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BackgroundThe Atribacterota are widely distributed in the subsurface biosphere. Recently, the first Atribacterota isolate was described and the number of Atribacterota genome sequences retrieved from environmental samples has increased significantly; however, their diversity, physiology, ecology, and evolution remain poorly understood.ResultsWe report the isolation of the second member of Atribacterota, Thermatribacter velox gen. nov., sp. nov., within a new family Thermatribacteraceae fam. nov., and the short-term laboratory cultivation of a member of the JS1 lineage, Phoenicimicrobium oleiphilum HX-OS.bin.34TS, both from a terrestrial oil reservoir. Physiological and metatranscriptomics analyses showed that Thermatribacter velox B11T and Phoenicimicrobium oleiphilum HX-OS.bin.34TS ferment sugars and n-alkanes, respectively, producing H2, CO2, and acetate as common products. Comparative genomics showed that all members of the Atribacterota lack a complete Wood-Ljungdahl Pathway (WLP), but that the Reductive Glycine Pathway (RGP) is widespread, indicating that the RGP, rather than WLP, is a central hub in Atribacterota metabolism. Ancestral character state reconstructions and phylogenetic analyses showed that key genes encoding the RGP (fdhA, fhs, folD, glyA, gcvT, gcvPAB, pdhD) and other central functions were gained independently in the two classes, Atribacteria (OP9) and Phoenicimicrobiia (JS1), after which they were inherited vertically; these genes included fumarate-adding enzymes (faeA; Phoenicimicrobiia only), the CODH/ACS complex (acsABCDE), and diverse hydrogenases (NiFe group 3b, 4b and FeFe group A3, C). Finally, we present genome-resolved community metabolic models showing the central roles of Atribacteria (OP9) and Phoenicimicrobiia (JS1) in acetate- and hydrocarbon-rich environments.ConclusionOur findings expand the knowledge of the diversity, physiology, ecology, and evolution of the phylum Atribacterota. This study is a starting point for promoting more incisive studies of their syntrophic biology and may guide the rational design of strategies to cultivate them in the laboratory. Video Abstract.

Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season. [ABSTRACT FROM AUTHOR]

Given the vast quantity of oil and gas input to the marine environment annually, hydrocarbon degradation by marine microorganisms is an essential ecosystem service. Linkages between taxonomy and hydrocarbon degradation capabilities are largely based on cultivation studies, leaving a knowledge gap regarding the intrinsic ability of uncultured marine microbes to degrade hydrocarbons. To address this knowledge gap, metagenomic sequence data from the Deepwater Horizon (DWH) oil spill deep-sea plume was assembled to which metagenomic and metatranscriptomic reads were mapped. Assembly and binning produced new DWH metagenome-assembled genomes that were evaluated along with their close relatives, all of which are from the marine environment (38 total). These analyses revealed globally distributed hydrocarbon-degrading microbes with clade-specific substrate degradation potentials that have not been reported previously. For example, methane oxidation capabilities were identified in all Cycloclasticus. Furthermore, all Bermanella encoded and expressed genes for non-gaseous n-alkane degradation; however, DWH Bermanella encoded alkane hydroxylase, not alkane 1-monooxygenase. All but one previously unrecognized DWH plume member in the SAR324 and UBA11654 have the capacity for aromatic hydrocarbon degradation. In contrast, Colwellia were diverse in the hydrocarbon substrates they could degrade. All clades encoded nutrient acquisition strategies and response to cold temperatures, while sensory and acquisition capabilities were clade specific. These novel insights regarding hydrocarbon degradation by uncultured planktonic microbes provides missing data, allowing for better prediction of the fate of oil and gas when hydrocarbons are input to the ocean, leading to a greater understanding of the ecological consequences to the marine environment. [ABSTRACT FROM AUTHOR]

Laccase is a multicopper oxidase enzyme that oxidizes a variety of substrates, including polyphenols and polycyclic aromatic hydrocarbons (PAHs). It catalyzes the four-electron reduction of molecular oxygen that results in the production of water as a by-product. Thus, laccase can play an important role in environmental care. Previously, we have successfully expressed Trametes trogii laccase (TtLcc1) in the yeast Saccharomyces cerevisiae. In this work, we have expressed in yeast another laccase, LacA from Trametes sp. AH28-2, and tested its function on PAHs. Yeast cells engineered to produce the two laccases performed efficient PAH degradation. Both TtLcc1 and LacA led to the construction of spatiotemporal fluorescence-pulse generators when combined with a benzoate/salicylate yeast biosensor in a two-population system. Moreover, laccases returned a visual output signal in yeast synthetic circuits—upon reacting with ABTS (2,2′-azino-bis (3-ethylbenzthiazoline-6-sulfonic acid)). Thus, in S. cerevisiae, laccases are a powerful alternative to fluorescent reporter proteins.

Plant growth promoting rhizobacteria (PGPR) play a key role in sustainable agricultural practices leading to increased crop productivity. Moreover, PGPR with ability to diminish abiotic stresses like salinity and hydrocarbon contamination in soil, can be developed into potent biofertilizers with maximum ecological benefits. Sundarbans mangrove region in West Bengal, a natural reservoir of diverse microbiota is an important source of PGPR adapted to high salinity and other abiotic stresses like hydrocarbon contamination due to oil spillage and water transport systems, rendering the soil unsuitable for farming. In the present study, a potent PGPR has been isolated from rhizospheric soil of Matla riverbed in mangrove areas of Sundarbans, with simultaneous nitrogen fixing, phosphate solubilizing and plant hormone like indole acetic acid (IAA) producing properties as well as high salt tolerance and hydrocarbon bioremediation abilities. The strain has been identified as Pseudomonas aeruginosa JCM 5962 (NCBI Accession number MK544832.1) on the basis of 16S rRNA analysis. The isolated Pseudomonas aeruginosa strain showed atmospheric nitrogen fixation (3612 ± 2 mg N/ Kg of soil), highest phosphate solubilization index of 3.0 ± 0.06 and 37.14 µg/mL of IAA production. This potent strain also showed salt tolerance upto 7% in culture broth and an uptake of 18.72% of salt. Highest hydrocarbon degradation was shown by this strain in presence of diesel as the sole carbon source. The isolated Pseudomonas aeruginosa strain showed overall improvement in growth of Abelmoschus esculentus (Okra) plants in pot experiments in different conditions like absence of any abiotic stress, presence of 5% salt stress and presence of 1% diesel contaminant. These results indicate that Pseudomonas aeruginosa JCM 5962 can be developed as a potent biofertilizer to be used in agricultural lands of Sundarbans mangrove regions and other areas which are plagued by high salinity and increasing hydrocarbons, particularly petroleum contamination. [ABSTRACT FROM AUTHOR]

The increase in environmental pollution caused by inadequate anthropogenic practices is emerging as a global threat to human health and ecosystems. Addressing this issue is crucial, and bioremediation stands out as a sustainable solution for remediating contaminated soils. This study evaluates the feasibility of bioremediation to mitigate soil contamination by petroleum hydrocarbons using laying hen manure as a biostimulating agent, in the forms of manure stabilized by simple drying and compost from fresh manure. The specific objectives included analyzing the interaction between manure and contaminants, evaluating the influence of physicochemical and microbiological variables, comparing the efficiency of different manure proportions, and assessing contaminant reduction rates. Physicochemical and biological monitoring and statistical analysis were conducted. The results indicate that the treatment with stabilized manure significantly differed from the control sample, achieving up to 98% reduction in total petroleum hydrocarbons concentrations within 60 days and microorganism populations of around 107 CFU/mL. In contrast, the treatment with compost did not show significant differences from the control. Furthermore, while both treatments increased microbial populations, only the compost treatments maintained non-toxic conditions for soybean seed germination and root elongation, highlighting its potential for agricultural applications post-remediation. Stabilized poultry manure, though effective in total petroleum hydrocarbons degradation, resulted in soil toxicity due to high salinity and potassium levels, necessitating careful management. Its combined application with sawdust is recommended to improve soil structure and counteract compaction. These findings underscore the effectiveness of stabilized manure in accelerating bioremediation and the potential of compost to enhance soil health, suggesting tailored applications depending on specific remediation goals. [ABSTRACT FROM AUTHOR]

The aim of the present work was to examine the hydrocarbon degradation potential of yeasts isolated from the mangrove sediments. Mangrove sediments around the world were considered to be heavily polluted with oil contaminants and the microbes dwelling in them were believed to be highly active in metabolizing and detoxifying the oil fractions. In the present study, 70 yeast isolates were screened for their lipolytic activity qualitatively and 35 of them which showed comparatively higher lipolysis were tested for their crude oil degradation ability. Screening of hydro-carbon utilizing isolates was performed on Bushnell Haas agar media overlaid with 1% crude oil and the appearance of colonies were considered a positive. Three isolates were selected based on this and were sequenced using ITS gene of the 18S region of the rDNA and identified to be Candida tropicalis. The extent of crude oil degra-dation was assessed by growing the isolates in basal medium supplemented with heavy crude oil as the carbon source for 21 days. The residual crude oil fractions were then analyzed using GC-MS to quantitatively measure the degradation potential of each isolate. Our results showed that the yeast strains under study could actively metabolize the crude oil including the higher chain fractions which make them efficient hydrocarbon degraders that can be used in the bioremediation processes.

Escalating oil consumption has resulted in an increase in accidental spills of petroleum hydrocarbons, causing severe environmental degradation, notably in vulnerable regions like the Niger Delta. Complex mixture of these hydrocarbons particularly long-chain alkanes presents unique challenges in restoration of polluted environment due to their chemical properties. This study aimed to investigate the long-chain hydrocarbon-degrading bacterial communities within long-term chronically polluted soil in Ogoniland, by utilizing both traditional cultivation methods and modern culture-independent techniques. Results revealed that surface-polluted soil (SPS) and subsurface soil (SPSS) exhibit significantly higher total organic carbon (TOC) ranging from 5.64 to 5.06% and total petroleum hydrocarbons (TPH) levels ranging from 36,775 ppm to 14,087 ppm, compared to unpolluted soil (UPS) with 1.97% TOC and 479 ppm TPH, respectively. Analysis of carbon chain lengths reveals the prevalence of longer-chain alkanes (C20-28) in the surface soil. Culture-dependent methods, utilizing crude oil enrichment (COE) and paraffin wax enrichment (PWE), yield 47 bacterial isolates subjected to a long-chain alkane degradation assay. Twelve bacterial strains demonstrate significant degradation abilities across all enriched media. Three bacterial members, namely Pseudomonas sp. (almA), Marinomonas sp. (almA), and Alteromonas (ladA), exhibit genes responsible for long-chain alkane degradation, demonstrating efficiency between 50 and 80%. Culture-independent analysis reveals that surface SPS samples exhibit greater species richness and diversity compared to subsurface SPSS samples. Proteobacteria dominates as the phylum in both soil sample types, ranging from 22.23 to 82.61%, with Firmicutes (0.2–2.22%), Actinobacteria (0.4–3.02%), and Acidobacteria (0.1–3.53%) also prevalent. Bacterial profiles at genus level revealed that distinct variations among bacterial populations between SPS and SPSS samples comprising number of hydrocarbon degraders and the functional predictions also highlight the presence of potential catabolic genes (nahAa, adh2, and cpnA) in the polluted soil. However, culture-dependent analysis only captured a few of the dominant members found in culture-independent analysis, implying that more specialized media or environments are needed to isolate more bacterial members. The findings from this study contribute valuable information to ecological and biotechnological aspects, aiding in the development of more effective bioremediation applications for restoring oil-contaminated environments. [ABSTRACT FROM AUTHOR]

Molecular biological techniques and bioinformatic analysis were used to investigate the phylogenetic and functional diversity of the prokaryotic complex of soil microcosms. The dominant organisms of the hydrolytic community were different in the samples from different climatic zones. In the soils subject to anthropogenic or abiogenic load, apart from decreased diversity and abundance of prokaryotes, the number of the genes marking the ability to degrade xenobiotics, as well as those encoding nitrogen conversion and metabolism of vitamins and cofactors, was found to increase. Under heavy oil contamination, the bacterial community was capable of nitrification; its role increased in the lower horizons of the soil profile. The patterns revealed in the work indicate high metabolic potential of the prokaryotic component of the studied soils. [ABSTRACT FROM AUTHOR]

Soil pollution is a growing global concern and one of the most challenging environmental issues today, involving the human sector as well. Innovative soil remediation strategies are needed to conserve the natural resources of the environment. Endophytes are present in all plants species, living symbiotically in a continuum dynamic mutualism. Among multiple changing roles, safeguarding the host in terms of increasing resistance to abiotic factors has been widely demonstrated. Following these physiological changes, host plants have beneficial potential in degrading pollutants from contaminated soils. Enzymes produced by host plants along with endophytes may also, degrade macromolecule compounds into small molecules or convert more toxic substances into less toxic substances to increase their adaptability. Phytoremediation technology with endophyte fungi is an ecological alternative strategy that has been documented as a promising technology for remedying contaminated soils. This review article aims to piece together the physiological, chemical and genetical mechanisms employed in phytoremediation techniques mediated by endophytic fungi and highlight the importance of the plant-microbiome ecology. [ABSTRACT FROM AUTHOR]

Careless handling of petroleum in petrochemical industries releases toxic hydrocarbons and metals to soil and water. The aim of the present study was to isolate hydrocarbon‐utilizing and metal‐tolerant bacteria. Hydrocarbon‐utilizing bacteria from petroleum‐contaminated soils were isolated on the Bushnell Hass medium. Hydrocarbon degradation by Pseudomonas taiwanensis strain YSA‐17 was observed by gas chromatography–mass spectrometry. Bioaccumulation of metals by strain YSA‐17 was assessed in nutrient broth. Among different strains, YSA‐17 showed the highest potential for hydrocarbon utilization. After 20 days of incubation, YSA‐17 completely degraded one compound and during its degradation, there was the formation of 13 new compounds which were absent in uninoculated control. Results of scanning electron microscope and Fourier transmission infrared (FTIR) indicated degradation of hydrocarbons. FTIR showed the formation of new functional groups in YSA‐17 inoculated medium. Expression of the total quantity of hydrocarbon‐degrading gene (AlkB and NehAc) in petroleum‐amended nutrient broth inoculated with strain YSA‐17 enhanced significantly during 20 days of incubation compared to control. YSA‐17 also significantly removed metals. This study concluded that bioinoculant can be utilized for the bioremediation of pollutants cocontaminated with hydrocarbons and metals. Petroleum‐contaminated soil will be remediated for pollutants. [ABSTRACT FROM AUTHOR]

This article, titled "Editorial: Microbial hydrocarbon degradation and bioremediation: from genes to pathways," discusses recent advancements in understanding the processes of hydrocarbon degradation and bioremediation by microbial species. The article highlights the potential of bacterial species to degrade toxic pollutants and emphasizes the versatility of microbial bioremediation strategies. It also explores the challenges and practical applications of applying these advancements to large-scale bioremediation projects. The article concludes by discussing future developments in synthetic biology, meta-omics, microbiome engineering, and bioinformatics as promising approaches to improving the degradation capabilities of microorganisms. [Extracted from the article]

Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzeneand naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through shortread metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments. [ABSTRACT FROM AUTHOR]

Bacterial degradation of crude oil is a promising strategy for reducing the concentration of hydrocarbons in contaminated environments. In the first part of this study, we report the enrichment of two bacterial consortia from deep sediments of the Gulf of Mexico with crude oil as the sole carbon and energy source. We conducted a comparative analysis of the bacterial community in the original sediment, assessing its diversity, and compared it to the enrichment observed after exposure to crude oil in defined cultures. The consortium exhibiting the highest hydrocarbon degradation was predominantly enriched with Rhodococcus (75%). Bacterial community analysis revealed the presence of other hydrocarbonoclastic members in both consortia. In the second part, we report the isolation of the strain Rhodococcus sp. GOMB7 with crude oil as a unique carbon source under microaerobic conditions and its characterization. This strain demonstrated the ability to degrade long-chain alkanes, including eicosane, tetracosane, and octacosane. We named this new strain Rhodococcus qingshengii GOMB7. Genome analysis revealed the presence of several genes related to aromatic compound degradation, such as benA, benB, benC, catA, catB, and catC; and five alkB genes related to alkane degradation. Although members of the genus Rhodococcus are well known for their great metabolic versatility, including the aerobic degradation of recalcitrant organic compounds such as petroleum hydrocarbons, this is the first report of a novel strain of Rhodococcus capable of degrading long-chain alkanes under microaerobic conditions. The potential of R. qingshengii GOMB7 for applications in bioreactors or controlled systems with low oxygen levels offers an energy-efficient approach for treating crude oil-contaminated water and sediments. [ABSTRACT FROM AUTHOR]

The current work deals with genomic analysis, possible ecological functions, and biotechnological potential of two bacterial strains, HO-A22T and SHC 2-14, isolated from unique subsurface environments, the Cheremukhovskoe oil field (Tatarstan, Russia) and nitrate- and radionuclide-contaminated groundwater (Tomsk region, Russia), respectively. New isolates were characterized using polyphasic taxonomy approaches and genomic analysis. The genomes of the strains HO-A22T and SHC 2-14 contain the genes involved in nitrate reduction, hydrocarbon degradation, extracellular polysaccharide synthesis, and heavy metal detoxification, confirming the potential for their application in various environmental biotechnologies. Genomic data were confirmed by cultivation studies. Both strains were found to be neutrophilic, chemoorganotrophic, facultatively anaerobic bacteria, growing at 15–33 °C and 0–1.6% NaCl (w/v). The 16S rRNA gene sequences of the strains were similar to those of the type strains of the genus Ensifer (99.0–100.0%). Nevertheless, genomic characteristics of strain HO-A22T were below the thresholds for species delineation: the calculated average nucleotide identity (ANI) values were 83.7–92.4% (<95%), and digital DNA–DNA hybridization (dDDH) values were within the range of 25.4–45.9% (<70%), which supported our conclusion that HO-A22T (=VKM B-3646T = KCTC 92427T) represented a novel species of the genus Ensifer, with the proposed name Ensifer oleiphilus sp. nov. Strain SHC 2-14 was assigned to the species 'Ensifer canadensis', which has not been validly published. This study expanded the knowledge about the phenotypic diversity among members of the genus Ensifer and its potential for the biotechnologies of oil recovery and radionuclide pollution treatment. [ABSTRACT FROM AUTHOR]

The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze-thaw cycle (FTC) alternating between -20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.

The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze-thaw cycle (FTC) alternating between -20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.

ABSTRACT Microbes play a significant role in the degradation of petroleum hydrocarbons in the oceans, yet little is known about the native bacteria that metabolize hydrocarbons before an oil spill. The Faroe-Shetland Channel (FSC) is a deepwater subarctic region of the North Atlantic with prominent oil production and a diverse microbial community associated with the degradation of petroleum. Here, we combine DNA-based stable-isotope probing (DNA-SIP) with metagenomics to elucidate the metabolic underpinnings of native alkane-degrading bacteria from the FSC. From two 13C n-hexadecane SIP experiments using seawater from 5 and 700 m depths in the FSC, we obtained 42 metagenome-assembled genomes (MAGs) belonging to 19 genera, including two previously overlooked hydrocarbon-degrading bacteria, Lentibacter (Alphaproteobacteria) and Dokdonia (Bacteroidetes). Diversity surveys indicated Lentibacter were dominant members of the FSC, constituting up to 17% of these communities. Many of the SIP-enriched MAGs (20/42) encoded a complete alkane oxidation pathway, including alkane monooxygenase (AlkB), rubredoxin reductase (AlkT), and rubredoxin-2 (AlkG). Fourteen Aphaproteobacteria MAGs lacked AlkG for electron transfer. Instead, they encoded novel disulfide isomerases with iron-binding cysteine motifs conserved across rubredoxins. Dokdonia lacked AlkT and AlkG, however, their central alkane-degradation catabolic pathways were complete. We describe previously unrecognized bacteria capable of hydrocarbon degradation, including the dominant genera Lentibacter, which may continuously purge hydrocarbons released from oil exploration activities in the FSC. This advances the understanding of the diversity and physiologies of alkane degradation in the North Atlantic and provides evidence of new mechanisms used to metabolize alkanes. IMPORTANCE Petroleum pollution in the ocean has increased because of rapid population growth and modernization, requiring urgent remediation. Our understanding of the metabolic response of native microbial communities to oil spills is not well understood. Here, we explored the baseline hydrocarbon-degrading communities of a subarctic Atlantic region to uncover the metabolic potential of the bacteria that inhabit the surface and subsurface water. We conducted enrichments with a 13C-labeled hydrocarbon to capture the fraction of the community actively using the hydrocarbon. We then combined this approach with metagenomics to identify the metabolic potential of this hydrocarbon-degrading community. This revealed previously undescribed uncultured bacteria with unique metabolic mechanisms involved in aerobic hydrocarbon degradation, indicating that temperature may be pivotal in structuring hydrocarbon-degrading baseline communities. Our findings highlight gaps in our understanding of the metabolic complexity of hydrocarbon degradation by native marine microbial communities.

Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.

Co-contamination of hydrocarbons with heavy metals in soils often complicates and hinders bioremediation. A comprehensive characterization of site-specific degraders at contaminated sites can help determine if in situ bioremediation processes are sufficient. This study aimed to identify differences in benzene and toluene degradation rates and the microbial communities enriched under aerobic conditions when different concentrations of Cd and Pb are introduced. Microcosms were used to study the degradation of 0.23 mM benzene or 0.19 mM toluene under various concentrations of Pb (up to 240 µM) and Cd (up to 440 µM). Soil collected from a stormwater retention basin receiving runoff from a large parking lot was utilized to seed the microcosms. The hydrocarbon degradation time and rates were measured. After further rounds of amendment and degradation of benzene and toluene, 16S rRNA gene amplicon sequencing and quantitative PCR were used to ascertain the microbial communities enriched under the various concentrations of the heavy metals. The initial degradation time for toluene and benzene was 7 to 9 days and 10 to 13 days, respectively. Degradation rates were similar for each hydrocarbon despite the concentration and presence of metal co-contaminant, however, the enriched microbial communities under each condition differed. Microcosms without metal co-contaminant contained a diversity of putative benzene and toluene degrading bacteria. Cd strongly reduced the richness of the microbial communities. With higher levels of heavy metals, genera such as Ralstonia, Cupriavidus, Azoarcus, and Rhodococcus became more dominant under various conditions. The study finds that highly efficient benzene- and toluene-degrading consortia can develop under variations of heavy metal co-contamination, but the consortia are dependent on the heavy metal type and concentrations. [ABSTRACT FROM AUTHOR]

Petroleum contamination to our biosphere particularly soil and water is due to release of petroleum products from petrochemical industries and is now a day's biggest problem to the mankind. Present work was conducted to assess capability of hydrocarbon-utilizing and metal tolerant bacteria to degrade hydrocarbons and remediate metals in the soil contaminated with petroleum with the aim to form super bio-inoculants to restore soil to its original state. In order to achieve above goal, petroleum contaminated soil was observed for hydrocarbons using GC-MS, a total of 25 hydrocarbons were found in petroleum polluted soil with hydrocarbon concentration of 3738 mg/kg. Petroleum polluted soil was also observed for total bacterial population which was observed as 2.10 × 106 CFU/g of soil. Strains YSA-7 and YSA-8 showed highest potential for hydrocarbon-utilization with an absorbance of 0.681 and 0.614 respectively. Strains were also highly tolerant to Cu and Zn with tolerance of 600 µg/ml (Cu) and 1500 µg/ml (Zn) by strain YSA-7 and 700 µg/ml (Cu) and 1800 (Zn) µg/ml by strain YSA-8. Strains YSA-7 and YSA-8 were identified by 16 SrRNA as Lysinibacillus fusiformis and Stenotrophomonas maltophilia, respectively. After 20 days of incubation, Lysinibacillus fusiformis strain YSA-7 and Stenotrophomonas maltophilia YSA8 degraded all twenty-five (25) compounds but there was complete degradation of 13 compounds by strain YSA-7 and 17 compounds by strain YSA-8 using GC-MS. Both strains (YSA-7 and YSA8) were significant and efficient for removing Cu and Zn using mechanism of biosorption at different pH, metal concentrations and time of incubation. Remediation of hydrocarbons and metals under in vitro conditions suggests that the inoculation of such bacteria to petroleum contaminated soil possessing mixture of contaminants such as hydrocarbons and metals can remove such pollutants from contaminated environment and can restore such habitat to its original state. [ABSTRACT FROM AUTHOR]

Oil spills during extraction and use are seriously threatening human health. Hence, effective bioremediation is a prerequisite for environmental and human well-being. In this study, bioremediation was performed by natural attenuation (NA), bioaugmentation (BA), and biostimulation (BS) microcosmic experiments. Gas chromatography and high-throughput sequencing were used to explore the changes in hydrocarbon degradation and bacterial community structure in different layers of contaminated soil, respectively. The results showed that the deep soil contained mainly C17‒C21 fractions. In 300 days, the degradation rates of soil total petroleum hydrocarbons in surface, middle, and deep soils were 99.87%, 96.04%, and 71.63% in the BA group; 99.75%, 95.73%, and 99.84% in the BS group; and 8.55%, 8.64%, and 9.84% in the NA group, respectively. Most of the petroleum hydrocarbon fractions were completely degraded by the end of remediation experiments. There were noticeable changes in the structure and relative abundance of soil bacteria in the different treatments compared to the original soil. Proteobacteria was the dominant phylum in all soil samples and Pseudomonas became the dominant genus in the BA group. In the BA and BS group, the germination rate of mung bean seeds was > 72.5% in all cases, which was six times higher than that of the NA group. Thus, bioremediation reduced the toxicity of contaminated soil in a shorter period of time than NA, and this study could act as a reference for treatment of contaminated soil in oil recovery areas. [ABSTRACT FROM AUTHOR]

BackgroundMicroorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy.ResultsHere, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondary recovery.ConclusionOur data expand current knowledge of the metabolic potential and role in hydrocarbon metabolism of individual members of thermophilic microbial communities from an oil reservoir. The study also reveals potential metabolic exchanges based on vitamin and amino acid auxotrophies indicating the presence of complex network of interactions between microbial taxa within the community.

Waxy crude oil is a problem to the oil and gas industry because wax deposition in pipelines reduces the quality of the crude oil. Currently, the industry uses chemicals to solve the problem but it is not environmentally friendly. As an alternative, the biodegradation approach is one of the options. Previously eleven thermophilic bacteria were isolated and exhibited high ability to degrade hydrocarbon up to 70% of waxy crude oil. However, despite the successful study on these single bacteria strains, it is believed that biodegradation of paraffin wax requires more than a single species. Five consortia were developed based on the biodegradation efficiency of 11 bacterial strains. Consortium 3 showed the highest biodegradation (77.77%) with more long-chain alkane degraded throughout the incubation compared to other consortia. Enhancement of hydrocarbon degradation was observed for all consortia especially in long chain alkane (C18-C40). Consortium 3 exhibited higher alkane monooxygenase, alcohol dehydrogenase, lipase, and esterase activities. Moreover, the dominant bacteria in the consortia were determined by denaturing gradient gel electrophoresis (DGGE), which showed the domination of genera Geobacillus, Parageobacillus, and Anoxybacillus. It can be concluded that the bacterial consortia showed higher biodegradation and improved degrading more long-chain hydrocarbon compared to a single isolate. [ABSTRACT FROM AUTHOR]

The halophilic consortia were enriched from water samples of Abhor, Red Sea, Jeddah, Saudi Arabia for the degradation of phenanthrene, fluorene, hexadecane, pyrene, and treatment of automobile service station wastewater under saline conditions (4%). Complete degradation of phenanthrene and fluorene was recorded up to a concentration of 500 mg.L-1 in 12 days, when the concentration was raised to 800 mg.L-1, the percentage of degradation of the two compounds was recorded by 84 and 90% within 14 days, while when the concentration increased to 1000 mg.L-1, a significant decline was recorded. Pyrene degradation was studied under saline conditions, where it recorded a degradation rate of 92 and 81% at a concentration of 50 and 100 mg.L-1 in 10 and 12 days, respectively, while when increasing the concentration, a severe decrease in the percentage of degradation was recorded that reached 57 and 44% at concentration 200 and 300 mg.L-1, respectively .Hexadecane recorded complete degradation at a concentration of 0.5 and 1%, within 4 and 6 days, respectively, while at a concentration of 1.5%, the rate of deterioration was 88% in 10 days. Record 93% removal of COD in CSTR within 40th day, when treatment of automobile service station wastewater with halophilic bacterial consortia. The existing bacterial strains were classified as potentially responsible for petroleum hydrocarbon degradation and treatment of automobile service station wastewater such as Ochrobactrum, Propionispira, Martelella, Bacillus, Marinobacter, and Azospira. The present study recommends that the hydrophilic consortia can be used in the treatment of automobile service station wastewater under saline conditions. [ABSTRACT FROM AUTHOR]

Sloping farmland increases soil erosion, but little is known about how soil erosion impacts microbial structures and functions in sloping farmland. Using high-throughput sequencing, we conducted a six-year in-situ experiment with gradients of 0° (CK), 5° (S1), 10° (S2), and 15° (S3) to investigate the effects of sloping farmland on soil microbial diversities, compositions, and functions related to nitrogen and carbon resource acquisition. The results showed that the S1, S2, and S3 treatments significantly decreased SOM and NO 3 − levels by 33.0%∼47.3% and 37.0%∼49.6%, respectively, in comparison to the CK treatment. The S1, S2, and S3 treatments had similar impacts on diversities and compositions of bacterial and fungal communities. Moreover, the S1, S2, and S3 treatments had same enriched and depleted core microbiota. Long-term sloping cultivation filtered these core microbiota mainly by reducing SOM and NO 3 − and increasing AK and AP. Compared with the CK treatment, the S1, S2, and S3 treatments significantly reduced the relative abundances of potential functions of nitrogen fixation, hydrocarbon degradation, and fermentation by 46.9%∼54.5%, 74.7%∼83.5%, and 28.1%∼54.1%, respectively. Sloping treatments reduced functions related to nitrogen fixation and soil hydrocarbon degradation mainly because the loss of SOM reduced the relative abundances of core microbiota. Generally, long-term sloping cultivation reduced core microbiota related to nitrogen fixation and soil hydrocarbon degradation mainly due to the loss of SOM. Our findings provided implications for the management and reclamation of sloping farmland. • Long-term sloping cultivation significantly decreased soil organic matter by 33.0%∼47.3%. • Sloping gradients within 5°∼15° similarly impacted microbial diversities and functions. • Long-term sloping cultivation reduced nitrogen and carbon resource acquisition. [ABSTRACT FROM AUTHOR]

[Display omitted] • Hydrocarbon-degrading consortia were dominated by homogeneous dispersal processes; • Nitrate addition promoted hydrocarbon degradation and undominated processes; • Pseudomonas can improve oil recovery by producing rhamnolipid; • Roseovarius -MAGs were the novel taxa oxidizing alkane and producing acetate; • Ca. Bacteroidia could potentially degrade hydrocarbons by fumarate addition. Hydrocarbon–degrading consortia (HDC) play an important role in petroleum exploitation. However, the real composition and metabolic mechanism of HDC in the microbial enhanced oil recovery (MEOR) process remain unclear. By combining 13C–DNA stable isotope probing microcosms with metagenomics, some newly reported phyla, including Chloroflexi, Synergistetes, Thermotogae, and Planctomycetes, dominated the HDC in the oil reservoirs. In the field trials, the HDC in the aerobic-facultative-anaerobic stage of oilfields jointly promoted the MEOR process, with monthly oil increments of up to 189 tons. Pseudomonas can improve oil recovery by producing rhamnolipid in the facultative condition. Roseovarius was the novel taxa potentially oxidizing alkane and producing acetate to improve oil porosity and permeability in the aerobic condition. Ca. Bacteroidia were the new members potentially degrading hydrocarbons by fumarate addition in the anaerobic environment. Comprehensive identification of the active HDC in oil reservoirs provides a novel theoretical basis for oilfield regulatory scheme. [ABSTRACT FROM AUTHOR]

The current work deals with genomic analysis, possible ecological functions, and biotechnological potential of two bacterial strains, HO-A22T and SHC 2-14, isolated from unique subsurface environments, the Cheremukhovskoe oil field (Tatarstan, Russia) and nitrate- and radionuclide-contaminated groundwater (Tomsk region, Russia), respectively. New isolates were characterized using polyphasic taxonomy approaches and genomic analysis. The genomes of the strains HO-A22T and SHC 2-14 contain the genes involved in nitrate reduction, hydrocarbon degradation, extracellular polysaccharide synthesis, and heavy metal detoxification, confirming the potential for their application in various environmental biotechnologies. Genomic data were confirmed by cultivation studies. Both strains were found to be neutrophilic, chemoorganotrophic, facultatively anaerobic bacteria, growing at 15–33 °C and 0–1.6% NaCl (w/v). The 16S rRNA gene sequences of the strains were similar to those of the type strains of the genus Ensifer (99.0–100.0%). Nevertheless, genomic characteristics of strain HO-A22T were below the thresholds for species delineation: the calculated average nucleotide identity (ANI) values were 83.7–92.4% (T (=VKM B-3646T = KCTC 92427T) represented a novel species of the genus Ensifer, with the proposed name Ensifer oleiphilus sp. nov. Strain SHC 2-14 was assigned to the species ‘Ensifer canadensis’, which has not been validly published. This study expanded the knowledge about the phenotypic diversity among members of the genus Ensifer and its potential for the biotechnologies of oil recovery and radionuclide pollution treatment.

The agricultural spreading of treated sewage sludge is a valid strategy in terms of circular economy for the management of this nutrient-rich waste. Anaerobic digestion (AD) can be applied to stabilize and hygienize sewage sludge, making it suitable for agricultural reuse, while producing biogas to be utilized as an energy vector. However, the presence of contaminants, including petroleum hydrocarbons, could limit the widespread agricultural utilization of sewage sludge. In this context, the impact of dewatering agents, such as cationic polyelectrolytes, on AD efficiency and hydrocarbon biodegradation has been poorly investigated, although it represents a noteworthy aspect when conditioned sludge is digested for agricultural use in centralized biogas plants. This work aims to elucidate the effect of cationic polyelectrolyte addition on biomethanation as well as the degradation and extractability of C10-C40 hydrocarbons during mesophilic AD of sewage sludge. The addition of 26.7 g/kgTS of cationic polyelectrolyte was observed to extend the AD lag phase, although similar methane yields (573–607 mLCH4 per g of degraded volatile solids) were observed for both conditioned and raw sludge. Furthermore, a significant impact on hydrocarbon degradation was observed due to chemical conditioning. Indeed, this work reveals that cationic polyelectrolytes can affect hydrocarbon extractability and suggests moreover that the presence of natural interferents (e.g., biogenic waxes) in sewage sludge may lead to an overestimation of potentially toxic C10-C40 hydrocarbon concentrations, potentially limiting the application of sludge-derived digestates in agriculture. [ABSTRACT FROM AUTHOR]

The high-altitude lakes are ecological habitats accommodating a vast diversity of microbial populations. These microbes are efficient sources for a variety of enzymes. The objective of this study is to perform in-depth metagenomic profiling of an artificial lake ecosystem located in the Sikkim Himalayan region, deciphering the hydrocarbon degradation potential of this site and mining biocatalysts of industrial importance. In the present study, metagenomic analysis of an artificial Himalayan lake, located in North Sikkim, India, was performed. A comprehensive taxonomic and functional profiling revealed gene mapped to pathways for degradation of hydrocarbons such as toluene, benzoate, ethylbenzene, etc. This site was rich in iron, and the metagenomic investigation revealed genomic signatures of the iron-reducing bacterium; Geothrix fermentans. The appraisal of the carbohydrate metabolic potential of this site divulged the predominance of β-galactosidase genes. The artificial lake metagenome was further compared to publicly available saline and freshwater lakes. At the taxonomic, as well as functional levels, it was found to be closer to freshwater lake metagenome, e.g., Medonta Lake, US, and freshwater Vanda Lake, Antarctica. The microbial community profiling and functional contribution of the artificial Himalayan lake would be beneficial for mining genes encoding various industrially relevant enzymes. [ABSTRACT FROM AUTHOR]

Petroleum contamination of our biosphere particularly soil and water is due to the release of petroleum products from petrochemical industries. The aim of the present study was to isolate hydrocarbon-utilising and metal-tolerant bacteria capable of hydrocarbon degradation and metal remediation. Petroleum contaminated soil from which the bacteria were isolated had a total hydrocarbon concentration of 3538 mg/kg and several metals. The soil was also observed for the total bacterial population which was observed as 2.23 × 106 CFU/g of soil. Among different strains, strain YSA-9 showed the highest potential for hydrocarbon-utilisation with an absorbance of 0.920. Strain YSA-9 also displayed high tolerance to Cr (VI) and Cu up to 900 μg/ml to each metal. Strain YSA-9 was identified by 16S rRNA as Klebsiella pneumoniae. Strain YSA-9 showed a wide range of hydrocarbon degradation, degrading many hydrocarbons with the formation of new compounds and remedying higher amounts of metals. Klebsiella pneumoniae YSA-9 significantly removed Cr (VI) and Cu by biosorption at different pH, metal concentrations, temperature and the time of incubation. A wide range of hydrocarbon degradation and higher metal remediation by strain YSA-9 makes strain YSA-9 a super bio-inoculant for the remediation of polluted soils. [ABSTRACT FROM AUTHOR]

The development of Arctic regions leads to pollution of marine and coastal environments with oil and petroleum products. The purpose of this work was to determine the diversity of microbial communities in seawater, as well as in littoral and coastal soil, and the potential ability of their members to degrade hydrocarbons degradation and to isolate oil-degrading bacteria. Using high-throughput sequencing of the V4 region of the 16S rRNA gene, the dominance of bacteria in polar communities was shown, the proportion of archaea did not exceed 2% (of the total number of sequences in the libraries). Archaea inhabiting the seawater belonged to the genera Nitrosopumilus and Nitrosoarchaeum and to the Nitrososphaeraceae family. In the polluted samples, members of the Gammaproteobacteria, Alphaproteobacteria, and Actinomycetes classes predominated; bacteria of the classes Bacteroidia, Clostridia, Acidimicrobiia, Planctomycetia, and Deltaproteobacteria were less represented. Using the iVikodak program and KEGG database, the potential functional characteristics of the studied prokaryotic communities were predicted. Bacteria were potentially involved in nitrogen and sulfur cycles, in degradation of benzoate, terephthalate, fatty acids, and alkanes. A total of 19 strains of bacteria of the genera Pseudomonas, Aeromonas, Oceanisphaera, Shewanella, Paeniglutamicibacter, and Rhodococcus were isolated from the studied samples. Among them were psychrotolerant and psychrophilic bacteria growing in seawater and utilizing crude oil, diesel fuel, and motor oils. The data obtained suggest that the studied microbial communities could participate in the removal of hydrocarbons from arctic seawater and coastal soils and suggested the possibility of the application of the isolates for the bioaugmentation of oil-contaminated polar environments. [ABSTRACT FROM AUTHOR]

Anaerobic microbial hydrocarbon degradation is a major biogeochemical process at marine seeps. Here we studied the response of the microbial community to petroleum seepage simulated for 190 days in a sediment core from the Caspian Sea using a sediment-oil-flow-through (SOFT) system. Untreated (without simulated petroleum seepage) and SOFT sediment microbial communities shared 43% bacterial genus-level 16S rRNA-based operational taxonomic units (OTU0.945) but shared only 23% archaeal OTU0.945. The community differed significantly between sediment layers. The detection of fourfold higher deltaproteobacterial cell numbers in SOFT than in untreated sediment at depths characterized by highest sulfate reduction rates and strongest decrease of gaseous and mid-chain alkane concentrations indicated a specific response of hydrocarbon-degrading Deltaproteobacteria. Based on an increase in specific CARD-FISH cell numbers, we suggest the following groups of sulfate-reducing bacteria to be likely responsible for the observed decrease in aliphatic and aromatic hydrocarbon concentration in SOFT sediments: clade SCA1 for propane and butane degradation, clade LCA2 for mid- to long-chain alkane degradation, clade Cyhx for cycloalkanes, pentane and hexane degradation, and relatives of Desulfobacula for toluene degradation. Highest numbers of archaea of the genus Methanosarcina were found in the methanogenic zone of the SOFT core where we detected preferential degradation of long-chain hydrocarbons. Sequencing of masD, a marker gene for alkane degradation encoding (1-methylalkyl)succinate synthase, revealed a low diversity in SOFT sediment with two abundant species-level MasD OTU0.96.

A novel bacterial strain, CH91, was isolated from a high-temperature oil reservoir. Morphological characterization, phylogenetic analyses of 16S rRNA gene sequence and genome relatedness indicated that the strain is a potential new species in the genus Rhodococcus. Strain CH91 could grow in the temperature range of 25–50 °C (optimally at 37 °C) and utilize a broad range of long-chain n-alkanes from hexadecane to hexatriacontane. The utilization of the n-alkanes mixture of strain CH91 revealed that the degradation rate was correlated to the length of the carbon chain. Two novel alkB genes encoding alkane 1-monooxygenase were found in the genome of this strain. The protein sequences of both alkane 1-monooxygenases showed a remarkable phylogenetic distance to other reported AlkB protein sequences. These results would help broaden our knowledge about alkane degradation by Rhodocuccus and its potential ecological role. The ability of the strain in the long-chain alkane degradation and thermal tolerance could also be further exploited for bioremediation of oil contaminations and microbial enhanced oil recovery. [ABSTRACT FROM AUTHOR]

The global increase in marine transportation of dilbit (diluted bitumen) can increase the risk of spills, and the application of chemical dispersants remains a common response practice in spill events. To reliably evaluate dispersant effects on dilbit biodegradation over time, we set large-scale (1,500 mL) microcosms without nutrient addition using a low dilbit concentration (30 ppm). Shotgun metagenomics and metatranscriptomics were deployed to investigate microbial community responses to naturally and chemically dispersed dilbit. We found that the large-scale microcosms could produce more reproducible community trajectories than small-scale (250 mL) ones based on the 16S rRNA gene amplicon sequencing. In the early-stage large-scale microcosms, multiple genera were involved in the biodegradation of dilbit, while dispersant addition enriched primarily Alteromonas and competed for the utilization of dilbit, causing depressed degradation of aromatics. The metatranscriptomic-based metagenome-assembled genomes (MAG) further elucidated early-stage microbial antioxidation mechanism, which showed that dispersant addition triggered the increased expression of the antioxidation process genes of Alteromonas species. Differently, in the late stage, the microbial communities showed high diversity and richness and similar compositions and metabolic functions regardless of dispersant addition, indicating that the biotransformation of remaining compounds can occur within the post-oil communities. These findings can guide future microcosm studies and the application of chemical dispersants for responding to a marine dilbit spill. IMPORTANCE In this study, we employed microcosms to study the effects of marine dilbit spill and dispersant application on microbial community dynamics over time. We evaluated the impacts of microcosm scale and found that increasing the scale is beneficial for reducing community stochasticity, especially in the late stage of biodegradation. We observed that dispersant application suppressed aromatics biodegradation in the early stage (6 days), whereas exerting insignificant effects in the late stage (50 days), from both substance removal and metagenomic/metatranscriptomic perspectives. We further found that Alteromonas species are vital for the early-stage chemically dispersed oil biodegradation and clarified their degradation and antioxidation mechanisms. These findings help us to better understand microcosm studies and microbial roles for biodegrading dilbit and chemically dispersed dilbit and suggest that dispersant evaluation in large-scale systems and even through field trails would be more realistic after marine oil spill response. [ABSTRACT FROM AUTHOR]

Oil reservoirs have an autochthonous microbiota that varies depending on factors such as temperature, pH, salinity, pressure and availability of nutrients. The following work had the objective of characterizing bacteria isolated from a Cuban crude oil. The isolated ones were identified through conventional tests and mass spectrometry. It was evaluated the capacity to assimilate different hydrocarbons as a carbon source. It was also determined the minimum inhibitory concentration to crude and the formation of biofilms. Six bacteria were isolated, five were located in the genus Bacillus and one in the genus Aeromonas. All the isolates used six hydrocarbons as a carbon and energy source, grew in concentrations greater than 15% (v / v) of the crude oil and degraded the saturated and aromatic fraction thereof. All bacteria produce biofilms and have characteristics that make them interesting for inclusion in crude oil extraction and bioremediation.

With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001). Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors) were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential "keystone" genes, defined as either "hubs" or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions.

The present study was conducted to reveal specific bacterial consortium belong to same genus capable of mineralizing petroleum hydrocarbons and also act as a valid indicator to locate the oil reservoir in Red Sea, Saudi Arabia. The study focused on area consist of hydrocarbons in briny water and sediment. The sites included Port Sudan Deep, Suakin Deep, Hatiba Deep, and Brian salt in the Red Sea, Saudi Arabia. The concept of the study is to identify crude oil reservoir using the presence of hydrocarbon degrading bacterial strains. The Marinobacter strains isolated were grown in different media such as marine broth with crude oil, tryptic soy agar and mineral salt medium with phenanthrene as sole carbon source at 40 g/L of NaCl concentration. The strains present in hydrocarbon reservoirs of different deeps were isolated and identified as Marinobacter hydrocarbonoclasticus strain MAM1 (MF716467), Marinobacter sp. strain MAM2 (MF716468) and Marinobacter hydrocarbonoclasticus strain MAM3 (MF716469). Marinobacter consortium was pertained by the mixture of the above strains (MAM1, MAM2 and MAM3) from different deep samples. The consortium potentially utilized PAHs (polycyclic aromatic hydrocarbons) such as phenanthrene (PHN) and pyrene (PY). The consortium degraded 72 ± 1.5% of PHN at 1500 mg/L concentration in 16 days under saline condition (4%). The degradation of PY (300 mg/L) by the consortium was 86 ± 1.1% in 12 days under saline condition (4%). Also the presence of Marinobacter strains in the deep water samples and crude oil drilling rig (core) samples, confirmed the relationship between the bacterial strains and oil reservoir. Thus the study confirmed Marinobacter can be used as a potential indicator strain in different deeps at Red Sea to identify the crude oil reservoir. [ABSTRACT FROM AUTHOR]

Computational and statistical analysis of shotgun metagenomes can predict gene abundance and is helpful for elucidating the functional and taxonomic compositions of environmental samples. Gene products are compared against physicochemical conditions or perturbations to shed light on the functions performed by the microbial community of an environmental sample; however, this information is not always available. The present study proposes a method for inferring the metabolic potential of metagenome samples by constructing a reference based on determining the probability distribution of the counts of each enzyme annotated. To test the methodology, we used marine water samples distributed worldwide as references. Then, the references were utilized to compare the annotated enzymes of two different water samples extracted from the Gulf of Mexico (GoM) to distinguish those enzymes with atypical behavior. The enzymes whose annotation counts presented frequencies significantly different from those of the reference were used to perform metabolic reconstruction, which naturally identified pathways. We found that several of the enzymes were involved in the biodegradation of petroleum, which is consistent with the impact of human hydrocarbon extraction activity and its ubiquitous presence in the GoM. The examination of other reconstructed pathways revealed significant enzymes indicating the presence of microbial communities characterizing each ocean depth and ocean cycle, providing a fingerprint of each sampled site. [ABSTRACT FROM AUTHOR]

Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation. [ABSTRACT FROM AUTHOR]

Soil samples from a transect from low to highly hydrocarbon‐contaminated soils were collected around the Brazilian Antarctic Station Comandante Ferraz (EACF), located at King George Island, Antarctica. Quantitative PCR (qPCR) analysis of bacterial 16S rRNA genes, 16S rRNA gene (iTag), and shotgun metagenomic sequencing were used to characterize microbial community structure and the potential for petroleum degradation by indigenous microbes. Hydrocarbon contamination did not affect bacterial abundance in EACF soils (bacterial 16S rRNA gene qPCR). However, analysis of 16S rRNA gene sequences revealed a successive change in the microbial community along the pollution gradient. Microbial richness and diversity decreased with the increase of hydrocarbon concentration in EACF soils. The abundance of Cytophaga, Methyloversatilis, Polaromonas, and Williamsia was positively correlated (p‐value = <.05) with the concentration of total petroleum hydrocarbons (TPH) and/or polycyclic aromatic hydrocarbons (PAH). Annotation of metagenomic data revealed that the most abundant hydrocarbon degradation pathway in EACF soils was related to alkyl derivative‐PAH degradation (mainly methylnaphthalenes) via the CYP450 enzyme family. The abundance of genes related to nitrogen fixation increased in EACF soils as the concentration of hydrocarbons increased. The results obtained here are valuable for the future of bioremediation of petroleum hydrocarbon‐contaminated soils in polar environments. [ABSTRACT FROM AUTHOR]

With the frequent occurrence of oil spills, the bioremediation of petroleum hydrocarbons pollution has attracted more and more attention. In this study, we investigated the biodegradation of crude oil by the biosurfactant-producing strain S-1. The strain was isolated from petroleum-contaminated soil and identified as Serratia marcescens according to partial 16S rDNA gene analysis. It was able to effectively degrade hydrocarbons with the concomitant production of biosurfactants at 20–30 °C, while there was no biosurfactant production and the degradation rate was lower at 37 °C. The biosurfactant was identified as serrawettin W1 by UPLC-ESI–MS, and was found to reduce the surface tension of water to 30 mN/m, with stable surface activity and emulsion activity at temperatures from 20 to 100 °C, pH of 2–10 and NaCl concentrations of 0–50 g/L. Serrawettin W1 significantly increased the cell surface hydrophobicity (CSH) and enhanced the bioavailability of hydrocarbon pollutants, which was conducive to the degradation of crude oil, including long-chain alkanes and aromatic hydrocarbons. Serratia marcescens S-1 has potential applications in bioremediation at low temperature. [ABSTRACT FROM AUTHOR]

Abstract Background Soils polluted with animal charcoal from skin and hide cottage industries harbour extremely toxic and carcinogenic hydrocarbon pollutants and thus require a bio-based eco-friendly strategy for their depuration. The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal-polluted soil was monitored for 6 weeks in field moist microcosms consisting of CFMM-treated soil (FN4) and an untreated control (FN1). Hydrocarbon degradation was monitored using gas chromatography-flame ionization detector (GC-FID), and changes in microbial community structure were monitored using Kraken, while functional annotation of putative open reading frames (ORFs) was done using KEGG KofamKOALA and NCBI’s conserved domain database (CDD). Results Gas chromatographic analysis of hydrocarbon fractions revealed the removal of 84.02% and 82.38% aliphatic and 70.09% and 70.14% aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure. In the FN4 metagenome, 92.97% of the population belong to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%) and Firmicutes (11.20%), and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%), were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for aromatic hydrocarbons, benzoate, xylene, chlorocyclohexane/chlorobenzene, toluene and several others in FN1 metagenome. In the FN4 metagenome, only seven hydrocarbon degradation genes were detected. Conclusion This study revealed that though CFMM amendment slightly increases the rate of hydrocarbon degradation, it negatively impacts the structural and functional properties of the animal charcoal-polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration.

Oily sludge generated by petroleum industries results in serious hazards to the environment due to its toxic effects. Microorganisms can survive in the harsh environment utilizing the pollutants as their sole source of carbon and energy. The present study was carried out to isolate and characterize the bacterial population present in the refinery wastes collected from Bongaigaon Refinery, Assam, India. The diversity of bacteria was significantly correlated (p< 0.05) with the physicochemical characteristics and level of hydrocarbon content of the studied samples. A total of 36 bacterial strains were isolated from the oily sludge sample. Two potent hydrocarbonoclastic bacteria were screened out based on their ability of degradation of petroleum hydrocarbon. The potent bacterial isolates also produced biosurfactants. The potent strains were identified as Pseudomonas sp. and Bacillus sp. Gravimetric estimation of hydrocarbon degradation and FTIR analysis revealed that these potent bacterial strains could remove different constituents of petroleum hydrocarbon. The indigenous bacterial isolates either alone or in consortium may be applied for degrading different fractions of hydrocarbon contaminants of the oily sludge to remediate the sludge polluted soil environment.