A novel phenanthrene dioxygenase from Nocardioides sp. Strain KP7: expression in Escherichia coli

Identification of an efficient phenanthrene-degrading Pseudarthrobacter sp. L1SW and characterization of its metabolites and catabolic pathway

Phenanthrene, a typical chemical of polycyclic aromatic hydrocarbons (PAHs) pollutants, severely threatens health of wild life and human being. Microbial degradation is effective and environment-friendly for PAH removal, while the phenanthrene-degrading mechanism in Gram-positive bacteria is unclear. In this work, one Gram-positive strain of plant growth-promoting rhizobacteria (PGPR), Pseudarthrobacter sp. L1SW, was isolated and identified with high phenanthrene-degrading efficiency and great stress tolerance. It degraded 96.3% of 500 mg/L phenanthrene in 72 h and kept stable degradation performance with heavy metals (65 mg/L of Zn2+, 5.56 mg/L of Ni2+, and 5.20 mg/L of Cr3+) and surfactant (10 CMC of Tween 80). Strain L1SW degraded phenanthrene mainly through phthalic acid pathway, generating intermediate metabolites including cis-3,4-dihydrophenanthrene-3,4-diol, 1-hydroxy-2-naphthoic acid, and phthalic acid. A novel metabolite (m/z 419.0939) was successfully separated and identified as an end-product of phenanthrene, suggesting a unique metabolic pathway. With the whole genome sequence alignment and comparative genomic analysis, 19 putative genes associated with phenanthrene metabolism in strain L1SW were identified to be distributed in three gene clusters and induced by phenanthrene and its metabolites. These findings advance the phenanthrene-degrading study in Gram-positive bacteria and promote the practical use of PGPR strains in the bioremediation of PAH-contaminated environments.

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

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

Microbiome based approaches for the degradation of polycyclic aromatic hydrocarbons (PAHs): A current perception

Globally, polycyclic aromatic hydrocarbons (PAHs) pollution is primarily driven by their release into the air through various combustion processes, including burning fossil fuels such as coal, oil, and gas in motor vehicles, power plants, and industries, as well as burning organic matter like wood, tobacco, and food in fireplaces, cigarettes, and grills. Apart from anthropogenic pollution sources, PAHs also occur naturally in crude oil, and their potential release during oil extraction, refining processes, and combustion further contributes to contamination and pollution concerns. PAHs are resistant and persistent in the environment because of their inherent features, viz., heterocyclic aromatic ring configurations, hydrophobicity, and thermostability. A wide range of microorganisms have been found to be effective degraders of these recalcitrant contaminants. The presence of hydrocarbons as a result of numerous anthropogenic activities is one of the primary environmental concerns. PAHs are found in soil, water, and the air, making them ubiquitous in nature. The presence of PAHs in the environment creates a problem, as their presence has a detrimental effect on humans and animals. For a variety of life forms, PAH pollutants are reported to be toxic, carcinogenic, mutation-inducing, teratogenic, and immune toxicogenics. Degradation of PAHs via biological activity is an extensively used approach in which diverse microorganisms (fungal, algal, clitellate, and protozoan) and plant species and their derived composites are utilized as biocatalysts and biosurfactants. Some microbes have the ability to transform and degrade these PAHs, allowing them to be removed from the environment. The goal of this review is to provide a critical overview of the existing understanding of PAH biodegradation. It also examines current advances in diverse methodologies for PAH degradation in order to shed light on fundamental challenges and future potential.

Environmental forensics using stable and radioactive isotopes in naturally attenuated soil after phenol-leakage accidents

Phenol is a carcinogenic and hazardous chemical used in multiple industries and poses a high risk of chemical spills into the environment. To date, environmental forensic research has not focused on chemically remediated soils. In this study, an advanced environmental forensic analysis was performed on microbial communities and breakdown products of phenol, carbon stable isotopes, and radioactive isotopes in phenol-contaminated soil. As indicators of phenol-spill accidents after natural attenuation, higher δ13C levels and lower 14C/12C ratios were observed in phenol-contaminated soil compared with uncontaminated soil. In addition, 16s rRNA gene analysis revealed that phenol-breakdown products identified by gas chromatography-mass spectrometry and the presence of soil bacteria, such as Nocardioides, Faecalibacterium, and Bacteroides, were indicators of phenol-leakage accidents. Therefore, the proposed environmental forensic strategy is a valuable tool for identifying the location of previously occurring chemical accidents and estimating the ecological impact after the natural attenuation of contaminated soils.

Microbial remediation of oil-contaminated shorelines: a review

Frequent marine oil spills have led to increasingly serious oil pollution along shorelines. Microbial remediation has become a research hotspot of intertidal oil pollution remediation because of its high efficiency, low cost, environmental friendliness, and simple operation. Many microorganisms are able to convert oil pollutants into non-toxic substances through their growth and metabolism. Microorganisms use enzymes' catalytic activities to degrade oil pollutants. However, microbial remediation efficiency is affected by the properties of the oil pollutants, microbial community, and environmental conditions. Feasible field microbial remediation technologies for oil spill pollution in the shorelines mainly include the addition of high-efficiency oil degrading bacteria (immobilized bacteria), nutrients, biosurfactants, and enzymes. Limitations to the field application of microbial remediation technology mainly include slow start-up, rapid failure, long remediation time, and uncontrolled environmental impact. Improving the environmental adaptability of microbial remediation technology and developing sustainable microbial remediation technology will be the focus of future research. The feasibility of microbial remediation techniques should also be evaluated comprehensively.

Oil-Contaminated Soil Remediation with Biodegradation by Autochthonous Microorganisms and Phytoremediation by Maize (Zea mays)

Biological methods are currently the most commonly used methods for removing hazardous substances from land. This research work focuses on the remediation of oil-contaminated land. The biodegradation of aliphatic hydrocarbons and PAHs as a result of inoculation with biopreparations B1 and B2 was investigated. Biopreparation B1 was developed on the basis of autochthonous bacteria, consisting of strains Dietzia sp. IN118, Gordonia sp. IN101, Mycolicibacterium frederiksbergense IN53, Rhodococcus erythropolis IN119, Rhodococcus globerulus IN113 and Raoultella sp. IN109, whereas biopreparation B2 was enriched with fungi, such as Aspergillus sydowii, Aspergillus versicolor, Candida sp., Cladosporium halotolerans, Penicillium chrysogenum. As a result of biodegradation tests conducted under ex situ conditions for soil inoculated with biopreparation B1, the concentrations of TPH and PAH were reduced by 31.85% and 27.41%, respectively. Soil inoculation with biopreparation B2 turned out to be more effective, as a result of which the concentration of TPH was reduced by 41.67% and PAH by 34.73%. Another issue was the phytoremediation of the pre-treated G6-3B2 soil with the use of Zea mays. The tests were carried out in three systems (system 1-soil G6-3B2 + Zea mays; system 2-soil G6-3B2 + biopreparation B2 + Zea mays; system 3-soil G6-3B2 + biopreparation B2 with γ-PGA + Zea mays) for 6 months. The highest degree of TPH and PAH reduction was obtained in system 3, amounting to 65.35% and 60.80%, respectively. The lowest phytoremediation efficiency was recorded in the non-inoculated system 1, where the concentration of TPH was reduced by 22.80% and PAH by 18.48%. Toxicological tests carried out using PhytotoxkitTM, OstracodtoxkitTM and Microtox® Solid Phase tests confirmed the effectiveness of remediation procedures and showed a correlation between the concentration of petroleum hydrocarbons in the soil and its toxicity. The results obtained during the research indicate the great potential of bioremediation practices with the use of microbial biopreparations and Zea mays in the treatment of soils contaminated with petroleum hydrocarbons.

A Review of Pyrene Bioremediation Using Mycobacterium Strains in a Different Matrix

Polycyclic aromatic hydrocarbons are compounds with 2 or more benzene rings, and 16 of them have been classified as priority pollutants. Among them, pyrene has been found in higher concentrations than recommended, posing a threat to the ecosystem. Many bacterial strains have been identified as pyrene degraders. Most of them belong to Gram-positive strains such as Mycobacterium sp. and Rhodococcus sp. These strains were enriched and isolated from several sites contaminated with petroleum products, such as fuel stations. The bioremediation of pyrene via Mycobacterium strains is the main objective of this review. The scattered data on the degradation efficiency, formation of pyrene metabolites, bio-toxicity of pyrene and its metabolites, and proposed degradation pathways were collected in this work. The study revealed that most of the Mycobacterium strains were capable of degrading pyrene efficiently. The main metabolites of pyrene were 4,5-dihydroxy pyrene, phenanthrene-4,5-dicarboxylate, phthalic acid, and pyrene-4,5-dihydrodiol. Some metabolites showed positive results for the Ames mutagenicity prediction test, such as 1,2-phenanthrenedicarboxylic acid, 1-hydroxypyrene, 4,5-dihydropyrene, 4-phenanthrene-carboxylic acid, 3,4-dihydroxyphenanthrene, monohydroxy pyrene, and 9,10-phenanthrenequinone. However, 4-phenanthrol showed positive results for experimental and prediction tests. This study may contribute to enhancing the bioremediation of pyrene in a different matrix.

Artificial Consortium of Three E. coli BL21 Strains with Synergistic Functional Modules for Complete Phenanthrene Degradation

Polycyclic aromatic hydrocarbons (PAHs) are highly toxic and persistent organic pollutions that can accumulate in the environment. In this study, an aromatic ring cleavage module, a salicylic acid synthesis module, and a catechol metabolism module were respectively constructed in three Escherichia coli BL21 strains. Subsequently, the engineered strains were cocultured as an artificial consortium for the biodegradation of phenanthrene, a typical PHA. Single factor experiments and response surface methodology were used to identify the optimal degradation conditions, including an inoculation interval of 6 h, inoculation ratio of 1:1:1, and IPTG concentration of 2 mM. Under these conditions, the 7-day degradation ratio of 100 mg/L phenanthrene reached 72.67%. Moreover, the engineered Escherichia coli BL21 strains showed good phenanthrene degradation ability at substrate concentrations 10 mg/L up to 500 mg/L. Enzyme activity assays combined with gas chromatography-mass spectrometry measurements confirmed that the three engineered strains behaved as a synergistic consortium in the phenanthrene degradation process. Based on the analysis of the key metabolites, the engineered bacteria were supplemented at 7-day intervals in batches so that each engineered strain maintained its optimal degradation ability. The 21-day degradation ratio finally reached 90.66%, which was much higher than what was observed with simultaneous inoculation. These findings suggest that the three engineered strains with separate modules constructed in this study offer an attractive solution for removing PAHs from the environment.

Phenanthrene-degrading Sphingobium xenophagum are widely distributed in the western Pacific Ocean

Six phenanthrene-degrading bacteria were isolated from surface sea water sampled from the western Pacific Ocean. They were identified as Sphingobium xenophagum (formerly Sphingomonas xenophaga) based on morphological, biochemical, and chemical characteristics and 16S rRNA sequences. Salinity ranges for the growth of these isolates were broader than those of seven reported Sphingomonas strains isolated from soil, and the optimum NaCl concentration in the growth medium was higher than that for soil sphingomonads. These isolates also exhibited higher phenanthrene-degrading activity in briny conditions than that of a phenanthrene-degrading Sphingomonas strain isolated from soil. A DNA fragment carrying nah genes, which are encoded on the naphthalene-catabolic plasmid NAH of Pseudomonas putida PpG7, hybridised less strongly with the total DNA of all isolates. Certain genes for phenanthrene degradation were also preliminarily characterised in all isolates. This is the first demonstration that S. xenophagum strains, that are able to degrade phenanthrene, are widely distributed in marine environments, and the growth and phenanthrene-degrading activity of these strains are adapted to briny conditions. Results also suggest that genes for phenanthrene degradation, which are dissimilar to the nah genes, were also ubiquitously distributed in marine strains.

Genetically engineered microbial remediation of soils co-contaminated by heavy metals and polycyclic aromatic hydrocarbons: Advances and ecological risk assessment

Soils contaminated with heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have been becoming a worldwide concerned environmental problem because of threatening public healthy via food chain exposure. Thus soils polluted by HMs and PAHs need to be remediated urgently. Physical and chemical remediation methods usually have some disadvantages, e.g., cost-expensiveness and incomplete removal, easily causing secondary pollution, which are hence not environmental-friendly. Conventional microbial approaches are mostly used to treat a single contaminant in soils and lack high efficiency and specificity for combined contaminants. Genetically engineered microorganisms (GEMs) have emerged as a desired requirement of higher bioremediation efficiency for soils polluted with HMs and PAHs and environmental sustainability, which can provide a more eco-friendly and cost-effective strategy in comparison with some conventional techniques. This review comments the recent advances about successful bioremediation techniques and approaches for soil contaminated with HMs and/or PAHs by GEMs, and discusses some challenges in the simultaneous removal of HMs and PAHs from soil by designing multi-functional genetic engineering microorganisms (MFGEMs), such as improvement of higher efficiency, strict environmental conditions, and possible ecological risks. Also, the modern biotechnological techniques and approaches in improving the ability of microbial enzymes to effectively degrade combined contaminants at a faster rate are introduced, such as reasonable gene editing, metabolic pathway modification, and protoplast fusion. Although MFGEMs are more potent than the native microbes and can quickly adapt to combined contaminants in soils, the ecological risk of MFGEMs needs to be evaluated under a regulatory, safety, or costs benefit-driving system in a way of stratified regulation. Nevertheless, the innovation of genetic engineering to produce MFGEMs should be inspired for the welfare of successful bioremediation for soils contaminated with HMs and PAHs but it must be supervised by the public, authorities, and laws.

Co-existing water and sediment bacteria are driven by contrasting environmental factors across glacier-fed aquatic systems

Glacier-fed aquatic ecosystems provide habitats for diverse and active bacterial communities. However, the environmental vulnerabilities of co-existing water and sediment bacterial communities in these ecosystems remain unclear. Here, 16S rRNA gene sequencing was used to investigate co-existing bacterial communities in paired water and sediment samples from multiple rivers and lakes that are mainly fed by glaciers from the southeast Tibetan Plateau. Overall, the bacterial communities were dissimilar between the water and sediment, which indicated that there were limited interactions between them. Bacterial diversity was greatest in the sediments, where it was mainly driven by changes in nitrogen compounds and pH. Meanwhile water bacterial diversity was more susceptible to evapotranspiration, elevation, and mean annual temperature. Water samples contained higher proportions of Proteobacteria and Bacteroidetes, while sediment harbored higher proportions of Acidobacteria, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Cyanobacteria, and Gemmatimonadetes. Bacterial community composition was significantly correlated with mean annual precipitation in water, but with nitrogen compounds in sediment. The co-occurrence network of water included more keystone species (e.g., CL500-29 marine group, Nocardioides spp., and Bacillus spp.) than the sediment network. These keystone species showed stronger phylogenetic signals than the species in the modular structures. Further, ecological clusters within the networks suggested that there were contrasting environmental vulnerabilities and preferences between water and sediment communities. These findings demonstrated that co-existing water and sediment bacterial communities and ecological clusters were shaped by contrasting environmental factors. This work provides a basis for understanding the importance of bacterial communities in maintaining glacier-fed aquatic ecosystems. Further, the results provide new perspectives for water resource management and water conservation in changing environments.

Exploitation of Potential Extremophiles for Bioremediation of Xenobiotics Compounds: A Biotechnological Approach

Microorganisms that are capable of live and adapt in hostile habitats of different environmental factors such as extremes temperature, salinity, nutrient availability and pressure are known as extremophiles. Exposure to xenobiotic compounds is global concern influencing the world population as a health hazard. Hence their removal is warranted using biological means that is very sustainable, potentially cost-effective and eco-friendly. Due to adaptation in extreme environments and unique defense mechanisms, they are receiving more attention for the bioremediation of the xenobiotic compounds. They possess robust enzymatic and biocatalytic systems that make them suitable for the effective removal of pollutants from the contaminated environment. Additionally, the extremophiles act as microfactories having specific genetic and biotechnological potential for the production of biomolecules. This mini review will provide an overview of microbial degradation metabolic pathways for bioremediation along with the molecular and physiological properties of diverse extremophiles from variety of habitats. Furthermore, the factors affecting the bioremediation process is also summarized.

Metagenomic analysis exploring microbial assemblages and functional genes potentially involved in di (2-ethylhexyl) phthalate degradation in soil

Widespread use of di (2-ethylhexyl) phthalate (DEHP) as a plasticizer has caused considerable soil pollution; however, little is known about indigenous microbial communities involved in its degradation in soil. In this study, metagenomic sequencing combined with metabolite determination was used to explore microorganisms and genes potentially involved in DEHP degradation in aerobic and anaerobic soils. The results showed that under both dryland aerobic and flooded anaerobic conditions, DEHP was initially hydrolyzed into mono (2-ethylhexyl) phthalate which was then hydrolyzed into phthalic acid; benzoic acid was the central intermediate during further metabolism steps. Bacteria were more responsive to DEHP presence than fungi/archaea, and potential degradative genes stimulated by DEHP were predominantly associated with bacteria, reflecting the dominant role of bacteria in DEHP degradation. Members of the Actinomycetales seemed to be the dominant degraders under aerobic conditions, while a number of phyla i.e. Gemmatimonadetes, Proteobacteria, Acidobacteria and Bacteroidetes appeared to be involved under anaerobic conditions. Interestingly, ~50% of esterase/lipase/cytochrome P450 genes enriched by DEHP under aerobic conditions were from Nocardioides, a bacterial genus that has not been previously directly linked to phthalate ester degradation. The results indicate that novel degraders may play an important role in DEHP degradation in natural soil environments. This study provides a better understanding of the phthalate ester biodegradation processes occurring in soil.

Symbiotic riboflavin degradation by Microbacterium and Nocardioides bacteria

Unlike its biosynthetic mechanisms and physiological function, current understanding of riboflavin degradation in soil is limited to a few bacteria that decompose it to lumichrome. Here, we isolated six Microbacterium and three Nocardioides strains. These strains utilized riboflavin and lumichrome, respectively, as carbon sources. Among these strains, we identified Microbacterium paraoxydans R16 (R16) and Nocardioides nitrophenolicus L16 (L16), which were isolated form the same enrichment culture. Co-cultured R16 and L16 reconstituted a riboflavin-degrading interspecies consortium, in which the R16 strain degraded riboflavin to lumichrome and ᴅ-ribose. The L16 strain utilized the lumichrome as a carbon source, indicating that R16 is required for L16 to grow in the consortium. Notably, rates of riboflavin degradation and growth were increased in co-cultured, compared with monocultured R16 cells. These results indicated that a beneficial symbiotic interaction between M. paraoxydans R16 and N. nitrophenolicus L16 results in the ability to degrade riboflavin.

Isolation and Characterization of Genes Responsible for Naphthalene Degradation from Thermophilic Naphthalene Degrader, Geobacillus sp. JF8

Geobacillus sp. JF8 is a thermophilic biphenyl and naphthalene degrader. To identify the naphthalene degradation genes, cis-naphthalene dihydrodiol dehydrogenase was purified from naphthalene-grown cells, and its N-terminal amino acid sequence was determined. Using a DNA probe encoding the N-terminal region of the dehydrogenase, a 10-kb DNA fragment was isolated. Upstream of nahB, a gene for dehydrogenase, there were two open reading frames which were designated as nahAc and nahAd, respectively. The products of nahAc and nahAd were predicted to be alpha and beta subunit of ring-hydroxylating dioxygenases, respectively. Phylogenetic analysis of amino acid sequences of NahB indicated that it did not belong to the cis-dihydrodiol dehydrogenase group that includes those of classical naphthalene degradation pathways. Downstream of nahB, four open reading frames were found, and their products were predicted as meta-cleavage product hydrolase, monooxygenase, dehydrogenase, and gentisate 1,2-dioxygenase, respectively. A reverse transcriptase-PCR analysis showed that transcription of nahAcAd was induced by naphthalene. These findings indicate that we successfully identified genes involved in the upper pathway of naphthalene degradation from a thermophilic bacterium.

A PAH-degrading bacterial community enriched with contaminated agricultural soil and its utility for microbial bioremediation

A bacterial community was enriched with polycyclic aromatic hydrocarbons (PAHs) polluted soil to better study PAH degradation by indigenous soil bacteria. The consortium degraded more than 52% of low molecular weight and 35% of high molecular weight (HMW) PAHs during 16 days in a soil leachate medium. 16S rRNA gene high-throughput sequencing and quantitative polymerase chain reaction analyses for alpha subunit genes of ring-hydroxylating-dioxygenase (RHDα) suggested that Proteobacteria and Actinobacteria at the phylum level, Pseudomonas, Methylobacillus, Nocardioides, Methylophilaceae, Achromobacter, Pseudoxanthomonas, and Caulobacter at the generic level were involved in PAH degradation and might have the ability to carry RHDα genes (nidA and nahAc). The community was selected and collected according to biomass and RHDα gene contents, and added back to the PAH-polluted soil. The 16 EPA priority PAHs decreased from 95.23 to 23.41 mg kg^-1 over 35 days. Compared with soil without the introduction of this bacterial community, adding the community with RHDα genes significantly decreased soil PAH contents, particularly HMW PAHs. The metabolic rate of PAHs in soil was positively correlated with nidA and nahAc gene contents. These results indicate that adding an indigenous bacterial consortium containing RHDα genes to contaminated soil may be a feasible and environmentally friendly method to clean up PAHs in agricultural soil.

Identification of proteins induced by polycyclic aromatic hydrocarbon and proposal of the phenanthrene catabolic pathway in Amycolatopsis tucumanensis DSM 45259

In the present study the polycyclic aromatic hydrocarbon removal and metabolic adaptation of Amycolatopsis tucumanensis DSM 45259 were investigated. Analysis of one-dimensional gel electrophoresis of crude cell extracts revealed differential synthesis of proteins which were identified by MALDI-TOF. To elucidate the phenanthrene metabolic pathway in A. tucumanensis DSM45259, two-dimensional electrophoresis and detection of phenanthrene degradation intermediates by GS-MS were performed. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in the metabolism of aromatic compounds, oxidative stress response, energy production and protein synthesis. The obtained results allowed us to clarify the phenanthrene catabolic pathway, by confirming the roles of several proteins involved in the degradation process and comprehensive adaptation. This may clear the way for more efficient engineering of bacteria in the direction of more effective bioremediation applications.

Synergistic plant-microbes interactions in the rhizosphere: a potential headway for the remediation of hydrocarbon polluted soils

Soil pollution is an unavoidable evil; many crude-oil exploring communities have been identified to be the most ecologically impacted regions around the world due to hydrocarbon pollution and their concurrent health risks. Several clean-up technologies have been reported on the removal of hydrocarbons in polluted soils but most of them are either very expensive, require the integration of advanced mechanization and/or cannot be implemented in small scale. However, "Bioremediation" has been reported as an efficient, cost-effective and environment-friendly technology for clean-up of hydrocarbon"s contaminated soils. Here, we suggest the implementation of synergistic mechanism of bioremediation such as the use of rhizosphere mechanism which involves the actions of plant and microorganisms, which involves the exploitation of plant and microorganisms for effective and speedy remediation of hydrocarbon"s contaminated soils. In this mechanism, plant"s action is synergized with the soil microorganisms through the root rhizosphere to promote soil remediation. The microorganisms benefit from the root metabolites (exudates) and the plant in turn benefits from the microbial recycling/solubilizing of mineral nutrients. Harnessing the abilities of plants and microorganisms is a potential headway for cost-effective clean-up of hydrocarbon"s polluted sites; such technology could be very important in countries with great oil producing activities/records over many years but still developing.

Exploring Marine Environments for the Identification of Extremophiles and Their Enzymes for Sustainable and Green Bioprocesses

Sea environments harbor a wide variety of life forms that have adapted to live in hard and sometimes extreme conditions. Among the marine living organisms, extremophiles represent a group of microorganisms that attract increasing interest in relation to their ability to produce an array of molecules that enable them to thrive in almost every marine environment. Extremophiles can be found in virtually every extreme environment on Earth, since they can tolerate very harsh environmental conditions in terms of temperature, pH, pressure, radiation, etc. Marine extremophiles are the focus of growing interest in relation to their ability to produce biotechnologically useful enzymes, the so-called extremozymes. Thanks to their resistance to temperature, pH, salt, and pollutants, marine extremozymes are promising biocatalysts for new and sustainable industrial processes, thus representing an opportunity for several biotechnological applications. Since the marine microbioma, i.e., the complex of microorganisms living in sea environments, is still largely unexplored finding new species is a central issue for green biotechnology. Here we described the main marine environments where extremophiles can be found, some existing or potential biotechnological applications of marine extremozymes for biofuels production and bioremediation, and some possible approaches for the search of new biotechnologically useful species from marine environments.

Aerobic and oxygen-limited enrichment of BTEX-degrading biofilm bacteria: dominance of Malikia versus Acidovorax species

Due to their high resistance against environmental challenges, bacterial biofilms are ubiquitous and are frequently associated with undesired phenomena in environmental industry (e. g. biofouling). However, because of the high phylogenetic and functional diversity, bacterial biofilms are important sources of biotechnologically relevant microorganisms, e.g. those showing bioremediation potential. In our previous work, the high phylogenetic and metabolic diversity of a clogging biofilm, developed in a simple aromatic hydrocarbon (BTEX)-contaminated groundwater well was uncovered. The determination of relationships between different groups of biofilm bacteria and certain metabolic traits has been omitted so far. Therefore, by setting up new biofilm-based enrichment microcosms, the research goal of the present study was to identify the aerobic/hypoxic BTEX-degrading and/or prolific biofilm-forming bacteria. The initial bacterial community composition as well as temporal dynamics due to the selective enrichment has been determined. The obtained results indicated that the concentration of dissolved oxygen may be a strong selective force on the evolution and final structure of microbial communities, developed in hydrocarbon-contaminated environments. Accordingly, members of the genus Malikia proved to be the most dominant community members of the aerobic BTEX-degrading enrichments. Acidovorax spp. dominated the oxygen-limited/hypoxic setup. During the study, a strain collection of 23 different bacterial species was obtained. Non-pathogenic members of this strain collection, with outstanding biodegradation (e.g. Pseudomonas, Variovorax isolates) and biofilm-forming potential (e.g. Rhizobium), may potentially be applied in the development of biofilm-based semipermeable reactive biobarriers.

Insight Into Metabolic Versatility of an Aromatic Compounds-Degrading Arthrobacter sp. YC-RL1

The genus Arthrobacter is ubiquitously distributed in different natural environments. Many xenobiotic-degrading Arthrobacter strains have been isolated and described; however, few have been systematically characterized with regard to multiple interrelated metabolic pathways and the genes that encode them. In this study, the biodegradability of seven aromatic compounds by Arthrobacter sp. YC-RL1 was investigated. Strain YC-RL1 could efficiently degrade p-xylene (PX), naphthalene, phenanthrene, biphenyl, p-nitrophenol (PNP), and bisphenol A (BPA) under both separated and mixed conditions. Based on the detected metabolic intermediates, metabolic pathways of naphthalene, biphenyl, PNP, and BPA were proposed, which indicated that strain YC-RL1 harbors systematic metabolic pathways toward aromatic compounds. Further, genomic analysis uncovered part of genes involved in the proposed pathways. Both intradiol and extradiol ring-cleavage dioxygenase genes were identified in the genome of strain YC-RL1. Meanwhile, gene clusters predicted to encode the degradation of biphenyl (bph), para-substituted phenols (npd) and protocatechuate (pca) were identified, and bphA1A2BCD was proposed to be a novel biphenyl-degrading gene cluster. The complete metabolic pathway of biphenyl was deduced via intermediates and functional gene analysis (bph and pca gene clusters). One of the these genes encoding ring-cleavage dioxygenase in bph gene cluster, a predicted 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) gene, was cloned and its activity was confirmed by heterologous expression. This work systematically illuminated the metabolic versatility of aromatic compounds in strain YC-RL1 via the combination of metabolites identification, genomics analysis and laboratory experiments. These results suggested that strain YC-RL1 might be a promising candidate for the bioremediation of aromatic compounds pollution sites.

Aerobic bacteria degrading both n-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility

Environmental pollution with petroleum toxic products has afflicted various ecosystems, causing devastating damage to natural habitats with serious economic implications. Some crude oil components may serve as growth substrates for microorganisms. A number of bacterial strains reveal metabolic capacities to biotransform various organic compounds. Some of the hydrocarbon degraders are highly biochemically specialized, while the others display a versatile metabolism and can utilize both saturated aliphatic and aromatic hydrocarbons. The extended catabolic profiles of the latter group have been subjected to systematic and complex studies relatively rarely thus far. Growing evidence shows that numerous bacteria produce broad biochemical activities towards different hydrocarbon types and such an enhanced metabolic potential can be found in many more species than the already well-known oil-degraders. These strains may play an important role in the removal of heterogeneous contamination. They are thus considered to be a promising solution in bioremediation applications. The main purpose of this article is to provide an overview of the current knowledge on aerobic bacteria involved in the mineralization or transformation of both n-alkanes and aromatic hydrocarbons. Variant scientific approaches enabling to evaluate these features on biochemical as well as genetic levels are presented. The distribution of multidegradative capabilities between bacterial taxa is systematically shown and the possibility of simultaneous transformation of complex hydrocarbon mixtures is discussed. Bioinformatic analysis of the currently available genetic data is employed to enable generation of phylogenetic relationships between environmental strain isolates belonging to the phyla Actinobacteria, Proteobacteria, and Firmicutes. The study proves that the co-occurrence of genes responsible for concomitant metabolic bioconversion reactions of structurally-diverse hydrocarbons is not unique among various systematic groups.

Microbial diversity and activity of an aged soil contaminated by polycyclic aromatic hydrocarbons

In-depth understanding of indigenous microbial assemblages resulted from aged contamination by polycyclic aromatic hydrocarbons (PAHs) is of vital importance in successful in situ bioremediation treatments. Soil samples of three boreholes were collected at 12 different vertical depths. Overall, the dominating three-ring PAHs (76.2%) were closely related to distribution patterns of soil dehydrogenase activity, microbial cell numbers, and Shannon biodiversity index (H') of indigenous microorganisms. High-molecular-weight PAHs tend to yield more diverse communities. Results from 16S rRNA analysis indicated that possible functional groups of PAH degradation include three species in Bacillus cereus group, Bacillus sp. SA Ant14, Nocardioides sp., and Ralstonia pickettii. Principal component analysis indicates significant positive correlations between the content of high-molecular-weight PAHs and the distribution of Bacillus weihenstephanensis KBAB4 and Nocardioides sp. The species B. cereus 03BB102, Bacillus thuringiensis, B. weihenstephanensis KBAB4, and Nocardioides sp. were recognized as main PAH degraders and thus recommended to be utilized in further bioremediation applications. The vertical distribution characteristics of PAHs in soil profiles (1-12 m) and the internal relationship between the transport mechanisms of PAHs and the response of soil biological properties help further understand the microbial diversity and activity in an aged site.

Characterization of a polycyclic aromatic ring-hydroxylation dioxygenase from Mycobacterium sp. NJS-P

Ring-hydroxylating dioxygenases (RHDs) play a critical role in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). In this study, genes pdoAB encoding a dioxygenase capable of oxidizing various PAHs with up to five-ring benzo[a]pyrene were cloned from Mycobacterium sp. NJS-P. The α-subunit of the PdoAB showed 99% and 93% identity to that from Mycobacterium sp. S65 and Mycobacterium sp. py136, respectively. An Escherichia coli expression experiment revealed that the enzyme is able to oxidize anthracene, phenanthrene, pyrene and benzo[a]pyrene, but not to fluoranthene and benzo[a]anthracene. Furthermore, the results of in silico analysis showed that PdoAB has a large substrate-binding pocket satisfying for accommodation of HMW PAHs, and suggested that the binding energy of intermolecular interaction may predict the substrate conversion of RHDs towards HMW PAHs, especially those may have steric constraints on the substrate-binding pocket, such as benzo[a]pyrene and benzo[a]anthracene.

Soil properties and microbial ecology of a paddy field after repeated applications of domestic and industrial sewage sludges

The effects of repeated application of two types of sewage sludge, domestic and industrial (petrochemical, PSS) sludges, into paddy fields over a 5-year period on the soil properties and microbial ecology were studied and compared with conventional NPK fertilizer application. Soil organic matter and total nitrogen contents were significantly higher in the two sludge treatments than that in fertilized plots after 5 years. Soil concentrations of potentially toxic metals were low after 5 years of both sludge treatments, but the polycyclic aromatic hydrocarbons (PAHs) showed differences between the two sludge types. Concentrations of high-molecular-weight PAHs were significantly higher (p < 0.05) in the petrochemical sludge treatment than the domestic sludge treatment or the fertilizer control, although the total concentrations of 16 types of PAH in the petrochemical sludge treatment were only slightly higher than in the domestic sludge treatment and the control. The biological toxicity of soil dimethyl sulfoxide extracts from the petrochemical sludge treatment was also significantly higher (p < 0.05) than those from the fertilizer control and the domestic sludge treatment when evaluated using Photobacterium phosphoreum T3. Both types of sewage sludge increased soil microbial activity, but only the petrochemical sludge led to enrichment with specific PAH degraders such as Mycobacterium, Nocardioides, and Sphingomonas.

Comparative proteomics reveal the mechanism of Tween80 enhanced phenanthrene biodegradation by Sphingomonas sp. GY2B

Previous study concerning the effects of surfactants on phenanthrene biodegradation focused on observing the changes of cell characteristics of Sphingomonas sp. GY2B. However, the impact of surfactants on the expression of bacterial proteins, controlling phenanthrene transport and catabolism, remains obscure. To overcome the knowledge gap, comparative proteomic approaches were used to investigate protein expressions of Sphingomonas sp. GY2B during phenanthrene biodegradation in the presence and absence of a nonionic surfactant, Tween80. A total of 23 up-regulated and 19 down-regulated proteins were detected upon Tween80 treatment. Tween80 could regulate ion transport (e.g. H⁺) in cell membrane to provide driving force (ATP) for the transmembrane transport of phenanthrene thus increasing its uptake and biodegradation by GY2B. Moreover, Tween80 probably increased GY2B vitality and growth by inducing the expression of peptidylprolyl isomerase to stabilize cell membrane, increasing the abundances of proteins involved in intracellular metabolic pathways (e.g. TCA cycle), as well as decreasing the abundances of translation/transcription-related proteins and cysteine desulfurase, thereby facilitating phenanthrene biodegradation. This study may facilitate a better understanding of the mechanisms that regulate surfactants-enhanced biodegradation of PAHs at the proteomic level.

Marine-Derived Biocatalysts: Importance, Accessing, and Application in Aromatic Pollutant Bioremediation

The aim of the present review is to highlight the potential use of marine biocatalysts (whole cells or enzymes) as an alternative bioprocess for the degradation of aromatic pollutants. Firstly, information about the characteristics of the still underexplored marine environment and the available scientific tools used to access novel marine-derived biocatalysts is provided. Marine-derived enzymes, such as dioxygenases and dehalogenases, and the involved catalytic mechanisms for the degradation of aromatic and halogenated compounds, are presented, with the purpose of underpinning their potential use in bioremediation. Emphasis is given on persistent organic pollutants (POPs) that are organic compounds with significant impact on health and environment due to their resistance in degradation. POPs bioaccumulate mainly in the fatty tissue of living organisms, therefore current efforts are mostly focused on the restriction of their use and production, since their removal is still unclear. A brief description of the guidelines and criteria that render a pollutant POP is given, as well as their potential biodegradation by marine microorganisms by surveying recent developments in this rather unexplored field.

The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective

Widespread pollution of terrestrial ecosystems with petroleum hydrocarbons (PHCs) has generated a need for remediation and, given that many PHCs are biodegradable, bio- and phyto-remediation are often viable approaches for active and passive remediation. This review focuses on phytoremediation with particular interest on the interactions between and use of plant-associated bacteria to restore PHC polluted sites. Plant-associated bacteria include endophytic, phyllospheric, and rhizospheric bacteria, and cooperation between these bacteria and their host plants allows for greater plant survivability and treatment outcomes in contaminated sites. Bacterially driven PHC bioremediation is attributed to the presence of diverse suites of metabolic genes for aliphatic and aromatic hydrocarbons, along with a broader suite of physiological properties including biosurfactant production, biofilm formation, chemotaxis to hydrocarbons, and flexibility in cell-surface hydrophobicity. In soils impacted by PHC contamination, microbial bioremediation generally relies on the addition of high-energy electron acceptors (e.g., oxygen) and fertilization to supply limiting nutrients (e.g., nitrogen, phosphorous, potassium) in the face of excess PHC carbon. As an alternative, the addition of plants can greatly improve bioremediation rates and outcomes as plants provide microbial habitats, improve soil porosity (thereby increasing mass transfer of substrates and electron acceptors), and exchange limiting nutrients with their microbial counterparts. In return, plant-associated microorganisms improve plant growth by reducing soil toxicity through contaminant removal, producing plant growth promoting metabolites, liberating sequestered plant nutrients from soil, fixing nitrogen, and more generally establishing the foundations of soil nutrient cycling. In a practical and applied sense, the collective action of plants and their associated microorganisms is advantageous for remediation of PHC contaminated soil in terms of overall cost and success rates for in situ implementation in a diversity of environments. Mechanistically, there remain biological unknowns that present challenges for applying bio- and phyto-remediation technologies without having a deep prior understanding of individual target sites. In this review, evidence from traditional and modern omics technologies is discussed to provide a framework for plant-microbe interactions during PHC remediation. The potential for integrating multiple molecular and computational techniques to evaluate linkages between microbial communities, plant communities and ecosystem processes is explored with an eye on improving phytoremediation of PHC contaminated sites.

Aerobic degradation of BDE-209 by Enterococcus casseliflavus: Isolation, identification and cell changes during degradation process

Decabromodiphenyl ether (BDE-209) is one of the most commonly used brominated flame retardants that have contaminated the environment worldwide. Microbial bioremediation has been considered as an effective technique to remove these sorts of persistent organic pollutants. Enterococcus casseliflavus, a gram-positive bacterium capable of aerobically transforming BDE-209, was isolated by our team from sediments in Guiyu, an e-waste dismantling area in Guangdong Province, China. To promote microbial bioremediation of BDE-209 and elucidate the mechanism behind its aerobic degradation, the effects of BDE-209 on the cell changes of E. casseliflavus were examined in this study. The experimental results demonstrated that the high cell surface hydrophobicity (CSH) of E. casseliflavus made the bacteria absorb hydrophobic BDE-209 more easily. E. casseliflavus responded to BDE-209 stress, resulting in an increase in cell membrane permeability and accumulation of BDE-209 inside the cell. The differential expression of intracellular protein was analyzed through two-dimensional gel electrophoresis (2-DE). More than 50 differentially expressed protein spots were reproducibly detected, including 25 up, and 25 down regulated after a 4 days exposure. Moreover, the apoptotic-like cell changes were observed during E. casseliflavus mediated degradation of BDE-209 by means of flow cytometry.

Phenanthrene bioaccumulation in the nematode Caenorhabditis elegans

The contribution of food to the bioaccumulation of xenobiotics and hence toxicity is still an ambiguous issue. It is becoming more and more evident that universal statements cannot be made, but that the relative contribution of food-associated xenobiotics in bioaccumulation depends on species, substance, and environmental conditions. Yet, small-sized benthic or soil animals such as nematodes have largely been disregarded so far. Bioaccumulation of the polycyclic aromatic hydrocarbon phenanthrene in the absence and presence of bacterial food was measured in the nematode Caenorhabditis elegans. Elimination of phenanthrene in the nematodes was biphasic, suggesting that there was a slowly exchanging pool within the nematodes or that biotransformation of phenanthrene took place. Even with food present, dissolved phenanthrene was still the major contributor to bioaccumulated compound in nematode tissues, whereas the diet only contributed about 9%. Toxicokinetic parameters in the treatment without food were different from the ones of the treatment with bacteria, possibly because nematodes depleted their lipid reserves during starvation.

Functional characterization of diverse ring-hydroxylating oxygenases and induction of complex aromatic catabolic gene clusters in Sphingobium sp. PNB

Sphingobium sp. PNB, like other sphingomonads, has multiple ring-hydroxylating oxygenase (RHO) genes. Three different fosmid clones have been sequenced to identify the putative genes responsible for the degradation of various aromatics in this bacterial strain. Comparison of the map of the catabolic genes with that of different sphingomonads revealed a similar arrangement of gene clusters that harbors seven sets of RHO terminal components and a sole set of electron transport (ET) proteins. The presence of distinctly conserved amino acid residues in ferredoxin and in silico molecular docking analyses of ferredoxin with the well characterized terminal oxygenase components indicated the structural uniqueness of the ET component in sphingomonads. The predicted substrate specificities, derived from the phylogenetic relationship of each of the RHOs, were examined based on transformation of putative substrates and their structural homologs by the recombinant strains expressing each of the oxygenases and the sole set of available ET proteins. The RHO AhdA1bA2b was functionally characterized for the first time and was found to be capable of transforming ethylbenzene, propylbenzene, cumene, p-cymene and biphenyl, in addition to a number of polycyclic aromatic hydrocarbons. Overexpression of aromatic catabolic genes in strain PNB, revealed by real-time PCR analyses, is a way forward to understand the complex regulation of degradative genes in sphingomonads.

Isolation and characterization of a novel phenanthrene (PHE) degrading strain Psuedomonas sp. USTB-RU from petroleum contaminated soil

The phenanthrene degrading novel bacterium strain USTB-RU was isolated from petroleum contaminated soil in Dagan oilfield, southeast of Tianjin, northeast China. The novel isolate was identified as Pseudomonas sp. USTB-RU on the basis of morphological, physicochemical characteristics and analysis of 16S rDNA gene sequence. The strain could degrade 86.65% of phenanthrene at an initial concentration of 100 mg L(-1) in 8 days and identified intermediate metabolite evident the biodegradation of phenanthrene through protocatechuate metabolic pathway. The strain showed the potential to produce surface-active compounds that may have caused for the resulted efficient biodegradation through enhancing the substrate bioavailability. The results highlighted that the adaptability of USTB-RU to grow in a range of temperature, pH and potential to utilize various commonly co-exist pollutants in contaminated site other than phenanthrene as sole carbon and energy source. Further, susceptibility of the strain for the tested antibiotics inferred the possibility to absence of risk of spreading drug resistant factor to other indigenous bacteria. Therefore, the isolated novel strain USTB-RU may have a high potential for application in in situ bioremediation of phenanthrene contaminated environment.

A gene expression study of the activities of aromatic ring-cleavage dioxygenases in Mycobacterium gilvum PYR-GCK to changes in salinity and pH during pyrene degradation

Polycyclic aromatic hydrocarbons (PAHs) are toxic pollutants found in the environment which can be removed through the use of physical and biological agents. The rate of PAH biodegradation is affected by environmental conditions of pH, salinity and temperature. Adaptation of the pyrene degrading bacteria, Mycobacterium gilvum PYR-GCK, to fluctuating environmental conditions during pyrene biodegrading activity was studied using the quantitative real time – Polymerase Chain Reaction (qRT-PCR) technique. Four aromatic ring-cleavage dioxygenase genes: phdF, phdI, pcaG and pcaH; critical to pyrene biodegradation, were studied in pH states of 5.5, 6.5, 7.5 and NaCl concentrations 0 M, 0.17 M, 0.5 M, 0.6 M, 1 M. First, we conducted a residual pyrene study using gas chromatography and flame ionization technologies. Central to a gene expression study is the use of a valid endogenous reference gene, making its determination our next approach, using the geNorm/NormFinder algorithms. Armed with a valid control gene, rpoB, we applied it to a gene expression study, using the comparative critical threshold (2^ΔΔCT) quantification method. The pyrene degrading activity of the strain was strongly functional in all the NaCl concentration states, with the least activity found at 1M (∼70% degraded after 48 hours of cultivation). The transcripts quantification of three genes backed this observation with high expression levels. The gene expression levels also revealed pH 6.5 as optimal for pyrene degradation and weak degradation activity at pH of 5.5, corroborating the residual pyrene analysis. The expression of these genes as proteins has already been studied in our laboratory using proteomics techniques and this validates our current study.

Draft genome sequence of Rhodococcus sp. strain P14, a biodegrader of high-molecular-weight polycyclic aromatic hydrocarbons

The genus Rhodococcus is known for its ability to degrade various xenobiotic compounds. Rhodococcus sp. strain P14 isolated from crude oil-contaminated sediments can degrade mineral oil and polycyclic aromatic hydrocarbons (PAHs). The draft genome sequence of Rhodococcus sp. P14 was obtained using Solexa technology, which provided an invaluable genetic background for further investigation of the ability of P14 to degrade xenobiotic compounds.

Characterization of the 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene (DDE) degradation system in Janibacter sp. TYM3221

Bacterial degradation of 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene (DDE) has been previously reported, however, its degradation enzyme system has not been characterized. In this study, a DDE-degrading bacterium, Janibacter sp. TYM3221, was isolated and characterized. Transformation of DDE was demonstrated by TYM3211 resting cells grown in LB in the presence and absence of biphenyl. Gas chromatography-mass spectrometry analysis revealed five metabolites of DDE containing a meta-ring cleavage product and 4-chlorobenzoic acid, suggesting that TYM3221 degrades DDE to 4-chlorobenzoic acid via a meta-ring cleavage product. A gene cluster, bphAaAbAcAd, which codes for biphenyl dioxygenase subunits, was cloned from TYM3221. A mutant strain with a bphAa-gene inactivation did not grow on biphenyl, and showed no DDE degradation activity. These results indicate that in strain TYM3221, the bphAa-coded biphenyl dioxygenase is involved not only in the metabolism of biphenyl but also in the degradation of DDE.

Expression in Escherichia coli of biphenyl 2,3-dioxygenase genes from a Gram-positive polychlorinated biphenyl degrader, Rhodococcus jostii RHA1

Rhodococcus jostii RHA1 is a polychlorinated biphenyl degrader. Multi-component biphenyl 2,3-dioxygenase (BphA) genes of RHA1 encode large and small subunits of oxygenase component and ferredoxin and reductase components. They did not express enzyme activity in Escherichia coli. To obtain BphA activity in E. coli, hybrid BphA gene derivatives were constructed by replacing ferredoxin and/or reductase component genes of RHA1 with those of Pseudomonas pseudoalcaligenes KF707. The results obtained indicate a lack of catalytic activity of the RHA1 ferredoxin component gene, bphAc in E. coli. To determine the cause of inability of RHA1 bphAc to express in E. coli, the bphAc gene was introduced into Rosetta (DE3) pLacI, which has extra tRNA genes for rare codons in E. coli. The resulting strain abundantly produced the bphAc product, and showed activity. These results suggest that codon usage bias is involved in inability of RHA1 bphAc to express its catalytic activity in E. coli.

Bacteria-mediated PAH degradation in soil and sediment

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the natural environment and easily accumulate in soil and sediment due to their low solubility and high hydrophobicity, rendering them less available for biological degradation. However, microbial degradation is a promising mechanism which is responsible for the ecological recovery of PAH-contaminated soil and sediment for removing these recalcitrant compounds compared with chemical degradation of PAHs. The goal of this review is to provide an outline of the current knowledge of biodegradation of PAHs in related aspects. Over 102 publications related to PAH biodegradation in soil and sediment are compiled, discussed, and analyzed. This review aims to discuss PAH degradation under various redox potential conditions, the factors affecting the biodegradation rates, degrading bacteria, the relevant genes in molecular monitoring methods, and some recent-year bioremediation field studies. The comprehensive understanding of the bioremediation kinetics and molecular means will be helpful for optimizing and monitoring the process, and overcoming its limitations in practical projects.

Substrate specificity and structural characteristics of the novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1

The Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs) NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1 have been implicated in the initial oxidation of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs), forming cis-dihydrodiols. To clarify how these two RHOs are functionally different with respect to the degradation of HMW PAHs, we investigated their substrate specificities to 13 representative aromatic substrates (toluene, m-xylene, phthalate, biphenyl, naphthalene, phenanthrene, anthracene, fluoranthene, pyrene, benz[a]anthracene, benzo[a]pyrene, carbazole, and dibenzothiophene) by enzyme reconstitution studies of Escherichia coli. Both Nid systems were identified to be compatible with type V electron transport chain (ETC) components, consisting of a [3Fe-4S]-type ferredoxin and a glutathione reductase (GR)-type reductase. Metabolite profiles indicated that the Nid systems oxidize a wide range of aromatic hydrocarbon compounds, producing various isomeric dihydrodiol and phenolic compounds. NidAB and NidA3B3 showed the highest conversion rates for pyrene and fluoranthene, respectively, with high product regiospecificity, whereas other aromatic substrates were converted at relatively low regiospecificity. Structural characteristics of the active sites of the Nid systems were investigated and compared to those of other RHOs. The NidAB and NidA3B3 systems showed the largest substrate-binding pockets in the active sites, which satisfies spatial requirements for accepting HMW PAHs. Spatially conserved aromatic amino acids, Phe-Phe-Phe, in the substrate-binding pockets of the Nid systems appeared to play an important role in keeping aromatic substrates within the reactive distance from the iron atom, which allows each oxygen to attack the neighboring carbons.

Advances in the field of high-molecular-weight polycyclic aromatic hydrocarbon biodegradation by bacteria

Interest in understanding prokaryotic biotransformation of high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs) has continued to grow and the scientific literature shows that studies in this field are originating from research groups from many different locations throughout the world. In the last 10 years, research in regard to HMW PAH biodegradation by bacteria has been further advanced through the documentation of new isolates that represent diverse bacterial types that have been isolated from different environments and that possess different metabolic capabilities. This has occurred in addition to the continuation of in-depth comprehensive characterizations of previously isolated organisms, such as Mycobacterium vanbaalenii PYR-1. New metabolites derived from prokaryotic biodegradation of four- and five-ring PAHs have been characterized, our knowledge of the enzymes involved in these transformations has been advanced and HMW PAH biodegradation pathways have been further developed, expanded upon and refined. At the same time, investigation of prokaryotic consortia has furthered our understanding of the capabilities of microorganisms functioning as communities during HMW PAH biodegradation.

Aromatic hydrocarbon degradation genes from chronically polluted Subantarctic marine sediments

AIM

The goal of this study was to identify functional targets to detect polycyclic aromatic hydrocarbon (PAH)-degrading bacterial populations in cold marine ecosystems.

METHODS AND RESULTS

We designed a degenerate primer set targeting genes encoding the alpha subunit of PAH-dioxygenases from Gram-positive bacteria. This primer set was used to amplify gene fragments from metagenomic DNA isolated from Subantarctic marine sediments (Ushuaia Bay, Argentina). These gene fragments were cloned and sequenced. We identified 14 distinct groups of genes, most of them showing significant relatedness with dioxygenases from Gram-positive bacteria of the genera Rhodococcus, Mycobacterium, Nocardioides, Terrabacter and Bacillus. The level of identity with these genes, however, was low to moderate (33-62% at the amino acid level).

CONCLUSION

These results indicate the presence of a high diversity of hitherto unidentified dioxygenase genes in this cold polluted environment.

SIGNIFICANCE AND IMPACT OF THE STUDY

Subantarctic marine ecosystems are particularly vulnerable to hydrocarbon pollution, and the development of environmental restoration strategies for these environments is pressing. The information obtained in this work will be the starting point for the design of quantitative molecular tools to analyse the abundance and dynamics of these aromatic hydrocarbon-degrading bacterial populations in the marine environment.

Identification of two vicinal operons for the degradation of 2-aminobenzenesulfonate encoded on plasmid pSAH in Alcaligenes sp. strain O-1

Alcaligenes sp. strain O-1 inducibly deaminates 2-aminobenzenesulfonate (ABS) via dioxygenation to 3-sulfocatechol, which is desulfonated during meta ring-cleavage to yield 2-hydroxymuconate. This intermediate is transformed through the oxalocrotonate-branch of the sulfocatechol meta-pathway (Scm). The complete pathway is encoded on the 180-kb plasmid pSAH, 20kb of which was sequenced. Twenty open reading frames (ORFs) were detected. Two clusters (abs and scm) with degradative genes were surrounded by several transposon-related ORFs. The six genes of the abs cluster were shown to be co-transcribed, and contained the genes for two characterised subunits of the oxygenase component of the ABS-dioxygenase system, and genes putatively encoding ABS-transport functions with similarities to (a) an ABC-type transporter system and (b) a putative major facilitator superfamily transporter. No gene encoding the reductase for the oxygenase system was present in the abs gene cluster, but a candidate gene was found in the scm cluster. The seven-gene scm cluster was also transcribed as single polycistronic message. Functions could be attributed to the gene products, but one enzyme, which was shown to be present, 2-hydroxymuconate isomerase, was not encoded in the scm cluster. No transcriptional regulator was found. This genetic information on the degradation of ABS in strain O-1 provides another example of both split operons and dispersed pathway genes.

Characterization of a pyrene-degrading Mycobacterium sp. strain CH-2

Mycobacterium sp strain CH-2 was isolated from a manufactured gas plant contaminated with polycyclic aromatic hydrocarbons (PAHs) and was identified by analysis of 16S rDNA sequences. Strain CH-2 was capable of mineralizing 3- and 4- ring PAHs, including phenanthrene, pyrene, and fluoranthene. In addition, strain CH-2 could utilize phenanthrene, pyrene and a wide range of alkanes as a sole carbon and energy source. Primers based upon the sequences of the polycyclic aromatic hydrocarbon (PAH) dioxygenases nidAB (from Mycobacterium vanbaalenii strain PYR-1) and pdoA2B2 (from Mycobacterium sp. Strain 6PY1) were used as molecular probes to amplify the dioxygenases. Degenerate primers were used to amplify a portion of an alkane monooxygenase gene. Mineralization assays and reverse transcriptase-polymerase chain reaction (RT-PCR) analysis indicated that the alkane monooxygenase was constitutively expressed, while nidAB and pdoA2B2 were expressed only in the presence of PAHs. A genomic library of strain CH-2 was created and then screened for the presence of biodegradative operons using the amplified PAH dioxygenases. The pdolocus included a partial pdoF, as well as pdoA2, pdoB2, orf 72, and putative genes for a ferredoxin, an araC-type regulator, and a reductase. The nid locus included a partial nidC, as well as nidB, nidA, and a putative promoter. Primer extension analysis of the nidlocus located the transcriptional start site 68bp upstream of the nidB start codon. The putatively identified promoter region and a promoter fragment lacking the -10 region were amplified, and the products were cloned into pRW50. This plasmid carries the lac operon without a promoter. The plasmid containing the full length promoter expressed the lacZ reporter gene, while expression by the promoter fragment was equivalent to the expression of cells carrying pRW50.