The Ohio State University
Fungi are increasingly recognized as active members of marine microbiomes, yet their roles in ocean carbon cycling remain far less understood than those of bacteria, archaea, and phytoplankton. Our lab studies how marine fungi participate in the transformation of particulate organic matter, especially complex polymers that are difficult to degrade.
Recent work from the eastern tropical North Pacific oxygen minimum zone (Peng and Valentine 2025) shows that fungi may play a disproportionately important role in polymer degradation. Although fungi represented a very small fraction of the total DNA and RNA pool, they accounted for a large fraction of expressed extracellular carbohydrate-active enzymes. In particular, fungal GH7 genes were highly expressed and may contribute to the degradation of cellulose- and chitosan-like polymers derived from marine particles, phytoplankton, zooplankton, and bacteria.
By combining metagenomics, metatranscriptomics, cultivation, and comparative genomics, we investigate how fungal hydrolytic activities influence carbon remineralization and how these activities may be coupled to nitrogen cycling in oxygen-deficient marine environments.
Nitrogen is a limiting element for biological productivity and has a strong influence on cycles of many other elements, including carbon, sulfur, and phosphorus. The transformation of different forms of nitrogen is primarily mediated by microorganisms, either for nitrogen assimilation or to gain energy. Anoxic and hypoxic environments are hot spots for dissimilatory reactions that account for most of the loss of biologically available nitrogen. We combine stable isotope-based techniques and ‘omics methods to investigate the microbial transformation of nitrogen across three connected marine settings: oxygen minimum zones, salt marsh sediments, and seasonally anoxic basin sediments.
Oxygen minimum zones (OMZs): In OMZs, we study microbial nitrogen cycling along steep oxygen gradients. Our work has shown that marine fungi are diverse and active in this environment and may contribute to nitrous oxide production near oxic–anoxic interfaces. We use stable isotope tracer experiments, metabarcoding, metagenomics, and metatranscriptomics to identify the organisms and metabolisms that regulate nitrogen transformations in oxygen-deficient waters.
Salt marsh sediments: Salt marsh sediments are hotspots for nitrogen cycling and can emit N2O, a potent greenhouse gas and ozone-depleting compound. While N2O production in sediments is often attributed to bacteria and archaea, our work asks whether salt marsh sediment fungi are overlooked contributors. We have isolated N2O-producing fungi from North Inlet salt marsh sediments in South Carolina and are examining their physiology, isotopomer signatures, molecular underpinning for N2O production, and environmental significance.
Santa Barbara Basin: We study nitrogen cycling in seasonally anoxic marine sediments. In the Santa Barbara Basin, our work examines how denitrification, anammox, DNRA, and N2O production respond to seasonal anoxia, nitrate availability, and sediment organic matter. These sediment studies help us understand how low-oxygen environments regulate both fixed nitrogen loss and fixed nitrogen retention.
Marine biogeochemical processes emerge from communities rather than from organisms acting alone. We investigate how competition, cross-feeding, parasitism, and metabolic cooperation between fungi and prokaryotes influence the degradation of organic matter and the cycling of carbon and nitrogen.
In the eastern tropical North Pacific oxygen minimum zone, size-fractionated community analyses indicated that putative fungal-prokaryotic interactions occur primarily on particles. Network analysis identified both positive and negative associations and implicated a particle-associated Cladosporium lineage as a putative keystone taxon (Thompson et al., 2024). Metatranscriptomic evidence further suggests a potential division of labor in which bacterial chitin deacetylation supplies chitosan for degradation by highly expressed fungal GH7 enzymes (Peng and Valentine, 2025).
Across salt and brackish marshes, the structure of these associations changes with habitat. Brackish-marsh sediments were dominated by negative fungal-prokaryotic connections consistent with resource competition, whereas surface waters contained many positive connections consistent with cross-feeding. In salt-marsh communities, positive associations between Ascomycota and sulfate-reducing Desulfobacteria suggest cooperation during complex organic matter degradation, while negative associations between chytrid fungi and Cyanobacteriota are consistent with parasitism (Thompson and Peng, 2025). We use these patterns to generate hypotheses that can be tested through cultivation, controlled experiments, and activity-based assays.
Marine fungi are often studied using tools and reference databases developed for terrestrial fungi, which can obscure the true diversity and evolutionary history of fungi in the ocean. Our lab works to improve detection, cultivation, and genomic characterization of marine fungi from open ocean and coastal environments.
We study the ecology of planktonic fungi, including their distribution across oxygen gradients, particle size fractions, and salinity gradients. In estuarine systems, our work shows that early diverging fungal lineages can be abundant and ecologically important, especially in brackish marsh sediments. These lineages are often missed or poorly resolved by commonly used fungal markers, highlighting the need for improved molecular approaches (Thompson et al. 2025).
We are also investigating the evolution of fungi isolated from the open ocean. Most fungal isolates with sequenced genomes come from terrestrial environments, leaving major gaps in our understanding of marine fungal evolution. Comparative genomics of marine isolates, including Rhodotorula sphaerocarpa ETNP2018, suggests that some open ocean fungi are evolutionarily and functionally distinct from their terrestrial counterparts, with genomic features consistent with adaptation to oligotrophic marine environments (Lane et al. 2023).
Together, these projects ask how fungi have adapted to marine environments, how their genomes encode marine lifestyles, and how their ecological roles differ from those of terrestrial fungi.