Earth Sciences Division (ESD) Department of Energy (DOE) Lawrence Berkeley National Laboratory (LBNL)

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Archaeome, Bacteriome in Biofilms

Sources: Dan Hawkes

The Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored, owing to the difficulty in accessing samples. In response, ESD’s Giovanni Birarda and others (including ESD’s Hoi-Ying Holman and Gary Andersen) recently investigated the microbiome relatedness of subsurface biofilms within two sulfidic springs in southeast Germany—springs that have similar physical and chemical parameters and are fed by one deep groundwater current. Because of their unique hydrogeological setting, these springs provided accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon.

The conversion of biofilm to string-of-pearls community in the spring water originating from the subsurface.

Comparative analysis of infrared imaging spectra demonstrated great variation 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 the 16S rRNA gene level, the 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.

The results provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses. 

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Citation: Probs, A.J., G. Birarda, H.-Y. N. Holman, T.Z. DeSantis, G. Wanner, G.L. Andersen, K.P. Alexandra, S. Meck, J. Völkel, H.A. Bechtel, R. Wirth, and C. Moissl-Eichinger (2014), Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacterome in subsurface biofilms that are dominated by the same Archaeal species. PLoS ONE, 9 (6), e99801; DOI: 10.1371/journal.pone.0099801.

Funding Source: BER, BSISB