Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: Metagenomics and metatranscriptomics in AMD : Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics      
keywords:
Other
ID:
PRJEB6277
description:
High-throughput sequencing technologies are expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of the rare and uncultured microbes in natural communities remains a major challenge. Here we used a divide and conquer strategy that partitioned the combined metagenomic and metatranscriptomic data (110 Gbp) into subsets based on K-mer frequency in sequence assembly to an acid mine drainage (AMD) microbial community, and successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare (relative abundance < 1% frequency) taxa. We reported the first composite genome of a naturally occurring Ferrovum population and its metabolic pathways, providing initial molecular insights into the ecological role of these less known but potentially important microorganisms in the AMD environment. Community gene transcriptional analysis revealed metabolic capabilities expressed in situ, including iron and sulfur oxidation which are key in energy acquisition and AMD generation, carbon and nitrogen related metabolisms associated with syntrophic interactions, and mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were executed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. This study demonstrates the potential of the divide and conquer strategy for ultra-high-throughput sequencing data for the genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.
accesstypes:
download
landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJEB6277
authentication:
none
authorization:
none
dateReleased:
07-07-2014
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject