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 by 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.
Highlights
The subsurface biosphere harbors an enormous portion of the Earth’s microbiome
PhyloChip G3, quantitative PCR (qPCR) and fluorescence in situ hybridization (FISH) revealed the predominance of Archaea in the subsurface biofilms samples from Muhlbacher Schwefelquelle (MSI-BF) and Sippenauer Moor (SM-BF) samples (Table 1)
QPCR showed that .97% of all 16S rRNA genes in Muhlbacher Schwefelquelle at Isling (MSI)-BF and Sippenauer Moor biofilm (SM-BF) samples were archaeal, but only 26% in the surface string-of-pearls community (SOPC)
Summary
The subsurface biosphere harbors an enormous portion of the Earth’s microbiome. It is estimated, that approximately 2.961029 and 2.5–2561029 prokaryotic cells reside below the surface layer in marine and terrestrial sediments, respectively [1,2]. Sulfidic springs are rather rare (10% of all terrestrial aquifers; [7]), they contain excellent energy sources for subsurface and surface life: Once mixed with oxygen as terminal electron acceptor nutrients from sulfidic subsurface aquifers can lead to high amounts of biomass in the outflow region [8,9,10,11,12,13,14] These biomasses, which are mostly complex microbial communities such as bacterial or archaeal/bacterial biofilms, have been the focus of many studies, yet the oxygen-free subsurface environment of sulfidic springs is lacking information concerning its biodiversity and variation over geographical location [15]
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