Current Status of the Degradation of Aliphatic and Aromatic Petroleum Hydrocarbons by Thermophilic Microbes and Future Perspectives

Microorganisms immobilized hydroxyethyl cellulose/luffa composite sponge for selective adsorption and biodegradation of oils in wastewater

The highly efficient removal of oils such as oils or dyes from wastewater has aroused wide concern and is of great significance for clean production and environmental remediation. The synthesis of a novel aerogel (designated as HEC/LS) is reported herein, achieved through a sol-gel method followed by freeze-drying utilizing loofa and hydroxyethyl cellulose as the raw materials. The new HEC/LS aerogel exhibits excellent porosity and specific surface area, with a porosity of 88.70 %, a total pore area of 0.607 m2 g-1, and a specific surface area of 230 m2 g-1. The prepared HEC/LS aerogel exhibits exceptional hydrophilicity and self-floatability, facilitating its rapid absorption of water up to 21 times its own weight within a mere 3 s. Additionally, it demonstrates good adsorption performance for methylene blue (MB), with a maximum adsorption capacity of 83.30 mg g-1. Subsequently, a new hydrophobic microorganisms-loaded composite aerogel (namely, Bn-HEC/LS) was obtained by doping microorganisms into the as-prepared HEC/LS in multiple enrichment followed by a hydrophobic and oleophilic surface modification. Based on its rich porous structure and oleophilic wettability, the as-synthesized Bn-HEC/LS exhibits excellent selective adsorption and degradation properties for the oil contamination, the diesel oil could be selectively absorbed in the Bn-HEC/LS and degraded by the loaded microorganisms. Among them, B5-HEC/LS displays the highest removal efficiency of 94.50 % within 180 h, while free microorganisms and HEC/LS aerogels show degradation efficiencies of only 21.70 % and 48.10 %, respectively. The fixation of microorganisms in the aerogel increases their number within the material and enhances the relative microorganisms removal capacity. The hydrophobic and lipophilic modifications improve the selective adsorption performance of the aerogel on diesel oil, resulting in a significantly high removal rate of Bn-HEC/LS for diesel oil. The results indicate that the immobilization of microorganisms into aerogel improves the activity of microorganisms, and the hydrophobic and oleophilic modification enhances the selective adsorption performance of aerogel to diesel oil, thus resulting in a very high removal rate of Bn-HEC/LS for diesel oil. This study is expected to provide a now possibility for the green and efficient bioremediation of oils.

Ecotoxicological effects, human and animal health risks of pollution and exposure to waste engine oils: a review

Waste engine oils are hazardous waste oils originating from the transportation sector and industrial heavy-duty machinery operations. Improper handling, disposal, and miscellaneous misuses cause significant air, soil, sediments, surface water, and groundwater pollution. Occupational exposure by prolonged and repeated contact poses direct or indirect health risks, resulting in short-term (acute) or long-term (chronic) toxicities. Soil pollution causes geotoxicity by disrupting the biocenosis and physicochemical properties of the soil, and phytotoxicity by impairing plant growth, physiology and metabolism. Surface water pollution impacts aquatic ecosystems and biodiversity. Air pollution from incineration causes the release of greenhouse gases creating global warming, noxious gases and particulate matter eliciting pulmonary disorders. The toxicity of waste engine oil is due to the total petroleum hydrocarbons (TPH) composition, including polycyclic aromatic hydrocarbons (PAHs), benzene, toluene, ethylbenzene, xylene (BTEX), polychlorinated biphenyls (PCBs) congeners, organometallic compounds, and toxic chemical additives. The paper aims to provide a comprehensive overview of the ecotoxicological effects, human and animal health toxicology and exposure to waste engine oils. It highlights the properties and functions of engine oil and describes waste engine oil generation, disposal and recycling. It provides intensive evaluations and descriptions of the toxicokinetics, metabolism, routes of exposure and toxicosis in human and animal studies based on toxicological, epidemiological and experimental studies. It emphasises the preventive measures in occupational exposure and recommends risk-based remediation techniques to mitigate environmental pollution. The review will assist in understanding the potential risks of waste engine oil with significant consideration of the public health benefits and importance.

Metagenomic analysis of a thermophilic bacterial consortium and its use in the bioremediation of a petroleum-contaminated soil

Biodegradation is difficult at high temperatures due to the limited capacity of microorganisms to survive and function outside their optimum temperature range. Here, a thermophilic petroleum-degrading consortium was enriched from compost at a temperature of 55 °C. 16S rDNA and metagenomic techniques were used to analyze the composition of the consortium and the mechanisms of degradation. The consortium degraded 17000 mg total petroleum hydrocarbons (TPHs) L-1 with a degradation efficiency of 81.5% in 14 days. The consortium utilized a range of substrates such as n-hexadecane, n-docosane, naphthalene and pyrene and grew well over a wide range of pH (4-10) and salinity (0-90 g L-1). The hydrocarbon-degrading extremophilic consortium contained, inter alia, (relative abundance >1%) Caldibacillus, Geobacillus, Mycolicibacterium, Bacillus, Chelatococcus, and Aeribacillus spp. Metagenomic analysis was conducted to discover the degradation and environmental tolerance functional genes of the consortium. Two alkane hydroxylase genes, alkB and ladA, were found. A microcosm study shows that the consortium promoted the bioremediation of soil TPHs. The results indicate that the consortium may be a good candidate for the high-temperature bioremediation of petroleum-contaminated soils.

Study on the accelerated biodegradation of PAHs in subsurface soil via coupled low-temperature thermally treatment and electron acceptor stimulation based on metagenomic sequencing

In situ anoxic bioremediation is a sustainable technology to remediate PAHs contaminated soils. However, the limited degradation rate of PAHs under anoxic conditions has become the primary bottleneck hindering the application of this technology. In this study, coupled low-temperature thermally treatment (<50 °C) and EA biostimulation was used to enhance PAH removal. Anoxic biodegradation of PAHs in soil was explored in microcosms in the absence and presence of added EAs at 3 temperatures (15 °C, 30 °C, and 45 °C). The influence of temperature, EA, and their interaction on the removal of PAHs were identified. A PAH degradation model based on PLSR analysis identified the importance and the positive/negative role of parameters on PAH removal. Soil archaeal and bacterial communities showed similar succession patterns, the impact of temperature was greater than that of EA. Soil microbial community and function were more influenced by temperature than EAs. Close and frequent interactions were observed among soil bacteria, archaea, PAH-degrading genes and methanogenic genes. A total of 15 bacterial OTUs, 1 PAH-degrading gene and 2 methanogenic genes were identified as keystones in the network. Coupled low-temperature thermally treatment and EA stimulation resulted in higher PAH removal efficiencies than EA stimulation alone and low-temperature thermally treatment alone.

Microplastics and associated chemicals in drinking water: A review of their occurrence and human health implications

Microplastics (MPs) have entered drinking water (DW) via various pathways, raising concerns about their potential health impacts. This study provides a comprehensive review of MP-associated chemicals, such as oligomers, plasticizers, stabilizers, and ultraviolet (UV) filters that can be leached out during DW treatment and distribution. The leaching of these chemicals is influenced by various environmental and operating factors, with three major ones identified: MP concentration and polymer type, pH, and contact time. The leaching process is substantially enhanced during the disinfection step of DW treatment, due to ultraviolet light and/or disinfectant-triggered reactions. The study also reviewed human exposure to MPs and associated chemicals in DW, as well as their health impacts on the human nervous, digestive, reproductive, and hepatic systems, especially the neuroendocrine toxicity of endocrine-disrupting chemicals. An overview of MPs in DW, including tap water and bottled water, was also presented to enable a background understanding of MPs-associated chemicals. In short, certain chemicals leached from MPs in DW can have significant implications for human health and demand further research on their long-term health impacts, mitigation strategies, and interactions with other pollutants such as disinfection byproducts (DBPs) and per- and polyfluoroalkyl substances (PFASs). This study is anticipated to facilitate the research and management of MPs in DW and beverages.

Impact of artisanal refining activities on bacterial diversity in a Niger Delta fallow land

Hydrocarbon pollution is a major ecological problem facing oil-producing countries, especially in the Niger Delta region of Nigeria. In this study, a site that had been previously polluted by artisanal refining activity was investigated using 16S rRNA Illumina high-throughput sequencing technology and bioinformatics tools. These were used to investigate the bacterial diversity in soil with varying degrees of contamination, determined with a gas chromatography-flame ionization detector (GC-FID). Soil samples were collected from a heavily polluted (HP), mildly polluted (MP), and unpolluted (control sample, CS) portion of the study site. DNA was extracted using the Zymo Research (ZR) Fungi/Bacteria DNA MiniPrep kit, followed by PCR amplification and agarose gel electrophoresis. The microbiome was characterized based on the V3 and V4 hypervariable regions of the 16S rRNA gene. QIIME (Quantitative Insights Into Microbial Ecology) 2 software was used to analyse the sequence data. The final data set covered 20,640 demultiplexed high-quality reads and a total of 160 filtered bacterial OTUs. Proteobacteria dominated samples HP and CS, while Actinobacteria dominated sample MP. Denitratisoma, Pseudorhodoplanes, and Spirilospora were the leading genera in samples HP, CS, and MP respectively. Diversity analysis indicated that CS [with 25.98 ppm of total petroleum hydrocarbon (TPH)] is more diverse than HP (with 490,630 ppm of TPH) and MP (with 5398 ppm of TPH). A functional prediction study revealed that six functional modules dominated the dataset, with metabolism covering up to 70%, and 11 metabolic pathways. This study demonstrates that a higher hydrocarbon concentration in soil adversely impacts microbial diversity, creating a narrow bacterial diversity dominated by hydrocarbon-degrading species, in addition to the obvious land and ecosystem degradation caused by artisanal refining activities. Overall, the artisanal refining business is significantly driving ecosystem services losses in the Niger Delta, which calls for urgent intervention, with focus on bioremediation.

Medium-chain alkane biodegradation and its link to some unifying attributes of alkB genes diversity

Hydrocarbon footprints in the environment, via biosynthesis, natural seepage, anthropogenic activities and accidents, affect the ecosystem and induce a shift in the healthy biogeochemical equilibrium that drives needed ecological services. In addition, these imbalances cause human diseases and reduce animal and microorganism diversity. Microbial bioremediation, which capitalizes on functional genes, is a sustainable mitigation option for cleaning hydrocarbon-impacted environments. This review focuses on the bacterial alkB functional gene, which codes for a non-heme di‑iron monooxygenase (AlkB) with a di‑iron active site that catalyzes C₈-C₁₆ medium-chain alkane metabolism. These enzymes are ubiquitous and share common attributes such as being controlled by global transcriptional regulators, being a component of most super hydrocarbon degraders, and their distributions linked to horizontal gene transfer (HGT) events. The phylogenetic approach used in the HGT detection suggests that AlkB tree topology clusters bacteria functionally and that a preferential gradient dictates gene distribution. The alkB gene also acts as a biomarker for bioremediation, although it is found in pristine environments and absent in some hydrocarbon degraders. For instance, a quantitative molecular method has failed to link alkB copy number to contamination concentration levels. This limitation may be due to AlkB homologues, which have other functions besides n-alkane assimilation. Thus, this review, which focuses on Pseudomonas putida GPo1 alkB, shows that AlkB proteins are diverse but have some unifying trends around hydrocarbon-degrading bacteria; it is erroneous to rely on alkB detection alone as a monitoring parameter for hydrocarbon degradation, alkB gene distribution are preferentially distributed among bacteria, and the plausible explanation for AlkB affiliation to broad-spectrum metabolism of hydrocarbons in super-degraders hitherto reported. Overall, this review provides a broad perspective of the ecology of alkB-carrying bacteria and their directed biodegradation pathways.

Genetic and functional characterization of multiple thermophilic organosulfur-removal systems reveals desulfurization potentials for waste residue oil cleaning

Heavy oil and petroleum refining residues usually contain high concentrations of recalcitrant hazardous organosulfur compounds, causing long-term serious global environmental pollution during leakage and combustion. Research conducted here identified a unique thermophilic bacterium Parageobacillus thermoglucosidasius W-36 with the notable ability of waste residue oil desulfurization, utilization and tolerance of multiplex hazardous organosulfur pollutants. Genome information mining revealed multiple desulfurization systems in three organosulfur-utilizing gene clusters. Enzymatic characterization, phylogenetic relationships, transcriptional performance and structural prediction indicated four novel key monooxygenases for diverse organosulfur removal. Importantly, all monooxygenases shared obvious commonalities in the predicted tertiary structure backbone and catalytic characteristics of C-S bond cleavage, implying the potential of genetic engineering for broad-spectrum hazardous organosulfur removal. Therefore, this work demonstrated the important application potential of thermophilic bacteria as a promising alternative biodesulfurization way for waste residue oil cleaning.

The ecological response and distribution characteristics of microorganisms and polycyclic aromatic hydrocarbons in a retired coal gas plant post-thermal remediation site

Thermal remediation is one of the most common approaches of removing organic pollutants in the retired contamination sites. However, little is known about the performance of bacterial community characteristics after in situ thermal remediation. In this study, the ecological response and spatial distributional characteristics of microorganisms and polycyclic aromatic hydrocarbons (PAHs) were investigated using a high throughput sequencing method in a retired coal gas plant site after in situ thermal remediation in Nanjing, China. Combination of Venn, clustering-correlation heatmap and two - factor correlation network analysis revealed that, microbial communities were obviously affected and classified by soil depths, temperature, and contamination level, respectively. The common and endemic microorganisms of each group were identified. The relative abundances of Thermaerobacter, Calditerricola, Brevibacillus, Ralstonia and Rhodococcus (aerobic bacteria) gradually declined with the increase of soil depth, while those of Bacillus, Fictibacillus, Paenibacillus, Rheinheimera presented opposite tendency. Some thermophilic degradation bacteria of PAHs, including Thermaerobacter, Calditerricola, Bacillus, Rhodococcus, unclassified_p__Firmicutes, Arthrobacter and Deinococcus, were identified and increased in the abundance at heavily polluted sites. Additionally, Proteobacteria, Bacteroidota, Deinococcota, Chloroflexi, Acidobacteriota, and Actinobacteriota showed negative response to the increase of soil depth, temperature and pollution level, while Firmicutes presented a positive response. This implied that Firmicutes has better stress resistance and adaptability to thermal remediation condition. The key environmental factors affecting microorganism composition and distribution were Temperature, Total nitrogen, Oxidation-Reduction Potential, Organic matters, and PAHs concentrations, which explains the dominant driving mechanism of soil depth, temperature, and contamination level on microbial characteristics in thermal remediation site. Our study could contribute to a better understanding of the resilience and adaptation mechanisms of microbial community at the contaminated site after the in situ thermal remediation.

Benzo[A]Pyrene Biodegradation by Multiple and Individual Mesophilic Bacteria under Axenic Conditions and in Soil Samples

To date, only a handful of bacterial strains that can independently degrade and utilize benzo[a]pyrene (BaP) as the sole carbon source has been isolated and characterized. Here, three new bacterial strains-JBZ1A, JBZ2B, and JBZ5E-were isolated from contaminated soil and, using 16S rRNA sequencing, were identified as Brad rhizobium japonicum, Micrococcus luteus, and Bacillus cereus, respectively. The growth ability of each individual strain and a consortium of all strains in the presence of BaP (4-400 µmol·L^-1, pH 7, 37 °C) was identified by the doubling time (dt). The results illustrate that dt decreased with increasing BaP concentrations for individual strains and the consortium. The optimum growth conditions of the consortium were 37 °C, 0.5% NaCl (w/v), and pH 7. Under these conditions, the degradation rate was 1.06 µmol·L^-1·day^-1, whereas that of individual strains ranged from 0.9 to 0.38 µmol·L^-1·day^-1. B. cereus had the strongest contribution to the consortium's activity, with a degradation rate of 0.9 µmol·L^-1·day^-1. The consortium could also remove BaP spiked with soil but at a lower rate (0.01 µmol L^-1.day^-1). High-performance liquid chromatography-high-resolution tandem mass spectrometry permitted the detection of the metabolites of these strains, and a biodegradation pathway is proposed.

Slurry phase biodegradation of heavy oily sludge and evidence of asphaltene biotransformation

Oily sludge management is a global environmental concern due to its hazardous nature. Oily sludge obtained from a refinery in India had 19-21% oil content. The oil was highly enriched in the asphaltene fraction. Slurry phase biodegradation of this oily sludge in presence of a 3-membered bacterial consortium was optimized in presence of Triton X-100 to increase the bioavailability of hydrocarbons. Triton X-100 at 4 times the critical micelle concentration (CMC) showed the highest degradation where oil removal of 53.1% was achieved from a 10% sludge slurry over 90 days. GCxGC analysis of n-alkanes present in the oily sludge after the biodegradation study showed an increase in the lower n-alkanes, i.e., dodecane and tridecane over the first 30 days, whereas the higher n-alkanes were removed to a much higher extent. Heptadecane showed the maximum extent of degradation with 94.9% removal in 90 days and an initial degradation rate of 0.079 day^-1. The, maximum rate of degradation was observed for pentacosane (0.083 day^-1) with 93.7% removal in 90 days. The increase in the lower n-alkanes may be attributed to biotic transformation of the asphaltene fraction which was also confirmed through FTIR and pyrolysis GCxGC analysis. Biodegradation was found to cause changes in the pyrolysis product of asphaltenes where four and three-ring pyrolysis products decreased while the one and two-ring pyrolysis products increased. In presence of the consortium asphaltene removal over 90 days was 12% whereas only 0.4% removal was obtained in the abiotic controls.

Sustainable strategies for combating hydrocarbon pollution: Special emphasis on mobil oil bioremediation

The global rise in industrialization and vehicularization has led to the increasing trend in the use of different crude oil types. Among these mobil oil has major application in automobiles and different machines. The combustion of mobil oil renders a non-usable form that ultimately enters the environment thereby causing problems to environmental health. The aliphatic and aromatic hydrocarbon fraction of mobil oil has serious human and environmental health hazards. These components upon interaction with soil affect its fertility and microbial diversity. The recent advancement in the omics approach viz. metagenomics, metatranscriptomics and metaproteomics has led to increased efficiency for the use of microbial based remediation strategy. Additionally, the use of biosurfactants further aids in increasing the bioavailability and thus biodegradation of crude oil constituents. The combination of more than one approach could serve as an effective tool for efficient reduction of oil contamination from diverse ecosystems. To the best of our knowledge only a few publications on mobil oil have been published in the last decade. This systematic review could be extremely useful in designing a micro-bioremediation strategy for aquatic and terrestrial ecosystems contaminated with mobil oil or petroleum hydrocarbons that is both efficient and feasible. The state-of-art information and future research directions have been discussed to address the issue efficiently.

Characterization of two novel strains of Pseudomonas aeruginosa on biodegradation of crude oil and its enzyme activities

Crude oil contaminant is one of the major problem to environment and its removal process considered as most challenging tool currently across the world. In this degradation study, crude oil hydrocarbons are degraded on various pH optimization conditions (pH 2, 4,6,7,8 and 10) by using two biosurfactant producing bacterial strains Pseudomonas aeruginosa PP3 and Pseudomonas aeruginosa PP4. During crude oil biodegradation, degradative enzymes alkane hydroxylase and alcohol dehydrogenase were examined and found to be higher in PP4 than PP3. Biodegradation efficiency (BE) of crude oil by both PP3 and PP4 were analysed by gas chromatography mass spectroscopy (GCMS). Based on strain PP3, the highest BE was observed in pH 2 and pH 4 were found to be 62% and 69% than pH 6, 7, 8 and 10 (47%, 47%, 49% and 45%). It reveals that PP3 was survived effectively in acidic condition and utilized the crude oil hydrocarbons. In contrast, the highest BE of PP4 was observed in pH 7 (78%) than pH4 (68%) and pH's 2, 6, 8 and 10 (52%, 52%, 43% and 53%) respectively. FTIR spectra results revealed that the presence of different functional group of hydrocarbons (OH, -CH₃, CO, C-H) in crude oil. GCMS results confirmed that both strains PP3 and PP4 were survived in acidic condition and utilized the crude oil hydrocarbons as sole carbon sources. This is the first observation on biodegradation of crude oil by the novel strains of Pseudomonas aeruginosa in acidic condition with higher BE. Overall, the extracellular enzymes and surface active compounds (biosurfactant) produced by bacterial strains were played a key role in crude oil biodegradation process.

Bioremediation of Soil from Petroleum Contamination

Petroleum is the most common global fossil fuel. It is a complex multi-component system mainly composed of various hydrocarbons such as alkanes, cycloalkanes, mono-, bi- and polyaromatic compounds, resins and asphaltenes. In spite of humanity’s need for petroleum, it negatively affects the environment due to its toxicity. The ecological problem is especially serious at petroleum mining sites or during petroleum transportation. Since it is not possible to replace petroleum with less toxic fuel, ways to reduce the toxic impact of petroleum hydrocarbons on the environment need to be developed. This review addresses bioremediation, a biological approach to petroleum degradation, which is mainly performed by microbes. The pathways of degradation of alkanes, alkenes and aromatic hydrocarbons are presented in detail. The effects of temperature, aeration and the presence of biogenic elements on microbial degradation of petroleum are discussed. Plant–microbe interactions involved with the bioremediation of petroleum-polluted soils are specifically addressed. The data presented in this review point to the great potential of bioremediation practices for cleaning soils of petroleum.

Adaptive Response of Thermophiles to Redox Stress and Their Role in the Process of dye Degradation From Textile Industry Wastewater

Release of dye-containing textile wastewater into the environment causes severe pollution with serious consequences on aquatic life. Bioremediation of dyes using thermophilic microorganisms has recently attracted attention over conventional treatment techniques. Thermophiles have the natural ability to survive under extreme environmental conditions, including high dye concentration, because they possess stress response adaptation and regulation mechanisms. Therefore, dye detoxification by thermophiles could offer enormous opportunities for bioremediation at elevated temperatures. In addition, the processes of degradation generate reactive oxygen species (ROS) and subject cells to oxidative stress. However, thermophiles exhibit better adaptation to resist the effects of oxidative stress. Some of the major adaptation mechanisms of thermophiles include macromolecule repair system; enzymes such as superoxide dismutase, catalase, and glutathione peroxidase; and non-enzymatic antioxidants like extracellular polymeric substance (EPSs), polyhydroxyalkanoates (PHAs), etc. In addition, different bacteria also possess enzymes that are directly involved in dye degradation such as azoreductase, laccase, and peroxidase. Therefore, through these processes, dyes are first degraded into smaller intermediate products finally releasing products that are non-toxic or of low toxicity. In this review, we discuss the sources of oxidative stress in thermophiles, the adaptive response of thermophiles to redox stress and their roles in dye removal, and the regulation and crosstalk between responses to oxidative stress.

Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate degradation in Variovorax sp. PAMC26660

Background

While the genus Variovorax is known for its aromatic compound metabolism, no detailed study of the peripheral and central pathways of aromatic compound degradation has yet been reported. Variovorax sp. PAMC26660 is a lichen-associated bacterium isolated from Antarctica. The work presents the genome-based elucidation of peripheral and central catabolic pathways of aromatic compound degradation genes in Variovorax sp. PAMC26660. Additionally, the accessory, core and unique genes were identified among Variovorax species using the pan genome analysis tool. A detailed analysis of the genes related to xenobiotic metabolism revealed the potential roles of Variovorax sp. PAMC26660 and other species in bioremediation.

Results

TYGS analysis, dDDH, phylogenetic placement and average nucleotide identity (ANI) analysis identified the strain as Variovorax sp. Cell morphology was assessed using scanning electron microscopy (SEM). On analysis of the core, accessory, and unique genes, xenobiotic metabolism accounted only for the accessory and unique genes. On detailed analysis of the aromatic compound catabolic genes, peripheral pathway related to 4-hydroxybenzoate (4-HB) degradation was found among all species while phenylacetate and tyrosine degradation pathways were present in most of the species including PAMC26660. Likewise, central catabolic pathways, like protocatechuate, gentisate, homogentisate, and phenylacetyl-CoA, were also present. The peripheral pathway for 4-HB degradation was functionally tested using PAMC26660, which resulted in the growth using it as a sole source of carbon.

Conclusions

Computational tools for genome and pan genome analysis are important to understand the behavior of an organism. Xenobiotic metabolism-related genes, that only account for the accessory and unique genes infer evolution through events like lateral gene transfer, mutation and gene rearrangement. 4-HB, an aromatic compound present among lichen species is utilized by lichen-associated Variovorax sp. PAMC26660 as the sole source of carbon. The strain holds genes and pathways for its utilization. Overall, this study outlines the importance of Variovorax in bioremediation and presents the genomic information of the species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08589-3.

Molecular signatures of Janthinobacterium lividum from Trinidad support high potential for crude oil metabolism

Background

Janthinobacterium lividum is considered to be a psychrotrophic bacterial species. For the first time in the literature, J. lividum strains were isolated from Trinidad presenting with atypical features - hydrocarbonoclastic and able to survive in a tropical environment.

Methods

Identification of the Trinidad strains was carried out through 16S rRNA phylogenetic analysis. Gene-specific primers were designed to target the VioA which encodes violacein pigment and the EstA/B gene which encodes secreted extracellular lipase. Bioinformatics analyses were carried out on the nucleotide and amino acid sequences of VioA and EstA/B genes of the Trinidad Janthinobacterium strains to assess functionality and phylogenetic relatedness to other Janthinobacterium sequences specifically and more broadly, to other members of the Oxalobacteraceae family of betaproteobacteria.

Results

16S rRNA confirmed the identity of the Trinidad strains as J. lividum and resolved three of the Trinidad strains at the intra-specific level. Typical motility patterns of this species were recorded. VioAp sequences were highly conserved, however, synonymous substitutions located outside of the critical sites for enzyme function were detected for the Trinidad strains. Comparisons with PDB 6g2p model from aa231 to aa406 further indicated no functional disruption of the VioA gene of the Trinidad strains. Phylogeny of the VioA protein sequences inferred placement of all J. lividum taxa into a highly supported species-specific clade (bs = 98%). EstA/Bp sequences were highly conserved, however, synonymous substitutions were detected that were unique to the Trinidad strains. Phylogenetic inference positioned the Trinidad consensus VioA and EstA protein sequences in a clearly distinct branch.

Conclusions

The findings showed that the primary sequence of VioAp and EstA/Bp were unique to the Trinidad strains and these molecular signatures were reflected in phylogenetic inference. Our results supported chemotaxis, possible elective inactivation of VioA gene expression and secreted lipase activity as survival mechanisms of the Trinidad strains in petrogenic conditions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02346-4.

A Novel Gene Cluster Is Involved in the Degradation of Lignin-Derived Monoaromatics in Thermus oshimai JL-2

A novel gene cluster involved in the degradation of lignin-derived monoaromatics such as p-hydroxybenzoate, vanillate, and ferulate has been identified in the thermophilic nitrate reducer Thermus oshimai JL-2. Based on conserved domain analyses and metabolic pathway mapping, the cluster was classified into upper- and peripheral-pathway operons. The upper-pathway genes, responsible for the degradation of p-hydroxybenzoate and vanillate, are located on a 0.27-Mb plasmid, whereas the peripheral-pathway genes, responsible for the transformation of ferulate, are spread throughout the plasmid and the chromosome. In addition, a lower-pathway operon was also identified in the plasmid that corresponds to the meta-cleavage pathway of catechol. Spectrophotometric and gene induction data suggest that the upper and lower operons are induced by p-hydroxybenzoate, which the strain can degrade completely within 4 days of incubation, whereas the peripheral genes are expressed constitutively. The upper degradation pathway follows a less common route, proceeding via the decarboxylation of protocatechuate to form catechol, and involves a novel thermostable γ-carboxymuconolactone decarboxylase homolog, identified as protocatechuate decarboxylase based on gene deletion experiments. This gene cluster is conserved in only a few members of the Thermales and shows traces of vertical expansion of catabolic pathways in these organisms toward lignoaromatics.IMPORTANCE High-temperature steam treatment of lignocellulosic biomass during the extraction of cellulose and hemicellulose fractions leads to the release of a wide array of lignin-derived aromatics into the natural ecosystem, some of which can have detrimental effects on the environment. Not only will identifying organisms capable of using such aromatics aid in environmental cleanup, but thermostable enzymes, if characterized, can also be used for efficient lignin valorization. However, no thermophilic lignin degraders have been reported thus far. The present study reports T. oshimai JL-2 as a thermophilic bacterium with the potential to use lignin-derived aromatics. The identification of a novel thermostable protocatechuate decarboxylase gene in the strain further adds to its significance, as such an enzyme can be efficiently used in the biosynthesis of cis,cis-muconate, an important intermediate in the commercial production of plastics.

Current Status of and Future Perspectives in Bacterial Degradation of Benzo[a]pyrene

Benzo[a]pyrene (BaP) is one the main pollutants belonging to the high-molecular-weight PAHs (HMW-PAHs) class and its degradation by microorganisms remains an important strategy for its removal from the environment. Extensive studies have been carried out on the isolation and characterisation of microorganisms that can actively degrade low-molecular-weight PAHs (LMW-PAHs), and to a certain extent, the HMW-PAH pyrene. However, so far, limited work has been carried out on BaP biodegradation. BaP consists of five fused aromatic rings, which confers this compound a high chemical stability, rendering it less amenable to biodegradation. The current review summarizes the emerging reports on BaP biodegradation. More specifically, work carried out on BaP bacterial degradation and current knowledge gaps that limit our understanding of BaP degradation are highlighted. Moreover, new avenues of research on BaP degradation are proposed, specifically in the context of the development of "omics" approaches.

Sustainable remediation of diesel-contaminated soil by low temperature thermal treatment: Improved energy efficiency and soil reusability

Thermal treatment can effectively remediate diesel-contaminated soil, but is considered unsustainable because of its energy-intensive nature and potential to damage soil properties. Here, we used low temperature thermal treatment (LTTT) as an energy-efficient technique to remediate diesel-contaminated soil. The impacts of LTTT on the physiochemical and ecological properties of soils were investigated to evaluate the reusability of heated soil. Heating at 250 °C for 10 min reduced the concentration of the total petroleum hydrocarbons from 6271 mg/kg to 359  mg/kg, which is lower than the Chinese risk screening level of 826 mg/kg. After LTTT, most soil physiochemical properties were nearly unchanged, and the NO₃^--N and NH₄⁺-N contents increased. Moreover, LTTT-remediated soil was favorable for the germination and early growth of wheat. The microbial community changed substantially, but recovered after being mixed with uncontaminated soil. Finally, exploration of the mechanisms of LTTT revealed that pyrolysis was the dominant mechanism of diesel removal. A biochar-like pyrolytic carbon was formed, which improved the soil reusability.

Biodegradation of aliphatic and polycyclic aromatic hydrocarbons by the thermophilic bioemulsifier-producing Aeribacillus pallidus strain SL-1

The utilization of thermophilic hydrocarbon-degrading microorganisms is a suitable strategy for improving biodegradation of petroleum hydrocarbons and PAHs, as well as enhancing oil recovery from high-temperature reservoirs. In this study, the thermophilic strain Aeribacillus pallidus SL-1 was evaluated for the biodegradation of crude oil and PAHs at 60 °C. Strain SL-1 was found to preferentially degrade short-chain n-alkanes (<C17) and aromatic hydrocarbons from crude oil. The highest degradation rate of 84% was obtained with 1000 mg/l naphthalene as sole carbon source. Additionally, the strain was able to degrade 80% of phenanthrene (200 mg/l) and 50% of pyrene (50 mg/l) within 5 days at 60 °C. The SL-bioemulsifier produced by strain SL-1 was identified as a glycoprotein with stable emulsifying activity over a wide range of environmental conditions. Chemical composition studies exhibited that the SL-bioemulsifier consisted of polysaccharides (65.6%) and proteins (13.1%), among them, proteins were the major emulsifying functional substrates. Furthermore, the SL-bioemulsifier was able to enhance the solubility of PAHs. Thus, the bioemulsifier-producing strain SL-1 has great potential for applications in high-temperature bioremediation.

Contribution of Yeast Extract, Activated Carbon, and an Electrostatic Field to Interspecies Electron Transfer for the Bioelectrochemical Conversion of Coal to Methane

The bioelectrochemical conversion of coal to methane was investigated in an anaerobic batch reactor containing yeast extract and activated carbon. In anaerobic degradation of coal, yeast extract was a good stimulant for the growth of anaerobic microorganisms, and activated carbon played a positive role. An electrostatic field of 0.67 V/cm significantly improved methane production from coal by promoting direct and mediated interspecies electron transfers between exoelectrogenic bacteria and electrotrophic methanogenic archaea. However, the accumulation of coal degradation intermediates gradually repressed the conversion of coal to methane, and the methane yield of coal was only 31.2 mL/g lignite, indicating that the intermediates were not completely converted to methane. By supplementing yeast extract and seed sludge into the anaerobic reactor, the intermediate residue could be further converted to methane under an electrostatic field of 0.67 V/cm, and the total methane yield of coal increased to 98.0 mL/g lignite. The repression of the intermediates to the conversion of coal to methane was a kind of irreversible substrate inhibition. The irreversible substrate inhibition in the conversion of coal to methane could be attenuated under the electrostatic field of 0.67 V/cm by ensuring sufficient biomass through biostimulation or bioaugmentation.

Biodegradation of mixed polycyclic aromatic hydrocarbons by pure and mixed cultures of biosurfactant producing thermophilic and thermo-tolerant bacteria

Applicability of thermophilic and thermo-tolerant microorganisms for biodegradation of polycyclic aromatic hydrocarbons (PAHs) with low water solubility is an interesting strategy for improving the biodegradation efficiency. In this study, we evaluated utility of thermophilic and thermo-tolerant bacteria isolated from Unkeshwar hot spring (India) for biodegradation of four different PAHs. Water samples were enriched in mineral salt medium (MSM) containing a mixture of four PAHs compounds (anthracene: ANT, fluorene: FLU, phenanthrene: PHE and pyrene: PYR) at 37 °C and 50 °C. After growth based screening, four potent strains obtained which were identified as Aeribacillus pallidus (UCPS2), Bacillus axarquiensis (UCPD1), Bacillus siamensis (GHP76) and Bacillus subtilis subsp. inaquosorum (U277) based on the 16S rRNA gene sequence analysis. Degradation of mixed PAH compounds was evaluated by pure as well as mixed cultures under shake flask conditions using MSM supplemented with 200 mg/L concentration of PAHs (50 mg/L of each compound) for 15 days at 37 °C and 50 °C. A relatively higher degradation of ANT (92%- 96%), FLU (83% - 86%), PHE (16% - 54%) and PYR (51% - 71%) was achieved at 50 °C by Aeribacillus sp. (UCPS2) and mixed culture. Furthermore, crude oil was used as a substrate to study the degradation of same PAHs using these organisms which also revealed with similar results with the higher degradation at 50 °C. Interestingly, PAH-degrading strains were also positive for biosurfactant production. Biosurfactants were identified as the variants of surfactins (lipopeptide biosurfactants) based on analytical tools and phylogenetic analysis of the surfactin genes. Overall, this study has shown that hot spring microbes may have a potential for PAHs degradation and also biosurfactant production at a higher temperature, which could provide a novel perspective for removal of PAHs residues from oil contaminated sites.