Antarctica is a continent of extremes, with a myriad of environmental pressures influencing its surprisingly complex and rich microbial communities. With photoautotrophic primary producers almost entirely absent in the hyper-arid soils of Eastern Antarctica, non-photosynthetic carbon fixation processes are predicted to play a significant ecological role. The novel process of atmospheric chemosynthesis, facilitated by high affinity 1h/5 NiFe hydrogenases and form 1E RuBisCO, has been proposed to be the main method of energy supply and primary production across such polar desert landscapes. One bacterial phylum with the genetic capacity to perform atmospheric chemosynthesis is the rare but widespread Candidatus Eremiobacterota, a novel candidate phylum found in typically low abundances of <0.1% in global terrestrial environments.
Access to Eastern Antarctic soils containing a high relative abundance of Ca. Eremiobacterota in 2019, in addition to new insights provided through metagenome-resolved genomics presented a unique opportunity to perform genome informed cultivation attempts on this uncultured clade. Newly designed, highly selective Ca. Eremiobacterota qPCR primers were validated and used to quantify growth in response to a genome informed cultivation strategy, alongside the presence of the atmospheric chemosynthesis associated functional genes 1h/5 NiFe hydrogenase and form 1E RuBisCO.
Over 8 months, qPCR monitoring revealed that enrichment cultures produced an up to 7,000-fold increase in relative abundance of Ca. Eremiobacterota from 0.37% to 25.7%. Building on these exciting results, a molecular beacon probe was produced and validated, using the previously developed, highly specific 16S rDNA Ca. Eremiobacterota primer sequence. The novel fixation-free labelling technique of FISH-TAMB (Fluorescent in situ hybridisation of transcript-annealing molecular beacons) is now being used alongside flow cytometry with the aim to produce the first isolate from this enigmatic novel phylum. Future characterisation of the functionally diverse Ca. Eremiobacterota will not only allow for a greater understanding of microbial dark matter, but also provide new insights into the role of the underexplored process of atmospheric chemosynthesis in global microbial carbon fixation.