Description of Clavibacter zhangzhiyongii sp. nov., a phytopathogenic actinobacterium isolated from barley seeds, causing leaf brown spot and decline

Clavibacter michiganensis is a Gram-stain-positive bacterium with eight subspecies, five of which have been redefined as different species on the basis of their genome sequence data. On the basis of the results of phylogenetic analysis of dnaA gene sequences, strains of members of the genus Clavibacter isolated from barley have been grouped in a separate clade from other species and subspecies of the genus Clavibacter . In this study, the biochemical, physiological, fatty acids and genetic characteristics of strains DM1T and DM3, which represented the barley isolates, were examined. On the basis of results from multi-locus sequence typing and other biochemical and physiological features, including colony colour, carbon source utilisation and enzyme activities, DM1T and DM3 are categorically differentiated from the aforementioned eight species and subspecies of the genus Clavibacter . Moreover, the results of genomic analysis reveal that the DNA G+C contents of DM1T and DM3 are 73.7 and 73.5 %, respectively, and the average nucleotide identity (ANI) values between DM1T and DM3 and other species and subspecies range from 90.4 to 92.0 %. The ANI value between DM1T and DM3 is 98.0 %. These results indicate that DM1T and DM3 are distinct from other known species and subspecies of the genus Clavibacter . Therefore, we propose a novel species, C. zhangzhiyongii, with DM1T (=CFCC 16553 T=LMG 31970T) as the type strain.

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism’s genotype. While manual reconstructions are laborious, automated reconstructions often fail to recapitulate known metabolic processes. Here we present (https://github.com/jotech/gapseq), a new tool to predict metabolic pathways and automatically reconstruct microbial metabolic models using a curated reaction database and a novel gap-filling algorithm. On the basis of scientific literature and experimental data for 14,931 bacterial phenotypes, we demonstrate that gapseq outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, and metabolic interactions within microbial communities.

Carbon source utilisation and evaluation of the Biolog system in the identification of Actinobacillus pleuropneumoniae

Sixty-eight Actinobacillus pleuropneumoniae strains were isolated from porcine acute pleuropneumonia cases from different parts of Hungary between 2000 and 2014. A total of 41 isolates were identified as A. pleuropneumoniae bio-type I and 27 strains as biotype II based on cultural, morphological and biochemical characteristics. The aim of this study was to evaluate metabolic fingerprinting in the species-level identification of A. pleuropneumoniae isolates. Utilisation of carbon sources by these field isolates and six reference strains was characterised by the Biolog system (GN2 Microplate, MicroLog3 Version 4.20.05 software). Twenty-nine field strains were correctly identified by the Biolog system as A. pleuropneumoniae, 36 strains as A. lignieresii, two strains as H. paraphrohaemolyticus and one strain as A. equuli after 24 h of incubation. Among the six A. pleuropneumoniae reference strains the Biolog system identified one strain as A. pleuropneumoniae, four as A. lignieresii and one as H. paraphrohaemolyticus. There was no correlation between biotypes and serotypes of A. pleuropneumoniae and the carbon source utilisation pattern and species identification by the Biolog system. our data indicate that the efficacy of the Biolog system used here could be improved by including phenotypes of more A. pleuropneumoniae strains representing a wider geographical occurrence into the database.

Identification of a proposed new serovar of Actinobacillus Pleuropneumoniae: Serovar 16

Five Actinobacillus pleuropneumoniae strains isolated from pathological lesions of porcine pleuropneumonia in Hungary could not be assigned to any of the accepted 15 serovars. Using hyperimmune serum raised against these unty-pable-serovar A. pleuropneumoniae strains in rabbits, indirect haemagglutination tests proved that they form a distinct group and there is no cross-reaction between them and the type strains of A. pleuropneumoniae. All five strains harboured the toxin-associated genes for the production (apxIA) and secretion (apxIB) of ApxI, the gene for the expression of ApxII and the largest-size (2800 bp) apxIV gene. The carbon source utilisation pattern and the sequence analysis of the 16S rRNA gene confirmed the species identification of the suggested type strain, A. pleuropneumoniae A-85/14. A new serovar of A. pleuropneumoniae — serovar 16 — is proposed with A. pleuropneumoniae A-85/14 as reference strain.

Comparative analysis of DNA-based microbial community composition and substrate utilisation patterns of activated sludge microorganisms from wastewater treatment plants operated under different conditions

In this study, the microbial community structure and carbon source utilisation profile of activated sludge samples collected from full-scale municipal wastewater treatment plants (WWTPs) operated under different conditions were characterised and compared, respectively, using terminal-restriction fragment length polymorphism (T-RFLP) analysis and Biolog assay. Samples were collected from each biological treatment tank of six conventional activated sludge, two anaerobic–oxic, two anaerobic–anoxic–oxic, and one step-aeration processes in eight full-scale WWTPs in Osaka, Japan. Results of the T-RFLP analysis of eubacterial 16S rDNA showed that microbial communities of activated sludge differed greatly among samples, and that they were affected by process-based operational conditions. In contrast, the carbon source utilisation profiles of activated sludge samples were mutually similar, but appeared to be influenced slightly by aerated conditions at each reaction tank. Similar carbon source utilisation profiles among all samples suggest that the activated sludge community possesses functions that are necessary for wastewater treatment even if the phylogenetic composition is different. Different results from the T-RFLP analysis and Biolog assay suggest that the phylogenetic composition of microbial community might not necessarily reflect the wastewater treatment functions of the activated sludge.