title: Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm.
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.
authors.affiliation: Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Probst
authors.forename: Hoi-Ying N
authors.initials: HY
authors.lastname: Holman
authors.forename: Todd Z
authors.initials: TZ
authors.lastname: DeSantis
authors.forename: Gary L
authors.initials: GL
authors.lastname: Andersen
authors.forename: Giovanni
authors.initials: G
authors.lastname: Birarda
authors.forename: Hans A
authors.initials: HA
authors.lastname: Bechtel
authors.forename: Yvette M
authors.initials: YM
authors.lastname: Piceno
authors.forename: Maria
authors.initials: M
authors.lastname: Sonnleitner
authors.forename: Kasthuri
authors.initials: K
authors.lastname: Venkateswaran
authors.forename: Christine
authors.initials: C
authors.lastname: Moissl-Eichinger
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000378:metabolism; D018407:Bacterial Physiological Phenomena; D044822:Biodiversity; D018441:Biofilms; D004269:DNA, Bacterial / Q000235:genetics; D050885:Hydrogensulfite Reductase / Q000235:genetics; D017404:In Situ Hybridization, Fluorescence; D060985:Natural Springs / Q000737:chemistry / Q000382:microbiology*; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D050885:Hydrogensulfite Reductase