Xanthobacter dioxanivorans sp. nov., a 1,4-dioxane-degrading bacterium.

A Gram-stain-negative bacterium, designated as YN2T, that is capable of degrading 1,4-dioxane, was isolated from active sludge collected from a wastewater treatment plant in Harbin, PR China. Cells of strain YN2T were aerobic, motile, pleomorphic rods, mostly twisted, and contained the water-insoluble yellow zeaxanthin dirhamnoside. Strain YN2T grew at 10-40 °C (optimum, 30 °C), pH 5.0-8.0 (pH 7.0) and with 0-1 % (w/v) NaCl (0.1 %). It also could grow chemolithoautotrophically and fix N2 when no ammonium or nitrate was supplied. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YN2T belongs to the genus Xanthobacter and shares the highest pairwise identity with Xanthobacter autotrophicus 7cT (98.6 %) and Xanthobacter flavus 301T (98.4 %). The major respiratory quinone was ubiquinone-10. Chemotaxonomic analysis revealed that the strain possesses C16 : 0, C19 : 0 cyclo ω8c and C18 : 1 ω7c as the major fatty acids. The DNA G+C content was 67.95 mol%. Based on genome sequences, the DNA-DNA hybridization estimate values between strain YN2T and X. autotrophicus 7cT, X. flavus 301T and X. tagetidis TagT2CT (the only three species of Xanthobacter with currently available genomes) were 31.70, 31.30 and 28.50 %; average nucleotide identity values were 85.23, 84.84 and 83.59 %; average amino acid identity values were 81.24, 80.23 and 73.57 %. Based on its phylogenetic, phenotypic, and physiological characteristics, strain YN2T is considered to represent a novel species of the genus Xanthobacter, for which the name Xanthobacter dioxanivorans sp. nov. is proposed. The type strain is YN2T (=CGMCC 1.19031T=JCM 34666T).

Xanthobacter oligotrophicus sp.nov., isolated from paper mill sewage.

A novel, aerobic nitrogen-fixing methylotrophic bacterium, strain 29kT, was enriched and isolated from sludge generated during wastewater treatment at a paper mill in Baikal, Russian Federation. Cells were Gram-stain-variable. The cell wall was of the negative Gram-type. Cells were curved oval rod-shaped, 0.5-0.7×1.7-3.4 µm and formed yellow-coloured colonies. Cells tended to be pleomorphic if grown on media containing succinate or coccoid if grown in the presence of methyl alcohol as the sole carbon source. Cells were non-motile, non-spore-forming and contained retractile (polyphosphate) and lipid (poly-ß-hydroxybutyrate) bodies. The major respiratory quinone was ubiquinone Q-10 and the predominant cellular fatty acids were C18:1 ω7, C19:0 cyclo and C16:0. The genomic DNA G+C content was 67.95 mol%. Strain 29kT was able to grow at 4-37 °C (optimum, 30 °C), at pH 6.0-8.5 (optimum, pH 6.5-7.0) and at salinities of 0-0.5% (w/v) NaCl (optimum, 0% NaCl). Catalase and oxidase were positive. Strain 29kT could grow chemolithoautotrophically in mineral media under an atmosphere of H2, O2 and CO2 as well as chemoorganoheterotrophically on methanol, ethanol, n-propanol, n-butanol and various organic acids. The carbohydrate utilization spectrum is limited by glucose and raffinose. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the newly isolated strain was a member of the genus Xanthobacter with Xanthobacter autotrophicus 7cT (99.9% similarity) and Xanthobacter viscosus 7dT (99.4 % similarity) as closest relatives among species with validly published names. The average nucleotide identity and digital DNA-DNA hybridization values of 92.7 and 44.9%, respectively, of the 29kT to the genome of the most closely related species, X. autotrophicus 7cT, were below the species cutoffs. Based on genotypic, phenotypic and chemotaxonomic characteristics, it is proposed that the isolate represents a novel species, Xanthobacter oligotrophicus sp. nov. The type strain is 29kT (=KCTC 72777T=VKM B-3453T).

Biodiversity of aerobic methylobacteria associated with the phyllosphere of the southern Moscow Oblast.

During the summer period (15­25°C), 34 strains of methylotrophic bacteria associated with different species of herbs, shrub, and trees in Pushchino (Moscow oblast, Russia) were isolated on the medium with methanol. Predominance of pink-colored Methylobacterium strains in the phyllosphere of many plants was confirmed by microscopy, enumeration of the colonies from grass leaves, and sequencing of the 16S rRNA genes. Colorless and yellow-pigmented methylotrophs belonged to the genera Methylophilus, Methylobacillus, Hansschlegelia, Methylopila, Xanthobacter, and Paracoccus. All isolates were able to synthesize plant hormones auxins from L-tryptophan (5−50 µg/mL) and are probably plant symbionts.

A New Catabolic Plasmid in Xanthobacter and Starkeya spp. from a 1,2-Dichloroethane-Contaminated Site.

UNLABELLED: 1,2-Dichloroethane (DCA) is a problematic xenobiotic groundwater pollutant. Bacteria are capable of biodegrading DCA, but the evolution of such bacteria is not well understood. In particular, the mechanisms by which bacteria acquire the key dehalogenase genes dhlA and dhlB have not been well defined. In this study, the genomic context of dhlA and dhlB was determined in three aerobic DCA-degrading bacteria (Starkeya novella strain EL1, Xanthobacter autotrophicus strain EL4, and Xanthobacter flavus strain EL8) isolated from a groundwater treatment plant (GTP). A haloalkane dehalogenase gene (dhlA) identical to the canonical dhlA gene from Xanthobacter sp. strain GJ10 was present in all three isolates, and, in each case, the dhlA gene was carried on a variant of a 37-kb circular plasmid, which was named pDCA. Sequence analysis of the repA replication initiator gene indicated that pDCA was a member of the pTAR plasmid family, related to catabolic plasmids from the Alphaproteobacteria, which enable growth on aromatics, dimethylformamide, and tartrate. Genes for plasmid replication, mobilization, and stabilization were identified, along with two insertion sequences (ISXa1 and ISPme1) which were likely to have mobilized dhlA and dhlB and played a role in the evolution of aerobic DCA-degrading bacteria. Two haloacid dehalogenase genes (dhlB1 and dhlB2) were detected in the GTP isolates; dhlB1 was most likely chromosomal and was similar to the canonical dhlB gene from strain GJ10, while dhlB2 was carried on pDCA and was not closely related to dhlB1 Heterologous expression of the DhlB2 protein confirmed that this plasmid-borne dehalogenase was capable of chloroacetate dechlorination. IMPORTANCE: Earlier studies on the DCA-degrading Xanthobacter sp. strain GJ10 indicated that the key dehalogenases dhlA and dhlB were carried on a 225-kb linear plasmid and on the chromosome, respectively. The present study has found a dramatically different gene organization in more recently isolated DCA-degrading Xanthobacter strains from Australia, in which a relatively small circular plasmid (pDCA) carries both dhlA and dhlB homologs. pDCA represents a true organochlorine-catabolic plasmid, first because its only obvious metabolic phenotype is dehalogenation of organochlorines, and second because acquisition of this plasmid provides both key enzymes required for carbon-chlorine bond cleavage. The discovery of the alternative haloacid dehalogenase dhlB2 in pDCA increases the known genetic diversity of bacterial chloroacetate-hydrolyzing enzymes.

[Activated Sludge Bacteria Transforming Cyanopyridines and Amides of Pyridinecarboxylic Acids].

Species diversity of bacteria from the activated sludge of Perm biological waste treatment facilities capable of transformation of cyanopyridines and amides of pyridinecarboxylic acids was investigated. Enrichment cultures in mineral media with 3-cyanopyridine as the sole carbon and nitrogen source were used to obtain 32 clones of gram-negative heterotrophic bacteria exhibiting moderate growth on solid and liquid media with 3- and 4-cyanopyridine. Sequencing of the 16S rRNA gene fragments revealed that the clones with homology of at least 99% belonged to the genera Acinetobacte, Alcaligenes, Delftia, Ochrobactrum, Pseudomonas, Stenotrophomonas, and Xanthobacter. PCR analysis showed that 13 out of 32 isolates contained the sequences (-1070 bp) homologous to the nitrilase genes reported previously in Alcaligenes faecalis JM3 (GenBank, D13419.1). Nine clones were capable of nitrile and amide transformation in minimal salt medium. Acinetobacter sp. 11 h and Alcaligenes sp. osv transformed 3-cyanopyridine to nicotinamide, while most of the clones possessed amidase activity (0.5 to 46.3 mmol/(g h) for acetamide and 0.1 to 5.6 mmol/(g h) for nicotinamide). Nicotinamide utilization by strain A. faecalis 2 was shown to result in excretion of a secondary metabolite, which was identified as dodecyl acrylate at 91% probability.

Biodegradation of three tetracyclines in swine wastewater.

Tetracyclines (TCs), including tetracycline (TC), oxytetracycline (OTC), and chlortetracycline (CTC), are amongst the most common antibiotics used in animal husbandry. Residual amounts of these antibiotics in the environment are a concern because they contribute to selection of resistant bacteria. In this study, we investigated the biodegradation of three TCs in swine wastewater. In batch experiments, OTC and CTC were completely degraded at d 18 and 20, respectively, but TC was remained at 7.1% after 20 d incubation. The degradation rates of TCs in the wastewater were in the order of OTC > CTC > TC. Degradation of the TCs was enhanced by the addition of enzyme extract from spent mushroom compost (SMC) of Pleurotus eryngii. The degradation rates were higher with the addition of extract-containing microcapsules than suspended enzyme extract in swine wastewater. In the bioreactor experiment, the addition of extract-containing microcapsules enhanced the removal rates of the three TCs, and adding TCs twice maintained enzyme activity in the swine wastewater. Of the microorganism strains isolated from the wastewater samples, strain HL2 (identified as Xanthobacter flavus) showed the best degrading ability.

Isolation and characterization of Xanthobacter polyaromaticivorans sp. nov. 127W that degrades polycyclic and heterocyclic aromatic compounds under extremely low oxygen conditions.

Two bacterial strains, 127W and T102, were isolated from anoxic crude oil tank sludge as effective degraders of dibenzothiophene (DBT), a model sulfur containing heterocyclic aromatic compound in crude oil. Strain 127W was more tolerant to oxygen limitation than T102 and was capable of degrading two- and three-ring polycyclic and heterocyclic aromatic compounds under both aerobic and low oxygen conditions. Strain 127W degraded 0.082, 0.055, and 0.064 mM of DBT, naphthalene, and anthracene, respectively, in one week with dissolved oxygen < or =0.2ppm (0.006 mM). Degradation by 127W cell-free extracts for DBT was increased by addition of sodium hydrogencarbonate under this oxygen concentration. Phylogenetic analysis of the 16S rRNA gene sequence and physiological characteristics indicate that the strains 127W and T102 belong to new species of the genus Xanthobacter and Pseudomonas stutzeri, respectively. We propose X. polyaromaticivorans sp. nov. 127W.

Bacterial composition of the biofilm on the surface of course sediment of the Danube: with special reference to the clinically important bacteria.

On monthly intervals and over a period of 14 months (November, 1993-December, 1994) biofilm samples from sediments taken at the Szentendre Island on the Danube were culturel and the isolated organisms were examined macromorphologically and micromorphogically and tested for oxidase and catalase production and their ability to oxidise and ferment glucose. The majority (85%) of the strains isolated were catalase positive. 43% were oxidase positive, 38% were glucose oxidisers and only 19% fermented glucose. In the sediment upmost biofilm layers Gram-negatives dominate (10 samples out of 14). A representative set strains has been subjected to complete identification using the Biolog automated identification system. The coryneform bacteria (e.g. Arthrobacter spp.) and members of the genus Rhodococcus dominated the Gram-positive bacteria while the dominant Gram-negative bacteria were facultative H2 autotrophs, methylotrophs (e.g. Xanthobacter flavus, Hydrogenophaga spp.) and different Aeromonas, Enterobacter and Pseudomonas species. Because the water supply of Budapest (the capital of Hungary) comes from bankwall filtred Danube water resources, the presence of clinically important microorganisms (i.e. Aeromonas, Enterobacter, Pseudomonas and Rhodococcus spp) in the Danube-sediments may pose a public health problem to the users (in particular the immunocompromised) of such water supplies.