Transformation of chlorinated phenolic compounds in the genusRhodococcus

The ability of strains of the genusRhodococcus to transform chlorinated phenolic compounds was studied. Noninduced cells of several strains ofRhodococcus, covering at least eight species, were found to attack mono-, di-, and trichlorophenols by hydroxylation at theortho position to chlorocatechols. 3-chlorophenol and 4-chlorophenol were converted to 4-chlorocatechol, 2,3-dichlorophenol to 3,4-dichlorocatechol, and 3,4-di-chlorophenol to 4,5-dichlorocatechol. The chlorocatechols accumulated to nearly stoichiometric amounts. Other mono- and dichlorophenols were not transformed. The ability of the strains to hydroxylate chlorophenols correlated with the ability to grow on unsubstituted phenol as the sole source of carbon and energy. SeveralRhodococcus strains attacked chlorophenolic compounds by both hydroxylation and O-methylation. 2,3,4-, 2,3,5- and 3,4,5-trichlorophenol were hydroxylated to trichlorocatechol and then sequentially O-methylated to chloroguaiacol and chloroveratrole. Tetrachlo-rohydroquinone was O-methylated sequentially to tetrachloro-4-methoxy-phenol and tetrachloro-1,4-dimethoxybenzene. Several of the active strains had no known history of exposure to any chloroaromatic compound. Rhodococci are widely distributed in soil and sludge and these results suggest that this genus may play an important role in transformation of chlorinated phenolic compounds in the environment.     

O-Methylation of Chlorinated para-Hydroquinones by Rhodococcus chlorophenolicus

Rhodococcus chlorophenolicus PCP-I, a degrader of polychlorinated phenols, guaiacols (2-methoxyphenols), and syringols (2,6-dimethoxyphenols), was shown to O-methylate the degradation intermediate, a chlorinated para-hydroquinone, into 4-methoxyphenol. O-methylation was constitutively expressed, whereas the degradation of chlorophenols and chlorohydroquinones was inducible in R. chlorophenolicus. The O-methylating reaction required two hydroxyl groups in positions para to each other. R. chlorophenolicus selectively methylated the hydroxyl group flanked by two chlorine substituents. Tetrachlorohydroquinone, trichlorohydroquinone, and 2,6-dichlorohydroquinone were methylated into tetrachloro-4-methoxyphenol, 2,3,5-trichloro-4-methoxyphenol, and 3,5-dichloro-4-methoxyphenol, respectively. Chlorohydroquinones with only one chlorine adjacent to a hydroxyl group were methylated only in trace amounts, and no metabolite was formed from hydroquinone. The degradation intermediates formed in hydroxylation of tetrachloroguaiacol and trichlorosyringol by R. chlorophenolicus were O-methylated into two isomeric trichlorodimethoxyphenols and two isomeric dichlorotrimethoxyphenols, respectively. R. chlorophenolicus also degraded the polychlorinated methylation products (tetrachlorinated and trichlorinated 4-methoxyphenols), but not mono- and dichlorinated 4-methoxyphenols.     

The diversity of extradiol dioxygenase (edo) genes in cresol degrading rhodococci from a creosote-contaminated site that express a wide range of degradative abilities

Analysis of the bacterial population of soil surface samples from a creosote-contaminated site showed that up to 50% of the culturable micro-organisms detected were able to utilise a mixture of cresols. From fifty different microbial isolates fourteen that could utilise more than one cresol isomer were selected and identified by 16S rRNA analysis. Eight isolates were Rhodococcus strains and six were Pseudomonas strains. In general, the Rhodococcus strains exhibited a broader growth substrate range than the Pseudomonas strains. The distribution of various extradiol dioxygenase (edo) genes, previously associated with aromatic compound degradation in rhodococci, was determined for the Rhodococcus strains by PCR detection and Southern-blot hybridization. One strain, Rhodococcus sp. I1 exhibited the broadest growth substrate range and possessed five different edogenes. Gene disruption experiments indicated that two genes (edoC and edoD) were associated with isopropylbenzene and naphthalene catabolism respectively. The other Rhodococcus strains also possessed some of the edo genes and one (edoB) was present in all of the Rhodococcus strains analysed. None of the rhodococcal edo genes analysed were present in the Pseudomonas strains isolated from the site. It was concluded that individual strains of Rhodococcus possess a wide degradative ability and may be very important in the degradation of complex mixtures of substrates found in creosote.     

Destruction of mixture of tri-hexa-chlorinated biphenyls by <Emphasis Type="Italic">Rhodococcus</Emphasis> genus strains

Destruction of polychlorinated biphenyls (PCBs) by strain-destructors Rhodococcus sp. B7a and Rhodococcus sp. G12a has been studied. It was shown that these strains destruct 78–95% of PCB mixture containing tri-hexa-chlorinated biphenyls. Rhodococcus destruct all components of the mixture of tri-, tetra-, penta-, and hexa-chlorinated biphenyls without accumulation of toxic chlorinated metabolites. The studied bacteria destruct PCB that are the most stable for oxidation, such as 2,5,2′,5′-CB; 3,4,3′,4′-CB; and 2,4,5,2′,4′,5′-CB. The most perspective strains are R. rubber P25, Rhodococcus sp. B7a and Rhodococcus sp. G12a whose metabolic potential can be used for biotechnological refinement of the environment from highly toxic pollutants.     

Characterization of selected actinomycetes degrading polyaromatic hydrocarbons in liquid culture and spiked soil

Summary Five strains of the Rhodococcus and Gordonia genera were evaluated for their potential use in bioremediation of polycyclic aromatic hydrocarbons (PAH) with or without another substrate (co-substrate). Their ability to produce biosurfactants or to degrade phenanthrene when growing on glucose, hexadecane and rapeseed oil was tested in liquid medium at 30 °C. All strains showed biosurfactant activity. The highest reduction in surface tension was recorded in whole cultures of Rhodococcus sp. DSM 44126 (23.1%) and R. erythropolis DSM 1069 (21.1%) grown on hexadecane and Gordonia sp. APB (20.4%) and R. erythropolis TA57 (18.2%) grown on rapeseed oil. Cultures of Gordonia sp. APB and G. rubripertincta formed emulsions when grown on rapeseed oil. After 14 days of incubation, Rhodococcus sp. DSM 44126 degraded phenanthrene (initial concentration 100 μg ml⁻¹) as sole carbon source (79.4%) and in the presence of hexadecane (80.6%), rapeseed oil (96.8%) and glucose (below the limit of detection). The other strains degraded less than 20%, and then with a co-substrate only. Rhodococcus sp. DSM 44126 was selected and its performance evaluated in soil spiked with a mixture of PAH (200 mg kg⁻¹). The effect of the addition of 0, 0.1 and 1% rapeseed oil as co-substrate was also tested. Inoculation enhanced the degradation of phenanthrene (55.7% and 95.2% with 0.1% oil and without oil respectively) and of anthracene (29.2% with 0.1% oil). Approximately 96% of anthracene and 62% of benzo(a)pyrene disappeared from the soil (inoculated and control) after 14 days and anthraquinone was detected as a metabolite. Rhodococcus sp. DSM 44126 was identified as Rhodococcus wratislaviensis by 16S rRNA sequencing and was able to degrade anthracene as sole carbon source in liquid culture.     

Degradation and O-methylation of chlorinated phenolic compounds by Rhodococcus and Mycobacterium strains.

Three polychlorophenol-degrading Rhodococcus and Mycobacterium strains were isolated independently from soil contaminated with chlorophenol wood preservative and from sludge of a wastewater treatment facility of a kraft pulp bleaching plant. Rhodococcus sp. strain CG-1 and Mycobacterium sp. strain CG-2, isolated from tetrachloroguaiacol enrichment, and Rhodococcus sp. strain CP-2, isolated from pentachlorophenol enrichment, mineralized pentachlorophenol and degraded several other polychlorinated phenols, guaiacols (2-methoxyphenols), and syringols (2,6-dimethoxyphenols) at micromolar concentrations and were sensitive to the toxic effects of pentachlorophenol. All three strains initiated degradation of the chlorophenols by para-hydroxylation, producing chlorinated para-hydroquinones, which were then further degraded. Parallel to degradation, strains CG-1, CG-2, and CP-2 also O-methylated nearly all chlorinated phenols, guaiacols, syringols, and hydroquinones. O-methylation of chlorophenols was a slow reaction compared with degradation. The preferred substrates of the O-methylating enzyme(s) were those with the hydroxyl group flanked by two chlorine substituents. O-methylation was constitutively expressed, whereas degradation of chlorinated phenolic compounds was inducible.     

Degradation and O-methylation of chlorinated phenolic compounds by Rhodococcus and Mycobacterium strains

Three polychlorophenol-degrading Rhodococcus and Mycobacterium strains were isolated independently from soil contaminated with chlorophenol wood preservative and from sludge of a wastewater treatment facility of a kraft pulp bleaching plant. Rhodococcus sp. strain CG-1 and Mycobacterium sp. strain CG-2, isolated from tetrachloroguaiacol enrichment, and Rhodococcus sp. strain CP-2, isolated from pentachlorophenol enrichment, mineralized pentachlorophenol and degraded several other polychlorinated phenols, guaiacols (2-methoxyphenols), and syringols (2,6-dimethoxyphenols) at micromolar concentrations and were sensitive to the toxic effects of pentachlorophenol. All three strains initiated degradation of the chlorophenols by para-hydroxylation, producing chlorinated para-hydroquinones, which were then further degraded. Parallel to degradation, strains CG-1, CG-2, and CP-2 also O-methylated nearly all chlorinated phenols, guaiacols, syringols, and hydroquinones. O-methylation of chlorophenols was a slow reaction compared with degradation. The preferred substrates of the O-methylating enzyme(s) were those with the hydroxyl group flanked by two chlorine substituents. O-methylation was constitutively expressed, whereas degradation of chlorinated phenolic compounds was inducible.     

Genomic and phenomic differentiation of Rhodococcus equi and related strains

16S rDNA sequence and pyrolysis mass spectrometric analyses were carried out on representatives of Rhodococcus equi and marker strains of genera that encompass mycolic acid containing actinomycetes. The R. equi strains formed a monophyletic clade within the evolutionary radiation occupied by members of the genera Nocardia and Rhodococcus. The 16S rDNA sequence data also showed R. equi to be an heterogeneous taxon. This heterogeneity was underscored by the pyrolysis mass spectrometric data. These observations are in line with those of previous studies where similar profiles of relatedness were found between pyrolysis mass spectral data and the results of DNA:DNA pairing and numerical phenetic studies.     

Enzyme Immobilization on Ion Exchangers by Forming an Enzyme Coating with Transglutaminase as a Crosslinker

Southern hybridization analysis using the genes encoding the α- and β-subunits of nitrile hydratase (NHase) from Rhodococcus sp. N-774 as probe suggested that two R. erythropolis strains, JCM6823 and JCM2892, among 31 strains mainly from Japan Culture of Microorganisms (JCM) have NHase genes. Restriction analysis of DNA fragments showing positive hybridization showed that each fragment carried a nucleotide sequence very similar to that of the NHase genes from Rhodococcus sp. N-774. Nucleotide sequence analysis of the DNA fragment cloned from R. erythropolis JCM6823 showed the presence of the genes encoding the α- and β-subunits of NHase, which show 94.7% and 96.2% identity in amino acid sequence to those of Rhodococcus sp. N-774, respectively, as well as a C-terminal portion of the amidase gene upstream from these genes. Despite the extremely high amino acid sequence similarity in both NHases and amidases from R. erythropolis JCM6823 and Rhodococcus sp. N-774, the NHases and amidases from R. erythropolis strains showed broader substrate specificity when compared to those from Rhodococcus sp. N-774. This suggests that a very limited number of amino acid residues are responsible for the difference in substrate specificity. Although the NHase of Rhodococcus sp. N-774 are constitutively produced, the NHases of both R. erythropolis strains were inducibly produced by addition of ε-caprolactam as an inducer.     

红球菌R04细胞的不对称分裂及其在联苯胁迫下的分裂抑制

【目的】研究红球菌R04细胞的分裂方式及联苯对其形态和细胞分裂的影响。【方法】以一株多氯联苯降解菌株(Rhodococcus sp.R04)为研究对象,利用荧光显微镜、扫描电子显微镜及透射电子显微镜分析红球菌R04在不同培养条件下的细胞分裂。【结果】红球菌R04细胞表现出对称分裂(约占30%)和不对称分裂(约占70%)两种分裂方式,且培养条件不影响不对称分裂细胞所占的比例。细胞分裂过程中,隔膜主要分布于细胞长度的30%–50%。在联苯的分解代谢过程中,红球菌R04细胞的生长分裂会受到联苯的抑制,但不影响红球菌R04细胞的分裂方式,在联苯胁迫下,细胞形成丝状化,表现出异常分裂,随着培养时间的延长,在细胞生长指数后期至转换期,细胞能够进行正常分裂。【结论】环境异生型化合物联苯/多氯联苯对其降解菌株——红球菌R04细胞的生长和分裂有较强影响,但是并不影响其分裂方式。     

Identification and characterization of <Emphasis Type="Italic">o</Emphasis>-xylene-degrading <Emphasis Type="Italic">Rhodococcus</Emphasis> spp. which were dominant species in the remediation of <Emphasis Type="Italic">o</Emphasis>-xylene-contaminated soils

Soils contaminated with o-xylene were more difficult to bioremediate than those contaminated with other BTEX hydrocarbons (benzene, toluene, ethylbenzene, m-xylene and p-xylene). In order to identify microorganisms responsible for o-xylene degradation in soil, microbial community structure analyses were carried out with two soil samples in the presence of o-xylene and mineral nutrients. In two different soil samples, Rhodococcus opacus became abundant. We were also able to isolate o-xylene degrading Rhodococcus species from these soil samples. A primer set was developed to specifically detect a cluster of this Rhodococcus group including isolated Rhodococcus strains, Rhodococcus opacus and Rhodococcus koreensis. The growth of this bacterial group in an o-xylene-contaminated soil was followed by competitive PCR (cPCR). The decrease in o-xylene clearly paralleled the growth of the Rhodococcus group.     

Fluorene Transformation by Bacteria of the Genus Rhodococcus

Of the four investigated Rhodococcus strains (R. rhodochrous172, R. opacus 4a and 557, and R. rhodnii 135), the first three strains were found to be able to completely transform fluorene when it was present in the medium as the sole source of carbon at a concentration of 12–25 mg/l. At a fluorene concentration of 50–100 mg/l in the medium, the rhodococci transformed 50% of the substrate in 14 days. The addition of casamino acids and sucrose (1–5 g/l) stimulated fluorene transformation, so that R. rhodochrous 172 could completely transform it in 2–5 days. Nine intermediates of fluorene transformation were isolated, purified, and structurally characterized. It was found that R. rhodnii 135 and R. opacus strains 4a and 557 hydroxylated fluorene with the formation of 2-hydroxyfluorene and 2,7-dihydroxyfluorene. R. rhodochrous 172 transformed fluorene via two independent pathways to a greater degree than the other rhodococci studied.     

Physiological aspects of hydrocarbon emulsification, metal resistance and DNA profile of biodegrading bacteria isolated from oil polluted sites

The production of biosurfactants was evaluated for seven bacterial strains isolated from different oil contaminated sites by the Emulsification Index using diesel oil as the hydrocarbon source. Minimum Inhibitory Concentrations of Mg²⁺, Cr³⁺ and Cu²⁺ were determined to identify the less sensitive bacteria in order to select the best strains for bioremediation. Plasmid extraction was also performed in order to search for gene sequences involved with biosurfactant synthesis. All strains were able to emulsify diesel oil. Rhodococcus ruber AC239 presented the best index (58%), followed by other Rhodococcus strains. Pseudomonas aeruginosa, R. ruber AC239, AC87 and R. erytropolis AC272 presented smallest sensitivities to heavy metals used, being suitable for use in sites contaminated with high concentrations of them. No plasmid DNA was detected showing that biosurfactant coding genes should be in the chromosomal DNA.     

Biodegradation of 4-nitroanisole by two Rhodococcus spp.

Two Rhodococcus strains, R. opacus strain AS2 and R. erythropolis strain AS3, that were able to use 4-nitroanisole as the sole source of carbon and energy, were isolated from environmental samples. The first step of the degradation involved the O-demethylation of 4-nitroanisole to 4-nitrophenol which accumulated transiently in the medium during growth. Oxygen uptake experiments indicated the transformation of 4-nitrophenol to 4-nitrocatechol and 1,2,4-trihydroxybenzene prior to ring cleavage and then subsequent mineralization. The nitro group was removed as nitrite, which accumulated in the medium in stoichiometric amounts. In R. opacus strain AS2 small amounts of hydroquinone were produced by a side reaction, but were not further degraded.     

Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

In this paper comparative genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7 were performed. Rhodococcus sp. BCP1 was selected for its ability to grow on short-chain n-alkanes and R. opacus R7 was isolated for its ability to grow on naphthalene and on o-xylene. Results of genome comparison, including BCP1, R7, along with other Rhodococcus reference strains, showed that at least 30% of the genome of each strain presented unique sequences and only 50% of the predicted proteome was shared. To associate genomic features with metabolic capabilities of BCP1 and R7 strains, hundreds of different growth conditions were tested through Phenotype Microarray, by using Biolog plates and plates manually prepared with additional xenobiotic compounds. Around one-third of the surveyed carbon sources was utilized by both strains although R7 generally showed higher metabolic activity values compared to BCP1. Moreover, R7 showed broader range of nitrogen and sulphur sources. Phenotype Microarray data were combined with genomic analysis to genetically support the metabolic features of the two strains. The genome analysis allowed to identify some gene clusters involved in the metabolism of the main tested xenobiotic compounds. Results show that R7 contains multiple genes for the degradation of a large set of aromatic and PAHs compounds, while a lower variability in terms of genes predicted to be involved in aromatic degradation was found in BCP1. This genetic feature can be related to the strong genetic pressure exerted by the two different environment from which the two strains were isolated. According to this, in the BCP1 genome the smo gene cluster involved in the short-chain n-alkanes degradation, is included in one of the unique regions and it is not conserved in the Rhodococcus strains compared in this work. Data obtained underline the great potential of these two Rhodococcus spp. strains for biodegradation and environmental decontamination processes.     

Purification and properties of p-hydroxybenzoate hydroxylases from Rhodococcus strains

Gram-positive bacteria of the genus Rhodococcus catabolize p-hydroxybenzoate (PHB) through the initial formation of 3,4-dihydroxybenzoate. High levels of p-hydroxybenzoate hydroxylase (PHBH) activity are induced in six different Rhodococcus species when these strains are grown on PHB as sole carbon source. The PHBH enzymes were purified to apparent homogeneity and appeared to be homodimers of about 95 kD with each subunit containing a relatively weakly bound FAD. In contrast to their counterparts from gram-negative microorganisms, the Rhodococcus PHBH enzymes prefer NADH to NADPH as external electron donor. All purified enzymes were inhibited by Cl^– and for five of six enzymes more pronounced substrate inhibition was observed in the presence of chloride ions.     

Methylcatechol 1,2-dioxygenase of <Emphasis Type="Italic">Rhodococcus opacus</Emphasis> 6a is a new type of the catechol-cleaving enzyme

The strains Rhodococcus sp. 400, R. rhodochrous 172, and R. opacus 6a utilize 4-methylbenzoate as the only carbon and energy source. 4-Methylcatechol is a key intermediate of biodegradation. Its further conversion by all the strains proceeds via ortho-cleavage. The specific activity of catechol 1,2-dioxygenase assayed in crude extracts of Rhodococcus sp. 400 and R. rhodochrous 172 with 3- and 4-methylcatechols does not exceed the enzyme activity assayed with catechol. Two catechol 1,2-dioxygenases have been purified from the biomass of R. opacus strain 6a grown with 4-methylbenzoate. These enzymes differed in molecular mass and physicochemical and catalytic properties. One of these enzymes belongs to the type of enzymes cleaving the catechol ring and known as methylcatechol 1,2-dioxygenases. In bacteria of the Rhodococcus genus, such an enzyme is described here for the first time.     

Microbial sensors for determination of aromatics and their chloroderivatives. Part II: Determination of chlorinated phenols using a Rhodococcus-containing biosensor

An amperometric biosensor for determination of phenol and chlorophenols using Rhodococcus has been developed. This sensor is more sensitive to phenol and chlorophenols, especially to mono- and dichlorinated phenol, than to benzoate and monochlorobenzoates. The incubation of the sensor with phenol and its chlorinated derivatives enhanced the activity of the microbial sensor for these compounds. A linear relationship between the current range and the concentration of phenol, 2-, 3- and 4-chlorophenol was observed up to 20 mol/l. The detection limit for all studied substrates was 4 mol/l. The current difference was reproducible within 5.5% when the test solution contained 40 mol phenol/l. Correspondence to: K. Riedel     

Purification and Characterization of an Alkaliphilic Choline Oxidase of Fusarium oxysporum

Uptake of cesium, potassium, and rubidium by Rhodococcus erythropolis CS98 and Rhodococcus sp. strain CS402 followed Michaelis-Menten saturation kinetics. The K_m’s for uptake of these monovalent cations by R. erythropolis CS98 and Rhodococcus sp. strain CS402 were 136 and 436μM for Cs⁺, 65 and 101μM for K⁺, and 102 and 113μM for Rb⁺, respectively. These values were significantly lower than those of Rhodobacter capsulatus and the Kup system in Escherichia coli. Potassium was a competitive inhibitor of cesium uptake by these strains, suggesting that cesium was accumulated by the potassium transport system. Although an uncoupler, FCCP, inhibited the cesium transport system, this system was not repressed by high concentrations of potassium in both Rhodococcus strains. However, the specificity in both Rhodococcus strains was different from the Trk system. These results suggest that the potassium transport system which can transport cesium in both Rhodococcus strains may be novel.     

Isolation for bacteria and fungi for the hydrolysis of phthalate and terephthalate esters

Bacterial and fungal strains were isolated from enrichment cultures using diethylphthalate, diethylterephthalate, or ethylene glycol dibenzoate as sole carbon sources.Aureobacterium, Flavobacterium, andMicrococcus species were isolated from diethylphthalate enrichments;Rhodococcus andXanthomonas species were isolated from diethylterephthalate enrichments;Rhodococcus andFusarium species were isolated from ethylene glycol dibenzoate enrichments.