cTo 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 the de novo reconstruction 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. Two Halomonas spp. 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 the Halomonas populations, one of the Rhodobacteraceae populations, and the Rhizobiales population. 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 sequence coverage (9؋ to 2,700؋) within the metagenomic data set.
Microdiversity refers to the diversity of organisms that are closely related phylogenetically yet exhibit different metabolic activities and therefore occupy distinct niches. Genomic studies comparing multiple strains of the same species have revealed that while much of the genome sequence is highly conserved, significant functional variation can exist, arising from changes in gene function due to mutation, the introduction of genes by horizontal gene transfer, or changes in gene regulation due to mutation or genome rearrangement. Microbial community diversity is usually measured via sequencing of either all or a part of the 16S rRNA gene. It is well established that bacteria that have near-identical or identical 16S rRNA sequences can have significantly divergent genome complements, cell morphologies, and metabolic functions (1-4).Recent developments in sequencing technologies and analysis have enabled cultivation-independent sequencing of intact microbial communities (metagenomics) and prediction of functional potential of individual microbial populations within a community. Early metagenomic work employed the same technology used for isolate genome sequencing, the Sanger method, which provided only a limited sequencing depth. Nonetheless, initial attempts to reconstruct member genomes in very-low-diversity communities or abundant members of complex communities were successful (5, 6)....