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Abstract As Earth’s principal reservoir of organic carbon and microbial biomass, the deep subsurface hosts microorganisms capable of mobilizing this once-sequestered carbon. Contrary to standard assumptions of eukaryotic scarcity, this study documents abundant fungal communities, ranging from 4.2 × 103 to 6.8 × 103 fungal cells ml−1, across a methane-producing organic-rich shale 247–556 meters below the surface. Although fungal:bacterial cell ratios ranged from 1:7028 to 1:713, application of biomass conversion factors developed for oceanic systems yielded a median fungal:bacterial biomass ratio of 1:4.7. 16S ribosomal ribonucleic acid (rRNA) gene amplicons revealed bacterial and archaeal communities mirroring those found in well-characterized extremophilic, carbon-degrading environments, while sequencing of 18S rRNA gene and internal transcribed spacer rRNA spacer amplicons collectively identified a eukaryotic hotspot with 689 fungal operational taxonomic units across six phyla. The dominant fungal classes, Agaricomycetes and Dothideomycetes, are well-established degraders of recalcitrant carbon compounds at the surface, suggesting they may similarly contribute to organic matter degradation and ecosystem maintenance in the subsurface. Cultivation and isolation efforts yielded 205 fungal strains, including 13 candidate novel taxa, underscoring the deep subsurface as an underexplored eukaryotic habitat. Stable carbon isotopes indicate methane is predominantly generated via microbial conversion of the fossil carbon, while water isotopes suggest in situ geochemical conditions have been relatively stable since the Late Pleistocene, with subglacial recharge as a plausible mechanism for microbial introduction. Collectively, these findings suggest that fungi are underrecognized contributors to organic matter transformation and functional diversity in the deep biosphere, revealing a critical gap in our understanding of deep subsurface ecosystem processes. 

Fungal communities are primary decomposers of detritus, including coarse woody debris (CWD). We investigated the succession of fungal decomposer communities in CWD through different stages of decay in the wide-ranging and early successional tree species Populus grandidentata (bigtooth aspen). We compared shifts in fungal communities over time with concurrent changes in substrate chemistry and in bacterial community composition, the latter deriving from an earlier study of the same system. We found that fungal communities were highly dynamic during the stages of CWD decay, rapidly colonizing standing dead trees and gradually changing in composition until the late stages of decomposed wood were integrated into soil organic matter. Fungal communities were most similar to neighboring stages of decay, with fungal diversity, abundance, and enzyme activity positively related to percent nitrogen, irrespective of decay class. In contrast to other studies, we found that species diversity remained unchanged across decay classes. Differences in enzyme profiles across CWD decay stages mirrored changes in carbon recalcitrance, as B-D-xylosidase, peroxidase, and Leucyl aminopeptidase activity increased as decomposition progressed. Finally, fungal and bacterial gene abundances were stable and increased, respectively, with the extent of CWD decay, suggesting that fungal-driven decomposition was associated with shifting community composition and associated enzyme functions rather than fungal quantities. 

Much of the diversity of microbes from natural habitats, such as soil and freshwater, comprise species and lineages that have never been isolated into pure culture. In part, this stems from a bias of culturing in favor of saprotrophic microbes over the myriad symbiotic ones that include parasitic and mutualistic relationships with other taxa. In the present study, we aimed to shed light on the ecological function and morphology of the many undescribed lineages of aquatic fungi by individually isolating and sequencing molecular barcodes from 127 cells of host-associated fungi using single-cell sequencing. By adding these sequences and their photographs into the fungal tree, we were able to understand the morphology of reproductive and vegetative structures of these novel fungi and to provide a hypothesized ecological function for them. These individual host-fungal cells revealed themselves to be complex environments despite their small size; numerous samples were hyper-parasitized with other zoosporic fungal lineages such as Rozellomycota. 

Synopsis What are the implications of misunderstanding sex as a binary, and why is it essential for scientists to incorporate a more expansive view of biological sex in our teaching and research? This roundtable will include many of our symposium speakers, including biologists and intersex advocates, to discuss these topics and visibilize the link between ongoing reification of dyadic sex within scientific communities and the social, political, and medical oppression faced by queer, transgender, and especially intersex communities. As with the symposium as a whole, this conversation is designed to bring together empirical research and implementation of equity, inclusion, and justice principles, which are often siloed into separate rooms and conversations at academic conferences. Given the local and national attacks on the rights of intersex individuals and access to medical care and bodily autonomy, this interdisciplinary discussion is both timely and urgent. 

ABSTRACT The impacts of microsporidia on host individuals are frequently subtle and can be context dependent. A key example of the latter comes from a recently discovered microsporidian symbiont ofDaphnia, the net impact of which was found to shift from negative to positive based on environmental context. Given this, we hypothesized low baseline virulence of the microsporidian; here, we investigated the impact of infection on hosts in controlled conditions and the absence of other stressors. We also investigated its phylogenetic position, ecology, and host range. The genetic data indicate that the symbiont isOrdospora pajunii, a newly described microsporidian parasite ofDaphnia. We show thatO. pajuniiinfection damages the gut, causing infected epithelial cells to lose microvilli and then rupture. The prevalence of this microsporidian could be high (up to 100% in the lab and 77% of adults in the field). Its overall virulence was low in most cases, but some genotypes suffered reduced survival and/or reproduction. Susceptibility and virulence were strongly host-genotype dependent. We found that North AmericanO. pajuniiwere able to infect multipleDaphniaspecies, including the European speciesDaphnia longispina, as well asCeriodaphniaspp. Given the low, often undetectable virulence of this microsporidian and potentially far-reaching consequences of infections for the host when interacting with other pathogens or food, thisDaphnia–O. pajuniisymbiosis emerges as a valuable system for studying the mechanisms of context-dependent shifts between mutualism and parasitism, as well as for understanding how symbionts might alter host interactions with resources. IMPORTANCEThe net outcome of symbiosis depends on the costs and benefits to each partner. Those can be context dependent, driving the potential for an interaction to change between parasitism and mutualism. Understanding the baseline fitness impact in an interaction can help us understand those shifts; for an organism that is generally parasitic, it should be easier for it to become a mutualist if its baseline virulence is relatively low. Recently, a microsporidian was found to become beneficial to itsDaphniahosts in certain ecological contexts, but little was known about the symbiont (including its species identity). Here, we identify it as the microsporidiumOrdospora pajunii. Despite the parasitic nature of microsporidia, we foundO. pajuniito be, at most, mildly virulent; this helps explain why it can shift toward mutualism in certain ecological contexts and helps establishO. pajuniiis a valuable model for investigating shifts along the mutualism-parasitism continuum.