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

BMC Genomics

Research Article

Brian C Thomas¹  Vincent J Denef²  Alexis P Yelton³  Jillian F Banfield⁴  Nicholas B Justice⁵  Cindy Castelle⁶  Luis R Comolli⁶ 

[1] Department of Earth and Planetary Sciences, University of California, 94720, Berkeley, CA, USA;Department of Earth and Planetary Sciences, University of California, 94720, Berkeley, CA, USA;Department of Ecology and Evolutionary Biology, University of Michigan, 48109, Ann Arbor, MI, USA;Department of Environmental Science, Policy, and Management, University of California, 94720, Berkeley, CA, USA;Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA;Department of Environmental Science, Policy, and Management, University of California, 94720, Berkeley, CA, USA;Department of Earth and Planetary Sciences, University of California, 94720, Berkeley, CA, USA;Department of Plant and Microbial Biology, University of California, 94720, Berkeley, CA, USA;Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA;

关键词: Metagenomics;    Acid mine drainage;    Thermoplasmatales;    Ferroplasma;    Iron oxidation;    Comparative genomics;   

DOI  :  10.1186/1471-2164-14-485

 received in 2013-02-28, accepted in 2013-07-15,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundMetal 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.ResultsWe 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.ConclusionThe 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.

【 授权许可】

Unknown   
© Yelton et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.