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PubMed1990

Coexisting bacterial populations responsible for multiphasic mineralization kinetics in soil.

Experiments were conducted to study populations of indigenous microorganisms capable of mineralizing 2,4-dinitrophenol (DNP) in two soils. Previous kinetic analyses indicated the presence of two coexisting populations of DNP-mineralizing microorganisms in a forest soil (soil 1). Studies in which eucaryotic and procaryotic inhibitors were added to this soil indicated that both populations were bacterial. Most-probable-number counts with media containing different concentrations of DNP indicated that more bacteria could mineralize low concentrations of DNP than could metabolize high concentrations of it. Enrichments with varying concentrations of DNP and various combinations of inhibitors consistently resulted in the isolation of the same two species of bacteria from soil 1. This soil contained a large number and variety of fungi, but no fungi capable of mineralizing DNP were isolated. The two bacterial isolates were identified as a Janthinobacterium sp. and a Rhodococcus sp. The Janthinobacterium sp. had a low mu(max) and a low K(m) for DNP mineralization, whereas the Rhodococcus sp. had much higher values for both parameters. These differences between the two species of bacteria were similar to differences seen when soil was incubated with different concentrations of DNP. Values for mu(max) from soil incubations were similar to mu(max) values obtained in pure culture studies. In contrast, K(s) and K(m) values showed greater variation between soil and pure culture studies. The results of this study help to confirm predictions that two physiologically distinct bacterial populations are responsible for the multiphasic mineralization kinetics observed in the soil studied.

Journal Article↗

PubMed1998

Computation of the electrical double layer properties of semipermeable membranes in multicomponent electrolytes

A methodology is presented for calculating of the surface potential, Donnan potential, and ion concentration profiles for semipermeable microbial membranes that is valid for an arbitrary electrolyte composition. This model for surface potential, Donnan potential, and charge density was applied to recently reported experimental data for gram-positive bacteria, including Bacillus brevis, Rhodococcus opacus, Rhodococcus erythropolis, and Corynebacterium species. These calculations show that previously unconsidered trace amounts of divalent and trivalent cations at very low concentrations (10(-6) M) can have significant effects on the calculated surface and Donnan potentials, at ionic strengths of I </= 0.01 M, and that these effects need to be considered in accurate modeling of microbial surface. In addition, the calculated ion concentration profiles show that owing to the relatively high surface charges that can develop in microbial membranes, electrostatic effects can act to significantly concentrate divalent (factors of 5 x 10(3)) and trivalent (factors of 2 x 10(4)) cations within the bacterial cell wall. Comparison of the calculated concentration factors with those derived from experiments shows that a significant fraction of the uptake of metal by bacteria can be explained by the proposed electrostatic model.

Journal Article↗

PubMed2000

Molecular analysis of surfactant-driven microbial population shifts in hydrocarbon-contaminated soil.

We analyzed the impact of surfactant addition on hydrocarbon mineralization kinetics and the associated population shifts of hydrocarbon-degrading microorganisms in soil. A mixture of radiolabeled hexadecane and phenanthrene was added to batch soil vessels. Witconol SN70 (a nonionic, alcohol ethoxylate) was added in concentrations that bracketed the critical micelle concentration (CMC) in soil (CMC') (determined to be 13 mg g(-1)). Addition of the surfactant at a concentration below the CMC' (2 mg g(-1)) did not affect the mineralization rates of either hydrocarbon. However, when surfactant was added at a concentration approaching the CMC' (10 mg g(-1)), hexadecane mineralization was delayed and phenanthrene mineralization was completely inhibited. Addition of surfactant at concentrations above the CMC' (40 mg g(-1)) completely inhibited mineralization of both phenanthrene and hexadecane. Denaturing gradient gel electrophoresis of 16S rRNA gene segments showed that hydrocarbon amendment stimulated Rhodococcus and Nocardia populations that were displaced by Pseudomonas and Alcaligenes populations at elevated surfactant levels. Parallel cultivation studies revealed that the Rhodococcus population can utilize hexadecane and that the Pseudomonas and Alcaligenes populations can utilize both Witconol SN70 and hexadecane for growth. The results suggest that surfactant applications necessary to achieve the CMC alter the microbial populations responsible for hydrocarbon mineralization.

Alkanes↗

PubMed2003

Distribution of the coenzyme M pathway of epoxide metabolism among ethene- and vinyl chloride-degrading Mycobacterium strains.

An epoxyalkane:coenzyme M (CoM) transferase (EaCoMT) enzyme was recently found to be active in the aerobic vinyl chloride (VC) and ethene assimilation pathways of Mycobacterium strain JS60. In the present study, EaCoMT activity and genes were investigated in 10 different mycobacteria isolated on VC or ethene from diverse environmental samples. In all cases, epoxyethane metabolism in cell extracts was dependent on CoM, with average specific activities of EaCoMT between 380 and 2,910 nmol/min/mg of protein. PCR with primers based on conserved regions of EaCoMT genes from Mycobacterium strain JS60 and the propene oxidizers Xanthobacter strain Py2 and Rhodococcus strain B-276 yielded fragments (834 bp) of EaCoMT genes from all of the VC- and ethene-assimilating isolates. The Mycobacterium EaCoMT genes form a distinct cluster and are more closely related to the EaCoMT of Rhodococcus strain B-276 than that of Xanthobacter strain Py2. The incongruence of the EaCoMT and 16S rRNA gene trees and the fact that isolates from geographically distant locations possessed almost identical EaCoMT genes suggest that lateral transfer of EaCoMT among the Mycobacterium strains has occurred. Pulsed-field gel electrophoresis revealed large linear plasmids (110 to 330 kb) in all of the VC-degrading strains. In Southern blotting experiments, the strain JS60 EaCoMT gene hybridized to many of the plasmids. The CoM-mediated pathway of epoxide metabolism appears to be universal in alkene-assimilating mycobacteria, possibly because of plasmid-mediated lateral gene transfer.

Biodegradation, Environmental↗

PubMed1992

High-performance liquid chromatography of corynomycolic acids as a tool in identification of Corynebacterium species and related organisms.

A high-performance liquid chromatography (HPLC) study of 307 strains of Corynebacterium species and related taxa revealed that strains classified as "Corynebacterium aquaticum"; "Corynebacterium asperum"; and Centers for Disease Control (CDC) groups 1, 2, A-3, A-4, A-5, B-1, B-3, E, F-2, and I-2 as well as some unidentified coryneforms do not contain any corynomycolic acids; therefore, they should not be included in the genus Corynebacterium. Such an HPLC method of identification permitted the correct assignment to the genus Rhodococcus of two unpigmented strains of coryneform bacteria whose mycolic acid profiles were comparable to those of Rhodococcus equi. Bacteria belonging to CDC groups ANF-1, ANF-3, F-1, G-1, G-2, and I-1, as well as some other Corynebacterium sp. strains, yielded corynomycolic acid HPLC patterns related to those of Corynebacterium species. Either similarities or differences were observed in the corynomycolic acid profiles of Corynebacterium species tested after culture on sheep blood agar and/or sheep blood agar supplemented with Tween 80, which demonstrated that identification at the species or group level is possible. However, Corynebacterium striatum and CDC group I-1 bacteria as well as CDC group G-1 and group G-2 bacteria had indistinguishable HPLC patterns. Conversely, some variations were observed within some species as Corynebacterium xerosis, C. striatum, and Corynebacterium minutissimum. The evaluation procedure of this HPLC method by mass spectrometry analysis of isolated eluted peaks revealed that analytical reverse-phase HPLC alone does not provide any structural information, since isomers with identical polarities coeluted as a single peak. Nevertheless, HPLC is a rapid and reliable method for identification of corynomycolic acid-containing bacteria in the clinical microbiological laboratory.

Chromatography, High Pressure Liquid↗

PubMed2005

Characterization and performance of a toluene-degrading biofilm developed on pumice stones.

BACKGROUND: Hydrocarbon-degrading biofilms in the treatment of contaminated groundwaters have received increasing attention due to the role played in the so-called "biobarriers". These are bioremediation systems in which a microbial consortium adherent to a solid support is placed across the flow of a contaminated plume, thus promoting biodegradation of the pollutant. RESULTS: A microbial consortium adherent to pumice granules (biofilm) developed from a toluene-enriched microflora in a mini-scale system, following continuous supply of a mineral medium containing toluene, over a 12-month period. Observation by scanning electron microscopy, together with quantification of the biomass attached to pumice, evidenced the presence of abundant exopolymeric material surrounding the cells in the biofilm. Toluene removal monitored during 12-month operation, reached 99%. Identification of the species, based on comparative 16S ribosomal DNA (rDNA) sequence analysis, revealed that Rhodococcus erythropolis and Pseudomonas marginalis were the predominant bacterial species in the microbial consortium. CONCLUSION: A structurally complex toluene-degrading biofilm, mainly formed by Rhodococcus erythropolis and Pseudomonas marginalis, developed on pumice granules, in a mini-scale apparatus continuously fed with toluene.

Journal Article↗

PubMed2002

Serum amyloid A (SAA) as an aid in the management of infectious disease in the foal: comparison with total leucocyte count, neutrophil count and fibrinogen.

Differentiation between infectious and noninfectious disease and rapid initiation of accurate treatment are essential in managing diseases in the neonatal and young foal. Identification of useful inflammatory markers for these purposes is, therefore, of great importance. The aim of this study was to compare the responses of the acute phase protein serum amyloid A (SAA) with the responses of fibrinogen and total leucocyte and neutrophil counts in infectious diseases encountered in the young foal, and to assess whether SAA measurements give additional information useful in the management of these diseases. In a prospective study, foals (n = 25) showing clinical signs indicative of infectious disease were blood sampled on admission and then daily or every second day during hospitalisation. The main presenting signs were neonatal weakness (n = 9), pneumonia (n = 6) and diarrhoea (n = 10). SAA and fibrinogen concentrations on admission were higher in foals with bacterial infections (n = 8) than in foals with nonbacterial or uncertain diagnoses (n = 17). On admission, weak foals with negative blood cultures (n = 3) had normal SAA and fibrinogen concentrations and varying total leucocyte and neutrophil counts. Foals with positive blood cultures (n = 2) had markedly increased SAA, decreased or increased fibrinogen concentration and leuco- and neutropenia. Those with ambiguous blood cultures (n = 3) had moderate to markedly increased SAA concentrations and normal fibrinogen concentration, leucocyte and neutrophil counts on admission. All foals with negative or ambiguous blood cultures recovered and had normal or decreasing SAA concentration on discharge. Both foals with a positive blood culture were subjected to euthanasia. One foal born with equine herpesvirus-1 infection had moderately increased SAA and normal fibrinogen concentration and leuco- and neutropenia. Foals with Rhodococcus equi pneumonia had increased concentrations of all parameters on admission. On discharge, recovered foals had normal SAA concentrations, whereas fibrinogen and total white blood cell count and neutrophil counts were still increased. There were no consistent inflammatory changes in the parameters measured in diarrhoeic foals and there was no statistical difference between rotavirus-positive (n = 4) and -negative (n = 6) foals in this respect. The results of this investigation suggest that SAA might be an aid in the differential diagnostic procedure of neonatally weak foals and in foals with diarrhoea as the main presenting clinical sign and that SAA measurements could add information in the monitoring of treatment in Rhodococcus equi pneumonia by responding more rapidly than the markers used to date.

Animals↗

PubMedDate not supplied

[Clusterization of halophilic and halotolerant eubacteria using whole-cell protein electrophoresis data].

Total cell proteins of the nineteen halophilic and halotolerant eubacteria isolated from marine sediments and highly mineralized formation waters of oil fields were investigated by SDS gel electrophoresis. The microorganisms studied, phenotypically identified as belonging to the genera Dietzia, Rhodococcus, Staphylococcus, Cytophaga, Brevibacterium, and Archangium, were found to form clearly distinguishable clusters (20-30% similarity at the generic level) on the dendrogram derived from electrophoretic protein patterns. Protein similarity data confirmed the heterogeneity of Rhodococcus maris and its relatedness to the genus Dietza.

Bacterial Proteins↗

PubMed2002

Fighting foam with phages?

Seventeen (17) phages infective for the mycolata were isolated from six samples of activated sludge using 21 prospective hosts from the genera Dietzia, Gordonia, Nocardia, Rhodococcus, Tsukamurella and Mycobacterium. Their morphology indicated that they were all members of the viral family Siphoviridae, but they varied in the size of the icosahedral head and length of non-contractile tail, suggesting they were different. This was confirmed by host-range studies with 47 strains of mycolata, which showed that each phage had a unique host-range, and this was polyvalent in the majority (15/17) of cases, with 12 phages infective for hosts representing two or three of the genera Gordonia, Nocardia and Rhodococcus. The potential for use of these phages in the control of foaming and other applications is discussed.

Actinobacteria↗

PubMed2002

Dispelling the "Nocardia amarae" myth: a phylogenetic and phenotypic study of mycolic acid-containing actinomycetes isolated from activated sludge foam.

Right-angle branched filaments and rods micromanipulated from activated sludge foam and mixed liquor were identified as putatively novel members of the genera Gordonia, Mycobacterium and Rhodococcus using a combination of chemical, molecular and morphological data. Pyrolysis mass spectrometric analyses of gordoniae isolated in both the present and a previous study revealed pyro-groups, distinct from validly described Gordonia species, which could be equated with those based on morphological properties and 16S rDNA data. Putative gordoniae assigned to one of these groups were found to be closely related to strains currently identified as "Rhodococcus australis". These strains were also found to have properties consistent with their classification in the genus Gordonia. The results of this study highlight the limitations of the microscopic approach to filament identification and cast further doubt on the view that foaming can be attributed to members of one or a few Nocardia species.

DNA, Bacterial↗

PubMed2004

Bacterial diversity of a soil sample from Schirmacher Oasis, Antarctica.

The bacterial diversity of a soil sample collected in the vicinity of Lake Zub, Schirmacher Oasis, Antarctica, was determined both by establishing pure colonies of culturable bacteria and by cloning the total 16S rDNA of the soil and establishing the phylogeny of the clones. Analysis of the 16S rRNA gene clones indicated that the bacteria belonged to the classes alpha-proteobacteria, beta-proteobacteria, gamma-proteobacteria, Gemmatimonas, Bacteriodetes, Actinobacteria, Chloroflexi and Chlamydiae. In addition, seven clones were categorized as unidentified and unculturable in the classes of beta-Proteobacteria, Actinobacteria, Chloroflexi and Chlamydiae. Further, the culturable bacteria from the same site were identified as belonging to the genera Pseudomonas, Sphingobacterium, Arthrobacter, Micrococcus, Brevondimonas, Rhodococcus and Microbacterium. These results identify for the first time the presence of bacteria belonging to the genera Brevundimonas, Microbacterium, Rhodococcus, Serratia, Enterobacter, Rhodopseudomonas, Sphingomonas, Acidovorax, Burkholderia, Nevskia, Gemmatimonas, Xanthomonas and Flexibacter in Antarctica. Further, comparison of the Antarctic soil bacterial diversity with other cold habitats of Antarctica like from sediments, ice and cyanobacterial mat samples indicated that the bacterial diversity in soil was similar to the diversity observed in the continental shelf sediment sample. The Antarctic soil clones also resembled the bacterial diversity of soils from other geographical regions, but were unique in that none of the clones from the soil belonged to the uncultured Y, O, G, A and B groups common to all soil samples.

Antarctic Regions↗

PubMed1998

Key enzymes for the degradation of benzoate, m- and p-hydroxybenzoate by some members of the order Actinomycetales.

A preliminary screening of numerous species of the order Actinomycetales, especially of the genera Mycobacterium, Nocardia, Rhodococcus, Pseudonocardia, and Streptomyces, showed that many of them are able to metabolize benzoate (B) and p-hydroxybenzoate (pHB) as indicated by growth and change of color of the pH-indicator of an agar medium. Subsequent experiments with liquid cultures which allowed the analysis of substrate utilization by thin layer chromatography confirmed these results. The study of the degradative pathway proved that B was metabolized via catechol (C), pHB via protocatechuate (P) and m-hydroxybenzoate (mHB) via gentisate (G). The aromatic ring of C and P was subjected to an ortho-cleavage; only one strain of Noc. asteroides degraded C via a meta-cleavage, but P via an ortho-cleavage. Cell free extracts of four selected organisms exhibited activity of C-1,2-dioxygenase (C-1,2-O) and/or P-3,4-dioxygenase (P-3,4-O), depending on the growth substrate used for precultivation. In Streptomyces C-1,2-O was only found in cells grown on B, and P-3,4-O only in cells grown on pHB. On the contrary, in Rhodococcus rhodochrous B-cells oxidized C as well as P, while P-cells possessed only P-3,4-O-activity.

Actinomycetales↗

PubMed2000

Light inhibits rifampicin inactivation and reduces rifampicin resistance due to a cloned mycobacterial ADP-ribosylation gene.

Rifampicin is a principal drug used to combat infections by mycobacteria and related organisms. Most strains of Mycobacterium are able to inactivate this antibiotic by ribosylation via an ADP-ribosylated intermediate. We found that this inactivation was inhibited by light at levels similar to those prevailing in laboratory environments. Rifampicin resistance arising from the cloned ADP-ribosyl transferase was also greatly diminished at these light levels. The cloned Rhodococcus equi monooxygenase which inactivates this antibiotic by a different mechanism was, in contrast, not inhibited by light.

Antibiotics, Antitubercular↗

PubMed1998

Multivesiculated macrophages: their implication in fine-needle aspiration cytology of lung mass lesions.

Alveolar macrophages are almost invariably present in percutaneous fine-needle aspiration cytology of the lung. They may predominate, appear foamy and finely vesiculated, or may reflect the cellular composition of the lung mass lesion. In a review of 172 cases of "negative for malignant cells" from the percutaneous lung fine-needle aspiration cytology file in an 8-year period at Hines VA Hospital, the vacuolated macrophages were evaluated qualitatively and quantitatively. Among the 53 cases (34%) showing vacuolated macrophages, only 5-25% of the cells were multivesiculated, the cytoplasmic vacuoles were few, focal, and occasionally global, and the majority of the vacuolated macrophages contained anthracotic or hemosiderin pigments. One case exhibited striking multivesiculation in at least 95% of macrophages and also in bronchial and alveolar cells, fibroblasts, and endothelial and inflammatory cells, a finding consistent with amiodarone toxicity (index case 1). The diagnosis was confirmed on subsequent transbronchial lung biopsy. In another patient with clinical HIV infection, the multivesiculation was also seen in 95% of the macrophages with associated acute inflammatory exudate, coccobacilli, and a positive culture for Rhodococcus equi (index case 2). In most cases, the vacuolated macrophages are reactive and inflammatory. Occasionally, as in our index cases they may actually indicate a specific diagnosis.

Actinomycetales Infections↗

PubMed1988

Microbial hydrolysis of organic nitriles and amides.

Nitrile-hydrating enzymes produced by bacteria and fungi catalyse the conversion of a large number of chemically diverse nitriles, including many economically important compounds used industrially for chemical synthesis of amides and acids. This paper presents data on two new, highly different nitrile-hydrolysing enzymes which were isolated in connection with our studies on enzymic nitrile transformations. Particular attention was paid to the enzymes' substrate specificities and sensitivity to substrate/product inhibition. One of our microbial isolates was a Rhodococcus sp. (strain CH5). This strain produces a constitutive hydratase that has a broad substrate spectrum, including aliphatic and aromatic nitriles, mononitriles and dinitriles, hydroxynitriles and amino-nitriles. It also produces a constitutive amidase of equally low substrate specificity. The hydratase/amidase system catalysed the hydrolysis of D,L-aminonitriles into racemic mixtures of amino acids. Strain CH5 is able to produce high concentrations of malonic acid monoamide from malononitrile and malonamide. The other isolate, Alcaligenes sp. (strain I4), can convert high concentrations of cyanoacetate into malonic acid, presumably by means of an aliphatic nitrilase that is specific for cyanoacetate. Enzyme kinetic experiments have shown that this enzyme is very resistant to both substrate and product inhibition.

Alcaligenes↗

PubMed2026

Identification of a Nonribosomal Peptide Analog With Activity Against Multiple Gram-Positive Bacteria via a Synthetic Bioinformatic Natural Product Discovery Approach.

Nonribosomal peptide (NRP) antibiotics exhibit potent biological activities and are broadly used in clinical therapy. Because most microorganisms are difficult to culture and many antibiotic biosynthetic genes are silent, traditional activity tracking approaches face major limitations in the discovery of novel NRPs. Here, based on a synthetic bioinformatic natural product (syn-BNP) discovery approach that integrates bioinformatics and chemical synthesis, a novel nonribosomal peptide synthetase (NRPS) gene cluster from the genome of Rhodococcus erythropolis D-1 was mined. A putative NRP scaffold synthesized by the NRPS encoded by this cluster was predicted. Through chemical synthesis and four rounds of structure-activity relationship (SAR) studies, 37 NRP analogs were ultimately generated. Among these analogs, ZURJC28 shows activity against multiple Gram-positive bacteria, including two drug-resistant strains. Mechanistic studies and metabolomics analyses revealed that ZURJC28 exerts membrane-disruptive activity associated with interaction with phosphatidylglycerol (PG)-enriched Gram-positive membranes, leading to membrane damage and widespread metabolic dysregulation. ZURJC28 also shows low cytotoxicity and low hemolytic activity, suggesting its preliminary in vitro safety profile.

Gram-Positive Bacteria↗

PubMed2001

Haloalkane hydrolysis with an immobilized haloalkane dehalogenase.

Haloalkane dehalogenase from Rhodococcus rhodochrous was covalently immobilized onto a polyethyleneimine impregnated gamma-alumina support. The dehalogenating enzyme was found to retain greater than 40% of its original activity after immobilization, displaying an optimal loading (max. activity/supported protein) of 70 to 75 mg/g with an apparent maximum (max. protein/support) of 156 mg/g. The substrate, 1,2,3-trichloropropane, was found to favorably partition (adsorb) onto the inorganic alumina carrier (10 to 20 mg/g), thereby increasing the local reactant concentration with respect to the catalyst's environment, whereas the product, 2,3-dichloropropan-1-ol, demonstrated no affinity. Additionally, the inorganic alumina support exhibited no adverse effects because of solvent/component incompatibilities or deterioration due to pH variance (pH 7.0 to 10.5). As a result of the large surface area to volume ratio of the support matrix and the accessibility of the bound protein, the immobilized biocatalyst was not subject to internal mass transfer limitations. External diffusional restrictions could be eliminated with simple agitation (mixing speed: 50 rpm; flux: 4.22 cm/min). The pH-dependence of the immobilized dehalogenase was essentially the same as that for the native enzyme. Finally, both the thermostability and resistance toward inactivation by organic solvent were improved by more than an order of magnitude after immobilization.

Aluminum Oxide↗

PubMed2003

Measurement of strain-dependent toxicity in the indene bioconversion using multiparameter flow cytometry.

The bionconversion of indene to cis-(1S,2R)-indandiol, a potential key intermediate in the synthesis of Merck's HIV protease inhibitor, CRIXIVAN trade mark, can be achieved using Rhodococcus, Pseudomonas putida, and Escherichia coli strains. This study reports on the application of multiparameter flow cytometry for the measurement of cytoplasmic membrane integrity and membrane depolarization as indicators of toxic effects of the substrate, product, and by-products using each of these strains. Measurements of oxygen uptake rate (OUR) and optical density (OD) as indicators of metabolic activity and biomass growth, respectively, were also made. Measurements of the cytoplasmic membrane potential, cell viability, and respiratory activity provided a sensitive set of parameters to assess toxicity in the indene bioconversion and provided the basis for process improvements and strain selection. The toxic concentrations of the substrate, product, and by-products for each strain have been determined. The results show that it is possible to accumulate cis-(1S,2R)-indandiol and cis-1-amino-2-indanol up to 20 g/L without significant negative effects on cell physiology using any of the strains tested. The Gram-negative P. putida (421-5 and GM 730) and E. coli strains were more resistant to indene and the isolated chemicals of the biotransformation than the Gram-positive Rhodoccoccus I24 strain, possibly due to the presence of the outer membrane and efflux pump mechanisms. P. putida GM 730 and the E. coli TDO 123 strains responded similarly to toxic effects, and the E. coli TDO 123 strain was more resistant than the P. putida 421-5 strain. In addition to the recommendations for strain selection, the identified targets for bioprocess improvement include a combination of genetic as well as process engineering approaches.

Bioreactors↗