Uncultivated archaea and associated bacteria in untapped biotopes

Despite the almost ubiquitous nature of Archaea about the planet, and an ever-increasing appreciation for the contribution they make to Earth’s energy cycles, the distribution and metabolic potential of these microorganisms remain poorly understood due to the lack of cultivated representatives. The overarching objective of this study was to significantly bolster the current understanding of the occurrence and function of archaea, and co-existing bacteria, in two so-far poorly explored biotopes. To date, archaea have yet to be isolated and cultivated under laboratory conditions from either of these environments, which necessitated the use of metagenomic and other emerging molecular approaches available in the field of microbial ecology. The first biotope investigated, spacecraft assembly cleanrooms, are strongly influenced by rigorous cleaning regimens, controlled humidity, and scarce nutrients. While the occurrence of Thaumarchaeota had already been reported in these environments, their origin and mode of ingress remained unknown and unexplored. Over the course of this investigation, Thaumarchaeota were identified to persist on human skin, and human activity was shown to be a source of the observed archaeal presence in spacecraft assembly facilities. In a parallel vein, a viability-dependent assay coupled to molecular microbiome profiling enabled the differentiation of living fraction of bacteria from the entire community profile. The results of these analyses represent a milestone in cleanroom monitoring, as they suggest that the viable fraction of the spacecraft assembly cleanroom microbiome accounts for a mere tenth of its total abundance and diversity. The second biotope investigated in this study were subsurface environments that are accessible through anaerobic, sulfidic springs. It had previously been demonstrated that, with regard to biodiversity and metabolic potential, the subsurface remains poorly characterized and thus represents a great reservoir for mining novel microbial lineages. More specifically, the upwelling of sulfidic springs near Regensburg has been shown to source extensive quantities of nearly mono-species biofilms of the recently discovered SM1 Euryarchaeon (95% purity). The findings of this investigation, for the first time ever, demonstrated that bacterial contingent of this primarily archaeal biome was actively taking part in sulfate-reduction. Comparative microbiome analysis of biofilms from two geographically distinct spring locations enabled the observation of extensive variation between communities without substantial change in their function. To resolve the metabolic capability and phylogenomic position of the SM1 Euryarchaeon, metagenomic approaches were utilized in concert with other state-of-theart techniques. The results of these efforts evidenced a distinct pyhlogenetic position of the SM1 Euryarchaea, for which the name “Candidatus Altiarchaeum hamiconnexum” (candidatus family “Altiarchaeaceae”, candidatus order “Altiarchaeales”) is proposed. The genome of this novel taxon was shown to encode the enzymes responsible for a novel, archaeal acetyl-CoA pathway free of Factor420. Such a pathway affords these double-membraned archaea to grow anaerobically, most likely via acetate oxidation. Genes for the genesis of the biofilms mediated by nano-grappling hooks and diverse extracellular polysaccharides were identified in the genome. It is hypothesized that the biofilm provides a competitive advantage with respect to fitness, as they help to outcompete other subsurface microorganisms by filtering and capturing nutrients that seep into the groundwater. The findings of the many investigations that make up this thesis significantly contributed to today’s much enhanced understanding of archaea and the roles they play alongside the co-occurring bacteriome in two distinct biotopes. At the same time, the results represent a remarkable example of how well the ecophysiology of novel archaeal lineages can be examined with current state-of-the-art technologies.