Morphology, Ultrastructure, and Molecular Phylogeny of Aphelidium collabens sp. nov. (Aphelida), a Parasitoid of a Green Alga Coccomyxa sp

Gene Expression in Aphelid Zoospores Reveals Their Transcriptional and Translational Activity and Alacrity for Invasion

In Aphelidium insulamus (Opisthokonta, Aphelida) zoospores, the expression of 7708 genes out of 7802 described genes was detected. For 589 of them, expression levels were shown to be more than 10 times higher than the median level. Among the highly expressed genes with known functions, the largest functional categories were "Cellular Metabolism", "Protein Synthesis", "Cell State Control", and "Nucleic Acid Processing". Unlike fungal zoospores, translational and transcriptional activity was demonstrated for A. insulamus zoospores. With increasing temperature, the expression of many zoospore genes changed dramatically; the expression of heat shock and chaperone protein genes multiplied more than 30 times, indicating the high sensitivity of aphelid zoospores and their response to environmental changes.

Inside the Host: Understanding the Evolutionary Trajectories of Intracellular Parasitism

This review explores the origins of intracellular parasitism, an intriguing facet of symbiosis, where one organism harms its host, potentially becoming deadly. We focus on three distantly related groups of single-celled eukaryotes, namely Kinetoplastea, Holomycota, and Apicomplexa, which contain multiple species-rich lineages of intracellular parasites. Using comparative analysis of morphological, physiological, and molecular features of kinetoplastids, microsporidians, and sporozoans, as well as their closest free-living relatives, we reveal the evolutionary trajectories and adaptations that enabled the transition to intracellular parasitism. Intracellular parasites have evolved various efficient mechanisms for host acquisition and exploitation, allowing them to thrive in a variety of hosts. Each group has developed unique features related to the parasitic lifestyle, involving dedicated protein families associated with host cell invasion, survival, and exit. Indeed, parallel evolution has led to distinct lineages of intracellular parasites employing diverse traits and approaches to achieve similar outcomes.

Santiago ALCM, Saxena RK, Schoutteten N, Wimalasena MK, Aleoshin VV, Al-Hatmi AMS, Ariyawansa KGSU, Assunção AR, Bamunuarachchige TC, Baral HO, Bhat DJ, Błaszkowski J, Boekhout T, Boonyuen N, Brysch-Herzberg M, Cao B, Cazabonne J, Chen XM, Coleine C, Dai DQ, Daniel HM, da Silva SBG, de Souza FA, Dolatabadi S, Dubey MK, Dutta AK, Ediriweera A, Egidi E, Elshahed MS, Fan X, Felix JRB, Galappaththi MCA, Groenewald M, Han LS, Huang B, Hurdeal VG, Ignatieva AN, Jerônimo GH, de Jesus AL, Kondratyuk S, Kumla J, Kukwa M, Li Q, Lima JLR, Liu XY, Lu W, Lumbsch HT, Madrid H, Magurno F, Marson G, McKenzie EHC, Menkis A, Mešić A, Nascimento ECR, Nassonova ES, Nie Y, Oliveira NVL, Ossowska EA, Pawłowska J, Peintner U, Pozdnyakov IR, Premarathne BM, Priyashantha AKH, Quandt CA, Queiroz MB, Rajeshkumar KC, Raza M, Roy N, Samarakoon MC, Santos AA, Santos LA, Schumm F, Selbmann L, Selçuk F, Simmons DR, Simakova AV, Smith MT, Sruthi OP, Suwannarach N, Tanaka K, Tibpromma S, Tomás EO, Ulukapı M, Van Vooren N, Wanasinghe DN, Weber E, Wu Q, Yang EF, Yoshioka R, Youssef NH, Zandijk A, Zhang GQ, Zhang JY, Zhao H, Zhao R, Zverkov OA, Thines M, Karpov SA. Classes and phyla of the kingdom Fungi

Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom Fungi, drawing upon a comprehensive phylogenomic analysis of Holomycota, with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of Fungi, viz. Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota, Sanchytriomycota, and Zoopagomycota. In the phylogenies, Caulochytriomycota resides in Chytridiomycota; thus, the former is regarded as a synonym of the latter, while Caulochytriomycetes is viewed as a class in Chytridiomycota. We provide a description of each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov is introduced as the only subphylum in Sanchytriomycota. The subclass Pneumocystomycetidae Kirk et al. in Pneumocystomycetes, Ascomycota is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.

Genomics and phylogenetic relationships of microsporidia and their relatives

Microsporidia are intracellular parasites that all possess a unique infection apparatus involving a polar tube. Upon contact with a host cell, this tube forms the conduit through which the parasite enters the host. Infecting mostly animals, microsporidian species can be transmitted vertically or horizontally, and exert various effects on their hosts: infections range from being relatively benign to lethal. Microsporidian genomes possess highly divergent sequences and are often substantially reduced in size. Their divergent sequences and unique morphology created early challenges to our understanding of their phylogenetic position within the tree of eukaryotes. Over the last couple of decades, advances in both sequencing technology and phylogenetic methodology supported a clear relationship between microsporidia and fungi. However, the specifics of this relationship were muddied by the lack of known microsporidian relatives. With increased taxon discovery and the morphological and molecular characterization of microsporidia-like taxa, rozellids and aphelids, a better resolved picture is emerging. Here we review the history of microsporidian taxonomy and current status of genomics of microsporidia and their nearest relatives, with an aim to understand their morphological and metabolic differences, along with their evolutionary relationships.

Diversity of Rhizophydiales (Chytridiomycota) in Thailand: unveiling the hidden gems of the Kingdom

Chytrids, often overshadowed by their other fungal counterparts, take center stage as we unravel the mysteries surrounding new species within Rhizophydiales and explore their unique characteristics. In the broader spectrum of chytrids, their significance lies not only in their roles as decomposers but also as key players in nutrient cycling within aquatic ecosystems as parasites and saprobes. Baited soil and aquatic samples collected from various provinces of Thailand, yielded new species of the Rhizophydiales (Chytridiomycota), some of which expanded previously single species genera. Our investigation incorporated a combination of morphological and phylogenetic approaches, enabling us to identify these isolates as distinct taxa. The novel isolates possess distinguishing features, such as variations in size and shape of the sporangium and zoospores, that somewhat differentiate them from described taxa. To confirm the novelty of the species, we employed robust phylogenetic analyses using maximum likelihood and bayesian methods. The results provided strong support for the presence of eight distinct lineages within the Rhizophydiales, representing our newly discovered species. Furthermore, we employed Poisson Tree Processes to infer putative species boundaries and supplement evidence for the establishment of our new Rhizophydiales species. By meticulously exploring their morphological characteristics and genetic makeup, we expand the known catalogue of fungal diversity by describing Alphamyces thailandicus, Angulomyces ubonensis, Gorgonomyces aquaticus, G. chiangraiensis, G. limnicus, Pateramyces pingflumenensis, Terramyces aquatica, and T. flumenensis and also provide valuable insights into the intricacies of this order. This newfound knowledge not only enriches our understanding of Rhizophydiales but also contributes significantly to the broader field of mycology, addressing a critical gap in the documentation of fungal species. The identification and characterization of these eight novel species mark a noteworthy stride towards a more comprehensive comprehension of fungal ecosystems and their vital role.

Microbial Diversity and Community Structure of Wastewater-Driven Microalgal Biofilms

Dwindling water sources increase the need for efficient wastewater treatment. Solar-driven algal turf scrubber (ATS) system may remediate wastewater by supporting the development and growth of periphytic microbiomes that function and interact in a highly dynamic manner through symbiotic interactions. Using ITS and 16S rRNA gene amplicon sequencing, we profiled the microbial communities of four microbial biofilms from ATS systems operated with municipal wastewater (mWW), diluted cattle and pig manure (CattleM and PigM), and biogas plant effluent supernatant (BGE) in comparison to the initial inocula and the respective wastewater substrates. The wastewater-driven biofilms differed significantly in their biodiversity and structure, exhibiting an inocula-independent but substrate-dependent establishment of the microbial communities. The prokaryotic communities were comparable among themselves and with other microbiomes of aquatic environments and were dominated by metabolically flexible prokaryotes such as nitrifiers, polyphosphate-accumulating and algicide-producing microorganisms, and anoxygenic photoautotrophs. Striking differences occurred in eukaryotic communities: While the mWW biofilm was characterized by high biodiversity and many filamentous (benthic) microalgae, the agricultural wastewater-fed biofilms consisted of less diverse communities with few benthic taxa mainly inhabited by unicellular chlorophytes and saprophytes/parasites. This study advances our understanding of the microbiome structure and function within the ATS-based wastewater treatment process.

Vegetative cell fusion and a new stage in the life cycle of the Aphelida (Opisthosporidia)

The aphelids, intracellular parasitoids of algae, represent a large cluster of species sister to Fungi in molecular phylogenetic trees. Sharing a common ancestor with Fungi, they are very important in terms of evolution of these groups of Holomycota. Aphelid life cycle being superficially similar to that of Chytridiomycetes is understudied. We have found in the aphelids a new stage-big multiflagellar and amoeboid cells, formed from a plasmodium that has two sorts of nuclei after trophic stage fusion. The families of protein-coding genes involved in the vegetative cell fusion in Opisthokonta were also discussed.

Niche and ecosystem preference of earliest diverging fungi in soils

Within the supergroup Rotosphaeromycetes, or "Holomycota"/"Nucletmycea", there are several well-recognised unicellular clades in the earliest diverging fungi (EDF). However, we know little about their occurrence. Here, we investigated EDF in the rhizosphere and bulk soils from cropland, forest, orchard, and wetland ecosystems around the Beijing-Hebei area, China, to illustrate their niche and ecosystem preference. More than 500 new operational taxonomic units (OTUs) of EDF were detected based on the 18S rRNA genes. Microsporida and Aphelida constitute dominant groups, whereas Rozellosporida was quite rare. Although the EDF community was site-specific, the soil chemical characteristics, vegetation, and other eukaryotic microorganisms were the key factors driving the occurrence of EDF. Moreover, the stochastic process consisted the most of the EDF community assembly.

Mucilage protects the planktonic desmid Staurodesmus sp. against parasite attack by a chytrid fungus

Zoosporic fungi of the phylum Chytridiomycota are ubiquitous parasites of phytoplankton in aquatic ecosystems, but little is known about phytoplankton defense strategies against parasitic chytrid attacks. Using a model chytrid-phytoplankton pathosystem, we experimentally tested the hypothesis that the mucilage envelope of a mucilage-forming desmid species provides protection against the parasitic chytrid Staurastromyces oculus. Mucilage-forming Staurodesmus cells were not accessible to the chytrid, whereas physical removal of the mucilage envelope rendered the same Staurodesmus sp. strain equally susceptible to chytrid infections as the original non-mucilage-forming host Staurastrum sp. Epidemic spread of the parasite only occurred in Staurastrum sp., whereas non-mucilage-bearing Staurodesmus sp. allowed for co-existence of host and parasite, and mucilage-bearing Staurodesmus sp. caused parasite extinction. In addition to the mucilage defense barrier, we also demonstrate the ability of both Staurastrum sp. and Staurodesmus sp. to resist infection by preventing chytrid development while still remaining viable and being able to reproduce and thus recover from an infection. This study extends our knowledge on phytoplankton defense traits and the functional role of mucilage in phytoplankton as a physical barrier against fungal parasites.

Genomic analysis reveals cryptic diversity in aphelids and sheds light on the emergence of Fungi

Over the past decade, molecular phylogenetics has reshaped our understanding of the fungal tree of life by unraveling a hitherto elusive diversity of the protistan relatives of Fungi. Aphelida constitutes one of these novel deep branches that precede the emergence of osmotrophic fungal lifestyle and hold particular significance as the pathogens of algae. Here, we obtain and analyze the genomes of aphelid species Amoeboaphelidium protococcarum and Amoeboaphelidium occidentale. Genomic data unmask the vast divergence between these species, hidden behind their morphological similarity, and reveal hybrid genomes with a complex evolutionary history in two strains of A. protococcarum. We confirm the proposed sister relationship between Aphelida and Fungi using phylogenomic analysis and chart the reduction of characteristic proteins involved in phagocytic activity in the evolution of Holomycota. Annotation of aphelid genomes demonstrates the retention of actin nucleation-promoting complexes associated with phagocytosis and amoeboid motility and also reveals a conspicuous expansion of receptor-like protein kinases, uncharacteristic of fungal lineages. We find that aphelids possess multiple carbohydrate-processing enzymes that are involved in fungal cell wall synthesis but do not display rich complements of algal cell-wall-processing enzymes, suggesting an independent origin of fungal plant-degrading capabilities. Aphelid genomes show that the emergence of Fungi from phagotrophic ancestors relied on a common cell wall synthetic machinery but required a different set of proteins for digestion and interaction with the environment.

Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits

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.

Aphelidium parallelum, sp. nov., a new aphelid parasitic on selenastracean green algae

Aphelids (phylum Aphelida = Aphelidiomycota) are intracellular parasitoids of algae and represent one of the early-diverging or sister lineages of the kingdom Fungi. Although aphelids are a small group comprising four genera and 17 species, molecular phylogenetic analyses revealed that numerous environmental DNA sequences represent undescribed lineages, indicating their hidden diversity. Here, we investigated a novel aphelid strain, KS114, that parasitizes selenastracean green algae. KS114 exhibited a life cycle typical of aphelids and produced posteriorly uniflagellate zoospores that resembled those of Aphelidium chlorococcorum f. majus in possessing a single apical filopodium but could be distinguished by ultrastructure features. In KS114, the kinetosome and nonflagellated centriole were aligned in parallel, a unique characteristic among the known aphelids. Kinetid-associated structures, such as fibrillar root and microtubules, were not found in the zoospores of KS114. In the molecular phylogeny of nuc 18S rDNA sequences, KS114 clustered with two environmental sequences and was distinct from all other sequenced species. Based on these results, we describe this aphelid as a new species, Aphelidium parallelum.http://www.zoobank.org/urn:lsid:zoobank.org:act:3CB658DB-1F12-41EF-A57D-2CBFCDE6A49A.