Sequence analysis of 16S rRNA, gyrB and catA genes and DNA-DNA hybridization reveal that Rhodococcus jialingiae is a later synonym of Rhodococcus qingshengii

The results of 16S rRNA, gyrB and catA gene sequence comparisons and reasserted DNA–DNA hybridization unambiguously proved that Rhodococcus jialingiae Wang et al. 2010 and Rhodococcus qingshengii Xu et al. 2007 represent a single species. On the basis of priority R. jialingiae must be considered a later synonym of R. qingshengii .</jats:p

Genome analysis provides insights into microaerobic toluene-degradation pathway of Zoogloea oleivorans BucT

Zoogloea oleivorans, capable of using toluene as a sole source of carbon and energy, was earlier found to be an active degrader under microaerobic conditions in aquifer samples. To uncover the genetic background of the ability of microaerobic toluene degradation in Z. oleivorans, the whole-genome sequence of the type strain Buc(T) was revealed. Metatranscriptomic sequence reads, originated from a previous SIP study on microaerobic toluene degradation, were mapped on the genome. The genome (5.68 Mb) had a mean G + C content of 62.5%, 5005 protein coding gene sequences and 80 RNA genes. Annotation predicted that 66 genes were involved in the metabolism of aromatic compounds. Genome analysis revealed the presence of a cluster with genes coding for a multicomponent phenol-hydroxylase system and a complete catechol meta-cleavage pathway. Another cluster flanked by mobile-element protein coding genes coded a partial catechol meta-cleavage pathway including a subfamily I.2.C-type extradiol dioxygenase. Analysis of metatranscriptomic data of a microaerobic toluene-degrading enrichment, containing Z . oleivorans as an active-toluene degrader revealed that a toluene dioxygenase-like enzyme was responsible for the ring-hydroxylation, while enzymes of the partial catechol meta-cleavage pathway coding cluster were responsible for further degradation of the aromatic ring under microaerobic conditions. This further advances our understanding of aromatic hydrocarbon degradation between fully oxic and strictly anoxic conditions

Plant polysaccharide degrading enzyme system of Thermobifida cellulosilytica TB100^T revealed by de novo genome project data

Thermobifidas are thermophilic, aerobic, lignocellulose decomposing actinomycetes. The Thermobifida genus includes four species: T. fusca, T. alba, T. cellulosilytica, and T. halotolerans. T. fusca YX is the far best characterized strain of this taxon and several cellulases and hemicellulases have been cloned from it for industrial purposes targeting paper industry, biofuel, and feed applications. Unfortunately, sequence data of such enzymes are almost exclusively restricted to this single species; however, we demonstrated earlier by zymography that other T. alba and T. cellulosilytica strains encode the same enzyme sets. Recently, the advances in whole genome sequencing by the use of next generation genomics platforms accelerated the selection process of valuable hydrolases from uncharacterized bacterial species for cloning purposes. For this purpose T. cellulosilytica TB100T type strain was chosen for de novo genome sequencing. We have assembled the genome of T. cellulosilytica strain TB100T into 168 contigs and 19 scaffolds, with reference length of 4 327 869 bps, 3 589 putative coding sequences, 53 tRNAs, and 4 rRNAs. The analysis of the annotated genome revealed the existence of 27 putative hydrolases belonging to 14 different glycoside hydrolase (GH) families. The investigation of identified, cloned, and heterologously multiple cellulases, mannanases, xylanases, and amylases may result in industrial applications beside gaining useful basic research related information

Lachgas(N2O)‐Freisetzung durch Streptomyces nitrosporeus in einem sandigen Lehmboden in Abhängigkeit von pO2, pH und Angebot an leicht mineralisierbarem Kohlenstoff

In model experiments under defined conditions (80%WHC, 300 mu g nitrate-N g(-1) dry soil, 30 degrees C) the effect of pO(2), pH and addition of easily decomposable organic matter on nitrous oxide production by Streptomyces nitrosporeus DSM 40023 from a sterilized sandy loam soil was studied. This streptomycete reduces nitrate to N2O but not to N-2. The strain was inoculated into a sterilized sandy loam sail (pH 6), enriched with nitrate and incubated at approximately 20 and 10% (v/v) O-2 for 26 days. In another series of experiments the pH was increased with NaOH-solution up to pH 7 or the soil was enriched with pulverized leaves (1%) to increase mineralization activity and the demand for electron accepters. In the headspace the concentration of O-2, CO2 and N2O was analysed by GC. The soil concentration of NO3-, NO2- and NH4+ was measured as well as the pH value. The population density was determined by the plate count method. At a decreased oxygen concentration of about 2.5% (v/v) in the headspace, S. nitrosporeus increased the release of N2O. In the experiments with an initial oxygen concentration of approximately 20% (v/v) this threshold of about 2.5%/(v/v) O-2 was hardly reached and consequently only little N2O was produced. Apparently, S. nitrosporeus uses O-2 in preference to nitrate, which is characteristical of nitrate respiration. A pH increase from pH 6 to 7 reduced the lag phase significantly and increased the rate of oxygen consumption, CO2 release and N2O production. Maximum nitrous oxide production was reached after 13 days. The result indicated that streptomycetes Like S. nitrosporeus may use nitrate, rate alternativly to O-2 to maintain energy conservation (ATP synthesis) with the release of N2O. So far, nothing is known about the role of streptomycetes in contributing to N2O production in natural soils

J. Bacteriol.

Here we report on the complete genome sequence of Cupriavidus basilensis OR16 NCAIM BO2487. The genome of strain OR16 contains 7,534 putative coding sequences, including a large set of xenobiotics-degrading genes and a unique glucose dehydrogenase gene that is absent from other Cupriavidus genomes

Mycotoxin-degradation profile of Rhodococcus strains

Mycotoxins are secondary fungal metabolites that may have mutagenic, carcinogenic, cytotoxic and endocrine disrupting effects. These substances frequently contaminate agricultural commodities despite efforts to prevent them, so successful detoxification tools are needed. The application of microorganisms to biodegrade mycotoxins is a novel strategy that shows potential for application in food and feed processing. In this study we investigated the mycotoxin degradation ability of thirty-two Rhodococcus strains on economically important mycotoxins: aflatoxin B-1, zearalenone, fumonisin B-1, T2 toxin and ochratoxin A, and monitored the safety of aflatoxin B-1 and zearalenone degradation processes and degradation products using previously developed toxicity profiling methods. Moreover, experiments were performed to analyse multi-mycotoxin-degrading ability of the best toxin degrader/detoxifier strains on aflatoxin B-1, zearalenone and T2 toxin mixtures. This enabled the safest and the most effective Rhodococcus strains to be selected, even for multi-mycotoxin degradation. We concluded that several Rhodococcus species are effective in the degradation of aromatic mycotoxins and their application in mycotoxin biodetoxification processes is a promising field of biotechnology. (C) 2013 Elsevier B.V. All rights reserved