Complete nucleotide sequence and evolutionary significance of a chromosomally encoded naphthalene-degradation lower pathway from Pseudomonas stutzeri AN10

Metabolic cross-feeding between the competent degrader Rhodococcus sp. strain p52 and an incompetent partner during catabolism of dibenzofuran: Understanding the leading and supporting roles

Microbial interactions, particularly metabolic cross-feeding, play important roles in removing recalcitrant environmental pollutants; however, the underlying mechanisms involved in this process remain unclear. Thus, this study aimed to elucidate the mechanism by which metabolic cross-feeding occurs during synergistic dibenzofuran degradation between a highly efficient degrader, Rhodococcus sp. strain p52, and a partner incapable of utilizing dibenzofuran. A bottom-up approach combined with pairwise coculturing was used to examine metabolic cross-feeding between strain p52 and Arthrobacter sp. W06 or Achromobacter sp. D10. Pairwise coculture not only promoted bacterial pair growth but also facilitated dibenzofuran degradation. Specifically, strain p52, acting as a donor, released dibenzofuran metabolic intermediates, including salicylic acid and gentisic acid, for utilization and growth, respectively, by the partner strains W06 and D10. Both salicylic acid and gentisic acid exhibited biotoxicity, and their accumulation inhibited dibenzofuran degradation. The transcriptional activity of the genes responsible for the catabolism of dibenzofuran and its metabolic intermediates was coordinately regulated in strain p52 and its cocultivated partners, thus achieving synergistic dibenzofuran degradation. This study provides insights into microbial metabolic cross-feeding during recalcitrant environmental pollutant removal.

The trade-off between individual metabolic specialization and versatility determines the metabolic efficiency of microbial communities

In microbial systems, a metabolic pathway can be either completed by one autonomous population or distributed among a consortium performing metabolic division of labor (MDOL). MDOL facilitates the system's function by reducing the metabolic burden; however, it may hinder the function by reducing the exchange efficiency of metabolic intermediates among individuals. As a result, the function of a community is influenced by the trade-offs between the metabolic specialization and versatility of individuals. To experimentally test this hypothesis, we deconstructed the naphthalene degradation pathway into four steps and introduced them individually or combinatorically into different strains with varying levels of metabolic specialization. Using these strains, we engineered 1,456 synthetic consortia and found that 74 consortia exhibited higher degradation function than both the autonomous population and rigorous MDOL consortium. Quantitative modeling provides general strategies for identifying the most effective MDOL configuration. Our study provides critical insights into the engineering of high-performance microbial systems.

Recombination in Bacterial Genomes: Evolutionary Trends

Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.

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.

Comparative genomics of Stutzerimonas balearica (Pseudomonas balearica): diversity, habitats, and biodegradation of aromatic compounds

Stutzerimonas balearica (Pseudomonas balearica) has been found principally in oil-polluted environments. The capability of S. balearica to thrive from the degradation of pollutant compounds makes it a species of interest for potential bioremediation applications. However, little has been reported about the diversity of S. balearica. In this study, genome sequences of S. balearica strains from different origins were analyzed, revealing that it is a diverse species with an open pan-genome that will continue revealing new genes and functionalities as the genomes of more strains are sequenced. The nucleotide signatures and intra- and inter-species variation of the 16S rRNA genes of S. balearica were reevaluated. A strategy of screening 16S rRNA gene sequences in public databases enabled the detection of 158 additional strains, of which only 23% were described as S. balearica. The species was detected from a wide range of environments, although mostly from aquatic and polluted environments, predominantly related to petroleum oil. Genomic and phenotypic analyses confirmed that S. balearica possesses varied inherent capabilities for aromatic compounds degradation. This study increases the knowledge of the biology and diversity of S. balearica and will serve as a basis for future work with the species.

Stutzerimonas decontaminans sp. nov. isolated from marine polluted sediments

Strains 19SMN4^T and ST27MN3 were isolated from marine sediments after enrichment with 2-methylnaphthalene and were classified as Pseudomonas stutzeri genomovar 4. Four other strains, BG 2, HT20, HT24, and A7, were isolated from sulphide-oxidizing bioreactors or activated sludge affiliated with the same clade in the 16S rRNA phylogenetic tree. P. stutzeri has been recently reclassified as a new genus, Stutzerimonas, and a preliminary analysis indicated that the strains in this study were distinct from any classified Stutzerimonas and are considered representatives of phylogenomic species 4 (pgs4). Strains 19SMN4^T and ST27MN3 were extensively characterized with phenotypic, chemotaxonomic, genomic and phylogenomic data. Strain 19SMN4^T had a well-characterized naphthalene degradative plasmid that has been compared with other plasmids, while in strain ST27MN3, the naphthalene degradative genes were detected in the chromosome sequence. Phylogenomic analysis of the core gene sequences showed that strains 19SMN4^T and ST27MN3 shared 3,995 genes and were closely related to members of the species "Stutzerimonas songnenensis" and Stutzerimonas perfectomarina, as well as to the Stutzerimonas phylogenomic species, pgs9, pgs16 and pgs24. The aggregate average nucleotide identity (ANI) indicated that strains 19SMN4^T and ST27MN3 belonged to the same genomic species, whereas the genomic indices with their closest-related type strains were below the accepted species threshold (95 %). We therefore conclude that strains 19SMN4^T and ST27MN3 represent a novel species of Stutzerimonas, for which the name Stutzerimonas decontaminans is proposed; the type strain is 19SMN4^T (=CCUG44593^T = DSM6084^T = LMG18521^T).

Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor

Microbial communities execute metabolic pathways to drive global nutrient cycles. Within a community, functionally specialized strains can perform different yet complementary steps within a linear pathway, a phenomenon termed metabolic division of labor (MDOL). However, little is known about how such metabolic behaviors shape microbial communities. Here, we derive a theoretical framework to define the assembly of a community that degrades an organic compound through MDOL. The framework indicates that to ensure community stability, the strains performing the initial steps should hold a growth advantage (m) over the "private benefit" (n) of the strain performing the last step. The steady-state frequency of the last strain is then determined by the quotient of n and m. Our experiments show that the framework accurately predicts the assembly of our synthetic consortia that degrade naphthalene through MDOL. Our results provide insights for designing and managing stable microbial systems for metabolic pathway optimization.

Current Methods for Recombination Detection in Bacteria

The role of genetic exchanges, i.e., homologous recombination (HR) and horizontal gene transfer (HGT), in bacteria cannot be overestimated for it is a pivotal mechanism leading to their evolution and adaptation, thus, tracking the signs of recombination and HGT events is importance both for fundamental and applied science. To date, dozens of bioinformatics tools for revealing recombination signals are available, however, their pros and cons as well as the spectra of solvable tasks have not yet been systematically reviewed. Moreover, there are two major groups of software. One aims to infer evidence of HR, while the other only deals with horizontal gene transfer (HGT). However, despite seemingly different goals, all the methods use similar algorithmic approaches, and the processes are interconnected in terms of genomic evolution influencing each other. In this review, we propose a classification of novel instruments for both HR and HGT detection based on the genomic consequences of recombination. In this context, we summarize available methodologies paying particular attention to the type of traceable events for which a certain program has been designed.

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 New ICEclc Subfamily Integrative and Conjugative Element Responsible for Horizontal Transfer of Biphenyl and Salicylic Acid Catabolic Pathway in the PCB-Degrading Strain Pseudomonas stutzeri KF716

Integrative and conjugative elements (ICEs) are chromosomally integrated self-transmissible mobile genetic elements. Although some ICEs are known to carry genes for the degradation of aromatic compounds, information on their genetic features is limited. We identified a new member of the ICEclc family carrying biphenyl catabolic bph genes and salicylic acid catabolic sal genes from the PCB-degrading strain Pseudomonas stutzeri KF716. The 117-kb ICE_bph-salKF716 contains common core regions exhibiting homology with those of degradative ICEclc from P. knackmussii B13 and ICE_XTD from Azoarcus sp. CIB. A comparison of the gene loci collected from the public database revealed that several putative ICEs from P. putida B6-2, P, alcaliphila JAB1, P. stutzeri AN10, and P. stutzeri 2A20 had highly conserved core regions with those of ICE_bph-salKF716, along with the variable region that encodes the catabolic genes for biphenyl, naphthalene, toluene, or phenol. These data indicate that this type of ICE subfamily is ubiquitously distributed within aromatic compound-degrading bacteria. ICE_bph-salKF716 was transferred from P. stutzeri KF716 to P. aeruginosa PAO1 via a circular extrachromosomal intermediate form. In this study, we describe the structure and genetic features of ICE_bph-salKF716 compared to other catabolic ICEs.

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

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

Biotechnological applications of marine bacteria in bioremediation of environments polluted with hydrocarbons and plastics

Marine ecosystems are some of the most adverse environments on Earth and contain a considerable portion of the global bacterial population, and some of these bacterial species play pivotal roles in several biogeochemical cycles. Marine bacteria have developed different molecular mechanisms to address fluctuating environmental conditions, such as changes in nutrient availability, salinity, temperature, pH, and pressure, making them attractive for use in diverse biotechnology applications. Although more than 99% of marine bacteria cannot be cultivated with traditional microbiological techniques, several species have been successfully isolated and grown in the laboratory, facilitating investigations of their biotechnological potential. Some of these applications may contribute to addressing some current global problems, such as environmental contamination by hydrocarbons and synthetic plastics. In this review, we first summarize and analyze recently published information about marine bacterial diversity. Then, we discuss new literature regarding the isolation and characterization of marine bacterial strains able to degrade hydrocarbons and petroleum-based plastics, and species able to produce biosurfactants. We also describe some current limitations for the implementation of these biotechnological tools, but also we suggest some strategies that may contribute to overcoming them. KEY POINTS: • Marine bacteria have a great metabolic capacity to degrade hydrocarbons in harsh conditions. • Marine environments are an important source of new bacterial plastic-degrading enzymes. • Secondary metabolites from marine bacteria have diverse potential applications in biotechnology.

Change the original microbial community structure in the hydrolysis acidification tank to enhance the COD removal performance of oily wastewater

The hydrolysis acidification tank mainly relies on microorganisms to treat oily sewage, but in many cases the chemical oxygen demand (COD) of the effluent from the hydrolysis acidification tank does not decrease or even increase. In this work, about 50 L of oily wastewater is treated in a facultative anaerobic hydrolysis acidification tank with a temperature of 29 °C, pH 6, high-throughput sequencing technology analyzes found that after long-term operation of the hydrolysis and acidification tank, the dominant bacterial Pseudomonas accounted for only 2.87%, at this time, the effluent COD of the hydrolysis and acidification tank was 450 mg/L. Pseudomonas stutzeri LH-42 a strain screened in the laboratory, was domesticated and colonized in the hydrolysis acidification tank. High-throughput sequencing and bioinformatics analysis showed that the proportion of Pseudomonas in the hydrolysis acidification tank reached 5.89%, the effluent COD of the hydrolysis and acidification tank was 200 mg/L. The above results indicate the importance of the proportion of Pseudomonas in the hydrolysis and acidification tank for the COD degradation of oily wastewater.

A novel temperate phage, vB_PstS-pAN, induced from the naphthalene-degrading bacterium Pseudomonas stutzeri AN10

A novel temperate phage named vB_PstS-pAN was induced by mitomycin C treatment from the naphthalene-degrading bacterium Pseudomonas stutzeri AN10. The phage particles have icosahedral heads and long non-contractile tails, and vB_PstS-pAN can therefore be morphologically classified as a member of the family Siphoviridae. The whole genome of vB_PstS-pAN is 39,466 bp in length, with an 11-nt 3' overhang cohesive end. There are 53 genes in the vB_PstS-pAN genome, including genes responsible for phage integration, replication, morphogenesis, and bacterial lysis. The vB_PstS-pAN genome has low similarity to other phage genomes in the GenBank database, suggesting that vB_PstS-pAN is a novel member of the family Siphoviridae.

Microbial Degradation of Naphthalene and Substituted Naphthalenes: Metabolic Diversity and Genomic Insight for Bioremediation

Low molecular weight polycyclic aromatic hydrocarbons (PAHs) like naphthalene and substituted naphthalenes (methylnaphthalene, naphthoic acids, 1-naphthyl N-methylcarbamate, etc.) are used in various industries and exhibit genotoxic, mutagenic, and/or carcinogenic effects on living organisms. These synthetic organic compounds (SOCs) or xenobiotics are considered as priority pollutants that pose a critical environmental and public health concern worldwide. The extent of anthropogenic activities like emissions from coal gasification, petroleum refining, motor vehicle exhaust, and agricultural applications determine the concentration, fate, and transport of these ubiquitous and recalcitrant compounds. Besides physicochemical methods for cleanup/removal, a green and eco-friendly technology like bioremediation, using microbes with the ability to degrade SOCs completely or convert to non-toxic by-products, has been a safe, cost-effective, and promising alternative. Various bacterial species from soil flora belonging to Proteobacteria (Pseudomonas, Pseudoxanthomonas, Comamonas, Burkholderia, and Novosphingobium), Firmicutes (Bacillus and Paenibacillus), and Actinobacteria (Rhodococcus and Arthrobacter) displayed the ability to degrade various SOCs. Metabolic studies, genomic and metagenomics analyses have aided our understanding of the catabolic complexity and diversity present in these simple life forms which can be further applied for efficient biodegradation. The prolonged persistence of PAHs has led to the evolution of new degradative phenotypes through horizontal gene transfer using genetic elements like plasmids, transposons, phages, genomic islands, and integrative conjugative elements. Systems biology and genetic engineering of either specific isolates or mock community (consortia) might achieve complete, rapid, and efficient bioremediation of these PAHs through synergistic actions. In this review, we highlight various metabolic routes and diversity, genetic makeup and diversity, and cellular responses/adaptations by naphthalene and substituted naphthalene-degrading bacteria. This will provide insights into the ecological aspects of field application and strain optimization for efficient bioremediation.

Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer

In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.

Comparative Transcriptome Analysis Reveals the Mechanism Underlying 3,5-Dibromo-4-Hydroxybenzoate Catabolism via a New Oxidative Decarboxylation Pathway

The compound 3,5-dibromo-4-hydroxybenzoate (DBHB) is both anthropogenically released into and naturally produced in the environment, and its environmental fate is of great concern. Aerobic and anaerobic reductive dehalogenations are the only two reported pathways for DBHB catabolism. In this study, a new oxidative decarboxylation pathway for DBHB catabolism was identified in a DBHB-utilizing strain, Pigmentiphaga sp. strain H8. The genetic determinants underlying this pathway were elucidated based on comparative transcriptome analysis and subsequent experimental validation. A gene cluster comprising orf420 to orf426, with transcripts that were about 33- to 4,400-fold upregulated in DBHB-induced cells compared with those in uninduced cells, was suspected to be involved in DBHB catabolism. The gene odcA (orf420), which is essential for the initial catabolism of DBHB, encodes a novel NAD(P)H-dependent flavin monooxygenase that mediates the oxidative decarboxylation of DBHB to 2,6-dibromohydroquinone (2,6-DBHQ). The substrate specificity of the purified OdcA indicated that the 4-hydroxyl group and its ortho-halogen(s) are important for hydroxylation of the C-1 site carboxyl group by OdcA. 2,6-DBHQ is then ring cleaved by the dioxygenase OdcB (Orf425) to 2-bromomaleylacetate, which is finally transformed to β-ketoadipate by the maleylacetate reductase OdcC (Orf426). These results provide a better understanding of the molecular mechanism underlying the catabolic diversity of halogenated para-hydroxybenzoates.IMPORTANCE Halogenated hydroxybenzoates (HBs), which are widely used synthetic precursors for chemical products and common metabolic intermediates from halogenated aromatics, exert considerable adverse effects on human health and ecological security. Microbial catabolism plays key roles in the dissipation of halogenated HBs in the environment. In this study, the discovery of a new catabolic pathway for 3,5-dibromo-4-hydroxybenzoate (DBHB) and clarification of the genetic determinants underlying the pathway broaden our knowledge of the catabolic diversity of halogenated HBs in microorganisms. Furthermore, the NAD(P)H-dependent flavin monooxygenase OdcA identified in Pigmentiphaga sp. strain H8 represents a novel 1-monooxygenase for halogenated para-HBs found in prokaryotes and enhances our knowledge of the decarboxylative hydroxylation of (halogenated) para-HBs.

The naphthalene catabolic protein NahG plays a key role in hexavalent chromium reduction in Pseudomonas brassicacearum LZ-4

Soil contamination by PAH and heavy metals is a growing problem. Here, we showed that a new isolate, Pseudomonas brassicacearum strain LZ-4, can simultaneously degrade 98% of 6 mM naphthalene and reduce 92.4% of 500 μM hexavalent chromium [Cr (VI)] within 68 h. A draft genome sequence of strain LZ-4 (6,219,082 bp) revealed all the genes in the naphthalene catabolic pathway and some known Cr (VI) reductases. Interestingly, genes encoding naphthalene pathway components were upregulated in the presence of Cr (VI), and Cr (VI) reduction was elevated in the presence of naphthalene. We cloned and expressed these naphthalene catabolic genes and tested for Cr (VI) reduction, and found that NahG reduced 79% of 100 μM Cr (VI) in 5 minutes. Additionally, an nahG deletion mutant lost 52% of its Cr (VI) reduction ability compared to that of the wild-type strain. As nahG encodes a salicylate hydroxylase with flavin adenine dinucleotide (FAD) as a cofactor for electron transfer, Cr (VI) could obtain electrons from NADH through NahG-associated FAD. To the best of our knowledge, this is the first report of a protein involved in a PAH-degradation pathway that can reduce heavy metals, which provides new insights into heavy metal-PAH contamination remediation.

Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions

Although polycyclic aromatic hydrocarbons (PAHs) are harmful to human health, their elimination from the environment is not easy. Biodegradation of PAHs is promising since many bacteria have the ability to use hydrocarbons as their sole carbon and energy sources for growth. Of various microorganisms that can degrade PAHs, Pseudomonas aeruginosa is particularly important, not only because it causes a series of diseases including infection in cystic fibrosis patients, but also because it is a model bacterium in various studies. The genes that are responsible for degrading PAHs have been identified in P. aeruginosa, however, no gene acts alone as various stresses often initiate different metabolic pathways, quorum sensing, biofilm formation, antibiotic tolerance, etc. Therefore, it is important to study how PAH degradation genes behave under different conditions. In this study, we apply network analysis to investigating how 46 PAH degradation genes reorganized among 5549 genes in P. aeruginosa PAO1 under nine different conditions using publicly available gene coexpression data from GEO. The results provide six aspects of novelties: (i) comparing the number of gene clusters before and after stresses, (ii) comparing the membership in each gene cluster before and after stresses, (iii) defining which gene changed its membership together with PAH degradation genes before and after stresses, (iv) classifying membership-changed-genes in terms of category in Pseudomonas Genome Database, (v) postulating unknown gene’s function, and (vi) proposing new mechanisms for genes of interests. This study can shed light on understanding of cooperative mechanisms of PAH degradation from the level of entire genes in an organism, and paves the way to conduct the similar studies on other genes.

Genome Sequences of Two Naphthalene-Degrading Strains of Pseudomonas balearica, Isolated from Polluted Marine Sediment and from an Oil Refinery Site

The genome sequences of Pseudomonas balearica strains LS401 (CCUG 66666) and st101 (CCUG 66667) have been determined. The strains were isolated as naphthalene degraders from polluted marine sediment and from a sample from an oil refinery site, respectively. These genomes provide essential data about the biodegradation capabilities and the ecological implications of P. balearica.

Strategy of Pseudomonas pseudoalcaligenes C70 for effective degradation of phenol and salicylate

Phenol- and naphthalene-degrading indigenous Pseudomonas pseudoalcaligenes strain C70 has great potential for the bioremediation of polluted areas. It harbours two chromosomally located catechol meta pathways, one of which is structurally and phylogenetically very similar to the Pseudomonas sp. CF600 dmp operon and the other to the P. stutzeri AN10 nah lower operon. The key enzymes of the catechol meta pathway, catechol 2,3-dioxygenase (C23O) from strain C70, PheB and NahH, have an amino acid identity of 85%. The metabolic and regulatory phenotypes of the wild-type and the mutant strain C70ΔpheB lacking pheB were evaluated. qRT-PCR data showed that in C70, the expression of pheB- and nahH-encoded C23O was induced by phenol and salicylate, respectively. We demonstrate that strain C70 is more effective in the degradation of phenol and salicylate, especially at higher substrate concentrations, when these compounds are present as a mixture; i.e., when both pathways are expressed. Moreover, NahH is able to substitute for the deleted PheB in phenol degradation when salicylate is also present in the growth medium. The appearance of a yellow intermediate 2-hydroxymuconic semialdehyde was followed by the accumulation of catechol in salicylate-containing growth medium, and lower expression levels and specific activities of the C23O of the sal operon were detected. However, the excretion of the toxic intermediate catechol to the growth medium was avoided when the growth medium was supplemented with phenol, seemingly due to the contribution of the second meta pathway encoded by the phe genes.

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.

Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review

Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.

Metabolic Degradation of 1,4-dichloronaphthalene by Pseudomonas sp. HY

There is increasing concern regarding the adverse health effects of polychlorinated naphthalenes (PCNs). The metabolic degradation of 1,4-dichloronaphthalene (1,4-DCN) as a model PCN, was studied using a strain of Pseudomonas sp. HY. The metabolites were analyzed by gas chromatography-mass spectrometry (GC-MS). A series of metabolites including dihydroxy-dichloro-naphthalene, epoxy-dichlorinated naphthalene, dichlorinated naphthol, and dichlorinated salicylic acid were identified. The time-concentration plots of the degradation curves of 1,4-DCN was also obtained from the experiments, which set the initial concentration of 1,4-DCN to 10 mg/L and 20 mg/L, respectively. The results showed that 98% removal could be achieved within 48 h at an initial 1,4-DCN concentration of 10 mg/L. Nevertheless, it took 144 h to reach the same degradation efficiency at an initial concentration of 20 mg/L. The degradation of 1,4-DCN may not remove the chloride ions during the processes and the metabolites may not benefit the bacterial growth. The research suggests a metabolic pathway of 1,4-DCN, which is critical for the treatment of this compound through biological processes.

Microbial Toluene Removal in Hypoxic Model Constructed Wetlands Occurs Predominantly via the Ring Monooxygenation Pathway

In the present study, microbial toluene degradation in controlled constructed wetland model systems, planted fixed-bed reactors (PFRs), was queried with DNA-based methods in combination with stable isotope fractionation analysis and characterization of toluene-degrading microbial isolates. Two PFR replicates were operated with toluene as the sole external carbon and electron source for 2 years. The bulk redox conditions in these systems were hypoxic to anoxic. The autochthonous bacterial communities, as analyzed by Illumina sequencing of 16S rRNA gene amplicons, were mainly comprised of the families Xanthomonadaceae, Comamonadaceae, and Burkholderiaceae, plus Rhodospirillaceae in one of the PFR replicates. DNA microarray analyses of the catabolic potentials for aromatic compound degradation suggested the presence of the ring monooxygenation pathway in both systems, as well as the anaerobic toluene pathway in the PFR replicate with a high abundance of Rhodospirillaceae. The presence of catabolic genes encoding the ring monooxygenation pathway was verified by quantitative PCR analysis, utilizing the obtained toluene-degrading isolates as references. Stable isotope fractionation analysis showed low-level of carbon fractionation and only minimal hydrogen fractionation in both PFRs, which matches the fractionation signatures of monooxygenation and dioxygenation. In combination with the results of the DNA-based analyses, this suggests that toluene degradation occurs predominantly via ring monooxygenation in the PFRs.

Structural and kinetic characterization of recombinant 2-hydroxymuconate semialdehyde dehydrogenase from Pseudomonas putida G7

The first enzyme in the oxalocrotonate branch of the naphthalene-degradation lower pathway in Pseudomonas putida G7 is NahI, a 2-hydroxymuconate semialdehyde dehydrogenase which converts 2-hydroxymuconate semialdehyde to 2-hydroxymuconate in the presence of NAD(+). NahI is in family 8 (ALDH8) of the NAD(P)(+)-dependent aldehyde dehydrogenase superfamily. In this work, we report the cloning, expression, purification and preliminary structural and kinetic characterization of the recombinant NahI. The nahI gene was subcloned into a T7 expression vector and the enzyme was overexpressed in Escherichia coli ArcticExpress as a hexa-histidine-tagged fusion protein. After purification by affinity and size-exclusion chromatography, dynamic light scattering and small-angle X-ray scattering experiments were conducted to analyze the oligomeric state and the overall shape of the enzyme in solution. The protein is a tetramer in solution and has nearly perfect 222 point group symmetry. Protein stability and secondary structure content were evaluated by a circular dichroism spectroscopy assay under different thermal conditions. Furthermore, kinetic assays were conducted and, for the first time, KM (1.3±0.3μM) and kcat (0.9s(-1)) values were determined at presumed NAD(+) saturation. NahI is highly specific for its biological substrate and has no activity with salicylaldehyde, another intermediate in the naphthalene-degradation pathway.

Molecular responses of Frankia sp. strain QA3 to naphthalene

The Frankia-actinorhizal plant symbiosis plays a significant role in plant colonization in soils contaminated with heavy metals and toxic aromatic hydrocarbons. The molecular response of Frankia upon exposure to soil contaminants is not well understood. To address this issue, we subjected Frankia sp. strain QA3 to naphthalene stress and showed that it could grow on naphthalene as a sole carbon source. Bioinformatic analysis of the Frankia QA3 genome identified a potential operon for aromatic compound degradation as well as several ring-hydroxylating dioxygenases. Under naphthalene stress, the expression of these genes was upregulated. Proteome analysis showed a differential protein profile for cells under naphthalene stress. Several protein spots were analyzed and used to identify proteins involved in stress response, metabolism, and energy production, including a lignostilbene dioxygenase. These results provide a model for understanding the molecular response of Frankia to common soil pollutants, which may be required for survival and proliferation of the bacterium and their hosts in polluted environments.

Complete genome sequence of the naphthalene-degrading bacterium Pseudomonas stutzeri AN10 (CCUG 29243)

Pseudomonas stutzeri AN10 (CCUG 29243) can be considered a model strain for aerobic naphthalene degradation. We report the complete genome sequence of this bacterium. Its 4.71-Mb chromosome provides insights into other biodegradative capabilities of strain AN10 (i.e., benzoate catabolism) and suggests a high number of horizontal gene transfer events.

A culture-independent approach to unravel uncultured bacteria and functional genes in a complex microbial community

Most microorganisms in nature are uncultured with unknown functionality. Sequence-based metagenomics alone answers ‘who/what are there?’ but not ‘what are they doing and who is doing it and how?’. Function-based metagenomics reveals gene function but is usually limited by the specificity and sensitivity of screening strategies, especially the identification of clones whose functional gene expression has no distinguishable activity or phenotypes. A ‘biosensor-based genetic transducer’ (BGT) technique, which employs a whole-cell biosensor to quantitatively detect expression of inserted genes encoding designated functions, is able to screen for functionality of unknown genes from uncultured microorganisms. In this study, BGT was integrated with Stable isotope probing (SIP)-enabled Metagenomics to form a culture-independent SMB toolbox. The utility of this approach was demonstrated in the discovery of a novel functional gene cluster in naphthalene contaminated groundwater. Specifically, metagenomic sequencing of the ¹³C-DNA fraction obtained by SIP indicated that an uncultured Acidovorax sp. was the dominant key naphthalene degrader in-situ, although three culturable Pseudomonas sp. degraders were also present in the same groundwater. BGT verified the functionality of a new nag2 operon which co-existed with two other nag and two nah operons for naphthalene biodegradation in the same microbial community. Pyrosequencing analysis showed that the nag2 operon was the key functional operon in naphthalene degradation in-situ, and shared homology with both nag operons in Ralstonia sp. U2 and Polaromonas naphthalenivorans CJ2. The SMB toolbox will be useful in providing deep insights into uncultured microorganisms and unravelling their ecological roles in natural environments.

Deepening TOL and TOU catabolic pathways of Pseudomonas sp. OX1: cloning, sequencing and characterization of the lower pathways

Pseudomonas sp. OX1 is able to metabolize toluene and o-xylene through the TOU catabolic pathway, whereas its mutant M1 strain was found to be able to use m- and p-xylene as carbon and energy source, using the TOL catabolic pathway. Here we report the complete nucleotide sequence of the phe lower operon of the TOU catabolic pathway, and the sequence of the last four genes of the xyl-like lower operon of the TOL catabolic pathway. DNA sequence analysis shows the gene order within the operons to be pheCDEFGHI (phe operon) and xyl-likeQKIH (xyl-like operon), identical to the order found for the isofunctional genes of meta operons in the toluene/xylene pathway of TOL plasmid pWW0 from Pseudomonas putida mt-2 and the phenol/methylphenol pathway of pVIl50 from Pseudomonas sp. CF600. The nucleotide and the deduced amino acid sequences are homologous to the equivalent gene and enzyme sequences from other Pseudomonas meta pathways. Recombinant 2-hydroxymuconic semialdehyde dehydrogenase (HMSD) and 2-hydroxymuconic semialdehyde hydrolase (HMSH), coded by pheCD genes, respectively, and ADA and HOA enzymes from both phe and xyl operons were expressed in E. coli and steady-state kinetic analysis was carried out. The analysis of the kinetic parameters of HMSD and HMSH showed that the enzymes from Pseudomonas sp. OX1 are more specialized to channel metabolites into the two branches of the lower pathway than homologous enzymes from other pseudomonads. The kinetics parameters of recombinant ADA from phe and xyl-like operon were found to be similar to those of homologous enzymes from other Pseudomonas strains. In addition, the enzyme from xyl-like operon showed a substrate affinity three times higher than the enzyme from phe operon.

An insight into the origin and functional evolution of bacterial aromatic ring-hydroxylating oxygenases

Bacterial aromatic ring-hydroxylating oxygenases (RHOs) are multicomponent enzyme systems which have potential utility in bioremediation of aromatic compounds in the environment. To cope with the enormous diversity of aromatic compounds in the environment, this enzyme family has evolved remarkably exhibiting broad substrate specificity. RHOs are multicomponent enzymes comprising of a homo- or hetero-multimeric terminal oxygenase and one or more electron transport (ET) protein(s). The present study attempts in depicting the evolutionary scenarios that might have occurred during the evolution of RHOs, by analyzing a set of available sequences including those obtained from complete genomes. A modified classification scheme identifying four new RHO types has been suggested on the basis of their evolutionary and functional behaviours, in relation to structural configuration of substrates and preferred oxygenation site(s). The present scheme emphasizes on the fact that the phylogenetic affiliation of RHOs is distributed among four distinct 'Similarity classes', independent of the constituent ET components. Similar combination of RHO components that was previously considered to be equivalent and classified together [Kweon et al., BMC Biochemistry 9, 11 (2008)] were found here in distinct similarity classes indicating the role of substrate-binding terminal oxygenase in guiding the evolution of RHOs irrespective of the nature of constituent ET components. Finally, a model for evolution of the multicomponent RHO enzyme system has been proposed, beginning from genesis of the terminal oxygenase components followed by recruitment of constituent ET components, finally evolving into various 'extant' RHO types.

Degradation of 2,3-dihydroxybenzoate by a novel meta-cleavage pathway

2,3-Dihydroxybenzoate is the precursor in the biosynthesis of several siderophores and an important plant secondary metabolite that, in bacteria, can be degraded via meta-cleavage of the aromatic ring. The dhb cluster of Pseudomonas reinekei MT1 encodes a chimeric meta-cleavage pathway involved in the catabolism of 2,3-dihydroxybenzoate. While the first two enzymes, DhbA and DhbB, are phylogenetically related to those involved in 2,3-dihydroxy-p-cumate degradation, the subsequent steps are catalyzed by enzymes related to those involved in catechol degradation (DhbCDEFGH). Characterization of kinetic properties of DhbA extradiol dioxygenase identified 2,3-dihydroxybenzoate as the preferred substrate. Deletion of the encoding gene impedes growth of P. reinekei MT1 on 2,3-dihydroxybenzoate. DhbA catalyzes 3,4-dioxygenation with 2-hydroxy-3-carboxymuconate as the product, which is then decarboxylated by DhbB to 2-hydroxymuconic semialdehyde. This compound is then subject to dehydrogenation and further degraded to citrate cycle intermediates. Transcriptional analysis revealed genes of the dhB gene cluster to be highly expressed during growth with 2,3-dihydroxybenzoate, whereas a downstream-localized gene encoding 2-hydroxymuconic semialdehyde hydrolase, dispensable for 2,3-dihydroxybenzoate metabolism but crucial for 2,3-dihydroxy-p-cumate degradation, was only marginally expressed. This is the first report describing a gene cluster encoding enzymes for the degradation of 2,3-dihydroxybenzoate.

Heterologous expression of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes from a novel pyrene-degrading betaproteobacterium

A betaproteobacterium within the family Rhodocyclaceae previously identified as a pyrene degrader via stable-isotope probing (SIP) of contaminated soil (designated pyrene group 1 or PG1) was cultivated as the dominant member of a mixed bacterial culture. A metagenomic library was constructed, and the largest contigs were analyzed for genes associated with polycyclic aromatic hydrocarbon (PAH) metabolism. Eight pairs of genes with similarity to the α- and β-subunits of ring-hydroxylating dioxygenases (RHDs) associated with aerobic bacterial PAH degradation were identified and linked to PG1 through PCR analyses of a simplified enrichment culture. In tandem with a ferredoxin and reductase found in close proximity to one pair of RHD genes, six of the RHDs were cloned and expressed in Escherichia coli. Each cloned RHD was tested for activity against nine PAHs ranging in size from two to five rings. Despite differences in their predicted protein sequences, each of the six RHDs was capable of transforming phenanthrene and pyrene. Three RHDs could additionally transform naphthalene and fluorene, and these genotypes were also associated with the ability of the E. coli constructs to convert indole to indigo. Only one of the six cloned RHDs was capable of transforming anthracene and benz[a]anthracene. None of the tested RHDs were capable of significantly transforming fluoranthene, chrysene, or benzo[a]pyrene.

Mangrove microniches determine the structural and functional diversity of enriched petroleum hydrocarbon-degrading consortia

In this study, the combination of culture enrichments and molecular tools was used to identify bacterial guilds, plasmids and functional genes potentially important in the process of petroleum hydrocarbon (PH) decontamination in mangrove microniches (rhizospheres and bulk sediment). In addition, we aimed to recover PH-degrading consortia (PHDC) for future use in remediation strategies. The PHDC were enriched with petroleum from rhizosphere and bulk sediment samples taken from a mangrove chronically polluted with oil hydrocarbons. Southern blot hybridization (SBH) assays of PCR amplicons from environmental DNA before enrichments resulted in weak positive signals for the functional gene types targeted, suggesting that PH-degrading genotypes and plasmids were in low abundance in the rhizosphere and bulk sediments. However, after enrichment, these genes were detected and strong microniche-dependent differences in the abundance and composition of hydrocarbonoclastic bacterial populations, plasmids (IncP-1α, IncP-1β, IncP-7 and IncP-9) and functional genes (naphthalene, extradiol and intradiol dioxygenases) were revealed by in-depth molecular analyses [PCR-denaturing gradient gel electrophoresis and hybridization (SBH and microarray)]. Our results suggest that, despite the low abundance of PH-degrading genes and plasmids in the environmental samples, the original bacterial composition of the mangrove microniches determined the structural and functional diversity of the PHDC enriched.

Characterization of indigenous Rhodococcus sp. 602, a strain able to accumulate triacylglycerides from naphthyl compounds under nitrogen-starved conditions

An indigenous bacterium (strain 602) isolated in this study from a polluted soil sample collected in Patagonia (Argentina) was investigated in relation to its metabolic responses under unbalanced growth conditions. This strain was identified as Rhodococcus sp. by molecular analyses. Strain 602 showed the ability to degrade a wide range of compounds and to synthesize triacylglycerols under nitrogen-limiting conditions. Cells were also able to accumulate triacylglycerols during cultivation on naphthalene and naphthyl-1-dodecanoate. Triacylglycerols produced by resting cells in the presence of naphthyl-1-dodecanoate contained only short-chain length fatty acids (from C(8) to C(12)), suggesting an initial attack of the substrate by an esterase releasing 1-naphthol and dodecanoic acid, which was subsequently degraded by beta-oxidation. On the other hand, naphthalene seemed to be degraded by a mono-oxygenase yielding 1-naphthol, which was then transformed to 4-hydroxy-1-tetralone and to other possible metabolic intermediates. On the basis of the results obtained, a pathway involved in the metabolism of both aromatic compounds under nitrogen starvation by strain 602 is proposed. The results also demonstrated that Rhodococcus sp. 602 maintains its metabolic activity even in the absence of a nitrogen source. Intracellular triacylglycerols may help cells to maintain their catabolic activities under these growth-restricting conditions.

TnpR encoded by an ISPpu12 isoform regulates transposition of two different ISL3-like insertion sequences in Pseudomonas stutzeri after conjugative interaction

Pseudomonas stutzeri AN10 has two ISL3-like insertion sequences (ISs). One of them has been recently described as ISPst9. In this study we show that the second IS, situated 4.5 kb upstream of ISPst9, is an isoform of ISPpu12 from Pseudomonas putida mt-2. Although both ISL3-like ISs are flanked by nearly identical (21/24 conserved residues) inverted repeats (IRs) and harbor similar transposases (93% amino acid identity), they differ in their accompanying genes. As described for ISPst9, the isoform of ISPpu12 also transposes by a conservative mechanism, forms circular double-stranded DNA (dsDNA) transposition intermediates, and is induced by interaction with the conjugative strain Escherichia coli S17-1lambda(pir) (conjugative interaction) but not with the nonconjugative E. coli DH5alpha. In fact, we demonstrate that ISPst9 transposition after conjugative interaction occurs only when ISPpu12 is present, indicating that ISPpu12 is upregulating transposition of both ISs under such conditions. We also demonstrate that this conjugative interaction-mediated induction of ISPpu12 is not exclusive to the P. stutzeri AN10 strain but is a more general phenomenon, at least in Pseudomonas. Mutation of TnpR, a MerR-like transcriptional regulator present in ISPpu12 but not in ISPst9, reduced the transcription of tnpA (ISPpu12 transposase-encoding gene) and decreased formation of circular dsDNA transposition intermediates after conjugative interaction. Complementation of the TnpR mutant restored the phenotype. In addition, the presence of TnpR in an ISPpu12-free genetic background did not induce ISPst9 after conjugative interaction. Thus, our results suggest that TnpR, after conjugative interaction, activates transcription of tnpA of ISPpu12. Then, TnpA of ISPpu12 would bind to IRs of both ISs, ISPpu12 and ISPst9, causing their transposition.

Degradation of chloroaromatics by Pseudomonas putida GJ31: assembled route for chlorobenzene degradation encoded by clusters on plasmid pKW1 and the chromosome

Pseudomonas putida GJ31 has been reported to grow on chlorobenzene using a meta-cleavage pathway with chlorocatechol 2,3-dioxygenase (CbzE) as a key enzyme. The CbzE-encoding gene was found to be localized on the 180 kb plasmid pKW1 in a cbzTEXGS cluster, which is flanked by transposases and encodes only a partial (chloro)catechol meta-cleavage pathway comprising ferredoxin reductase, chlorocatechol 2,3-dioxygenase, an unknown protein, 2-hydroxymuconic semialdehyde dehydrogenase and glutathione S-transferase. Downstream of cbzTEXGS are located cbzJ, encoding a novel type of 2-hydroxypent-2,4-dienoate hydratase, and a transposon region highly similar to Tn5501. Upstream of cbzTEXGS, traNEOFG transfer genes were found. The search for gene clusters possibly completing the (chloro)catechol metabolic pathway of GJ31 revealed the presence of two additional catabolic gene clusters on pKW1. The mhpRBCDFETP cluster encodes enzymes for the dissimilation of 2,3-dihydroxyphenylpropionate in a novel arrangement characterized by the absence of a gene encoding 3-(3-hydroxyphenyl)propionate monooxygenase and the presence of a GntR-type regulator, whereas the nahINLOMKJ cluster encodes part of the naphthalene metabolic pathway. Transcription studies supported their possible involvement in chlorobenzene degradation. The upper pathway cluster, comprising genes encoding a chlorobenzene dioxygenase and a chlorobenzene dihydrodiol dehydrogenase, was localized on the chromosome. A high level of transcription in response to chlorobenzene revealed it to be crucial for chlorobenzene degradation. The chlorobenzene degradation pathway in strain GJ31 is thus a mosaic encoded by four gene clusters.

Bioactive substances produced by marine isolates of Pseudomonas

Pseudomonas is a genus of non-fermentative gram-negative Gammaproteobacteria found both on land and in the water. Many terrestrial isolates of this genus have been studied extensively. While many produce bioactive substances, enzymes, and biosurfactants, other Pseudomonas isolates are used for biological control of plant diseases and bioremediation. In contrast, only a few marine isolates of this genus have been described that produce novel bioactive substances. The chemical structures of the bioactive substances from marine Pseudomonas are diverse, including pyroles, pseudopeptide pyrrolidinedione, phloroglucinol, phenazine, benzaldehyde, quinoline, quinolone, phenanthren, phthalate, andrimid, moiramides, zafrin and bushrin. Some of these bioactive compounds are antimicrobial agents, and dibutyl phthalate and di-(2-ethylhexyl) phthalate have been reported to be cathepsin B inhibitors. In addition to being heterogeneous in terms of their structures, the antibacterial substances produced by Pseudomonas also have diverse mechanisms of action: some affect the bacterial cell membrane, causing bacterial cell lysis, whereas others act as acetyl-CoA carboxylase and nitrous oxide synthesis inhibitors. Marine Pseudomonas spp. have been isolated from a wide range of marine environments and are a potential untapped source for medically relevant bioactive substances.

Purine utilization by Klebsiella oxytoca M5al: genes for ring-oxidizing and -opening enzymes

The enterobacterium Klebsiella oxytoca uses a variety of inorganic and organic nitrogen sources, including purines, nitrogen-rich compounds that are widespread in the biosphere. We have identified a 23-gene cluster that encodes the enzymes for utilizing purines as the sole nitrogen source. Growth and complementation tests with insertion mutants, combined with sequence comparisons, reveal functions for the products of these genes. Here, we report our characterization of 12 genes, one encoding guanine deaminase and the others encoding enzymes for converting (hypo)xanthine to allantoate. Conventionally, xanthine dehydrogenase, a broadly distributed molybdoflavoenzyme, catalyzes sequential hydroxylation reactions to convert hypoxanthine via xanthine to urate. Our results show that these reactions in K. oxytoca are catalyzed by a two-component oxygenase (HpxE-HpxD enzyme) homologous to Rieske nonheme iron aromatic-ring-hydroxylating systems, such as phthalate dioxygenase. Our results also reveal previously undescribed enzymes involved in urate oxidation to allantoin, catalyzed by a flavoprotein monooxygenase (HpxO enzyme), and in allantoin conversion to allantoate, which involves allantoin racemase (HpxA enzyme). The pathway also includes the recently described PuuE allantoinase (HpxB enzyme). The HpxE-HpxD and HpxO enzymes were discovered independently by de la Riva et al. (L. de la Riva, J. Badia, J. Aguilar, R. A. Bender, and L. Baldoma, J. Bacteriol. 190:7892-7903, 2008). Thus, several enzymes in this K. oxytoca purine utilization pathway differ from those in other microorganisms. Isofunctional homologs of these enzymes apparently are encoded by other species, including Acinetobacter, Burkholderia, Pseudomonas, Saccharomyces, and Xanthomonas.

Conjugative interaction induces transposition of ISPst9 in Pseudomonas stutzeri AN10

ISPst9 is an ISL3-like insertion sequence (IS) that was recently described in the naphthalene-degrading organism Pseudomonas stutzeri strain AN10. In this paper we describe a novel strong IS regulation stimulus; transposition of ISPst9 is induced in all P. stutzeri AN10 cells after conjugative interaction with Escherichia coli. Thus, we observed that in all P. stutzeri AN10 cells that received genetic material by conjugation the ISPst9 genomic dose and/or distribution was changed. Furthermore, ISPst9 transposition was also observed when P. stutzeri AN10 cells were put in contact with the plasmidless conjugative strain E. coli S17-1lambda(pir), but not when they were put in contact with E. coli DH5alpha (a nonconjugative strain). The mechanism of ISPst9 transposition was analyzed, and transposition was shown to proceed by excision from the donor DNA using a conservative mechanism, which generated 3- to 10-bp deletions of the flanking DNA. Our results indicate that ISPst9 transposes, forming double-stranded DNA circular intermediates consisting of the IS and a 5-bp intervening DNA sequence probably derived from the ISPst9 flanking regions. The kinetics of IS circle formation are also described.

Resolving genetic functions within microbial populations: in situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization

Prokaryotes represent one-half of the living biomass on Earth, with the vast majority remaining elusive to culture and study within the laboratory. As a result, we lack a basic understanding of the functions that many species perform in the natural world. To address this issue, we developed complementary population and single-cell stable isotope ((13)C)-linked analyses to determine microbial identity and function in situ. We demonstrated that the use of rRNA/mRNA stable isotope probing (SIP) recovered the key phylogenetic and functional RNAs. This was followed by single-cell physiological analyses of these populations to determine and quantify in situ functions within an aerobic naphthalene-degrading groundwater microbial community. Using these culture-independent approaches, we identified three prokaryote species capable of naphthalene biodegradation within the groundwater system: two taxa were isolated in the laboratory (Pseudomonas fluorescens and Pseudomonas putida), whereas the third eluded culture (an Acidovorax sp.). Using parallel population and single-cell stable isotope technologies, we were able to identify an unculturable Acidovorax sp. which played the key role in naphthalene biodegradation in situ, rather than the culturable naphthalene-biodegrading Pseudomonas sp. isolated from the same groundwater. The Pseudomonas isolates actively degraded naphthalene only at naphthalene concentrations higher than 30 muM. This study demonstrated that unculturable microorganisms could play important roles in biodegradation in the ecosystem. It also showed that the combined RNA SIP-Raman-fluorescence in situ hybridization approach may be a significant tool in resolving ecology, functionality, and niche specialization within the unculturable fraction of organisms residing in the natural environment.

Microbial biodegradation of polyaromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are widespread in various ecosystems and are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. Because of their hydrophobic nature, most PAHs bind to particulates in soil and sediments, rendering them less available for biological uptake. Microbial degradation represents the major mechanism responsible for the ecological recovery of PAH-contaminated sites. The goal of this review is to provide an outline of the current knowledge of microbial PAH catabolism. In the past decade, the genetic regulation of the pathway involved in naphthalene degradation by different gram-negative and gram-positive bacteria was studied in great detail. Based on both genomic and proteomic data, a deeper understanding of some high-molecular-weight PAH degradation pathways in bacteria was provided. The ability of nonligninolytic and ligninolytic fungi to transform or metabolize PAH pollutants has received considerable attention, and the biochemical principles underlying the degradation of PAHs were examined. In addition, this review summarizes the information known about the biochemical processes that determine the fate of the individual components of PAH mixtures in polluted ecosystems. A deeper understanding of the microorganism-mediated mechanisms of catalysis of PAHs will facilitate the development of new methods to enhance the bioremediation of PAH-contaminated sites.

Cloning and characterization of a catechol-degrading gene cluster from 3,4-dichloroaniline degrading bacterium Pseudomonas sp. KB35B

We recently isolated a bacterium, Pseudomonas sp. KB35B, capable of growth on 3,4-dichloroaniline (DCA) as a sole carbon source. The isolated strain showed a high level of catechol 2,3-dioxygenase (CD-2,3) activity in the presence of 3,4-DCA. In an attempt to elucidate the relationship between biodegradation of 3,4-DCA and CD-2,3 activity, the genes encoding enzymes for the catabolic pathway of catechol were cloned and sequenced from the chromosomal DNA. The sequence analysis of the 10752 bp DNA fragment revealed 12 open reading frames in the order of nahRGTHINLOMKJX. Among the 12 genes, nahHINLOMK genes encode enzymes for the metabolism of catechol to TCA cycle intermediates. The nahR gene is the LysR type transcriptional regulator, and the nahH gene encodes CD-2,3 for meta-cleavages of catechol. 2-Hydroxymuconic semialdehyde hydrolase, 2-oxypent-4-dienoate hydratase, and 4-hydroxy-2-oxovalerate aldolase encoded by nahLMN genes are responsible for the three steps after meta-cleavages of catechol. The current results suggested that Pseudomonas sp. KB35B degrades 3,4-DCA via the meta-cleavage pathway of catechol.

Cross-regulation of biphenyl- and salicylate-catabolic genes by two regulatory systems in Pseudomonas pseudoalcaligenes KF707

Pseudomonas pseudoalcaligenes KF707 grows on biphenyl and salicylate as sole sources of carbon. The biphenyl-catabolic (bph) genes are organized as bphR1A1A2(orf3)A3A4BCX0X1X2X3D, encoding the enzymes for conversion of biphenyl to acetyl coenzyme A. In this study, the salicylate-catabolic (sal) gene cluster encoding the enzymes for conversion of salicylate to acetyl coenzyme A were identified 6.6-kb downstream of the bph gene cluster along with a second regulatory gene, bphR2. Both the bph and sal genes were cross-regulated positively and/or negatively by the two regulatory proteins, BphR1 and BphR2, in the presence or absence of the effectors. The BphR2 binding sequence exhibits homology with the NahR binding sequences in various naphthalene-degrading bacteria. Based on previous studies and the present study we propose a new regulatory model for biphenyl and salicylate catabolism in strain KF707.