Mycobacterium diversity and pyrene mineralization in petroleum-contaminated soils

Bioremediation of polycyclic aromatic hydrocarbons contaminated soils: recent progress, perspectives and challenges

The life of all creatures is supported directly or indirectly by soil, which is a significant environmental matrix. The soil has been polluted partly due to increased human activities and population growth, releasing several foreign substances and persistent contaminants. When toxic substances like polycyclic aromatic hydrocarbons (PAHs) are disposed of, the characteristics of the soil are changed, microbial biodiversity is impacted, and items are destroyed. Because of the mutagenicity, carcinogenicity, and toxicity of petroleum hydrocarbons, the restoration and cleanup of PAH-polluted areas represent a severe technological and environmental challenge for long-term growth and development. Although there are several ways to clean up PAH-contaminated soils, much attention is paid to intriguing bacteria, fungus, and their enzymes. Various factors influence PAH breakdown, including pH, temperature, airflow, moisture level, nutrient availability, and degrading microbial populations. This review discusses how PAHs affect soil characteristics and shows that secondary metabolite and carbon dioxide decomposition are produced due to microbial breakdown processes. Furthermore, the advantages of bioremediation strategies were assessed for correct evaluation and considered dependable on each legislative and scientific research level, as analyzed in this review.

Removal of organic and inorganic contaminants from the air, soil, and water by algae

Rapid increases in human populations and development has led to a significant exploitation of natural resources around the world. On the other hand, humans have come to terms with the consequences of their past mistakes and started to address current and future resource utilization challenges. Today's primary challenge is figuring out and implementing eco-friendly, inexpensive, and innovative solutions for conservation issues such as environmental pollution, carbon neutrality, and manufacturing effluent/wastewater treatment, along with xenobiotic contamination of the natural ecosystem. One of the most promising approaches to reduce the environmental contamination load is the utilization of algae for bioremediation. Owing to their significant biosorption capacity to deactivate hazardous chemicals, macro-/microalgae are among the primary microorganisms that can be utilized for phytoremediation as a safe method for curtailing environmental pollution. In recent years, the use of algae to overcome environmental problems has advanced technologically, such as through synthetic biology and high-throughput phenomics, which is increasing the likelihood of attaining sustainability. As the research progresses, there is a promise for a greener future and the preservation of healthy ecosystems by using algae. They might act as a valuable tool in creating new products.

Assessment of the impact of small-scale mining on soil contamination by mercury and hydrocarbons in the kadey catchment (East Cameroon)

The objective of the present study was to assess soil contamination by mercury and hydrocarbon products used in gold mining in the Kadey catchment area. The results obtained show that gold mining by the small mine is the cause of chemical contamination of the soil caused by hydrocarbon products with concentrations 800 times higher than the threshold value on certain points of the former mining sites. The use of mercury has led to an increase in its concentration to values that are still below the critical thresholds. It also appears from this work that organic matter plays a very important role in the retention of mercury on the soil surface. In the case of hydrocarbons are concerned, although high concentrations above are found exclusively at the surface, the rainfall contributes to their infiltration into the soil and to a horizontal redistribution of the contamination.

Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil

Iron and steel industries are the major contributors to persistent organic pollutants (POPs). The microbial community present at such sites has the potential to remediate these contaminants. The present study highlights the metabolic potential of the resident bacterial community of PAHs and PCB contaminated soil nearby Bhilai steel plant, Chhattisgarh (India). The GC-MS/MS analysis of soil samples MGB-2 (sludge) and MGB-3 (dry soil) resulted in identification of different classes of POPs including PAHs {benzo[a]anthracene (nd; 17.69%), fluorene (15.89%, nd), pyrene (nd; 18.7%), benzo(b)fluoranthene (3.03%, nd), benzo(k)fluoranthene (11.29%; nd), perylene (5.23%; nd)} and PCBs (PCB-15, PCB-95, and PCB-136). Whole-genome metagenomic analysis by Oxford Nanopore GridION Technology revealed predominance of domain bacteria (97.4%; 97.5%) followed by eukaryote (1.4%; 1.5%), archaea (1.2%; 0.9%) and virus (0.02%; 0.04%) in MGB-2 and MGB-3 respectively. Proteobacteria (44.3%; 50.0%) to be the prominent phylum followed by Actinobacteria (22.1%; 19.5%) in MBG-2 and MBG-3, respectively. However, Eukaryota microbial communities showed a predominance of phylum Ascomycota (20.5%; 23.6%), Streptophyta (18.5%, 17.0%) and unclassified (derived from Eukaryota) (12.1%; 12.2%) in MGB-2 and MGB-3. The sample MGB-3 was richer in macronutrients (C, N, P), supporting high microbial diversity than MGB-2. The presence of reads for biphenyl degradation, dioxin degradation, PAH degradation pathways can be further correlated with the presence of PCB and PAH as detected in the MGB-2 and MGB-3 samples. Further, taxonomic vis-à-vis functional analysis identified Burkholderia, Bradyrhizobium, Mycobacterium, and Rhodopseudomonas as the keystone degrader of PAH and PCB. Overall, our results revealed the importance of metagenomic and physicochemical analysis of the contaminated site, which improves the understanding of metabolic potential and adaptation of bacteria growing under POP contaminated environments.

Advances in research on petroleum biodegradability in soil

With the increased demand for petroleum and petroleum products from all parts of the society, environmental pollution caused by petroleum development and production processes is becoming increasingly serious. Soil pollution caused by petroleum seriously affects environmental quality in addition to human lives and productivity. At present, petroleum in soil is mainly degraded by biological methods. In their natural state, native bacteria in the soil spontaneously degrade petroleum pollutants that enter the soil; however, when the pollution levels increase, the degradation rates decrease, and it is necessary to add nutrients, dissolved oxygen, biosurfactants and other additives to improve the degradation ability of the native bacteria in the soil. The degradation process can also be enhanced by adding exogenous petroleum-degrading bacteria, microbial immobilization technologies, and microbial fuel cell technologies.

Bacterial diversity of the green turtle (Chelonia mydas) nest environment

The green turtle is an endangered species that is highly sensitive to environmental pollution that can adversely affect the healthy development of eggs. Moreover, the presence of some bacteria in nests can be regarded as an indicator of the pollution level in nesting areas. In our study, nest sand and egg contents were collected from Sugözü Beaches (Turkey), in the Mediterranean. Phenotypic and genotypic identification of bacteria were carried out by using conventional phenotypic methods, 16S rRNA gene sequencing respectively. The extended-spectrum beta-lactamase presence and carbapenem resistance of bacteria isolated from egg contents were determined. This is the first report of carbapenem resistance in the eggs. All strains were evaluated in three different categories including growth promoters in agriculture and aquaculture, pathogens that are found in human and animal, and biomonitoring aquatic pollution. According to our analysis, 67 bacterial species were identified from samples. This study is the first record of Alcaligenes, Zobellella, Lysinibacillus, Sphingobacterium, Achromobacter, Acinetobacter, Alcanivorax, Ochrobactrum, Microbacterium, Rhodococcus, and Stenotrophomonas isolated from sea turtles. Pathogens detected in the bacterial flora can threaten both sea turtles and field workers. These data can contribute to the development of new conservation strategies on the treatment of sea turtles, nest protection, and pollution detection on nesting beaches.

Bioaugmentation Treatment of a PAH-Polluted Soil in a Slurry Bioreactor

A bioslurry reactor was designed and used to treat loamy clay soil polluted with polycyclic aromatic hydrocarbons (PAHs). To this end, biostimulation alone, or combined with bioaugmentation with two bacterial strains (Rhodocccus erythropolis and Pseudomonas stuzeri) previously isolated from the polluted site, was applied. The PAH concentrations decreased notably after 15 days in all of the treatments. The concentrations of the two- and three-ring compounds fell by >80%, and, remarkably, the four- to six-ring PAHs also showed a marked decrease (>70%). These results thus indicate the capacity of bioslurry treatments to improve, notably, the degradation yields obtained in a previous real-scale remediation carried out using biopiles. In this sense, the remarkable results for recalcitrant PAHs can be attributed to the increase pollutants’ bioavailability achieves in the slurry bioreactors. Regarding bioaugmentation, although treatment with R. erythropolis led to a somewhat greater reduction of lighter PAHs at 15 days, the most time-effective treatment was achieved using P. stutzeri, which led to an 84% depletion of total PAHs in only three days. The effects of microbial degradation of other organic compounds were also monitored by means of combined qualitative and quantitative gas chromatography mass spectrometry (GC–MS) tools, as was the evolution of microbial populations, which was analyzed by culture and molecular fingerprinting experiments. On the basis of our findings, bioslurry technology emerges as a rapid and operative option for the remediation of polluted sites, especially for fine soil fractions with a high load of recalcitrant pollutants.

Nutrient drip irrigation for refractory hydrocarbon removal and microbial community shift in a historically petroleum-contaminated soil

An adequate amount of nutrients is required to enable biodegradation of refractory hydrocarbons in petroleum-contaminated soil. In this study, a microcosm experiment was conducted using a drip fertigation method for petroleum-contaminated soil remediation. Nitrogen and phosphorus were homogeneously and periodically sprayed into a historically contaminated soil using a modified horticultural drip irrigation device. Various petroleum hydrocarbon fraction contents were then determined by gravimetry and gas chromatography (GC), and changes in the soil microbial community were analyzed by high throughput sequencing. After 90 days of remediation, the removal efficiencies of total petroleum hydrocarbon (TPH), saturates, aromatics, C7-C30 n-alkanes, and 16 PAHs were respectively enhanced by 21.5%, 25.5%, 12.4%, 10.4%, and 19.6% compared with the use of a single nutrient amendment application. The high throughput sequencing result showed that obvious changes had occurred in the soil microbial community compositions during drip fertigation; however, fungi were more sensitive to drip fertigation than bacteria. The resulting predominant bacterial and fungal genera were Dietzia, Nocardioides, Mycobacterium, Sphaerobacter, Leifsonia, and Aspergillus, Scolecobasidium, and Fusarium, respectively. Remediating polluted soils by regular fertigation ensures the automatic addition of even amounts of nutrients, which achieves high refractory hydrocarbon removal efficiencies. It is expected that this method can be applied in the in-situ remediation of petroleum-contaminated soil on a large scale.

Methyl t-butyl ether-degrading bacteria for bioremediation and biocontrol purposes

A total of fifteen potential methyl t-butyl ether (MtBE)-degrading bacterial strains were isolated from contaminated soil. They have been identified as belonging to the genera Bacillus, Pseudomonas, Kocuria, Janibacter, Starkeya, Bosea, Mycolicibacterium, and Rhodovarius. Bacillus aryabhattai R1B, S. novella R8b, and M. mucogenicum R8i were able to grow using MtBE as carbon source, exhibiting different growth behavior and contaminant degradation ability. Their biocontrol ability was tested against various fungal pathogens. Both S. novella R8b and B. aryabhattai were effective in reducing the development of necrotic areas on leaves within 48 hours from Botritys cinerea and Alternaria alternata inoculation. Whereas, M. mucogenicum effectively controlled B. cinerea after 72 hours. Similar results were achieved using Pythium ultimum, in which the application of isolated bacteria increased seed germination. Only M. mucogenicum elicited tomato plants resistance against B. cinerea. This is the first report describing the occurrence of bioremediation and biocontrol activities in M. mucogenicum, B. aryabhattai and S. novella species. The production of maculosin and its antibiotic activity against Rhizoctonia solani has been reported for first time from S. novella. Our results highlight the importance of multidisciplinary approaches to achieve a consistent selection of bacterial strains useful for plant protection and bioremediation purposes.

DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil organic pollutants. Although PAH-degrading bacteria are present in almost all soils, their selection and enrichment have been shown in historically high PAH contaminated soils. We can wonder if the effectiveness of PAH biodegradation and the PAH-degrading bacterial diversity differ among soils. The stable isotope probing (SIP) technique with 13C-phenanthrene (PHE) as a model PAH was used to: (i) compare for the first time a range of 10 soils with various PAH contamination levels, (ii) determine their PHE-degradation efficiency and (iii) identify the active PHE-degraders using 16S rRNA gene amplicon sequencing from 13C-labeled DNA. Surprisingly, the PHE degradation rate was not directly correlated to the initial level of total PAHs and phenanthrene in the soils, but was mostly explained by the initial abundance and richness of soil bacterial communities. A large diversity of PAH-degrading bacteria was identified for seven of the soils, with differences among soils. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE degraders. A positive correlation between PHE-degradation level and the diversity of active PHE-degraders (Shannon index) supported the hypothesis that cooperation between strains led to a more efficient PAH degradation.

Effects of tillage managements and maize straw returning on soil microbiome using 16S rDNA sequencing

Agricultural practices could affect bacterial diversity and community structure by altering soil physical and chemical properties. Straw returning and tillage practices are widely used in agriculture, however, the effects of these agricultural practices on microbiomes are still unclear. In the present study, we compared the 18 bacterial communities of soil with different straw returning and tillage treatment combinations. The V3-V4 regions of the 16S ribosomal RNA were amplified and analyzed by high-throughput sequencing technology. The results showed that the bacterial communities were consistently dominated by Acidobacteria, Proteobacteria, Actinobacteria, and Chloroflexi. Short-term straw returning and tillage practices significantly altered the diversity, relative abundance and functions of the soil microbiome. Soil subjected to rotary tillage and straw returning (RTS) combination possessed the highest bacterial diversity and lowest ratio of G+/G- bacteria, indicating that RTS could be an efficient integrated management system to improve microbiome in the short term. Double verifications based on relative abundance and network analysis, revealed close relationships of Mycobacterium and Methylibium with RTS, indicating they could serve as biomarkers for RTS. Investigating microbial changes under different agricultural practices will provide valuable foundations for land sustainable utilization and increase crop yields.

Long-term effect of biochar amendment on the biodegradation of petroleum hydrocarbons in soil microbial fuel cells

Biochar is extensively applied in amendment of contaminated soils. However, the effect of biochar on the biodegradation of petroleum hydrocarbons and electricity generation in soil microbial fuel cells (MFCs) remains unclear. Here, three biochars respectively derived from poultry (chicken manure, CB), agriculture (wheat straw, SB) and forestry industries (wood sawdust, WB) were investigated after 223 days of amendment. Consequently, high removal for alkanes was in CB with the mineral nutrition and phosphorus while aromatics were in SB with the most N content and the highest molecular polarity. The lowest removal efficiency of total petroleum hydrocarbons was observed in WB with the highest surface area, whereas the most charge was obtained. The different performance of soil MFCs was due to physicochemical properties of biochar and colonized microbial communities of bacteria and archaea. The abundance of Actinotalea increased by 144-263% in SB and CB while that of Desulfatitalea distinctly increased in WB. Meanwhile, species from Methanosarcina, Methanoculleus, Halovivax and Natronorubrum exerted probably a methanogenic degrading role. This study revealed that the degrader, azotobacter and electricigens exhibited a close relationship in order to degrade hydrocarbons and generate electricity in soil bioelectrochemical remediation systems.

Influence of rhamnolipid biosurfactant and Brij-35 synthetic surfactant on 14C-Pyrene mineralization in soil

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous contaminants in soil and are considered priority pollutants due to their carcinogenicity. Bioremediation of PAH-contaminated soils is often limited by the low solubility and strong sorption of PAHs in soil. Synthetic surfactants and biosurfactants have been used to enhance the bioavailability of PAHs and to accelerate microbial degradation. However, few studies have compared synthetic and biosurfactants in their efficiency in promoting PAH biodegradation in either native or bioaugmented soils. In this study, we evaluated mineralization of ¹⁴C-pyrene in soils with or without the augmentation of Mycobacterium vanbaalenii PYR-1, and characterized the effect of Brij-35 (synthetic) and rhamnolipid biosurfactant at different amendment rates. Treatment of rhamnolipid biosurfactant at 140 or 1400 μg surfactant g-dry soil^-1 rates resulted in a significantly longer lag period in ¹⁴C-pyrene mineralization in both native and bioaugmented soils. In contrast, amendment of Brij-35 generally increased ¹⁴C-pyrene degradation, and the greatest enhancement occurred at 21.6 or 216 μg surfactant g-dry soil^-1 rates, which may be attributed to increased bioavailability. Brij-35 and rhamnolipid biosurfactant were found to be non-toxic to M. vanbaalenii PYR-1 at 10X CMC, thus indicating rhamnolipid biosurfactant likely served as a preferential carbon source to the degrading bacteria in place of ¹⁴C-pyrene, leading to delayed and inhibited ¹⁴C-pyrene degradation. Mineralization of ¹⁴C-pyrene by M. vanbaalenii PYR-1 was rapid in the unamended soils, and up to 60% of pyrene was mineralized to ¹⁴CO₂ after 10 d in the unamended or Brij-35 surfactant-amended soils. Findings of this study suggest that application of surfactants may not always lead to enhanced PAH biodegradation or removal. If the surfactant is preferentially used as an easier carbon substrate than PAHs for soil microorganisms, it may actually inhibit PAH biodegradation. Selection of surfactant types is therefore crucial for the effectiveness of surfactant-aided bioremediation of PAH-contaminated soils.

Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil

Analyzing the microbial community structure and functions become imperative for ecological processes. To understand the impact of spent engine oil (SEO) contamination on microbial community structure of an agricultural soil, soil microcosms designated 1S (agricultural soil) and AB1 (agricultural soil polluted with SEO) were set up. Metagenomic DNA extracted from the soil microcosms and sequenced using Miseq Illumina sequencing were analyzed for their taxonomic and functional properties. Taxonomic profiling of the two microcosms by MG-RAST revealed the dominance of Actinobacteria (23.36%) and Proteobacteria (52.46%) phyla in 1S and AB1 with preponderance of Streptomyces (12.83%) and Gemmatimonas (10.20%) in 1S and Geodermatophilus (26.24%), Burkholderia (15.40%), and Pseudomonas (12.72%) in AB1, respectively. Our results showed that soil microbial diversity significantly decreased in AB1. Further assignment of the metagenomic reads to MG-RAST, Cluster of Orthologous Groups (COG) of proteins, Kyoto Encyclopedia of Genes and Genomes (KEGG), GhostKOALA, and NCBI's CDD hits revealed diverse metabolic potentials of the autochthonous microbial community. It also revealed the adaptation of the community to various environmental stressors such as hydrocarbon hydrophobicity, heavy metal toxicity, oxidative stress, nutrient starvation, and C/N/P imbalance. To the best of our knowledge, this is the first study that investigates the effect of SEO perturbation on soil microbial communities through Illumina sequencing. The results indicated that SEO contamination significantly affects soil microbial community structure and functions leading to massive loss of nonhydrocarbon degrading indigenous microbiota and enrichment of hydrocarbonoclastic organisms such as members of Proteobacteria and Actinobacteria.

Biodegradation of Xenobiotic Compounds

The continuous accumulation of recalcitrant xenobiotic compounds into the ecosystem released from various sources caused a serious global concern. Xenobiotics compounds are carcinogenic, mutagenic, causing teratogenic effect and persist over a long period of time in the environment. Therefore there is an urgent need for the detoxification of these compounds. Biodegradation is a technique that employs natural biological processes to completely degrade toxic contaminants from the environment. The microorganisms possess a wide range of catabolic biodegradation pathways and, thus, use these toxic xenobiotics as the sole source of carbon and energy. Bacteria and fungi are source of xenobiotic degradation. For the development of successful and improved bioremediation processes, understanding of the biochemical and molecular aspects of xenobiotics biodegradation is required. The chapter aims to provide an overview of xenobiotic compounds, factors affecting biodegradation, the metabolic pathways and genetic adaptation in microorganisms for degradation of recalcitrant xenobiotic compounds.

Separating and characterizing functional alkane degraders from crude-oil-contaminated sites via magnetic nanoparticle-mediated isolation

Uncultivable microorganisms account for over 99% of all species on the planet, but their functions are yet not well characterized. Though many cultivable degraders for n-alkanes have been intensively investigated, the roles of functional n-alkane degraders remain hidden in the natural environment. This study introduces the novel magnetic nanoparticle-mediated isolation (MMI) technology in Nigerian soils and successfully separates functional microbes belonging to the families Oxalobacteraceae and Moraxellaceae, which are dominant and responsible for alkane metabolism in situ. The alkR-type n-alkane monooxygenase genes, instead of alkA- or alkP-type, were the key functional genes involved in the n-alkane degradation process. Further physiological investigation via a BIOLOG PM plate revealed some carbon (Tween 20, Tween 40 and Tween 80) and nitrogen (tyramine, l-glutamine and d-aspartic acid) sources promoting microbial respiration and n-alkane degradation. With further addition of promoter carbon or nitrogen sources, the separated functional alkane degraders significantly improved n-alkane biodegradation rates. This suggests that MMI is a promising technology for separating functional microbes from complex microbiota, with deeper insight into their ecological functions and influencing factors. The technique also broadens the application of the BIOLOG PM plate for physiological research on functional yet uncultivable microorganisms.

Degradation of polynuclear aromatic hydrocarbons by two strains of Pseudomonas

The goal of this investigation was to isolate competent polynuclear aromatic hydrocarbons degraders that can utilize polynuclear aromatic hydrocarbons of former industrial sites at McDoel Switchyard in Bloomington, Indiana. Using conventional enrichment method based on soil slurry, we isolated, screened and purified two bacterial species strains PB1 and PB2. Applying the ribotyping technique using the 16S rRNA gene analysis, the strains were assigned to the genus Pseudomonas (Pseudomonas plecoglossicida strain PB1 and Pseudomonas sp. PB2). Both isolates showed promising metabolic capacity on pyrene sprayed MS agar plates during the preliminary investigations. Using time course studies in the liquid cultures at calculated concentrations 123, 64, 97 and 94ppm for naphthalene, chrysene, fluroanthene and pyrene, P. plecoglossicida strain PB1 and Pseudomonas sp. PB2 showed partial utilization of the polynuclear aromatic hydrocarbons. Naphthalene was degraded between 26% and 40%, chrysene 14% and 16%, fluroanthene 5% and 7%; pyrene 8% and 13% by P. plecoglossicida strain PB1 and Pseudomonas sp. PB2 respectively. Based on their growth profile, we developed a model R(2)=1 to predict the degradation rate of slow polynuclear aromatic hydrocarbon-degraders where all the necessary parameters are constant. From this investigation, we confirm that the former industrial site soil microbial communities may be explored for the biorestoration of the industrial site.

Making soy sauce from defatted soybean meal without the mejus process by submerged cultivation using thermophilic bacteria

The diversity of thermophilic bacteria was not significantly altered while growing in a defatted soybean meal (DFSM) slurry at 60 °C for 10, 20, and 30 days. Five species of thermophilic bacteria, which belong to the genera Aeribacillus (temperature gradient gel electrophoresis [TGGE] band no. 1), Saccharococcus (TGGE band no. 2), Geobacillus (TGGE band no. 3), Bacillus (TGGE band no. 4), and Anoxybacillus (TGGE band no. 5), were detected in the fermenting DFSM slurry. The cell-free culture fluid obtained from the fermenting DFSM slurry on day 14 hydrolyzed starch and soy protein at 60 °C but not at 30 °C. Soy sauce (test soy sauce) was prepared from the fermented DFSM slurry after a 30 day cultivation at 60 °C and a 60 day ripening at 45 °C. Free amino acid (AA) and organic acid contents in the soy sauce increased in proportion to the fermentation period, whereas ammonium decreased proportionally. Mg and Ca contained in the soy sauce decreased proportionally during fermentation and were lower than those in the non-fermented DFSM extract (control). Spectral absorbance of soy sauce prepared from the fermented DFSM slurry was maximal at 430 nm and increased slightly in proportion to the fermentation period. The aroma and flavor of the test soy sauce were significantly different from those of traditional Korean soy sauce. Conclusively, soy sauce may be prepared directly from the fermented DFSM slurry without meju-preparing process and fermentation period may be a factor for control of soy sauce quality.

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.

The hidden 'mycobacteriome' of the human healthy oral cavity and upper respiratory tract

The incidence of opportunistic non-tuberculous mycobacteria (NTM) infections has increased considerably in the past decades causing an array of infections, including respiratory and soft-tissue infections. NTM are ubiquitous and can be found in numerous environments, including households and water plants. However, NTM have not been reported to be associated with the healthy human oral microbiome. Since the oral cavity and upper respiratory track are the main ports of entry of microorganisms into the human body, elucidating NTM diversity and prevalence will assist in the assessment of the potential risks of infection elicited by these opportunistic pathogens. Here, we report the identification of a ‘non-tuberculous mycobacteriome’ in healthy individuals. We employed a modified DNA extraction procedure in conjunction with mycobacterial-specific primers to screen niches in the oral cavity (buccal mucosa and dental plaque) and upper respiratory tract (nostrils and oropharynx) of 10 healthy subjects. A total of 50 prevalent operational taxonomic units sequenced on MiSeq (Illumina) using 16S rRNA V3–V4 region were detected across all screened niches, showing the presence of diverse NTM communities. NTM DNA was detected in the nostrils of all 10 subjects, in buccal mucosa of 8 subjects, in the oropharynx of 7 subjects, and in the dental plaques of 5 subjects. Results from quantitative PCR showed each individual harbored 10³–10⁴ predicted NTM per each screened niche. The modification of standard DNA isolation methods to increase sensitivity toward mycobacterial species represents an important step to advance the knowledge of the oral as well as the overall human microbiome. These findings clearly reveal for the first time that healthy individuals harbor a ‘non-tuberculous mycobacteriome’ in their oral cavity and upper respiratory tract and may have important implications in our understanding of infections caused by NTM.

Microbial metabolism and community structure in response to bioelectrochemically enhanced remediation of petroleum hydrocarbon-contaminated soil

This study demonstrates that electrodes in a bioelectrochemical system (BES) can potentially serve as a nonexhaustible electron acceptor for in situ bioremediation of hydrocarbon contaminated soil. The deployment of BES not only eliminates aeration or supplement of electron acceptors as in contemporary bioremediation but also significantly shortens the remediation period and produces sustainable electricity. More interestingly, the study reveals that microbial metabolism and community structure distinctively respond to the bioelectrochemically enhanced remediation. Tubular BESs with carbon cloth anode (CCA) or biochar anode (BCA) were inserted into raw water saturated soils containing petroleum hydrocarbons for enhancing in situ remediation. Results show that total petroleum hydrocarbon (TPH) removal rate almost doubled in soils close to the anode (63.5-78.7%) than that in the open circuit positive controls (37.6-43.4%) during a period of 64 days. The maximum current density from the BESs ranged from 73 to 86 mA/m(2). Comprehensive microbial and chemical characterizations and statistical analyses show that the residual TPH has a strongly positive correlation with hydrocarbon-degrading microorganisms (HDM) numbers, dehydrogenase activity, and lipase activity and a negative correlation with soil pH, conductivity, and catalase activity. Distinctive microbial communities were identified at the anode, in soil with electrodes, and soil without electrodes. Uncommon electrochemically active bacteria capable of hydrocarbon degradation such as Comamonas testosteroni, Pseudomonas putida, and Ochrobactrum anthropi were selectively enriched on the anode, while hydrocarbon oxidizing bacteria were dominant in soil samples. Results from genus or phylum level characterizations well agree with the data from cluster analysis. Data from this study suggests that a unique constitution of microbial communities may play a key role in BES enhancement of petroleum hydrocarbons biodegradation in soils.

Isolation and Identification of Mycobacteria from Soils at an Illegal Dumping Site and Landfills in Japan

In order to study the diversity and community of genus Mycobacterium in polluted soils, we tried to isolate mycobacteria from 11 soil samples collected from an illegal dumping site and 3 landfills in Japan. Using culture methods with or without Acanthamoeba culbertsoni, a total of 19 isolates of mycobacteria were obtained from 5 soil samples and 3 of them were isolated only by the co-culture method with the amoeba. Conventional biochemical tests and sequencing of the hsp65, rpoB, and 16S rRNA genes were performed for species identification of 17 of the 19 isolates. Among the 17 isolates, there was one isolate each of Mycobacterium vanbaalenii, Mycobacterium mageritense, Mycobacterium frederiksbergense, M. vanbaalenii or Mycobacterium austroafricanum, and Mycobacterium chubuense or Mycobacterium chlorophenolicum. The remaining 12 isolates could not be precisely identified at the species level. A phylogenic tree based on the hsp65 sequences indicated that 2 of the 12 isolates were novel species. In addition, 4 isolates were phylogenically close to species that degrade polycyclic aromatic hydrocarbons, which induce some cancers in humans. These results demonstrated that there were many hitherto-unreported mycobacteria in the polluted soils, and suggested that some mycobacteria might play roles in the natural attenuation and engineered bioremediation of contaminated sites with other microorganisms.

The roles of biological interactions and pollutant contamination in shaping microbial benthic community structure

Biological interactions between metazoans and the microbial community play a major role in structuring food webs in aquatic sediments. Pollutants can also strongly affect the structure of meiofauna and microbial communities. This study aims investigating, in a non-contaminated sediment, the impact of meiofauna on bacteria facing contamination by a mixture of three PAHs (fluoranthene, phenanthrene and pyrene). Sediment microcosms were incubated in the presence or absence of meiofauna during 30 days. Bioremediation treatments, nutrient amendment and addition of a hydrocarbon-degrading bacterium, were also tested to enhance PAH biodegradation. Results clearly show the important role of meiofauna as structuring factor for bacterial communities with significant changes observed in the molecular fingerprints. However, these structural changes were not concomitant with changes in biomass or function. PAH contamination had a severe impact on total meiofaunal abundance with a strong decrease of nematodes and the complete disappearance of polychaetes and copepods. In contrast, correspondence analysis, based on T-RFLP fingerprints, showed that contamination by PAH resulted in small shifts in microbial composition, with or without meiofauna, suggesting a relative tolerance of bacteria to the PAH cocktail. The PAH bioremediation treatments were highly efficient with more than 95% biodegradation. No significant difference was observed in presence or absence of meiofauna. Nutrient addition strongly enhanced bacterial and meiofaunal abundances as compared to control and contaminated microcosms, as well as inducing important changes in the bacterial community structure. Nutrients thus were the main structural factor in shaping bacterial community composition, while the role of meiofauna was less evident.

Profiles ofMycobacteriumcommunities under polycyclic aromatic hydrocarbon contamination stress in the Shenfu Irrigation Area, northeast China

Indigenous Mycobacterium communities play an important role in the degradation of polycyclic aromatic hydrocarbons (PAHs), but little is known about Mycobacterium distribution in situ at PAH-contaminated sites. In this study, the diversity and distribution of Mycobacterium communities were investigated in sediments and soils at sites upstream, midstream, and downstream of an oil-sewage irrigation channel, using denaturing gradient gel electrophoresis (DGGE). The results show that heavy PAH contamination in upstream sites negatively affected Mycobacterium community diversity compared with midstream and downstream sites in all 3 sample types (sediments, corn field soils, and rice field soils). There was a correlation between the distribution of Mycobacterium communities and PAH contamination, as indicated by canonical correspondence analysis. Mycobacterium diversity and distribution was found to vary between the 3 sample types.

A global proteome study of Mycobacterium gilvum PYR-GCK grown on pyrene and glucose reveals the activation of glyoxylate, shikimate and gluconeogenetic pathways through the central carbon metabolism highway

Various hydrocarbons have been released into the environment as a result of industrialization. An effective way of removing these materials without further environmental contamination is microbial bioremediation. Mycobacterium gilvum PYR-GCK, a bacteria isolated from a PAH polluted estuary, was studied using comparative shotgun proteomics to gain insight on its molecular activity while using pyrene and glucose as sole carbon and energy sources. Based on annotated genomic information, a confirmation analysis was first performed to confirm its pyrene degradation activity, using gas chromatography-mass spectrometry technology. One dimensional gel electrophoresis and liquid chromatography-mass spectrometry technologies employed in the proteomics analysis revealed the expression of pyrene degrading gene products along with upregulated expression of proteins functioning in the glyoxylate and shikimate pathways, in the pyrene-induced cells. The study also revealed the pathway of pyrene degraded intermediates, via partial gluconeogenesis, into the pentose phosphate pathway to produce precursors for nucleotides and amino acids biosynthesis.

Microbial diversity and PAH catabolic genes tracking spatial heterogeneity of PAH concentrations

We analyzed the within-site spatial heterogeneity of microbial community diversity, polyaromatic hydrocarbon (PAH) catabolic genotypes, and physiochemical soil properties at a creosote contaminated site. Genetic diversity and community structure were evaluated from an analysis of denaturant gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified sequences of 16S rRNA gene. The potential PAH degradation capability was determined from PCR amplification of a suit of aromatic dioxygenase genes. Microbial diversity, evenness, and PAH genotypes were patchily distributed, and hot and cold spots of their distribution coincided with hot and cold spots of the PAH distribution. The analyses revealed a positive covariation between microbial diversity, biomass, evenness, and PAH concentration, implying that the creosote contamination at this site promotes diversity and abundance. Three patchily distributed PAH-degrading genotypes, NAH, phnA, and pdo1, were identified, and their abundances were positively correlated with the PAH concentration and the fraction of soil organic carbon. The covariation of the PAH concentration with the number and spatial distribution of catabolic genotypes suggests that a field site capacity to degrade PAHs may vary with the extent of contamination.

Natural attenuation of contaminated marine sediments from an old floating dock Part II: changes of sediment microbial community structure and its relationship with environmental variables

Changes of microbial community structure and its relationship with various environmental variables in surface marine sediments were examined for a one-year period after the removal of an old floating dock in Hong Kong SAR, South China. Temporal variations in the microbial community structure were clearly revealed by principal component analysis (PCA) of the microbial ester-linked fatty acid methyl ester (EL-FAME) profiles. The most obvious shift in microbial community structure was detected 6 months after the removal of the dock, although no significant decline in the levels of pollutants could be detected. As determined by EL-FAME profiles, the microbial diversity recovered and the predominance of gram-negative bacteria was gradually replaced by gram-positive bacteria and fungi in the impacted stations. With redundancy analysis (RDA), the concentration of total polycyclic aromatic hydrocarbons (PAHs) was found to be the second important determinant of microbial community structure, next to Time. The relative abundance of 18:1ω9c and hydroxyl fatty acids enriched in the PAH hot spots, whereas 16:1ω9 and 18:1ω9t were negatively correlated to total PAH concentration. The significant relationships observed between microbial EL-FAME profiles and pollutants, exampled by PAHs in the present study, suggested the potential of microbial community analysis in the assessment of the natural attenuation process in contaminated environments.

Pyrene degradation by Pseudomonas sp. and Burkholderia sp. enriched from coking wastewater sludge

A pyrene-degrading consortium was enriched from sludge of coking wastewater treatment plant which included a combination of aerobic and anaerobic reactors. Biodegradation of pyrene by the consortium follows first-order kinetics. Addition of a co-substrate (glucose or anthraquinone) facilitated pyrene degrading. The highest degradation rate was achieved at 35°C and pH 7.0, as glucose was added. In this case, pyrene (100 mg L(-1)) was degraded by 93.1 % within 36 h. An intermediate, 1-naphthol was detected via GC-MS analysis, indicating that pyrene degradation by the consortium proceeded with a pathway different from that associated with Mycobacterium sp. By comparisons of 16S rRNA gene sequences, two strains in this consortium were identified as Pseudomonas sp. and Burkholderia sp. The enriched pyrene-degrading consortium from coking wastewater treatment system shows highest pyrene-degrading activity compared with the reported pyrene degraders.

Environmental mycobacteria: a threat to human health?

In many cases, bacterial pathogens are close relatives to nonpathogens. Pathogens seem to be limited lineages within nonpathogenic bacteria. Nonpathogenic isolates are generally more diverse and widespread in the environment and it is generally considered that environmental bacteria do not pose a risk to human health as clinical isolates do; this may not be the case with mycobacteria, but environmental mycobacteria have not been well studied. It is documented that several environmental mycobacteria constitute a source for human infections. Diverse mycobacterial environmental isolates are rarely involved in human disease. Environmental mycobacteria may have a role in degradation of different compounds. Environmental mycobacteria have had a long interaction with humans, maybe as long as the human species, and may have contributed to human evolution.

Accelerated biodegradation of pyrene and benzo[a]pyrene in the Phragmites australis rhizosphere by bacteria-root exudate interactions

We investigated the biodegradation of pyrene and benzo[a]pyrene in Phragmites australis rhizosphere sediment. We collected P. australis plants, rhizosphere sediments, and unvegetated sediments from natural aquatic sites and conducted degradation experiments using sediments spiked with pyrene or benzo[a]pyrene. Accelerated removal of pyrene and benzo[a]pyrene was observed in P. australis rhizosphere sediments with plants, whereas both compounds persisted in unvegetated sediments without plants and in autoclaved rhizosphere sediments with sterilized plants, suggesting that the accelerated removal resulted largely from biodegradation by rhizosphere bacteria. Initial densities of pyrene-utilizing bacteria were substantially higher in the rhizosphere than in unvegetated sediments, but benzo[a]pyrene-utilizing bacteria were not detected in rhizosphere sediments. Mycobacterium gilvum strains isolated from rhizosphere sediments utilized pyrene aerobically as a sole carbon source and were able to degrade benzo[a]pyrene when induced with pyrene. Phragmites australis root exudates containing phenolic compounds supported growth as a carbon source for the one Mycobacterium strain tested, and induced benzo[a]pyrene-degrading activity of the strain. The stimulatory effect on benzo[a]pyrene biodegradation and the amounts of phenolic compounds in root exudates increased when P. australis was exposed to pyrene. Our results show that Mycobacterium-root exudate interactions can accelerate biodegradation of pyrene and benzo[a]pyrene in P. australis rhizosphere sediments.

Temporal changes in Sphingomonas and Mycobacterium populations in mangrove sediments contaminated with different concentrations of polycyclic aromatic hydrocarbons (PAHs)

The change in community diversity and structure of the indigenous, dominant, polycyclic aromatic hydrocarbon (PAH)-degrading bacterial genera, Sphingomonas and Mycobacterium, due to contamination in the environment is not very well known. A combination of PCR-DGGE with specific primers and a cultivation-dependent microbiological method was used to detect different populations of Sphingomonas and Mycobacterium in mangrove sediments. The structure of the entire bacterial community (including Sphingomonas) did not show a shift due to environmental contamination, whereas the diversity of Mycobacterium populations in mangrove sediments with higher PAH contamination increased from exposure between Day 0 and Day 30. The isolated Mycobacterium strains migrated to the same position as the major bands of the bacterial communities in Mycobacterium-specific DGGE. A dioxygenase gene system, nidA, which is commonly found in PAH-degrading Mycobacterium strains, was also detected in the more highly contaminated sediment slurries. The present study revealed that Mycobacterium species were the dominant PAH-degraders and played an important role in degrading PAHs in contaminated mangrove sediments.

Isolation of polycyclic aromatic hydrocarbons (PAHs)-degrading Mycobacterium spp. and the degradation in soil

The goal of this study was to isolate PAHs degraders that can utilize PAHs associated with soil particulates and investigate the biodegradation of PAHs on agar plate, in liquid culture and soil. Two Mycobacterium strains (NJS-1 and NJS-P) were isolated from PAHs-contaminated farmland soil using enrichment based on soil slurry. The isolates could degrade five test PAHs including pyrene, phenanthrene, fluoranthene, anthracene and benzo[a]pyrene on plate, but showed different effects in liquid culture, especially for fluoranthene. Isolate NJS-1 was capable of utilizing benzo[a]pyrene as a sole carbon and energy source, and an enhanced degradation was observed when pyrene was supplied as cometabolic substrate. Reintroduction of the isolates into sterile contaminated soil resulted in a significant removal of aged pyrene and fluoranthene (over 40%) in 2-months incubation. In pyrene-spiked soil, the degradation of pyrene and fluoranthene increased to 90% and 50%, respectively. Comparing PAHs degradation on plate, in liquid culture and soil, we can conclude that there was corresponding degradation in different test systems. In addition, the degradation of aged PAHs in soil suggested the potential application of two isolates in further bioremediation.

Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils

This study investigates the dynamics of pyrene degradation rates, microbial communities, and functional gene copy numbers during the incubation of pyrene-spiked soils. Spiking pyrene to the soil was found to have negligible effects on the bacterial community present. Our results demonstrated that there was a significant difference in nidA gene copy numbers between sampling dates in QZ soil. Mycobacterium 16S rDNA clone libraries showed that more than 90% mycobacteria detected were closely related to fast-growing PAH-degrading Mycobacterium in pyrene-spiked soil, while other sequences related to slow-growing Mycobacterium were only detected in the control soil. It is suggested that nidA gene copy number and fast-growing PAH-degrading Mycobacterium could be used as indicators to predict pyrene contamination and its degradation activity in soils.

Multiple responses of gram-positive and gram-negative bacteria to mixture of hydrocarbons

Most of our knowledge about pollutants and the way they are biodegraded in the environment has previously been shaped by laboratory studies using hydrocarbon-degrading bacterial strains isolated from polluted sites. In present study Gram-positive (Mycobacterium sp. IBBPo1, Oerskovia sp. IBBPo2, Corynebacterium sp. IBBPo3) and Gram-negative (Chryseomonas sp. IBBPo7, Pseudomonas sp. IBBPo10, Burkholderia sp. IBBPo12) bacteria, isolated from oily sludge, were found to be able to tolerate pure and mixture of saturated hydrocarbons, as well as pure and mixture of monoaromatic and polyaromatic hydrocarbons. Isolated Gram-negative bacteria were more tolerant to mixture of saturated (n-hexane, n-hexadecane, cyclohexane), monoaromatic (benzene, toluene, ethylbenzene) and polyaromatic (naphthalene, 2-methylnaphthalene, fluorene) hydrocarbons than Gram-positive bacteria. There were observed cellular and molecular modifications induced by mixture of saturated, monoaromatic and polyaromatic hydrocarbons to Gram-positive and Gram-negative bacteria. These modifications differ from one strain to another and even for the same bacterial strain, according to the nature of hydrophobic substrate.

Isolation and characterization of pyrene metabolizing microbial consortia from the plant rhizoplane

Most research on the ecology of PAH degrading bacteria in the rhizosphere has focused on individual strains that grow on specific PAHs. Thus, there are fundamental questions as to importance of microbial consortia for PAH degradation in the plant rhizosphere. The study reported here characterized cultivable pyrene degrading rhizoplane microbial communities from two different plant species using a root printing technique on agar plates. Colonies were revealed by formation of clearing zones on medium containing a thin film of pyrene on the surface of a mineral nutrient agar. Prints of the rhizoplane colonies were obtained from roots of Melilotus officinalis (sweet yellow clover) and Andropogon gerardii (big bluestem) plants. Phylogenetic characterizations of selected pyrene degrading colonies were assessed by PCR-DGGE and DNA sequencing. Results showed that different populations of cultivable pyrene degraders were obtained from representative consortia that were examined. Many of the PAH degrading consortia consisted of mixtures of bacterial species that were unable to degrade pyrene by themselves. While this study focused on culturable PAH degraders, the results suggest that pyrene degradation in the rhizosphere commonly involves the activity of bacterial consortia in which various species of bacteria interact to achieve PAH degradation.

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.

Plant-associated bacterial degradation of toxic organic compounds in soil

A number of toxic synthetic organic compounds can contaminate environmental soil through either local (e.g., industrial) or diffuse (e.g., agricultural) contamination. Increased levels of these toxic organic compounds in the environment have been associated with human health risks including cancer. Plant-associated bacteria, such as endophytic bacteria (non-pathogenic bacteria that occur naturally in plants) and rhizospheric bacteria (bacteria that live on and near the roots of plants), have been shown to contribute to biodegradation of toxic organic compounds in contaminated soil and could have potential for improving phytoremediation. Endophytic and rhizospheric bacterial degradation of toxic organic compounds (either naturally occurring or genetically enhanced) in contaminated soil in the environment could have positive implications for human health worldwide and is the subject of this review.

Molecular detection and phylogenetic analysis of the catechol 1,2-dioxygenase gene from Gordonia spp

The C12O gene (catA gene) encodes for catechol 1,2-dioxygenase, which is a key enzyme involved in the first step catalysis of the aromatic ring in the ortho-cleavage pathway. This functional gene can be used as a marker to assess the catabolic potential of bacteria in bioremediation. C12OF and C12OR primers were designed based on the conserved regions of the CatA amino acid sequence of Actinobacteria for amplifying the catA gene from the genus Gordonia (16 Gordonia representing 11 species). The amplified catA genes (382bp) were sequenced and analyzed. In the phylogenetic tree based on the translated catA amino acid sequences, all the Gordonia segregated clearly from other closely related genera. The sequence similarity of the catA gene in Gordonia ranged from 72.4% to 99.5%, indicating that the catA gene might have evolved faster than rrn operons or the gyrB gene at the inter-species level. A single nucleotide deletion of the catA gene was observed in Gordonia amicalis CC-MJ-2a, Gordonia rhizosphera and Gordonia sputi at nucleotide position 349. This deletion led to an encoding frame shift downstream of 11 amino acid residues, from WPSVAARAPAP to GHPWRPAHLHL, which was similar to most of the non-Gordonia Actinobacteria. Such variations might influence the catabolic activities or substrate utilization patterns of catechol 1,2-dioxygenase among Gordonia.

Bacterial degradation of aromatic compounds

Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.