13 research outputs found
Blastn results
Applying blastn to obtain the taxonomic information of each direct shotgun sequencing read that contain 16S rRNA gene sequenc
Additional file 1: of Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
Supplimentary material on metagemic analysis. (DOCX 312 kb
Bacterial Communities of Three Saline Meromictic Lakes in Central Asia
<div><p>Meromictic lakes located in landlocked steppes of central Asia (~2500 km inland) have unique geophysiochemical characteristics compared to other meromictic lakes. To characterize their bacteria and elucidate relationships between those bacteria and surrounding environments, water samples were collected from three saline meromictic lakes (Lakes Shira, Shunet and Oigon) in the border between Siberia and the West Mongolia, near the center of Asia. Based on in-depth tag pyrosequencing, bacterial communities were highly variable and dissimilar among lakes and between oxic and anoxic layers within individual lakes. <i>Proteobacteria</i>, <i>Bacteroidetes</i>, <i>Cyanobacteria</i>, <i>Actinobacteria</i> and <i>Firmicutes</i> were the most abundant phyla, whereas three genera of purple sulfur bacteria (a novel genus, <i>Thiocapsa</i> and <i>Halochromatium)</i> were predominant bacterial components in the anoxic layer of Lake Shira (~20.6% of relative abundance), Lake Shunet (~27.1%) and Lake Oigon (~9.25%), respectively. However, few known green sulfur bacteria were detected. Notably, 3.94% of all sequencing reads were classified into 19 candidate divisions, which was especially high (23.12%) in the anoxic layer of Lake Shunet. Furthermore, several hydro-parameters (temperature, pH, dissolved oxygen, H<sub>2</sub>S and salinity) were associated (P< 0.05) with variations in dominant bacterial groups. In conclusion, based on highly variable bacterial composition in water layers or lakes, we inferred that the meromictic ecosystem was characterized by high diversity and heterogenous niches.</p></div
Location of sampling sites; Lake Shira and Lake Shunet in Khakassia, Russia and Lake Oigon in western Mongolia.
<p>Location of sampling sites; Lake Shira and Lake Shunet in Khakassia, Russia and Lake Oigon in western Mongolia.</p
Number of shared OTUs in Lakes Shira, Shunet and Oigon, visualized by a heat map.
<p>Relative abundance of OTUs were standardized to the total number of OTUs (per-lake basis).</p
Relative abundance of bacterial communities at the phylum level according to depth in Lakes Shira, Shunet and Oigon.
<p>Relative abundance of bacterial communities at the phylum level according to depth in Lakes Shira, Shunet and Oigon.</p
Estimated diversity indices and richness for the bacterial communities as represented in the 16S rRNA gene libraries<sup>a</sup>.
<p>Estimated diversity indices and richness for the bacterial communities as represented in the 16S rRNA gene libraries<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0150847#t002fn001" target="_blank"><sup>a</sup></a>.</p