Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1

Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes

Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggested a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.

Remediation potential of an immobilized microbial consortium with corn straw as a carrier in polycyclic aromatic hydrocarbons contaminated soil

Polycyclic aromatic hydrocarbons (PAHs) are widespread in soils and threaten human health seriously. The immobilized microorganisms (IM) technique is an effective and environmentally sound approach for remediating PAH-contaminated soil. However, the knowledge of the remedial efficiency and the way IM operates using natural organic materials as carriers in complex soil environments is limited. In this study, we loaded a functional microbial consortium on corn straw to analyze the effect of IM on PAH concentration and explore the potential remediation mechanisms of IM in PAH-contaminated soil. The findings revealed that the removal rate of total PAHs in the soil was 88.25% with the application of IM after 20 days, which was 39.25% higher than the control treatment, suggesting that IM could more easily degrade PAHs in soil. The findings from high-throughput sequencing and quantitative PCR revealed that the addition of IM altered the bacterial community structure and key components of the bacterial network, enhanced cooperative relationships among bacteria, and increased the abundance of bacteria and functional gene copies such as nidA and nahAc in the soil, ultimately facilitating the degradation of PAHs in the soil. This study enhances our understanding of the potential applications of IM for the treatment of PAH-contaminated soil.

Biochar inoculated with Pseudomonas putida alleviates its inhibitory effect on biodegradation pathways in phenanthrene-contaminated soil

Controversial results are reported whereby biodegradation of polycyclic aromatic hydrocarbons (PAHs) can be promoted or inhibited by biochar amendment of soil. Metabolomics was applied to analyze the metabolic profiles of amendment with biochar (BB) and biochar inoculated with functional bacteria (Pseudomonas putida) (BP) involved in phenanthrene (PHE) degradation. Additionally, metagenomic analysis was utilized to assess the impact of different treatments on PHE degradation by soil microorganisms. Results indicated that BB treatment decreased the PHE biodegradation of the soil indigenous bacterial consortium, but BP treatment alleviated this inhibitory effect. Metabolomics revealed the differential metabolite 9-phenanthrol was absent in the BB treatment, but was found in the control group (CK), and in the treatment inoculated with the Pseudomonas putida (Ps) and the BP treatment. Metagenomic analysis showed that biochar decreased the abundance of the cytochrome P450 monooxygenase (CYP116), which was detected in the Pseudomonas putida, thus alleviating the inhibitory effect of biochar on PHE degradation. Moreover, a noticeable delayed increase of functional gene abundance and enzymes abundance in the BB treatment was observed in the PHE degradation pathway. Our findings elucidate the mechanism of inhibition with biochar amendment and the alleviating effect of biochar inoculated with degrading bacteria.

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.

Characterization of three rapidly growing novel Mycobacterium species with significant polycyclic aromatic hydrocarbon bioremediation potential

Mycobacterium species exhibit high bioremediation potential for the degradation of polycyclic aromatic hydrocarbons (PAHs) that are significant environmental pollutants. In this study, three Gram-positive, rapidly growing strains (YC-RL4T, MB418T, and HX176T) were isolated from petroleum-contaminated soils and were classified as Mycobacterium within the family Mycobacteriaceae. Genomic average nucleotide identity (ANI; < 95%) and digital DNA-DNA hybridization (dDDH; < 70%) values relative to other Mycobacterium spp. indicated that the strains represented novel species. The morphological, physiological, and chemotaxonomic characteristics of the isolates also supported their affiliation with Mycobacterium and their delineation as novel species. The strains were identified as Mycobacterium adipatum sp. nov. (type strain YC-RL4T = CPCC 205684T = CGMCC 1.62027T), Mycobacterium deserti sp. nov. (type strain MB418T = CPCC 205710T = KCTC 49782T), and Mycobacterium hippophais sp. nov. (type strain HX176T = CPCC 205372T = KCTC 49413T). Genes encoding enzymes involved in PAH degradation and metal resistance were present in the genomes of all three strains. Specifically, genes encoding alpha subunits of aromatic ring-hydroxylating dioxygenases were encoded by the genomes. The genes were also identified as core genes in a pangenomic analysis of the three strains along with 70 phylogenetically related mycobacterial strains that were previously classified as Mycolicibacterium. Notably, strain YC-RL4T could not only utilize phthalates as their sole carbon source for growth, but also convert di-(2-ethylhexyl) phthalate into phthalic acid. These results indicated that strains YC-RL4T, MB418T, and HX176T were important resources with significant bioremediation potential in soils contaminated by PAHs and heavy metals.

Bioremediation of polycyclic aromatic hydrocarbons: An updated microbiological review

A class of organic priority pollutants known as PAHs is of critical public health and environmental concern due to its carcinogenic properties as well as its genotoxic, mutagenic, and cytotoxic properties. Research to eliminate PAHs from the environment has increased significantly due to awareness about their negative effects on the environment and human health. Various environmental factors, including nutrients, microorganisms present and their abundance, and the nature and chemical properties of the PAH affect the biodegradation of PAHs. A large spectrum of bacteria, fungi, and algae have ability to degrade PAHs with the biodegradation capacity of bacteria and fungi receiving the most attention. A considerable amount of research has been conducted in the last few decades on analyzing microbial communities for their genomic organization, enzymatic and biochemical properties capable of degrading PAH. While it is true that PAH degrading microorganisms offer potential for recovering damaged ecosystems in a cost-efficient way, new advances are needed to make these microbes more robust and successful at eliminating toxic chemicals. By optimizing some factors like adsorption, bioavailability and mass transfer of PAHs, microorganisms in their natural habitat could be greatly improved to biodegrade PAHs. This review aims to comprehensively discuss the latest findings and address the current wealth of knowledge in the microbial bioremediation of PAHs. Additionally, recent breakthroughs in PAH degradation are discussed in order to facilitate a broader understanding of the bioremediation of PAHs in the environment.

Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach

BACKGROUND

Polycyclic aromatic hydrocarbon (PAH) contamination has been a worldwide environmental issue because of its impact on ecosystems and human health. Biodegradation plays an important role in PAH removal in natural environments. To date, many PAH-degrading strains and degradation genes have been reported. However, a comprehensive PAH-degrading gene database is still lacking, hindering a deep understanding of PAH degraders in the era of big data. Furthermore, the relationships between the PAH-catabolic genotype and phenotype remain unclear.

RESULTS

Here, we established a bacterial PAH-degrading gene database and explored PAH biodegradation capability via a genome-function relationship approach. The investigation of functional genes in the experimentally verified PAH degraders indicated that genes encoding hydratase-aldolase could serve as a biomarker for preliminarily identifying potential degraders. Additionally, a genome-centric interpretation of PAH-degrading genes was performed in the public genome database, demonstrating that they were ubiquitous in Proteobacteria and Actinobacteria. Meanwhile, the global phylogenetic distribution was generally consistent with the culture-based evidence. Notably, a few strains affiliated with the genera without any previously known PAH degraders (Hyphomonas, Hoeflea, Henriciella, Saccharomonospora, Sciscionella, Tepidiphilus, and Xenophilus) also bore a complete PAH-catabolic gene cluster, implying their potential of PAH biodegradation. Moreover, a random forest analysis was applied to predict the PAH-degrading trait in the complete genome database, revealing 28 newly predicted PAH degraders, of which nine strains encoded a complete PAH-catabolic pathway.

CONCLUSIONS

Our results established a comprehensive PAH-degrading gene database and a genome-function relationship approach, which revealed several potential novel PAH-degrader lineages. Importantly, this genome-centric and function-oriented approach can overcome the bottleneck of conventional cultivation-based biodegradation research and substantially expand our current knowledge on the potential degraders of environmental pollutants.

Characterizations of highly efficient moderately halophilic toluene degrading exiguobacterium mexicanum M7 strain isolated from Egyptian saline sediments

Toluene and other monoaromatic compounds are released into the environment particularly saline habitats due to the inappropriate disposal methods of petroleum products. Studying the bio-removal strategy is required to clean up these hazardous hydrocarbons that threaten all ecosystem life using halophilic bacteria with higher biodegradation efficiency of monoaromatic compounds as a sole carbon and energy source. Therefore, sixteen pure halophilic bacterial isolates were obtained from saline soil of Wadi An Natrun, Egypt, which have the ability to degrade toluene and consume it as the only source of carbon and energy. Amongst these isolates, isolate M7 exhibited the best growth with considerable properties. This isolate was selected as the most potent strain and identified based on phenotypic and genotypic characterizations. The strain M7 was belonging to Exiguobacterium genus and founded to be closely matched to the Exiguobacterium mexicanum with a similarity of 99%. Using toluene as sole carbon source, strain M7 showed good growth at a wide range temperature degree (20-40ºC), pH (5-9), and salt concentrations (2.5-10%, w/v) with optimal growth conditions at 35ºC, pH 8, and 5%, respectively. The biodegradation ratio of toluene was estimated at above optimal conditions and analyzed using Purge-Trap GC-MS. The results showed that strain M7 has the potentiality to degraded 88.32% of toluene within greatly short time (48 h). The current study findings support the potential ability to use strain M7 as a biotechnological tool in many applications such as effluent treatment and toluene waste management.

Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.

Negative correlations between cultivable and active-yet-uncultivable pyrene degraders explain the postponed bioaugmentation

Bioaugmentation is an effective approach to remediate soils contaminated by polycyclic aromatic hydrocarbons (PAHs), but suffers from unsatisfactory performance in engineering practices, which is hypothetically explained by the complicated interactions between indigenous microbes and introduced degraders. This study isolated a cultivable pyrene degrader (Sphingomonas sp. YT1005) and an active pyrene degrading consortium (Gp16, Streptomyces, Pseudonocardia, Panacagrimonas, Methylotenera and Nitrospira) by magnetic-nanoparticle mediated isolation (MMI) from soils. Pyrene biodegradation was postponed in bioaugmentation with Sphingomonas sp. YT1005, whilst increased by 30.17% by the active pyrene degrading consortium. Pyrene dioxygenase encoding genes (nidA, nidA3 and PAH-RHDα-GP) were enriched in MMI isolates and positively correlated with pyrene degradation efficiency. Pyrene degradation by Sphingomonas sp. YT1005 only followed the phthalate pathway, whereas both phthalate and salicylate pathways were observed in the active pyrene degrading consortium. The results indicated that the uncultivable pyrene degraders were suitable for bioaugmentation, rather than cultivable Sphingomonas sp. YT1005. The negative correlations between Sphingomonas sp. YT1005 and the active-yet-uncultivable pyrene degraders were the underlying mechanisms of bioaugmentation postpone in engineering practices.

A thermophile Hydrogenibacillus sp. strain efficiently degrades environmental pollutants polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants threatening ecosystems and human health. Here, we isolated and characterized a new strain, Hydrogenibacillus sp. N12, which is a thermophilic PAH-degrader. Strain N12 utilizes naphthalene as a sole carbon and energy source above 60°C and co-metabolizes many other PAHs as well. The metabolites were identified in the catabolism of naphthalene by gas chromatography-mass spectrometry (GC-MS) and stable isotopic analysis. Based on the identified metabolites, we proposed two possible metabolic pathways, one via salicylic acid and the other via phthalic acid. Whole-genome sequencing reveals that strain N12 possesses a small chromosome of 2.6 Mb. Combining genetic and transcriptional information, we reveal a new gene cluster for the naphthalene degradation. The genes, designated as narAaAb that are predicted to encode the alpha and beta subunits of naphthalene dioxygenase, were subsequently subcloned into Escherichia coli and the enzyme activity was detected by whole-cell transformation. Capacity to degrade several other tricyclic-PAHs was also characterized, suggesting co-existence of other constitutively expressed enzyme systems in strain N12 in addition to the naphthalene degradation gene cluster. Our study provides insights into the potential of the thermophilic PAH-degrader in biotechnology and environmental management applications.

A review on the enzymes and metabolites identified by mass spectrometry from bacteria and microalgae involved in the degradation of high molecular weight PAHs

High molecular weight PAHs (HMW PAHs) are dangerous pollutants widely distributed in the environment. The use of microorganisms represents an important tool for HMW PAHs bioremediation, so, the understanding of their biochemical pathways facilitates the development of biodegradation strategies. For this reason, the potential role of species of microalgae, bacteria, and microalga-bacteria consortia in the degradation of HMW PAHs is discussed. The identification of their metabolites, mostly by GC-MS and LC-MS, allows a better approach to the enzymes involved in the key steps of the metabolic pathways of HMW PAHs biodegradation. So, this review intends to address the proteomic research on enzyme activities and their involvement in regulating essential biochemical functions that help bacteria and microalgae in the biodegradation processes of HMW PAHs. It is noteworthy that, given that to the best of our knowledge, this is the first review focused on the mass spectrometry identification of the HMW PAHs metabolites; whereby and due to the great concern of the presence of HMW PAHs in the environment, this material could help the urgency of developing new bioremediation methods. The elucidation of the metabolic pathways of persistent pollutant degrading microorganisms should lead to a better knowledge of the enzymes involved, which could contribute to a very ecological route to the control of environmental contamination in the future.

Overview of Approaches to Improve Rhizoremediation of Petroleum Hydrocarbon-Contaminated Soils

Soil contamination with petroleum hydrocarbons (PHCs) has become a global concern and has resulted from the intensification of industrial activities. This has created a serious environmental issue; therefore, there is a need to find solutions, including application of efficient remediation technologies or improvement of current techniques. Rhizoremediation is a green technology that has received global attention as a cost-effective and possibly efficient remediation technique for PHC-polluted soil. Rhizoremediation refers to the use of plants and their associated microbiota to clean up contaminated soils, where plant roots stimulate soil microbes to mineralize organic contaminants to H2O and CO2. However, this multipartite interaction is complicated because many biotic and abiotic factors can influence microbial processes in the soil, making the efficiency of rhizoremediation unpredictable. This review reports the current knowledge of rhizoremediation approaches that can accelerate the remediation of PHC-contaminated soil. Recent approaches discussed in this review include (1) selecting plants with desired characteristics suitable for rhizoremediation; (2) exploiting and manipulating the plant microbiome by using inoculants containing plant growth-promoting rhizobacteria (PGPR) or hydrocarbon-degrading microbes, or a combination of both types of organisms; (3) enhancing the understanding of how the host–plant assembles a beneficial microbiome, and how it functions, under pollutant stress. A better understanding of plant–microbiome interactions could lead to successful use of rhizoremediation for PHC-contaminated soil in the future.

Colonization and performance of a pyrene-degrading bacterium Mycolicibacterium sp. Pyr9 on root surfaces of white clover

Some rhizosphere bacteria could colonize on the root surface of plants, or even form biofilm to promote plant growth, enhance plant resistance to harsh external environments and block the soil contamination. In this study, to explore the effects of pyrene-degrading bacterium on root surface on plant uptake of pyrene, a pyrene-degrading bacterium Mycolicibacterium sp. Pyr9 was isolated from the root surface of Eleusine indica L. Gaertn. in PAH-contaminated fields; after antibiotic labeling, it was colonized onto the root surface of white clover (Trifolium repens L.), and its distribution and performance were monitored under different levels of pyrene contamination. Strain Pyr9 could degrade 98% of pyrene (with an initial concentration of 50 mg L^-1) in culture solution within 8 d; it also owns a variety of plant growth promoting characteristics and appreciable tolerance to harsh environments. The transcription of pyrene catabolic genes in Pyr9 enhanced obviously when induced by pyrene. Pyr9 colonized and grew well on the root surface of white clover via root inoculation; some cells could even enter into the root tissues and move to the shoots. Compared with the Pyr9-free treatment, the pyrene contents in the roots and shoots of Pyr9-inoculated white clover decreased by 25%-30% and 33%-42%, respectively. Correspondingly, the pyrene accumulation and translocation factors in white clover decreased as well. These results indicate that Pyr9 would be a good potential to circumvent plant pyrene pollution. This research may provide a theoretical basis and technical support for the safety of agricultural products and human health in PAH-contaminated sites.

Hydroxylation at Multiple Positions Initiated the Biodegradation of Indeno[1,2,3-cd]Pyrene in Rhodococcus aetherivorans IcdP1

Nowadays, contamination by polycyclic aromatic hydrocarbons (PAHs) has become a serious problem all over the world; in particular, high-molecular-weight PAHs (HWM PAHs, four to seven rings) are more harmful to human health and environment due to their more complex structure and metabolic pathway. Biodegradation of PAHs with six or more rings, such as indeno[1,2,3-cd]pyrene (IcdP), was rarely described. An IcdP-degrading strain, Rhodococcus aetherivorans IcdP1, was isolated from HWM PAH-contaminated soil. It could grow on and efficiently degrade various HWM PAHs, such as IcdP, benzo[a]pyrene, and benzo[j]fluoranthene. It showed highest degrading ability toward IcdP (> 70% within 10 days). The IcdP degradation was initiated by ring hydroxylation with multiple pathways, including the hydroxylation at the 1,2 and 7,8 positions, according to the relevant metabolites detected, e.g., cyclopenta[cd]pyrene-3,4-dicarboxylic acid and 2,3-dimethoxy-2,3-dihydrofluoranthene. The transcriptional patterns of the genes encoding ring-hydroxylating oxygenases (RHOs) and cytochrome P450 monooxygenases (CYP450s) under the induction of IcdP, pyrene, and benzo[b]fluoranthene (BbF) were compared to determine the key initial RHOs in the conversion of IcdP. The expression of genes encoding RHOs 1892-1894, 1917-1920, and 4740-4741 was induced strictly by IcdP, and the amino acid sequences of these proteins showed very low identities with their homologs. These results suggested that IcdP was degraded through a dioxygenation-initiated metabolism pattern, and RHOs 1892-1894, 1917-1920, and 4740-4741 responded to the initial ring cleavage of IcdP through 1,2-dihydrodiol or 7,8-dihydrodiol. The studies would contribute to the understanding of the molecular mechanism of initial degradation of IcdP.

Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches

Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.

iTRAQ-Based Comparative Proteomic Analysis of Acinetobacter baylyi ADP1 Under DNA Damage in Relation to Different Carbon Sources

DNA damage response allows microorganisms to repair or bypass DNA damage and maintain the genome integrity. It has attracted increasing attention but the underlying influential factors affecting DNA damage response are still unclear. In this work, isobaric tags for relative and absolute quantification (iTRAQ)-based proteomic analysis was used to investigate the influence of carbon sources on the translational response of Acinetobacter baylyi ADP1 to DNA damage. After cultivating in a nutrient-rich medium (LB) and defined media supplemented with four different carbon sources (acetate, citrate, pyruvate, and succinate), a total of 2807 proteins were identified. Among them, 84 proteins involved in stress response were significantly altered, indicating the strong influence of carbon source on the response of A. baylyi ADP1 to DNA damage and other stresses. As the first study on the comparative global proteomic changes in A. baylyi ADP1 under DNA damage across nutritional environments, our findings revealed that DNA damage response in A. baylyi ADP1 at the translational level is significantly altered by carbon source, providing an insight into the complex protein interactions across carbon sources and offering theoretical clues for further study to elucidate their general regulatory mechanism to adapt to different nutrient environments.

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.

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.

Low molecular weight organic acids enhance the high molecular weight polycyclic aromatic hydrocarbons degradation by bacteria

The biodegradation potential of three bacterial cultures isolated from the rhizosphere of maize (Zea mays) and Sudan grass (Sorghum sudanense) grown in PAHs contaminated soils to degrade benzo[a]pyrene (BaP) and pyrene (PYR) was assessed. Of the three bacterial cultures isolated, two belonged to Gram-positive bacteria of phylum Actinobacteria namely Arthrobacter sp. MAL3 and Microbacterium sp. MAL2. The Gram-negative bacterial culture was Stenotrophomonas sp. MAL1, from the phylum Proteobacteria. The cultures were grown in the presence of BaP and PYR as sole carbon sources and with the addition of low molecular weight organic acids (LMWOAs) mixture. After 10-14 days of exposure, all the bacterial isolates exhibited a complete degradation of PYR with the addition of LMWOAs mixture, whereas only 38.7% of BaP was degraded by Stenotrophomonas sp. MAL1 with the addition of LMWOAs mixture. In addition, enhanced PAHs biodegradation by bacterial culture was observed when the PAHs present as mixture (BaP + PYR) with the addition of LMWOAs. Dioxygenase genes were detected in Stenotrophomonas sp. MAL1 (phnAC), and Arthrobacter sp. MAL3 (nidA and PAH-RHDα). Therefore, this study provides new insights on the influence of LMWOAs in enhancing the degradation of high molecular weight (HMW) PAHs in soil by rhizosphere bacterial cultures.

Contribution of the Kodama and 4S pathways to the dibenzothiophene biodegradation in different coastal wetlands under different C/N ratios

Dibenzothiophene (DBT) degradation mechanisms and the transformation of pathways during the incubation of three types of coastal sediments with C/N ratios ranging from 1 to 9 were investigated. The DBT degradation efficiencies were clearly improved with increasing C/N ratio in reed wetland sediments, tidal wetlands sediments and estuary wetland sediments. The quantitative response relationships between DBT degradation rates and related functional genes demonstrate that the Kodama pathway-related gene groups were dominant factors at low C/N ratios, while the 4S-related gene groups mainly determined the degradation rate when the C/N ratio was up to 5. Network analysis also shows that the pathway shifts from the Kodama pathway to the 4S pathway occurred through changes in the connections between functional genomes and rates. Furthermore, there were competition and collaboration between the Kodama and 4S pathways. The 4S pathway-related bacteria were more active in estuary wetland sediments compared with reed wetland sediments and tidal wetland sediments. The higher degradation efficiency in estuary wetland sediments may indicate the greater participation of the 4S pathway in the DBT biodegradation reaction. And the effects of ring cleavage of Kodama pathway caused more complete metabolizing of DBT.

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.

Mutation of Phenylalanine-223 to Leucine Enhances Transformation of Benzo[a]pyrene by Ring-Hydroxylating Dioxygenase of Sphingobium sp. FB3 by increasing Accessibility of the Catalytic Site

Burning of agricultural biomass generates polycyclic aromatic hydrocarbons (PAHs) including the carcinogen benzo[a]pyrene, of which the catabolism is primarily initiated by a ring-hydroxylating dioxygenase (RHD). This study explores catalytic site accessibility and its role in preferential catabolism of some PAHs over others. The genes flnA1f, flnA2f, flnA3, and flnA4, encoding the oxygenase α and β subunits, ferredoxin, and ferredoxin reductase, respectively, of the RHD enzyme complex (FlnA) were cloned from Sphingobium sp. FB3 and coexpressed in E. coli BL21. The FlnA effectively transformed fluoranthene but not benzo[a]pyrene. Substitution of the bulky phenylalanine-223 by leucine reduces the steric constraint in the substrate entrance to make the catalytic site of FlnA more accessible to large substrates, as visualized by 3D modeling, and allows the FlnA mutant to efficiently transform benzo[a]pyrene. Accessibility of the catalytic site to PAHs is a mechanism of RHD substrate specificity. The results shed light on why some PAHs are more recalcitrant than others.

Assessment of biodegradation potential at a site contaminated by a mixture of BTEX, chlorinated pollutants and pharmaceuticals using passive sampling methods - Case study

The present study describes a pilot remediation test of a co-mingled plume containing BTEX, chlorinated pollutants and pharmaceuticals. Remediation was attempted using a combination of various approaches, including a pump and treat system applying an advanced oxidation process and targeted direct push injections of calcium peroxide. The remediation process was monitored intensively and extensively throughout the pilot test using various conventional and passive sampling methods, including next-generation amplicon sequencing. The results showed that the injection of oxygen-saturated treated water with residual hydrogen peroxide and elevated temperature enhanced the in situ removal of monoaromatics and chlorinated pollutants. In particular, in combination with the injection of calcium peroxide, the conditions facilitated the in situ bacterial biodegradation of the pollutants. The mean groundwater concentration of benzene decreased from 1349μg·L^-1 prior to the test to 3μg·L^-1 within 3months after the calcium peroxide injections; additionally, monochlorobenzene decreased from 1545μg·L^-1 to 36μg·L^-1, and toluene decreased from 143μg·L^-1 to 2μg·L^-1. Furthermore, significant degradation of the contaminants bound to the soil matrix in less permeable zones was observed. Based on a developed 3D model, 90% of toluene and 88% of chlorobenzene bound to the soil were removed during the pilot test, and benzene was removed almost completely. On the other hand, the psychopharmaceuticals were effectively removed by the employed advanced oxidation process only from the treated water, and their concentration in groundwater remained stagnant due to inflow from the surroundings and their absence of in situ degradation. The employment of passive sampling techniques, including passive diffusion bags (PDB) for volatile organic pollutants and their respective transformation products, polar organic compound integrative samplers (POCIS) for the pharmaceuticals and in situ soil microcosms for microbial community analysis, was proven to be suitable for monitoring remediation in saturated zones.

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.

Insights in the regulation of the degradation of PAHs in Novosphingobium sp. HR1a and utilization of this regulatory system as a tool for the detection of PAHs

Novosphingobium sp. HR1a is able to grow using diverse polycyclic aromatic hydrocarbons (PAHs) as the sole carbon sources. We have identified two transposons that contain genes encoding several ring-hydroxylating dioxygenases and we have demonstrated the crucial role of one of these dioxygenases in the PAH metabolism in this strain; a mutant in the large subunit of this dioxygenase was unable to growth with 2-, 3-, or 4-rings aromatic hydrocarbons. Using a construction of lacZ gene fused with the pathway promoter, we determined that the expression of the dioxygenase gene was specifically induced in the presence of some PAHs and intermediates of their metabolic pathway. In silico analysis of the ORFs within the transposons and construction of the corresponding knock-out mutants allowed us to identify the main regulatory protein involved in PAH degradation in Novosphingobium sp. HR1a. To our knowledge this is the first time that a regulatory protein controlling the degradation pathway of high-molecular weight PAHs has been investigated. A deeper knowledge of the regulatory circuits that control the expression of PAH degradation has allowed us to design two biosensors for monitoring environments contaminated with oil-derived mixtures. Novosphingobium sp. HR1a (pKSR-1), the biosensor based on the promoter of the regulatory protein PahR, was more sensitive and faster in the detection of aromatic contaminants in environmental samples than Novosphingobium sp. HR1a (pKSA-1), the biosensor that is based on the PAHs-dioxygenase promoter (P_pahA). Novosphingobium sp. HR1a (pKSR-1) was able to detect PAHs in the range of μgl^-1 (ppb).

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.

Biodegradation of high concentrations of mixed polycyclic aromatic hydrocarbons by indigenous bacteria from a river sediment: a microcosm study and bacterial community analysis

This study assessed the biodegradation of mixtures of polycyclic aromatic hydrocarbons (PAHs) by indigenous bacteria in river sediment. Microcosms were constructed from sediment from the Chao Phraya River (the main river in Thailand) by supplementation with high concentrations of fluorene, phenanthrene, pyrene (300 mg kg^-1 of each PAH), and acenaphthene (600 mg kg^-1). Fluorene and phenanthrene were completely degraded, whereas 50% of the pyrene and acenaphthene were removed at the end of the incubation period (70 days). Community analyses revealed the dynamics of the bacterial profiles in the PAH-degrading microcosms after PAH exposure. Actinobacteria predominated and became significantly more abundant in the microcosms after 14 days of incubation at room temperature under aerobic conditions. Furthermore, the remaining PAHs and alpha diversity were positively correlated. The sequencing of clone libraries of the PAH-RHDα genes also revealed that the dioxygenase genes of Mycobacterium sp. comprised 100% of the PAH-RHDα library at the end of the microcosm setup. Moreover, two PAH-degrading Actinobacteria (Arthrobacter sp. and Rhodococcus ruber) were isolated from the original sediment sample and showed high activity in the degradation of phenanthrene and fluorene in liquid cultivation. This study reveals that indigenous bacteria had the ability to degrade high concentrations of mixed PAHs and provide clear evidence that Actinobacteria may be potential candidates to play a major role in PAH degradation in the river sediment.

Insight of Proteomics and Genomics in Environmental Bioremediation

Bioremediation of hazardous substances from environment is a major human and environmental health concern but can be managed by the microorganism due to their variety of properties that can effectively change the complexity. Microorganisms convey endogenous genetic, biochemical and physiological assets that make them superlative proxies for pollutant remediation in habitat. But, the crucial step is to degrade the complex ring structured pollutants. Interestingly, the integration of genomics and proteomics technologies that allow us to use or alter the genes and proteins of interest in a given microorganism towards a cell-free bioremediation approach. Resultantly, efforts have been finished by developing the genetically modified (Gm) microbes for the remediation of ecological contaminants. Gm microorganisms mediated bioremediation can affect the solubility, bioavailability and mobility of complex hazardous.

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.

Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants

Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today's scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.

Kinetics of nutrient enhanced crude oil degradation by Pseudomonas aeruginosa AKS1 and Bacillus sp. AKS2 isolated from Guwahati refinery, India

Bacterial degradation of crude oil in response to nutrient treatments has been vastly studied. But there is a paucity of information on kinetic parameters of crude oil degradation. Here we report the nutrient stimulated kinetic parameters of crude oil degradation assessed in terms of CO2 production and oil removal by Pseudomonas aeruginosa AKS1 and Bacillus sp. AKS2. The hydrocarbon degradation rate of P. aeruginosa AKS1 in oil only amended sediment was 10.75 ± 0.65 μg CO2-C g(-1) sediment day(-1) which was similar to degradation rate in sediments with no oil. In presence of both inorganic N & P, the degradation rate increased to 47.22 ± 1.32 μg CO2-C g(-1) sediment day(-1). The half-saturation constant (Ks) and maximum degradation rate (Vmax) for P. aeruginosa AKS1 under increasing N and saturating P concentration were 13.57 ± 0.53 μg N g(-1) sediment and 39.36 ± 1.42 μg CO2-C g(-1) sediment day(-1) respectively. The corresponding values at increasing P and a constant N concentration were 1.60 ± 0.13 μg P g(-1) sediment and 43.90 ± 1.03 μg CO2-C g(-1) sediment day(-1) respectively. Similarly the degradation rate of Bacillus sp. AKS2 in sediments amended with both inorganic nutrients N & P was seven fold higher than the rates in oil only or nutrient only treated sediments. The Ks and Vmax estimates of Bacillus sp. AKS2 under increasing N and saturating P concentration were 9.96 ± 1.25 μg N g(-1) sediment and 59.96 ± 7.56 μg CO2-C g(-1) sediment day(-1) respectively. The corresponding values for P at saturating N concentration were 0.46 ± 0.24 μg P g(-1) sediment and 63.63 ± 3.54 μg CO2-C g(-1) sediment day(-1) respectively. The rates of CO2 production by both isolates were further stimulated when oil concentration was increased above 12.5 mg g(-1) sediment. However, oil degradation activity declined at oil concentration above 40 mg g(-1) sediment when treated with constant nutrient: oil ratio. Both isolates exhibited alkane hydroxylase activity but aromatic degrading catechol 1, 2-dioxygenase and catechol 2, 3-dioxygenase activities were shown by P. aeruginosa AKS1 only.

Simultaneous Biodegradation of Polyaromatic Hydrocarbons by a Stenotrophomonas sp: Characterization of nid Genes and Effect of Surfactants on Degradation

A polyaromatic hydrocarbon degrading bacterium was isolated from a petroleum contaminated site and designated as Stenotrophomonas sp. strain IITR87. It was found to utilize pyrene, phenanthrene and benzo(a)pyrene as sole carbon source, but not anthracene, chrysene and fluoranthene. Gas chromatography and mass spectroscopy analysis resulted in identification of pyrene metabolites namely monohydroxypyrene, 4-oxa-pyrene-5-one, dimethoxypyrene and monohydroxyphenanthrene. Southern hybridization using naphthalene dioxygenase gene (nidA) as probe against the DNA of strain IITR87 revealed the presence of nidA gene. PCR analysis suggests dispersed occurrence of nid genes in the genome instead of a cluster as reported in a PAH-degrading Mycobacterium vanbaalenii PYR-1. The nid genes in strain IITR87, dioxygenase large subunit (nidA), naphthalene dioxygenase small subunit (nidB) and aldehyde dehydrogenase gene (nidD) showed more than 97 % identity to the reported nid genes from Mycobacterium vanbaalenii PYR-1. Most significantly, the biodegradation of PAHs was enhanced 25-60 % in the presence of surfactants rhamnolipid and Triton X-100 due to increased solubilization and bioavailability. These results could be useful for the improved biodegradation of high-molecular-weight PAHs in contaminated habitats.

Effects of Polycyclic Aromatic Hydrocarbon Mixtures on Degradation, Gene Expression, and Metabolite Production in Four Mycobacterium Species

Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental contaminants that are hazardous to human health. It has been demonstrated that members of the Mycobacterium genus are among the most effective degraders of PAHs, but few studies have focused on the degradation of PAH mixtures. In this study, single and mixed PAH metabolism was investigated in four phylogenetically distinct Mycobacterium species with respect to (i) parent compound degradation, (ii) bacterial growth, (iii) catabolic gene expression, and (iv) metabolite production. Synergistic and antagonistic effects on four model PAH compounds (benzo[a]pyrene, pyrene, fluoranthene, and phenanthrene) characterized degradation of mixtures in a strain- and mixture-dependent manner. The mixture of pyrene and phenanthrene, in particular, resulted in antagonized degradation by three out of four bacterial species, and further studies were narrowed to investigate the degradation of this mixture. Antagonistic effects persisted over time and were correlated with reduced bacterial growth. Antagonized degradation of PAH was not caused by preferential degradation of secondary PAHs, nor were mixture compounds or concentrations toxic to cells growing on sugars. Reverse transcription-PCR (RT-PCR) studies of the characterized catabolic pathway of phenanthrene showed that in one organism, antagonism of mixture degradation was associated with downregulated gene expression. Metabolite profiling revealed that antagonism in mixture degradation was associated with the shunting of substrate through alternative pathways not used during the degradation of single PAHs. The results of this study demonstrate metabolic differences between single and mixed PAH degradation with consequences for risk assessment and bioremediation of PAH-contaminated sites.

IMPORTANCE

Mycobacterium species are promising organisms for environmental bioremediation because of their ubiquitous presence in soils and their ability to catabolize aromatic compounds. PAHs can be degraded effectively as single compounds, but mixed substrates often are subject to degradative inhibition, which may explain the persistence of these pollutants in soils. Single and mixed PAH degradation by diverse Mycobacterium species was compared, with associated bacterial growth, gene expression, and metabolite production. The results demonstrate that antagonism characterized degradation in a strain- and mixture-dependent manner. One strain that was versatile in its pathway use of single chemicals also efficiently degraded the mixture, whereas antagonism in other the strains was associated with altered metabolic profiles, indicating unusual pathway use. The impacts of this work on risk assessment and bioremediation modeling studies indicate the need to account for mixture-generated intermediates and to recognize mixture degradation as a property distinct from that of PAH substrate range.

Direct evidences on bacterial growth pattern regulating pyrene degradation pathway and genotypic dioxygenase expression

Pyrene degradation by Mycobacterium sp. strain A1-PYR was investigated in the presence of nutrient broth, phenanthrene and fluoranthene, respectively. Fast bacterial growth in the nutrient broth considerably enhanced pyrene degradation rate, whereas degradation efficiency per cell was substantially decreased. The addition of nutrient broth could not alter the transcription levels of all dioxygenase genotypes. In the PAH-only substrates, bacterial growth completely relied on biological conversion of PAHs into the effective carbon sources, which led to a higher degradation efficiency of pyrene per cell than the case of nutrient broth. Significant correlations were only observed between nidA-related dioxygenase expression and pyrene degradation or bacterial growth. The highest pyrene degradation rate in the presence of phenanthrene was consistent with the highest transcription level of nidA and 4,5-pyrenediol as the sole initial metabolite. This study reveals that bacterial growth requirement can invigorate degradation of PAHs by regulating metabolic pathway and genotypic enzyme expression.

PbaR, an IclR family transcriptional activator for the regulation of the 3-phenoxybenzoate 1',2'-dioxygenase gene cluster in Sphingobium wenxiniae JZ-1T

The 3-phenoxybenzoate (3-PBA) 1',2'-dioxygenase gene cluster (pbaA1A2B cluster), which is responsible for catalyzing 3-phenoxybenzoate to 3-hydroxybenzoate and catechol, is inducibly expressed in Sphingobium wenxiniae strain JZ-1(T) by its substrate 3-PBA. In this study, we identified a transcriptional activator of the pbaA1A2B cluster, PbaR, using a DNA affinity approach. PbaR is a 253-amino-acid protein with a molecular mass of 28,000 Da. PbaR belongs to the IclR family of transcriptional regulators and shows 99% identity to a putative transcriptional regulator that is located on the carbazole-degrading plasmid pCAR3 in Sphingomonas sp. strain KA1. Gene disruption and complementation showed that PbaR was essential for transcription of the pbaA1A2B cluster in response to 3-PBA in strain JZ-1(T). However, PbaR does not regulate the reductase component gene pbaC. An electrophoretic mobility shift assay and DNase I footprinting showed that PbaR binds specifically to the 29-bp motif AATAGAAAGTCTGCCGTACGGCTATTTTT in the pbaA1A2B promoter area and that the palindromic sequence (GCCGTACGGC) within the motif is essential for PbaR binding. The binding site was located between the -10 box and the ribosome-binding site (downstream of the transcriptional start site), which is distinct from the location of the binding site in previously reported IclR family transcriptional regulators. This study reveals the regulatory mechanism for 3-PBA degradation in strain JZ-1(T), and the identification of PbaR increases the variety of regulatory models in the IclR family of transcriptional regulators.

Genetic determinants involved in the biodegradation of naphthalene and phenanthrene in Pseudomonas aeruginosa PAO1

Pseudomonas sp. are predominant isolates of degradation-competent strains while very few studies have explored the degradation-related genes and pathways in most of the degrading strains. P. aeruginosa PAO1 was found capable of degrading naphthalene and phenanthrene efficiently. In order to investigate the degradation-related genes of naphthalene and phenanthrene in P. aeruginosa PAO1, a random promoter library of about 5760 strains was constructed. Thirty-two clones for differentially expressed promoters were obtained by screening in the presence of sub-inhibitory concentration of naphthalene and phenanthrene. Among them, 13 genes were up-regulated and 15 were down-regulated in the presence of naphthalene as well as phenanthrene. The four remaining genes have different regulation tendencies by naphthalene or phenanthrene. By comparing the growth between the wild type and mutants as well as the complementations, the roles of seven selected up-regulated genes on naphthalene and phenanthrene degradation were investigated. Five of the seven selected up-regulated genes, like PA2666 and PA4780, were found playing key roles on the degradation in P. aeruginosa PAO1. Also, the results imply that these genes participate in the overlapping part of naphthalene and phenanthrene degradation pathways in PAO1. Results in the article offer the convenience quick method and platform for searching degradation-related genes. It also laid a foundation for understanding of the role of the regulated genes.

Dynamic Response of Mycobacterium vanbaalenii PYR-1 to BP Deepwater Horizon Crude Oil

We investigated the response of the hydrocarbon-degrading Mycobacterium vanbaalenii PYR-1 to crude oil from the BP Deepwater Horizon (DWH) spill, using substrate depletion, genomic, and proteome analyses. M. vanbaalenii PYR-1 cultures were incubated with BP DWH crude oil, and proteomes and degradation of alkanes and polycyclic aromatic hydrocarbons (PAHs) were analyzed at four time points over 30 days. Gas chromatography-mass spectrometry (GC-MS) analysis showed a chain length-dependent pattern of alkane degradation, with C12 and C13 being degraded at the highest rate, although alkanes up to C28 were degraded. Whereas phenanthrene and pyrene were completely degraded, a significantly smaller amount of fluoranthene was degraded. Proteome analysis identified 3,948 proteins, with 876 and 1,859 proteins up- and downregulated, respectively. We observed dynamic changes in protein expression during BP crude oil incubation, including transcriptional factors and transporters potentially involved in adaptation to crude oil. The proteome also provided a molecular basis for the metabolism of the aliphatic and aromatic hydrocarbon components in the BP DWH crude oil, which included upregulation of AlkB alkane hydroxylase and an expression pattern of PAH-metabolizing enzymes different from those in previous proteome expression studies of strain PYR-1 incubated with pure or mixed PAHs, particularly the ring-hydroxylating oxygenase (RHO) responsible for the initial oxidation of aromatic hydrocarbons. Based on these results, a comprehensive cellular response of M. vanbaalenii PYR-1 to BP crude oil was proposed. This study increases our fundamental understanding of the impact of crude oil on the cellular response of bacteria and provides data needed for development of practical bioremediation applications.

Diversity and distribution of actinobacterial aromatic ring oxygenase genes across contrasting soil properties

The diversity of a gene family encoding Actinobacterial aromatic ring oxygenases (AAROs) was detected by the PCR-cloning approach using a newly designed PCR primer set. The distribution of AAROs was investigated in 11 soils representing different land management and vegetation zones and was correlated with several geochemical parameters including pH, organic matter (OM), total Kjeldahl nitrogen (TKN), and nitrogen oxides (NO(x)-N: mostly NO3(-)-N). The distribution of individual clades encoding enzymes with potentially different substrates were correlated with different environmental factors, suggesting differential environmental controls on the distribution of specific enzymes as well as sequence diversity. For example, individual clades associated with phthalate dioxygenases were either strongly negatively correlated with pH, or not correlated with pH but showed strong positive correlation with organic carbon content. A large number of clones clustering in a clade related to PAH oxygenases were positively correlated with pH and nitrogen, but not with organic matter. This analysis may yield insight into the ecological forces driving the distribution of these catabolic genes.

Comparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium

Background

The bacterial genus Mycobacterium is of great interest in the medical and biotechnological fields. Despite a flood of genome sequencing and functional genomics data, significant gaps in knowledge between genome and phenome seriously hinder efforts toward the treatment of mycobacterial diseases and practical biotechnological applications. In this study, we propose the use of systematic, comparative functional pan-genomic analysis to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon (PAH) metabolism in the genus Mycobacterium.

Results

Phylogenetic, phenotypic, and genomic information for 27 completely genome-sequenced mycobacteria was systematically integrated to reconstruct a mycobacterial phenotype network (MPN) with a pan-genomic concept at a network level. In the MPN, mycobacterial phenotypes show typical scale-free relationships. PAH degradation is an isolated phenotype with the lowest connection degree, consistent with phylogenetic and environmental isolation of PAH degraders. A series of functional pan-genomic analyses provide conserved and unique types of genomic evidence for strong epistatic and pleiotropic impacts on evolutionary trajectories of the PAH-degrading phenotype. Under strong natural selection, the detailed gene gain/loss patterns from horizontal gene transfer (HGT)/deletion events hypothesize a plausible evolutionary path, an epistasis-based birth and pleiotropy-dependent death, for PAH metabolism in the genus Mycobacterium. This study generated a practical mycobacterial compendium of phenotypic and genomic changes, focusing on the PAH-degrading phenotype, with a pan-genomic perspective of the evolutionary events and the environmental challenges.

Conclusions

Our findings suggest that when selection acts on PAH metabolism, only a small fraction of possible trajectories is likely to be observed, owing mainly to a combination of the ambiguous phenotypic effects of PAHs and the corresponding pleiotropy- and epistasis-dependent evolutionary adaptation. Evolutionary constraints on the selection of trajectories, like those seen in PAH-degrading phenotypes, are likely to apply to the evolution of other phenotypes in the genus Mycobacterium.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-015-0302-8) contains supplementary material, which is available to authorized users.

Evident bacterial community changes but only slight degradation when polluted with pyrene in a red soil

Understanding the potential for Polycyclic aromatic hydrocarbons (PAH) degradation by indigenous microbiota and the influence of PAHs on native microbial communities is of great importance for bioremediation and ecological evaluation. Various studies have focused on the bacterial communities in the environment where obvious PAH degradation was observed, little is known about the microbiota in the soil where poor degradation was observed. Soil microcosms were constructed with a red soil by supplementation with a high-molecular-weight PAH (pyrene) at three dosages (5, 30, and 70 mg ⋅ kg(-1)). Real-time PCR was used to evaluate the changes in bacterial abundance and pyrene dioxygenase gene (nidA) quantity. Illumina sequencing was used to investigate changes in diversity, structure, and composition of bacterial communities. After 42 days of incubation, no evident degradation was observed. The poor degradation ability was associated with the stability or significant decrease of abundance of the nidA gene. Although the abundance of the bacterial 16S rRNA gene was not affected by pyrene, the bacterial richness and diversity were decreased with increasing dosage of pyrene and the community structure was changed. Phylotypes affected by pyrene were comprehensively surveyed: (1) at the high taxonomic level, seven of the abundant phyla/classes (relative abundance >1.0%) including Chloroflexi, AD3, WPS-2, GAL5, Alphaproteobacteria, Actinobacteria, and Deltaproteobacteria and one rare phylum Crenarchaeota were significantly decreased by at least one dosage of pyrene, while three phyla/classes (Acidobacteria, Betaproteobacteria, and Gammaproteobacteria) were significantly increased; and (2) at the lower taxonomic level, the relative abundances of twelve orders were significantly depressed, whereas those of nine orders were significantly increased. This work enhanced our understanding of the biodegradation potential of pyrene in red soil and the effect of pyrene on soil ecosystems at the microbial community level.

Metabolic engineering of Arabidopsis for remediation of different polycyclic aromatic hydrocarbons using a hybrid bacterial dioxygenase complex

The widespread presence of polycyclic aromatic hydrocarbons (PAHs) and their potential harm to various organisms has generated interest in efficiently eliminating these compounds from the environment. Phytoremediation is an efficient technology for cleaning up pollutants. However, unlike microorganisms, plants lack the catabolic pathway for complete degradation of these dangerous groups of compounds. One way to enhance the potential of plants for remediation of these compounds is by transferring genes involved in xenobiotic degradation from microbes to plants. In this paper, four genes, namely nidA and nidB (encoding the large and small subunits of naphthalene dioxygenase of Mycobacterium vanbaalenii PYR-1) as well as NahAa and NahAb (encoding flavoprotein reductase and ferredoxin of the electron-transport chain of the Pseudomonas putida G7 naphthalene dioxygenase system), were transferred and ectopically expressed in Arabidopsis thaliana. Transgenic Arabidopsis plants overexpressing the heterozygous naphthalene dioxygenase system exhibited enhanced tolerance toward 2-4 rings PAHs. Transgenic plants assimilated PAHs from the culture media faster and accumulated less in vivo than wild-type plants. Furthermore, examination of metabolic intermediates by gas chromatography-mass spectrometry revealed that the naphthalene metabolic pathway in transgenic plants mainly involves the dioxygenase pathway. Taken together, our findings suggest that grafting the naphthalene dioxygenase complex into plants is a possible strategy to breed PAH-tolerant plants to efficiently degrade PAHs in the environment.

Pleiotropic and epistatic behavior of a ring-hydroxylating oxygenase system in the polycyclic aromatic hydrocarbon metabolic network from Mycobacterium vanbaalenii PYR-1

Despite the considerable knowledge of bacterial high-molecular-weight (HMW) polycyclic aromatic hydrocarbon (PAH) metabolism, the key enzyme(s) and its pleiotropic and epistatic behavior(s) responsible for low-molecular-weight (LMW) PAHs in HMW PAH-metabolic networks remain poorly understood. In this study, a phenotype-based strategy, coupled with a spray plate method, selected a Mycobacterium vanbaalenii PYR-1 mutant (6G11) that degrades HMW PAHs but not LMW PAHs. Sequence analysis determined that the mutant was defective in pdoA2, encoding an aromatic ring-hydroxylating oxygenase (RHO). A series of metabolic comparisons using high-performance liquid chromatography (HPLC) analysis revealed that the mutant had a lower rate of degradation of fluorene, anthracene, and pyrene. Unlike the wild type, the mutant did not produce a color change in culture media containing fluorene, phenanthrene, and fluoranthene. An Escherichia coli expression experiment confirmed the ability of the Pdo system to oxidize biphenyl, the LMW PAHs naphthalene, phenanthrene, anthracene, and fluorene, and the HMW PAHs pyrene, fluoranthene, and benzo[a]pyrene, with the highest enzymatic activity directed toward three-ring PAHs. Structure analysis and PAH substrate docking simulations of the Pdo substrate-binding pocket rationalized the experimentally observed metabolic versatility on a molecular scale. Using information obtained in this study and from previous work, we constructed an RHO-centric functional map, allowing pleiotropic and epistatic enzymatic explanation of PAH metabolism. Taking the findings together, the Pdo system is an RHO system with the pleiotropic responsibility of LMW PAH-centric hydroxylation, and its epistatic functional contribution is also crucial for the metabolic quality and quantity of the PAH-MN.