Search

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 - 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.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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Ltd.)

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 13 C-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., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

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.IMPORTANCEMicrobial degradation of hydrocarbons is a critically important process promoting ecosystem health, yet much of what is known about this process is based on physiological experiments with a few hydrocarbon substrates and cultured microbes. Thus, the ability to degrade the diversity of hydrocarbons that comprise oil and gas by microbes in the environment, particularly in the ocean, is not well characterized. Therefore, this study aimed to utilize non-cultivation-based 'omics data to explore novel genomes of uncultured marine microbes involved in degradation of oil and gas. Analyses of newly assembled metagenomic data and previously existing genomes from other marine data sets, with metagenomic and metatranscriptomic read recruitment, revealed globally distributed hydrocarbon-degrading marine microbes with clade-specific substrate degradation potentials that have not been previously reported. This new understanding of oil and gas degradation by uncultured marine microbes suggested that the global ocean harbors a diversity of hydrocarbon-degrading bacteria, which can act as primary agents regulating ecosystem health., Competing Interests: The authors declare no conflict of interest.

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., (© 2024. The Author(s).)

Databases of genes and enzymes involved in hydrocarbon degradation have been previously reported. However, these databases specialize on only a specific group of hydrocarbons and/or are constructed partly based on enzyme sequences with putative functions indicated by in silico research, with no experimental evidence. Here, we present a curated database of Hydrocarbon Aerobic Degradation Enzymes and Genes (HADEG) containing proteins and genes involved in alkane, alkene, aromatic, and plastic aerobic degradation and biosurfactant production based solely on experimental evidence, which are present in bacteria, and fungi. HADEG includes 259 proteins for petroleum hydrocarbon degradation, 160 for plastic degradation, and 32 for biosurfactant production. This database will help identify and predict hydrocarbon degradation genes/pathways and biosurfactant production in genomes., Competing Interests: Declaration of Competing Interest All the authors have read and approved the final version of the manuscript and declare there are no conflicts of interest., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

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 13 C-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., Competing Interests: The authors declare no conflict of interest.

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., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Soil contamination with diesel oil is quite common during processes of transport and storage. Bioremediation is considered a safe, economical, and environmentally friendly approach for contaminated soil treatment. In this context, studies using hydrocarbon bioremediation have focused on total petroleum hydrocarbon (TPH) analysis to assess process effectiveness, while ecotoxicity has been neglected. Thus, this study aimed to select a microbial consortium capable of detoxifying diesel oil and apply this consortium to the bioremediation of soil contaminated with this environmental pollutant through different bioremediation approaches. Gas chromatography (GC-FID) was used to analyze diesel oil degradation, while ecotoxicological bioassays with the bioindicators Artemia sp., Aliivibrio fischeri (Microtox), and Cucumis sativus were used to assess detoxification. After 90 days of bioremediation, we found that the biostimulation and biostimulation/bioaugmentation approaches showed higher rates of diesel oil degradation in relation to natural attenuation (41.9 and 26.7%, respectively). Phytotoxicity increased in the biostimulation and biostimulation/bioaugmentation treatments during the degradation process, whereas in the Microtox test, the toxicity was the same in these treatments as that in the natural attenuation treatment. In both the phytotoxicity and Microtox tests, bioaugmentation treatment showed lower toxicity. However, compared with natural attenuation, this approach did not show satisfactory hydrocarbon degradation. Based on the microcosm experiments results, we conclude that a broader analysis of the success of bioremediation requires the performance of toxicity bioassays.

The Role of microorganisms in the petroleum industry is wide-ranging. To understand the role of microorganisms in hydrocarbon transformation, identification of such microorganisms is vital, especially the ones capable of in situ degradation. Microorganisms play a pivotal role in the degradation of hydrocarbons and remediation of heavy metals. Anaerobic microorganisms such as Sulphate Reducing Bacteria (SRB), responsible for the production of hydrogen sulphide (H 2 S) within the reservoir, reduces the oil quality by causing reservoir souring and reduction in oil viscosity. This paper reviews the diversity of SRB, methanogens, Nitrogen Reducing Bacteria (NRB), and fermentative bacteria present in oil reservoirs. It also reviews the extensive diversity of these microorganisms, their applications in petroleum industries, characteristics and adaptability to survive in different conditions, the potential to alter the petroleum hydrocarbons properties, the propensity to petroleum hydrocarbon degradation, and remediation of metals.

Bacteria from the genus Geobacillus are generally obligately thermophilic, with a unique bioenergy production capacity and unique enzymes. Geobacillus species were isolated primarily from hot springs, oilfields, and associated soils. They often exhibit unique survival patterns in these extreme oligotrophic environments. With the development of the microbial resources found in oilfields, Geobacillus spp. have been proven as valuable bacteria in many reports related to oilfields. After the isolation of Geobacillus by culture methods, more evidence was found that they possess the abilities of hydrocarbon utilization and bioemulsifier production. This paper mainly summarizes some characteristics of the Geobacillus species found in the oilfield environment, focusing on the inference and analysis of hydrocarbon degradation and bioemulsifier synthesis based on existing research, which may reveal their potential value in microbial enhanced oil recovery. It also provides references for understanding microbes in extreme environments.

Background: The Mariana Trench is the deepest known site in the Earth's oceans, reaching a depth of ~ 11,000 m at the Challenger Deep. Recent studies reveal that hadal waters harbor distinctive microbial planktonic communities. However, the genetic potential of microbial communities within the hadal zone is poorly understood., Results: Here, implementing both culture-dependent and culture-independent methods, we perform extensive analysis of microbial populations and their genetic potential at different depths in the Mariana Trench. Unexpectedly, we observed an abrupt increase in the abundance of hydrocarbon-degrading bacteria at depths > 10,400 m in the Challenger Deep. Indeed, the proportion of hydrocarbon-degrading bacteria at > 10,400 m is the highest observed in any natural environment on Earth. These bacteria were mainly Oleibacter, Thalassolituus, and Alcanivorax genera, all of which include species known to consume aliphatic hydrocarbons. This community shift towards hydrocarbon degraders was accompanied by increased abundance and transcription of genes involved in alkane degradation. Correspondingly, three Alcanivorax species that were isolated from 10,400 m water supplemented with hexadecane were able to efficiently degrade n-alkanes under conditions simulating the deep sea, as did a reference Oleibacter strain cultured at atmospheric pressure. Abundant n-alkanes were observed in sinking particles at 2000, 4000, and 6000 m (averaged 23.5 μg/gdw) and hadal surface sediments at depths of 10,908, 10,909, and 10,911 m (averaged 2.3 μg/gdw). The δ 2 H values of n-C 16/18 alkanes that dominated surface sediments at near 11,000-m depths ranged from - 79 to - 93‰, suggesting that these sedimentary alkanes may have been derived from an unknown heterotrophic source., Conclusions: These results reveal that hydrocarbon-degrading microorganisms are present in great abundance in the deepest seawater on Earth and shed a new light on potential biological processes in this extreme environment.

Leaves are covered by a cuticle composed of long (C11-C20) and very-long chain hydrocarbons (>C20), e.g. alkanes, fatty acids, alcohols, aldehydes, ketones and esters. In addition to these aliphatics, cyclic hydrocarbons may be present. Leaves are colonised by a variety of so-called epiphytic bacteria, which may have adapted to be able to utilise cuticle hydrocarbons. We tested the ability of a wide range of phylogenetically different epiphytic bacteria to utilise and grow on diesel and petroleum benzine and show that out of the 21 strains tested, nine had the ability to utilise diesel for growth. Only one strain was able to utilise petroleum benzine for growth. The ability to utilise hydrocarbons for growth correlated with the ability of the strains to produce surfactants and out of the 21 tested strains, 12 produced surfactants. Showing that 75% of the strains producing surfactants were able to degrade hydrocarbons. Our findings suggest that the ability to degrade hydrocarbons and to produce surfactants is highly prevalent in epiphytic bacteria. It is unclear if epiphytic bacteria utilise hydrocarbons originating from the cuticle of living leaves. The application of surfactant producing, hydrocarbon-utilising, epiphytic bacteria might serve as a method for hydrocarbon bioremediation., (© FEMS 2019.)

The oil drilling process generates large volumes of waste with inadequate treatments. Here, oil drilling waste (ODW) microbial communities demonstrate different hydrocarbon degradative abilities when exposed to distinct nutrient enrichments as revealed by comparative metagenomics. The ODW was enriched in Luria Broth (LBE) and Potato Dextrose (PDE) media to examine the structure and functional variations of microbial consortia. Two metagenomes were sequenced on Ion Torrent platform and analyzed using MG-RAST. The STAMP software was used to analyze statistically significant differences amongst different attributes of metagenomes. The microbial diversity presented in the different enrichments was distinct and heterogeneous. The metabolic pathways and enzymes were mainly related to the aerobic hydrocarbons degradation. Moreover, our results showed efficient biodegradation after 15 days of treatment for aliphatic hydrocarbons (C8-C33) and polycyclic aromatic hydrocarbons (PAHs), with a total of about 50.5% and 46.4% for LBE and 44.6% and 37.9% for PDE, respectively. The results obtained suggest the idea that the enzymatic apparatus have the potential to degrade petroleum compounds., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Aims: The aim of this study was the baseline description of oil-degrading sediment bacteria along a depth transect in the Faroe-Shetland Channel (FSC) and the identification of biomarker taxa for the detection of oil contamination in FSC sediments., Methods and Results: Oil-degrading sediment bacteria from 135, 500 and 1000 m were enriched in cultures with crude oil as the sole carbon source (at 12, 5 and 0°C respectively). The enriched communities were studied using culture-dependent and culture-independent (clone libraries) techniques. Isolated bacterial strains were tested for hydrocarbon degradation capability. Bacterial isolates included well-known oil-degrading taxa and several that are reported in that capacity for the first time (Sulfitobacter, Ahrensia, Belliella, Chryseobacterium). The orders Oceanospirillales and Alteromonadales dominated clone libraries in all stations but significant differences occurred at genus level particularly between the shallow and the deep, cold-water stations. Alcanivorax constituted 64% of clones at FSC135 but was absent at deeper stations. Pseudoalteromonas and Oleispira dominated the bacterial community at 500 and 1000 m., Conclusions: The genus Oleispira emerged as a major player in the early stages of crude oil degradation in deep-sea sediments of the FSC particularly at subzero temperatures. This finding is offering a direction for future research into biomonitoring tools for the detection of low levels of crude oil contamination in the deep FSC, and possibly high latitude cold waters in general., Significance and Impact of the Study: Oil and gas exploration in the FSC occurs at depths >1000 m but baseline environmental data necessary for the assessment of ecosystem recovery to prespill conditions in the event of an oil spill are lacking. This study will contribute to our ability to assess the impact of oil release in the FSC and guide the direction of bioremediation strategies tailored to the area., (© 2018 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of The Society for Applied Microbiology.)

Mangroves are coastal ecosystems of transition between terrestrial and marine environments, that have been particularly contaminated in the last decades. Organic compounds are part of these contaminants, which have increased in the environment due to industrial activities and accidental oil spills. These contaminants are toxic to higher organisms, but microorganisms can metabolize most of these compounds and thus offer a tool for bioremediation purposes. The aim of the present study was to characterize the microbial potential and activity for degradation of aromatic compounds in sediment samples from mangroves using metagenomic and metatranscriptomic approaches. Sediment samples were collected for DNA and RNA extraction from each of the mangrove sites: highly oil-impacted (Oil Mgv), anthropogenically impacted (Ant Mgv) and pristine (Prs Mgv) mangrove. Hydrocarbon concentrations in Oil Mgv sediments were higher than those observed in Ant Mgv and Prs Mgv. Genes and transcripts associated with aromatic compound degradation, particularly the meta and ortho-pathways, were more abundant in Oil Mgv and Ant Mgv suggesting that many of the aromatic compounds are being aerobically degraded by the microbiome in these sites. Functions involved in the degradation of aromatic compounds were also found in pristine site, although in lower abundance. Members of the genera Aromatoleum, Desulfococcus, Desulfatibacillum, Desulfitobacterium and Vibrio were actively involved in the detoxification of sediments affected by the oil spill. Results obtained from this study provided strong evidence that microbial degradation of aromatic compounds plays an active role in the biological response to mangrove sediment pollution and subsequent ecosystem recovery., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Some studies have described the isolation and 16S rRNA gene sequence-based identification of hydrocarbon-degrading bacteria living associated with marine eukaryotic phytoplankton, and thus far the direct visual observation of these bacteria on micro-algal cell surfaces ('phycosphere') has not yet been reported. Here, we developed two new 16S rRNA-targeted oligonucleotide probes, PCY223 and ALGAR209, to respectively detect and enumerate the obligate hydrocarbonoclastic bacteria Polycyclovorans algicola and Algiphilus aromaticivorans by Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH). To enhance the hybridization specificity with the ALGAR209 probe, a competitor probe was developed. These probes were tested and optimized using pure cultures, and then used in enrichment experiments with laboratory cultures of micro-algae exposed to phenanthrene, and with coastal water enriched with crude oil. Microscopic analysis revealed these bacteria are found in culture with the micro-algal cells, some of which were found attached to algal cells, and whose abundance increased after phenanthrene or crude oil enrichment. These new probes are a valuable tool for identifying and studying the ecology of P. algicola and A. aromaticivorans in laboratory and field samples of micro-algae, as well as opening new fields of research that could harness their ability to enhance the bioremediation of contaminated sites., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Hydrocarbon degradation (HD) potential by autochthonous microorganisms in the coastal sediments of the NW area of Portugal (coastal sandy beaches and estuaries of the rivers Minho and Douro) was evaluated, investigating if water and sediment contamination/characteristics influence it. Sediments were characterized for microbial abundance (by DAPI), HD microorganisms' abundance (by MPN), microbial community structure (by ARISA), hydrocarbons (by FTIR and SPME-GC-MS), hazardous and noxious substances (SPME-GC-MS) and metals (by AAS). To our knowledge, this is the first time all these pollutants, including the selected HNS, were measured simultaneously in sediments of the selected coastal area. Higher contaminants concentrations were, generally, registered in Douro samples. A clear differentiation of the microbial community structure between beaches and estuaries was observed, as well as, between Douro and Minho river estuaries. BIO-ENV analysis indicated both sediment characteristics (e.g. OM content) and contaminants presence/concentrations (e.g. tetrachloroethylene presence) affected the structure of the microbial community along the studied areas. In all the selected sites, the characterized autochthonous microbial communities showed potential for hydrocarbons degradation, with HD microorganisms being found in all collected sediments. These microorganisms can be a valuable asset to recover contaminated areas, but sediment characteristics and contaminants presence/levels need to be taken into account as they can affect their bioremediation potential and the success of their application as biotechnological tool., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Joostella strains are emerging candidates for biosurfactant production. Here such ability was analyzed for Joostella strain A8 in comparison with Alcanivorax strain A53 and Pseudomonas strain A6, all previously isolated from hydrocarbon enrichment cultures made of polychaete homogenates. In pure cultures Joostella sp. A8 showed the highest stable emulsion percentage (78.33%), hydrophobicity rate (62.67%), and an optimal surface tension reduction during growth in mineral medium supplemented with diesel oil (reduction of about 12mN/m), thus proving to be highly competitive with Alcanivorax and Pseudomonas strains. During growth in pure culture different level of biodegradation were detected for Alcanivorax strain A53 (52.7%), Pseudomonas strain A6 (38.2%) and Joostella strain A8 (26.8%). When growing in consortia, isolates achieved similar abundance values, with the best efficiency that was observed for the Joostella-Pseudomonas co-culture. Gas-chromatographic analysis revealed an increase in the biodegradation efficiency in co-cultures (about 90%), suggesting that the contemporary action of different bacterial species could improve the process. Results were useful to compare the efficiencies of well-known biosurfactant producers (i.e. Pseudomonas and Alcanivorax representatives) with a still unknown biosurfactant producer, i.e. Joostella, and to confirm them as optimal biosurfactant-producing candidates., (Copyright © 2017. Published by Elsevier B.V.)

In this study, a novel isolate of Enterobacter aerogenes isolated from contaminated soils with hydrocarbons had extracellular phytate-degrading activity. Enterobacter aerogenes isolates were identified by biochemical tests and confirmed by16S rRNA gene products (amplified size 211bp) for genotypic detection. The phytase activity was reached to maximum activity when this isolate was cultivated under the optimal conditions which consisted of using minimal salt medium containing 1%(w/v) rice bran as a sole source for carbon and 2% (w/v) yeast extract at pH 5.5 and temperature of 50°C for 48 h. The phytase had purified to homogeneity by 50% ammonium sulphate precipitation, ion exchange and gel filtration chromatography with 75.7 fold of purification and a yield of 30.35%. The purified phytase is a single peptide with approximate molecular mass of 42 kDa as assessed by SDS-PAGE. The highest degradative ability by Enterobacter aerogenes of black oil, white oil and used engine oil had observed after 72 h of incubation. Rapid degradation of black oil and used engine oil had also observed while slow degradation of white oilat all time of incubation. The purified phytase inhibited biofilm formation ability in a dose-dependent manner for all Gram-negative and Gram-positive biofilm-forming bacteria and a significant difference in cell surface hydrophobicity was observed after exposure of planktonic cells to phytase for hour. The hydrolyzing effect of phytase released by Enterobacter aerogenes for complex salts of phosphorus that are insoluble in the soil led to increase of phosphorus concentrations and enhanced the ability of Enterobacter aerogenes to degrade a specific hydrocarbon in contaminated soil so that the phytase has a promising application in bioremediation of contaminated soils with hydrocarbons., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Biodegradation is an important process for hydrocarbon weathering that influences its fate and transport, yet little is known about in situ biodegradation rates of specific hydrocarbon compounds in the deep ocean. Using data collected in the Gulf of Mexico below 700m during and after the Deepwater Horizon oil spill, we calculated first-order degradation rate constants for 49 hydrocarbons and inferred degradation rate constants for an additional 5 data-deficient hydrocarbons. Resulting calculated (not inferred) half-lives of the hydrocarbons ranged from 0.4 to 36.5days. The fastest degrading hydrocarbons were toluene (k=-1.716), methylcyclohexane (k=-1.538), benzene (k=-1.333), and C1-naphthalene (k=-1.305). The slowest degrading hydrocarbons were the large straight-chain alkanes, C-26 through C-33 (k=-0.0494 through k=-0.007). Ratios of C-18 to phytane supported the hypothesis that the primary means of degradation in the subsurface was microbial biodegradation. These degradation rate constants can be used to improve models describing the fate and transport of hydrocarbons in the event of an accidental deep ocean oil spill., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Background: Bacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem pollution caused by crude oil accidents and their use. Initially, the scientific community studied the role of individual microbial species by characterizing and optimizing their biosurfactant and oil degradation genes, studying their individual distribution. However, with the advances in genomics, in particular with the use of New-Generation-Sequencing and Metagenomics, it is now possible to have a macro view of the complex pathways related to the symbiotic degradation of hydrocarbons and surfactant production. It is now possible, although more challenging, to obtain the DNA information of an entire microbial community before automatically characterizing it. By characterizing and understanding the interconnected role of microorganisms and the role of degradation and biosurfactant genes in an ecosystem, it becomes possible to develop new biotechnological approaches for bioremediation use. This paper analyzes 46 different metagenome samples, spanning 20 biomes from different geographies obtained from different research projects., Results: A metagenomics bioinformatics pipeline, focused on the biodegradation and biosurfactant-production pathways, genes and organisms, was applied. Our main results show that: (1) surfactation and degradation are correlated events, and therefore should be studied together; (2) terrestrial biomes present more degradation genes, especially cyclic compounds, and less surfactation genes, when compared to water biomes; and (3) latitude has a significant influence on the diversity of genes involved in biodegradation and biosurfactant production. This suggests that microbiomes found near the equator are richer in genes that have a role in these processes and thus have a higher biotechnological potential., Conclusion: In this work we have focused on the biogeographical distribution of hydrocarbon degrading and biosurfactant producing genes. Our principle results can be seen as an important step forward in the application of bioremediation techniques, by considering the biostimulation, optimization or manipulation of a starting microbial consortia from the areas with higher degradation and biosurfactant producing genetic diversity.

Natural biodegradation of heavy oil in the marine environment can be accelerated by the addition of nutrients or seeding of pre-selected microorganisms. In this study, a microcosm experiment was conducted to investigate the effects of inorganic nutrient supplementation (biostimulation) and bacterial consortium amendment (bioaugmentation) on the natural degradative processes of artificially contaminated sediment. Our results revealed that the addition of nutrients had greater effect on remediation than the addition of bacterial cells. Supplementation of inorganic nutrients promoted and sustained the growth of oil-degrading and heterotrophic bacteria throughout the experimental period. Highest reduction in the total petroleum hydrocarbons, and of their components, n-alkanes, polycylic aromatic hydrocarbons (PAHs) and alkyl PAHs, were obtained in the biostimulated microcosms. Changes in the bacterial community were monitored by the PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) method targeting the 16S rDNA gene. Results revealed different responses of the bacterial community to the addition of heavy oil and remediation agents. Shifts in the bacterial communities in the seawater were more dynamic than in the sediment. Results of this study showed that addition of remediation agents significantly enhanced the natural biodegradation of heavy oil in a sediment-seawater microcosm trial.

In this study chemical analyses and ecotoxicity tests were applied for the assessment of a heavily hydrocarbon-contaminated soil prior and after the application of a remediation procedure that consisted in the stimulation of soil autochthonous populations of hydrocarbon degraders in static-ventilated biopiles. Terrestrial bioassays were applied in mixtures of test soils and artificial control soil and studied the survival and reproduction of Eisenia fetida and the avoidance response of E. fetida and Folsomia candida. Effects on aquatic organisms were studied by means of acute tests with Vibrio fischeri, Raphidocelis subcapitata, and Daphnia magna performed on aqueous elutriates from test soils. The bioremediation procedure led to a significant reduction in the concentration of hydrocarbons (from 34264 to 3074 mg kg(-1), i.e., 91 % decrease) and toxicity although bioassays were not able to report a percentage decrease of toxicity as high as the percentage reduction. Sublethal tests proved the most sensitive terrestrial bioassays and avoidance tests with earthworms and springtails showed potential as monitoring tools of hydrocarbon remediation due to their high sensitivity and short duration. The concentrations of hydrocarbons in water extracts from test soils were 130 and 100 μg L(-1) before and after remediation, respectively. Similarly to terrestrial tests, most aquatic bioassays detected a significant reduction in toxicity, which was almost negligible at the end of the treatment. D. magna survival was the most affected by soil elutriates although toxicity to the crustacean was associated to the salinity of the samples rather than to the concentration of hydrocarbons. Ecotoxicity tests with aqueous soil elutriates proved less relevant in the assessment of hydrocarbon-contaminated soils due to the low hydrosolubility of hydrocarbons and the influence of the physicochemical parameters of the aquatic medium.

In the present study, acrylic coupons with a thin layer of oil on the surface were incubated in the coastal water of Trindade Island, Brazil, for 60 days. The microorganisms adhered to the coupons were isolated using enrichment medium with hexadecane and naphthalene as the sole carbon and energy source. A total of 15 bacterial isolates were obtained, and the ability of these isolates to use different hydrocarbons as the source of carbon and energy was investigated. None of the isolates produced biosurfactants under our experimental conditions. Subsequently, identification methods such as partial sequencing of the 16S rRNA gene and analysis of fatty acids (MIDI) profile were employed. Among the 15 isolates, representatives of Actinobacteria, Firmicutes, and Alphaproteobacteria were detected. The isolates Rhodococcus rhodochrous TRN7 and Nocardia farcinica TRH1 were able to use all the hydrocarbons added to the culture medium (toluene, octane, xylene, naphthalene, phenanthrene, pyrene, hexadecane, anthracene, eicosane, tetracosane, triacontane, and pentacontane). Polymerase chain reaction amplification of the DNA isolated by employing primers for catechol 2,3-dioxygenase, alkane dehydrogenase and the alpha subunit of hydroxylating dioxygenases polycyclic aromatic hydrocarbon rings genes demonstrated that various isolates capable of utilizing hydrocarbons do not exhibit genes of known routes of catabolism, suggesting the existence of unknown catabolic pathways in these microorganisms. Our findings suggest that the microbiota associated to the coast of tropical oceanic islands has the ability to assist in environmental regeneration in cases of accidents involving oil spills in its shore. Thus, it motivates studies to map bioremediation strategies using the autochthonous microbiota from these environments., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

The Deepwater Horizon oil spill in the northern Gulf of Mexico represents the largest marine accidental oil spill in history. It is distinguished from past spills in that it occurred at the greatest depth (1,500 m), the amount of hydrocarbon gas (mostly methane) lost was equivalent to the mass of crude oil released, and dispersants were used for the first time in the deep sea in an attempt to remediate the spill. The spill is also unique in that it has been characterized with an unprecedented level of resolution using next-generation sequencing technologies, especially for the ubiquitous hydrocarbon-degrading microbial communities that appeared largely to consume the gases and to degrade a significant fraction of the petroleum. Results have shown an unexpectedly rapid response of deep-sea Gammaproteobacteria to oil and gas and documented a distinct succession correlated with the control of the oil flow and well shut-in. Similar successional events, also involving Gammaproteobacteria, have been observed in nearshore systems as well.

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]

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]

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]

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]

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 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]

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]

Mesopelagic water from the deep Eastern Mediterranean Sea (EMS) was collected under disrupted (REPRESS) or undisturbed (HP) pressure conditions and was acclimated to oil (OIL) or dispersed-oil (DISPOIL) under in situ pressure and temperature (10 MPa, 14 °C). Decompression resulted in oil-acclimatised microbial communities of lower diversity despite the restoration of in situ pressure conditions during the 1-week incubation. Further biodiversity loss was observed when oil-acclimatised communities were transferred to ONR7 medium to facilitate the isolation of oil-degrading bacteria. Microbial diversity loss impacted the degradation of recalcitrant oil compounds, especially PAHs, as low-abundance taxa, linked with PAH degradation, were outcompeted in the enrichment process. Thalassomonas, Pseudoalteromonas, Halomonas and Alcanivorax were enriched in ONR7 under all experimental conditions. No effect of dispersant application on the microbial community structure was identified. A. venustensis was isolated under all tested conditions suggesting a potential key role of this species in hydrocarbons removal in the deep EMS. [Display omitted] • Maintaining pressure during sampling is crucial for preserving microbial diversity. • Several key crude-oil degraders were outcompeted in nutrient-rich ONR7 medium. • Alcanivorax, Halomonas and Pseudoalteromonas acted as typical r-strategists in ONR7. • Heavy alkanes and PAHs degradation capacity were impacted by biodiversity loss. • Alcanivorax venustensis dominated the oil-enriched consortia from the deep EMS. [ABSTRACT FROM AUTHOR]

The most dangerous pollution in the environment are the unwanted hydrocarbon in form of oil and petroleum which is the result of leak from the coastal oil refiners and to overcomes these situations use of microbes are the only ecofriendly method and they are the main contributor to maintain a safer environment. Current study aimed to evaluate the fungi and bacteria as a bio-degrader of hydrocarbon, for his bacteria and fungi were first isolate and identify from the oil contaminated soil collected from the different workshops of Sargodha city. Result reveled that upper layer (0-2m) contain diverse and large number of bacteria and fungi specie (bacteria 50%; fungi 50%), while lowest layer (3-4m) contain less diverse and low number of bacterial and fungi species (bacteria 6.66%; fungi 13.6%). After identification it was found that total 4 strains of fungi were isolate in which Aspergillustubingensis and Alternariatenuissima were dominantIn case of bacteria 7 strains were identified. Among which E. coli were dominant. Followed by the Pseudomonas spp. after biodegradation test it was found that fungal strain Aspergillustubingensis was the excellent bio-degrader (1.69x109) followed by the Aspergillums niger (1.40x108). On the other hands among the bacterial strains Staphylococcus aureus utilizes high amount of the hydrocarbon as energy source (1.76x107) followed by the Pseudomonas aeruginosa (1.67x109). in conclusion Introducing these microbes to the oil contaminated environment can solve the problems of hydrocarbon pollution. But future research should be conducted to better understand the molecular mechanism of hydrocarbon degradation in order to better utilize these microorganisms for the welfare of human beings. [ABSTRACT FROM AUTHOR]

The Gulf of Mexico (GoM) is a particular environment that is continuously exposed to hydrocarbon compounds that may influence the microbial community composition. We carried out a metagenomic assessment of the bacterial community to get an overall view of this geographical zone. We analyzed both taxonomic and metabolic markers profiles to explain how the indigenous GoM microorganims participate in the biogeochemical cycling. Two geographically distant regions in the GoM, one in the north-west (NW) and one in the south-east (SE) of the GoM were analyzed and showed differences in their microbial composition and metabolic potential. These differences provide evidence the delicate equilibrium that sustains microbial communities and biogeochemical cycles. Based on the taxonomy and gene groups, the NW are more oxic sediments than SE ones, which have anaerobic conditions. Both water and sediments show the expected sulfur, nitrogen, and hydrocarbon metabolism genes, with particularly high diversity of the hydrocarbon-degrading ones. Accordingly, many of the assigned genera were associated with hydrocarbon degradation processes, Nitrospira and Sva0081 were the most abundant in sediments, while Vibrio , Alteromonas , and Alcanivorax were mostly detected in water samples. This basal-state analysis presents the GoM as a potential source of aerobic and anaerobic hydrocarbon degradation genes important for the ecological dynamics of hydrocarbons and the potential use for water and sediment bioremediation processes. [ABSTRACT FROM AUTHOR]

The most common type of environmental contamination is petroleum hydrocarbons. Sustainable and environmentally friendly treatment strategies must be explored in light of the increasing challenges of toxic and critical wastewater contamination. This paper deals with the bacteria-producing biosurfactant and their employment in the bioremediation of hydrocarbon-containing waste through a microbial fuel cell (MFC) with Pseudomonas aeruginosa (exoelectrogen) as co-culture for simultaneous power generation. Staphylococcus aureus is isolated from hydrocarbon-contaminated soil and is effective in hydrocarbon degradation by utilizing hydrocarbon (engine oil) as the only carbon source. The biosurfactant was purified using silica-gel column chromatography and characterised through FTIR and GCMS, which showed its glycolipid nature. The isolated strains are later employed in the MFCs for the degradation of the hydrocarbon and power production simultaneously which has shown a power density of 6.4 W/m3 with a 93% engine oil degradation rate. A biogenic Fe 2 O 3 nanoparticle (NP) was synthesized using Bambusa arundinacea shoot extract for anode modification. It increased the power output by 37% and gave the power density of 10.2 W/m3. Thus, simultaneous hydrocarbon bioremediation from oil-contamination and energy recovery can be achieved effectively in MFC with modified anode. [Display omitted] • Bacterial co-culture in MFC yield power of 6.4 W/m3 with 93% engine oil degradation. • Modified anode with Fe 2 O 3 particles enhanced power by 37% and redox current in MFC. • Bioelectrochemical analyses show anodic activity boost for oil removal with Fe 2 O 3. • S. aureus as hydrocarbon-degrading strain co-cultured with P. aeruginosa in MFC. • 89–93% oil degradation, 78% organic removal was achieved in modified MFC. [ABSTRACT FROM AUTHOR]

Dispersant application is a primary emergency oil spill response strategy and yet the efficacy and unintended consequences of this approach in marine ecosystems remain controversial. To address these uncertainties, ex situ incubations were conducted to quantify the impact of dispersant on petroleum hydrocarbon (PHC) biodegradation rates and microbial community structure at as close as realistically possible to approximated in situ conditions [2 ppm v/v oil with or without dispersant, at a dispersant to oil ratio (DOR) of 1:15] in surface seawater. Biodegradation rates were not substantially affected by dispersant application at low mixing conditions, while under completely dispersed conditions, biodegradation was substantially enhanced, decreasing the overall half-life of total PHC compounds from 15.4 to 8.8 days. While microbial respiration and growth were not substantially altered by dispersant treatment, RNA analysis revealed that dispersant application resulted in pronounced changes to the composition of metabolically active microbial communities, and the abundance of nitrogen-fixing prokaryotes, as determined by qPCR of nitrogenase (nifH) genes, showed a large increase. While the Gammaproteobacteria were enriched in all treatments, the Betaproteobacteria and different families of Alphaproteobacteria predominated in the oil and dispersant treatment, respectively. Results show that mixing conditions regulate the efficacy of dispersant application in an oil slick, and the quantitative increase in the nitrogen-fixing microbial community indicates a selection pressure for nitrogen fixation in response to a readily biodegradable, nitrogen-poor substrate. [ABSTRACT FROM AUTHOR]

Guaymas Basin is a young marginal rift basin in the Gulf of California characterized by active seafloor spreading, rapid deposition of organic-rich sediments, and steep geothermal gradients where sedimentary organic material of photosynthetic origin turns into hydrocarbons - potential microbial substrates. After introducing the sources of hydrocarbons in the subsurface, this short overview discusses the phylogenetic diversity, temperature range and occurrence patterns of novel alkane-oxidizing bacteria and archaea in the hydrothermal sediments of Guaymas Basin. Many of these alkane-degrading specialists function as syntrophic consortia, where sulfate-reducing bacteria accept electron from methane- or alkane-oxidizing archaea. As a source of metagenomes, enrichments, and cultures of these methodologically and conceptually challenging microorganisms, Guaymas Basin stands out as an indispensable field site that has consistently catalyzed new insights into the microbiology of anaerobic hydrocarbon oxidation and assimilation. • Phylogenetic and physiological diversity of hydrocarbon-oxidizing bacteria and archaea. • Hydrothermal sediments of Guaymas Basin. • Recent microbial discoveries of hydrocarbon-oxidizing bacteria and archaea in Guaymas Basin. • Complementing extensive genome-based and physiological overviews on hydrocarbon-oxidizing bacteria and archaea. [ABSTRACT FROM AUTHOR]

Oil reserves in deep-sea sediments are currently subject to intense exploration, with associated risks of oil spills. Previous research suggests that microbial communities from deep-sea sediment (>1000m) can degrade hydrocarbons (HCs), but have a lower degradation ability than shallow (<200m) communities, probably due to in situ temperature. This study aimed to assess the effect of marine origin on microbial HC degradation potential while separating the influence of temperature, and to characterise associated HC-degrading bacterial communities. Microbial communities from 135 and 1000 m deep sediments were selectively enriched on crude oil at in situ temperatures and both consortia were subsequently incubated for 42 days at 20°C with two HC mixtures: diesel fuel or model oil. Significant HC biodegradation occurred rapidly in the presence of both consortia, especially of low molecular weight HCs and was concomitant with microbial community changes. Further, oil degradation was higher with the shallow consortium than with the deep one. Dominant HC-degrading bacteria differed based on both spatial origin of the consortia and supplemented HC types. This study provides evidence for influence of sediment spatial origin and HC composition on the selection and activity of marine HC-degrading bacterial communities and is relevant for future bioremediationdevelopments. This study describes the effect of seabed sediment origin on microbial hydrocarbon degradation rates and the influence of different HC mixtures on bacterial consortia composition. [ABSTRACT FROM AUTHOR]

Bacterial endophytes (BEs) are non-pathogenic residents of healthy plant tissues that can confer benefits to plants. Many Bacterial endophytes have been shown to contribute to plant growth and health, alleviation of plant stress and to in-planta contaminant-degradation. This study examined the endophytic bacterial communities of plants growing abundantly in a heavily hydrocarbon contaminated site, and compared them to those found in the same species at a non-contaminated. We used culture- dependent and independent methods to characterize the community structure, hydrocarbon degrading capabilities, and plant growth promoting traits of cultivable endophytes isolated from Achillea millefolium, Solidago Canadensis , and Daucus carota plants from these two sites. Culture- dependent and independent analyses revealed class Gammaproteobacteria predominated in all the plants regardless of the presence of petroleum hydrocarbon, with Pantoea spp. as largely dominant. It was interesting to note a >50% taxonomic overlap (genus level) of 16s rRNA high throughput amplicon sequences with cultivable endophytes. PERMANOVA analysis of TRFLP fragments revealed significant structural differences between endophytic bacterial communities from hydrocarbon-contaminated and non-contaminated soils—however, there was no marked difference in their functional capabilities. Pantoea spp. demonstrated plant beneficial characteristics, such as P solubilization, indole-3-acetic acid production and presence of 1-aminocyclopropane-1-carboxylate deaminase. Our findings reveal that functional capabilities of bacterial isolates being examined were not influenced by the presence of contamination; and that the stem endosphere supports ubiquitous BEs that were consistent throughout plant hosts and sites. [ABSTRACT FROM AUTHOR]

Cytochrome P450 enzyme isolated from an extremophile Bacillus Stratosphericus sp. was used as the recognition element for an ion-sensitive field effect transistor (ISFET)-based biosensor. The fabricated ISFET is Schottky-based and has silicon dioxide as a sensing layer. The cytochrome P450 component in its present purified form (pH-7.2) in 5% agarose was laid over the SiO2 gate to examine its capability of generating electronic response in the presence of n-hexadecane and reduced nicotinamide adenine dinucleotide phosphate. The partially purified preparation was obtained from the lysozyme treated spheroplast via ion exchange chromatography followed by the gel filtration chromatography. The variation of potential difference between the gate and the source with respect to pH for the bare ISFET and the variation of gate and source potential difference with respect to the concentration of the measurand at constant current have been recorded for analyses. The observed correlation showed good repeatability of the sensor output suggesting a potential functional sensing device for hydrocarbon detection. The sensitivity parameters for the device have been determined to be 50.65 mV/pH and 54.34 mV/molar for the bare ISFET and enzyme field-effect transistor, respectively. [ABSTRACT FROM AUTHOR]

Little is known about the microbial ecology of the subsurface oil sands in Northern Alberta, Canada. Biodegradation of low molecular weight hydrocarbons by indigenous microbes has enriched high molecular weight hydrocarbons, resulting in highly viscous bitumen. This extreme subsurface environment is further characterized by low nutrient availability and limited access to water, thus resulting in low microbial biomass. Improved DNA isolation protocols and increasingly sensitive sequencing methods have allowed an in-depth investigation of the microbial ecology of this unique subsurface environmental niche. Community analysis was performed on core samples (n = 62) that were retrieved from two adjacent sites located in the Athabasca Oil Sands at depths from 220 to 320 m below the surface. Microbial communities were dominated by aerobic taxa, including Pseudomonas and Acinetobacter. Only one core sample microbial community was dominated by anaerobic taxa, including the methanogen Methanoculleus, as well as Desulfomicrobium and Thauera. Although the temperature of the bitumen-containing subsurface is low (8° C), two core samples had high fractions of the potentially thermophilic taxon, Thermus. Predominance of aerobic taxa in the subsurface suggests the potential for in situ aerobic hydrocarbon degradation; however, more studies are required to determine the functional role of these taxa within this unique environment. [ABSTRACT FROM AUTHOR]

The genus Acinetobacter encompasses biotechnologically relevant species and nosocomial pathogens. In this study, nine isolates recovered from different oil reservoir samples showed the ability to grow with petroleum as the only carbon source and possessed the ability to emulsify kerosene. The whole genomes of the nine strains were sequenced and analyzed. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of all strains were compared to the reference strains, and the results were below the reference values (<97.88 and 82, respectively), suggesting that the isolates belong to a new subspecies of Acinetobacter baumannii. The name Acinetobacter baumannii oleum ficedula is proposed. A comparison of the whole genome repertoire of 290 Acinetobacter species indicated that the strains in this study resemble non-pathogenic Acinetobacter strains. However, the new isolates resemble A. baumannii when comparing virulence factors. The isolates in this study carry many genes involved in hydrocarbon degradation, indicating the potential to degrade most toxic compounds listed by environmental regulatory agencies such as ATSDR, EPA, and CONAMA. In addition, despite the absence of known biosurfactant or bioemulsifier genes, the strains showed emulsifying activity, suggesting the presence of new pathways or genes related to this process. This study investigated the genomic, phenotypic, and biochemical features of the novel environmental subspecies A. baumannii oleum ficedula , revealing their potential to degrade hydrocarbons and to produce biosurfactants or bioemulsifiers. Applying these environmental subspecies in bioaugmentation strategies sheds light on future approaches to bioremediation. The study shows the importance of genomic analysis of environmental strains and their inclusion in metabolic pathways databases, highlighting unique enzymes/alternative pathways for consuming hazardous hydrocarbons. [Display omitted] • Acinetobacter baumannii strains were isolated from oil reservoirs. • The phenotypic and genomic characterization indicates a novel subspecies. • A. baumannii oleum ficedula shows hydrocarbon degradation specialization. • A potential new pathway of biosurfactant production was suggested. • This subspecies has unique genes for the degradation of hazardous hydrocarbons. [ABSTRACT FROM AUTHOR]

Crude oil contamination of soils and waters is a worldwide problem, which has been actively addressed in recent years. Sequencing genomes of microorganisms involved in the degradation of hydrocarbons have allowed the identification of several promoters, genes, and degradation pathways of these contaminants. This knowledge allows a better understanding of the functional dynamics of microbial degradation. Here, we report a first draft of the 44.2 Mbp genome assembly of an environmental strain of the fungus Scedosporium apiospermum. The assembly consisted of 178 high-quality DNA scaffolds with 1.93% of sequence repeats identified. A total of 11,195 proteincoding genes were predicted including a diverse group of gene families involved in hydrocarbon degradation pathways like dioxygenases and cytochrome P450. The metabolic pathways identified in the genome can potentially degrade hydrocarbons like chloroalkane/alkene, chorocyclohexane, and chlorobenzene, benzoate, aminobenzoate, fluorobenzoate, toluene, caprolactam, geraniol, naphthalene, styrene, atrazine, dioxin, xylene, ethylbenzene, and polycyclic aromatic hydrocarbons. The comparison analysis between this strain and the previous sequenced clinical strain showed important differences in terms of annotated genes involved in the hydrocarbon degradation process. [ABSTRACT FROM AUTHOR]

Background: Over three-fifths of the world's known crude oil cannot be recovered using state-of-the-art techniques, but microbial conversion of petroleum hydrocarbons trapped in oil reservoirs to methane is one promising path to increase the recovery of fossil fuels. The process requires cooperation between syntrophic bacteria and methanogenic archaea, which can be affected by sulfate-reducing prokaryotes (SRPs). However, the effects of sulfate on hydrocarbon degradation and methane production remain elusive, and the microbial communities involved are not well understood. Results: In this study, a methanogenic hexadecane-degrading enrichment culture was treated with six different concentrations of sulfate ranging from 0.5 to 25 mM. Methane production and maximum specific methane production rate gradually decreased to 44 and 56% with sulfate concentrations up to 25 mM, respectively. There was a significant positive linear correlation between the sulfate reduction/methane production ratio and initial sulfate concentration, which remained constant during the methane production phase. The apparent methanogenesis fractionation factor (αapp) gradually increased during the methane production phase in each treatment, the αapp for the treatments with lower sulfate (0.5-4 mM) eventually plateaued at ~1.047, but that for the treatment with 10-25 mM sulfate only reached ~1.029. The relative abundance levels of Smithella and Methanoculleus increased almost in parallel with the increasing sulfate concentrations. Furthermore, the predominant sulfate reducer communities shifted from Desulfobacteraceae in the low-sulfate cultures to Desulfomonile in the high-sulfate cultures. Conclusion: The distribution of hexadecane carbon between methane-producing and sulfate-reducing populations is dependent on the initial sulfate added, and not affected during the methane production period. There was a relative increase in hydrogenotrophic methanogenesis activity over time for all sulfate treatments, whereas the total activity was inhibited by sulfate addition. Both Smithella and Methanoculleus, the key alkane degraders and methane producers, can adapt to sulfate stress. Specifically, different SRP populations were stimulated at various sulfate concentrations. These results could help to evaluate interactions between sulfate-reducing and methanogenic populations during anaerobic hydrocarbon degradation in oil reservoirs. [ABSTRACT FROM AUTHOR]

Background: Bacterial and Archaeal communities have a complex, symbiotic role in crude oil bioremediation. Their biosurfactants and degradation enzymes have been in the spotlight, mainly due to the awareness of ecosystem pollution caused by crude oil accidents and their use. Initially, the scientific community studied the role of individual microbial species by characterizing and optimizing their biosurfactant and oil degradation genes, studying their individual distribution. However, with the advances in genomics, in particular with the use of New-Generation-Sequencing and Metagenomics, it is now possible to have a macro view of the complex pathways related to the symbiotic degradation of hydrocarbons and surfactant production. It is now possible, although more challenging, to obtain the DNA information of an entire microbial community before automatically characterizing it. By characterizing and understanding the interconnected role of microorganisms and the role of degradation and biosurfactant genes in an ecosystem, it becomes possible to develop new biotechnological approaches for bioremediation use. This paper analyzes 46 different metagenome samples, spanning 20 biomes from different geographies obtained from different research projects. Results: A metagenomics bioinformatics pipeline, focused on the biodegradation and biosurfactant-production pathways, genes and organisms, was applied. Our main results show that: (1) surfactation and degradation are correlated events, and therefore should be studied together; (2) terrestrial biomes present more degradation genes, especially cyclic compounds, and less surfactation genes, when compared to water biomes; and (3) latitude has a significant influence on the diversity of genes involved in biodegradation and biosurfactant production. This suggests that microbiomes found near the equator are richer in genes that have a role in these processes and thus have a higher biotechnological potential. Conclusion: In this work we have focused on the biogeographical distribution of hydrocarbon degrading and biosurfactant producing genes. Our principle results can be seen as an important step forward in the application of bioremediation techniques, by considering the biostimulation, optimization or manipulation of a starting microbial consortia from the areas with higher degradation and biosurfactant producing genetic diversity. [ABSTRACT FROM AUTHOR]

Bioaugmentation, Biostimulation and Horizontal gene transfer (HGT) of catabolic genes have been proven for their role in bioremediation of hydrocarbons. It also has been proved that selection of either biostimulation or bioremediation varies for every contaminated site. The reliability of HGT compared to biostimulation and bioremediation was not tested. The present study focuses on reliability of biostimulatiion, bioaugmentation and HGT during biodegradation of Diesel oil and Non aqueous phase liquids (NAPL). Pseudomonas aeruginosa (AEBBITS1) having alk B and NDO genes was used for bioaugmentation and the experiment was conducted using seawater as medium. Based on Gas chromatography results diesel was found to be degraded to 100% in both presence and absence of AEBBITS1. Denturing gradient gel electrophoresis result showed same pattern in presence and absence of AEBBITS1 indicating no HGT. NAPL degradation was found to be more by Biostimulated Bioaugmentation compared to biostimulation and bioaugmentation alone. This proves that biostimulated bioaugmentation is better strategy for oil contamination (tarabll) in Velsao beach, Goa. [ABSTRACT FROM AUTHOR]