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Community genomics in microbial ecology and evolution

Nature Reviews Microbiology volume 3, pages 489–498 (2005)Cite this article

Key Points

  • Genomic analyses of microbial communities can reveal the metabolic potential of uncultivated microorganisms.

  • Community genomics emphasizes the analysis of natural coexisting species populations through cultivation-independent environmental genome sequencing. The approach enables post-genomic functional assays to be carried out to understand the ecology and evolution of microbial consortia.

  • It possible to reconstruct near-complete, and possibly complete, genome sequences directly from environmental samples. However, heterogeneity in gene content and sequence identity, and genomic rearrangements in strain populations presents a fundamental challenge in reconstructing species genomes from mixed communities. Resolution of strain-level genomic heterogeneity is a fundamental goal of community genomic analysis. Comparative genome assembly that uses a sequenced strain as an assembly scaffold is a rapid and efficient method for analysis of the corresponding environmental population.

  • Comparative genomics of DNA sequences from members of strain populations can reveal the extent to which individuals are representative of their associated populations, the form of genomic heterogeneity, and the importance of processes such as lateral gene transfer and recombination in genome evolution over relatively short timescales.

  • Genomic data from communities can enable analyses of metabolic activity using gene-expression-array-based and proteomic methods. Analyses that evaluate gene expression have the potential to reveal the extent to which metabolic functions are partitioned among community members and how this changes as communities establish and develop.

  • To understand the processes of adaptation and evolution, it is important to find ways in which genome and environmental change can be placed on the same timescale.

Abstract

It is possible to reconstruct near-complete, and possibly complete, genomes of the dominant members of microbial communities from DNA that is extracted directly from the environment. Genome sequences from environmental samples capture the aggregate characteristics of the strain population from which they were derived. Comparison of the sequence data within and among natural populations can reveal the evolutionary processes that lead to genome diversification and speciation. Community genomic datasets can also enable subsequent gene expression and proteomic studies to determine how resources are invested and functions are distributed among community members. Ultimately, genomics can reveal how individual species and strains contribute to the net activity of the community.

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Figure 1: Resolving strain-level heterogeneity.
Figure 2: Genomic heterogeneity in Ferroplasma species and strains.
Figure 3: Integrating community genomics and functional assays in situ.

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Acknowledgements

We thank G. W. Tyson and anonymous reviewers for helpful comments. Support for our work from the Department of Energy Microbial Genome Program, National Science Foundation (NSF) Biocomplexity Program, NASA Astrobiology Institute, and the NSF Postdoctoral Research Fellowship Program in Microbial Biology (E.E.A.) is gratefully acknowledged.

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Authors and Affiliations

  1. Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, 94720, California, USA

    Eric E. Allen

  2. Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, 94720, California, USA

    Jillian F. Banfield

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Correspondence to Jillian F. Banfield.

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DATABASES

Entrez Gene

Ferroplasma acidarmanus strain fer1

Leptospirillum group III

FURTHER INFORMATION

Jillian Banfield's laboratory

Genomes Online Database

Glossary

CLONE LIBRARY

A collection of targeted DNA sequences, such as the 16S rRNA gene, most often derived from PCR amplification and subsequent cloning into a vector. Specifically, 16S rRNA gene clone libraries are often used in surveys of microbial diversity from environmental samples.

CONSORTIUM

Physical association between cells of two or more types of microorganism. Such an association might be advantageous to at least one of the microorganisms.

COVERAGE

The average number of times a nucleotide is represented by a high-quality base in the sequence data; full genome coverage is usually attained at 8–10X coverage.

ABIOTIC

The non-living physical and chemical attributes of a system, which include pH, temperature, pressure, osmotic strength, and chemical composition.

SYNTENY

Refers to the presence of two or more genes on the same chromosome. However, the term is often used to refer to the shared colinearity in orthologous gene content and gene order between genomes.

SCAFFOLD

A genome fragment constructed by the ordering and orienting of sets of unlinked contigs generated from raw shotgun sequence data by using additional information (such as paired-end sequence information or homology data) to determine proper contig linkage and placement along the chromosome. Scaffolds can be comprised of multiple contigs.

PANMICTIC

Characterized by a lack of restriction in genetic exchange within the population; all individuals within the species population are potential recombination partners.

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Allen, E., Banfield, J. Community genomics in microbial ecology and evolution. Nat Rev Microbiol 3, 489–498 (2005). https://doi.org/10.1038/nrmicro1157

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