Title: Coupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species

Abstract

Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed bymore » dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation) and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses.« less

Authors:

Probst, Alexander J. ^[1]; Birarda, Giovanni ^[2]; Holman, Hoi-Ying N. ^[2]; DeSantis, Todd Z. ^[3]; Wanner, Gerhard ^[4]; Andersen, Gary L. ^[2]; Perras, Alexandra K. ^[5]; Meck, Sandra ^[5]; Völkel, Jörg ^[6]; Bechtel, Hans A. ^[7]; Wirth, Reinhard ^[5]; Moissl-Eichinger, Christine ^[5]

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+ Show Author Affiliations

1. Univ. of Regensburg (Germany). Inst. for Microbiology and Archaea Center; Second Genome Inc., South San Francisco, CA (United States). Dept. for Bioinformatics
2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Center for Evironmental Biotechnology
3. Second Genome Inc., South San Francisco, CA (United States). Dept. for Bioinformatics
4. Ludwig Maximilian Univ. of Munich, Munich (Germany). Biozentrum. Dept. of Biology
5. Univ. of Regensburg (Germany). Inst. for Microbiology and Archaea Center
6. Technische Univ. Munchen, Freising (Germany). Center of Life and Food Sciences Weihenstephan. Dept. of Geomorphology and Soil Science
7. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS)

Publication Date:

Fri Jun 27 00:00:00 EDT 2014

Research Org.:

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

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

OSTI Identifier:

1627703

Grant/Contract Number:  

AC02-05CH11231

Resource Type:

Accepted Manuscript

Journal Name:

PLoS ONE

Additional Journal Information:

Journal Volume: 9; Journal Issue: 6; Journal ID: ISSN 1932-6203

Publisher:

Public Library of Science

Country of Publication:

United States

Language:

English

Subject:

54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; Science & Technology - Other Topics