Ecophysiology of a sulfate-reducing rare biosphere member

Methane emission from peatlands contributes substantially to global warming but is significantly reduced by sulfate reduction, which is fuelled by globally increasing aerial sulfur pollution. However, the biology behind sulfate reduction in terrestrial ecosystems is not well understood. We recently identified a Desulfosporosinus sp. to be an important sulfate reducer in a long-term experimental peatland site, which at the same time represented a member of the `rare biosphere` (0.006% of the total bacterial and archaeal community). Currently, knowledge about the `rare biosphere` is mainly restricted to inventories of 16S rRNA genes, which occur at low abundance in the environment. In particular, information on the genomic content and the ecophysiology of `rare biosphere` members that contribute substantially to biogeochemical processes is virtually absent. In this project, we want to gain insights into the ecophysiology of the rare peatland Desulfosporosinus by (i) studying its genome using selective metagenomics and comparing it to four genomes of distinct pure culture Desulfosporosinus spp., (ii) testing how its metabolic potential is reflected in the substrates that are actually used in situ (fundamental vs. realized niche), (iii) analyzing its main activated pathways involved in energy metabolism, assimilation, and stress response by probing its major transcripts under in situ conditions using selective metatranscriptomics, and (iv) identifying its indispensible nutritional and physicochemical requirements by cultivation. The easily accessible and well- characterized Schlöppnerbrunnen II peatland, which serves as a long-term experimental field site, represents an ideal habitat for studying this `rare biosphere` microorganism and its impact on sulfate reduction. Novel methodological approaches like the combination of DNA stable isotope probing with metagenomics as well as the combination of RNA stable isotope probing with metatranscriptomics will be applied to selectively target this rare microorganism. These tools and the knowledge gained will be of great value to other studies of the under-explored `rare biosphere`, its impact on ecosystems, and general concepts in microbial ecology.

Wetlands are important carbon sinks but at the same time a major global source of the greenhouse gas methane. How wetland microorganisms will respond to global warming and increasing aerial sulphur pollution in the upcoming decades to centuries is one of the largest unknowns in environmental and climate research. Although regarded primarily as methanogenic environments, a hidden sulphur cycle exerts important ecosystem functions in wetlands. Dissimilatory sulphate reduction is thermodynamically favourable relative to methanogenic processes and often occurs in wetlands at high rates, despite low sulphate concentrations. The underlying interspecies resource competition thus effectively controls gross production of methane in wetlands. Our previous work revealed that rare Desulphosporosinus species have the potential to substantially contribute to sulphate reduction in an acidic peatland. Through this project, we have (i) furthered our understanding of sulphate reducer ecophysiology in peatlands, (ii) highlighted the possible interactions and impact of different peat soil microbes during anaerobic carbon degradation under different environmentally relevant conditions, (iii) deciphered the genome of the rare Desulphosporosinus species by a new combination of metagenomic approaches, and (iv) isolated representative peat soil Desulphosporosinus strains in pure culture. In conclusion, we have deepened our knowledge of the ecology of sulphate-reducing microorganisms in peatlands and provide a showcase approach for analysing the ecological impact of members of the rare microbial biosphere on nutrient cycling in other environments.