Ca. Eremiobacterota; an enigmatic, versatile bacterial phylum that dominates Antarctic soils.

Candidatus Eremiobacterota (previously WPS-2) is a yet-to-be cultured bacterial phylum.  We recently proposed that members of this group are capable of using the energy derived from atmospheric hydrogen oxidation to fix carbon dioxide via a process coined atmospheric chemosynthesis.

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Our laboratory has been interested in this enigmatic phylum for several years because we believe that the ability to ‘live on air’ allows this usually rare bacterial phylum to thrive and support primary production in the extreme, oligotrophic soils of the Antarctic continent. In our publication, “Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations”, we present unique insights into the metabolic potential and environmental determinants of Ca. Eremiobacterota. We also provide the first microscopic images of these mystery bacteria (see image below).

Visualization of Candidatus Eremiobacteria using fluorescence in-situ hybridisation on cells isolated from an Antarctic desert soil. Photo by Kate Montgomery, UNSW Sydney.

To uncover insights into the metabolic potential of Ca. Eremiobacterota we analysed 72 metagenome-assembled genomes (MAGS) from previously published datasets and newly sequenced metagenomes from Mitchell Peninsula in Eastern Antarctica, where Ca. Eremiobacterota dominates. We found a close phylogenetic affiliation of Ca. Eremiobacterota to phylum Armatimonadota, and separation of Ca. Eremiobacterota into two classes, Ca. Eremiobacteria and the new class Ca. Xenobia, clarifying decades of debate on the classification of Ca. Eremiobacterota. 

Our functional analysis of Ca. Eremiobacterota MAGs revealed that they have the potential for versatile lifestyles, particularly with respect to carbon acquisition. In addition to the widespread potential for atmospheric chemosynthesis within Ca. Eremiobacterota, certain genera (e.g., Ca. Velthaea, Ca. Hemerobacter) have the potential for both anoxygenic photosynthesis and trace gas oxidation-mediated carbon fixation. In addition to these autotrophic capacities, Ca. Eremiobacterota members are genetically capable of degrading a range of different plant- and insect-derived organic compounds such as cellulose, chitin, and even aromatic compounds.

Finally, we performed a meta-analysis using the 16S rRNA gene amplicon sequencing dataset for Australian (AusMicrobiome) and Polar soils (Australian Antarctic Data Centre) with > 60 soil physicochemical factors to identify environmental determinants of Ca. Eremiobacterota in polar soils. Among other factors, pH was found to be the key driver of Ca. Eremiobacterota richness and relative abundance. This supports our hypothesis that phylum Ca. Eremiobacterota are acid-tolerant, with a preference for acidophilic environments and capacities to survive under nutrient poor conditions.

In summary, Ca. Eremiobacterota taxa are highly diverse, metabolically flexible, and specialized. They are armed with a suite of carbon acquisition and acid tolerance mechanisms, which earns them a special niche in terrestrial environments and allows them to dominate the cold, dry, and acidic-oligotrophic conditions of Mitchell Peninsula, in the Windmil Islands region of Eastern Antarctica (Image on banner; Photo taken by Daniel Wilkins of the Australian Antarctic Division).