The wetland sulfur microbiome

Wetlands are responsible for about a third of the global annual emission of the potent greenhouse gas methane and are key ecosystems in global carbon cycling and climate change. Sulfur-cycling microorganisms have an important but undervalued role in organic matter degradation and controlling methane emissions from wetlands by diverting the carbon flow away from methane- producing archaea. While a few studies provided first insights into the identity and ecological role of sulfate-reducing bacteria, microorganisms involved in the various individual steps of sulfur cycling in wetlands are under-characterized. A deeper understanding of microbial ecology in wetlands is necessary for assessing how the microbial communities in these vulnerable ecosystems will respond to future climate changes such as rising global temperature. This project thus aims at establishing the first comprehensive overview of the sulfur microbiome in wetlands. Selected research questions that will be addressed are: What is the identity and ecophysiology of microorganisms that reduce or oxidize sulfur compounds of intermediate oxidation states, e.g. sulfite, thiosulfate, tetrathionate, elemental sulfur, for energy generation? What is the physiological interplay between generalists that utilise diverse sulfur compounds of various oxidation states and specialists that utilise only selected sulfur compounds? How is sulfur metabolism in wetland microorganisms linked to complementary utilization of compounds of other element cycles such as carbon, nitrogen, and iron? We will initially draw on available metagenome, metatranscriptome, and supporting biogeochemical data from diverse native wetlands or wetland experiments to establish a genome collection of uncultured sulfur microorganisms and reveal their putative physiological functions and interspecies interactions. Genome-based physiological predictions will be evaluated through monitoring microbial activities in a series of defined soil microcosm experiments by molecular biology, stable isotope probing, and biogeochemical analyses. The combination of modern genome-centric and strain-level Omics approaches with experiments designed to test specific metabolic hypotheses will lead to a better understanding of the identity and distribution of sulfur-cycling microorganisms and the physiological mechanisms that allow them to provide central ecosystem services in the different wetlands.

Wetlands are the largest natural source of methane, a major greenhouse gas. How much methane they emit depends strongly on microorganisms that process sulfur, because an active sulfur cycle can limit methane production. Yet until recently, we lacked a clear picture of who these sulfur-cycling microbes are, how widespread they are, and how they interact with the methane cycle. This project has now provided the most complete prediction of microbial sulfur cycling capacity across the tree of life and different environments on Earth to date. We created a curated catalog of all major genes involved in sulfur metabolism, enabling much more accurate identification of sulfur-metabolizing microbes in environmental DNA. Using this framework, we analyzed tens of thousands of genomes and thousands of metagenomes across diverse environments. The results expanded the known diversity of sulfur-cycling microorganisms and revealed that different habitats host distinct sulfur-processing pathways and microbial groups. A central discovery is the identification of two previously overlooked microbial processes that reshape our understanding of how wetlands recycle sulfur and control methane emissions. First, we uncovered a new microbial energy metabolism, microbial iron oxide respiration coupled to sulfide oxidation (MISO), in which microorganisms oxidize sulfide using solid iron minerals. This process regenerates sulfate in oxygen-free conditions. It helps explain long-standing observations that sulfate reduction remains active for months in wetlands, thereby suppressing methane formation. Second, a microorganism traditionally viewed as a methane oxidizer was isolated and was found to also respire sulfur compounds. It was demonstrated experimentally that methane oxidation and sulfur oxidation are metabolically compatible and can occur simultaneously within a single cell. Through this discovery, a previously unknown group of mixotrophic methane/sulfur-oxidizing bacteria was revealed, which may significantly influence both methane consumption and sulfur recycling in natural and engineered wetlands. Together, these findings show that wetland microbes are far more metabolically versatile and interconnected than previously thought. The project delivers essential tools and new concepts for understanding how the cycling of carbon, sulfur, and iron are connected via microorganisms and how wetlands regulate greenhouse gas emissions in a changing climate.