The evolution of pathways for aromatic hydrocarbon oxidation in Pseudomonas

Engineering of Rieske dioxygenase variants with improved cis-dihydroxylation activity for benzoates

Rieske dioxygenases have a long history of being utilized as green chemical tools in the organic synthesis of high-value compounds, due to their capacity to perform the cis-dihydroxylation of a wide variety of aromatic substrates. The practical utility of these enzymes has been hampered however by steric and electronic constraints on their substrate scopes, resulting in limited reactivity with certain substrate classes. Herein, we report the engineering of a widely used member of the Rieske dioxygenase class of enzymes, toluene dioxygenase (TDO), to produce improved variants with greatly increased activity for the cis-dihydroxylation of benzoates. Through rational mutagenesis and screening, TDO variants with substantially improved activity over the wild-type enzyme were identified. Homology modeling, docking studies, molecular dynamics simulations, and substrate tunnel analysis were applied in an effort to elucidate how the identified mutations resulted in improved activity for this polar substrate class. These analyses revealed modification of the substrate tunnel as the likely cause of the improved activity observed with the best-performing enzyme variants.

The Complete Genome Sequence of a Gossypol-Degrading Bacterial Strain, Raoultella sp. YL01

Cottonseed meal is an important source of plant protein for the meal fodder materials. But its usage in animal breeding industry is limited by a type of toxic phenol, gossypol, that has toxic effects on animal health. Microbial degradation is a promising way to lower down gossypol in cottonseed meal. However, the molecular mechanisms of bio-degradation of gossypol is still unclear. In this study we isolated a gossypol-degrading bacterial strain, YL01, and sequenced its complete genome via Oxford Nanopore sequencing method. There is a chromosome (5,737,005 bp) and a plasmid (136,446 bp) in YL01. 5489 protein coding genes in total were functionally annotated. 16S rRNA analysis showed that YL01 taxonomically belongs to the genus of Raoultella. YL01 is the first published complete genome sequence of microbes capable of gossypol degradation. Gene function annotation showed that 126 protein coding genes may involve in gossypol catabolism. Sequence similarity analysis showed that, as the only gossypol-degrading strain in the genus of Raoultella, YL01 uniquely holds 260 genes that are not possessed by other Raoultella strains. Our work gives a preliminary list for genes responsible for gossypol degradation but further investigations are needed to completely disclose this molecular processes.

Bacteria are better predictive biomarkers of environmental estrogen transmission than fungi

The heavy reliance on estrogens in the food industry worldwide greatly contributes to the environmental release of these compounds, begetting serious public concern of their fate. Various microorganisms capable of estrogen degradation, and their catabolic pathways, have been isolated, suggesting that they can eliminate estrogens in both engineered and natural environments. Nonetheless, it remains little understood as to how potential estrogen-degrading microorganisms are distributed within those habitats. An estrogen transmission chain from swine manure to compost, compost-amended soil, and neighboring agricultural soil was investigated in five suburban areas of Beijing, China. The concentrations of major estrogen classes decreased by > 90% from manure to soils, which did not co-vary with environmental antibiotics and heavy metal concentrations. Many bacterial taxa, such as Lactobacillus and Bacteroides, could serve as potential biomarkers of estrogen concentrations, while fungi were only occasionally accurate. To explain this phenomenon, stochasticity was found to be dominant in shaping the fungal communities across all samples, while deterministic selection, arising from biotic interactions, was important for bacterial communities. Metabolic genes involved in oxidizing phenol and catalyzing oxidative ring cleavage of catechol were detected, co-varying with estrogen concentrations. These findings are important as identifying microbial biomarkers of estrogen dynamics, spanning the levels of both taxonomy and functional genes, provides valuable information for assessing estrogen bioavailability and biomarking of estrogen fate in the environment.

The Chironomid Microbiome Plays a Role in Protecting Its Host From Toxicants

Organisms are assemblages of the host and their endogenous bacteria, which are defined as microbiomes. The host and its microbiome undergo a mutual evolutionary process to adapt to changes in the environment. Chironomids (Diptera; Chironomidae), are aquatic insects that grow and survive in polluted environments; however, the mechanisms that protect them under these conditions are not fully understood. Here we present evidence that the chironomids’ microbiome enables them to survival in polluted environments. It has been demonstrated that about 40% of the microbiota that inhabit Chironomus transvaalensis egg masses and larvae has the potential to detoxify different toxicants. Metagenomic analysis of Chironomus ramosus larvae demonstrated the presence of genes in the insects’ microbiome that can help the insects to survive in hostile environments. A set of experiments demonstrated that short exposure of C. transvaalensis larvae to metals significantly changed their microbiota composition in comparison to unexposed larvae. Another experiment, that followed Koch’s postulates, demonstrated that disinfected C. transvaalensis larvae can survive toxic lead and chromium exposure when they are recolonized with bacteria that can detoxify these toxic metals. This accumulating research, points to the conclusion that the chironomid microbiome plays a role in protecting its host from toxicants.

Genome analysis of the metabolically versatile Pseudomonas umsongensis GO16: the genetic basis for PET monomer upcycling into polyhydroxyalkanoates

The throwaway culture related to the single-use materials such as polyethylene terephthalate (PET) has created a major environmental concern. Recycling of PET waste into biodegradable plastic polyhydroxyalkanoate (PHA) creates an opportunity to improve resource efficiency and contribute to a circular economy. We sequenced the genome of Pseudomonas umsongensis GO16 previously shown to convert PET-derived terephthalic acid (TA) into PHA and performed an in-depth genome analysis. GO16 can degrade a range of aromatic substrates in addition to TA, due to the presence of a catabolic plasmid pENK22. The genetic complement required for the degradation of TA via protocatechuate was identified and its functionality was confirmed by transferring the tph operon into Pseudomonas putida KT2440, which is unable to utilize TA naturally. We also identified the genes involved in ethylene glycol (EG) metabolism, the second PET monomer, and validated the capacity of GO16 to use EG as a sole source of carbon and energy. Moreover, GO16 possesses genes for the synthesis of both medium and short chain length PHA and we have demonstrated the capacity of the strain to convert mixed TA and EG into PHA. The metabolic versatility of GO16 highlights the potential of this organism for biotransformations using PET waste as a feedstock.

Development and application of a high throughput assay system for the detection of Rieske dioxygenase activity

Herein we report the development of a new periodate-based reactive assay system for the fluorescent detection of the cis-diol metabolites produced by Rieske dioxygenases. This sensitive and diastereoselective assay system successfully evaluates the substrate scope of Rieske dioxygenases and determines the relative activity of a rationally designed Rieske dioxygenase variant library. The high throughput capacity of the assay system enables rapid and efficient substrate scope investigations and screening of large dioxygenase variant libraries.

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

Wastewater treatment plants (WWTPs) are crucial for producing clean effluents from polluting sources such as hospitals, industries, and municipalities. In recent decades, many new organic compounds have ended up in surface waters in concentrations that, while very low, cause (chronic) toxicity to countless organisms. These organic micropollutants (OMPs) are usually quite recalcitrant and not sufficiently removed during wastewater treatment. Microbial degradation plays a pivotal role in OMP conversion. Microorganisms can adapt their metabolism to the use of novel molecules via mutations and rearrangements of existing genes in new clusters. Many catabolic genes have been found adjacent to mobile genetic elements (MGEs), which provide a stable scaffold to host new catabolic pathways and spread these genes in the microbial community. These mobile systems could be engineered to enhance OMP degradation in WWTPs, and this review aims to summarize and better understand the role that MGEs might play in the degradation and wastewater treatment process. Available data about the presence of catabolic MGEs in WWTPs are reviewed, and current methods used to identify and measure MGEs in environmental samples are critically evaluated. Finally, examples of how these MGEs could be used to improve micropollutant degradation in WWTPs are outlined. In the near future, advances in the use of MGEs will hopefully enable us to apply selective augmentation strategies to improve OMP conversion in WWTPs.

Complete Genome Sequence and Biodegradation Characteristics of Benzoic Acid-Degrading Bacterium Pseudomonas sp. SCB32

Allelochemicals are metabolites produced by living organisms that have a detrimental effect on other species when released into the environment. These chemicals play critical roles in the problems associated with crop replanting. Benzoic acid is a representative allelochemical found in root exudates and rhizosphere soil of crops and inhibits crop growth. The bioremediation of allelochemicals by microorganisms is an efficient decontamination process. In this research, a bacterial strain capable of degrading benzoic acid as the sole carbon source was isolated. The genome of the strain was sequenced, and biodegradation characteristics and metabolic mechanisms were examined. Strain SCB32 was identified as Pseudomonas sp. based on 16S rRNA gene analysis coupled with physiological and biochemical analyses. The degradation rate of 800 mg L-1 benzoic acid by strain SCB32 was greater than 97.0% in 24 h. The complete genome of strain SCB32 was 6.3 Mbp with a GC content of 64.6% and 5960 coding genes. Potential benzoic acid degradation genes were found by comparison to the KEGG database. Some key intermediate metabolites of benzoic acid, such as catechol, were detected by gas chromatography-mass spectrometry. The biodegradation pathway of benzoic acid, the ortho pathway, is proposed for strain SCB32 based on combined data from genome annotation and mass spectrometry. Moreover, the benzoic acid degradation products from strain SCB32 were essentially nontoxic to lettuce seedlings, while seeds in the benzoic acid-treated group showed significant inhibition of germination. This indicates a possible application of strain SCB32 in the bioremediation of benzoic acid contamination in agricultural environments.

Biodegradation of phenol by Chlamydomonas reinhardtii

The data presented in this particular study demonstrate that the biodegradation of phenol by Chlamydomonas reinhardtii is a dynamic bioenergetic process mainly affected by the production of catechol and the presence of a growth-promoting substrate in the culture medium. The study focused on the regulation of the bioenergetic equilibrium resulting from production of catechol after phenol oxidation. Catechol was identified by HPLC-UV and HPLC-ESI-MS/MS. Growth measurements revealed that phenol is a growth-limiting substrate for microalgal cultures. The Chlamydomonas cells proceed to phenol biodegradation because they require carbon reserves for maintenance of homeostasis. In the presence of acetic acid (a growth-promoting carbon source), the amount of catechol detected in the culture medium was negligible; apparently, acetic acid provides microalgae with sufficient energy reserves to further biodegrade catechol. It has been shown that when microalgae do not have sufficient energy reserves, a significant amount of catechol is released into the culture medium. Chlamydomonas reinhardtii acts as a versatile bioenergetic machine by regulating its metabolism under each particular set of growth conditions, in order to achieve an optimal balance between growth, homeostasis maintenance and biodegradation of phenol. The novel findings of this study reveal a paradigm showing how microalgal metabolic versatility can be used in the bioremediation of the environment and in potential large-scale applications.

Response of aquatic microbial communities and bioindicator modelling of hydraulic fracturing flowback and produced water

The response of microbial communities to releases of hydraulic fracturing flowback and produced water (PW) may influence ecosystem functions. However, knowledge of the effects of PW spills on freshwater microbiota is limited. Here, we conducted two separate experiments: 16S rRNA gene sequencing combined with random forests modelling was used to assess freshwater community changes in simulated PW spills by volume from 0.05% to 50%. In a separate experiment, live/dead cell viability in a freshwater community was tested during exposure to 10% PW by volume. Three distinct patterns of microbial community shifts were identified: (i) indigenous freshwater genera remained dominant in <2.5% PW, (ii) from 2.5% to 5% PW, potential PW organic degraders such as Pseudomonas, Rheinheimera and Brevundimonas became dominant, and (iii) no significant change in the relative abundance of taxa was observed in >5% PW. Microbial taxa including less abundant genera such as Cellvibrio were potential bioindicators for the degree of contamination with PW. Additionally, live cells were quickly damaged by adding 10% PW, but cell counts recovered in the following days. Our study shows that the responses of freshwater microbiota vary by spill size, and these responses show promise as effective fingerprints for PW spills in aquatic environments.

Biochar as simultaneous shelter, adsorbent, pH buffer, and substrate of Pseudomonas citronellolis to promote biodegradation of high concentrations of phenol in wastewater

Microbial degradation is an elimination method for removal of organic contaminants from soil and water. However, the main factor limiting its practical application is high bacterial sensitivity to environmental factors such as pH, toxicity, and mass transfer. In this study, biochar was produced pyrolytically from peanut shells at 350 °C, 550 °C, and 750 °C (referred to as BC350, BC550, and BC750, respectively) and their promotion on phenol biodegradation in wastewater by the bacterium Pseudomonas citronellolis was investigated. Higher initial phenol concentration (>400 mg L^-1) showed obvious inhibition on biodegradation with the removal efficiencies being less than 46%, and even the bacterium failed to survive at the phenol concentrations of higher than 1000 mg L^-1. With biochar incorporated, the removal efficiencies of phenol increased from below 46% to up to 99% at the initial concentrations of 400-1200 mg L^-1. Immobilization of strains in biochar by calcium alginate further increased the microbial tolerance to high concentrations of phenol (i.e., 63% removal at 1200 mg L^-1). Scanning electron microscopy demonstrated that biochar acted as shelter to support the bacterium to struggle with extreme conditions. The initial adsorption of phenol by biochar alleviated the initial toxicity of phenol to bacterium and the subsequent gradual desorption controlled the bioavailability of phenol. In this regard, BC350 showed a comparable sorption capacity with BC550 and BC750, while a higher desorption potential than them, thus balanced better the toxicity and bioavailability of phenol to microbes. Alkalinity of BC550 and BC750 played important roles in rescuing the microbes from being damaged by pH shock via neutralizing the fast generation of acidic intermediates. The extractable organic substances in BC350 could be consumed by bacterium as substrates, which was confirmed by incubating the strains in water-extractable solution. Results of this study indicate that incorporation of microbes with biochar could promote the biodegradation of high concentration organic wastewater.

Evaluation of aromatic hydrocarbon decomposition catalyzed by the dioxygenase system and substitution of ferredoxin and ferredoxin reductase

In this study, the catalytic activity and kinetic characteristics of the aromatic hydrocarbon dioxygenase system and the possibility of substituting its ferredoxin and ferredoxin reductase components were evaluated. The genes encoding toluene dioxygenase and toluene dihydrodiol dehydrogenase were cloned from Pseudomonas putida F1, and the corresponding enzymes were overexpressed and purified to homogeneity. Oxidative hydroxylation of toluene to cis-toluene dihydrodiol was catalyzed by toluene dioxygenase, and its subsequent dehydrogenation to 3-methylcatechol was catalyzed by toluene dihydrodiol dehydrogenase. The specific activity of the dioxygenase was 2.82 U/mg-protein, which is highly remarkable compared with the values obtained in previous researches conducted with crude extracts or insoluble forms of enzymes. Kinetic parameters, as characterized by the Hill equation, were v_max = 497.2 μM/min, K_M = 542.4 μM, and n_H = 2.2, suggesting that toluene dioxygenase has at least three cooperative binding sites for toluene. In addition, the use of alternative ferredoxins and reductases was examined. Ferredoxin cloned from CYP153 could transfer electrons to the iron sulfur protein component of toluene dioxygenase. The ferredoxin could be reduced by ferredoxin, rubredoxin, and putidaredoxin reductases of CYP153, alkane-1 monooxygenase, and camphor 5-monooxygenase, respectively. The results provide useful information regarding the effective enzymatic biotreatment of hazardous aromatic hydrocarbon contaminants.

Isolation of a novel platform bacterium for lignin valorization and its application in glucose-free cis,cis-muconate production

Microbial production of cis,cis-muconate (ccMA) from phenolic compounds obtained by chemical depolymerization of lignin is a promising approach to valorize lignin. Because microbial production requires a large amount of carbon and energy source, it is desirable to establish a ccMA-producing strain that utilizes lignin-derived phenols instead of general sources like glucose. We isolated Pseudomonas sp. strain NGC7 that grows well on various phenolic compounds derived from p-hydroxyphenyl, guaiacyl, and syringyl units of lignin. An NGC7 mutant of protocatechuate (PCA) 3,4-dioxygenase and ccMA cycloisomerase genes (NGC703) lost the ability to grow on vanillate and p-hydroxybenzoate but grew normally on syringate. Introduction of a plasmid carrying genes encoding PCA decarboxylase, flavin prenyltransferase, vanillate O-demethylase, and catechol 1,2-dioxygenase into NGC703 enabled production of 3.2 g/L ccMA from vanillate with a yield of 75% while growing on syringate. This strain also produced ccMA from birch lignin-derived phenols. All these results indicate the utility of NGC7 in glucose-free ccMA production.

Genome-based analysis for the identification of genes involved in o-xylene degradation in Rhodococcus opacus R7

BACKGROUND

Bacteria belonging to the Rhodococcus genus play an important role in the degradation of many contaminants, including methylbenzenes. These bacteria, widely distributed in the environment, are known to be a powerhouse of numerous degradation functions, due to their ability to metabolize a wide range of organic molecules including aliphatic, aromatic, polycyclic aromatic compounds (PAHs), phenols, and nitriles. In accordance with their immense catabolic diversity, Rhodococcus spp. possess large and complex genomes, which contain a multiplicity of catabolic genes, a high genetic redundancy of biosynthetic pathways and a sophisticated regulatory network. The present study aimed to identify genes involved in the o-xylene degradation in R. opacus strain R7 through a genome-based approach.

RESULTS

Using genome-based analysis we identified all the sequences in the R7 genome annotated as dioxygenases or monooxygenases/hydroxylases and clustered them into two different trees. The akb, phe and prm sequences were selected as genes encoding respectively for dioxygenases, phenol hydroxylases and monooxygenases and their putative involvement in o-xylene oxidation was evaluated. The involvement of the akb genes in o-xylene oxidation was demonstrated by RT-PCR/qPCR experiments after growth on o-xylene and by the selection of the R7-50 leaky mutant. Although the akb genes are specifically activated for o-xylene degradation, metabolic intermediates of the pathway suggested potential alternative oxidation steps, possibly through monooxygenation. This led us to further investigate the role of the prm and the phe genes. Results showed that these genes were transcribed in a constitutive manner, and that the activity of the Prm monooxygenase was able to transform o-xylene slowly in intermediates as 3,4-dimethylphenol and 2-methylbenzylalcohol. Moreover, the expression level of phe genes, homologous to the phe genes of Rhodococcus spp. 1CP and UPV-1 with a 90% identity, could explain their role in the further oxidation of o-xylene and R7 growth on dimethylphenols.

CONCLUSIONS

These results suggest that R7 strain is able to degrade o-xylene by the Akb dioxygenase system leading to the production of the corresponding dihydrodiol. Likewise, the redundancy of sequences encoding for several monooxygenases/phenol hydroxylases, supports the involvement of other oxygenases converging in the o-xylene degradation pathway in R7 strain.

Agdc1p - a Gallic Acid Decarboxylase Involved in the Degradation of Tannic Acid in the Yeast Blastobotrys (Arxula) adeninivorans

Tannins and hydroxylated aromatic acids, such as gallic acid (3,4,5-trihydroxybenzoic acid), are plant secondary metabolites which protect plants against herbivores and plant-associated microorganisms. Some microbes, such as the yeast Arxula adeninivorans are resistant to these antimicrobial substances and are able to use tannins and gallic acid as carbon sources. In this study, the Arxula gallic acid decarboxylase (Agdc1p) which degrades gallic acid to pyrogallol was characterized and its function in tannin catabolism analyzed. The enzyme has a higher affinity for gallic acid (Km -0.7 ± 0.2 mM, kcat -42.0 ± 8.2 s-1) than to protocatechuic acid (3,4-dihydroxybenzoic acid) (Km -3.2 ± 0.2 mM, kcat -44.0 ± 3.2 s-1). Other hydroxylated aromatic acids, such as 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, 2,3-dihydroxybenzoic acid, 2,4-dihydroxybenzoic acid and 2,5-dihydroxybenzoic acid are not gallic acid decarboxylase substrates. A. adeninivorans G1212/YRC102-AYNI1-AGDC1, which expresses the AGDC1 gene under the control of the strong nitrate inducible AYNI1 promoter achieved a maximum gallic acid decarboxylase activity of 1064.4 U/l and 97.5 U/g of dry cell weight in yeast grown in minimal medium with nitrate as nitrogen source and glucose as carbon source. In the same medium, gallic acid decarboxylase activity was not detected for the control strain G1212/YRC102 with AGDC1 expression under the control of the endogenous promoter. Gene expression analysis showed that AGDC1 is induced by gallic acid and protocatechuic acid. In contrast to G1212/YRC102-AYNI1-AGDC1 and G1212/YRC102, A. adeninivorans G1234 [Δagdc1] is not able to grow on medium with gallic acid as carbon source but can grow in presence of protocatechuic acid. This confirms that Agdc1p plays an essential role in the tannic acid catabolism and could be useful in the production of catechol and cis,cis-muconic acid. However, the protocatechuic acid catabolism via Agdc1p to catechol seems to be not the only degradation pathway.

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.

Quantitative response relationships between degradation rates and functional genes during the degradation of beta-cypermethrin in soil

In the present study, the degradation mechanisms of beta-cypermethrin and its metabolites in soil were explored through the quantitative response relationships between the degradation rates and related functional genes. We found that the degradation rate of beta-cypermethrin was rapid in unsterilized soil but not in sterilized soil, which indicated that the degradation process is microbially based. Moreover, three metabolites (3-phenoxybenzoic acid, phenol and protocatechuic acid) were detected during the degradation process and used to identify the degradation pathway and functional genes related to the degradation process. The key rate-limiting functional genes were pytH and pobA, and the relative contributions of these genes to the degradation process were examined with a path analysis. The path analysis revealed that the genes pobA and pytH had the greatest direct effects on the degradation of beta-cypermethrin (pobA), alpha-cypermethrin (pobA), theta-cypermethrin (pytH) and 3-phenoxybenzoic acid (pytH).

Chironomid microbiome

Chironomids are abundant insects in freshwater habitats. They undergo a complete metamorphosis of four life stages: eggs, larvae, and pupae in water, and a terrestrial adult stage. Chironomids are known to be pollution-tolerant, but little is known about their resistance mechanisms to toxic substances. Here we review current knowledge regarding the chironomid microbiome. Chironomids were found as natural reservoirs of Vibrio cholerae and Aeromonas spp. A stable bacterial community was found in the egg masses and the larvae when both culture-dependent and -independent methods were used. A large portion of the endogenous bacterial species was closely related to species known as toxicant degraders. Bioassays based on Koch's postulates demonstrated that the chironomid microbiome plays a role in protecting its host from toxic hexavalent chromium and lead. V. cholerae, a stable resident in chironomids, is present at low prevalence. It degrades the egg masses by secreting haemagglutinin/protease, prevents eggs from hatching, and exhibits host pathogen interactions with chironomids. However, the nutrients from the degraded egg masses may support the growth of the other microbiome members and consequently control V. cholerae numbers in the egg mass. V. cholerae, other chironomid endogenous bacteria, and their chironomid host exhibit complex mutualistic relationships.

A framework to gauge the epidemic potential of plant pathogens in environmental reservoirs: the example of kiwifruit canker

New economically important diseases on crops and forest trees emerge recurrently. An understanding of where new pathogenic lines come from and how they evolve is fundamental for the deployment of accurate surveillance methods. We used kiwifruit bacterial canker as a model to assess the importance of potential reservoirs of new pathogenic lineages. The current kiwifruit canker epidemic is at least the fourth outbreak of the disease on kiwifruit caused by Pseudomonas syringae in the mere 50 years in which this crop has been cultivated worldwide, with each outbreak being caused by different genetic lines of the bacterium. Here, we ask whether strains in natural (non-agricultural) environments could cause future epidemics of canker on kiwifruit. To answer this question, we evaluated the pathogenicity, endophytic colonization capacity and competitiveness on kiwifruit of P. syringae strains genetically similar to epidemic strains and originally isolated from aquatic and subalpine habitats. All environmental strains possessing an operon involved in the degradation of aromatic compounds via the catechol pathway grew endophytically and caused symptoms in kiwifruit vascular tissue. Environmental and epidemic strains showed a wide host range, revealing their potential as future pathogens of a variety of hosts. Environmental strains co-existed endophytically with CFBP 7286, an epidemic strain, and shared about 20 virulence genes, but were missing six virulence genes found in all epidemic strains. By identifying the specific gene content in genetic backgrounds similar to known epidemic strains, we developed criteria to assess the epidemic potential and to survey for such strains as a means of forecasting and managing disease emergence.

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

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

Metagenomic screening for aromatic compound-responsive transcriptional regulators

We applied a metagenomics approach to screen for transcriptional regulators that sense aromatic compounds. The library was constructed by cloning environmental DNA fragments into a promoter-less vector containing green fluorescence protein. Fluorescence-based screening was then performed in the presence of various aromatic compounds. A total of 12 clones were isolated that fluoresced in response to salicylate, 3-methyl catechol, 4-chlorocatechol and chlorohydroquinone. Sequence analysis revealed at least 1 putative transcriptional regulator, excluding 1 clone (CHLO8F). Deletion analysis identified compound-specific transcriptional regulators; namely, 8 LysR-types, 2 two-component-types and 1 AraC-type. Of these, 9 representative clones were selected and their reaction specificities to 18 aromatic compounds were investigated. Overall, our transcriptional regulators were functionally diverse in terms of both specificity and induction rates. LysR- and AraC- type regulators had relatively narrow specificities with high induction rates (5-50 fold), whereas two-component-types had wide specificities with low induction rates (3 fold). Numerous transcriptional regulators have been deposited in sequence databases, but their functions remain largely unknown. Thus, our results add valuable information regarding the sequence–function relationship of transcriptional regulators.

The protective role of endogenous bacterial communities in chironomid egg masses and larvae

Insects of the family Chironomidae, also known as chironomids, are distributed worldwide in a variety of water habitats. These insects display a wide range of tolerance toward metals and organic pollutions. Bacterial species known for their ability to degrade toxicants were identified from chironomid egg masses, leading to the hypothesis that bacteria may contribute to the survival of chironomids in polluted environments. To gain a better understanding of the bacterial communities that inhabit chironomids, the endogenous bacteria of egg masses and larvae were studied by 454-pyrosequencing. The microbial community of the egg masses was distinct from that of the larval stage, most likely due to the presence of one dominant bacterial Firmicutes taxon, which consisted of 28% of the total sequence reads from the larvae. This taxon may be an insect symbiont. The bacterial communities of both the egg masses and the larvae were found to include operational taxonomic units, which were closely related to species known as toxicant degraders. Furthermore, various bacterial species with the ability to detoxify metals were isolated from egg masses and larvae. Koch-like postulates were applied to demonstrate that chironomid endogenous bacterial species protect the insect from toxic heavy metals. We conclude that chironomids, which are considered pollution tolerant, are inhabited by stable endogenous bacterial communities that have a role in protecting their hosts from toxicants. This phenomenon, in which bacteria enable the continued existence of their host in hostile environments, may not be restricted only to chironomids.

The organization of naphthalene degradation genes in Pseudomonas putida strain AK5

The Pseudomonas putida АК5 that was isolated from the slime pit of a Nizhnekamsk oil chemical factory can metabolize naphthalene via salicylate and gentisate. Catabolic genes are localized on non-conjugative IncP-7 plasmid pAK5 of about 115 kb in size. The "classical"nah-1 operon and the novel sgp-operon (salicylate-gentisate pathway) are both involved in naphthalene degradation by P. putida АК5, that was first described for Pseudomonas. The sgp-operon includes six open reading frames (ORFs) (sgpAIKGHB). The four ORFs code for the entire salicylate 5-hydroxylase - oxidoreductase component (sgpA), large and small subunits of the oxigenase component (sgpG and sgpH) and 2Fe-2S ferredoxin (sgpB). Genes for gentisate 1, 2-dioxygenase (sgpI) and fumarylpyruvate hydrolase (sgpK) are located in salicylate 5-hydroxylase genes clustering between sgpA and sgpG. The putative positive regulator for the sgp-operon (sgpR) was found upstream of the sgpA gene and oriented in the opposite direction from sgpA. The putative maleylacetoacetate isomerase gene is located apart, directly downstream from the sgp-operon. The sgp-operon organization and phylogenetic analysis of deduced amino acid sequences indicate that this operon has a mosaic structure according to the modular theory of the evolution of modern catabolic pathways.

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.

Bacterial community composition associated with chironomid egg masses

Chironomids (Diptera: Chironomidae) are the most widely distributed and often the most abundant insect in freshwater. They undergo a complete metamorphosis of four life stages, of which the egg, larva, and pupae are aquatic and the adult is terrestrial. Chironomid egg masses were found to be natural reservoirs of Vibrio cholerae and Aeromonas species. To expand the knowledge of the endogenous bacterial community associated with chironomid egg masses, denaturing gradient gel electrophoresis and clone analysis of 16S rRNA gene libraries were used in this study. Bacterial community composition associated with chironomid egg masses was found to be stable among different sampling periods. Cloned libraries of egg masses revealed that about 40% of the clones were related to bacteria known to degrade various toxicants. These findings were further supported when bacterial species that showed resistance to different toxic metals were isolated from egg masses and larval samples. Chironomids are found under a wide range of water conditions and are able to survive pollutants. However, little is known about their protective mechanisms under these conditions. Chironomid egg masses are inhabited by a stable endogenous bacterial community, which may potentially play a role in protecting chironomids from toxicants in polluted environments. Further study is needed to support this hypothesis.

Metabolic characterization and genes for the conversion of biphenyl in Dyella ginsengisoli LA-4

A complete bph gene cluster (bphLA-4) containing 12,186 bp was amplified from Dyella ginsengisoli LA-4. The bphLA-4 was composed of bphABCXD, and an additional gene encoding a meta-fission product hydrolase was located in the bphX region. BphLA-4 was independently transcribed by the two operons, bphA1A2orf1A3A4BCX0 and bphX1orf2X2X3D, and significantly differed from bphKF707. Both benzoate and catechol induced the expression of both operons. 2-Hydroxypenta-2,4-dienoate was identified as the intermediate of the biphenyl degradation by strain LA-4. This finding suggested that there existed a novel lower pathway of biphenyl degradation in strain LA-4.

Purification and Characterization of Catechol 1,2-Dioxygenase from Acinetobacter sp. DS002 and Cloning, Sequencing of Partial catA Gene

Catechol 1,2-dioxygenase (C12O) was purified to electrophoretic homogeneity from Acinetobacter sp. DS002. The pure enzyme appears to be a homodimer with a molecular mass of 66 kDa. The apparent K(m) and V(max) for intradiol cleavage of catechol were 1.58 μM and 2 units per mg of protein respectively. Unlike other C12Os reported in the literature, the catechol 1,2-dioxygenase of Acinetobacter showed neither intradiol nor extradiol cleavage activity when substituted catechols were used as substrates. However, it has shown mild intradiol cleavage activity when benzenetriol was used as substrate. As determined by two dimensional electrophoresis (2DE) followed MALDI-TOF/TOF analyses and gel permeation chromatography, no isoforms of C12O was observed in Acinetobacter sp. DS002. Further, the C12O was seen only in cultures grown in benzoate and it was completely absent in succinate grown cultures. Based on the sequence information obtained from MS/MS data, degenerate primers were designed to amplify catA gene from the genomic DNA of Acinetobacter sp. DS002. The sequence of the PCR amplicon and deduced amino acid sequence showed 97% similarity with a catA gene of Acinetobacter baumannii AYE (YP_001713609).

Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis

Several types of environmental bacteria that can aerobically degrade various aromatic compounds have been identified. The catabolic genes in these bacteria have generally been found to form operons, which promote efficient and complete degradation. However, little is known about the degradation pathways in bacteria that are difficult to culture in the laboratory. By functionally screening a metagenomic library created from activated sludge, we had earlier identified 91 fosmid clones carrying genes for extradiol dioxygenase (EDO), a key enzyme in the degradation of aromatic compounds. In this study, we analyzed 38 of these fosmids for the presence and organization of novel genes for aromatics degradation. Only two of the metagenomic clones contained complete degradation pathways similar to those found in known aromatic compound-utilizing bacteria. The rest of the clones contained only subsets of the pathway genes, with novel gene arrangements. A circular 36.7-kb DNA form was assembled from the sequences of clones carrying genes belonging to a novel EDO subfamily. This plasmid-like DNA form, designated pSKYE1, possessed genes for DNA replication and stable maintenance as well as a small set of genes for phenol degradation; the encoded enzymes, phenol hydroxylase and EDO, are capable of the detoxification of aromatic compounds. This gene set was found in 20 of the 38 analyzed clones, suggesting that this 'detoxification apparatus' may be widespread in the environment.

Benzoate-mediated changes on expression profile of soluble proteins in Serratia sp. DS001

AIM

To assess differences in protein expression profile associated with shift in carbon source from succinate to benzoate in Serratia sp. DS001 using a proteomics approach.

METHODS AND RESULTS

A basic proteome map was generated for the soluble proteins extracted from Serratia sp. DS001 grown in succinate and benzoate. The differently and differentially expressed proteins were identified using ImageMaster 2D Platinum software (GE Healthcare). The identity of the proteins was determined by employing MS or MS/MS. Important enzymes such as Catechol 1,2 dioxygenase and transcriptional regulators that belong to the LysR superfamily were identified.

CONCLUSIONS

Nearly 70 proteins were found to be differentially expressed when benzoate was used as carbon source. Based on the protein identity and degradation products generated from benzoate it is found that ortho pathway is operational in Serratia sp. DS001.

SIGNIFICANCE AND IMPACT OF THE STUDY

Expression profile of the soluble proteins associated with shift in carbon source was mapped. The study also elucidates degradation pathway of benzoate in Serratia sp. DS001 by correlating the proteomics data with the catabolites of benzoate.

Phylogeny vs genome reshuffling: horizontal gene transfer

The evolutionary events in organisms can be tracked to the transfer of genetic material. The inheritance of genetic material among closely related organisms is a slow evolutionary process. On the other hand, the movement of genes among distantly related species can account for rapid evolution. The later process has been quite evident in the appearance of antibiotic resistance genes among human and animal pathogens. Phylogenetic trees based on such genes and those involved in metabolic activities reflect the incongruencies in comparison to the 16S rDNA gene, generally used for taxonomic relationships. Such discrepancies in gene inheritance have been termed as horizontal gene transfer (HGT) events. In the post-genomic era, the explosion of known sequences through large-scale sequencing projects has unraveled the weakness of traditional 16S rDNA gene tree based evolutionary model. Various methods to scrutinize HGT events include atypical composition, abnormal sequence similarity, anomalous phylogenetic distribution, unusual phyletic patterns, etc. Since HGT generates greater genetic diversity, it is likely to increase resource use and ecosystem resilience.

Naphthalene metabolism in Nocardia otitidiscaviarum strain TSH1, a moderately thermophilic microorganism

The thermophilic bacterium Nocardia otitidiscaviarum strain TSH1, originally isolated in our laboratory from a petroindustrial wastewater contaminated soil in Iran, grows at 50 degrees C on a broad range of hydrocarbons. Transformation of naphthalene by strain TSH1 which is able to use this two ring-polycyclic aromatic hydrocarbon (PAH) as a sole source of carbon and energy was investigated. The metabolic pathway was elucidated by identifying metabolites, biotransformation studies and monitoring enzyme activities in cell-free extracts. The identification of metabolites suggests that strain TSH1 initiates its attack on naphthalene by dioxygenation at its C-1 and C-2 positions to give 1,2-dihydro-1,2-dihydroxynaphthalene. The intermediate 2-hydroxycinnamic acid, characteristic of the meta-cleavage of the resulting diol was identified in the acidic extract. Apart from typical metabolites of naphthalene degradation known from mesophiles, benzoic acid was identified as an intermediate for the naphthalene pathway of this Nocardia strain. Neither phthalic acid nor salicylic acid metabolites were detected in culture extracts. Enzymatic experiments with cell extract showed the catechol 1,2-dioxygenase activity while transformation of phthalic acid and protocatechuic acid was not observed. The results of enzyme activity assays and identification of benzoic acid in culture extract provide strong indications that further degradation goes through benzoate and beta-ketoadipate pathway. Our results indicate that naphthalene degradation by thermophilic N. otitidiscaviarum strain TSH1 differs from the known pathways found for the thermophilic Bacillus thermoleovorans Hamburg 2 and mesophilic bacteria.

Metabolic Diversity in Bacterial Degradation of Aromatic Compounds

Aromatic compounds pose a major threat to the environment, being mutagenic, carcinogenic, and recalcitrant. Microbes, however, have evolved the ability to utilize these highly reduced and recalcitrant compounds as a potential source of carbon and energy. Aerobic degradation of aromatics is initiated by oxidizing the aromatic ring, making them more susceptible to cleavage by ring-cleaving dioxygenases. A preponderance of aromatic degradation genes on plasmids, transposons, and integrative genetic elements (and their shuffling through horizontal gene transfer) have lead to the evolution of novel aromatic degradative pathways. This enables the microorganisms to utilize a multitude of aromatics via common routes of degradation leading to metabolic diversity. In this review, we emphasize the exquisiteness and relevance of bacterial degradation of aromatics, interlinked degradative pathways, genetic and metabolic regulation, carbon source preference, and biosurfactant production. We have also explored the avenue of metagenomics, which opens doors to a plethora of uncultured and uncharted microbial genetics and metabolism that can be used effectively for bioremediation.

Molecular and biochemical characterization of 3-hydroxybenzoate 6-hydroxylase from Polaromonas naphthalenivorans CJ2

Prior research revealed that Polaromonas naphthalenivorans CJ2 carries and expresses genes encoding the gentisate metabolic pathway for naphthalene. These metabolic genes are split into two clusters, comprising nagRAaGHAbAcAdBFCQEDJI'-orf1-tnpA and nagR2-orf2I''KL (C. O. Jeon, M. Park, H. Ro, W. Park, and E. L. Madsen, Appl. Environ. Microbiol. 72:1086-1095, 2006). BLAST homology searches of sequences in GenBank indicated that the orf2 gene from the small cluster likely encoded a salicylate 5-hydroxylase, presumed to catalyze the conversion of salicylate into gentisate. Here, we report physiological and genetic evidence that orf2 does not encode salicylate 5-hydroxylase. Instead, we have found that orf2 encodes 3-hydroxybenzoate 6-hydroxylase, the enzyme which catalyzes the NADH-dependent conversion of 3-hydroxybenzoate into gentisate. Accordingly, we have renamed orf2 nagX. After expression in Escherichia coli, the NagX enzyme had an approximate molecular mass of 43 kDa, as estimated by gel filtration, and was probably a monomeric protein. The enzyme was able to convert 3-hydroxybenzoate into gentisate without salicylate 5-hydroxylase activity. Like other 3-hydroxybenzoate 6-hydroxylases, NagX utilized both NADH and NADPH as electron donors and exhibited a yellowish color, indicative of a bound flavin adenine dinucleotide. An engineered mutant of P. naphthalenivorans CJ2 defective in nagX failed to grow on 3-hydroxybenzoate but grew normally on naphthalene. These results indicate that the previously described small catabolic cluster in strain CJ2 may be multifunctional and is essential for the degradation of 3-hydroxybenzoate. Because nagX and an adjacent MarR-type regulatory gene are both closely related to homologues in Azoarcus species, this study raises questions about horizontal gene transfer events that contribute to operon evolution.

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.

Bioremediation and monitoring of aromatic-polluted habitats

Bioremediation may restore contaminated soils through the broad biodegradative capabilities evolved by microorganisms towards undesirable organic compounds. Understanding bioremediation and its effectiveness is rapidly advancing, bringing available molecular approaches for examining the presence and expression of the key genes involved in microbial processes. These methods are continuously improving and require further development and validation of primer- and probe-based analyses and expansion of databases for alternative microbial markers. Phylogenetic marker approaches provide tools to determine which organisms are present or generally active in a community; functional gene markers provide only information concerning the distribution or transcript levels (deoxyribonucleic acid [DNA]- or messenger ribonucleic acid [mRNA]-based approaches) of specific gene populations across environmental gradients. Stable isotope probing methods offer great potential to identify microorganisms that metabolize and assimilate specific substrates in environmental samples, incorporating usually a rare isotope (i.e., (13)C) into their DNA and RNA. DNA and RNA in situ characterization allows the determination of the species actually involved in the processes being measured. DNA microarrays may analyze the expression of thousands of genes in a soil simultaneously. A global analysis of which genes are being expressed under various conditions in contaminated soils will reveal the metabolic status of microorganisms and indicate environmental modifications accelerating bioremediation.

Nucleotide sequence of plasmid pCNB1 from comamonas strain CNB-1 reveals novel genetic organization and evolution for 4-chloronitrobenzene degradation

The nucleotide sequence of a new plasmid pCNB1 from Comamonas sp. strain CNB-1 that degrades 4-chloronitrobenzene (4CNB) was determined. pCNB1 belongs to the IncP-1beta group and is 91,181 bp in length. A total of 95 open reading frames appear to be involved in (i) the replication, maintenance, and transfer of pCNB1; (ii) resistance to arsenate and chromate; and (iii) the degradation of 4CNB. The 4CNB degradative genes and arsenate resistance genes were located on an extraordinarily large transposon (44.5 kb), proposed as TnCNB1. TnCNB1 was flanked by two IS1071 elements and represents a new member of the composite I transposon family. The 4CNB degradative genes within TnCNB1 were separated by various truncated genes and genetic homologs from other DNA molecules. Genes for chromate resistance were located on another transposon that was similar to the Tn21 transposon of the class II replicative family that is frequently responsible for the mobilization of mercury resistance genes. Resistance to arsenate and chromate were experimentally confirmed, and transcriptions of arsenate and chromate resistance genes were demonstrated by reverse transcription-PCR. These results described a new member of the IncP-1beta plasmid family, and the findings suggest that gene deletion and acquisition as well as genetic rearrangement of DNA molecules happened during the evolution of the 4CNB degradation pathway on pCNB1.

Metabolism of 2-, 3- and 4-hydroxybenzoates by soil isolatesAlcaligenessp. strain PPH andPseudomonassp. strain PPD

Pseudomonas sp. strain PPD and Alcaligenes sp. strain PPH isolated from soil by enrichment culture technique utilize 2-, 3- and 4-hydroxybenzoates as the sole source of carbon and energy. The degradation pathways were elucidated by performing whole-cell O(2) uptake, enzyme activity and induction studies. Depending on the mixture of carbon source and the preculture condition, strain PPH was found to degrade 2-hydroxybenzoate either via the catechol or gentisate route and has both salicylate 1-hydroxylase and salicylate 5-hydroxylase. Strain PPD utilizes 2-hydroxybenzoate via gentisate. Both strains degrade 3- and 4-hydroxybenzoate via gentisate and protocatechuate, respectively. Enzymes were induced by respective hydroxybenzoate. Growth pattern, O(2) uptake and enzyme activity profiles on the mixture of three hydroxybenzoates as a carbon source suggest coutilization by both strains. When 3- or 4-hydroxybenzoate grown culture was used as an inoculum, strain PPH failed to utilize 2-hydroxybenzoate via catechol, indicating the modulation of the metabolic pathways, thus generating metabolic diversity.

Benzoate catabolite repression of the phthalate degradation pathway in Rhodococcus sp. strain DK17

Rhodococcus sp. strain DK17 exhibits a catabolite repression-like response when provided simultaneously with benzoate and phthalate as carbon and energy sources. Benzoate in the medium is depleted to detection limits before the utilization of phthalate begins. The transcription of the genes encoding benzoate and phthalate dioxygenase paralleled the substrate utilization profile. Two mutant strains with defective benzoate dioxygenases were unable to utilize phthalate in the presence of benzoate, although they grew normally on phthalate in the absence of benzoate.

Novel upper meta-pathway extradiol dioxygenase gene diversity in polluted soil

For the determination of the catabolic community diversity that is related to biodegradation potential, we developed a protocol for the assessment of catabolic marker genes in polluted soils. Primers specific to upper pathway extradiol dioxygenase genes were designed which amplified a 469-bp product from Sphingomonas sp. HV3. The constructed primers were used in PCR amplification of upper pathway ring cleavage genes from DNA directly isolated from a mineral oil polluted landfill site, a mineral oil landfarming site and a birch rhizosphere-associated soil that was either artificially polluted with a PAH mixture or not polluted. Amplicons were cloned and subjected to restriction fragment length polymorphism analysis dividing the HhaI-digested products into operational taxonomic units. Altogether 26 different operational taxonomic units were detected with the sequence similarity to known catabolic genes of Alpha-, Beta-, and Gammaproteobacteria. Phylogenetic analysis divided the operational taxonomic units from the polluted soils into seven clusters. Two contained exclusively sequences with no close homologues in the database, therefore representing novel catabolic genes. This large proportion of novel extradiol sequences shows that there is an extensive unknown catabolic diversity in polluted environments.