Microbial responses to the Deepwater Horizon oil spill: from coastal wetlands to the deep sea

Autochthonous psychrophilic hydrocarbonoclastic bacteria and its ecological function in contaminated cold environments

Petroleum hydrocarbon (PH) pollution has mostly been caused by oil exploration, extraction, and transportation activities in colder regions, particularly in the Arctic and Antarctic regions, where it serves as a primary source of energy. Due to the resilience feature of nature, such polluted environments become the realized ecological niches for a wide community of psychrophilic hydrocarbonoclastic bacteria (PHcB). In contrast, to other psychrophilic species, PHcB is extremely cold-adapted and has unique characteristics that allow them to thrive in greater parts of the cold environment burdened with PHs. The stated group of bacteria in its ecological niche aids in the breakdown of litter, turnover of nutrients, cycling of carbon and nutrients, and bioremediation. Although such bacteria are the pioneers of harsh colder environments, their growth and distribution remain under the influence of various biotic and abiotic factors of the environment. The review discusses the prevalence of PHcB community in colder habitats, the metabolic processes involved in the biodegradation of PH, and the influence of biotic and abiotic stress factors. The existing understanding of the PH metabolism by PHcB offers confirmation of excellent enzymatic proficiency with high cold stability. The discovery of more flexible PH degrading strategies used by PHcB in colder environments could have a significant beneficial outcome on existing bioremediation technologies. Still, PHcB is least explored for other industrial and biotechnological applications as compared to non-PHcB psychrophiles. The present review highlights the pros and cons of the existing bioremediation technologies as well as the potential of different bioaugmentation processes for the effective removal of PH from the contaminated cold environment. Such research will not only serve to investigate the effects of pollution on the basic functional relationships that form the cold ecosystem but also to assess the efficacy of various remediation solutions for diverse settings and climatic conditions.

Limited impact of weathered residues from the Deepwater Horizon oil spill on the gut-microbiome and foraging behavior of sheepshead minnows (Cyprinodon variegatus)

The Deepwater Horizon disaster of April 2010 was the largest oil spill in U.S. history and exerted catastrophic effects on several ecologically important fish species in the Gulf of Mexico (GoM). Within fish, the microbiome plays a key symbiotic role in maintaining host health and aids in acquiring nutrients, supporting immune function, and modulating behavior. The aim of this study was to examine if exposure to weathered oil might produce significant shifts in fish gut-associated microbial communities as determined from taxa and genes known for hydrocarbon degradation, and whether foraging behavior was affected. The gut microbiome (16S rRNA and shotgun metagenomics) of sheepshead minnow (Cyprinodon variegatus) was characterized after fish were exposed to oil in High Energy Water Accommodated Fractions (HEWAF; tPAH = 81.1 ± 12.4 µg/L) for 7 days. A foraging behavioral assay was used to determine feeding efficiency before and after oil exposure. The fish gut microbiome was not significantly altered in alpha or beta diversity. None of the most abundant taxa produced any significant shifts as a result of oil exposure, with only rare taxa showing significant shifts in abundance between treatments. However, several bioindicator taxa known for hydrocarbon degradation were detected in the oil treatment, primarily Sphingomonas and Acinetobacter. Notably, the genus Stenotrophomonas was detected in high abundance in 16S data, which previously was not described as a core member of fish gut microbiomes. Data also demonstrated that behavior was not significantly affected by oil exposure. Potential low bioavailability of the oil may have been a factor in our observation of minor shifts in taxa and no behavioral effects. This study lays a foundation for understanding the microbiome of captive sheepshead minnows and indicates the need for further research to elucidate the responses of the fish gut-microbiome under oil spill conditions.

Functional response of microbial communities in lab-controlled oil-contaminated marine sediment

Crude oil contamination is one of the biggest problems in modern society. As oil enters into contact with the environment, especially if the point of contact is a body of water, it begins a weathering process by mixing and spreading. This is dangerous to local living organisms' communities and can impact diversity. However, despite unfavorable conditions, some microorganisms in these environments can survive using hydrocarbons as a nutrient source. Thus, understanding the local community dynamics of contaminated areas is essential. In this work, we analyzed the 16S rRNA amplicon sequencing and metatranscriptomic data of uncontaminated versus contaminated shallow marine sediment from publicly available datasets. We investigated the local population's taxonomic composition, species diversity, and fluctuations over time. Co-expression analysis coupled with functional enrichment showed us a prevalence of hydrocarbon-degrading functionality while keeping a distinct transcriptional profile between the late stages of oil contamination and the uncontaminated control. Processes related to the degradation of aromatic compounds and the metabolism of propanoate and butanoate were coupled with evidence of enhanced activity such as flagellar assembly and two-component system. Many enzymes of the anaerobic toluene degradation pathways were also enriched in our results. Furthermore, our diversity and taxonomical analyses showed a prevalence of the class Desulfobacteria, indicating interesting targets for bioremediation applications on marine sediment.

Metatranscriptomic responses and microbial degradation of background polycyclic aromatic hydrocarbons in the coastal Mediterranean and Antarctica

Although microbial degradation is a key sink of polycyclic aromatic hydrocarbons (PAH) in surface seawaters, there is a dearth of field-based evidences of regional divergences in biodegradation and the effects of PAHs on site-specific microbial communities. We compared the magnitude of PAH degradation and its impacts in short-term incubations of coastal Mediterranean and the Maritime Antarctica microbiomes with environmentally relevant concentrations of PAHs. Mediterranean bacteria readily degraded the less hydrophobic PAHs, with rates averaging 4.72 ± 0.5 ng L h-1. Metatranscriptomic responses showed significant enrichments of genes associated to horizontal gene transfer, stress response, and PAH degradation, mainly harbored by Alphaproteobacteria. Community composition changed and increased relative abundances of Bacteroidota and Flavobacteriales. In Antarctic waters, there was no degradation of PAH, and minimal metatranscriptome responses were observed. These results provide evidence for factors such as geographic region, community composition, and pre-exposure history to predict PAH biodegradation in seawater.

Alteration in Community Dynamics of Chaetoceros curvisetus and Bacterioplankton Communities in Response to Surfactin Exposure

The use of surfactin is a promising method to mitigate algal blooms. However, little is known about surfactin toxicity to algae and bacterioplankton. Here, we treated Chaetoceros curvisetus, the dominant species of algal blooms in the East China Sea, with 0, 0.5, 1, 2, 3, and 4 mg/L of surfactin for 96 h to investigate temporal variability. Our results showed that low concentrations of surfactin (<2 mg/L) changed the cell morphology of C. curvisetus, and higher concentrations (>3 mg/L) had lethal effects. Meanwhile, we examined the community dynamics of the free-living (FL, 0.22-5 μm) and particle-attached (PA, >5 μm) bacterioplankton of C. curvisetus in response to different surfactin concentrations and cultivation periods. Both PA and FL bacterioplankton were mainly composed of Proteobacteria, Actinobacteria, and Bacteroidetes, while FL bacterioplankton were more diverse than PA bacterioplankton. The variations of FL and PA bacterioplankton were significantly constrained by the surfactin concentration. Surfactin changed the lifestyle of some bacterioplankton from FL to PA, which mainly belonged to abundant bacterioplankton. Furthermore, we identified some surfactin-sensitive species/taxa. Our study will help enhance the ability to predict marine microbial responses under the effect of surfactin, providing a research foundation for this new harmful algal bloom mitigation method.

Functional redundancy in response to runoff input upholds microbial community in hydrocarbon-contaminated land-sea continuum

An experimental approach mimicking the land-sea continuum in microcosms was developed in order to determine the effect of the terrigenous inputs by soil runoff on the microbial functional potential in hydrocarbon (HC) contaminated marine coastal sediment. We hypothesized that the coalescent event increases the functional potential of microbial communities in marine coastal sediments, influencing the fate of HC in marine coastal ecosystems. The microbial functional potential including the HC degradation ability was assessed by DNA-array to compare the sediment receiving or not terrigenous inputs. The removal of HC and the functional gene richness in sediment was unchanged with the terrigenous inputs. However, the gene variants (GVs) composition was modified indicating functional redundancy. In addition, functional indicators including GVs related to sulfite reduction, denitrification and polyaromatic degradation were identified in higher proportion in sediment receiving terrigenous inputs. The terrigenous inputs modified the functional co-occurrence networks, showing a reorganization of the GVs associations with an increase of the network complexity. Different keystone GVs ensuring similar functions were identified in networks with or without terrigenous inputs, further confirming functional redundancy. We argue that functional redundancy maintains the structure of microbial community in hydrocarbon-contaminated land-sea continuum mixing zone. Our results provide helpful functional information for the monitoring and management of coastal environment affected by human land-based activities.

Multi-year seabed environmental baseline in deep-sea offshore oil prospective areas established using microbial biodiversity

Microorganisms are the ocean's first responders to marine pollution events, yet baseline studies rarely focus on microbial communities. Temporal and spatial microbial biodiversity baselines were established using bacterial 16S rRNA gene amplicon sequencing of seafloor sediments in a deep-water oil prospective area along the Scotian Slope off Canada's east coast sampled during 2015-2018. Bacterial diversity was generally similar in space and time, with members of the family Woeseiaceae detected consistently in >1 % relative abundance, similar to seabed sediments in other parts of the world. Anomalous biodiversity results at one site featured lower Woeseiaceae as well as higher levels of bacterial groups specifically associated with cold seeps such as Aminicenantes. This was unexpected given that site selection was based on sediment geochemistry not revealing any petroleum hydrocarbons in these locations. This finding highlights the sensitivity and specificity of microbial DNA sequencing in environmental monitoring. Microbiome assessments like this one represent an important strategy for incorporating microbial biodiversity as a new and useful metric for establishing robust environmental baselines that are necessary for understanding ecosystem responses to marine pollution.

The shifting research landscape for PAH bioremediation in water environment: a bibliometric analysis on three decades of development

Polycyclic aromatic hydrocarbons (PAHs) with their carcinogenic, teratogenic, and mutagenic effects can cause great damage to the ecosystem and public health when present in water. With bioremediation, PAH contamination in water environment can be greatly reduced in an eco-friendly manner. It has thus become the research focus for many environmental scientists. In this study, a bibliometric analysis on three-decade (1990-2022) development of PAH bioremediation in water environment was conducted from temporal and spatial dimensions using CiteSpace. A total of 2480 publications, obtained from Web of Science core collection database, were used to explore the basic characteristics, hotspots, and prospects of the research area. The results showed that (1) bioremediation/biodegradation of PAHs in water environment has been getting researchers' attention since 1990, and is gaining even more traction as time goes on. (2) In terms of countries, China and the USA were the major contributors in this research area, while at the institutional level, the Chinese Academy of Sciences has produced the most research results. However, international cooperation across regions was lacking in the field. (3) Environment Science and Technology, Chemosphere, Applied and Environment Microbiology, Journal of Hazardous Materials, and Environment Pollution were the 5 most cited journals in this field. (4) There were three major stages the field has gone through, each with distinct research hotspots, including initial stage (1990-1994), mechanism investigation (1995-2000), and application exploration (2001-2010; 2011-2022). Finally, research perspectives were proposed, covering three directions, namely, bioavailability, immobilization, and viable but nonculturable (VBNC) bacteria.

Dosage concentration and pulsing frequency affect the degradation efficiency in simulated bacterial polycyclic aromatic hydrocarbon-degrading cultures

A major source of anthropogenic polycyclic aromatic hydrocarbon (PAH) inputs into marine environments are diffuse emissions which result in low PAH concentrations in the ocean water, posing a potential threat for the affected ecosystems. However, the remediation of low-dosage PAH contaminations through microbial processes remains largely unknown. Here, we developed a process-based numerical model to simulate batch cultures receiving repeated low-dosage naphthalene pulses compared to the conventionally used one-time high-dosage. Pulsing frequency as well as dosage concentration had a large impact on the degradation efficiency. After 10 days, 99.7%, 97.2%, 86.6%, or 83.5% of the 145 mg L^-1 naphthalene was degraded when given as a one-time high-dosage or in 2, 5, or 10 repeated low-concentration dosages equally spaced throughout the experiment, respectively. If the simulation was altered, giving the system that received 10 pulses time to recover to 99.7%, pulsing patterns affected the degradation of naphthalene. When pulsing 10 days at once per day, naphthalene accumulated following each pulse and if the degradation was allowed to continue until the recovered state was reached, the incubation time was prolonged to 17 days with a generation time of 3.81 days. If a full recovery was conditional before the next pulse was added, the scenario elongated to 55 days and generation time increased to 14.15 days. This indicates that dissolution kinetics dominate biodegradation kinetics, and the biomass concentration of PAH-degrading bacteria alone is not a sufficient indicator for quantifying active biodegradation. Applying those findings to the environment, a one-time input of a high dosage is potentially degraded faster than repeated low-dosage PAH pollution and repeated low-dosage input could lead to PAH accumulation in vulnerable pristine environments. Further research on the overlooked field of chronic low-dosage PAH contamination is necessary.

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

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

Impacts of dispersants on microbial communities and ecological systems

Accidental oil spills can result in catastrophic ecological insults and therefore require rapid intervention to mitigate the potential impacts to aquatic ecosystems. One of the largest oil spills, known as the Deepwater Horizon oil spill, occurred in the Spring of 2010 near the coast of Louisiana (USA) due to an explosion during oil drilling activities. Millions of gallons of oil were released into the Gulf of Mexico, impacting thousands of ocean miles and coastal areas linked to the gulf. Among the actions taken during the remediation efforts was the unprecedented large use of Corexit dispersants, including at the subsurface to prevent oil from reaching the surface. While there is evidence that dispersants can accelerate the biodegradation of oil, reports on their potential toxicity to aquatic biota and to microbial functions have also been documented. In this review, we will examine the most recent literature on the impact of dispersants on microbial communities implicated in oil degradation and overall ecological networks. The primary focus will be on studies using Corexit but other dispersants will be discussed if data are available. We will share the literature gaps identified and discuss future work that is needed to reconcile some of the discrepancies found on the effectiveness of dispersants on oil degradation and their potential toxicity. KEY POINTS: • Chemical dispersants have been applied as a chemical response measure for oil spills. • The effects of chemical dispersants on microbial communities have been the subject of substantial research. • This work seeks to review recent work on the impact of chemical dispersants on oil biodegradation, microbial communities, and ecosystems.

Anthropogenic impact accelerates antibiotic resistome diversity in the mangrove sediment of Indian Sundarban

Mangroves are situated in convergence zones between fresh and marine water and are prone to pollution and deforestation. This study explored the microbiome structure, function and antibiotic resistome of Indian Sundarban. The taxonomic Chao1 estimated diversity was highest in uninhabited Kalash (1204.64 ± 12.72) and lowest in Godkhali, which experiences considerable human activities (1158.76 ± 11.18). The alpha diversity showed negative correlation (p < 0.05) with PAH such as Acenaphthene (r = -0.56), Acenaphthylene (r = -0.62), Fluoranthene (r = -0.59), Fluorene (r = -0.55), Phenanthrene (r = -0.57), while the biochemical parameters phosphate (r = 0.58) and salinity (r = 0.58) had a significant (p < 0.05) positive correlation. The data suggest the importance of physicochemical parameters in maintaining the mangrove microbiome. The taxonomic composition was dominated by Proteobacteria (54.12 ± 0.37). All sites were dominated by ARGs such as rpoB2, cpxR, ompR, camP, and bacA. Comparing the Sundarban mangrove sediment resistome with mangrove from other sites in India (Kerala) and China (Guangxi, Hainan, and Shenzhen) suggested that resistome from Indian mangrove has a significantly (p < 0.05) higher ARG diversity compared to Chinese mangroves. Yet, the abundance of the ARG was significantly (p < 0.05) lower in the Indian mangroves posing a much greater risk if enriched. The study suggests that anthropogenic activities and pollution degrade the microbiome diversity, disturb the microbiome functions, and enrich ARGs.

Genome-resolved analyses show an extensive diversification in key aerobic hydrocarbon-degrading enzymes across bacteria and archaea

Background

Hydrocarbons (HCs) are organic compounds composed solely of carbon and hydrogen that are mainly accumulated in oil reservoirs. As the introduction of all classes of hydrocarbons including crude oil and oil products into the environment has increased significantly, oil pollution has become a global ecological problem. However, our perception of pathways for biotic degradation of major HCs and key enzymes in these bioconversion processes has mainly been based on cultured microbes and is biased by uneven taxonomic representation. Here we used Annotree to provide a gene-centric view of the aerobic degradation ability of aliphatic and aromatic HCs in 23,446 genomes from 123 bacterial and 14 archaeal phyla. 

Results

Apart from the widespread genetic potential for HC degradation in Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes, genomes from an additional 18 bacterial and 3 archaeal phyla also hosted key HC degrading enzymes. Among these, such degradation potential has not been previously reported for representatives in the phyla UBA8248, Tectomicrobia, SAR324, and Eremiobacterota. Genomes containing whole pathways for complete degradation of HCs were only detected in Proteobacteria and Actinobacteriota. Except for several members of Crenarchaeota, Halobacterota, and Nanoarchaeota that have tmoA, ladA, and alkB/M key genes, respectively, representatives of archaeal genomes made a small contribution to HC degradation. None of the screened archaeal genomes coded for complete HC degradation pathways studied here; however, they contribute significantly to peripheral routes of HC degradation with bacteria.

Conclusion

Phylogeny reconstruction showed that the reservoir of key aerobic hydrocarbon-degrading enzymes in Bacteria and Archaea undergoes extensive diversification via gene duplication and horizontal gene transfer. This diversification could potentially enable microbes to rapidly adapt to novel and manufactured HCs that reach the environment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08906-w.

Preparation and oil absorption performance of ATP/P(MMA-BMA-St)/Fe

In this paper, oil-in-water-in-oil (O/W/O) double Pickering emulsions were prepared by purified and modified attapulgite (ATP), and modified nano-Fe3O4 as stable particles. By using the Pickering emulsion as a template and using methyl methacrylate (MMA), butyl methacrylate ester (BMA) and styrene (St) as monomers, ATP/P(MMA-BMA-St)/Fe3O4 composite porous resins were then prepared. The oil absorption performance of the composites was investigated. The results showed that the composite materials prepared by the double Pickering emulsion template method exhibited a three-dimensional (3D) porous structure. When using the optimal conditions (mMMA:mBMA = 3:2, m(MMA+BMA):mSt = 1:2, initiator = 5.33%, crosslinking agent = 20%, modified attapulgite = 0.33% and oil phase/water phase = 1:4), the prepared porous material had the best oil absorption performance, resulting in a diesel oil absorption rate and oil retention rate of 897.29 and 84.76% respectively. This study provides a simple, economic and environmentally friendly method for the preparation of inorganic–organic composite porous materials, which has great application potential in the field of oil treatment.

Snorkels enhance alkanes respiration at ambient and increased hydrostatic pressure (10 MPa) by either supporting the TCA cycle or limiting alternative routes for acetyl-CoA metabolism

The impact of piezosensitive microorganisms is generally underestimated in the ecology of underwater environments exposed to increasing hydrostatic pressure (HP), including the biodegradation of crude oil components. Yet, no isolated pressure-loving (piezophile) microorganism grows optimally on hydrocarbons, and no isolated piezophile at all has a HP optimum <10 MPa (e.g. 1000 m below sea water level). Piezosensitive heterotrophs are thus largely accountable for oil clean up < 10 MPa, however, they are affected by such a mild HP increase in ways which are not completely clear. In a first study, the application of a bioelectrochemical system (called "oil-spill snorkel") enhanced the alkane oxidation capacity in sediments collected at surface water but tested up to 10 MPa. Here, the fingerprint left on transcript abundance was studied to explore which metabolic routes are 1) supported by snorkels application and 2) negatively impacted by HP increase. Transcript abundance was comparable for beta-oxidation across all treatments (also at a taxonomical level), while the metabolism of acetyl-CoA was highly impacted: at either 0.1 or 10 MPa, snorkels supported acetyl-CoA oxidation within the TCA cycle, while in negative controls using non-conductive rods several alternative routes for acetyl-CoA were stimulated (including those leading to internal carbon reserves e.g. 2,3 butanediol and dihydroxyacetone). In general, increased HP had opposite effects as compared to snorkels, thus indicating that snorkels could enhance hydrocarbons oxidation by alleviating in part the stressing effects imposed by increased HP on the anaerobic, respiratory electron transport chain. 16S rRNA gene analysis of sediments and biofilms on snorkels suggest a crosstalk between oil-degrading, sulfate-reducing microorganisms and sulfur oxidizers. In fact, no sulfur was deposited on snorkels, however, iron, aluminum and phosphorous were found to preferentially deposit on snorkels at 10 MPa. This data indicates that a passive BES such as the oil-spill snorkel can mitigate the stress imposed by increased HP on piezosensitive microorganisms (up to 10 MPa) without being subjected to passivation. An improved setup applying these principles can further support this deep-sea bioremediation strategy.

Assessing Microbial Corrosion Risk on Offshore Crude Oil Production Topsides under Conditions of Nitrate and Nitrite Treatment for Souring

Oilfield souring is a detrimental effect caused by sulfate-reducing microorganisms that reduce sulfate to sulfide during their respiration process. Nitrate or nitrite can be used to mitigate souring, but may also impart a corrosion risk. Produced fluids sampled from the topside infrastructure of two floating, production, storage, and offloading (FPSO) vessels (Platform A and Platform B) were assessed for microbial corrosion under nitrate and nitrite breakthrough conditions using microcosm tests incubated at 54 °C. Microbial community compositions on each individual FPSO were similar, while those between the two FPSO vessels differed. Platform B microbial communities responded as expected to nitrate breakthrough conditions, where nitrate-reducing activity was enhanced and sulfate reduction was inhibited. In contrast, nitrate treatments of Platform A microbial communities were not as effective in preventing sulfide production. Nitrite breakthrough conditions had the strongest sulfate reduction inhibition in samples from both platforms, but exhibited the highest pitting density. Live experimental replicates with no nitrate or nitrite additive yielded the highest general corrosion rates in the study (up to 0.48 mm/year), while nitrate- or nitrite-treated fluids revealed general corrosion rates that are considered low or moderate (<0.12 mm/year). Overall, the results of this study provide a description of nitrogen- and sulfur-based microbial activities under thermophilic conditions, and their risk for MIC that can occur along fluid processing lines on FPSO topsides that process fluids during offshore oil production operations.

Biosurfactants and chemotaxis interplay in microbial consortium-based hydrocarbons degradation

Hydrocarbons are routinely detected at low concentrations, despite the degrading metabolic potential of ubiquitous microorganisms. The potential drivers of hydrocarbons persistence are lower bioavailability and mass transfer limitation. Recently, bioremediation strategies have developed rapidly, but still, the solution is not resilient. Biosurfactants, known to increase bioavailability and augment biodegradation, are tightly linked to bacterial surface motility and chemotaxis, while chemotaxis help bacteria to locate aromatic compounds and increase the mass transfer. Harassing the biosurfactant production and chemotaxis properties of degrading microorganisms could be a possible approach for the complete degradation of hydrocarbons. This review provides an overview of interplay between biosurfactants and chemotaxis in bioremediation. Besides, we discuss the chemical surfactants and biosurfactant-mediated biodegradation by microbial consortium.

Biodiversity and Biogeography of Abundant and Rare Microbial Assemblages in the Western Subtropical Pacific Ocean

The levels of chlorophyll a and nutrient concentrations in the surface waters of the western subtropical Pacific Ocean are among the lowest globally. In addition, our knowledge of basin-scale diversity and biogeography of microbial communities in this vast extremely oligotrophic environment is still rather limited. Here, high-throughput sequencing was used to examine the biodiversity and biogeography of abundant and rare microbial assemblages throughout the water column from the surface to a depth of 3,000 m across a horizontal distance of 1,100 km in the western Pacific Ocean. Microbial alpha diversity in the 200-m layer was higher than at other depths, with Gammaproteobacteria, Alphaproteobacteria, and Clostridia as the dominant classes in all samples. Distinctly vertical distributions within the microbial communities were revealed, with no difference horizontally. Some microbes exhibited depth stratification. For example, the relative abundances of Cyanobacteria and Alphaproteobacteria decreased with depth, while Nitrososphaeria, Actinobacteria, and Gammaproteobacteria increased with depth in the aphotic layers. Furthermore, we found that environmental (selective process) and spatial (neutral process) factors had different effects on abundant and rare taxa. Geographical distance showed little effect on the dispersal of all and abundant taxa, while statistically significant distance-decay relationships were observed among the rare taxa. Temperature and chlorophyll a were strongly associated with all, abundant, and rare taxa in the photic layers, while total inorganic nitrogen was recognized as the crucial factor in the aphotic layers. Variance partitioning analysis indicated that environmental selection played a relatively important role in shaping all and abundant taxa, while the variation in rare taxa explained by environmental and spatial processes was relatively low, as more than 70% of the variation remained unexplained. This study provides novel knowledge related to microbial community diversity in the western subtropical Pacific Ocean, and the analyzes biogeographical patterns among abundant and rare taxa.

Natural attenuation of oil in marine environments: A review

Natural attenuation is an important process for oil spill management in marine environments. Natural attenuation affects the fate of oil by physical, chemical, and biological processes, which include evaporation, dispersion, dissolution, photo-oxidation, emulsification, oil particle aggregation, and biodegradation. This review examines the cumulative knowledge regarding these natural attenuation processes as well as their simulation and prediction using modelling approaches. An in-depth discussion is provided on how oil type, microbial community and environmental factors contribute to the biodegradation process. It describes how our understanding of the structure and function of indigenous oil degrading microbial communities in the marine environment has been advanced by the application of next generation sequencing tools. The synergetic and/or antagonist effects of oil spill countermeasures such as the application of chemical dispersants, in-situ burning and nutrient enrichment on natural attenuation were explored. Several knowledge gaps were identified regarding the synergetic and/or antagonistic effects of active response countermeasures on the natural attenuation/biodegradation process. This review highlighted the need for field data on both the effectiveness and potential detrimental effects of oil spill response options to support modelling and decision-making on their selection and application.

Dissolved organic matter production from herder application and in-situ burning of crude oil at high latitudes: Bioavailable molecular composition patterns and microbial community diversity effects

Chemical herders and in-situ burning (ISB) are designed to mitigate the effects that oil spills may have on the high latitude marine environment. Little information exists on the water solubilization of petroleum residues stemming from chemically herded ISB and whether these bioavailable compounds have measurable impacts on marine biota. In this experiment, we investigated the effects of Siltech OP40 and crude oil ISB on a) petroleum-derived dissolved organic matter (DOM_HC) composition and b) seawater microbial community diversity over 28 days at 4 °C in aquarium-scale mesocosms. Ultra-high resolution mass spectrometry and fluorescence spectroscopy revealed increases in aromaticity over time, with ISB and ISB+OP40 samples having higher % aromatic classes in the initial incubation periods. ISB+OP40 contained a nearly 12-fold increase in the number of DOM_HC formulae relative to those before ISB. 16S rRNA gene sequencing identified differences in microbial alpha diversity between seawater, ISB, OP40, and ISB+OP40. Microbial betadiversity shifts were observed that correlated strongly with aromatic/condensed relative abundance and incubation time. Proteobacteria, specifically from the genera Marinomonas and Perlucidibaca experienced -22 and +24 log₂-fold changes in ISB+OP40 vs. seawater, respectively. These findings provide an important opportunity to advance our understanding of chemical herders and ISB in the high latitude marine environment.

Chemical Diversity and Antimicrobial Potential of Cultivable Fungi from Deep-Sea Sediments of the Gulf of Mexico

A collection of 29 cultivable fungal strains isolated from deep-sea sediments of the Gulf of Mexico were cultivated under the “one strain, many compounds” approach to explore their chemical diversity and antimicrobial potential. From the 87 extracts tested, over 50% showed antimicrobial activity, and the most active ones were those from cultures grown at 4 °C in darkness for 60 days (resembling deep-sea temperature). PCA analysis of the LC-MS data of all the extracts confirmed that culture temperature is the primary factor in the variation of the 4462 metabolite features, accounting for 21.3% of the variation. The bioactivity-guided and conventional chemical studies of selected fungal strains allowed the identification of several active and specialized metabolites. Finally, metabolomics analysis by GNPS molecular networking and manual dereplication revealed the biosynthetic potential of these species to produce interesting chemistry. This work uncovers the chemical and biological study of marine-derived fungal strains from deep-sea sediments of the Gulf of Mexico.

Oil contamination drives the transformation of soil microbial communities: Co-occurrence pattern, metabolic enzymes and culturable hydrocarbon-degrading bacteria

The land-based oil extraction activity has led to serious pollution of the soil. While microbes may play an important role in the remediation of contaminated soils, ecological effects of oil pollution on soil microbial relationships remain poorly understood. Here, typical contaminated soils and undisturbed soils from seven oilfields of China were investigated in terms of their physicochemical characteristics, indigenous microbial assemblages, bacterial co-occurrence patterns, and metabolic enzymes. Network visualization based on k-core decomposition illustrated that oil pollution reduced correlations between co-existing bacteria. The core genera were altered to those related with oil metabolism (Pseudarthrobacter, Alcanivorax, Sphingomonas, Chromohalobacter and Nocardioides). Under oil pollution pressure, the indigenous bacteria Gammaproteobacteria was domesticated as biomarker and the enzyme expression associated with the metabolism of toxic benzene, toluene, ethylbenzene, xylene and polycyclic aromatic hydrocarbons was enhanced. Functional pathways of xenobiotics biodegradation were also stimulated under oil contamination. Finally, twelve culturable hydrocarbon-degrading microbes were isolated from these polluted soils and classified into Stenotrophomonas, Delftia, Pseudomonas and Bacillus. These results show that the soil microbial communities are transformed under oil pollution stress, and also provide useful information for future bioremediation processes.

Bacteria-Oil Microaggregates Are an Important Mechanism for Hydrocarbon Degradation in the Marine Water Column

Following oil spills in aquatic environments, oil-associated flocculants observed within contaminated waters ultimately lead to the sedimentation of oil as marine oil snow (MOS). To better understand the role of aggregates in hydrocarbon degradation and transport, we experimentally produced a MOS sedimentation event using Gulf of Mexico coastal waters amended with oil or oil plus dispersant. In addition to the formation of MOS, smaller micrometer-scale (10- to 150-μm) microbial aggregates were observed. Visual inspection of these microaggregates revealed that they were most abundant in the oil-amended treatments and frequently associated with oil droplets, linking their formation to the presence of oil. The peak abundance of the microaggregates coincided with the maximum rates of biological hydrocarbon oxidation estimated by the mineralization of 14C-labeled hexadecane and naphthalene. To elucidate the potential of microaggregates to serve as hot spots for hydrocarbon degradation, we characterized the free-living and aggregate-associated microbial assemblages using 16S rRNA gene sequencing. The microaggregate population was found to be bacterially dominated and enriched with putative hydrocarbon-degrading taxa. Direct observation of some of these taxa using catalyzed reporter deposition fluorescence in situ hybridization confirmed their greater abundance within microaggregates relative to the surrounding seawater. Metagenomic sequencing of these bacteria-oil microaggregates (BOMAs) further supported their community's capacity to utilize a wide variety of hydrocarbon compounds. Taken together, these data highlight that BOMAs are inherent features in the biological response to oil spills and likely important hot spots for hydrocarbon oxidation in the ocean. IMPORTANCE 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. In addition to MOS, we observed micrometer-scale (10- to 150-μm) aggregates whose abundance coincided with maximum rates of hydrocarbon degradation and whose composition was dominated by hydrocarbon-degrading bacteria with the genetic potential to metabolize a range of these compounds. This targeted study examining the role of these bacteria-oil microaggregates in hydrocarbon degradation reveals details of this fundamental component of the biological response to oil spills, and with it, alterations to biogeochemical cycling in the ocean.

Phylogeny and diversity of alkane-degrading enzyme gene variants in the laurentian great lakes and western atlantic

Many aquatic environments are at risk for oil contamination and alkanes are one of the primary constituents of oil. The alkane hydroxylase (AlkB) is a common enzyme used by microorganisms to initiate the process of alkane-degradation. While many aspects of alkane bioremediation have been studied, the diversity and evolution of genes involved in hydrocarbon degradation from environmental settings is relatively understudied. The majority of work done to-date has focused on the marine environment. Here we sought to better understand the phylogenetic diversity of alkB genes across marine and freshwater settings using culture-independent methods. We hypothesized that there would be distinct phylogenetic diversity of alkB genes in freshwater relative to the marine environment. Our results confirm that alkB has distinct variants based on environment while our diversity analyses demonstrate that freshwater and marine alkB communities have unique responses to oil amendments. Our results also demonstrate that in the marine environment, depth is a key factor impacting diversity of alkB genes.

Bacterial responses to background organic pollutants in the northeast subarctic Pacific Ocean

Thousands of man-made synthetic chemicals are released to oceans and compose the anthropogenic dissolved organic carbon (ADOC). Little is known about the effects of this chronic pollution on marine microbiome activities. In this study, we measured the pollution level at three sites in the Northeast Subarctic Pacific Ocean (NESAP) and investigated how mixtures of three model families of ADOC at different environmentally relevant concentrations affected naturally occurring marine bacterioplankton communities' structure and metabolic functioning. The offshore northernmost site (North) had the lowest concentrations of hydrocarbons, as well as organophosphate ester plasticizers, contrasting with the two other continental shelf sites, the southern coastal site (South) being the most contaminated. At North, ADOC stimulated bacterial growth and promoted an increase in the contribution of some Gammaproteobacteria groups (e.g. Alteromonadales) to the 16 rRNA pool. These groups are described as fast responders after oil spills. In contrast, minor changes in South microbiome activities were observed. Gene expression profiles at Central showed the coexistence of ADOC degradation and stress-response strategies to cope with ADOC toxicities. These results show that marine microbial communities at three distinct domains in NESAP are influenced by background concentrations of ADOC, expanding previous assessments for polar and temperate waters.

Effects of Dispersants and Biosurfactants on Crude-Oil Biodegradation and Bacterial Community Succession

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.

Distinct microbial community along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents

The Persian Gulf, hosting ca. 48% of the world's oil reserves, has been chronically exposed to natural oil seepage. Oil spill studies show a shift in microbial community composition in response to oil pollution; however, the influence of chronic oil exposure on the microbial community remains unknown. We performed genome-resolved comparative analyses of the water and sediment samples along Persian Gulf's pollution continuum (Strait of Hormuz, Asalouyeh, and Khark Island). Continuous exposure to trace amounts of pollution primed the intrinsic and rare marine oil-degrading microbes such as Oceanospirillales, Flavobacteriales, Alteromonadales, and Rhodobacterales to bloom in response to oil pollution in Asalouyeh and Khark samples. Comparative analysis of the Persian Gulf samples with 106 oil-polluted marine samples reveals that the hydrocarbon type, exposure time, and sediment depth are the main determinants of microbial response to pollution. High aliphatic content of the pollution enriched for Oceanospirillales, Alteromonadales, and Pseudomonadales whereas, Alteromonadales, Cellvibrionales, Flavobacteriales, and Rhodobacterales dominate polyaromatic polluted samples. In chronic exposure and oil spill events, the community composition converges towards higher dominance of oil-degrading constituents while promoting the division of labor for successful bioremediation.

High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments

Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.

Genome sequence analysis of deep sea Aspergillus sydowii BOBA1 and effect of high pressure on biodegradation of spent engine oil

A deep-sea fungus Aspergillus sydowii BOBA1 isolated from marine sediment at a depth of 3000 m was capable of degrading spent engine (SE) oil. The response of immobilized fungi towards degradation at elevated pressure was studied in customized high pressure reactors without any deviation in simulating in situ deep-sea conditions. The growth rate of A. sydowii BOBA1 in 0.1 MPa was significantly different from the growth at 10 MPa pressure. The degradation percentage reached 71.2 and 82.5% at atmospheric and high pressure conditions, respectively, within a retention period of 21 days. The complete genome sequence of BOBA1 consists of 38,795,664 bp in size, comprises 2582 scaffolds with predicted total coding genes of 18,932. A total of 16,247 genes were assigned with known functions and many families found to have a potential role in PAHs and xenobiotic compound metabolism. Functional genes controlling the pathways of hydrocarbon and xenobiotics compound degrading enzymes such as dioxygenase, decarboxylase, hydrolase, reductase and peroxidase were identified. The spectroscopic and genomic analysis revealed the presence of combined catechol, gentisate and phthalic acid degradation pathway. These results of degradation and genomic studies evidenced that this deep-sea fungus could be employed to develop an eco-friendly mycoremediation technology to combat the oil polluted marine environment. This study expands our knowledge on piezophilic fungi and offer insight into possibilities about the fate of SE oil in deep-sea.

Comparison of Hydrocarbon-Degrading Consortia from Surface and Deep Waters of the Eastern Mediterranean Sea: Characterization and Degradation Potential

The diversity and degradation capacity of hydrocarbon-degrading consortia from surface and deep waters of the Eastern Mediterranean Sea were studied in time-series experiments. Microcosms were set up in ONR7a medium at in situ temperatures of 25 °C and 14 °C for the Surface and Deep consortia, respectively, and crude oil as the sole source of carbon. The Deep consortium was additionally investigated at 25 °C to allow the direct comparison of the degradation rates to the Surface consortium. In total, ~50% of the alkanes and ~15% of the polycyclic aromatic hydrocarbons were degraded in all treatments by Day 24. Approximately ~95% of the total biodegradation by the Deep consortium took place within 6 days regardless of temperature, whereas comparable levels of degradation were reached on Day 12 by the Surface consortium. Both consortia were dominated by well-known hydrocarbon-degrading taxa. Temperature played a significant role in shaping the Deep consortia communities with Pseudomonas and Pseudoalteromonas dominating at 25 °C and Alcanivorax at 14 °C. Overall, the Deep consortium showed a higher efficiency for hydrocarbon degradation within the first week following contamination, which is critical in the case of oil spills, and thus merits further investigation for its exploitation in bioremediation technologies tailored to the Eastern Mediterranean Sea.

A Review and Bibliometric Analysis on Applications of Microbial Degradation of Hydrocarbon Contaminants in Arctic Marine Environment at Metagenomic and Enzymatic Levels

The globe is presently reliant on natural resources, fossil fuels, and crude oil to support the world’s energy requirements. Human exploration for oil resources is always associated with irreversible effects. Primary sources of hydrocarbon pollution are instigated through oil exploration, extraction, and transportation in the Arctic region. To address the state of pollution, it is necessary to understand the mechanisms and processes of the bioremediation of hydrocarbons. The application of various microbial communities originated from the Arctic can provide a better interpretation on the mechanisms of specific microbes in the biodegradation process. The composition of oil and consequences of hydrocarbon pollutants to the various marine environments are also discussed in this paper. An overview of emerging trends on literature or research publications published in the last decade was compiled via bibliometric analysis in relation to the topic of interest, which is the microbial community present in the Arctic and Antarctic marine environments. This review also presents the hydrocarbon-degrading microbial community present in the Arctic, biodegradation metabolic pathways (enzymatic level), and capacity of microbial degradation from the perspective of metagenomics. The limitations are stated and recommendations are proposed for future research prospects on biodegradation of oil contaminants by microbial community at the low temperature regions of the Arctic.

Solid inoculants as a practice for bioaugmentation to enhance bioremediation of hydrocarbon contaminated areas

Vacuum freeze-drying is a scientifically advanced method to prepare solid inoculants from oil degrading bacterium. The introduction of oil-degrading microbes or bioaugmentation can be an efficient way to bioremediate oil spills in marine areas, where oil-degrading bacteria are deficient. The purpose of this study is to evaluate the potential use of solid inoculants of LZ-2 bacteria to enhance the degradation rate of crude oil. In this study, response surface methodology (RSM) was incorporated into the experimental design to optimize a response, which is influenced by different protectants. Our results showed that five factors have interactive and synergistic protective effects on the growth of LZ-2. Optimal growth of freeze-dried LZ-2 (63.8%) was observed with a 10.5% solution of skim milk supplemented with 14.3% sucrose, 14.4% of trehalose, 4.9% of glycerin and 14.7% of β-cyclodextrin. The culture grew in medium containing crude oil (3 g L^-1) at 37 °C at 150 rpm for 30 d, GC and GC-MS analysis showed biodegradation of 44.2 and 21.6% for total saturate and aromatic hydrocarbons respectively. These results indicated that the solid inoculants of LZ-2 bacteria had the potential to be used for ex-situ bioremediation of hydrocarbon pollutants associated with crude oil.

Crude oil pollution and biodegradation at the Persian Gulf: A comprehensive and review study

The Persian Gulf consider as the fundamental biological marine condition between the seas. There is a different assortment of marine life forms including corals, wipes, and fish in this marine condition. Mangrove timberlands are found all through this sea-going biological system. Sullying of the Persian Gulf to oil-based goods is the principle of danger to this marine condition and this contamination can effectively affect this differing marine condition. Numerous specialists examined the result of oil contamination on Persian Gulf marine creatures including corals sponges, bivalves, and fishes. These analysts affirmed this oil contamination on the Persian Gulf significantly diminished biodiversity. Diverse microorganisms fit to consume oil-based commodities detailed by various scientists from the Persian Gulf and their capacity to the debasement of unrefined petroleum has been examined. There has additionally been little exploration of cyanobacteria, yeast, and unrefined petroleum debasing organisms in this sea-going environment. Biosurfactants are amphipathic molecules that upgrade the disintegration of oil and increment their bioavailability to corrupt microscopic organisms. Additionally, biosurfactant-producing bacteria were discovered from the Persian Gulf, and the capability to degradation of crude oil in microscale was evaluated. The current review article aims to collect the finding of various researches performed in the Persian Gulf on oil pollution and crude-oil biodegradation. It is expected that by applying biological methods in combination with mechanical and chemical methods, the hazard consequences of crude-oil contamination on this important aquatic ecosystem at the world will be mitigated and a step towards preserving this diverse marine environment.

Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes

Marine microbes are known to degrade hydrocarbons; however, microbes inhabiting deep-sea sediments remain largely unexplored. Previous studies into the classical pathways of marine microbial metabolism reveal diverse chemistries; however, metabolic profiling of marine microbes cultured with hydrocarbons is limited. In this study, taxonomic (amplicon sequencing) profiles of two environmental deep-sea sediments (>1,200 m deep) were obtained, along with taxonomic and metabolomic (mass spectrometry-based metabolomics) profiles of microbes harbored in deep-sea sediments cultured with hydrocarbons as the sole energy source. Samples were collected from the Gulf of México (GM) and cultured for 28 days using simple (toluene, benzene, hexadecane, and naphthalene) and complex (petroleum API 40) hydrocarbon mixtures as the sole energy sources. The sediment samples harbored diverse microbial communities predominantly classified into Woeseiaceae and Kiloniellaceae families, whereas Pseudomonadaceae and Enterobacteriaceae families prevailed after sediments were cultured with hydrocarbons. Chemical profiling of microbial metabolomes revealed diverse chemical groups belonging primarily to the lipids and lipid-like molecules superclass, as well as the organoheterocyclic compound superclass (ClassyFire annotation). Metabolomic data and prediction of functional profiles indicated an increase in aromatic and alkane degradation in samples cultured with hydrocarbons. Previously unreported metabolites, identified as intermediates in the degradation of hydrocarbons, were annotated as hydroxylated polyunsaturated fatty acids and carboxylated benzene derivatives. In summary, this study used mass spectrometry-based metabolomics coupled to chemoinformatics to demonstrate how microbes from deep-sea sediments could be cultured in the presence of hydrocarbons. This study also highlights how this experimental approach can be used to increase the understanding of hydrocarbon degradation by deep-sea sediment microbes.IMPORTANCE High-throughput technologies and emerging informatics tools have significantly advanced knowledge of hydrocarbon metabolism by marine microbes. However, research into microbes inhabiting deep-sea sediments (>1,000 m) is limited compared to those found in shallow waters. In this study, a nontargeted and nonclassical approach was used to examine the diversity of bacterial taxa and the metabolic profiles of hydrocarbon-degrading deep-sea microbes. In conclusion, this study used metabolomics and chemoinformatics to demonstrate that microbes from deep-sea sediment origin thrive in the presence of toxic and difficult-to-metabolize hydrocarbons. Notably, this study provides evidence of previously unreported metabolites and the global chemical repertoire associated with the metabolism of hydrocarbons by deep-sea microbes.

Difference in the rhizosphere microbiome of Melia azedarach during removal of benzo(a)pyrene from cadmium co-contaminated soil

Benzo(a)pyrene (BaP) is a highly persistent biohazard polyaromatic hydrocarbon and often reported to be present in soils co-contaminated with heavy metals. The present study explains the rhizodegradation of BaP using bacterial consortium in the rhizosphere of Melia azedarach, along with a change in taxonomical and functional properties of the rhizosphere microbiome. The relative abundance of most dominant phylum Proteobacteria was 2% higher with BaP, while in the presence of both BaP and Cd, its abundance was 2.2% lower. Functional metagenome analysis also revealed the shifting of microbial community and functional gene abundance in the favor of xenobiotic compound degradation upon augmentation of bacterial consortium. Interestingly, upon the addition of BaP the range of functional abundance for genes of PAH degradation (0.165-0.19%), was found to be decreasing. However, augmentation of a bacterial consortium led to an increase in its abundance including genes for degradation of benzoate (0.55-0.64%), toluene (0.2-0.22%), naphthalene (0.25-0.295%) irrespective of the addition of BaP and Cd. Moreover, under greenhouse condition, the application of M. azedarach-bacterial consortium enhanced the degradation of BaP in the rhizosphere (88%) after 60 days, significantly higher than degradation in bulk soil (68.22%). The analysis also showed an increase in degradation of BaP by 15% with plant-native microbe association than in bulk soil. Therefore, the association of M. azedarach-bacterial consortium enhanced the degradation of BaP in soil along with the taxonomical and functional attributes of the rhizosphere microbiome.

Characteristics of long-term changes in microbial communities from contaminated sediments along the west coast of South Korea: Ecological assessment with eDNA and physicochemical analyses

The environmental DNA (eDNA) metabarcoding was applied to assess benthic ecological health in the west coast of South Korea by investigating a long-term microbial community change (2015-17). The ecological interaction among microorganisms, from phylum to family level, and their associations to environmental variables across the five regions were highlighted. As part of the study, the available chemistry and toxicological data in the regions during the monitoring periods were incorporated into an integrated sediment triad assessment. The bacterial communities were dominated by Proteobacteria (34.2%), Bacteroidetes (13.8%), and Firmicutes (10.8%). Proteobacteria and Bacteroidetes dominated consistently across regions and years, while Firmicutes and Cyanobacteria significantly varied by region and years (p < 0.05). The abundance of this phylum declined over time with the increasing abundance of Cyanobacteria, indicating their independent interactions to certain environmental changes. Planctomycetes and Gemmatimonadetes linked to some contaminants (ΣPAHs and Cu), implying indicator taxa. Overall, eDNA-based microbial community analysis combined with exposures of contaminants and responses of microorganisms is a promising strategy for the assessment of benthic ecological health in contaminated sediments from coastal waters.

Metagenomic Insights Into the Mechanisms for Biodegradation of Polycyclic Aromatic Hydrocarbons in the Oil Supply Chain

Petroleum is a very complex and diverse organic mixture. Its composition depends on reservoir location and in situ conditions and changes once crude oil is spilled into the environment, making the characteristics associated with every spill unique. Polycyclic aromatic hydrocarbons (PAHs) are common components of the crude oil and constitute a group of persistent organic pollutants. Due to their highly hydrophobic, and their low solubility tend to accumulate in soil and sediment. The process by which oil is sourced and made available for use is referred to as the oil supply chain and involves three parts: (1) upstream, (2) midstream and (3) downstream activities. As consequence from oil supply chain activities, crude oils are subjected to biodeterioration, acidification and souring, and oil spills are frequently reported affecting not only the environment, but also the economy and human resources. Different bioremediation techniques based on microbial metabolism, such as natural attenuation, bioaugmentation, biostimulation are promising approaches to minimize the environmental impact of oil spills. The rate and efficiency of this process depend on multiple factors, like pH, oxygen content, temperature, availability and concentration of the pollutants and diversity and structure of the microbial community present in the affected (contaminated) area. Emerging approaches, such as (meta-)taxonomics and (meta-)genomics bring new insights into the molecular mechanisms of PAH microbial degradation at both single species and community levels in oil reservoirs and groundwater/seawater spills. We have scrutinized the microbiological aspects of biodegradation of PAHs naturally occurring in oil upstream activities (exploration and production), and crude oil and/or by-products spills in midstream (transport and storage) and downstream (refining and distribution) activities. This work addresses PAH biodegradation in different stages of oil supply chain affecting diverse environments (groundwater, seawater, oil reservoir) focusing on genes and pathways as well as key players involved in this process. In depth understanding of the biodegradation process will provide/improve knowledge for optimizing and monitoring bioremediation in oil spills cases and/or to impair the degradation in reservoirs avoiding deterioration of crude oil quality.

Streptomyces sp. S501, a Marine Petroleum-Degrading Actinobacterium Isolated from Sediment of Yalujiang Estuary, Northern China, and Its Genome Annotation

Streptomyces sp. S501, which was isolated from the sediment of Yalujiang Estuary in China, was the first marine Streptomyces species discovered to act as an excellent petroleum degrader. We analyzed the effect of pH, temperature, and concentration of NH₄NO₃ on the petroleum degradation of strain S501, and the optimum biodegradation rate reached 63.02% under the condition of 2 g/L NH₄NO₃ addition at 30 °C and pH 8. The complete genome sequence of Streptomyces sp. S501 was determined by using the PacBio RSII platform, which contains a linear chromosome with 7,173,651 bp and a linear plasmid with 288,181 bp, with GC contents of 71.19% and 67.57%, respectively. The genome sequence suggests that Streptomyces sp. S501 has the ability to degrade several hazardous pollutants, as well as the ability to biosynthesize diverse secondary metabolites and enzymes. There are fifty annotated genes involved in oil component degradation, and there are three genes without known annotation information in Streptomyces sp. S501, which have high homology with genes encoding P450 family enzymes and should be novel genes involved in alkane degradation. This study provides useful genetic information for investigating the molecular mechanisms of marine Streptomyces, with biodegradation and application potential.

Niche Partitioning between Coastal and Offshore Shelf Waters Results in Differential Expression of Alkane and Polycyclic Aromatic Hydrocarbon Catabolic Pathways

In the wake of the Deepwater Horizon oil spill, the taxonomic response of marine microbial communities to oil and dispersants has been extensively studied. However, relatively few studies on the functional response of these microbial communities have been reported, especially in a longitudinal fashion. Moreover, despite the fact that marine oil spills typically impact thousands of square kilometers of both coastal and offshore marine environments, little information is available on how the microbial response to oil and dispersants might differ between these biomes. The results of this study help fill this critical knowledge gap and provide valuable insight into how oil spill response efforts, such as chemically dispersing oil, may have differing effects in neighboring coastal and offshore marine environments.

Marine oil spills can impact both coastal and offshore marine environments, but little information is available on how the microbial response to oil and dispersants might differ between these biomes. Here, we describe the compositional and functional response of microbial communities to different concentrations of oil and chemically dispersed oil in coastal and offshore surface waters from the Texas-Louisiana continental shelf. Using a combination of analytical chemistry and 16S rRNA amplicon and metatranscriptomic sequencing, we provide a broad, comparative overview of the ecological response of hydrocarbon-degrading bacteria and their expression of hydrocarbon-degrading genes in marine surface waters over time between two oceanic biomes. We found evidence for the existence of different ecotypes of several commonly described hydrocarbon-degrading bacterial taxa which behaved differentially in coastal and offshore shelf waters despite being exposed to similar concentrations of oil, dispersants, and nutrients. This resulted in the differential expression of catabolic pathways for n-alkanes and polycyclic aromatic hydrocarbons (PAHs)—the two major categories of compounds found in crude oil—with preferential expression of n-alkane degradation genes in coastal waters while offshore microbial communities trended more toward the expression of PAH degradation genes. This was unexpected as it contrasts with the generally held view that n-alkanes, being more labile, are attacked before the more refractory PAHs. Collectively, our results provide new insights into the existence and potential consequences of niche partitioning of hydrocarbon-degrading taxa between neighboring marine environments.

IMPORTANCE In the wake of the Deepwater Horizon oil spill, the taxonomic response of marine microbial communities to oil and dispersants has been extensively studied. However, relatively few studies on the functional response of these microbial communities have been reported, especially in a longitudinal fashion. Moreover, despite the fact that marine oil spills typically impact thousands of square kilometers of both coastal and offshore marine environments, little information is available on how the microbial response to oil and dispersants might differ between these biomes. The results of this study help fill this critical knowledge gap and provide valuable insight into how oil spill response efforts, such as chemically dispersing oil, may have differing effects in neighboring coastal and offshore marine environments.

Microbial Communities across Global Marine Basins Show Important Compositional Similarities by Depth

The environmental surveys following the 2010 Deepwater Horizon (DWH) spill identified a variety of hydrocarbon-degrading microorganisms, and laboratory studies with field-collected water samples then demonstrated faster-than-expected hydrocarbon biodegradation rates at 5°C. Knowledge about microbial community composition, diversity, and functional metabolic capabilities aids in understanding and predicting petroleum biodegradation by microbial communities in situ and is therefore an important component of the petroleum spill response decision-making process. This study investigates the taxonomic composition of microbial communities in six different global basins where petroleum and gas activities occur. Shallow-water communities were strikingly similar across basins, while deep-water communities tended to show subclusters by basin, with communities from the epipelagic, mesopelagic, and bathypelagic zones sometimes appearing within the same cluster. Microbial taxa that were enriched in the water column in the Gulf of Mexico following the DWH spill were found across marine basins. Several hydrocarbon-degrading genera (e.g., Actinobacteria, Pseudomonas, and Rhodobacteriacea) were common across all basins. Other genera such as Pseudoalteromonas and Oleibacter were highly enriched in specific basins.IMPORTANCE Marine microbial communities are a vital component of global carbon cycling, and numerous studies have shown that populations of petroleum-degrading bacteria are ubiquitous in the oceans. Few studies have attempted to distinguish all of the taxa that might contribute to petroleum biodegradation (including, e.g., heterotrophic and nondesignated microbes that respond positively to petroleum and microbes that grow on petroleum as the sole carbon source). This study quantifies the subpopulations of microorganisms that are expected to be involved in petroleum hydrocarbon biodegradation, which is important information during the decision-making process in the event of a petroleum spill accident.

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

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

Biophysical methods to quantify bacterial behaviors at oil-water interfaces

Motivated by the need for improved understanding of physical processes involved in bacterial biodegradation of catastrophic oil spills, we review biophysical methods to probe bacterial motility and adhesion at oil-water interfaces. This review summarizes methods that probe bulk, average behaviors as well as local, microscopic behaviors, and highlights opportunities for future work to bridge the gap between biodegradation and biophysics.

Microbial eco-physiological strategies for salinity-mediated crude oil biodegradation

Salinity variability strongly affects the behaviors of oil degrading bacteria for spilled oil biodegradation in the marine environment. However, limited studies explored the strategies of microbes on salinity-mediated crude oil biodegradation. In this study, a halotolerant bio-emulsifier producer, Exiguobacterium sp. N41P, was examined as a model strain for Alaska North Slope (ANS) crude oil (0.5%, v/v) biodegradation. Results indicated that Exiguobacterium sp. N41P could tolerant a wide range of salinity (0-120 g/L NaCl) and achieve the highest degradation efficiency under the salinity of 15 g/L NaCl due to the highest biofilm formation ability. Moreover, increased salinity induced decreased cell surface hydrophobicity and a migration of microbial growth from oil phase to aqueous phase, leading to limited bio-emulsifier productivity and depressed degradation of insoluble long-chain n-alkanes while enhancing the degradation of relative soluble naphthalene. Research findings illustrated the microbial eco-physiological mechanism for spilled oil biodegradation under diverse salinities and advanced the understanding of sophisticated marine crude oil biodegradation process.

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

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

Natural attenuation of spilled crude oil by cold-adapted soil bacterial communities at a decommissioned High Arctic oil well site

Romulus C-42 is a decommissioned oil well on Ellesmere Island in the Canadian High Arctic, and is the northernmost well to have produced oil and gas anywhere in the world. The remote site has been untouched since a crude oil spill in 1972, offering a rare opportunity to examine natural attenuation in Arctic soils >40 years after a pollution event. Bacterial community composition in crude oil contaminated soils was significantly different from adjacent background soils. Two members of the genus Rhodanobacter (Alphaproteobacteria) were found consistently in contaminated soils, whereas two members of the genus Sphingomonas (Gammaproteobacteria) appeared opposite to each other, one consistently within the oil contaminated soil and the other consistently in non-oil contaminated soils. GC of soil hydrocarbon extracts revealed moderate levels of biodegradation relative to the original oil produced in 1972. Despite conditions permissive for bacterial activity (>0 °C) being limited to only a few months each year, natural attenuation by cold adapted soil microbial communities has taken place since the oil spill over 40 years ago. Rhodanobacter and Sphingomonas lineages are associated with contaminated and baseline conditions in this extreme environment, revealing the utility of bacterial diversity measurements for assessing long-term responses of Arctic soils to pollution. ORIGINALITY-SIGNIFICANCE STATEMENT: Romulus C-42, the northernmost onshore drilling well in the world, was decommissioned following a small crude oil spill in 1972. Soil bacterial diversity profiles obtained >40 years later revealed significant differences in oil contaminated soils relative to adjacent non-oil contaminated background soils, consistent with evidence for moderate biodegradation of spilled crude oil having taken place since 1972. The results indicate that microbial diversity profiling is an effective tool for assessing natural attenuation in remote High Arctic soils with a history of oil pollution.

Changes in microbial community in the presence of oil and chemical dispersant and their effects on the corrosion of API 5L steel coupons in a marine-simulated microcosm

The influence of crude oil and chemical dispersant was evaluated over planktonic bacteria and biofilms grown on API 5L steel surfaces in microcosm systems. Three conditions were simulated, an untreated marine environment and a marine environment with the presence of crude oil and a containing crude oil and chemical dispersant. The results of coupon corrosion rates indicated that in the oil microcosm, there was a high corrosion rate when compared with the other two systems. Analysis of bacterial communities by 16S rRNA gene sequencing described a clear difference between the different treatments. In plankton communities, the Bacilli and Gammaproteobacteria classes were the most present in numbers of operational taxonomic unit (OTUs). The Vibrionales, Oceanospirillales, and Alteromonadales orders were predominant in the treatment with crude oil, whereas in the microcosm containing oil and chemical dispersant, mainly members of Bacillales order were detected. In the communities analyzed from biofilms attached to the coupons, the most preponderant class was Alphaproteobacteria, followed by Gammaproteobacteria. In the control microcosm, there was a prevalence of the orders Rhodobacterales, Aeromonadales, and Alteromonadales, whereas in the dispersed oil and oil systems, the members of the order Rhodobacterales were present in a larger number of OTUs. These results demonstrate how the presence of a chemical dispersant and oil influence the corrosion rate and bacterial community structures present in the water column and biofilms grown on API 5L steel surfaces in a marine environment. KEY POINTS: • Evaluation of the effects of oil and chemical surfactants on the corrosion of API 5L. • Changes in microbial communities do not present corrosive biofilm on API 5L coupons.

Measuring the biological impact of drilling waste on the deep seafloor: An experimental challenge

The depletion of traditional oil fields is driving the oil & gas industry to explore new exploitation sites previously considered as unprofitable. Deep-sea oil fields represent one of these new areas of exploitation. Well drilling during exploration and production operations generate large quantities of drilling waste whose biological impact on the deep-sea floor remains largely unknown. Because of the harsh abiotic factors characterizing this environment, the evaluation of this impact remains challenging. High hydrostatic pressure is the prominent factor which will affect in-situ biological processes. This review will examine the feedback on the various strategies used to evaluate the biological impact of deep-sea drilling waste deposition as well as the current technological limitations. Given the complexity of this issue, a good perspective strategy would be to trend towards the research and development of more relevant bioassays, especially considering the crucial factor of hydrostatic pressure.