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

Author

Listed:
  • Gene W. Tyson

    (University of California)

  • Jarrod Chapman

    (University of California
    Joint Genome Institute)

  • Philip Hugenholtz

    (University of California)

  • Eric E. Allen

    (University of California)

  • Rachna J. Ram

    (University of California)

  • Paul M. Richardson

    (Joint Genome Institute)

  • Victor V. Solovyev

    (Joint Genome Institute)

  • Edward M. Rubin

    (Joint Genome Institute)

  • Daniel S. Rokhsar

    (University of California
    Joint Genome Institute)

  • Jillian F. Banfield

    (University of California
    University of California)

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.

Suggested Citation

  • Gene W. Tyson & Jarrod Chapman & Philip Hugenholtz & Eric E. Allen & Rachna J. Ram & Paul M. Richardson & Victor V. Solovyev & Edward M. Rubin & Daniel S. Rokhsar & Jillian F. Banfield, 2004. "Community structure and metabolism through reconstruction of microbial genomes from the environment," Nature, Nature, vol. 428(6978), pages 37-43, March.
  • Handle: RePEc:nat:nature:v:428:y:2004:i:6978:d:10.1038_nature02340
    DOI: 10.1038/nature02340
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    Cited by:

    1. Ágnes Becsei & Alessandro Fuschi & Saria Otani & Ravi Kant & Ilja Weinstein & Patricia Alba & József Stéger & Dávid Visontai & Christian Brinch & Miranda Graaf & Claudia M. E. Schapendonk & Antonio Ba, 2024. "Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Jean-Sebastien Gounot & Minghao Chia & Denis Bertrand & Woei-Yuh Saw & Aarthi Ravikrishnan & Adrian Low & Yichen Ding & Amanda Hui Qi Ng & Linda Wei Lin Tan & Yik-Ying Teo & Henning Seedorf & Niranjan, 2022. "Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    3. Luis E. Valentin-Alvarado & Kathryn E. Appler & Valerie Anda & Marie C. Schoelmerich & Jacob West-Roberts & Veronika Kivenson & Alexander Crits-Christoph & Lynn Ly & Rohan Sachdeva & Chris Greening & , 2024. "Asgard archaea modulate potential methanogenesis substrates in wetland soil," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    4. Xiaoquan Su & Weihua Pan & Baoxing Song & Jian Xu & Kang Ning, 2014. "Parallel-META 2.0: Enhanced Metagenomic Data Analysis with Functional Annotation, High Performance Computing and Advanced Visualization," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-13, March.
    5. Shibu Yooseph & Granger Sutton & Douglas B Rusch & Aaron L Halpern & Shannon J Williamson & Karin Remington & Jonathan A Eisen & Karla B Heidelberg & Gerard Manning & Weizhong Li & Lukasz Jaroszewski , 2007. "The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families," PLOS Biology, Public Library of Science, vol. 5(3), pages 1-35, March.
    6. Kelly J. Whaley-Martin & Lin-Xing Chen & Tara Colenbrander Nelson & Jennifer Gordon & Rose Kantor & Lauren E. Twible & Stephanie Marshall & Sam McGarry & Laura Rossi & Benoit Bessette & Christian Baro, 2023. "O2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    7. Angelina Beavogui & Auriane Lacroix & Nicolas Wiart & Julie Poulain & Tom O. Delmont & Lucas Paoli & Patrick Wincker & Pedro H. Oliveira, 2024. "The defensome of complex bacterial communities," Nature Communications, Nature, vol. 15(1), pages 1-15, December.

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