Chytrids (phylum Chytridiomycota) are zoosporic fungi that play key roles as parasites of aquatic microorganisms, yet they are understudied and genomic resources for algal-infecting chytrids remain scarce. Here, we present the first comparative genomic analysis of multiple isolates of a single chytrid species (order Rhizophydiales) infecting the cyanobacterium Planktothrix agardhii. Isolates were collected from Sandusky Bay, Lake Erie, across two bloom years (2018 and 2019). Using single cell sequencing and metagenomic assembly, we generated individual genomes averaging 15.36 ± 0.12 Mbp in size with 75

Aquatic fungi play critical roles in carbon cycling through complex interactions with dissolved organic matter (DOM). However, their community associations with DOM across reservoir ecosystems remain poorly understood. This study investigated the relationships between fungal community structure and chromophoric DOM across Japanese reservoirs based on fungal sequencing and the optical properties of DOM. Fungal α-diversity showed positive correlations with DOM quantitative indicators (absorption coefficients and fluorescence peaks) and quality indicators such as peak M: T (ratio of humic-like to protein-like fluorescence), suggesting that greater DOM quantity and humification were associated with higher fungal α-diversity across reservoirs. Permutational multivariate analysis of variance based on Jaccard dissimilarity revealed that DOM humification indicators were associated with fungal community β-diversity in univariate models; for example, humification degree (peak M: T) explained 2.8

Parasitic oomycetes are ubiquitous in marine ecosystems, yet their phylogeny remains poorly characterized. While metabarcoding confirms their high diversity, the lack of formal descriptions leaves most of the sequences unclassified. In this study, we describe Miracula nipponica sp. nov., a parasitic oomycete from Sagami Bay, infecting the bloom-forming diatom Leptocylindrus sp. Phylogenetic analysis based on 18S rDNA sequences showed that all isolated strains were placed as a distinct lineage within the genus Miracula. Detailed microscopic observations revealed the formation of primary and secondary zoospores in the new species life cycle, with an occasional cyst cluster formation at the orifice of the discharge tube. Notably, the encysted stage demonstrated a long-term viability in the absence of hosts. Finally, laboratory experiments revealed a broad host range with low infection prevalence that includes other common diatoms from the study area. As the first parasitic oomycete infecting phytoplankton described in Japanese coastal waters, this study highlights their overlooked diversity and widespread presence of fungi-like organisms in marine ecosystems.

Aquatic fungi play an important role in the material cycling, yet the factors structuring the spatial distribution of aquatic fungal communities remain poorly understood. In this study, we investigated fungal community composition across 50 reservoirs in Japan using DNA metabarcoding. Chytridiomycota (chytrids) dominated fungal communities in many reservoirs and constituted a core component of fungal assemblage. Notably, diatom-parasitic taxa were detected in all reservoirs, indicating their ubiquitous occurrence. In contrast, rare and transient components were mainly composed of Dikarya (Ascomycota and Basidiomycota), likely influenced by stochastic processes, such as episodic inputs from terrestrial habitats. Variation partitioning showed that environmental, spatial, and host-related factors each explained only a small proportion of variation in both the total fungal community and chytrids, with spatial effects being slightly stronger for total fungi, whereas environmental and host-related factors contributed relatively more to chytrid communities. Our results indicate reservoir fungal communities are characterized by a ubiquitous chytrid core and substantial unexplained variation reflecting stochastic and within-lake processes.

Zoosporic eufungi (i.e., chytrids, sensu lato) comprise a phylogenetically and ecologically diverse guild of early diverging fungal phyla (Chytridiomycota, Monoblepharomycota, Neocallimastigomycota, Blastocladiomycota, Sanchytriomycota, Aphelidiomycota, Cryptomycota/Rozellomycota, and Olpidiomycota). While most circumscribed zoosporic eufungi function as decomposers of recalcitrant materials, such as pollen, chitin, and keratin, many taxa are parasites of algae and other microorganisms, land plants, and animals in terrestrial and aquatic ecosystems. The effects of parasitic chytrids on their hosts—and the downstream ecological consequences—are generally poorly understood, particularly when compared to better characterized host-parasite systems in the Dikarya. The most infamous chytrid fungus is the amphibian pathogen Batrachochytrium dendrobatidis, and its discovery and effect on global amphibian populations spurred a renewed interest in the diversity of zoosporic eufungi. Increasingly, research in freshwater and marine habitats has demonstrated that zoosporic eufungi regulate algal communities and serve as an important link between trophic levels in aquatic food webs. As pathogens of land plants, zoosporic eufungi can result in yield losses directly both as a pathogen or by serving as a vector for plant viruses. This chapter explores the diversity of chytrid fungi sensu lato in light of recent reclassifications with an emphasis on species that are parasites and pathogens of a variety of hosts ranging from autotrophs (algae and land plants), unicellular microorganisms (e.g., amoebae, flagellated heterotrophs), and invertebrate and vertebrate animals. The ecosystem dynamics of zoosporic eufungi parasites and pathogens are discussed, highlighting their impact on agriculture and industry.

In Kochi Prefecture, Japan, Passalora nattrassii, cause of eggplant leaf mold, is the most prevalent pathogen of eggplant because of its fungicide resistance. Sequencing analysis revealed amino acid substitutions including SdhB-H268C, SdhB-H268R, SdhB-I270V, SdhC-N83S, and SdhC-H149R. In efficacy trials of SDHI fungicides, isofetamid and pyraziflumid were effective against all five mutants except for SdhB-I270V and SdhB-H268C, respectively. Pyribencarb provided higher efficacy than azoxystrobin against QoI-resistant isolates with cytb-G143A. These results indicate that different mutations at the target sites are responsible for the different sensitivity patterns in P. nattrassii.

Similar to the term algae, the term fungi does not refer to a monophyletic group, but instead refers to a polyphyletic group with shared traits that evolved due to ecological niche similarity. As such, fungi are eukaryotic organisms that generally take up nutrients from their surrounding environment by absorbing and transporting them into the cell for further use. This sets them apart from animals and protozoans, which take food up into their bodies for digestion, and from autotrophic plants and protists, which produce complex carbohydrates by absorbing and reducing carbon dioxide. However, some fungal groups, such as Aphelidiomycota and Rozellomycota, are also capable of phagocytosis.

Stephanodiscus binderanus is a bloom-forming diatom abundant in winter and persisting into spring in the Laurentian Great Lakes. Climate change impacts these blooms by altering ice cover, turbidity, light penetration, and water temperature. Fungal parasites, especially Chytridiomycota, can suppress phytoplankton growth and alter bloom succession. To address the effects of both biotic and abiotic factors on S. binderanus in the face of a changing climate, we tested a range of temperatures (9.4-24 degrees C) and light intensities (15, 30, 50, 100 mu mol m-2 s-1) on infected and uninfected cultures. We also conducted an RNAseq analysis of both host and parasite across the described environmental parameters. Stephanodiscus binderanus can rapidly adapt to the above conditions, growing slowest at the lowest temperature and under low light, while adjusting its chlorophyll a (Chl a) content in lower light treatments to be more efficient at light harvesting. Chytrid infections were more prevalent at either end of the tested temperature range, despite downregulation of zoospore mitotic cycle genes at elevated temperatures. Elevated temperatures also induced reproductive stress in S. binderanus, marked by downregulation of meiosis-related genes. These effects, combined with nutrient depletion, likely contribute to seasonal declines in diatom populations as green algae and cyanobacteria emerge in late spring and early summer. It is anticipated that host response to lower light availability and the ability of the chytrid to infect under warming waters will contribute to a decline in filamentous diatom biomass in Lake Erie, especially as climate change increases the frequency of ice-free winters.

This study describes a novel parasitic fungus that infects the benthic and epiphytic dinoflagellate Ostreopsis cf. ovata during a coastal microalgal bloom in the Mediterranean Sea. Microscopic observations revealed a distinctive, irregularly shaped zoosporangium during the mature stages and spherical, posteriorly uniflagellate zoospores. This supports its affiliation within the phylum Chytridiomycota. Concatenated phylogenetic analysis based on 18S, 5.8S, and 28S ribosomal DNA placed the fungus within the order Lobulomycetales, thus establishing it as a distinct lineage separate from previously described species. Additional phylogenetic analyses including environmental DNA sequences revealed a close phylogenetic relationship with previously reported freshwater sequences. This suggests a possible ecological link between marine and freshwater habitats. Cross-infection experiments confirmed the ability of the fungus to infect healthy cells of both dinoflagellate and diatom species, rendering it the first known chytrid with a broad phytoplankton host range. Additionally, it is the first member of this order known to parasitize dinoflagellate species and only the second known to parasitize marine algae. Infection prevalence was higher in dinoflagellates than in diatoms. Furthermore, under laboratory conditions, the chytrid also developed zoosporangia on pollen grains, using them as an alternative nutrient source. Based on these findings, this study describes a new genus and species of zoosporic fungus, Algophthora mediterranea, within the order Lobulomycetales.

Chytridiomycota (chytrids) include a wide range of taxa with diverse trophic strategies, ranging from obligate parasites to saprotrophs. However, their taxonomic and functional diversity, particularly among those attached to phytoplankton, is often overlooked in field surveys given their morphological similarity. In this study, we examined the relationships between two large desmids (Micrasterias hardyi and Staurastrum dorsidentiferum) and associated chytrids in Lake Biwa. The analysis of spatiotemporal distribution revealed contrasting effects: S. dorsidentiferum's population dynamics were significantly influenced by chytrids, whereas M. hardyi remained unaffected. Single-spore DNA analysis identified both parasitic and saprotrophic chytrids on S. dorsidentiferum, but only saprotrophic chytrids on M. hardyi. Our findings indicate that chytrids attached to phytoplankton show taxonomic and functional diversity and do not always control host population dynamics. However, considering the feeding mode and substrate specificity of chytrids is important for elucidating their impact on phytoplankton dynamics and material flows in lakes.

To date, standard rRNA marker genes have had limited success in resolving the phylogeny of the phylum Chytridiomycota. Whereas the conserved and easily alignable ribosomal small subunit 18S rRNA gene had problems resolving nodes relating orders, the internal transcribed spacer 2 (ITS2) has been claimed to not be alignable for this group of organisms. Although the ITS2 is a fast-evolving locus, its secondary structure is well conserved. To improve the accuracy and robustness of Chytridiomycota phylogeny, in this study, we attempt, for the first, time to reconstruct an ITS2 sequence-structure phylogeny using the primary sequence and the secondary structure information simultaneously in inferring alignments and trees. Although currently only possible for a fraction of the available data, we show a well-supported ITS2 tree for selected organisms. The results are promising for further exploration of the large number of available ITS2 sequences.

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 of Daphnia , 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 is Ordospora pajunii , a newly described microsporidian parasite of Daphnia . We show that O. pajunii infection 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 American O. pajunii were able to infect multiple Daphnia species, including the European species Daphnia longispina , as well as Ceriodaphnia spp. 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, this Daphnia–O. pajunii symbiosis 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. IMPORTANCE The 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 its Daphnia hosts in certain ecological contexts, but little was known about the symbiont (including its species identity). Here, we identify it as the microsporidium Ordospora pajunii . Despite the parasitic nature of microsporidia, we found O. pajunii to be, at most, mildly virulent; this helps explain why it can shift toward mutualism in certain ecological contexts and helps establish O. pajunii is a valuable model for investigating shifts along the mutualism-parasitism continuum.

QuestionsNumerous studies on community assembly processes have been conducted in natural ecosystems. However, we know little about community assembly processes in human-dominated urban ecosystems. Here, we asked: (1) how are the composition and functional diversity of native and exotic plant species shaped by local environment and landscape factors across urban vacant lots; and (2) how is microbial (bacterial and fungal) community composition influenced by the local environment, landscape factors, and plant species composition across urban vacant lots?LocationWe investigated 69 urban vacant lots in Yokohama, Japan.MethodsBy using a variation partitioning approach, we examined the relative importance of local environmental and landscape factors (including land use and spatial structure) in explaining variation in plant species composition and functional diversity of native or exotic species. We also explored the relative importance of local environmental and landscape factors, and plant species composition in explaining variation in microbial community composition.ResultsThe spatial structure of vacant lots determined the species composition and functional diversity of plant communities, suggesting that plant community assembly is determined by dispersal limitation. However, the functional diversity of the exotic species varied randomly, which reduced the relative importance of the spatial structure of vacant lots. Plant species composition as well as the spatial structure of vacant lots were the important drivers of the composition of soil microbial communities, despite a higher proportion of unexplained variation in their composition. Finally, we found an essential contribution of earthmoving methods in explaining the variations in both plant and microbial community composition.ConclusionPlant and microbial community composition would be largely determined by dispersal limitation across urban vacant lots. Understanding urban community assembly is critical for predicting plant and microbial communities that play an essential role in regulating urban ecosystem functioning and services. We know little about community assembly processes in human-dominated urban ecosystems. Here, we showed that plant and microbial community composition would be largely determined by dispersal limitation across urban vacant lots. Understanding urban community assembly is critical for predicting plant and microbial communities that play an essential role in regulating urban ecosystem functioning and services.image

AbstractRecent advances in fungal genome sequencing have dramatically altered our understanding of the phylogeny and evolution of Fungi. However, there are still many poorly studied obligate parasitic or symbiotic fungi for which we lack any genomic information or knowledge of where they fit in the fungal phylogeny.Ancylistes,an endoparasite of desmid green algae, is such an understudied fungal genus. This genus has been taxonomically placed in the group of arthropod pathogens and saprobes, Entomophthoromycotina in Zoopagomycota. Understanding the phylogenetic position ofAncylistesprovides insights into the nutritional evolution of Zoopagomycota, which is primarily composed of animal-associated fungi. In this study, we found and cultivatedAncylistes closteriiwith its hostClosteriumsp. and sequenced its genome to investigate its phylogenetic position and evolution. Phylogenetic analyses using rDNA and genome-scale datasets showed thatA. closteriiwas sister to other Entomophthoromycotina fungi, confirming the taxonomic position ofAncylistes. Despite the ecological distinctiveness betweenAncylistesand other Entomophthoromycotina fungi, our comparative genomic analyses revealed many shared traits of these fungi such as lineage-specific subtilases and hybrid histidine kinases.Ancylistesalso possessed unique genes among Zoopagomycota fungi, such as plant cell wall degrading enzymes which could be important for infection of algae.SignificanceImproved taxon sampling is important for inferring a robust phylogeny of Fungi. However, there are still poorly studied obligate parasitic taxa whose DNA sequencing is challenging, especially in Zoopagomycota, one of the early diverging lineages of Fungi. This study focused on a long-neglected algal parasite,Ancylistes closterii, which belongs to the arthropod-associated group, Entomophthoromycotina. We rediscoveredA. closteriiand established a dual culture of fungus and its host alga, which enabled the first molecular analysis of this enigmatic parasite. Our results provide new insights into the nutritional evolution of primarily animal-associated Zoopagomycota.

Cladochytriales comprises a taxonomic order and lineage of chytrid fungi that are primarily saprobes of organic matter in aquatic and terrestrial ecosystems. The order contains species from 12 genera, though molecular confirmations of almost all type species are lacking, and many genera are considered polyphyletic. We conducted phylogenetic analyses of ribosomal RNA genes and developmental morphology of Cladochytriales isolates from the Collection of Zoosporic Eufungi at the University of Michigan and noted some strains that were distinct from described genera. In our phylogenetic analysis, Endochytriaceae represented by only one strain of Endochytrium ramosum was sister to Septochytriaceae while the incertae sedis lineage formed by the new species Thomasia carolinae was sister to Nowakowskiellaceae . Additionally, the phylogenetic relatedness of the other two new species, Dogmamyces elongatus and Allochytrium aureum , was also highly supported. A thorough revision of the order is needed because some genera, such as Catenochytridium and Nephrochytrium , remain polyphyletic or paraphyletic. In addition to indicating these problems, our updated phylogeny supports the description of two new genera and three new species and thereby begins to bring the knowledge of the Cladochytriales up to date.

Recent advances in fungal genome sequencing have dramatically altered our understanding of the phylogeny and evolution of Fungi. However, there are still many poorly studied obligate parasitic or symbiotic fungi for which we lack any genomic information or knowledge of where they fit in the fungal phylogeny. Ancylistes, an endoparasite of desmid green algae, is such an understudied fungal genus. This genus has been taxonomically placed in the group of arthropod pathogens and saprobes, Entomophthoromycotina in Zoopagomycota. Understanding the phylogenetic position of Ancylistes provides insights into the nutritional evolution of Zoopagomycota, which is primarily composed of animal-associated fungi. In this study, we found and cultivated Ancylistes closterii with its host Closterium sp. and sequenced its genome to investigate its phylogenetic position and evolution. Phylogenetic analyses using rDNA and genome-scale datasets showed that A. closterii was sister to other Entomophthoromycotina fungi, confirming the taxonomic position of Ancylistes . Despite the ecological distinctiveness between Ancylistes and other Entomophthoromycotina fungi, our comparative genomic analyses revealed many shared traits of these fungi such as lineage-specific subtilases and hybrid histidine kinases. Ancylistes also possessed unique genes among Zoopagomycota fungi, such as plant cell wall degrading enzymes which could be important for infection of algae. Significance Improved taxon sampling is important for inferring a robust phylogeny of Fungi. However, there are still poorly studied obligate parasitic taxa whose DNA sequencing is challenging, especially in Zoopagomycota, one of the early diverging lineages of Fungi. This study focused on a long-neglected algal parasite, Ancylistes closterii , which belongs to the arthropod-associated group, Entomophthoromycotina. We rediscovered A. closterii and established a dual culture of fungus and its host alga, which enabled the first molecular analysis of this enigmatic parasite. Our results provide new insights into the nutritional evolution of primarily animal-associated Zoopagomycota. ### Competing Interest Statement The authors have declared no competing interest.

IntroductionMicrobial communities are important components of glacier and snowpack ecosystems that influence biogeochemical cycles and snow/ice melt. Recent environmental DNA surveys have revealed that chytrids dominate the fungal communities in polar and alpine snowpacks. These could be parasitic chytrids that infect snow algae as observed microscopically. However, the diversity and phylogenetic position of parasitic chytrids has not been identified due to difficulties in establishing their culture and subsequent DNA sequencing. In this study, we aimed to identify the phylogenetic positions of chytrids infecting the snow algae, Chloromonas spp., bloomed on snowpacks in Japan.MethodsBy linking a microscopically picked single fungal sporangium on a snow algal cell to a subsequent sequence of ribosomal marker genes, we identified three novel lineages with distinct morphologies.ResultsAll the three lineages belonged to Mesochytriales, located within “Snow Clade 1”, a novel clade consisting of uncultured chytrids from snow-covered environments worldwide. Additionally, putative resting spores of chytrids attached to snow algal cells were observed.DiscussionThis suggests that chytrids may survive as resting stage in soil after snowmelt. Our study highlights the potential importance of parasitic chytrids that infect snow algal communities.

Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.

Kickxellomycotina encompasses two fungal groups: a saprobic group in excrement and soil and an arthropod gut-inhabiting group. The evolutionary transition between these two lifestyles is unclear due to the lack of knowledge on intermediate forms and lifestyles. Here, we describe a new species, Unguispora rhaphidophoridarum, that was isolated from the excrement of cave crickets (Rhaphidophoridae) in Japan. This species has a novel lifestyle that is intermediate between the saprobic and gut-inhabiting groups. The new genus Unguispora is a member of the Kickxellales and characterized by the sterile appendages born on the sporocladium and by the claw-like ornamentation of the sporangiole. Phylogenetic analysis based on 18S and 28S nuclear ribosomal DNA showed that this fungus is distinct from all known kickxellalean genera and is sister to Linderina. The sporangiospore of the new species germinated only in anaerobiosis and grew in a yeast-like form. The yeast-like cells, defined as "secondary spores," germinated into hyphae in aerobiosis. In the alimentary tract of cave crickets, the sporangiola are attached to the proventriculus (foregut) by the claw-like ornamentation and multiplicate in the same yeast-like form as under culture. We introduce a new term, "amphibious fungi," to describe fungi that have two life stages, one outside and the other inside the host gut, like U. rhaphidophoridarum. The discovery of an amphibious fungus in Kickxellales, which was formerly considered to be only saprobic, suggests that Kickxellomycotina has evolved in association with the animal gut.

A new chytrid genus and species was isolated and cultured from samples obtained in the Baltic Sea during a dinoflagellate bloom event. This species is characterized by having a spherical sporangium without papillae and zoospores of 2-3 mu m in diameter that are released through 3 discharge pores. Molecular phylogeny based on ribosomal operon showed its sister position to the Dinomyces cluster in Rhizophydiales. Zoospores lack fenestrated cisternae but contain a paracrystalline inclusion, found in a Rhizophydiales representative for the first time. Additionally, the kinetid features are uncommon for Rhizophydiales and only observed in Dinomyces representatives so far. These morphological features and its phylogenetic relationships justify the description of the new genus and speciesParadinomyces triforaminorum gen. nov. sp. nov. belonging to the family Dinomycetaceae. The chytrid was detected during a high-biomass bloom of the dinoflagellate Kryptoperidinium foliaceum. Laboratory experiments suggest this species is highly specific and demonstrate the impact it can have on HAB development. The chytrid co-occurred with three other parasites belonging to Chytridiomycota (Fungi) and Perkinsea (Alveolata), highlighting that parasitic interactions are common during HABs in brackish and marine systems, and these multiple parasites compete for similar hosts.