Flavobacterium ammonificans sp. nov. and Flavobacterium ammoniigenes sp. nov., ammonifying bacteria isolated from surface river water.

Three aerobic, Gram-stain-negative, non-motile, rod-shaped bacteria, designated as strains SHINM13T, GENT5T and GENT11 were isolated from surface river water (Saitama Prefecture, Japan). SHINM13T and GENT11 were positive for catalase, whereas GENT5T was negative. Phylogenetic analyses based on the 16S rRNA gene (1341 bp) or 40 marker gene (34,513 bp) sequences revealed that the strains formed distinct phylogenetic lineages within the genus Flavobacterium. The three strains shared 99.3-99.6 % 16S rRNA gene sequence similarity among each other. The average nucleotide identity by orthology (OrthoANI) and digital DNA-DNA hybridization (dDDH) values between strains SHINM13T and GENT11 were 96.56 and 82.1 %, respectively, and those between SHINM13T and GENT5T were 83.46 % and 52.9 %, respectively. The major cellular fatty acids were C15 : 1ω6c, iso-C15 : 0, iso-C15 : 1G, anteiso-C15 : 0 and iso-C15 : 0 3-OH. The major polar lipid was phosphatidylethanolamine. SHINM13T and GENT5T contained menaquinone-6 (MK-6) as the predominant respiratory quinone, and their DNA G+C contents were 34.4 and 35.1 mol%, respectively. Genome sequencing of the three isolates revealed a genome size of 2.26-2.40 Mbp. Furthermore, all three isolates converted dissolved organic nitrogen to ammonium during cell growth. On the basis of the results of phenotypic and phylogenetic analyses, strains SHINM13T and GENT11 and GENT5T represent two distinct novel species in the genus Flavobacterium, for which the names Flavobacterium ammonificans sp. nov. (type strain SHINM13T =JCM 34684T =NCIMB 15379T) and Flavobacterium ammoniigenes sp. nov. (type strain GENT5T =JCM 32249T=NCIMB 15380T) are proposed.

Ecological niche separation in the Polynucleobacter subclusters linked to quality of dissolved organic matter: a demonstration using a high sensitivity cultivation-based approach.

The free-living, cosmopolitan, freshwater betaproteobacterial bacterioplankton genus Polynucleobacter was detected in different years in 11 lakes of varying types and a river using the size-exclusion assay method (SEAM). Of the 350 strains isolated, 228 (65.1%) were affiliated with the Polynucleobacter subclusters PnecC (30.0%) and PnecD (35.1%). Significant positive correlations between fluorescence in situ hybridization and SEAM data were observed in the relative abundance of PnecC and PnecD bacteria to Polynucleobacter communities (PnecC + PnecD). Isolates were mainly PnecC bacteria in the samples with a high specific UV absorbance at 254 nm (SUVA(254) ), and a low total hydrolysable neutral carbohydrate and amino acid (THneutralCH + THAA) content of the dissolved organic matter (DOM) fraction, which is known to be correlated with a high humic content. In contrast, the PnecD bacteria were abundant in samples with high chlorophyll a and/or THneutralCH + THAA concentrations, indicative of primary productivity. With few exceptions, differences in the relative abundance of PnecC and PnecD in each sample, determined using a high-sensitivity cultivation-based approach, were due to DOM quality. These results suggest that the major DOM component in the field, which is allochthonously or autochthonously derived, is a key factor for ecological niche separation between PnecC and PnecD subclusters.