Biosurfactant Production and Growth Kinetics Studies of the Waste Canola Oil-Degrading Bacterium Rhodococcus erythropolis AQ5-07 from Antarctica

With the progressive increase in human activities in the Antarctic region, the possibility of domestic oil spillage also increases. Developing means for the removal of oils, such as canola oil, from the environment and waste "grey" water using biological approaches is therefore desirable, since the thermal process of oil degradation is expensive and ineffective. Thus, in this study an indigenous cold-adapted Antarctic soil bacterium, Rhodococcus erythropolis strain AQ5-07, was screened for biosurfactant production ability using the multiple approaches of blood haemolysis, surface tension, emulsification index, oil spreading, drop collapse and "MATH" assay for cellular hydrophobicity. The growth kinetics of the bacterium containing different canola oil concentration was studied. The strain showed β-haemolysis on blood agar with a high emulsification index and low surface tension value of 91.5% and 25.14 mN/m, respectively. Of the models tested, the Haldane model provided the best description of the growth kinetics, although several models were similar in performance. Parameters obtained from the modelling were the maximum specific growth rate (qmax), concentration of substrate at the half maximum specific growth rate, Ks% (v/v) and the inhibition constant Ki% (v/v), with values of 0.142 h-1, 7.743% (v/v) and 0.399% (v/v), respectively. These biological coefficients are useful in predicting growth conditions for batch studies, and also relevant to "in field" bioremediation strategies where the concentration of oil might need to be diluted to non-toxic levels prior to remediation. Biosurfactants can also have application in enhanced oil recovery (EOR) under different environmental conditions.

Production of Lipopeptide Biosurfactant by a Hydrocarbon-Degrading Antarctic Rhodococcus

Rhodococci are renowned for their great metabolic repertoire partly because of their numerous putative pathways for large number of specialized metabolites such as biosurfactant. Screening and genome-based assessment for the capacity to produce surface-active molecules was conducted on Rhodococcus sp. ADL36, a diesel-degrading Antarctic bacterium. The strain showed a positive bacterial adhesion to hydrocarbon (BATH) assay, drop collapse test, oil displacement activity, microplate assay, maximal emulsification index at 45% and ability to reduce water surface tension to < 30 mN/m. The evaluation of the cell-free supernatant demonstrated its high stability across the temperature, pH and salinity gradient although no correlation was found between the surface and emulsification activity. Based on the positive relationship between the assessment of macromolecules content and infrared analysis, the extracted biosurfactant synthesized was classified as a lipopeptide. Prediction of the secondary metabolites in the non-ribosomal peptide synthetase (NRPS) clusters suggested the likelihood of the surface-active lipopeptide production in the strain’s genomic data. This is the third report of surface-active lipopeptide producers from this phylotype and the first from the polar region. The lipopeptide synthesized by ADL36 has the prospect to be an Antarctic remediation tool while furnishing a distinctive natural product for biotechnological application and research.

NarL, a Novel Repressor for CYP108j1 Expression during PAHs Degradation in Rhodococcus sp. P14

Rhodococcus sp. P14 was isolated from crude-oil-contaminated sediments, and a wide range of polycyclic aromatic hydrocarbons (PAHs) could be used as the sole source of carbon and energy. A key CYP450 gene, designated as cyp108j1 and involved in the degradation of PAHs, was identified and was able to hydroxylate various PAHs. However, the regulatory mechanism of the expression of cyp108j1 remains unknown. In this study, we found that the expression of cyp108j1 is negatively regulated by a LuxR (helix-turn-helix transcription factors in acyl-homoserine lactones-mediated quorum sensing) family regulator, NarL (nitrate-dependent two-component regulatory factor), which is located upstream of cyp108j1. Further analysis revealed that NarL can directly bind to the promoter region of cyp108j1. Mutational experiments demonstrated that the binding site between NarL and the cyp108j1 promoter was the palindromic sequence GAAAGTTG-CAACTTTC. Together, the finding reveal that NarL is a novel repressor for the expression of cyp108j1 during PAHs degradation.

Pb2+ biosorption from aqueous solutions by live and dead biosorbents of the hydrocarbon-degrading strain Rhodococcus sp. HX-2

In this study, the Pb²⁺ biosorption potential of live and dead biosorbents of the hydrocarbon-degrading strain Rhodococcus sp. HX-2 was analyzed. Optimal biosorption conditions were determined via single factor optimization, which were as follows: temperature, 25°C; pH, 5.0, and biosorbent dose, 0.75 g L⁻¹. A response surface software (Design Expert 10.0) was used to analyze optimal biosorption conditions. The biosorption data for live and dead biosorbents were suitable for the Freundlich model at a Pb²⁺ concentration of 200 mg L⁻¹. At this same concentration, the maximum biosorption capacity was 88.74 mg g⁻¹ (0.428 mmol g⁻¹) for live biosorbents and 125.5 mg g⁻¹ (0.606 mmol g⁻¹) for dead biosorbents. Moreover, in comparison with the pseudo-first-order model, the pseudo-second-order model seemed better to depict the biosorption process. Dead biosorbents seemed to have lower binding strength than live biosorbents, showing a higher desorption capacity at pH 1.0. The order of influence of competitive metal ions on Pb²⁺ adsorption was Cu²⁺ > Cd²⁺ > Ni⁺. Fourier-transform infrared spectroscopy analyses revealed that several functional groups were involved in the biosorption process of dead biosorbents. Scanning electron microscopy showed that Pb²⁺ attached to the surface of dead biosorbents more readily than on the surface of live biosorbents, whereas transmission electron microscopy confirmed the transfer of biosorbed Pb²⁺ into the cells in the case of both live and dead biosorbents. It can thus be concluded that dead biosorbents are better than live biosorbents for Pb²⁺ biosorption, and they can accordingly be used for wastewater treatment.

Metabolic engineering of Rhodococcus ruber Chol-4: A cell factory for testosterone production

Rhodococcus ruber Chol-4 is a potent steroid degrader that has a great potential as a biotechnological tool. As proof of concept, this work presents testosterone production from 4-androstene-3,17-dione by tailoring innate catabolic enzymes of the steroid catabolism inside the strain. A R. ruber quadruple mutant was constructed in order to avoid the breakage of the steroid nucleus. At the same time, an inducible expression vector for this strain was developed. The 17-ketoreductase gene from the fungus Cochliobolus lunatus was cloned and overexpressed in this vector. The engineered strain was able to produce testosterone from 4-androstene-3,17-dione using glucose for cofactor regeneration with a molar conversion of 61%. It is important to note that 91% of the testosterone was secreted outside the cell after 3 days of cell biotransformation. The results support the idea that Rhodococcus ruber Chol-4 can be metabolically engineered and can be used for the production of steroid intermediates.

Strongly Enhanced Antibacterial Action of Copper Oxide Nanoparticles with Boronic Acid Surface Functionality

Copper oxide nanoparticles (CuONPs) have been widely recognized as good antimicrobial agents but are heavily regulated due to environmental concerns of their postuse. In this work, we have developed and tested a novel type of formulation for copper oxide (CuONPs) which have been functionalized with (3-glycidyloxypropyl)trimethoxysilane (GLYMO) to allow further covalent coupling of 4-hydroxyphenylboronic acid (4-HPBA). As the boronic acid (BA) groups on the surface of CuONPs/GLYMO/4-HPBA can form reversible covalent bonds with the diol groups of glycoproteins on the bacterial cell surface, they can strongly bind to the cells walls resulting in a very strong enhancement of their antibacterial action which is not based on electrostatic adhesion. Scanning electron microscopy and transmission electron microscopy imaging revealed that 4-HPBA-functionalized CuO nanoparticles could accumulate more on the cell surface than nonfunctionalized ones. We demonstrate that the CuONPs with boronic acid surface functionality are far superior antibacterial agents compared to bare CuONPs. Our results showed that the antibacterial impact of the 4-HPBA-functionalized CuONPs on Rhodococcus rhodochrous and Escherichia coli is 1 order of magnitude higher than that of bare CuONPs or CuONPs/GLYMO. We also observed a marked increase of the 4-HPBA-functionalized CuONPs antibacterial action on these microorganisms at shorter incubation times compared with the bare CuONPs at the same conditions. Significantly, we show that the cytotoxicity of CuONPs functionalized with 4-HPBA as an outer layer can be controlled by the concentration of glucose in the media, and that the effect is reversible as glucose competes with the sugar residues on the bacterial cell walls for the BA-groups on the CuONPs. Our experiments with human keratinocyte cell line exposure to CuONPs/GLYMO/4-HPBA indicated lack of measurable cytotoxicity at particle concentration which are effective as an antibacterial agent for both R. rhodochrous and E. coli. We envisage that formulations of CuONPs/GLYMO/4-HPBA can be used to drastically reduce the overall CuO concentration in antimicrobial formulations while strongly increasing their efficiency.

iTRAQ-based comparative proteomic analysis of differentially expressed proteins in Rhodococcus sp. BAP-1 induced by fluoranthene

To reveal the molecular mechanism at the level of regulation of proteins in Rhodococcus sp. BAP-1 induced by fluoranthene comparative proteomic analysis was performed on proteins extracted from fluoranthene-exposed cells on 1 d, 3 d, 6 d and 8 d compared with control cells using isobaric tags for relative and absolute quantization (iTRAQ) labeling and LC-MS/MS analysis to access differentially expressed proteins. As a result, we detected a total of 897 significantly differentially expressed proteins, including 30 shared proteins in four comparison clusters. We were able to short-list 190, 329, 101 and 90 proteins that were over-represented, and 394, 234, 65 and 49 under-represented proteins, in 1d/control, 3d/control, 6d/control and 8d/control comparisons, respectively. Functional analysis relied on Clusters of Orthologous Groups (COG), gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that fluoranthene significantly altered the expression of proteins involved in metabolic and biosynthesis processes. Furthermore, BAP-1 up-regulates aldehyde dehydrogenase, cytochrome c oxidase, and oligopeptide transport ATP-binding protein, while down-regulates several other proteins in order to adapt to fluoranthene exposure. These findings provide important clues to reveal fluoranthene degradation mechanism in BAP-1 and promote its bioremediation applications.

Comparative Proteomic Analysis of Propane Metabolism in Mycobacterium sp. Strain ENV421 and Rhodococcus sp. Strain ENV425

While growing on propane as a sole source of carbon, many strains cometabolically degrade environmental pollutants, such as ethers and chlorinated hydrocarbons. To gain insights into the molecular basis behind such a high metabolic versatility of propanotrophs, we examined the propane-inducible protein expression patterns of 2 soil actinobacteria that are known to degrade a variety of ethers (i.e., Mycobacterium sp. strain ENV421 and Rhodococcus sp. strain ENV425). In both strains, soluble diiron monooxygenase(s), that would catalyze the first step of the pathway, were induced by propane. However, despite their phylogenetic similarity, different sets of additional putative propane oxygenases (e.g., cytochrome P450 and particulate methane monooxygenases) were overexpressed in the 2 strains. They also diverged in the expression of enzymes responsible for downstream reactions. This study revealed a diversity of expression of putative propane oxygenases, which may be responsible for xenobiotic degradation, as well as a variety of metabolic pathways for propane in these bacterial species.

Generation of novel family of reductases from PCR based library for the synthesis of chiral alcohols and amines

Biocatalysis has shown tremendous potential in the synthesis of drugs and drug intermediates in the last decade. Screening of novel biocatalysts from the natural genome space is the growing trend to replenish the harsh chemical synthetic routes, commonly used in the pharmaceutical and chemical industry. Here, we report a novel ketoreductase (KERD) and a nitrile reductase isolated from the PCR based library generated from the genome of Rhodococcus ruber and Bacillus subtilis, respectively. Both the proteins are hypothetical in nature as there is no putative homology found in the database, although both the enzymes have significant activity towards the synthesis of chiral alcohols and amines. Enzyme activity over a wide range of substrates (aromatic and aliphatic) for both the novel catalysts was observed. From the unique gene sequence to activity over a broad range of substrate and >99% conversion at higher concentrations (100 mM and above) entitles both the hypothetical enzymes as novel. The novel KERD has shown >99% selectivity for the synthesis of (S)-phenylethanol which makes it a potential candidate for industrial catalysis. The novel nitrile reductase has also shown promising activity for the synthesis of (R)-2-phenylethanolamine, which is a difficult moiety to synthesize chemically. In this report, starting from a homology based library, two highly potent whole cell biocatalysts are obtained.

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.

Bioconversion of ecotoxic dehydroabietic acid using Rhodococcus actinobacteria

Actinobactrial strains Rhodococcus erythropolis IEGM 267 and R. rhodochrous IEGM 107 were used to study biodegradation of dehydroabietic acid (DHA), a toxic tricyclic diterpenoid. The experiments were carried out in batch cultures of pre-grown rhodococci in the presence of 0.1% (v/v) n-hexadecane under aerobic conditions for 7 days. It was shown that R. erythropolis IEGM 267 and R. rhodochrous IEGM 107 partially and completely degraded DHA (500 mg/L), respectively. Characteristic physicochemical (reduced zeta potential) and morphological-physiological (increased average size of single cells and cell aggregates, increased root-mean-square roughness) changes in DHA-exposed actinobacteria were revealed. Products of DHA bioconversion by R. erythropolis IEGM 267 were analyzed and exhibited a previously unidentified metabolite 5α-hydroxy-abieta-8,11,13-triene-18-oat. The obtained experimental data widen the knowledge on the catalytic activity of rhodococci and their possible contribution to decontamination of natural ecosystems from pollutants.

Predicting the accumulation of storage compounds by Rhodococcus jostii RHA1 in the feast-famine growth cycles using genome-scale flux balance analysis

Feast-famine cycles in biological wastewater resource recovery systems select for bacterial species that accumulate intracellular storage compounds such as poly-β-hydroxybutyrate (PHB), glycogen, and triacylglycerols (TAG). These species survive better the famine phase and resume rapid substrate uptake at the beginning of the feast phase faster than microorganisms unable to accumulate storage. However, ecophysiological conditions favouring the accumulation of either storage compounds remain to be clarified, and predictive capabilities need to be developed to eventually rationally design reactors producing these compounds. Using a genome-scale metabolic modelling approach, the storage metabolism of Rhodococcus jostii RHA1 was investigated for steady-state feast-famine cycles on glucose and acetate as the sole carbon sources. R. jostii RHA1 is capable of accumulating the three storage compounds (PHB, TAG, and glycogen) simultaneously. According to the experimental observations, when glucose was the substrate, feast phase chemical oxygen demand (COD) accumulation was similar for the three storage compounds; when acetate was the substrate, however, PHB accumulation was 3 times higher than TAG accumulation and essentially no glycogen was accumulated. These results were simulated using the genome-scale metabolic model of R. jostii RHA1 (iMT1174) by means of flux balance analysis (FBA) to determine the objective functions capable of predicting these behaviours. Maximization of the growth rate was set as the main objective function, while minimization of total reaction fluxes and minimization of metabolic adjustment (environmental MOMA) were considered as the sub-objective functions. The environmental MOMA sub-objective performed better than the minimization of total reaction fluxes sub-objective function at predicting the mixture of storage compounds accumulated. Additional experiments with ¹³C-labelled bicarbonate (HCO₃⁻) found that the fluxes through the central metabolism reactions during the feast phases were similar to the ones during the famine phases on acetate due to similarity in the carbon sources in the feast and famine phases (i.e., acetate and poly-β-hydroxybutyrate, respectively); this suggests that the environmental MOMA sub-objective function could be used to analyze successive environmental conditions such as the feast and famine cycles while the metabolically similar carbon sources are taken up by microorganisms.

Impact of the composition of the bacterial population and additional carbon source on the pathway and kinetics of degradation of endosulfan isomers

Abiotic and bacterial degradation is presented for the two isomers α- and β- of the organochlorine pesticide endosulfan, denoted as ES-1 and ES-2, respectively. Biodegradation studies were conducted with two indigenous species Pseudomonas putida (P. putida) and Rhodococcus sp. Both ES isomers rapidly hydrolyzed in water at pH ≥ 7 but the hydrolysis was inhibited in the presence of biomass. The pesticide partitioned onto the biomass making it unavailable for abiotic hydrolytic reaction. Spontaneous temperature dependent abiotic conversion of ES-2 to ES-1 was reported in the presence of dual air-water phases but was not observed in the abiotic aqueous phase. Biodegradation experiments with pure isomers showed a small amount of interconversion (∼5%) in either direction and ruled out any preferential interconversion of the ES-2 isomer to ES-1 or vice versa. Both the species were shown to degrade ES-2 at a higher rate compared to ES-1 which may lead to enrichment of ES-1 in agricultural fields in short-term following application of the pesticide. P. putida degraded both the ES isomers through oxidative and hydrolytic pathways while the Rhodococcus sp. used only the hydrolytic pathway. Since ES-S (product of the oxidative pathway) is orders of magnitude more toxic than the parent isomers, the short term toxicity of a field following the application of the pesticide may increase if the composition of the indigenous bacterial population is such that the oxidative pathway is preferred over the hydrolytic one. The presence of an additional carbon source increased the rates of degradation of both the isomers but the enhancement was greater for the degradation rate of ES-2 than ES-1.

Effects of synthetic iron and aluminium oxide surface charge and hydrophobicity on the formation of bacterial biofilm

In this research, bacterial cell attachments to hematite, goethite and aluminium hydroxide were investigated. The aim was to study the effects of these minerals' hydrophobicity and pH-dependent surface charge on the extent of biofilm formation using six genetically diverse bacterial strains: Rhodococcus spp. (RC92 & RC291), Pseudomonas spp. (Pse1 & Pse2) and Sphingomonas spp. (Sph1 & Sph2), which had been previously isolated from contaminated environments. The surfaces were prepared in a way that was compatible with the naturally occurring coating process in aquifers: deposition of colloidal particles from the aqueous phase. The biofilms were evaluated using a novel, in situ and non-invasive technique developed for this purpose. A manufactured polystyrene 12-well plate was used as the reference surface to be coated with synthesized minerals by deposition of their suspended particles through evaporation. Planktonic phase growth indicates that it is independent of the surface charge and hydrophobicity of the studied surfaces. The hydrophobic similarities failed to predict biofilm proliferation. Two of the three hydrophilic strains formed extensive biofilms on the minerals. The third one, Sph2, showed anomalies in contrast to the expected electrostatic attraction between the minerals and the cell surface. Further research showed how the solution's ionic strength affects Sph2 surface potential and shapes the extent of its biofilm formation; reducing the ionic strength from ≈200 mM to ≈20 mM led to a tenfold increase in the number of cells attached to hematite. This study provides a technique to evaluate biofilm formation on metal-oxide surfaces, under well-controlled conditions, using a simple yet reliable method. The findings also highlight that cell numbers in the planktonic phase do not necessarily show the extent of cell attachment, and thorough physicochemical characterization of bacterial strains, substrata and the aquifer medium is fundamental to successfully implementing any bioremediation projects.

[Physiological function of membrane protein RHOGL009301 involved in transport of benzoate in Rhodococcus sp. R04]

OBJECTIVE

The physiological function of membrane protein RHOGL009301 in Rhodococcus sp. R04 and the metabolic properties of the mutant strain were studied to determine the relationship between the physiological function of the membrane protein and the transport of benzoate.

METHODS

The RHOGL009301 gene and the green fluorescent protein gene were fused for expressing in Rhodococcus erythropolis, and the location of RHOGL009301 was observed by Delta Vision. The RHOGL009301 gene was knocked out by homologous recombination, and the growth of wild strain and deficient strain in different carbon sources were compared. The internal and external metabolites of the wild strain and the deficient strain when grown on biphenyl and benzoate were measured by HPLC, and the changes of metabolite concentration in different growth conditions were analyzed.

RESULTS

A fusion gene that contained RHOGL009301 gene and the green fluorescent protein gene was co-expressed in Rhodococcus erythropolis and localized on the cell membrane. The deficient strain R04ΔMP of RHOGL009301 gene was obtained. The biomass of the deficient strain was significantly reduced in biphenyl and benzoate culture, and its growth rate was slowed down. HPLC analysis showed that the deletion of RHOGL009301 gene inhibited the transport of benzoate.

CONCLUSION

RHOGL009301 membrane protein is one of the proteins involved in metabolism and transport of benzoate. Based on sequence homology analysis, we can conclude that the membrane protein is a novel benzoate transport protein.

Biodegradation and metabolic pathway of nicotine in Rhodococcus sp. Y22

Nicotine in tobacco is harmful to health and the environment, so there is an environmental requirement to remove nicotine from tobacco and tobacco wastes. In this study, the biotransformation of nicotine by Rhodococcus sp. Y22 was investigated, and three metabolites (NIC1, NIC4 and NIC5) were isolated by column separation, preparative TLC and solid plate's method, respectively. NIC1 was identified as 6-hydoxynicotine based on the results of NMR, MS, HPLC-UV and HRESIMS analysis; NIC4 was a novel compound and identified as 5-(3-methyl-[1,3]oxazinan-2-ylidene)-5H-pyridin-2-one based on the results of NMR, MS and UV analysis; NIC5 was identified as nicotine blue based on the results of NMR and MS analysis. Meanwhile, two metabolites NIC2 and NIC3 were identified as 6-hydroxy-N-methylmyosmine and 6-hydroxypseudooxynicotine by HRESIMS analysis, respectively. According to these metabolites, the possible pathway of nicotine degradation by Rhodococcus sp. Y22 was proposed. The nicotine can be transformed to nicotine blue through two pathways (A and B), and 6-hydroxy-N-methylmyosmine is the key compound, which can be converted to 6-hydroxypseudooxynicotine (pathway A) and 5-(3-methyl-[1,3]oxazinan-2-ylidene)-5H-pyridin-2-one (pathway B), respectively. Moreover, the encoding gene of nicotine dehydrogenase, ndh, was amplified from Rhodococcus sp. Y22, and its transcriptional level could be up-regulated obviously under nicotine induction. Our studies reported the key metabolites and possible biotransformation pathway of nicotine in Rhodococcus sp. Y22, and provided new insights into the microbial metabolism of nicotine.

Application of 2,4-Dinitrophenylhydrazine (DNPH) in High-Throughput Screening for Microorganism Mutants Accumulating 9α-Hydroxyandrost-4-ene-3,17-dione (9α-OH-AD)

To develop a quick method for the preliminarily screening of mutant strains that can accumulate 9α-hydroxyandrost-4-ene-3,17-dione (9α-OH-AD), a high-throughput screening method was presented by applying the principle that 2,4-dinitrophenylhydrazine (DNPH) can react with ketones to produce precipitation. The optimal color assay conditions were the substrate androst-4-ene-3,17-dione (AD) concentration at 2.0 g/L, the ratio of AD to DNPH solution at 1:4, and the sulfuric acid and ethanol solution percentages in DNPH solution at 2% and 35%, respectively. This method was used to preliminarily screen the mutants of Rhodococcus rhodochrous DSM43269, from which the three ones obtained could produce more 9α-OH-AD. This DNPH color assay method not only broadens screening methods and increases screening efficiency in microbial mutation breeding but also establishes a good foundation for obtaining strains for industrial application.

Inoculation methods using Rhodococcus erythropolis strain P30 affects bacterial assisted phytoextraction capacity of Nicotiana tabacum

In this study different bacterial inoculation methods were tested for tobacco plants growing in a mine-soil contaminated with Pb, Zn, and Cd. The inoculation methods evaluated were: seed inoculation, soil inoculation, dual soil inoculation event, and seed+soil inoculation. Each inoculum was added at two bacterial densities (10(6) CFUs mL(-1) and 10(8) CFUs mL(-1)). The objectives were to evaluate whether or not the mode of inoculation or the number of applied microorganisms influences plant response. The most pronounced bacterial-induced effect was found for biomass production, and the soil inoculation treatment (using 10(6) CFUs mL(-1)) led to the highest increase in shoot dry weight yield (up to 45%). Bacterial-induced effects on shoot metal concentrations were less pronounced; although a positive effect was found on shoot Pb concentration when using 10(8) CFUs mL(-1) in the soil inoculation (29% increase) and in the seed+soil inoculation (34% increase). Also shoot Zn concentration increased by 24% after seed inoculation with 10(6) CFUs mL(-1). The best effects on the total metal yield were not correlated with an increasing number of inoculated bacteria. In fact the best results were found after a single soil inoculation using the lower cellular density of 10(6) CFUs mL(-1).

[Transcriptomic and benzoate metabolic pathways of Rhodococcus sp. R04 cultured in biphenyl]

OBJECTIVE

Studying transcriptional characteristics of Rhodococcus sp. R04 is to find the genes that participate in the transportation, metabolism and regulation of polychlorinated biphenyls (PCBs), and disclose the molecular mechanism of biodegradation of PCBs.

METHODS

Strain R04 was separately cultivated on ethanol, glucose and biphenyl. The total RNA of the above different cultures was extracted, and the cDNA was obtained by reverse transcription and determined by high-throughput sequencing. The data obtained by sequencing were analyzed to find the correlation among the PCBs metabolic network, gene transcription regulation and metabolic response.

RESULTS

The sequencing results showed that 375 genes were up-regulated during grown on biphenyl, relative to growth on glucose, and 332 genes were up-regulated, relative to growth on ethanol. Those genes were found to participate in multiple biological processes of biphenyl metabolite. Among the genes relative to biphenyl/PCBs degradation, the genes located on the gene cluster in the upper biphenyl pathway were significantly up-regulated, while bphC4 and bphD2 were up-regulated slightly. By contrast, the other genes encoding BphC and BphD isozymes in the biphenyl pathway were down-regulated even if growth on biphenyl.

CONCLUSION

Transcriptomic analysis suggested that benzoate was degraded via ortho cleavage pathway, meta cleavage pathway or protocatechuic acid pathway, which provide more valuable data for us to reveal the characteristics and regulation of downstream metabolic pathways of biphenyl and PCBs.

[Effect of water isotopic composition on Rhodococcus erythropolis biomass production]

The effect of water isotopic composition on concentration of oil-oxidizing actinobacteria Rhodococcus erythropolis VKM Ac-2017D cellular biomass is observed during cultivation in liquid nutrient media. The value for the effect was determined by experimental conditions, including consecutive use of hydrophilic and hydrophobic nutritious substrates--saccharose and hexadecane. It is shown, that when Rhodococcus erythropolis VKM Ac-2017D cells, cultivated in media with sucrose and 71 and 98 ppm deuterium content in water were inoculated into the similar in mineral and isotopic composition media with hexadecane, a considerable increase in cellular biomass production is observed if compared to a control sample in which water with 150 ppm deuterium concentration was used.

Diversity of endophytic bacteria in Lolium perenne and their potential to degrade petroleum hydrocarbons and promote plant growth

The aim of this study was to assess the ability of twenty-nine endophytic bacteria isolated from the tissues of ryegrass (Lolium perenne L.) to promote plant growth and the degradation of hydrocarbon. Most of the isolates belonged to the genus Pseudomonas and showed multiple plant growth-promoting abilities. All of the bacteria that were tested exhibited the ability to produce indole-3-acetic acid and were sensitive to streptomycin. These strains were capable of phosphate solubilization (62%), cellulolytic enzyme production (62%), a capacity for motility (55%) as well as for the production of siderophore (45%), ammonium (41%) and hydrogen cyanide (38%). Only five endophytes had the emulsification ability that results from the production of biosurfactants. The 1-aminocyclopropane-1-carboxylate deaminase (ACCD) gene (acdS) was found in ten strains. These bacteria exhibited ACCD activities in the range from 1.8 to 56.6 μmol of α-ketobutyrate mg(-1)h(-1), which suggests that these strains may be able to modulate ethylene levels and enhance plant growth. The potential for hydrocarbon degradation was assessed by PCR amplification on the following genes: alkH, alkB, C23O, P450 and pah. The thirteen strains that were tested had the P450 gene but the alkH and pah genes were found only in the Rhodococcus fascians strain (L11). Four endophytic bacteria belonging to Microbacterium sp. and Rhodococcus sp. (L7, S12, S23, S25) showed positive results for the alkB gene.

Effects of a static magnetic field on phenol degradation effectiveness and Rhodococcus erythropolis growth and respiration in a fed-batch reactor

The aim of this study was to evaluate the impact of short-term repeated exposure to a static magnetic field (induction 370 mT) on the Rhodococcus erythropolis cells. Specifically, it was ascertained the magnetic field's potential to influence degradation of a phenol substrate, cell growth and respiration activity (oxygen consumption) during substrate biodegradation. The experiment took place over 3 days, with R. erythropolis exposed to the magnetic field for the first day. During the experiment, different recirculation rates between the reactor and the magnetic contactor has been tested. Use of the magnetic field at higher recirculation rates (residence time in contactor was less than 7 min) stimulated substrate (phenol) oxidation by around 34%; which, in turn, promoted R. erythropolis growth by around 28% by shortening the lag- and exponential-phases and increasing bacterial respiration activity by around 10%.

Isolation and functional analysis of a glycolipid producing Rhodococcus sp. strain IITR03 with potential for degradation of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT)

A 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degrading bacterium strain IITR03 producing trehalolipid was isolated and characterized from a pesticides contaminated soil. The strain IITR03 was identified as a member of the genus Rhodococcus based on polyphasic studies. Under aqueous culture conditions, the strain IITR03 degraded 282 μM of DDT and could also utilize 10mM concentration each of 4-chlorobenzoic acid, 3-chlorobenzoic acid and benzoic acid as sole carbon and energy source. The catechol 1,2-dioxygenase enzyme activity resulted in conversion of catechol to form cis,cis-muconic acid. Cloning and sequencing of partial nucleotide sequence of catechol 1,2-dioxygenase gene (cat) from strain IITR03 revealed its similarity to catA gene present in Rhodococcus sp. strain Lin-2 (97% identity) and Rhodococcus strain AN22 (96% identity) degrading benzoate and aniline, respectively. The results suggest that the strain IITR03 could be useful for field bioremediation studies of DDT-residues and chlorinated aromatic compounds present in contaminated sites.

Bacteria induced degradation of fluoranthene in minimal salt medium mediated by catabolic enzymes in vitro condition

Fluoranthene is highly toxic and ubiquitous in the environment. A study on degradation of 200 ppm of fluoranthene in MSM by two bacterial strains Pseudomonas aeruginosa PSA5, Rhodococcus sp. NJ2 and their consortium revealed that fluoranthene was degraded 74% by Rhodococcus sp. NJ2, 61% by Pseudomonas sp. PSA5 and 97% by their consortium. Higher degradation in the consortium may be attributed to synergistic action between two bacteria. It was also observed that several degradative enzymes catechol 1,2 dioxygenase, catechol 2,3 dioxygenase, protocatechuate 2,3 dioxygenase, protocatechuate 3,4 dioxygenase, protocatechuate 4,5 dioxygenase, salicylate hydroxylase and 2-carboxybenzaldehyde dehydrogenase were differentially induced at different stages of fluoranthene degradation. Biodegradation kinetics indicated half life period of fluoranthene degradation. Besides, glycolipid, as a biosurfactant, was induced to facilitate the degradation process. Hence, both the bacteria may be used individually or in combination for effective decontamination of oil and sludge contaminated soil.

Mixed-species biofilms cultured from an oil sand tailings pond can biomineralize metals

Here, we used an in vitro biofilm approach to study metal resistance and/or tolerance of mixed-species biofilms grown from an oil sand tailings pond in northern Alberta, Canada. Metals can be inhibitory to microbial hydrocarbon degradation. If microorganisms are exposed to metal concentrations above their resistance levels, metabolic activities and hydrocarbon degradation can be slowed significantly, if not inhibited completely. For this reason, bioremediation strategies may be most effective if metal-resistant microorganisms are used. Viability was measured after exposure to a range of concentrations of ions of Cu, Ag, Pb, Ni, Zn, V, Cr, and Sr. Mixed-species biofilms were found to be extremely metal resistant; up to 20 mg/L of Pb, 16 mg/L of Zn, 1,000 mg/L of Sr, and 3.2 mg/L of Ni. Metal mineralization was observed by visualization with scanning electron microscopy with metal crystals of Cu, Ag, Pb, and Sr exuding from the biofilms. Following metal exposure, the mixed-species biofilms were analyzed by molecular methods and were found to maintain high levels of species complexity. A single species isolated from the community (Rhodococcus erythropolis) was used as a comparison against the mixed-community biofilm and was seen to be much less tolerant to metal stress than the community and did not biomineralize the metals.

Cultivation of lipid-producing bacteria with lignocellulosic biomass: effects of inhibitory compounds of lignocellulosic hydrolysates

Lignocellulosic biomass has been recognized as a promising feedstock for the fermentative production of biofuel. However, the pretreatment of lignocellulose generates a number of by-products, such as furfural, 5-hydroxylmethyl furfural (5-HMF), vanillin, vanillic acids and trans-p-coumaric acid (TPCA), which are known to inhibit microbial growth. This research explores the ability of Rhodococcus opacus PD630 to use lignocellulosic biomass for production of triacylglycerols (TAGs), a common lipid raw material for biodiesel production. This study reports that R. opacus PD630 can grow well in R2A broth in the presence of these model inhibitory compounds while accumulating TAGs. Furthermore, strain PD630 can use TPCA, vanillic acid, and vanillin as carbon sources, but can only use TPCA and vanillic acid for TAG accumulation. Strain PD630 can also grow rapidly on the hydrolysates of corn stover, sorghum, and grass to accumulate TAGs, suggesting that strain PD630 is well-suited for bacterial lipid production from lignocellulosic biomass.

[Adaptation of coimmobilized Rhodococcus cells to oil hydrocarbons in a column bioreactor]

The possible adaptation of the association of Rhodococcus ruber and Rhodococcus opacus strains immobilized on modified sawdust to oil hydrocarbons in a column bioreactor was investigated. In the bioreactor, the bacterial population showed higher hydrocarbon and antibiotic resistance accompanied by the changes in cell surface properties (hydrophobicity, electrokinetic potential) and in the content of cellular lipids and biosurfactants. The possibility of using adapted Rhodococcus strains for the purification of oil-polluted water in the bioreactor was demonstrated.

Partial characterization of a crude cold-active lipase from Rhodococcus cercidiphylli BZ22

Cold-active lipase production by the psychrophilic strain Rhodococcus cercidiphylli BZ22 isolated from hydrocarbon-contaminated alpine soil was investigated. Depending on the medium composition, high cell densities were observed at a temperature range of 1-10 °C in Luria-Bertani (LB) broth or 1-30 °C in Reasoner's 2A (R2A). Maximum enzyme production was achieved at a cultivation temperature of 1-10 °C in LB medium. About 70-80% of the secreted enzyme was bound to the cell and was highly active as a cell-immobilized lipase which exhibited good reusability; more than 60% of the initial lipase activity was retained after five-fold reuse. The properties of the lipase produced by the investigated strain were compared with those of a mesophilic porcine pancreatic lipase (PPL). The thermal stability of the cell-immobilized bacterial lipase was higher than that of the extracellular enzyme. Highest activity was detected at 30 °C for the cell-immobilized enzyme and for PPL, while the extracellular enzyme displayed highest activity at 10-20 °C. The bacterial lipase hydrolyzed p-nitrophenyl (p-NP) esters with different acyl chain lengths (C2-C18). The highest hydrolytic activity was obtained with p-NP-butyrate (C4) as substrate, while the highest substrate affinity was obtained with p-NP-dodecanoate (C12) as substrate, indicating a clear preference of the enzyme for medium acyl chain lengths.

[Synthesis of surfactants by Rhodococcus erythropolis IMV Ac-5017, Acinetobacter calcoaceticus IMV B-7241 and Nocardia vaccinii IMV B-7405 on industrial waste]

The synthesis of surfactants by Rhodococcus erythropolis IMV Ac-5017, Acinetobacter calcoaceticus IMV B-7241 and Nocardia vaccinii IMV B-7405 on industrial waste (food and oil-processing industry, production of biodiesel) was investigated. The possibility of replacing the expensive substrates (n-hexadecane and ethanol) by industrial waste (oil and fat industry, fried sunflower oil, glycerol, liquid paraffin) for the surfactant biosynthesis was established. The conditional concentration of surfactants was maximal on oil containing substrates and exceeded those on n-hexadecane and ethanol 2-3 times. The highest rates of surfactants synthesis were observed on fried sunflower oil with the use of inoculum grown on carbohydrate substrates (glucose, molasses). It was established that the addition of glucose (0.1%) was accompanied by 2-4-fold intensification of surfactants synthesis by R. erythropolis IMV Ac-5017 and N. vaccinii IMV B-7405 on fried sunflower oil (2%).

[Effect of surface-active substances of Acinetobacter calcoaceticus IMV B-7241, Rhodococcus erythropolis IMV Ac-5017, and Nocardia vaccinii K-8 on phytopathogenic bacteria]

The effect of surface-active substances (SAS's) of Acinetobacter calcoaceticus IMV B-7241, Rhodococcus erythropolis IMV Ac-5017, and Nocardia vaccinii K-8 on phytopathogenic bacteria has been studied. It was shown that the survival of cells (10(5)-10(7) in a milliliter) of the Pseudomonas and Xanthomonas phytopathogenic bacteria was found to be 0-33% after treatment with SAS preparations of the IMV Ac-5017 and IMV B-7241 strains for 2 h (0.15-0.4 mg/mL). In the presence of N. vaccinii K-8 SAS preparations (0.085-0.85 mg/mL), the number of cells of the majority of the studied phytopathogenic bacteria decreased by 95-100%. These data show prospects for using microbial SAS's for the construction of ecologically friendly drugs for regulating the number of phytopathogenic bacteria.

Cholesterol to cholestenone oxidation by ChoG, the main extracellular cholesterol oxidase of Rhodococcus ruber strain Chol-4

The choG ORF of Rhodococcus ruber strain Chol-4 (referred from now as Chol-4) encodes a putative extracellular cholesterol oxidase. In the Chol-4 genome this ORF is located in a gene cluster that includes kstD3 and hsd4B, showing the same genomic context as that found in other Rhodococcus species. The putative ChoG protein is grouped into the class II of cholesterol oxidases, close to the Rhodococcus sp. CECT3014 ChoG homolog. The Chol-4 choG was cloned and expressed in a CECT3014 ΔchoG host strain in order to assess its ability to convert cholesterol into cholestenone. The RT-PCR analysis showed that choG gene was constitutively expressed in all the conditions assayed, but a higher induction could be inferred when cells were growing in the presence of cholesterol. A Chol-4 ΔchoG mutant strain was still able to grow in minimal medium supplemented with cholesterol, although at a slower rate. A comparative study of the removal of both cholesterol and cholestenone from the culture medium of either the wild type Chol-4 or its choG deletion mutant revealed a major role of ChoG in the extracellular production of cholestenone from cholesterol and, therefore, this enzyme may be related with the maintenance of a convenient supply of cholestenone for the succeeding steps of the catabolic pathway.

[Molecular biological characterization of biphenyl-degrading bacteria and identification of the biphenyl 2,3-dioxygenase α-subunit genes]

Bacterial isolates from soils contaminated with (chlorinated) aromatic compounds, which degraded biphenyl/chlorinated biphenyls (CB) and belonged to the genera Rhodococcus and Pseudomonas were studied. Analysis of the 16S rRNA gene sequences was used to determine the phylogenetic position of the isolates. The Rhodococcus cells were found to contain plasmids of high molecular mass (220-680 kbp). PCR screening for the presence of the bphA1 gene, a marker indicating the possibility for induction of 2,3-dioxygenase (biphenyl/toluene dioxygenase subfamily) revealed the presence of the bphAl genes with 99-100% similarity to the homologous genes of bacteria of the relevant species in all pseudomonad and most Rhodococcus isolates. A unique bphA1 gene, which had not been previously reported for the genus, was identified in Rhodococcus sp. G10. The absence of specific amplification of the bphA1 genes in some biphenyl-degrading bacteria (Rhodococcus sp. B7b, B106a, G12a, P2kr, P2(51), and P2m), as well as in an active biphenyl degrader Rhodococcus ruber P25 indicated the absence of the genes encoding the proteins of the biphenyl/toluene dioxygenase subfamily and participation of the enzymes other than this protein family in biphenyl/CB degradation.

Effects of growth substrate on triclosan biodegradation potential of oxygenase-expressing bacteria

Triclosan is an antimicrobial agent, an endocrine disrupting compound, and an emerging contaminant in the environment. This is the first study investigating triclosan biodegradation potential of four oxygenase-expressing bacteria: Rhodococcus jostii RHA1, Mycobacterium vaccae JOB5, Rhodococcus ruber ENV425, and Burkholderia xenovorans LB400. B. xenovorans LB400 and R. ruber ENV425 were unable to degrade triclosan. Propane-grown M. vaccae JOB5 can completely degrade triclosan (5 mg L(-1)). R. jostii RHA1 grown on biphenyl, propane, and LB medium with dicyclopropylketone (DCPK), an alkane monooxygenase inducer, was able to degrade the added triclosan (5 mg L(-1)) to different extents. Incomplete degradation of triclosan by RHA1 is probably due to triclosan product toxicity. The highest triclosan transformation capacity (Tc, defined as the amount of triclosan degraded/the number of cells inactivated; 5.63×10(-3) ng triclosan/16S rRNA gene copies) was observed for biphenyl-grown RHA1 and the lowest Tc (0.20×10(-3) ng-triclosan/16S rRNA gene copies) was observed for propane-grown RHA1. No triclosan degradation metabolites were detected during triclosan degradation by propane- and LB+DCPK-grown RHA1. When using biphenyl-grown RHA1 for degradation, four chlorinated metabolites (2,4-dichlorophenol, monohydroxy-triclosan, dihydroxy-triclosan, and 2-chlorohydroquinone (a new triclosan metabolite)) were detected. Based on the detected metabolites, a meta-cleavage pathway was proposed for triclosan degradation.

[Characterization of phenol-degrading Rhodococcus sp. strain P1 from coking wastewater]

OBJECTIVE

The removal of phenolic compounds was a key problem for coking wastewater treatment. This study focused on the isolation and characterization of anefficient phenol-degrading bacterial strain from coking wastewater.

METHODS

Phenol-degrading bacterium was screened by using phenol as the sole carbon source, strain was identified according to the morphological properties and 16S rRNA sequence analysis, the phenol-degrading characteristics and the potential for removal of phenol in the coking wastewater were evaluated.

RESULTS

Strain P1 was identified as the genus Rhodococcus sp. with morphological properties and 16S rRNA gene sequence. This strain could survive at the presence of phenol with concentration up to 1400 mg/L. The optimal conditions for biodegradation of 600 mg/L phenol in mineral medium were at 32 - 42 degrees C, pH 7.0 and 0 - 4% NaCl. The phenol-degrading efficiency by P1 strain was different in response to various heavy metal ions, Ni2+, Mn2+ and low concentration of Pb2+ had no effect on the phenol degradation. However, Cu2+, Ni2+ and Cd2+ seriously inhibited phenol degradation by strain P1. The 279.9 mg/L phenols from 1/3 coking wastewater were completely degraded after incubation for 2 days.

CONCLUSION

Strain P1 is an efficient phenol-degrading bacterium and has of the potential for removing phenolic compounds in coking wastewater.

Metabolism of 2-chloro-4-nitroaniline via novel aerobic degradation pathway by Rhodococcus sp. strain MB-P1

2-chloro-4-nitroaniline (2-C-4-NA) is used as an intermediate in the manufacture of dyes, pharmaceuticals, corrosion inhibitor and also used in the synthesis of niclosamide, a molluscicide. It is marked as a black-listed substance due to its poor biodegradability. We report biodegradation of 2-C-4-NA and its pathway characterization by Rhodococcus sp. strain MB-P1 under aerobic conditions. The strain MB-P1 utilizes 2-C-4-NA as the sole carbon, nitrogen, and energy source. In the growth medium, the degradation of 2-C-4-NA occurs with the release of nitrite ions, chloride ions, and ammonia. During the resting cell studies, the 2-C-4-NA-induced cells of strain MB-P1 transformed 2-C-4-NA stoichiometrically to 4-amino-3-chlorophenol (4-A-3-CP), which subsequently gets transformed to 6-chlorohydroxyquinol (6-CHQ) metabolite. Enzyme assays by cell-free lysates prepared from 2-C-4-NA-induced MB-P1 cells, demonstrated that the first enzyme in the 2-C-4-NA degradation pathway is a flavin-dependent monooxygenase that catalyzes the stoichiometric removal of nitro group and production of 4-A-3-CP. Oxygen uptake studies on 4-A-3-CP and related anilines by 2-C-4-NA-induced MB-P1 cells demonstrated the involvement of aniline dioxygenase in the second step of 2-C-4-NA degradation. This is the first report showing 2-C-4-NA degradation and elucidation of corresponding metabolic pathway by an aerobic bacterium.

Phenol degrading ability of Rhodococcus pyrinidivorans and Pseudomonas aeruginosa isolated from activated sludge plants in South Africa

Phenol, a common constituent in many industrial wastewaters is a major pollutant and has several adverse effects on the environment. The potential of various microorganisms to utilize phenol for their metabolic activity has been observed to be an effective means of remediating this toxic compound from the environment particularly wastewater. Five indigenous bacterial isolates (PD1-PD5) were obtained from phenol bearing industrial wastewater using the mineral salts medium. The isolates were further characterized based on their morphology, biochemical reactions and 16S rRNA phylogeny. The 16S rRNA sequence analysis using universal primers (27f/1492r) revealed that PD1, PD2, PD3 and PD4 were closely related to the actinomycete Rhodococcus pyrinidivorans (99%) and PD5 to Pseudomonas aeruginosa (99%). Growth kinetic patterns and phenol degradation abilities of the two representative isolates (PD1 and PD5) were also evaluated. Both the species were effective in utilizing phenol as the sole carbon source and could tolerate phenol concentrations of up to 500 to 600 mg/L. The ability of these isolates to utilize higher concentrations of phenol as their sole carbon source makes them potential candidates and better competitors in the bioremediation process.

Mathematic modeling for optimum conditions on aflatoxin B₁degradation by the aerobic bacterium Rhodococcus erythropolis

Response surface methodology was employed to optimize the degradation conditions of AFB₁ by Rhodococcus erythropolis in liquid culture. The most important factors that influence the degradation, as identified by a two-level Plackett-Burman design with six variables, were temperature, pH, liquid volume, inoculum size, agitation speed and incubation time. Central composite design (CCD) and response surface analysis were used to further investigate the interactions between these variables and to optimize the degradation efficiency of R. erythropolis based on a second-order model. The results demonstrated that the optimal parameters were: temperature, 23.2 °C; pH, 7.17; liquid volume, 24.6 mL in 100-mL flask; inoculum size, 10%; agitation speed, 180 rpm; and incubation time, 81.9 h. Under these conditions, the degradation efficiency of R. erythropolis could reach 95.8% in liquid culture, which was increased by about three times as compared to non-optimized conditions. The result by mathematic modeling has great potential for aflatoxin removal in industrial fermentation such as in food processing and ethanol production.

Simultaneous heterotrophic nitrification and aerobic denitrification by bacterium Rhodococcus sp. CPZ24

Rhodococcus sp. CPZ24 was isolated from swine wastewater and identified. Batch (0.25 L flask) experiments of nitrogen removal under aerobic growth conditions showed complete removal of 50 mg L(-1) ammonium nitrogen within 20 h, while nitrate nitrogen removal reached 67%. A bioreactor (50 L) was used to further assess the heterotrophic nitrification and aerobic denitrification abilities of Rhodococcus sp. CPZ24. The results showed that 85% of the ammonium nitrogen (100 mg L(-1)) was transformed to nitrification products (NO(3)(-)-N and NO(2)(-)-N) (13%), intracellular nitrogen (24%), and gaseous denitrification products (48%) within 25 h. The ammonium nitrogen removal rate was 3.4 mg L(-1)h(-1). The results indicate that the strain CPZ24 carries out simultaneous nitrification and denitrification, demonstrating a potential use of the strain for wastewater treatment.

Biosynthesis of benzoylformic acid from benzoyl cyanide by a newly isolated Rhodococcus sp. CCZU10-1 in toluene-water biphasic system

Benzoylformic acid was synthesized from the hydrolysis of benzoyl cyanide by a newly isolated Rhodococcus sp. CCZU10-1. In this study, an aqueous-toluene biphasic system was developed for highly efficient production of benzoylformic acid from the hydrolysis of benzoyl cyanide. In the aqueous-toluene biphasic system, the phase volume ratio, buffer pH and reaction temperature were optimized. Using fed-batch method, a total of 932 mM benzoylformic acid accumulated in the reaction mixture after the 10th feed. Moreover, enzymatic hydrolysis of benzoyl cyanide using calcium alginate entrapped resting cells was carried out in the aqueous-toluene biphasic system, and efficient biocatalyst recycling was achieved as a result of cell immobilization in calcium alginate, with a product-to-biocatalyst ratio of 14.26g benzoylformic acid g(-1) dry cell weight (DCW) cell after 20 cycles of repeated use.

Plant-derived auxin plays an accessory role in symptom development upon Rhodococcus fascians infection

The biotrophic phytopathogen Rhodococcus fascians has a profound impact on plant development, mainly through its principal virulence factors, a mix of synergistically acting cytokinins that induce shoot formation. Expression profiling of marker genes for several auxin biosynthesis routes and mutant analysis demonstrated that the bacterial cytokinins stimulate the auxin biosynthesis of plants via specific targeting of the indole-3-pyruvic acid (IPA) pathway, resulting in enhanced auxin signaling in infected tissues. The double mutant tryptophan aminotransferase 1-1 tryptophan aminotransferase related 2-1 (taa1-1 tar2-1) of Arabidopsis (Arabidopsis thaliana), in which the IPA pathway is defective, displayed a decreased responsiveness towards R. fascians infection, although bacterial colonization and virulence gene expression were not impaired. These observations implied that plant-derived auxin was employed to reinforce symptom formation. Furthermore, the increased auxin production and, possibly, the accumulating bacterial cytokinins in infected plants modified the polar auxin transport so that new auxin maxima were repetitively established and distributed, a process that is imperative for symptom onset and maintenance. Based on these findings, we extend our model of the mode of action of bacterial and plant signals during the interaction between R. fascians and Arabidopsis.

[Identification and biological characterization of an acetonitrile degrading strain]

OBJECTIVE

To identify and characterize an acetonitrile degrading strain BX2, thus to assess its potentials in the treatment of acetonitrile containing wastewater.

METHODS

By means of phenotype and physio-biochemical characterization as well as phylogenetic analysis, we identified strain BX2. The optimum culture conditions of the strain were studied with single factor test, and the degradation of acetonitrile under the optimal growth conditions was determined. Additionally, NaCl tolerance was investigated.

RESULTS

The phenotype and physio-biochemical characteristics of strain BX2 were similar to those of Rhodococcus sp.. The phylogenetic analysis based on 16S rRNA, gyrB and secA1 gene suggested strain BX2 was the closest relative of Rhodococcus rhodochrous with 99.37%, 99.29% and 97.87% sequence similarity respectively. The optimal conditions for cell growth were 35 degrees C, initial pH 7.5, and 1% inoculum. Under these conditions, the degradation rate of acetonitrile was 95.87% (800mg/L) within 16 h. Strain BX2 was able to grow in defined medium containing NaCl up to 6%.

CONCLUSION

Strain BX2 was identified as Rhodococcus rhodochrous and named Rhodococcus rhodochrous BX2. It showed great environmental adaptation and high capability of degrading acetonitrile.

Study of an aquifer contaminated by ethyl tert-butyl ether (ETBE): site characterization and on-site bioremediation

Ethyl tert-butyl ether (ETBE) was detected at high concentration (300mgL(-1)) in the groundwater below a gas-station. No significant carbon neither hydrogen isotopic fractionation of ETBE was detected along the plume. ETBE and BTEX biodegradation capacities of the indigenous microflora Pz1-ETBE and of a culture (MC-IFP) composed of Rhodococcus wratislaviensis IFP 2016, Rhodococcus aetherivorans IFP 2017 and Aquincola tertiaricarbonis IFP 2003 showed that ETBE and BTEX degradation rates were in the same range (ETBE: 0.91 and 0.83 mg L(-1)h(-1) and BTEX: 0.64 and 0.82 mg L(-1)h(-1), respectively) but tert-butanol (TBA) accumulated transiently at a high level using Pz1-ETBE (74 mg L(-1)). An on-site pilot plant (2m(3)) filled with polluted groundwater and inoculated by MC-IFP, successfully degraded four successive additions of ETBE and gasoline. However, an insignificant ETBE isotopic fractionation was also accompanying this decrease which suggested the involvement of low fractionating-strains using EthB enzymes, but required of additional proofs. The ethB gene encoding a cytochrome P450 involved in ETBE biodegradation (present in R. aetherivorans IFP 2017) was monitored by quantitative real-time polymerase chain reaction (q-PCR) on DNA extracted from water sampled in the pilot plant which yield up to 5×10(6) copies of ethB gene per L(-1).

[Detoxification of high concentrations of trinitrotoluene by bacteria]

The ability of the strains-destructors of various aromatic compounds to utilize trinitrotoluene (TNT) up to concentration of 70 mg/1 was shown. An increase in the TNT concentration from 100 to 150 mg/1 did not inhibit its conversion rate by the Kocuria palustris RS32 strain. The Acinetobacter sp. VT 11 strain utilized TNT as a sole substrate for growth; 3,5-dinitro-4-methyl anilide acetate and 2,6-dinitro-4-aminotoluene were identified as intermediates of TNT degradation by active strains of Pseudomonas sp. VT-7W and Kocuria rosea RS51. At the same time, 4-methyl-3,5-dinitroformamide was discovered for the first time upon the TNT destruction by the bacteria strains of Rhodococcus opacus 1G and Rhodococcus sp. VT-7. The active bacterial strains achieved an 82-90% destruction of TNT when they were introduced into the soil.

[Diversity of culturable butane-oxidizing bacteria in oil and gas field soil]

Butane-oxidizing bacteria in soil sample sites from Puguang gas field in Sichuan province and Jianghan oil field in Hubei province were isolated and 16S rRNA gene sequence and phylogenetic analysis were applied. The differences of number and phylogenetic position and population diversity of hydrocarbon-oxidizing bacteria in different environment were investigated. The results show that 25 strains of butane-oxidizing bacteria were isolated. Based on sequencing of 16S rRNA gene, the species of bacteria in two samples are classified into 3 phyla including Firmicutes, Actinobacteria and Proteobacteria. The community structure of butane-oxidizing bacteria isolated from two oil samples is simple, both of them contain 4 genus including Bacillus, Pseudomonas, Rhodococcus and Arthrobacter. Strains in the genus of Ochrobactrum and Mycobacterium were only isolated from Puguang gas field. The number and population diversity of butane-oxidizing bacteria in Puguang gas field was more than those in Jianghan oil field.

Screening, cultivation, and biocatalytic performance of Rhodococcus boritolerans FW815 with strong 2,2-dimethylcyclopropanecarbonitrile hydratase activity

In this work, a mild, efficient bioconversion of 2,2-dimethylcyclopropanecarbonitrile (DMCPCN) to 2,2-dimethylcyclopropanecarboxamide (DMCPCA) in distilled water system was developed. The isolate FW815 was screened using the enrichment culture technique, displaying strong DMCPCN hydratase activity, and was identified as Rhodococcus boritolerans based on morphological, physiological, biochemical tests and 16S rRNA gene sequencing. Cultivation outcomes indicated that R. boritolerans FW815 was a neutrophile, with a growth optimum of 28-32°C; its DMCPCN hydratase belonged to the Fe-type family, and was most active at 38-42°C, pH 7.0, with maximal activity of 4.51 × 10(4) U g(-1) DCW. R. boritolerans FW815 was found to be DMCPCA amidase-negative, eliminating the contamination of dimethylcyclopropanecarboxylic acid. Moreover, it displayed high activity and acceptable reusability in the non-buffered distilled water system, comparable to those in pH 7.0 phosphate buffer (50.0 mmol l(-1)).

[Effect of citric acid on synthesis of surfactants in Rhodococcus erythropolis IMV Ac-5017]

Expediency of sodium citrate (regulator of lipids synthesis) substitution is shown in the medium of cultivation of Rhodococcus erythropolis IMV Ac-5017 with ethanol (or hexadecane) and fumarate (gluconeogenesis precursor) by citric acid for pH maintenance at the level optimal for synthesis of surfactants. It has been established the maximum synthesis of surfactants of R. erythropolis IMV Ac-5017 was observed at pH 8.0. Introduction of 0.2% sodium fumarate at the end of experimental growth phase of the strain IMV Ac-5017 in the medium with 2% of ethanol with further periodic acidification of culture liquid by citric acid up to pH 8.0 was accompanied by the increase of conditional concentration of surfactants by 30, 40 and 95% as compared with an analogous process without pH regulation, by the use of sodium citrate as the regulator of lipids synthesis on the medium with ethanol as well as without organic acids, respectively.

Biochemical features of the degradation of pollutants by Rhodococcus as a basis for contaminated wastewater and soil cleanup

Rhodococcus bacteria are considered to be promising degraders of persistent pollutants and are the basis of biological preparations for contaminated wastewater and soil cleanup. Biotechnological application of this group of bacteria is based on the peculiaraties of their metabolism. This review briefly discusses the following main points: I. Growth of Rhodococcus on various aromatic substrates, II. Chloro/methylcatechol transformation pathways, 3-Chlorocatechol branch of the modified ortho-pathway, 4-Chlorocatechol branch of the modified ortho-pathway, Modified 3-chlorocatechol branch in Rhodococcus opacus 1CP, Meta-cleavage ofchlorocatechols, Modified pathway for methylcatechol degradation, III. Approaches to the enhancement of degradation activity, IV. Rhodococcus-based biopreparations, IV. Prospects.

Improved xenobiotic-degrading activity of Rhodococcus opacus strain 1cp after dormancy

The goals of the present work were as follows: to obtain the dormant forms of R. opacus 1cp; to study the phenotypic variability during their germination; to compare phenotypic variants during the growth on selective and elective media; and to reveal changes in the ability of the strain to destruct xenobiotics that had not been degradable before dormancy. It was shown that Rhodococcus opacus 1cp (the strain degrading chlorinated phenols) became able to utilize a broader spectrum of xenobiotics after storage in the dormant state. Germination of the dormant forms of R. opacus 1cp on an agarized medium was followed by emergence and development of phenotypic variants that could grow on 4-chlorophenol and 2,4,6-trichlorophenol without adaptation. The cells of R. opacus 1cp phenotypic variants also utilized all of the tested chlorinated phenols: 2,3-, 2,5-, and 2,6-dichloro-, 2,3,4- and 2,4,5-trichloro-, pentachlorophenol, and 1,2,4,5-tetrachlorobenzene in concentrations up to 60 mg/L, though at the lower rates than 4-CP and 2,4,6-TCP. The improved degradation of chlorinated phenols by R. opacus strain 1cp exposed to the growth arrest conditions demonstrates the significance of dormancy for further manifestation of the adaptive potential of populations. A new principle of selection of variants with improved biodegradative properties was proposed. It embraces introduction of the dormancy stage into the cell life cycle with subsequent direct inoculation of morphologically different colonies into the media with different toxicants, including those previously not degraded by the strain.

[Intensification of surfactant synthesis in Rhodococcus erythropolis EK-1 cultivated on hexadecane]

Activity of key enzymes of n-alkane metabolism was determined in cells of Rhodococcus erythropolis EK-1, a surfactant producer grown on n-hexadecane. Potassium cations were found to inhibit alkane hydroxylase and NADP(+)-dependent aldehyde dehydrogenase, while sodium cations were found to activate these enzymes. Decreased potassium concentration (to 1 mM), increased sodium concentration (to 35 mM), and addition of 36 micromol/l Fe(II), required for alkane hydroxylase activity, resulted in increased activity of the enzymes of n-hexadecane metabolism and in a fourfold increase of surfactant synthesis. A 1.5-1.7-fold increase in surfactant concentration after addition of 0.2% fumarate (gluconeogenesis precursor) and 0.1% citrate (lipid synthesis regulator) to the medium with n-hexadecane results from enhanced synthesis of trehalose mycolates, as evidenced by a 3-5-fold increase in phosphoenolpyruvate synthetase and trehalose phosphate synthase, respectively.