Abstract
Archaea are usually minor components of a microbial community and dominated by a large and diverse bacterial population. In contrast, the SM1 Euryarchaeon dominates a sulfidic aquifer by forming subsurface biofilms that contain a very minor bacterial fraction (5%). These unique biofilms are delivered in high biomass to the spring outflow that provides an outstanding window to the subsurface. Despite previous attempts to understand its natural role, the metabolic capacities of the SM1 Euryarchaeon remain mysterious to date. In this study, we focused on the minor bacterial fraction in order to obtain insights into the ecological function of the biofilm. We link phylogenetic diversity information with the spatial distribution of chemical and metabolic compounds by combining three different state-of-the-art methods: PhyloChip G3 DNA microarray technology, fluorescence in situ hybridization (FISH) and synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectromicroscopy. The results of PhyloChip and FISH technologies provide evidence for selective enrichment of sulfate-reducing bacteria, which was confirmed by the detection of bacterial dissimilatory sulfite reductase subunit B (dsrB) genes via quantitative PCR and sequence-based analyses. We further established a differentiation of archaeal and bacterial cells by SR-FTIR based on typical lipid and carbohydrate signatures, which demonstrated a co-localization of organic sulfate, carbonated mineral and bacterial signatures in the biofilm. All these results strongly indicate an involvement of the SM1 euryarchaeal biofilm in the global cycles of sulfur and carbon and support the hypothesis that sulfidic springs are important habitats for Earth’s energy cycles. Moreover, these investigations of a bacterial minority in an Archaea-dominated environment are a remarkable example of the great power of combining highly sensitive microarrays with label-free infrared imaging.
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Acknowledgements
Technical assistance by Lauren Tom as well as review and discussion provided by Robert Huber and Reinhard Wirth are much appreciated. Work at University of Regensburg was performed under the DFG grant MO19773–1 given to Christine Moissl-Eichinger. Phylogenetic work at Lawrence Berkeley National Laboratory was performed under the auspices of the U.S. Department of Energy under contract no. DE-AC02–05CH11231. The SR-FTIR and associated imaging work were performed under the Berkeley Synchrotron Infrared Structural Biology (BSISB) Program and the Subsurface Science Scientific Focus Area funded by the U.S. Department of Energy, Office of Science and Office of Biological and Environmental Research through contracts DE-AC02–05CH11231. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the U.S. Department of Energy under contract no. DE-AC02–05CH11231. The authors are grateful to PreSens (Germany, Regensburg) for providing the oxygen dipping probe PSt6 and the Fibox 3, LCD trace. Alexander J Probst was supported by the German National Academic Foundation (Studienstiftung des deutschen Volkes).
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Probst, A., Holman, HY., DeSantis, T. et al. Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm. ISME J 7, 635–651 (2013). https://doi.org/10.1038/ismej.2012.133
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