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Cited by 2,417Metal Extraction and BioleachingGenomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Community structure and metabolism through reconstruction of microbial genomes from the environment

Tyson, Gene W., Chapman, Jarrod, Hugenholtz, Philip, Allen, Eric E., Ram, Rachna J., Richardson, Paul M., Solovyev, Victor V., Rubin, Edward M. +2 more·2004·Nature
DOI 10.1038/nature02340
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Abstract

Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant form of heterogeneity at the strain level. The Leptospirillum group II genome had remarkably few nucleotide polymorphisms, despite the existence of low-abundance variants. The Ferroplasma type II genome seems to be a composite from three ancestral strains that have undergone homologous recombination to form a large population of mosaic genomes. Analysis of the gene complement for each organism revealed the pathways for carbon and nitrogen fixation and energy generation, and provided insights into survival strategies in an extreme environment.

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Crossref · 10.1038/nature02340

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  • Many aspects of intercellular and inter-species signaling, short- and long-term evolution, and regulatory programs are exercised by microbes in their natural settings and are extremely difficult to recapitulate in a controlled setting.

    “Since early studies of environmental and host-associated microbial communities (Gill et al., 2006; Tyson et al., 2004; Venter et al., 2004), it has been clear that many aspects of intercellular and inter-species signaling, short- and long-term evolution, and regulatory programs are exercised by microbes in their natural settings and extremely difficult to recapitulate in a controlled setting.”

    From Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2021) · cites this paper as Tyson et al., 2004

  • Assembly binning was first achieved by Tyson et al. (2004) from an acidophilic biofilm.

    “Assembly binning refers to the construction of complete or near complete microbial genomes directly from metagenomic sequencing data, and was first achieved by Tyson et al. (2004) from an acidophilic biofilm.”

    From Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future (2018) · cites this paper as Tyson et al., 2004

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Authors
Tyson, G. W., Chapman, J., Hugenholtz, P., Allen, E. E., Ram, R. J., Richardson, P. M., Solovyev, V. V., Rubin, E. M., Rokhsar, D. S., & Banfield, J. F.
Affiliations
  • University of California, Berkeley (US)
  • Joint Genome Institute (US)
Corresponding author
Banfield, Jillian F.
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2004-02-01
Volume
428
Issue
6978
Pages
37-43
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/nature02340
OpenAlex
W2124637227
Cited by
2,417
References
43
Citations by year
2026: 64 · 2025: 61 · 2024: 89 · 2023: 74 · 2022: 96 · 2021: 78 · 2020: 88 · 2019: 80 · 2018: 91 · 2017: 107 · 2016: 113 · 2015: 151 · 2014: 129 · 2013: 142 · 2012: 121
FWCI
98.61
Type
journal article
Language
en
Open access
closed
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
Topics
  • Physical Sciences › Engineering › Biomedical Engineering › Metal Extraction and Bioleaching
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Keywords
metagenome assembly, unculturable microorganisms, single nucleotide polymorphisms, strain heterogeneity, genome rearrangement, homologous recombination, mosaic genomes, CO2 fixation, nitrogen fixation, energy metabolism, extreme environments, microbial community structure
MeSH terms
Archaea, Bacteria, Base Composition, Base Sequence, Carbon, Environmental Microbiology, Genes, Bacterial, Genetic Complementation Test, Molecular Sequence Data, Nitrogen Fixation, Phylogeny, Recombination, Genetic, RNA, Ribosomal, 16S, Species Specificity, Open Reading Frames, Genome, Bacterial, Sequence Analysis, DNA, Ecosystem, Biofilms, Genes, Archaeal, Polymorphism, Single Nucleotide, Genome, Archaeal, Genomics

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