Diesel and Crude Oil Biodegradation by Cold-Adapted Microbial Communities in the Labrador Sea

Enhanced crude oil degradation observed in sea ice following bioaugmentation with arctic bacteria

Petroleum-derived contamination is a growing hazard for the Arctic Ocean and northern marine transportation corridors. In northern settings where the accessibility to oil spills can be limited, natural attenuation is the most promising remediation process. The goal of the presented research is to evaluate the impact of biodegradation on crude oil inside sea ice. To this end, a bioremediation experiment was conducted at the Sea-ice Environmental Research Facility, University of Manitoba. The experiment utilized two mesocosm tanks (Augmented and Native) filled with nutrient-enriched artificial seawater (i.e., biostimulation). The water in the Augmented tank also contained oil-acclimated bacteria enriched from Arctic surface seawater from Cambridge Bay, Canada (i.e., bioaugmentation). The Native tank was not inoculated, but both tanks contained a bacterial community originating with the artificial seawater preparation. Crude oil was added under the naturally formed ice cover within each tank, creating areas that contained different oil concentrations. The Augmented tank contained 22 distinct bacterial genera compared to the Native tank, presumably due to the inoculation. The abundance of distinct bacterial genera was maximal in the water column and in low-contaminated ice core samples (<0.21 g oil/L). In these ice cores, bioaugmentation affected the concentration of low-molecular-weight aliphatic compounds ( Collapse

Key Words

• Arctic
• Bioaugmentation
• Biodegradation
• Biostimulation (nutrient amendment)
• Crude oil
• Sea ice

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MESH Headings

• Petroleum/metabolism
• Ice Cover/microbiology
• Biodegradation, Environmental
• Arctic Regions
• Bacteria/metabolism
• Water Pollutants, Chemical/metabolism
• Seawater/microbiology
• Petroleum Pollution

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Affiliation(s)

Diana Saltymakova University of Manitoba, Winnipeg, MB, Canada
Durell S Desmond University of Manitoba, Winnipeg, MB, Canada.
Alastair F Smith University of Calgary, Calgary, AB, Canada
María A Bautista University of Calgary, Calgary, AB, Canada
Eric Collins University of Manitoba, Winnipeg, MB, Canada
Katarzyna Polcwiartek University of Manitoba, Winnipeg, MB, Canada
Nolan Snyder University of Manitoba, Winnipeg, MB, Canada
Teresinha Wolfe University of Manitoba, Winnipeg, MB, Canada
Casey Hubert University of Calgary, Calgary, AB, Canada
Dustin Isleifson University of Manitoba, Winnipeg, MB, Canada
Gary Stern University of Manitoba, Winnipeg, MB, Canada

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Oil spills in coastal regions of the Arctic and Subarctic: Environmental impacts, response tactics, and preparedness

Coastal areas of the Arctic and Subarctic are vulnerable to accidental oil spills, impacting the ecosystem, society, and economy. This article provides a comprehensive overview of oil spill pollution issues in cold regions, focusing on environmental impacts, oil transport and fate, coastal/shoreline response measures, and the state of current international policies and regulations. Numerous studies have described the potential effects of oil pollution (crude oil and refined products) on wildlife (invertebrates, fish, birds, and marine mammals) and coastal communities within the Arctic and Subarctic regions. The observed detrimental effects are influenced by the oil fate and transport processes, including physiochemical attenuation and biodegradation, natural dissolution/dispersion following point-source release (surface and subsurface), entrainment by sea ice, and stranding onto shorelines (in which the residual oil may be translocated). Measures such as natural attenuation, bioremediation, manual removal, in situ burning, and washing/flooding are available for spill response in coastal regions. Case studies in cold regions are illustrated for a better analysis of practical response methods, implying that shoreline cleanup operations in the Arctic and Subarctic are more challenging than those in more temperate and populated regions because of environmental and logistical challenges. Regarding preparedness, a number of national and international policies, regulations, and guidelines have been established to advance oil spill prevention and response measures within the Arctic and Subarctic regions. Based on the state of knowledge presented in this review, recommendations are made for future research on oil spill pollution in coastal regions of the Arctic and Subarctic.

Seawater warming rather than acidification profoundly affects coastal geochemical cycling mediated by marine microbiome

The most concerning consequences of climate change include ocean acidification and warming, which can affect microbial communities and thus the biogeochemical cycling they mediate. Therefore, it is urgent to study the impact of ocean acidification and warming on microbial communities. In the current study, metagenomics was utilized to reveal how the structure and function of marine microorganisms respond to ocean warming and acidification. In terms of community structure, Non-metric Multidimensional Scaling analysis visualized the similarity or difference between the control and the warming or acidification treatments, but the inter-group differences were not significant. In terms of gene functionality, warming treatments showed greater effects on microbial communities than acidification. After treatment with warming, the relative abundance of genes associated with denitrification increased, suggesting that ocean nitrogen loss can increase with increased temperature. Conversely, acidification treatments apparently inhibited denitrification. Warming treatment also greatly affected sulfur-related microorganisms, increasing the relative abundance of certain sulfate-reducing prokaryote, and enriched microbial carbon-fixation pathways. These results provide information on the response strategies of coastal microorganisms in the changing marine environments.

A review of oil spill research in Canadian Arctic marine environments

The Canadian Arctic is a large and diverse geographic area that encompasses a wide variety of environmental conditions and ecosystems. Over recent decades, marine transportation has increased across the Arctic and, as a result, so has the likelihood of an oil spill. The study of oil spills in the Arctic presents unique challenges compared to temperate marine environments, due to remoteness, cold temperatures and the presence of snow and ice throughout much of the year. This review summarizes and discusses the fate of oil in the Canadian Arctic. A brief introduction to the Canadian Arctic and sources of potential petroleum spills is provided, followed by discussions of the behaviour of oil in ice and freezing temperatures, oil-sediment interactions, and the weathering and natural remediation of oil under Arctic conditions. A summary of perspectives concludes the review, with emphasis on possible areas of future work to address research gaps.

Arctic's hidden hydrocarbon degradation microbes: investigating the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on microbial communities and hydrocarbon biodegradation pathways in high-Arctic beaches

BACKGROUND

Canadian Arctic summer sea ice has dramatically declined due to global warming, resulting in the rapid opening of the Northwest Passage (NWP), slated to be a major shipping route connecting the Atlantic and Pacific Oceans by 2040. This development elevates the risk of oil spills in Arctic regions, prompting growing concerns over the remediation and minimizing the impact on affected shorelines.

RESULTS

This research aims to assess the viability of nutrient and a surface washing agent addition as potential bioremediation methods for Arctic beaches. To achieve this goal, we conducted two semi-automated mesocosm experiments simulating hydrocarbon contamination in high-Arctic beach tidal sediments: a 32-day experiment at 8 °C and a 92-day experiment at 4 °C. We analyzed the effects of hydrocarbon contamination, biostimulation, and a surface washing agent on the microbial community and its functional capacity using 16S rRNA gene sequencing and metagenomics. Hydrocarbon removal rates were determined through total petroleum hydrocarbon analysis. Biostimulation is commonly considered the most effective strategy for enhancing the bioremediation process in response to oil contamination. However, our findings suggest that nutrient addition has limited effectiveness in facilitating the biodegradation process in Arctic beaches, despite its initial promotion of aliphatic hydrocarbons within a constrained timeframe. Alternatively, our study highlights the promise of a surface washing agent as a potential bioremediation approach. By implementing advanced -omics approaches, we unveiled highly proficient, unconventional hydrocarbon-degrading microorganisms such as Halioglobus and Acidimicrobiales genera.

CONCLUSIONS

Given the receding Arctic sea ice and the rising traffic in the NWP, heightened awareness and preparedness for potential oil spills are imperative. While continuously exploring optimal remediation strategies through the integration of microbial and chemical studies, a paramount consideration involves limiting traffic in the NWP and Arctic regions to prevent beach oil contamination, as cleanup in these remote areas proves exceedingly challenging and costly.

Novel oil-associated bacteria in Arctic seawater exposed to different nutrient biostimulation regimes

The Arctic Ocean is an oligotrophic ecosystem facing escalating threats of oil spills as ship traffic increases owing to climate change-induced sea ice retreat. Biostimulation is an oil spill mitigation strategy that involves introducing bioavailable nutrients to enhance crude oil biodegradation by endemic oil-degrading microbes. For bioremediation to offer a viable response for future oil spill mitigation in extreme Arctic conditions, a better understanding of the effects of nutrient addition on Arctic marine microorganisms is needed. Controlled experiments tracking microbial populations revealed a significant decline in community diversity along with changes in microbial community composition. Notably, differential abundance analysis highlighted the significant enrichment of the unexpected genera Lacinutrix, Halarcobacter and Candidatus Pseudothioglobus. These groups are not normally associated with hydrocarbon biodegradation, despite closer inspection of genomes from closely related isolates confirming the potential for hydrocarbon metabolism. Co-occurrence analysis further revealed significant associations between these genera and well-known hydrocarbon-degrading bacteria, suggesting potential synergistic interactions during oil biodegradation. While these findings broaden our understanding of how biostimulation promotes enrichment of endemic hydrocarbon-degrading genera, further research is needed to fully assess the suitability of nutrient addition as a stand-alone oil spill mitigation strategy in this sensitive and remote polar marine ecosystem.

Metagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches

BACKGROUND

Decreasing sea ice coverage across the Arctic Ocean due to climate change is expected to increase shipping activity through previously inaccessible shipping routes, including the Northwest Passage (NWP). Changing weather conditions typically encountered in the Arctic will still pose a risk for ships which could lead to an accident and the uncontrolled release of hydrocarbons onto NWP shorelines. We performed a metagenomic survey to characterize the microbial communities of various NWP shorelines and to determine whether there is a metabolic potential for hydrocarbon degradation in these microbiomes.

RESULTS

We observed taxonomic and functional gene evidence supporting the potential of NWP beach microbes to degrade various types of hydrocarbons. The metagenomic and metagenome-assembled genome (MAG) taxonomy showed that known hydrocarbon-degrading taxa are present in these beaches. Additionally, we detected the presence of biomarker genes of aerobic and anaerobic degradation pathways of alkane and aromatic hydrocarbons along with complete degradation pathways for aerobic alkane degradation. Alkane degradation genes were present in all samples and were also more abundant (33.8 ± 34.5 hits per million genes, HPM) than their aromatic hydrocarbon counterparts (11.7 ± 12.3 HPM). Due to the ubiquity of MAGs from the genus Rhodococcus (23.8% of the MAGs), we compared our MAGs with Rhodococcus genomes from NWP isolates obtained using hydrocarbons as the carbon source to corroborate our results and to develop a pangenome of Arctic Rhodococcus. Our analysis revealed that the biodegradation of alkanes is part of the core pangenome of this genus. We also detected nitrogen and sulfur pathways as additional energy sources and electron donors as well as carbon pathways providing alternative carbon sources. These pathways occur in the absence of hydrocarbons allowing microbes to survive in these nutrient-poor beaches.

CONCLUSIONS

Our metagenomic analyses detected the genetic potential for hydrocarbon biodegradation in these NWP shoreline microbiomes. Alkane metabolism was the most prevalent type of hydrocarbon degradation observed in these tidal beach ecosystems. Our results indicate that bioremediation could be used as a cleanup strategy, but the addition of adequate amounts of N and P fertilizers, should be considered to help bacteria overcome the oligotrophic nature of NWP shorelines.

Driving mechanisms for the adaptation and degradation of petroleum hydrocarbons by native microbiota from seas prone to oil spills

Offshore waters have a high incidence of oil pollution, which poses an elevated risk of ecological damage. The microbial community composition and metabolic mechanisms influenced by petroleum hydrocarbons vary across different marine regions. However, research on metabolic strategies for in-situ petroleum degradation and pollution adaptation remains in its nascent stages. This study combines metagenomic techniques with gas chromatography-mass spectrometry (GC-MS) analysis. The data show that the genera Pseudoalteromonas, Hellea, Lentisphaera, and Polaribacter exhibit significant oil-degradation capacity, and that the exertion of their degradation capacity is correlated with nutrient and oil pollution stimuli. Furthermore, tmoA, badA, phdF, nahAc, and fadA were found to be the key genes involved in the degradation of benzene, polycyclic aromatic hydrocarbons, and their intermediates. Key genes (INSR, SLC2A1, and ORC1) regulate microbial adaptation to oil-contaminated seawater, activating oil degradation processes. This process enhances the biological activity of microbial communities and accounts for the geographical variation in their compositional structure. Our results enrich the gene pool for oil pollution adaptation and degradation and provide an application basis for optimizing bioremediation intervention strategies.

Bioremediation for the recovery of oil polluted marine environment, opportunities and challenges approaching the Blue Growth

The Blue Growth strategy promises a sustainable use of marine resources for the benefit of the society. However, oil pollution in the marine environment is still a serious issue for human, animal, and environmental health; in addition, it deprives citizens of the potential economic and recreational advantages in the affected areas. Bioremediation, that is the use of bio-resources for the degradation of pollutants, is one of the focal themes on which the Blue Growth aims to. A repertoire of marine-derived bio-products, biomaterials, processes, and services useful for efficient, economic, low impact, treatments for the recovery of oil-polluted areas has been demonstrated in many years of research around the world. Nonetheless, although bioremediation technology is routinely applied in soil, this is not still standardized in the marine environment and the potential market is almost underexploited. This review provides a summary of opportunities for the exploiting and addition of value to research products already validated. Moreover, the review discusses challenges that limit bioremediation in marine environment and actions that can facilitate the conveying of valuable products/processes towards the market.

High Arctic seawater and coastal soil microbiome co-occurrence and composition structure and their potential hydrocarbon biodegradation

The accelerated decline in Arctic sea-ice cover and duration is enabling the opening of Arctic marine passages and improving access to natural resources. The increasing accessibility to navigation and resource exploration and production brings risks of accidental hydrocarbon releases into Arctic waters, posing a major threat to Arctic marine ecosystems where oil may persist for many years, especially in beach sediment. The composition and response of the microbial community to oil contamination on Arctic beaches remain poorly understood. To address this, we analyzed microbial community structure and identified hydrocarbon degradation genes among the Northwest Passage intertidal beach sediments and shoreline seawater from five high Arctic beaches. Our results from 16S/18S rRNA genes, long-read metagenomes, and metagenome-assembled genomes reveal the composition and metabolic capabilities of the hydrocarbon microbial degrader community, as well as tight cross-habitat and cross-kingdom interactions dominated by lineages that are common and often dominant in the polar coastal habitat, but distinct from petroleum hydrocarbon-contaminated sites. In the polar beach sediment habitats, Granulosicoccus sp. and Cyclocasticus sp. were major potential hydrocarbon-degraders, and our metagenomes revealed a small proportion of microalgae and algal viruses possessing key hydrocarbon biodegradative genes. This research demonstrates that Arctic beach sediment and marine microbial communities possess the ability for hydrocarbon natural attenuation. The findings provide new insights into the viral and microalgal communities possessing hydrocarbon degradation genes and might represent an important contribution to the removal of hydrocarbons under harsh environmental conditions in a pristine, cold, and oil-free environment that is threatened by oil spills.

Nocardioides: "Specialists" for Hard-to-Degrade Pollutants in the Environment

Nocardioides, a genus belonging to Actinomycetes, can endure various low-nutrient conditions. It can degrade pollutants using multiple organic materials such as carbon and nitrogen sources. The characteristics and applications of Nocardioides are described in detail in this review, with emphasis on the degradation of several hard-to-degrade pollutants by using Nocardioides, including aromatic compounds, hydrocarbons, haloalkanes, nitrogen heterocycles, and polymeric polyesters. Nocardioides has unique advantages when it comes to hard-to-degrade pollutants. Compared to other strains, Nocardioides has a significantly higher degradation rate and requires less time to break down substances. This review can be a theoretical basis for developing Nocardioides as a microbial agent with significant commercial and application potential.

Potential for natural attenuation of crude oil hydrocarbons in benthic microbiomes near coastal communities in Kivalliq, Nunavut, Canada

Oil spilled in marine environments can settle to the seafloor through aggregation and sedimentation processes. This has been predicted to be especially relevant in the Arctic due to plankton blooms initiated by melting sea ice. These conditions exist in the Kivalliq region in Nunavut, Canada, where elevated shipping traffic has increased the risk of accidental spills. Experimental microcosms combining surface sediment and crude oil were incubated at 4 °C over 21 weeks to evaluate the biodegradation potential of seabed microbiomes. Sediments sampled near the communities of Arviat and Chesterfield Inlet were assessed for biodegradation capabilities by combining hydrocarbon geochemistry with 16S rRNA gene and metagenomic sequencing, revealing decreased microbial diversity but enrichment of oil-degrading taxa. Alkane and aromatic hydrocarbon losses corresponded to detection of genes and genomes that encode enzymes for aerobic biodegradation of these compounds, pointing to the utility of marine microbiome surveys for predicting the fate of oil released into Arctic marine environments.

Ribosomal RNA gene operon copy number, a functional trait indicating the hydrocarbon degradation level of bacterial communities

The lack of universal indicators for predicting microbial biodegradation potential and assessing remediation effects limits the generalization of bioremediation. The community-level ribosomal RNA gene operon (rrn) copy number, an important functional trait, has the potential to serve as a key indicator of the bioremediation of organic pollutants. A meta-analysis based on 1275 samples from 26 hydrocarbon-related studies revealed a positive relationship between the microbial hydrocarbon biodegradation level and the community-level rrn copy number in soil, seawater and culture. Subsequently, a microcosm experiment was performed to decipher the community-level rrn copy number response mechanism during total petroleum hydrocarbon (TPH) biodegradation. The treatment combining straw with resuscitation-promoting factor (Rpf) exhibited the highest community-level rrn copy number and the most effective biodegradation compared with other treatments, and the initial TPH content (20,000 mg kg-1) was reduced by 67.67% after 77 days of incubation. TPH biodegradation rate was positively correlated with the average community-level rrn copy number (p = 0.001, R2 = 0.5781). Both meta and community analyses showed that rrn copy number may reflect the potential of hydrocarbon degradation and microbial dormancy. Our findings provide insight into the applicability of the community-level rrn copy number to assess bacterial biodegradation for pollution remediation.

Effects of marine diesel on microbial diversity and activity in high Arctic beach sediments

Global warming induced sea ice loss increases Arctic maritime traffic, enhancing the risk of ecosystem contamination from fuel spills and nutrient loading. The impact of marine diesel on bacterial metabolic activity and diversity, assessed by colorimetric assay, 16S rRNA and metagenomic sequencing, of Northwest Passage (Arctic Ocean) beach sediments was assessed with nutrient amendment at environmentally relevant temperatures (5 and 15 °C). Higher temperature and nutrients stimulated microbial activity, while diesel reduced it, with metabolism inhibited at and above 0.01 % (without nutrients) and at 1 % (with nutrients) diesel inclusions. Diesel exposure significantly decreased microbial diversity and selected for Psychrobacter genus. Microbial hydrocarbon degradation, organic compound metabolism, and exopolysaccharide production gene abundances increased under higher diesel concentrations. Metagenomic binning recovered nine MAGs/bins with hydrocarbon degradation genes. We demonstrate a nutrients' rescue-type effect in diesel contaminated microbial communities via enrichment of microorganisms with stress response, aromatic compound, and ammonia assimilation metabolisms.

Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench

BACKGROUND

The Kuril-Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment.

RESULTS

As for the bacterial communities, we found that Proteobacteria (56.1-74.5%), Bacteroidetes (6.5-19.1%), and Actinobacteria (0.9-16.1%) were the most represented bacterial phyla over all samples. Thaumarchaeota (52.9-91.1%) was the most abundant phylum in the archaeal communities. The archaeal diversity was highly represented by the ammonia-oxidizing Nitrosopumilus, and the potential hydrocarbon-degrading bacteria Acinetobacter, Zhongshania, and Colwellia were the main bacterial genera. The α-diversity analysis evidenced that both prokaryotic communities were characterized by low evenness, as indicated by the high Gini index values (> 0.9). The β-diversity analysis (Redundancy Analysis) indicated that, as expected, the depth significantly affected the structure of the prokaryotic communities. The co-occurrence network revealed seven prokaryotic groups that covaried across the abyssal-hadal zone of the Kuril-Kamchatka Trench. Among them, the main group included the most abundant archaeal and bacterial OTUs (Nitrosopumilus OTU A2 and OTU A1; Acinetobacter OTU B1), which were ubiquitous across the trench.

CONCLUSIONS

This manuscript represents the first attempt to characterize the prokaryotic communities of the KKT abyssal-hadal zone. Our results reveal that the most abundant prokaryotes harbored by the abyssal-hadal zone of Kuril-Kamchatka Trench were chemolithotrophic archaea and heterotrophic bacteria, which did not show a distinctive pattern distribution according to depth. In particular, Acinetobacter, Zhongshania, and Colwellia (potential hydrocarbon degraders) were the main bacterial genera, and Nitrosopumilus (ammonia oxidizer) was the dominant representative of the archaeal diversity.

Exploring the use of sodium caseinate-assisted responsive separation for the treatment of washing effluents in shoreline oil spill response

The produced effluents after shoreline washing contain a certain number of oil droplets and further treatment is necessary. In this study, the innocuous, widely available, and biodegradable sodium caseinate (NaCas) was deployed to capture oil pollutants from oily wastewater. Oil droplets can be effectively and rapidly captured by NaCas and subsequently removed after pH-triggered separation, producing a clean supernatant with low turbidity. The removal efficiency was enhanced by increasing NaCas concentration and separation time. The salinity inhibited the oil removal by increasing the interfacial tension of NaCas and reducing their sorption sites caused by the large particle size. Humic acid negatively influenced the oil separation performance of NaCas because of the competitive sorption and enhanced repulsion force between oil and NaCas. In addition, the increasing temperature was found to augment the oil removal. Factorial analysis revealed the individual factors and two-factor interactions that had significant effects on oil removal. Biotoxicity experiments proved that NaCas can fully offset the inhibitory effect of oil on the photosynthesis of algae and thus promote algae growth. Two post-treatment methods, namely thermal treatment, and biodegradation, can be used for the post-treatment of NaCas/oil precipitation residues. The use of NaCas-assisted responsive separation in the treatment of washing effluents can help achieve a sustainable shoreline oil spill response.

Microbial degradation mechanisms of surface petroleum contaminated seawater in a typical oil trading port

Petroleum hydrocarbons are significant new persistent organic pollutants for marine oil spill risk areas. Oil trading ports, in turn, have become major bearers of the risk of offshore oil pollution. However, studies on the molecular mechanisms of microbial degradation of petroleum pollutants by natural seawater are limited. Here, an in situ microcosm study was conducted. Combined with metagenomics, differences in metabolic pathways and in the gene abundances of total petroleum hydrocarbons (TPH) are revealed under different conditions. About 88% degradation of TPH was shown after 3 weeks of treatment. The positive responders to TPH were concentrated in the genera Cycloclasticus, Marivita and Sulfitobacter of the orders Rhodobacterales and Thiotrichales. The genera Marivita, Roseobacter, Lentibacter and Glaciecola were key degradation species when mixing dispersants with oil, and all of the above are from the Proteobacteria phylum. The analysis showed that the biodegradability of aromatic compounds, polycyclic aromatic hydrocarbon and dioxin were enhanced after the oil spill, and genes with higher abundances of bphAa, bsdC, nahB, doxE and mhpD were found, but the photosynthesis-related mechanism was inhibited. The dispersant treatment effectively stimulated the microbial degradation of TPH and then accelerated the succession of microbial communities. Meanwhile, functions such as bacterial chemotaxis and carbon metabolism (cheA, fadeJ and fadE) were better developed, but the degradation of persistent organic pollutants such as polycyclic aromatic hydrocarbons was weakened. Our study provides insights into the metabolic pathways and specific functional genes for oil degradation by marine microorganisms and will help improve the application and practice of bioremediation.

Response of microbial communities in North Saskatchewan River to diluted bitumen and conventional crude under freeze-thaw-refreeze cycle

Microorganisms are the first responder to oil spills and their response provides insight into the ecological effects of oils on aquatic ecosystems. Limited information is available about the impact of oil spills on freshwater ecosystems under seasonal river-ice regimes. This study aimed to investigate the microbial response of North Saskatchewan River water to diluted bitumen (DB) and conventional crude (CC) during the freeze-thaw-refreeze cycle. In two separate experiments, equivalent to 2 L of fresh DB and CC were spilled on the ice-covered river water within a mesoscale spill tank. The microbial response (changes in abundance and diversity) to oils under the freeze, thaw, and refreeze cycles were assessed for 10 days using 16S rRNA gene sequencing. The results showed that microbial communities exhibited different responses to the DB and CC oils. The effect of oils was more pronounced than that of the freeze or thaw cycles. The river microbial community rapidly responded to both spills, which coincided with a steady increase in the organic content of water throughout the freeze-thaw-refreeze cycle. Microbial diversity increased after the DB spill, but remain unchanged after the CC spill, regardless of the cycles. A higher number of new taxa emerged during the ice-covered period, while more microbial enrichment (increase in abundance) was observed during the thaw cycle. Flavobacterium (37 ± 5%) and Pseudomonas (36 ± 4%) remained the most predominant genera post-DB and CC spill, respectively. The results of this study suggest that ice coverage of 5 cm did not prevent the microbial communities from the effects of oils. Thus, a quick clean-up response to an oil spill on ice-covered water is equally critical to avoid the effects of oils on the underlying freshwater ecosystems.

Long-term patterns of hydrocarbon biodegradation and bacterial community composition in epipelagic and mesopelagic zones of an Arctic fjord

Oil spill attenuation in Arctic marine environments depends on oil-degrading bacteria. However, the seasonally harsh conditions in the Arctic such as nutrient limitations and sub-zero temperatures limit the activity even for bacteria capable of hydrocarbon metabolism at low temperatures. Here, we investigated whether the variance between epipelagic (seasonal temperature and inorganic nutrient variations) and mesopelagic zone (stable environmental conditions) could limit the growth of oil-degrading bacteria and lead to lower oil biodegradation rates in the epipelagic than in the mesopelagic zone. Therefore, we deployed absorbents coated with three oil types in a SW-Greenland fjord system at 10-20 m (epipelagic) and 615-650 m (mesopelagic) water depth for one year. During this period we monitored the development and succession of the bacterial biofilms colonizing the oil films by 16S rRNA gene amplicon quantification and sequencing, and the progression of oil biodegradation by gas chromatography - mass spectrometry oil fingerprinting analysis. The removal of hydrocarbons was significantly different, with several polycyclic aromatic hydrocarbons showing longer half-life times in the epipelagic than in the mesopelagic zone. Bacterial community composition and density (16S rRNA genes/ cm²) significantly differed between the two zones, with total bacteria reaching to log-fold higher densities (16S rRNA genes/cm²) in the mesopelagic than epipelagic oil-coated absorbents. Consequently, the environmental conditions in the epipelagic zone limited oil biodegradation performance by limiting bacterial growth.

Bioaugmentation enhance the bioremediation of marine crude oil pollution: Microbial communities and metabolic pathways

Bioaugmentation is an effective strategy used to speed up the bioremediation of marine oil spills. In the present study, a highly efficient petroleum degrading bacterium (Pseudomonas aeruginosa ZS1) was applied to the bioremediation of simulated crude oil pollution in different sampling sites in the South China Sea. The metabolic pathways of ZS1 to degrade crude oil, the temporal dynamics of the microbial community response to crude oil contamination, and the biofortification process were investigated. The results showed that the abundance and diversity of the microbial community decreased sharply after the occurrence of crude oil contamination. The best degradation rate of crude oil, which was achieved in the samples from the sampling site N3 after the addition of ZS1 bacteria, was 50.94% at 50 days. C13 alkanes were totally oxidized by ZS1 in the 50 days. The degradation rate of solid n-alkanes (C18-C20) was about 70%. Based on the whole genome sequencing and the metabolites analysis of ZS1, we found that ZS1 degraded n-alkanes through the terminal oxidation pathway and aromatic compounds through the catechol pathway. This study provides data support for further research on biodegradation pathways of crude oil and contributes to the subsequent development of more reasonable bioremediation strategies.

Genome-based taxonomic rearrangement of Oceanobacter-related bacteria including the description of Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. and emended description of the genus Thalassolituus

Oceanobacter-related bacteria (ORB) are a group of oligotrophic marine bacteria play an underappreciated role in carbon cycling. They have been frequently described as one of the dominant bacterial groups with a wide distribution in coastal and deep seawater of global oceans. To clarify their taxonomic affiliation in relation to alkane utilization, phylogenomic and comparative genomics analyses were performed based on currently available genomes from GenBank and four newly isolated strains, in addition to phenotypic and chemotaxonomic characteristics. Consistently, phylogenomic analysis robustly separated them into two groups, which are accordingly hydrocarbon-degrading (HD, Thalassolituus and Oleibacter) and non-HD (NHD, Oceanobacter). In addition, the two groups can also be readily distinguished by several polyphasic taxonomic characteristics. Furthermore, both AAI and POCP genomic indices within the HD group support the conclusion that the members of the genus Oleibacter should be transferred into the genus Thalassolituus. Moreover, HD and NHD bacteria differed significantly in terms of genome size, G + C content and genes involved in alkane utilization. All HD bacteria contain the key gene alkB encoding an alkane monooxygenase, which can be used as a marker gene to distinguish the members of closely related genera Oceanobacter and Thalassolituus. Pangenome analysis revealed that the larger accessory genome may endow Thalassolituus with the flexibility to cope with the dynamics of marine environments and thrive therein, although they possess smaller pan, core- and unique-genomes than Oceanobacter. Within the HD group, twelve species were clearly distinguished from each other by both dDDH and ANI genomic indices, including two novel species represented by the newly isolated strains alknpb1M-1 ^T and 59MF3M-4 ^T , for which the names Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. are proposed. Collectively, these findings build a phylogenetic framework for the ORB and contribute to understanding of their role in marine carbon cycling.

Degradation Rates and Bacterial Community Compositions Vary among Commonly Used Bioplastic Materials in a Brackish Marine Environment

Plastic pollution threatens both terrestrial and aquatic ecosystems. As a result of the pressures of replacing oil-based materials and reducing the accumulation of litter in the environment, the use of bioplastics is increasing, despite little being known about their accurate biodegradation in natural conditions. Here, we investigated the weight attrition and degradation behavior of four different bioplastic materials compared to conventional oil-based polyethylene during a 1-year in situ incubation in the brackish Baltic Sea and in controlled 1 month biodegradation experiments in the laboratory. Bacterial communities were also investigated to verify whether putative plastic-degrading bacteria are enriched on bioplastics. Poly-l-lactic acid showed no signs of degradation, whereas poly(3-hydroxybutyrate/3-hydroxyvalerate) (PHB/HV), plasticized starch (PR), and cellulose acetate (CA) degraded completely or almost completely during 1-year in situ incubations. In accordance, bacterial taxa potentially capable of using complex carbon substrates and belonging, e.g., to class Gammaproteobacteria were significantly enriched on PHB/HV, PR, and CA. An increase in gammaproteobacterial abundance was also observed in the biodegradation experiments. The results show substantial differences in the persistence and biodegradation rates among bioplastics, thus highlighting the need for carefully selecting materials for applications with risk of becoming marine litter.

Study on the Changes in Immobilized Petroleum-Degrading Bacteria Beads in a Continuous Bioreactor Related to Physicochemical Performance, Degradation Ability, and Microbial Community

Continuous bioreactors for petroleum degradation and the effect factors of these bioreactors have rarely been mentioned in studies. In addition, indigenous bacteria living in seawater could influence the performance of continuous bioreactors with respect to petroleum degradation in practice. In this paper, a bioreactor fitted with immobilized petroleum-degrading bacteria beads was designed for further research. The results indicated that the diesel degradation rate of the bioreactor could remain above 50% over 27 days, while degradation performance decreased with bioremediation time. Intriguingly, the diameters of immobilized petroleum-degrading bacteria beads were reduced by 32.49% after 45 days remediation compared with the initial size of the immobilized petroleum-degrading bacteria beads. Change in immobilized petroleum-degrading bacteria beads was considered to correlate remarkably with reduced degradation efficiency. Therefore, this paper will be helpful for further study and improvement of bioreactors in the practical context of oil-spill accident recovery.

Bioremediation by oil degrading marine bacteria: An overview of supplements and pathways in key processes

Oil spillage is one of the most common pollutants which brings greater economic loss and damage to the environment. The intensity and amount of the damage may vary depending on factors such as the type of oil, the location of the spill, and the climatic parameters in the area. As for any pollution management, the guidelines are Reduce, Re-use, Recover and Disposal. Amongst the other remediation processes, Bioremediation is amongst the most significant environmentally friendly and cost-effective approaches for marine biological restoration because it allows complex petroleum hydrocarbons in spilt oil to decompose completely into harmless compounds. Mainly, the necessity and essence of bioremediation were talked about. This review discussed the bacteria identified which are capable of degrading various oil related pollutants and their components. Also, it covered the various media components used for screening and growing the oil degrading bacteria and the pathways that are associated with oil degradation. This article also reviewed the recent research carried out related to the oil degrading bacteria.

Floating treatment wetlands for the bioremediation of oil spills: A review

Conventional oil spill recovery may cause significant damage to shoreline habitats during the removal of oiled material and from human and equipment interaction. In addition, these methods are costly and can leave a significant amount of residual oil in the environment. Biological remediation strategies may be a less invasive option for recovering oil from sensitive regions, with potential to increase recovery. Floating treatment wetlands are a growing area of interest for biodegradation of oil facilitated by plant-bacterial partnerships. Plants are able to stimulate microbial colonization in the rhizosphere, creating greater opportunity for contaminant interaction and degradation. A literature review analysis revealed thirteen articles researching this topic, and found that floating treatment wetlands have high potential to degrade oil contaminants. In some instances, plants and inoculated bacteria exhibited the highest degradation potential, however, plants alone had higher degradation potential than bacteria alone. Research is needed to explore how floating treatment wetlands perform in field-based trials and under variable environmental conditions.

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.

Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature

The development of oil exploration activities and an increase in shipping in Arctic areas have increased the risk of oil spills in this cold marine environment. The objective of this experimental study was to assess the effect of biostimulation on microbial community abundance, structure, dynamics, and metabolic potential for oil hydrocarbon degradation in oil-contaminated Arctic seawater. The combination of amplicon-based and shotgun sequencing, together with the integration of genome-resolved metagenomics and omics data, was applied to assess microbial community structure and metabolic properties in naphthenic crude oil-amended microcosms. The comparison of estimates for oil-degrading microbial taxa obtained with different sequencing and taxonomic assignment methods showed substantial discrepancies between applied methods. Consequently, the data acquired with different methods was integrated for the analysis of microbial community structure, and amended with quantitative PCR, producing a more objective description of microbial community dynamics and evaluation of the effect of biostimulation on particular microbial taxa. Implementing biostimulation of the seawater microbial community with the addition of nutrients resulted in substantially elevated prokaryotic community abundance (103-fold), a distinctly different bacterial community structure from that in the initial seawater, 1.3-fold elevation in the normalized abundance of hydrocarbon degradation genes, and 12% enhancement of crude oil biodegradation. The bacterial communities in biostimulated microcosms after four months of incubation were dominated by Gammaproteobacterial genera Pseudomonas, Marinomonas, and Oleispira, which were succeeded by Cycloclasticus and Paraperlucidibaca after eight months of incubation. The majority of 195 compiled good-quality metagenome-assembled genomes (MAGs) exhibited diverse hydrocarbon degradation gene profiles. The results reveal that biostimulation with nutrients promotes naphthenic oil degradation in Arctic seawater, but this strategy alone might not be sufficient to effectively achieve bioremediation goals within a reasonable timeframe.