skip to main content

Title: Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia

To gain a predictive understanding of the interspecies interactions within microbial communities that govern community function, the genomic complement of every member population must be determined. Although metagenomic sequencing has enabled thede novoreconstruction of some microbial genomes from environmental communities, microdiversity confounds current genome reconstruction techniques. To overcome this issue, we performed short-read metagenomic sequencing on parallel consortia, defined as consortia cultivated under the same conditions from the same natural community with overlapping species composition. The differences in species abundance between the two consortia allowed reconstruction of near-complete (at an estimated >85% of gene complement) genome sequences for 17 of the 20 detected member species. TwoHalomonasspp. indistinguishable by amplicon analysis were found to be present within the community. In addition, comparison of metagenomic reads against the consensus scaffolds revealed within-species variation for one of theHalomonaspopulations, one of theRhodobacteraceaepopulations, and theRhizobialespopulation. Genomic comparison of these representative instances of inter- and intraspecies microdiversity suggests differences in functional potential that may result in the expression of distinct roles in the community. In addition, isolation and complete genome sequence determination of six member species allowed an investigation into the sensitivity and specificity of genome reconstruction processes, demonstrating robustness across a wide range of sequencemore » coverage (9× to 2,700×) within the metagenomic data set.« less
Authors:
ORCiD logo ; ; ; ; ;
Publication Date:
OSTI Identifier:
1243198
Report Number(s):
PNNL-SA-111129
Journal ID: ISSN 0099-2240; KP1601010
DOE Contract Number:
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Applied and Environmental Microbiology; Journal Volume: 82; Journal Issue: 1
Publisher:
American Society for Microbiology
Research Org:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US)
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
microdiversity; metagenomic sequencing; parallel consortia