Culture-independent study of bacterial communities in tropical river sediment

<p>Ubiquitous microbial communities in river sediments actively govern organic matter decomposition, nutrient recycling, and remediation of toxic compounds. In this study, prokaryotic diversity in two major rivers in central Thailand, the Chao Phraya (CP) and the Tha Chin (TC) distributary was investigated. Significant differences in sediment physicochemical properties, particularly silt content, were noted between the two rivers. Tagged 16S rRNA sequencing on a 454 platform showed that the sediment microbiomes were dominated by <i>Gammaproteobacteria</i> and sulfur/sulfate reducing <i>Deltaproteobacteria</i>, represented by orders <i>Desulfobacteriales</i> and <i>Desulfluromonadales</i> together with organic degraders <i>Betaproteobacteria</i> (orders <i>Burkholderiales</i> and <i>Rhodocyclales</i>) together with the co-existence of <i>Bacteroidetes</i> predominated by <i>Sphingobacteriales</i>. Enrichment of specific bacterial orders was found in the clayey CP and silt-rich TC sediments, including various genera with known metabolic capability on decomposition of organic matter and xenobiotic compounds. The data represent one of the pioneered works revealing heterogeneity of bacteria in river sediments in the tropics.</p> <p>Analysis of bacterial diversity by tagged 16S rRNA sequencing revealed enrichment of specific taxa in CP and TC rivers.</p

<i>Proteobacteria</i> and <i>Bacteroidetes</i> are major phyla of filterable bacteria passing through 0.22 μm pore size membrane filter, in Lake Sanaru, Hamamatsu, Japan

<p>141 filterable bacteria that passed through a 0.22 μm pore size filter were isolated from Lake Sanaru in Hamamatsu, Japan. These belonged to <i>Proteobacteria</i>, <i>Bacteroidetes</i>, <i>Firmicutes</i>, or <i>Actinobacteria</i> among which the first two phyla comprised the majority of the isolates. 48 isolates (12 taxa) are candidates assignable to new bacterial species or genera of <i>Proteobacteria</i> or <i>Bacteroidetes</i>.</p

Additional file 3: Table S3. of Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method

Comparison of CRISPR-associated proteins of strain UCH007 with those of other strains. (XLSX 10 kb

Additional file 1: Table S1. of Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method

Phylogenetic analysis using whole genome sequences and 16S rRNA genes. (XLSX 12 kb

Additional file 2: Table S2. of Complete genome sequencing of Dehalococcoides sp. strain UCH007 using a differential reads picking method

Comparison of reductive dehalogenases of strain UCH007 with those of other strains. (XLSX 12 kb