Aerobic and anaerobic toluene degradation by a newly isolated denitrifying bacterium, Thauera sp. strain DNT-1. (1/35)

A newly isolated denitrifying bacterium, Thauera sp. strain DNT-1, grew on toluene as the sole carbon and energy source under both aerobic and anaerobic conditions. When this strain was cultivated under oxygen-limiting conditions with nitrate, first toluene was degraded as oxygen was consumed, while later toluene was degraded as nitrate was reduced. Biochemical observations indicated that initial degradation of toluene occurred through a dioxygenase-mediated pathway and the benzylsuccinate pathway under aerobic and denitrifying conditions, respectively. Homologous genes for toluene dioxygenase (tod) and benzylsuccinate synthase (bss), which are the key enzymes in aerobic and anaerobic toluene degradation, respectively, were cloned from genomic DNA of strain DNT-1. The results of Northern blot analyses and real-time quantitative reverse transcriptase PCR suggested that transcription of both sets of genes was induced by toluene. In addition, the tod genes were induced under aerobic conditions, whereas the bss genes were induced under both aerobic and anaerobic conditions. On the basis of these results, it is concluded that strain DNT-1 modulates the expression of two different initial pathways of toluene degradation according to the availability of oxygen in the environment.  (+info)

Petrobacter succinatimandens gen. nov., sp. nov., a moderately thermophilic, nitrate-reducing bacterium isolated from an Australian oil well. (2/35)

A novel Gram-negative, aerobic and moderately thermophilic bacterium, strain 4BON(T), was isolated from a non-water-flooded Australian terrestrial oil reservoir. Cells were non-spore-forming straight rods, which were motile by means of a polar flagellum. The optimum growth conditions were 55 degrees C, pH 6.9 and 0.5 % NaCl. Strain 4BON(T) was oxidase- and catalase-positive; it grew on fumarate, pyruvate, succinate, formate, ethanol and yeast extract in the presence of oxygen or nitrate as terminal electron acceptor. Nitrate was reduced to nitrous oxide. The DNA G+C content of the strain was 58.6 mol%. The closest phylogenetic relative of strain 4BON(T) was Hydrogenophilus thermoluteolus (similarity of 91.8 %), of the beta-Proteobacteria. As strain 4BON(T) is physiologically and phylogenetically different from H. thermoluteolus, it is proposed that it be assigned to a novel species of a novel genus, Petrobacter succinatimandens gen. nov., sp. nov. The type strain is 4BON(T) (=DSM 15512(T)=CIP 107790(T)).  (+info)

A third lineage with two-piece tmRNA. (3/35)

tmRNA combines tRNA and mRNA properties and helps bacteria to cope with stalled ribosomes. Its termini normally pair in the tRNA domain, closing the mRNA portion into a looping domain. A striking variation is a two-piece form that effectively breaks open the mRNA domain loop, resulting from independent gene permutation events in alphaproteobacteria and cyanobacteria. Convergent evolution to a similar form in separate bacterial lineages suggests that loop-opening benefits tmRNA function. This argument is strengthened by the discovery of a third bacterial lineage with a loop-opened two-piece tmRNA. Whereas most betaproteobacteria have one-piece tmRNA, a permuted tmRNA gene was found for Dechloromonas aromatica and close relatives. Correspondingly, two tmRNA pieces were identified, at approximately equal abundance and at a level one-fifteenth that of ribosomes, a 189 nt mRNA piece and a 65 nt aminoacylatable piece. Together these pieces were active with purified Escherichia coli translational components, but not alone. The proposed secondary structure combines common tmRNA features differently from the structures of other two-piece forms. The origin of the gene is unclear; horizontal transfer may be indicated by the similarity of the tRNA domain to that from a cyanobacterial two-piece tmRNA, but such transfer would not appear simple since the mRNA domain is most similar to that of other betaproteobacteria.  (+info)

Microautoradiographic study of Rhodocyclus-related polyphosphate-accumulating bacteria in full-scale enhanced biological phosphorus removal plants. (4/35)

The ecophysiology of uncultured Rhodocyclus-related polyphosphate-accumulating organisms (PAO) present in three full-scale enhanced biological phosphorus removal (EBPR) activated sludge plants was studied by using microautoradiography combined with fluorescence in situ hybridization. The investigations showed that these organisms were present in all plants examined and constituted 5 to 10, 10 to 15, and 17 to 22% of the community biomass. The behavior of these bacteria generally was consistent with the biochemical models proposed for PAO, based on studies of lab-scale investigations of enriched and often unknown PAO cultures. Rhodocyclus-related PAO were able to accumulate short-chain substrates, including acetate, propionate, and pyruvate, under anaerobic conditions, but they could not assimilate many other low-molecular-weight compounds, such as ethanol and butyrate. They were able to assimilate two substrates (e.g., acetate and propionate) simultaneously. Leucine and thymidine could not be assimilated as sole substrates and could only be assimilated as cosubstrates with acetate, perhaps serving as N sources. Glucose could not be assimilated by the Rhodocyclus-related PAO, but it was easily fermented in the sludge to products that were subsequently consumed. Glycolysis, and not the tricarboxylic acid cycle, was the source that provided the reducing power needed by the Rhodocyclus-related PAO to form the intracellular polyhydroxyalkanoate storage compounds during anaerobic substrate assimilation. The Rhodocyclus-related PAO were able to take up orthophosphate and accumulate polyphosphate when oxygen, nitrate, or nitrite was present as an electron acceptor. Furthermore, in the presence of acetate growth was sustained by using oxygen, as well as nitrate or nitrite, as an electron acceptor. This strongly indicates that Rhodocyclus-related PAO were able to denitrify and thus played a role in the denitrification occurring in full-scale EBPR plants.  (+info)

Dechloromonas hortensis sp. nov. and strain ASK-1, two novel (per)chlorate-reducing bacteria, and taxonomic description of strain GR-1. (5/35)

Recent studies on the occurrence of (per)chlorate-reducing bacteria have resulted in the characterization of strains capable of dissimilatory (per)chlorate reduction. Phylogenetic analysis has shown that these bacteria are members of the Proteobacteria. Strains have been isolated from polluted and pristine sites, but only strains from polluted sites have been characterized in detail and deposited in culture collections. Herein we describe the isolation and characterization of perchlorate-reducing bacterium strain MA-1(T) and chlorate-reducing bacterium strain ASK-1, respectively isolated from a pristine and a chlorate-polluted site. Both isolates are members of the Proteobacteria. The 16S rRNA gene sequence similarity of MA-1(T) to Dechloromonas agitata DSM 13637(T) is 97.6%, but the relatedness in DNA-DNA reassociation is only 37%. Therefore, we propose to classify strain MA-1(T) (=DSM 15637(T)=ATCC BAA-776(T)) as the type strain of a novel species, Dechloromonas hortensis sp. nov. Strain ASK-1 and a previously described strain GR-1 show 100 and 99% 16S rRNA gene sequence similarity to Pseudomonas chloritidismutans DSM 13592(T) and Dechlorosoma suillum DSM 13638(T), respectively. DNA-DNA hybridization studies indicated that strains ASK-1 and GR-1 are related at the species level to P. chloritidismutans DSM 13592(T) (79%) and Dechlorosoma suillum DSM 13638(T) (85%), respectively. As suggested previously, Dechlorosoma suillum appears to be a later heterotypic synonym of Azospira oryzae. Although strain ASK-1 is identified as P. chloritidismutans, its morphology and growth requirements are different from those of the type strain.  (+info)

Characterization of denitrifying polyphosphate-accumulating organisms in activated sludge based on nitrite reductase gene. (6/35)

Nitrite reductase gene (nirS) fragments in the activated sludge obtained from a sequencing batch reactor (SBR) under anaerobic-aerobic condition were cloned and classified by restriction fragment length polymorphism (RFLP) analysis, and representative fragments were sequenced. One of the nirS clones was approximately 70% of all nirS clones in anaerobic/aerobic (existing oxygen and nitrate) cycle operation in which a large amount of anoxic phosphate uptake was observed. Although the activated sludge samples analyzed might contain bacteria that did not accumulate polyphosphate, it was likely that this nirS fragment sequence was that from denitrifying polyphosphate-accumulating organisms (DNPAOs) which can utilize both oxygen and nitrate as electron acceptors. The sequence was similar to the nirS sequences of Thauera mechernichensis (83% similarity) and Azoarcus tolulyticus (83% similarity) both of which belong to the Rhodocyclus group.  (+info)

Nitrous oxide reductase genes (nosZ) of denitrifying microbial populations in soil and the earthworm gut are phylogenetically similar. (7/35)

Earthworms emit nitrous oxide (N2O) and dinitrogen (N2). It has been hypothesized that the in situ conditions of the earthworm gut activates ingested soil denitrifiers during gut passage and leads to these in vivo emissions (M. A. Horn, A. Schramm, and H. L. Drake, Appl. Environ. Microbiol. 69:1662-1669, 2003). This hypothesis implies that the denitrifiers in the earthworm gut are not endemic to the gut but rather are regular members of the soil denitrifier population. To test this hypothesis, the denitrifier populations of gut and soil from three different sites were comparatively assessed by sequence analysis of nosZ, the gene for the terminal enzyme in denitrification, N2O reductase. A total of 182 and 180 nosZ sequences were retrieved from gut and soil, respectively; coverage of gene libraries was 79 to 100%. Many of the nosZ sequences were heretofore unknown, clustered with known soil-derived sequences, or were related to N2O reductases of the genera Bradyrhizobium, Brucella, Dechloromonas, Flavobacterium, Pseudomonas, Ralstonia, and Sinorhizobium. Although the numbers of estimators for genotype richness of sequence data from the gut were higher than those of soil, only one gut-derived nosZ sequence did not group phylogenetically with any of the soil-derived nosZ sequences. Thus, the phylogenies of nosZ from gut and soil were not dissimilar, indicating that gut denitrifiers are soil derived.  (+info)

Azonexus caeni sp. nov., a denitrifying bacterium isolated from sludge of a wastewater treatment plant. (8/35)

A polyphasic taxonomic study was carried out to determine the taxonomic position of a newly isolated denitrifying bacterium, designated Slu-05T, which had been isolated from sludge from the main aerobic treatment tanks of a municipal sewage treatment plant. Phylogenetic analysis based on comparative 16S rRNA gene sequencing indicated that strain Slu-05T was closely related to Azonexus fungiphilus LMG 19178T (96.4 % sequence similarity), the sole species in the genus Azonexus. Strain Slu-05T comprised Gram-negative, motile, non-spore-forming and slightly curved rods. The predominant respiratory lipoquinone was Q-8. The major fatty acids were C16:1omega7c, C16:0, C18:1 isomers and C10:0 3-OH. The G+C content of the genomic DNA was 65.6 mol%. The results of DNA-DNA hybridization (15.6 %) together with phenotypic determination showed that strain Slu-5T could be distinguished from A. fungiphilus. Moreover, some phenotypic properties concerning enzyme activity, the substrates utilized as carbon sources and growth conditions distinguish strain Slu-5T from A. fungiphilus. On the basis of the results obtained in this study, Slu-05T (=DSM 17719T=KCTC 12530T=CCBAU 10199T) is the type strain of a novel species of Azonexus, for which the name Azonexus caeni sp. nov. is proposed.  (+info)

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