the environmental impact of pesticide-polluted soils, microbial bioremediation approaches and associated technologies should be widely developed and applied in the future (Ergüven and Yildirim 2016;Yildirim et al. 2018;Ergüven and Yildirim 2019). At present, bioremediation of environmental reservoirs is accomplished using primarily natural, non-engineered bacteria that have been isolated from contaminated sources and exhibit ability to degrade the target contaminant (Dubinsky et al. 2013). Nevertheless, research efforts on dimethoate-degrading bacteria so far are limited to the bacteria Paracoccus sp. ...
Article
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High toxicity of dimethoate requires efficient ways for detoxification and removal of its residues in contaminated environments. Microbial remediation is a process that utilizes the degradation potential of microbes to provide a cost-effective and reliable approach for pesticide abatement. For this purpose, a dimethoate-degrading bacterium Brucella sp. was isolated from a contaminated agricultural soil sample in Multan, Pakistan. This isolate was found to tolerate up to 100 ppm of dimethoate in minimal salt medium and was further evaluated for plant growth-promoting traits. The strain gave positive results for amylase, ammonia, and catalase production, while other traits such as indole acetic acid production and potassium solubilization were also confirmed. Thus, the strain could play an important role for plant nutrient transmission in the plant rhizosphere. Optimization of growth parameters (i.e., pH and temperature) depicted the potential of PS4 to be best tolerating dimethoate, with maximum cell density at λ 600 nm. Optimum pH and temperature for growth were found to be 6 and 35 °C, respectively. Based on optimization results as well as different attributes, the rhizospheric bacterial isolate PS4 was further subjected to a batch degradation experiment under different concentrations of dimethoate (25, 50, 75, and 100 ppm). This promising dimethoate-degrading isolate was found to degrade 83% of dimethoate (at 100 ppm) within a period of 7 days. In addition, it degraded 88% of dimethoate at 50 ppm, indicating that the bacterial isolate utilized dimethoate solely as a source of energy. The strain followed the first order reaction kinetics, depicting its dependence on dimethoate as energy and carbon source. Molecular profiling further supported its role in plant growth promotion and multi-stress tolerance. This research showed that Brucella sp. is capable of degrading dimethoate, and therefore, it would be useful in the investigation of novel bioremediation techniques at pesticide-polluted sites.
... Although the biodegradation process is affected by environmental such as the composition and concentration of petroleum hydrocarbons, temperature, and salinity, the decisive factor is the degradation ability of the microorganisms. Some wild-type petroleum hydrocarbon-degrading microorganisms screened out in petroleum-contaminated sites are subject to slow natural evolution speed, and their biological digestibility cannot meet our need (Dubinsky et al. 2013). ...
Article
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With the enhancement of environmental protection awareness, research on the bioremediation of petroleum hydrocarbon environmental pollution has intensified. Bioremediation has received more attention due to its high efficiency, environmentally friendly by-products, and low cost compared with the commonly used physical and chemical restoration methods. In recent years, bacterium engineered by systems biology strategies have achieved biodegrading of many types of petroleum pollutants. Those successful cases show that systems biology has great potential in strengthening petroleum pollutant degradation bacterium and accelerating bioremediation. Systems biology represented by metabolic engineering, enzyme engineering, omics technology, etc., developed rapidly in the twentieth century. Optimizing the metabolic network of petroleum hydrocarbon degrading bacterium could achieve more concise and precise bioremediation by metabolic engineering strategies; biocatalysts with more stable and excellent catalytic activity could accelerate the process of biodegradation by enzyme engineering; omics technology not only could provide more optional components for constructions of engineered bacterium, but also could obtain the structure and composition of the microbial community in polluted environments. Comprehensive microbial community information lays a certain theoretical foundation for the construction of artificial mixed microbial communities for bioremediation of petroleum pollution. This article reviews the application of systems biology in the enforce of petroleum hydrocarbon degradation bacteria and the construction of a hybrid-microbial degradation system. Then the challenges encountered in the process and the application prospects of bioremediation are discussed. Finally, we provide certain guidance for the bioremediation of petroleum hydrocarbon-polluted environment.
... The enhancement in the degradation achieved in the presence of NH3NO4 (Figure 4a) may be explained by the fact that hydrocarbons exist in a reduced state, and they are oxidised by microbes using electron acceptors. Since oxygen can also become a limiting factor, electron acceptors added to substitute for oxygen may indicate that the nitrate ion provided the next best alternative [86]. Nitrate gives high oxidation potential for the removal of hydrocarbon contamination [87]. ...
Article
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Hydrocarbon pollution is widespread around the globe and, even in the remoteness of Antarctica, the impacts of hydrocarbons from anthropogenic sources are still apparent. Antarctica’s chronically cold temperatures and other extreme environmental conditions reduce the rates of biological processes, including the biodegradation of pollutants. However, the native Antarctic microbial diversity provides a reservoir of cold-adapted microorganisms, some of which have the potential for biodegradation. This study evaluated the diesel hydrocarbon-degrading ability of a psychrotolerant marine bacterial consortium obtained from the coast of the north-west Antarctic Peninsula. The consortium’s growth conditions were optimised using one-factor-at-a-time (OFAT) and statistical response surface methodology (RSM), which identified optimal growth conditions of pH 8.0, 10 °C, 25 ppt NaCl and 1.5 g/L NH4NO3. The predicted model was highly significant and confirmed that the parameters’ salinity, temperature, nitrogen concentration and initial diesel concentration significantly influenced diesel biodegradation. Using the optimised values generated by RSM, a mass reduction of 12.23 mg/mL from the initial 30.518 mg/mL (4% (w/v)) concentration of diesel was achieved within a 6 d incubation period. This study provides further evidence for the presence of native hydrocarbon-degrading bacteria in non-contaminated Antarctic seawater.
... Methane oxidation was also stimulated early in the discharge (Crespo-Medina et al., 2014) and may have transmitted organic matter into the food web (Chanton et al., 2012;Wilson et al., 2016;Rogers et al., 2019). Oxidation of oil components occurs through the activities of a series of microbial populations, each pre-ferring a specialized substrate (oil constituent) (Dubinsky et al., 2013). Some oil-degrading bacteria produce natural biosurfactants (Head et al., 2006;Das et al., 2014) to enhance their access to oil and expedite biodegradation. ...
Article
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The Gulf of Mexico is a place where the environment and the economy both coexist and contend. It is a resilient large marine ecosystem that has changed in response to many drivers and pressures that we are only now beginning to fully understand. Coastlines of the states that border the Gulf comprise about half of the US southern seaboard, and those states are capped by the vast Midwest. The Gulf drains most of North America and is both an economic keystone and an unintended waste receptacle. It is a renowned resource for seafood markets, recreational fishing, and beach destinations and an international maritime highway fueled by vast, but limited, hydrocarbon reserves. Today, more is known about the Gulf than was imagined possible only a few years ago. That gain in knowledge was driven by one of the greatest environmental disasters of this country’s history, the Deepwater Horizon oil spill. The multitude of response actions and subsequent funded research significantly contributed to expanding our knowledge and, perhaps most importantly, to guiding the work needed to restore the damage from that oil spill. Funding for further work should not wait for the next major disaster, which will be too late; progress must be maintained to ensure that the Gulf continues to be resilient.
... These species were later supplanted mainly by Colwellia spp. and, to a lesser degree, Cycloclasticus and Pseudoalteromonas spp., which peaked when linear and simple aromatic hydrocarbons were abundant (Dubinsky et al., 2013;Kleindienst et al., 2015a). Employing metagenomics, scientists confirmed that the different hydrocarbon degradation genes and pathways present at different time points corresponded with abundances of different substrates within the plume (Mason et al., 2012;Redmond and Valentine, 2012). ...
Article
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The Deepwater Horizon oil spill represents one of the most damaging environmental catastrophes of our generation. It contaminated vast areas of the open ocean, the deep sea, and the shoreline of the Gulf region and disrupted its ecosystems, with both residual and long-term impacts. At the core of all of these ecosystems are microbial communities that perform essential biogeochemical processes and ecosystem services such as carbon and nutrient cycling. Despite their importance, relatively little was known about marine microbes that degrade hydrocarbons in the Gulf of Mexico prior to the Deepwater Horizon spill, nor the effect of hydrocarbons on the microbiology of the Gulf region. Research carried out through the Gulf of Mexico Research Initiative (GoMRI) revealed cooperative microbial communities operating at the heart of bioremediation services with highly adaptive and complex dynamics. In addition, these efforts established new methods for assessing and monitoring ecosystem health, whereby microbial population genetics can serve as indicators of biogeochemical disruptions and/or restoration status in marine and coastal environments. Although much research is still needed to fully understand and engage microbially mediated bioremediation services, GoMRI constructed a strong foundation of methods, discoveries, and overarching principles to build upon. These insights and tools will help scientists better prepare for, and respond to, future environmental catastrophes, from oil tanker spills to long-term disruptions of climate change.
... After the DwH spill, responding oil degraders comprised largely of Gammaproteobacteria in the genus Colwellia and the order Oceanospirillales (Hazen et al. 2010;Mason et al. 2012;Baelum et al. 2012;Dubinsky et al. 2013;Gutierrez et al., 2013Gutierrez et al., , 2016Yang et al., 2016). Studies show genera of Marinobacter, Alcanovorax, Cycloclasticus, and other putative hydrocarbon oxidizers increase in relative abundance within 12-24 hours of oil addition in surface waters of the Gulf of Mexico (Doyle et al. 2018(Doyle et al. , 2020. ...
Article
The Deepwater Horizon oil spill is the largest in US history in terms of oil released and the amount of dispersants applied. It is also the first spill in which the incorporation of oil and/or dispersant into marine snow was directly observable. Marine snow formation, incorporation of oil (MOS – marine oil snow) and subsequent settling to the seafloor, has been termed MOSSFA: Marine Oil Snow Sedimentation and Flocculent Accumulation. This pathway accounts for a significant fraction of the total oil returning back to the sea floor. GOMRI funded studies have determined that important drivers of MOSSFA include, but are not limited to, an elevated and extended Mississippi River discharge, which enhanced phytoplankton production and suspended particle concentrations, zooplankton grazing, and enhanced mucus formation (operationally defined as EPS, TEP, marine snow). Efforts thus far to understand the mechanisms driving these processes are being used to aid in the development of response strategies. These include modeling efforts towards predicting plume dynamics. Although much has been learned during the GOMRI program (reviewed herein and elsewhere), there are still important unknowns that need to be addressed. Understanding of the conditions under which significant MOSSFA events occur, the consequences to the biology, the sinking velocity and distribution of the MOSSFA as well as its ultimate fate are amongst the most important consideration for future studies. Also important is the modification of the oil and dispersant within the MOS and its transport as part of MOSSFA. Ongoing studies are needed to further develop our understanding of these complex and interrelated phenomena.
... When the relative abundance of alkanes decreased in the weeks following the spill, polycyclic aromatic hydrocarbon (PAH) degrading species became more prolific. 44 Bioremediation is limited by the capabilities of indigenous species to metabolize oil and the rate at which communities can adapt to oil as the sole carbon or energy source. The abundance of each species is dependent on oil composition and concentration and environmental factors including weather, salinity, temperature, and nutrient availability. ...
Article
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Oil seepage and spills have lasting detrimental effects on the environment, especially on nearby marine ecosystems. Despite quick and safe removal of contaminating oil being of utmost importance, remediation methods have remained largely unchanged over the last 20+ years. Removal methods such as skimmers, in situ burning, and sorbents can be difficult to implement in inclement weather. Marine microorganisms consume spilled oil as a primary energy source in a method known as bioremediation. Recently the introduction of nanoparticles to areas contaminated by oil has emerged as a potential method to enhance the efficacy of oil degradation by marine microorganisms. Nanoparticles have been primarily utilized as magnetic sorbents but can also act as emulsifiers, increasing the bioavailability of the oil by giving microbes a surface (droplets) to which they can attach and facilitate proliferation. Emulsification increases the oil–water interfacial area and often leads to an increase in the amount of oil degraded by microorganisms. Nanoenhanced bioremediation is effective on a variety of oil compositions and is minimally impacted by weather. It offers a sustainable alternative to traditional remediation methods, i.e., chemical dispersants, sorbents, and in situ burning, which are often toxic and ineffective.
... Organisms sharing an ecological range appear to have a high frequency of HGT [46]. Studies on Deepwater Horizon oil spill show early abundance of order Oceanospirillales and P. aeruginosa, indicating adaptation to metabolize similar substrates [47]. Hence, the affinity between these two groups could be due to HGT. ...
Article
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Proteobacteria is one of the largest and phenotypically most diverse divisions within the domain bacteria. Due to the economic importance, this phylum demands an urgent need for a clear and scientifically sound classification system to streamline their characterization. The goal of our study was to carefully reevaluate the current system of classification and suggest changes wherein necessary. Phylogenetic trees of 84 Proteobacteria were constructed using single gene-based phylogeny involving 16S rRNA genes and protein sequences of 85 conserved genes, whole genome-based phylogenetic tree using CVtree3.0, amino acid Identity matrix tree, and concatenated tree with aforementioned conserved genes. The results of our study confirm the polyphyletic relationship between Desulfurella acetivorans, a Deltaproteobacteria with Epsilonproteobacteria. The group Syntrophobacterales was found to be polyphyletic with respect to Desulfarculus baarsii and the group Thiotrichales was found to be splitting in different phylogenetic trees. Placement of phylogenetic groups belonging to Rhodocyclales, Oceonospirilalles, and Chromatiales is controversial and requires further study and revisions. Based on our analysis, we strongly support reclassification of Magnetococcales as a separate class Etaproteobacteria. From our results, we conclude that concatenated trees of conserved proteins are a more accurate method for phylogenetic analysis, as compared to other methods used.
... However, the collection of deep-sea microbial communities typically involved depressurization of the sample during retrieval and in most cases, subsequent incubation at atmospheric pressure [12][13][14][15][16][17][18][19][20][21]. In situ studies during DWH, using fluorometry, mass spectrometry, dissolved oxygen monitoring and next generation sequencing techniques have provided most of the documented data on microbial activity, accurately depicted the shifts in microbial communities, and pointed out the key microbial taxa that are involved in hydrocarbon degradation [9,[22][23][24][25][26][27][28][29], without providing any information on biodegradation rates. Ever since, the interest for more accurate measurement of the metabolic activities of deep-sea microbial communities regarding oil degradation has led to studies where high-pressure is applied. ...
Article
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Hydrocarbon biodegradation rates in the deep-sea have been largely determined under atmospheric pressure, which may lead to non-representative results. In this work, we aim to study the response of deep-sea microbial communities of the Eastern Mediterranean Sea (EMS) to oil contamination at in situ environmental conditions and provide representative biodegradation rates. Seawater from a 600 to 1000 m depth was collected using a high-pressure (HP) sampling device equipped with a unidirectional check-valve, without depressurization upon retrieval. The sample was then passed into a HP-reactor via a piston pump without pressure disruption and used for a time-series oil biodegradation experiment at plume concentrations, with and without dispersant application, at 10 MPa and 14οC. The experimental results demonstrated a high capacity of indigenous microbial communities in the deep EMS for alkane degradation regardless of dispersant application (>70%), while PAHs were highly degraded when oil was dispersed (>90%) and presented very low half-lives (19.4 to 2.2 days), compared to published data. To our knowledge, this is the first emulation study of deep-sea bioremediation using undisturbed deep-sea microbial communities.
... One OTU identified as Colwellia was significantly more abundant in the CEWAF/Bacteria/Recovery treatment compared to Seawater Control and Bacteria/Recovery. This genus contains strains that are known crude oil degraders (29) and dominate microbial communities of diluted plumes (47), pointing to a role in later stages of degradation. In a mesocosm study, the genus Colwellia was dominant only in treatments that received dispersant, and it was hypothesized that these bacteria participate in the metabolism of the sulfur compounds resulting from dispersant use (48). ...
Article
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Fish skin is an immunologically active tissue. It harbors a complex community of microorganisms vital to host homeostasis as, in healthy fish, they competitively exclude pathogens found in the surrounding aquatic environment.
... These thermogenic compounds, produced over centuries, strongly affect the ecology of marine ecosystems and trigger activity by numerous aerobic and anaerobic oil-degrading microorganisms 2 . Microbial degradation of hydrocarbons in marine environments has been extensively studied in deep-sea sediment seepages [3][4][5][6][7] , and following oil spills 8- 10 . Detailed investigations following the Deepwater Horizon oil spill in the Gulf of Mexico revealed multiple naturally occurring microbial lineages able to degrade hydrocarbons, and this list is expanding rapidly with metagenomic sequencing and data analysis. ...
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Cyanobacteria produce vast quantities of long-chain alkanes in the ocean, yet these do not accumulate in the water column, suggesting rapid co-localized biodegradation. The identities of microbes in this cryptic hydrocarbon cycle are mostly unknown, and are unexplored across marine-freshwater gradients. Analyzing genes and metagenome assembled genomes from a remote, pristine, petroleum-free and meromictic lake in the High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes and Verrucomicrobia had pathways for hydrocarbon production, providing additional sources of biogenic hydrocarbons. Classic oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identified in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae and Marinimicrobia. This suggests that biogenic hydrocarbons could sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications.
... Moreover, some genera, such as Paraglaciecola and Shewanella, with known versatile potential for oil hydrocarbon degradation [36,66], emerged among the dominant HDO-containing genera only in the SIO metagenome. All three MAGs derived from the SIO metagenome were affiliated with taxa containing HDOs (Bermanella, Glaciecola, and Rhodobacteraceae) [67,68]. ...
Article
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The anthropogenic release of oil hydrocarbons into the cold marine environment is an increasing concern due to the elevated usage of sea routes and the exploration of new oil drilling sites in Arctic areas. The aim of this study was to evaluate prokaryotic community structures and the genetic potential of hydrocarbon degradation in the metagenomes of seawater, sea ice, and crude oil encapsulating the sea ice of the Norwegian fjord, Ofotfjorden. Although the results indicated substantial differences between the structure of prokaryotic communities in seawater and sea ice, the crude oil encapsulating sea ice (SIO) showed increased abundances of many genera-containing hydrocarbon-degrading organisms, including Bermanella, Colwellia, and Glaciecola. Although the metagenome of seawater was rich in a variety of hydrocarbon degradation-related functional genes (HDGs) associated with the metabolism of n-alkanes, and mono-and polyaromatic hydrocarbons, most of the normalized gene counts were highest in the clean sea ice metagenome, whereas in SIO, these counts were the lowest. The long-chain alkane degradation gene almA was detected from all the studied metagenomes and its counts exceeded ladA and alkB counts in both sea ice meta-genomes. In addition, almA was related to the most diverse group of prokaryotic genera. Almost all 18 good-and high-quality metagenome-assembled genomes (MAGs) had diverse HDGs profiles. The MAGs recovered from the SIO metagenome belonged to the abundant taxa, such as Glaciecola, Bermanella, and Rhodobacteracea, in this environment. The genera associated with HDGs were often previously known as hydrocarbon-degrading genera. However, a substantial number of new associations , either between already known hydrocarbon-degrading genera and new HDGs or between genera not known to contain hydrocarbon degraders and multiple HDGs, were found. The super-imposition of the results of comparing HDG associations with taxonomy, the HDG profiles of MAGs, and the full genomes of organisms in the KEGG database suggest that the found relationships need further investigation and verification.
... The petroleum hydrocarbons released into the environment are eventually metabolized or degraded by indigenous bacterial species to release the physiological stress caused by the petroleum hydrocarbons in the microbial community and utilize them as a carbon source for their growth and multiplication. Various studies have reported many hydrocarbons assimilating bacteria from several oil reservoirs and oil-polluted environments (Dubinsky et al., 2013;Yang et al., 2015b). Several bacterial species such as Pseudomonas, Staphylococcus, Streptococcus, Streptobacillus, Acinetobacter, Enterobacter, Marinobacter, and Mycobacterium to possess petroleum hydrocarbons degradation ability (Atlas et al., 2015;Varjani and Upasani, 2016;Sarkar et al., 2017). ...
Article
Increased tolerance to toxic pollutants and enhanced degradation capabilities of the bacterial biofilm is often attributed to the matrix of extracellular polymeric substances (EPS). This biopolymeric matrix provides structure, stability, and shelter to the cells within a biofilm and the major constituent of this matrix is exopolysaccharides. However, the role of EPS extends beyond offering protection to the bacterial cells under stress. Bacterial EPS exhibits a double-layered structure consisting of the loosely bound EPS (LB-EPS) and the tightly bound EPS (TB-EPS). Both these EPS layers interact with noxious environmental pollutants through emulsification, solubilization, binding, precipitation, complexation, and ion exchange. Different functional groups of EPS, such as carboxyl, amide, phosphoryl, and hydroxyl, are involved in the removal of toxic pollutants from contaminated environments. Biofilm-EPS participate in several remedial functions such as sequestration of heavy metals, emulsification of petroleum hydrocarbons, binding and solubilization of polycyclic aromatic hydrocarbons (PAHs), and sorption and degradation of dyes and pesticides. Thus, bacterial biofilm and EPS present an attractive solution for decontaminating heavily polluted environments. This review discusses a comprehensive account of biofilm physiology, EPS components, and synthesis mechanisms of exopolysaccharides. The interaction mechanisms of bacterial biofilm and EPS with pollutants have been discussed in detail, and the application of biofilm-forming bacteria and associated EPS in the bioremediation of the environment has been summarized. A deeper understanding of the bacterial biofilm and EPS-mediated pollutant removal will help develop technologies for field-scale applications.
... Results of previous studies have shown changes in bacterial communities during degradation of oil might be attributed to a preferences by various bacteria for hydrocarbon degradation intermediates as sources of carbon (Lea-Smith et al., 2015;Uribe-Flores et al., 2019). Changes in structures of bacterial communities would be dependent on compositions of hydrocarbons present in oil during process of degradation of oil, in the order of alkanes, cycloalkanes, aromatics, resins, and finally asphalt (Dubinsky et al., 2013). ...
Article
Ecotoxicological effects of spilled oils are well documented, but study of recovery of marine benthic communities is limited. Long-term recovery of hard bottom communities during physical and biological remediations after a spill was monitored. A 60-day experiment was conducted using a mesocosm with monitoring of eight endpoints by use of the sediment quality triad (SQT). First, physical treatment of hot water + high pressure flushing maximally removed residual oils (max=93%), showing the greatest recovery among SQT variables (mean=72%). Physical cleanup generally involved adverse effects such as depression of the microphytobenthic community during the initial period. Next, biological treatments, such as fertilizer, emulsifier, enzyme and augmentation of the microbes, all facilitated removal of oil (max=66%) enhancing ecological recovery. Analysis of the microbiome confirmed that oil-degrading bacteria, such as Dietzia sp. and Rosevarius sp. were present. A mixed bioremediation, including fertilizer + multi-enzyme + microbes (FMeM) maximized efficacy of remediation as indicated by SQT parameters (mean=47%). Natural attenuation with “no treatment” showed comparable recovery to other remediations. Considering economic availability, environmental performance, and technical applicability, of currently available techniques, combined treatments of physical removal via hand wiping followed by FMeM could be most effective for recovery of the rocky shore benthic community.
... Members of this order are commonly found in association with oyster larvae [23] and adults [22], and are symbiotic with the gills of many bivalves [80][81][82]. Additionally, they are known for their capacity to break down organic compounds in the environment and their abundance in crude-oil containing seawater [83,84]. Their symbiotic capabilities with bivalves indicate that Oceanospirillales may confer beneficial effects to their larvae host and may be more useful at some larval stages than others. ...
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... The Rhodobacteraceae family was found to be the most abundant family on the plastic samples and higher than of seawater. Members of this family are known as hydrocarbon degraders of which Rhodococcus ruber has been shown to degrade PE (Gilan et al., 2004;Dubinsky et al., 2013). Several studies have reported a high abundance of the family Rhodobacteraceae on plastic samples (Bryant et al., 2016;Dussud et al., 2018). ...
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The increasing demand for petroleum products generates needs for innovative and reliable methods for cleaning up crude oil spills. Annually, several oil spills occur around the world, which brings numerous ecological and environmental disasters on the surface of deep seawaters like oceans. Biological and physico-chemical remediation technologies can be efficient in terms of spill cleanup and microorganisms—mainly bacteria—are the main ones responsible for petroleum hydrocarbons (PHCs) degradation such as crude oil. Currently, biodegradation is considered as one of the most sustainable and efficient techniques for the removal of PHCs. However, environmental factors associated with the functioning and performance of microorganisms involved in hydrocarbon-degradation have remained relatively unclear. This has limited our understanding on how to select and inoculate microorganisms within technologies of cleaning and to optimize physico-chemical remediation and degradation methods. This review article presents the latest discoveries in bioremediation techniques such as biostimulation, bioaugmentation, and biosurfactants as well as immobilization strategies for increasing the efficiency. Besides, environmental affecting factors and microbial strains engaged in bioremediation and biodegradation of PHCs in marines are discussed.
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Chapter
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Chapter
Organophosphorus pesticides (OPPs), being an attractive alternative to persistent organochlorine pesticides, are widely used in agriculture. The OPPs are the main components of herbicides, insecticides, and pesticides. They are derivatives of phosphoric acid having amide, ester, or thiol group possessing aliphatic, cyclic, or heterocyclic structure. The OPPs are soluble in water as well as organic solvents owing to their degradable organic nature. Currently more than 140 OPPs are being used all over the world and their careless handling, and inappropriate application contaminating environment by negatively affecting non-target species of humans, birds, animals, and plants through both systematic and non-systematic actions. The OPPs are utilized as fertilizers, agrochemicals, fungicides, pesticides, insecticides, acaricides, herbicides, plasticizers, flame retardants, plant growth factors, chemical warfare agents in agriculture, industrial sectors, as well as for household purposes. The injudicious utilization of OPPs is casting serious threats to global environment and health of living organisms. Nervous system of aquatic and terrestrial fauna is affected due to anti-acetylcholinestrase activity of OPPs such as chlorpyriphos, dimethoate, phorate, trichlorfon, glyphosate, etc. Their soluble nature makes them part of water bodies, thus because of various biotic and abiotic factors, OPPs become part of food chain. Regarding huge devastation caused by OPPs, it is needs of time to eliminate them from ecosystem. Therefore, their detoxification from the environment is necessary. There are various chemical, physical, and biological methods which have been used to reduce OPPs. The photocatalytic degradation of various OPP compounds has been investigated using UV light and TiO2 as photocatalyst. Chlorination of water has been reported to degrade OPPs. Bioremediation is considered as eco-friendly and economical process for the removal of these toxins as compared to other chemical and physical methods. Various microorganisms have been investigated which can degrade OPPs into less toxic compounds. Microbes use OPPs as carbon, phosphorous, and sulfur source, and electron donor by disrupting OPPs native structure, ultimately converting them to fewer toxic compounds in favourable conditions. This chapter highlights toxicokinetic study of organophosphates and their mechanism of action in living organisms. This chapter also highlights various microorganisms, i.e., bacteria, fungi, and algae, potentially involved in biodegradation of OPPs and their mechanism of bioremediation.
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Chapter
Bioremediation refers to the clean-up of pollution from soil, groundwater, surface water and air using biological, usually microbiological, processes. It has left the laboratory and is established in some parts of the world, especially the United States, as a full-scale, biotechnology-based industry. Key Concepts • Hydrocarbon and metal pollutants from anthropogenic sources are very diverse in types and microbes often biodegrade specific hydrocarbons. • Bioremediation involves the engineered biodegradation of pollutants in soil and water. • Bioremediation under aerobic conditions is the best understood and the most often applied. • Anaerobic biodegradation of hydrocarbons is more common than once thought due to advances in the detection of microorganisms without the necessity of culturing. • A range of engineering options is available for deliberate bioremediation of contaminated sites. • Knowledge of bioremediation capabilities of natural communities has been facilitated by modern –omics technologies such as metagenomics. • Synthetic biology offers solutions to outstanding questions regarding fundamental knowledge and future engineered bioremediation practice.
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Organophosphate pesticides (OPs) are used extensively for crop protection worldwide due to their high water solubility and relatively low persistence in the environment compared to other pesticides, such as organochlorines. Dimethoate is a broad-spectrum insecticide that belongs to the thio-organophosphate group of OPs. It is applied to cash crops, animal farms, and houses. It has been used in Pakistan since the 1960s, either alone or in a mixture with other OPs or pyrethroids. However, the uncontrolled use of this pesticide has resulted in residual accumulation in water, soil, and tissues of plants via the food chain, causing toxic effects. This review article has compiled and analyzed data reported in the literature between 1998 and 2021 regarding dimethoate residues and their microbial bioremediation. Different microorganisms such as bacteria, fungi, and algae have shown potential for bioremediation. However, an extensive role of bacteria has been observed compared to other microorganisms. Twenty bacterial, three fungal, and one algal genus with potential for the remediation of dimethoate have been assessed. Active bacterial biodegraders belong to four classes (i) alpha-proteobacteria, (ii) gamma-proteobacteria, (iii) beta-proteobacteria, and (iv) actinobacteria and flavobacteria. Microorganisms, especially bacterial species, are a sustainable technology for dimethoate bioremediation from environmental samples. Yet, new microbial species or consortia should be explored.
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Omics studies (metagenomics, transcriptomics, metabolomics, proteomics) for marine oil biodegradation research increased rapidly after the 2010 Deepwater Horizon (DWH) accident in the Gulf of Mexico. Since then, it has been demonstrated how omics techniques can be used to model and better understand pre-spill environments, monitoring during a spill and post-spill. Data that encompass everything from the ecosystem to the molecular level are needed for understanding the complicated process of petroleum biodegradation in marine environments. Consequently, using omics for monitoring oil in the ocean will help in developing more robust systems models and would make responses to spills much more defensible in terms of risks to the environment and people. Omics is enabling for a Systems Biology approach to oil spills which allows a search for hidden interactions and attributes at different trophic levels because ‘the whole is greater than the sum of its parts’.
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The application of dispersants to an oil-slick is a key remediation tool and thus understanding its effectiveness is vital. Two in situ oil slicks were created in the North Sea (off the coast of The Netherlands), one left to natural processes whilst dispersant (Slickgone NS) was applied to the other. GC-MS analysis of seawater from the surface slick, and at 1.5 and 5 m below the slick, revealed only two samples with measurable hydrocarbons (221 ± 92 μg ml−1 seawater), from the surface of the “Slickgone Dispersed” oil-slick ~25.5 hours after oil-slick formation, which was likely due to environmental conditions hindering sampling. Additionally, 16S rRNA gene quantitative PCR and amplicon analysis revealed extremely limited growth of obligate hydrocarbonoclastic bacteria (OHCB), detected at a relative abundance of <1×10-6 %. Furthermore, the Ecological Index of Hydrocarbon Exposure (EIHE) score, which quantifies the proportion of the bacterial community with hydrocarbon-biodegradation potential, was extremely low at 0.012 (scale of 0 – 1). This very low abundance of hydrocarbon-degrading bacteria at the time of sampling, even in samples with measurable hydrocarbons, could potentially be attributed to nutrient limitation (~25.5 hours after oil-slick creation total inorganic nitrogen was 3.33 μM and phosphorus was undetectable). The results of this study highlight a limited capacity for the environment, during this relatively short period, to naturally attenuate oil.
Chapter
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Hydrocarbon-degrading bacteria in the oceans and seas occur in relatively low abundances, but they become enriched in the presence of hydrocarbons, such as during oil spills. Though some species, mainly those found in anoxic sediments, are capable of anaerobic degradation of hydrocarbons, most marine hydrocarbon-degrading bacteria are strictly aerobic. Those with an almost exclusive preference for hydrocarbons as a sole source of carbon and energy are the obligate hydrocarbon degraders—organisms that are fundamentally important in the natural purging of oil-polluted marine environments. One mechanism through which these bacteria degrade hydrocarbons is via their production of biosurfactants that reduce the interfacial tension between water and oil, and break up oil into small droplets, in turn making the oil more accessible to these bacteria for degradation. Hydrocarbon-degrading bacteria, and the biosurfactants they produce, have found enormous use in bioremediation and in enhanced oil recovery.
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The biological effects and expected fate of the vast amount of oil in the Gulf of Mexico from the Deepwater Horizon blowout are unknown owing to the depth and magnitude of this event. Here, we report that the dispersed hydrocarbon plume stimulated deep-sea indigenous -Proteobacteria that are closely related to known petroleum degraders. Hydrocarbon-degrading genes coincided with the concentration of various oil contaminants. Changes in hydrocarbon composition with distance from the source and incubation experiments with environmental isolates demonstrated faster-than-expected hydrocarbon biodegradation rates at 5 C. Based on these results, the potential exists for intrinsic bioremediation of the oil plume in the deep-water column without substantial oxygen drawdown.
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We hypothesized that methane from the Deepwater Horizon oil spill was quantitatively consumed and presented results from four tests supporting this finding. Subsequent published studies provide further support for our conclusions. We refute the criticisms by Joye et al., which are incorrect, internally contradictory, based on flow-rate estimates that exceed consensus values, and overall do not disprove our hypothesis or invalidate its underlying assumptions.
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The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.
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Phytoplankton blooms characterize temperate ocean margin zones in spring. We investigated the bacterioplankton response to a diatom bloom in the North Sea and observed a dynamic succession of populations at genus-level resolution. Taxonomically distinct expressions of carbohydrate-active enzymes (transporters; in particular, TonB-dependent transporters) and phosphate acquisition strategies were found, indicating that distinct populations of Bacteroidetes, Gammaproteobacteria, and Alphaproteobacteria are specialized for successive decomposition of algal-derived organic matter. Our results suggest that algal substrate availability provided a series of ecological niches in which specialized populations could bloom. This reveals how planktonic species, despite their seemingly homogeneous habitat, can evade extinction by direct competition.
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