Arenibacter amylolyticus sp. nov., an amylase- producing bacterium of the family Flavobacteriaceae isolated from marine water in India

A novel Gram- stain- negative, curved rod- shaped, 0.5?0.7 ?m wide and 3.0?10.0 ?m long, non- motile bacterium, designated strain AK53T, was isolated from a 5 m depth water sample collected from the Bay of Bengal, Visakhapatnam, India. Colonies on marine agar were circular, small, dark orange, shiny, smooth, translucent, flat, with an entire margin. The major fatty acids included iso-C15:0, iso-C15: 0 3OH, anteiso- C15:0, iso-C15: 1 G, iso- C17: 0 3OH and summed feature 3 (C16:1 ?7c and/or C16:1 ?6c and/or iso-C15:0- 2OH). Polar lipids included phosphatidylethanolamine and five unidentified lipids. The DNA G+C content of the strain AK53T was found to be 40.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain AK53T was closely related to Arenibacter latericius KMM 426T and Arenibacter certesii KMM3941T (pair- wise sequence similarity of 99.17 and 98.89 %, respectively), forming a distinct branch within the genus Arenibacter and clustering with A. latericius. Strain AK53T shared average nucleotide identity (ANIb, based on BLAST) of 78.07 and 77.44 % with A. latericius JCM 13508T and A. certesii JCM 13507T, respectively. Based on the observed phenotypic, chemotaxonomic characteristics and phylogenetic analysis, strain AK53T is described in this study as representing a novel species in the genus Arenibacter, for which the name Arenibacter amylolyticus sp. nov. is proposed. The type strain of Arenibacter amylolyticus is AK53T (=MTCC 12004T= JCM 19206T=KCTC 62553T)

Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum

Artículo de publicación ISIFlavobacterium psychrophilum is a fish pathogen in salmonid aquaculture worldwide that causes cold water disease (CWD) and rainbow trout fry syndrome (RTFS). Comparative genome analyses of 11 F. psychrophilum isolates representing temporally and geographically distant populations were used to describe the F. psychrophilum pan-genome and to examine virulence factors, prophages, CRISPR arrays, and genomic islands present in the genomes. Analysis of the genomic DNA sequences were complemented with selected phenotypic characteristics of the strains. The pan genome analysis showed that F. psychrophilum could hold at least 3373 genes, while the core genome contained 1743 genes. On average, 67 new genes were detected for every new genome added to the analysis, indicating that F. psychrophilum possesses an open pan genome. The putative virulence factors were equally distributed among isolates, independent of geographic location, year of isolation and source of isolates. Only one prophage-related sequence was found which corresponded to the previously described prophage 6H, and appeared in 5 out of 11 isolates. CRISPR array analysis revealed two different loci with dissimilar spacer content, which only matched one sequence in the database, the temperate bacteriophage 6H. Genomic Islands (GIs) were identified in F. psychrophilum isolates 950106-1/1 and CSF 259-93, associated with toxins and antibiotic resistance. Finally, phenotypic characterization revealed a high degree of similarity among the strains with respect to biofilm formation and secretion of extracellular enzymes. Global scale dispersion of virulence factors in the genomes and the abilities for biofilm formation, hemolytic activity and secretion of extracellular enzymes among the strains suggested that F. psychrophilum isolates have a similar mode of action on adhesion, colonization and destruction of fish tissues across large spatial and temporal scales of occurrence. Overall, the genomic characterization and phenotypic properties may provide new insights to the mechanisms of pathogenicity in F. psychrophilum.Danish Directorate for Food, Fisheries and Agri Business 3414-09-02613 Danish Strategic Research Council (ProAqua) 09-072829 EU-IRSES (AQUAPHAGE) 69175 EU-IRSE

Analysis of bacterial diversity and biogeography at the Central Arizona-Phoenix Long Term Ecological Research (CAP LTER) site

The limiting factor involved in past assessments of soil bacterial diversity when using culture-independent techniques has often been the lack of sampling and replication. As a result, analyses of community structural shifts across soil environments have lacked statistical power. In this study, 23 16S rRNA gene clone libraries consisting of over 11,000 clones were constructed from soils at the Central Arizona Phoenix Long Term Ecological Research (CAP LTER) site. Subsequent ARDRA fingerprinting and partial 16S rRNA gene sequencing allowed for a more robust investigation of various components that may explain any observed variations in bacterial species composition. The designated land use type of the soils best explained the overall diversity gradient. Based on Simpson’s reciprocal index, diversity was found to significantly increase when comparing urbanized and agricultural soils to open desert samples located outside the metropolitan region. Land use type appears to be a powerful indicator of overall diversity due to irrigation methods that differ greatly across land use types. Experiment-wise comparisons of complete CAP LTER clone libraries via the LIBSHUFF method yielded no statistical similarity in sequence libraries, except for two replicate libraries constructed from one urban soil. However, inter-phylum LIBSHUFF analysis of the clones also shows degrees of phylogenetic partitioning between land use categories and that open desert remnant patches located within the city limits more closely resemble those urban soils than the open deserts outside of Phoenix. Examination of constructed 16S rRNA phylogenetic trees that include CAP LTER phylotypes indicate some distinct clustering of sequences appears to be driven by land use type rather than geography, and that most of these groups may be endemic to the region. However, some ubiquitous phylotype groups were discovered and were used as templates for specific PCR primer design, allowing for the detection of ten of these groups in all soil samples analyzed. Overall, this study suggests that anthropogenic factors have altered soil bacterial communities, the biogeography of many species is controlled in some manner by land use type, and that a small subset of taxa is ecologically tolerant despite the heterogeneity of habitats within the site