Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

Yelton, Alexis P.; Comolli, Luis R.; Justice, Nicholas B.; Castelle, Cindy; Denef, Vincent J.; Thomas, Brian C.; Banfield, Jillian F.

doi:10.1186/1471-2164-14-485

Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

Journal Article · Tue Jan 01 04:00:00 EST 2013 · BMC Genomics

DOI:https://doi.org/10.1186/1471-2164-14-485· OSTI ID:1626419

Yelton, Alexis P. ^[1]; Comolli, Luis R. ^[2]; Justice, Nicholas B. ^[3]; Castelle, Cindy ^[2]; Denef, Vincent J. ^[4]; Thomas, Brian C. ^[4]; Banfield, Jillian F. ^[5]

Univ. of California, Berkeley, CA (United States). Dept of Environmental Science, Policy, and Management; DOE/OSTI
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division
Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
Univ. of California, Berkeley, CA (United States). Dept of Environmental Science, Policy, and Management

Background: Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order. Results: We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis. Conclusion: The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231; FG02-05ER64134

OSTI ID:: 1626419

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Journal Issue: 1 Vol. 14; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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Biotechnology & Applied Microbiology
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Iron oxidation
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Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

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