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PubMed1998

Molybdopterin radical in bacterial aldehyde dehydrogenases.

The EPR spectra of three different molybdoprotein aldehyde dehydrogenases, one purified from Comamonas testosteroni and two purified from Amycolatopsis methanolica, showed in their oxidized state a novel type of signal. These three enzymes contain two different [2Fe-2S] centers, one flavin and one molybdopterin cytosine dinucleotide, as cofactors all of which are expected to be EPR silent in the oxidized state. The new EPR signal is isotropic with g = 2.004 both at X-band and Q-band frequencies, consists of six partially resolved lines, and shows Curie temperature behavior suggesting that the signal is due to an organic radical with S = 1/2. The EPR spectra of Comamonas testosteroni aldehyde dehydrogenase obtained after cultivation in media containing 15NH4Cl and/or after substitution of H2O for D2O show the presence of both nitrogen and proton hyperfine interactions. Simulations of the spectra of the four possible isotope combinations yield a single set of hyperfine coupling constants. The electron spin shows hyperfine interaction with a single I = 1 (0.9 mT) ascribed to a N nucleus, with a single I = 1/2 (1.5 mT) ascribed to one nonexchangeable H nucleus, and with two, exchangeable, identical I = 1/2 spins (0.6 mT) ascribed to two identical exchangeable protons. Taken together, the observations and simulations rule out amino acid residues or flavin as the origin of the radical. The values of the various hyperfine coupling constants are consistent with the properties expected for a molybdenum(VI)-trihydropterin radical in which the N5 atom is engaged in two hydrogen-bonding interactions with the protein. The majority of the electron (spin) density of the radical is located at and around the N5 atom and at the proton bound to the C6 atom of the pterin ring. The EPR spectrum of the molybdopterin radical broadens above 65 K and is no longer detectable above 168 K, indicating that it is not magnetically isolated. The line broadening is ascribed to cross-relaxation with a nearby, rapidly relaxing, oxidized [2Fe-2S] center involving its magnetic S = 1 excited state in this process. The amount of radical was apparently not changed by addition of aldehydes or oxidants, but it disappeared upon reduction by sodium dithionite. Therefore, whether the molybdenum(VI) trihydropterin radical as detected here is a functional intermediate in catalysis remains to be investigated further.

Actinobacteria↗

PubMed2001

Relationships within the Proteobacteria of plant pathogenic Acidovorax species and subspecies, Burkholderia species, and Herbaspirillum rubrisubalbicans by sequence analysis of 16S rDNA, numerical analysis and determinative tests.

Sequence data for 16S rDNA of the type strains of Acidovorax avenae subsp. avenae, A. avenae subsp. cattleyae, A. avenae subsp. citrulli, A. konjaci and Herbaspirillum rubrisubalbicans were compared with GenBank library accessions of Burkholderia spp., Comamonas sp., Ralstonia solanacearum and Variovorax sp. Maximum Parsimony analysis produced two clusters: 1. Acidovorax spp., Comamonas sp., and Variovorax sp. (all in the Comamonadaceae), and 2. Burkholderia spp., Ralstonia solanacearum, and Herbaspirillum rubrisubalbicans. Maximum Likelihood analysis produced only one cluster (of the Comamonadaceae). Using nutritional and laboratory tests, all Acidovorax spp., Burkholderia spp., and Herbaspirillum rubrisubalbicans were discriminated in distinct clusters at the species level, and could be identified by selected determinative tests. There were no phenotypic tests constituted as a circumscription of the genera and which permitted the allocation of strains to genera. Strain identification as species allowed allocation to genera only by inference. The nomenclatural implications of these data are discussed.

Base Sequence↗

PubMed1992

Identification of xenobiotic-degrading isolates from the beta subclass of the Proteobacteria by a polyphasic approach including 16S rRNA partial sequencing.

Nineteen gram-negative, aerobic, biodegradative isolates were identified by using a polyphasic taxonomic approach. The presence of the specific polyamine 2-hydroxyputrescine and the presence of a ubiquinone with eight isoprenoid units in the side chain (ubiquinone Q-8) allowed allocation of these organisms to the beta subclass of the Proteobacteria. On the basis of the results of additional characterization experiments (i.e., API 20NE tests, determinations of soluble protein patterns, and DNA-DNA hybridization experiments), we classified six isolates as either Comamonas testosteroni, Comamonas acidovorans, or Alcaligenes xylosoxidans subsp. denitrificans. By using the same criteria we allocated two additional isolates to the genus Alcaligenes. A comparison of a 16S rRNA fragment (positions 1220 to 1377; Escherichia coli nomenclature) indicated that the remaining isolates should be allocated as follows: one is a member of C. testosteroni and one is a member of Acidovorax facilis, as confirmed by the results of additional DNA-DNA hybridizations; two others probably belong to the family Alcaligenaceae; six are related to "Alcaligenes eutrophus"; and one, strain NRRL 12228, occupies an isolated position.

Bacterial Proteins↗

PubMed2001

Xenophilus azovorans gen. nov., sp. nov., a soil bacterium that is able to degrade azo dyes of the Orange II type.

The taxonomy of strain KF46FT, which was isolated previously after an aerobic enrichment with the azo compound 1-(4'-carboxyphenylazo)-2-naphthol as the sole source of energy and carbon, was investigated by a polyphasic approach. The organism contained a quinone system with ubiquinone Q-8 and 2-hydroxyputrescine and putrescine as the major polyamines, suggesting that strain KF46FT belonged to the beta-subclass of the Proteobacteria. The polar lipid profile consisted mainly of phosphatidylethanolamine and minor amounts of phosphatidylglycerol and diphosphatidylglycerol. Sequencing of the 16S rRNA gene supported its placement in the family Comamonadaceae, but the sequence similarities to the most closely related species of the genera Hydrogenophaga, Acidovorax, Comamonas and Xylophilus were only in the range 95.0 to 96.1%. Different methods for the construction of phylogenetic trees showed the separate position of strain KF46FT 'between' the genera Hydrogenophaga, Variovorax, Comamonas and Xylophilus. Analysis of the fatty acids revealed an unusual profile, with the presence of 8:0 3-OH, 10:0 3-OH, 16:1 2-OH, 16:0 2-OH and 18:1 2-OH in addition to 17:0 cyclo, which is unique among the previously described genera of the family Comamonadaceae. Thus, a new taxon is proposed for strain KF46FT, with the name Xenophilus azovorans gen. nov., sp. nov.

Azo Compounds↗

PubMed1992

Pseudomonas infections in patients with AIDS and AIDS-related complex.

We identified and reviewed retrospectively all the cases of infection by Pseudomonas and related genera in patients with AIDS and AIDS-related complex (ARC) who were hospitalized at our Institution over a 36-month period. We recorded 48 episodes of infection in 34 of 355 patients with AIDS, and in two of 73 patients with ARC: 25 pneumonias (9 community-acquired and 16 of nosocomial origin). 20 urinary tract infections, two soft tissue infections and one sepsis. In 14 of 16 patients with nosocomial pneumonia but in only one of nine patients with community-acquired pneumonia did we find coexisting opportunistic lung diseases. The following micro-organisms were isolated: P. aeruginosa in 41 cases, P. fluorescens in three cases, Xanthomonas maltophilia (P. maltophilia) in two cases, P. putida in one case. Comamonas testosteronis (P. testosteronis) and Comamonas acidovorans (P. acidovorans) in one case. Amikacin and ceftazidime, alone or in combination, appear to be the optimal choice of therapy for severe Pseudomonas infections in HIV-infected patients, although in our study six of 47 isolates were resistant in vitro to amikacin, and nine of 31 isolates were resistant to ceftazidime.

AIDS-Related Complex↗

PubMed1996

Taxonomic identification of Streptomyces exfoliatus K10 and characterization of its poly(3-hydroxybutyrate) depolymerase gene.

The poly(3-hydroxyalkanoate) (PHA) degrading isolate K10 was identified as Streptomyces exfoliatus. This bacterium is distinguished from other PHA-degrading strains by its ability to utilize both poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxyoctanoate) (PHO). A PHA depolymerase structural gene of S. exfoliatus (phaZ(Sex) was cloned, expressed and partially purified from recombinant Escherichia coli. The depolymerase was specific for PHB and did not hydrolyze PHO. This indicated the presence of at least one additional gene in S. exfoliatus which encodes a PHO depolymerase. 3-Hydroxybutyrate was identified as the only product of PHB hydrolysis. Comparison of the DNA-deduced amino acid sequence revealed high homology to the PHB depolymerase of Comamonas sp. and low to medium homologies to other PHA depolymerases. The PHB depolymerases of S. exfoliatus and Comamonas sp. represent a subgroup within the family of PHA(SCL) depolymerases. To our knowledge, the S. exfoliatus PHB depolymerase is the first briefly characterized PHA depolymerase of a Gram-positive.

Amino Acid Sequence↗

PubMed1993

Use of a simplified cell blot technique and 16S rRNA-directed probes for identification of common environmental isolates.

A simple technique in which rRNA-targeted oligodeoxynucleotide probes are used to identify bacteria immobilized on membranes is described. By using colony lifts, bacteria are directly transferred from plates to untreated nitrocellulose membranes. Alternatively, cells resuspended from colonies can be applied to membranes by using a vacuum manifold under high-salt conditions. Blotted cells are baked and hybridized under stringent conditions by using standard protocols. Treatment of blotted cells with sodium dodecyl sulfate, urea, formaldehyde, or protease had no apparent effect on hybridization signals. Hybridization to rRNA from cells that had been stored refrigerated for 6 days was readily detected; however, fivefold more cells (approximately 10(7) cells) were required to obtain hybridization signals comparable to those generated by cells not subjected to storage. The sequences of oligonucleotide probes specific for Pseudomonas cepacia, Comamonas testosteroni, and Acinetobacter calcoaceticus and a group probe identifying Pseudomonas aeruginosa, Pseudomonas mendocina, Pseudomonas fluorescens, Comamonas acidovorans, and "Flavobacterium" lutescens are presented. In conjunction with the colony lift hybridization procedure, bacteria isolated from river water were identified by using these probes.

Bacteria↗

PubMed1997

Development and application of monoclonal antibodies for in situ detection of indigenous bacterial strains in aquatic ecosystems.

Strain-specific monoclonal antibodies (MAbs) were developed for three different bacterial isolates obtained from a freshwater environment (Lake Plusssee) in the spring of 1990. The three isolates, which were identified by molecular methods, were as follows: Cytophaga johnsonae PX62, Comamonas acidovorans PX54, and Aeromonas hydrophila PU7718. These strains represented three species that were detected in high abundance during a set of mesocosm experiments in Lake Plusssee by the direct analysis of low-molecular-weight RNAs from bacterioplankton. We developed one MAb each for the bacterial isolates PX54 and PU7718 that did not show any cross-reactivity with other bacterial strains by immunofluorescence microscopy. Each MAb recognized the general lipopolysaccharide fraction of the homologous strain. These MAbs were tested successfully for their ability to be used for the in situ detection and counting of bacteria in lake water by immunofluorescence microscopy. During the spring of 1993, A. hydrophila PU7718 showed a depth distribution in Lake Plusssee with a pronounced maximum abundance at 6 m, whereas Comamonas acidovorans PX54 showed a depth distribution with a maximum abundance at the surface. The application of these MAbs to the freshwater samples enabled us to determine the cell morphologies and microhabitats of these strains within their natural environment. The presence of as many as 8,000 cells of these strains per ml in their original habitats 3 years after their initial isolation demonstrated the persistence of individual strains of heterotrophic bacteria over long time spans in pelagic habitats.

Aeromonas↗

PubMed2001

Genetic diversity among 3-chloroaniline- and aniline-degrading strains of the Comamonadaceae.

We examined the diversity of the plasmids and of the gene tdnQ, involved in the oxidative deamination of aniline, in five bacterial strains that are able to metabolize both aniline and 3-chloroaniline (3-CA). Three strains have been described and identified previously, i.e., Comamonas testosteroni I2 and Delftia acidovorans CA28 and BN3.1. Strains LME1 and B8c were isolated in this study from linuron-treated soil and from a wastewater treatment plant, respectively, and were both identified as D. acidovorans. Both Delftia and Comamonas belong to the family Comamonadaceae. All five strains possess a large plasmid of ca. 100 kb, but the plasmids from only four strains could be transferred to a recipient strain by selection on aniline or 3-CA as a sole source of carbon and/or nitrogen. Plasmid transfer experiments and Southern hybridization revealed that the plasmid of strain I2 was responsible for total aniline but not 3-CA degradation, while the plasmids of strains LME1 and B8c were responsible only for the oxidative deamination of aniline. Several transconjugant clones that had received the plasmid from strain CA28 showed different degradative capacities: all transconjugants could use aniline as a nitrogen source, while only some of the transconjugants could deaminate 3-CA. For all four plasmids, the IS1071 insertion sequence of Tn5271 was found to be located on a 1.4-kb restriction fragment, which also hybridized with the tdnQ probe. This result suggests the involvement of this insertion sequence element in the dissemination of aniline degradation genes in the environment. By use of specific primers for the tdnQ gene from Pseudomonas putida UCC22, the diversity of the PCR-amplified fragments in the five strains was examined by denaturing gradient gel electrophoresis (DGGE). With DGGE, three different clusters of the tdnQ fragment could be distinguished. Sequencing data showed that the tdnQ sequences of I2, LME1, B8c, and CA28 were very closely related, while the tdnQ sequences of BN3.1 and P. putida UCC22 were only about 83% identical to the other sequences. Northern hybridization revealed that the tdnQ gene is transcribed only in the presence of aniline and not when only 3-CA is present.

Aniline Compounds↗

PubMed1992

Chemical and cultural characterization of CDC group WO-1, a weakly oxidative gram-negative group of organisms isolated from clinical sources.

Ninety-six strains of weakly oxidative gram-negative rods isolated primarily from clinical specimens form a distinct group that has been designated Centers for Disease Control (CDC) group WO-1 (WO stands for weak oxidizer). The phenotypic characteristics of CDC group WO-1 were most similar to those of Comamonas acidovorans, Pseudomonas mallei, and CDC pink coccoid group III. The WO-1 group can be differentiated from C. acidovorans by the oxidation of glucose (often weak and sometimes delayed), motility by means of one or two polar flagella, and, when positive, the complete reduction of nitrate and nitrite. Motility and usually the failure to produce arginine dihydrolase distinguish this group from P. mallei. The WO-1 strains differ from the pink coccoid group III by the absence of pink growth pigment, the lack of predominantly coccoid cellular morphology, and usually the inability to produce acid from xylose. The cellular fatty acid compositions of 29 group WO-1 strains were characterized by large amounts of C16:0 and C16:1w7c; smaller amounts of C18:1w7c, C14:0, C12:0, and 3-OH-C10:0; and trace to small amounts of C15:1w6 and C17:0 acids. The fatty acid profile of WO-1, compared with the profiles of other bacteria we have tested previously, was most similar to the profiles of two phenotypically different organisms, Comamonas terrigena (a nonoxidative, multipolar gram-negative rod) and Chromobacterium violaceum (a fermentative gram-negative rod). Ubiquinone-8 was the major quinone in the five WO-1 strains examined. Eighty-five percent of the WO-1 strains were isolated from human specimens. Thirty-three percent were from blood, and 10% were from cerebrospinal fluid.

Cell Movement↗

PubMed2003

Novel growth media for rearing larval horn flies, Haematobia irritans (Diptera: Muscidae).

Experiments were conducted to develop an agar-based medium for rearing immature horn flies, Hematobia irritans (L.). Larval survival was determined on sterilized manure inoculated with pure and mixed cultures of Acinetobacter sp., Bacillus pumilus Meyer & Gottheil, Comamonas acidovorans den Dooren de Jong, Pseudomonas mendocina Palleroni, Flavobacterium sp. and Empedobacter breve (Holmes & Owen). Rearing larvae on mixed cultures enhanced pupal weight but not survival. Horn fly larvae failed to survive when reared on standard bacteriological media inoculated with pure and mixed cultures of Acinetobacter sp., P. mendocina, and C. acidovorans. Larvae completed development on a minimal medium supplemented with alfalfa, egg proteins, and vitamins. Medium with low alfalfa content (30 g alfalfa/500 ml minimal medium) had enhanced survival when supplemented with egg yolk protein and vitamins. Medium with high alfalfa content (130 g alfalfa/500 ml minimal medium) had enhanced survival when supplemented with whole egg protein and vitamins. Survival was also favored when media were inoculated with pure cultures of Acinetobacter or Acinetobacter mixed with either Pseudomonas or Comamonas. Individual plates could support larvae developing from up to 40 eggs, and survival was least variable when plates were inoculated with greater numbers of eggs. This rearing system shows promise as a means for conducting standardized bioassays on a meridic diet.

Animals↗

PubMed1977

[Seasonal dynamics of the abundance of vibrios and related microorganisms in the Don River].

The density of bacteria of the Vibrio, Aeromonas and Comamonas genera the Don river was subject to seasonal variations. The maximal vibrio concentration was recorded at the water temperature of 22 degrees C, and of Aeromonas and Comamonas--at lower temperature. Unlike Aeromonas, vibrios displayed a reverse dependence of the density on the extent of water contamination.

Aeromonas↗

PubMed2004

[Investigation of the bacteria in the seawater of Xisha in the South China Sea and their antibiotic sensitivity profile].

OBJECTIVE: To investigate the distribution and antibiotic sensitivity of the bacteria in the seawater of Xisha in the South China Sea. METHODS: The samples of the seawater in Xisha were collected for bacterial counting, identification and antibiotic sensitivity tests. RESULT: Of the 84 bacterial strains isolated from the 80 seawater samples, 38 (45.24%) belonged to Vibrio alginolyticus, 11 (13.10%) to Sphingomonas, 9 (10.72%) to Comamonas terrigena, 7 (8.33%) to Werepseudomonas, 6 (7.14%) to Moraxella, 5 (5.95%) to Cedeceadavisae, and 8 to other bacteria including 2 Aeromona, 2 Acinetobacter, 1 Pantoea agglomerans, 1 Kingella kingae, 1 Shewanella putrefaciens and 1 Suttonella indologenes. Tests of the antibiotic sensitivity showed that all the bacteria were high sensitive to 16 kinds of the antibiotics with the exception of Vibrio alginolyticus, Sphingomonas and comamonas terrigena that were less sensitive to aztreonam or piperacillin and Sphingomonas to cefotaxime or cefepime. CONCLUSION: The investigation will be of great significance for early-stage prevention and cure of bacterial infection acquired from the seawater.

Anti-Bacterial Agents↗

PubMed2003

Evaluation of effective diffusion coefficient and intrinsic kinetic parameters on azo dye biodegradation using PVA-immobilized cell beads.

An immobilized mixed culture (Aeromonas hydrophila, Comamonas testosteroni, and Acinetobacter baumannii) was prepared by entrapment into phosphorylated polyvinyl alcohol (PVA) gel beads. The unsteady-state diffusion mechanism in a gel bead was applied to estimate the effective diffusion coefficients (D(e)) and the partition coefficients (K(p)) of azo dye. In addition, a simple method was developed to determine the intrinsic kinetic parameters of immobilized cells from observed reaction rates and the intrinsic kinetic parameters were then verified by fitting the experimental data into the reaction-diffusion model in a batch reactor running at a well-stirred state. The calculated effectiveness factor (eta(cal)) approached unity at Thiele modulus (Phi) < 0.3 (i.e., d(p) < 0.475 mm). The experimental effectiveness factor (eta(exp)) was in the range of 0.71-0.45 for a corresponding sphere diameter (d(p)) of 1.91 +/- 0.16 to 4.43 +/- 0.07 mm at an initial dye concentration of 200 mg/L. The results show that intraparticle diffusion resistance has a significant effect on the azo dye biodegradation rate.

Acinetobacter baumannii↗

PubMed2000

Dihexyl sulfosuccinate biodegradation by mixed cultures.

The primary biodegradation of dihexyl sulfosuccinate has been demonstrated using two single cultures and three mixed bacterial cultures of Comamonas terrigena. Primary biodegradation was found in all variants. The highest biotransformation rate and efficiency was observed in one of the single strains. No synergistic effect on degradation was found in mixed cultures.

Biodegradation, Environmental↗

PubMed2000

Effect of starvation and chloramphenicol on acceleration of bacterial dihexyl sulfosuccinate biotransformation.

Starvation for carbon and energy sources accelerated the biotransformation of the anion-active surfactant dihexyl sulfosuccinate (DHS) by Comamonas terrigena cells. Chloramphenicol (Cm) added at different time intervals to non-starved cells inhibited the DHS transformation. The largest difference between cells treated and non-treated by Cm was observed for a 16-h-starvation period. Protein synthesis de novo during starvation enhanced the DHS biotransformation efficiency. A partial transformation of DHS in the presence of Cm indicated the constitutive character of enzymes involved in primary DHS biodegradation.

Bacterial Proteins↗

PubMed2006

Oxidative stress by biphenyl metabolites induces inhibition of bacterial cell separation.

Cell-cell separation of a polychlorinated biphenyl (PCB)-degrading bacterium Comamonas testosteroni TK102 was monitored by flow cytometry. When monohydroxy metabolites of biphenyl (BP) (2-hydroxybiphenyl and 3-hydroxybiphenyl) were added to the culture, cell-cell separation of strain TK102 was inhibited at stationary phase. This inhibition was reproduced on non-PCB degrading bacteria such as Pseudomonas putida PpY101 and Escherichia coli MV1184, but was not observed on Pseudomonas aeruginosa PAO1. An opportunistic pathogen, P. aeruginosa PAO1, produces exopolysaccharide, which is known to scavenge damaging chemicals such as reactive oxygen species (ROS). The higher level of ROS and lipid peroxidants were detected in the cells treated by monohydroxybiphenyls. Fat-soluble vitamin E, which is a lipid radical scavenger, maintained bacterial cell separation during monohydroxybiphenyls treatment. Our results demonstrated that intracellular oxidative stress played an important role in the inhibition of bacterial cell separation during BP metabolism. This study shows that metabolites of environmental pollutants, such as monohydroxylated BP, inhibit bacterial cell separation by oxidative stress.

Antioxidants↗

PubMed2001

Diversity in kinetics of trichloroethylene-degrading activities exhibited by phenol-degrading bacteria.

Whole-cell kinetics of phenol- and trichloroethylene (TCE)-degrading activities expressed by 13 phenol-degrading bacteria were analyzed. The Ks (apparent affinity constant in Haldane's equation) values for TCE were unexpectedly diverse, ranging from 11 microM to over 800 microM. The Vmax/Ks values for phenol were three orders of magnitude higher than the values for TCE in all bacteria analyzed, suggesting that these bacteria preferentially degrade phenol rather than TCE. A positive correlation between Ks for phenol and Ks for TCE was found, i.e., bacteria exhibiting high Ks values for phenol showed high Ks values for TCE, and vice versa. A comparison of the Ks values allowed grouping of these bacteria into three types, i.e., low-, moderate- and high-Ks types. Pseudo-first-order degradation-rate constants for TCE at 3.8 microM were found to be adequate to rapidly discriminate among the three types of bacteria. When bacteria were grown on phenol at the initial concentration of 2 mM, Comamonas testosteroni strain R5, a representative of low-Ks bacteria, completely degraded TCE at 3.8 microM, while strain P-8, a representative of high-Ks bacteria, did not. A mixed culture of these two bacteria poorly degraded TCE under the same conditions, where P-8 outgrew R5. These results suggest that low-Ks bacteria should be selectively grown for effective bioremediation of TCE-contaminated groundwater.

Betaproteobacteria↗