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Community Genomics

 Community genome sequencing

Recent advances in sequencing technologies make it possible to sequence microbial genomes in a entire microbial community, but this potential has not yet been fully demonstrated or validated. Since surface soil communities are extremely complex, fundamental understanding of microbial community structure and dynamics is likely to be achieved more efficiently and rapidly with simpler systems than with complex surface soil microbial communities. Thus, our basic strategy to address the challenges presented by biological complexity is to focus on less complex natural communities. To provide a fundamental and comprehensive understanding of microbial community diversity, we are sequencing at JGI a groundwater microbial community with manageable diversity and complexity (~10 phylotypes) at the Environmental Research Science Program (ERSP)-Field Research Center (FRC) using shotgun approach. This study will be the first metagenomic study of sequencing microbial community at contaminated sites.

The whole community sequence information will provide baseline information for understanding how contaminants affect microbial communities. This study will also help design strategies for remediating mixed contaminants. In addition, the whole community sequence information, along with microarray-based genomic technologies, will provide an unprecedented opportunity to test ecological and evolutionary theories about the relationship between phylogenetic diversity and functional properties of ecosystems. These issues are central to current concerns about biodiversity, and are also directly relevant to understanding and managing microbial communities for bioremediation and other purposes.   

Novel microarray-assisted approach for community sequencing

The most commonly used approach to access the genetic content of uncultured microorganisms is to directly isolate DNA from environmental samples, followed by cloning high-molecular-weight DNA fragments into artificial bacterial chromosomes (BACs) or fosmid vectors for direct or random shotgun sequence determination of the whole community.  One of the main challenges for such metagenomic approaches is that, in most of the cases, communities are very diverse with many complex interactions between community members. Another challenge is the unequal abundance of community members. The shot-gun approach will be inefficient when applied to the sequencing of whole complex communities, because the coverage will be excessive for the most dominant members and too little or absent for the less dominant members. In addition, some of the microbial populations within the different communities are identical or closely related. It is unnecessary to sequence all closely related strains from different communities. Thus, we are also developing microarray-based new strategy to pre-select clones for community genome sequencing.   

Linking genomics to community processes and functions

The availability of entire genome sequences from many organisms has the potential to open innovative and efficient research avenues for studying biological systems at different levels. However, how to use genome sequence information and related genomic technologies to understand how biological systems function at different levels of organization in nature is very difficult. One of the main challenges of studying natural microbial communities is that, in most of the cases, communities are very diverse with many complex interactions between community members. This complexity limits our ability to resolve the cause-and-effect relationships needed to develop a mechanistic understanding of the communities. Controlled experimentation with simplified systems is necessary to understand the fundamental principles of community dynamics. Thus, in an attempt to linking genomics to community functions, at the initial stage, we have focused on very simple systems with two species. By collaborating with other scientists, we are studying the genomic basis and mechanisms for the syntrophic interactions between sulfate-reducing bacteria (H₂ production) and methanogen (H₂ consumption). The syntrophic interaction between D. vulgaris (sulfate-reducer) and M. maripaludis (methanogen) has been established and meta-genome microarrays containing sequence information from both genomes were designed and constructed. We are using the meta-genome arrays to understand how these two populations interact each other at the genomic scale.   

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