The diversity of fungal genome

The genome size of an organism varies from species to species. The C-value paradox enigma is a very complex puzzle with regards to vast diversity in genome sizes in eukaryotes. Here we reported the detailed genomic information of 172 fungal species among different fungal genomes and found that fungal genomes are very diverse in nature. In fungi, the diversity of genomes varies from 8.97 Mb to 177.57 Mb. The average genome sizes of Ascomycota and Basidiomycota fungi are 36.91 and 46.48 Mb respectively. But higher genome size is observed in Oomycota (74.85 Mb) species, a lineage of fungus-like eukaryotic microorganisms. The average coding genes of Oomycota species are almost doubled than that of Acomycota and Basidiomycota fungus.

A without-prejudice list of generic names of fungi for protection under the International Code of Nomenclature for algae, fungi, and plants

As a first step towards the production of a List of Protected Generic Names for Fungi, a without-prejudice list is presented here as a basis for future discussion and the production of a List for formal adoption. We include 6995 generic names out of the 17072 validly published names proposed for fungi and invite comments from all interested mycologists by 31 March 2014. The selection of names for inclusion takes note of recent major publications on different groups of fungi, and further the decisions reached so far by international working groups concerned with particular families or genera. Changes will be sought in the Code to provide for this and lists at other ranks to be protected against any competing unlisted names, and to permit the inclusion of names of lichen-forming fungi. A revised draft will be made available for further discussion at the 10^th International Mycological Congress in Bangkok in August 2014. A schedule is suggested for the steps needed to produce a list for adoption by the International Botanical Congress in August 2017. This initiative provides mycologists with an opportunity to place nomenclature at the generic level on a more secure and stable base.

Cytology and molecular phylogenetics of Monoblepharidomycetes provide evidence for multiple independent origins of the hyphal habit in the Fungi

The evolution of filamentous hyphae underlies an astounding diversity of fungal form and function. We studied the cellular structure and evolutionary origins of the filamentous form in the Monoblepharidomycetes (Chytridiomycota), an early-diverging fungal lineage that displays an exceptional range of body types, from crescent-shaped single cells to sprawling hyphae. To do so, we combined light and transmission electron microscopic analyses of hyphal cytoplasm with molecular phylogenetic reconstructions. Hyphae of Monoblepharidomycetes lack a complex aggregation of secretory vesicles at the hyphal apex (i.e. Spitzenkörper), have centrosomes as primary microtubule organizing centers and have stacked Golgi cisternae instead of tubular/fenestrated Golgi equivalents. The cytoplasmic distribution of actin in Monoblepharidomycetes is comparable to the arrangement observed previously in other filamentous fungi. To discern the origins of Monoblepharidomycetes hyphae, we inferred a phylogeny of the fungi based on 18S and 28S ribosomal DNA sequence data with maximum likelihood and Bayesian inference methods. We focused sampling on Monoblepharidomycetes to infer intergeneric relationships within the class and determined 78 new sequences. Analyses showed class Monoblepharidomycetes to be monophyletic and nested within Chytridiomycota. Hyphal Monoblepharidomycetes formed a clade sister to the genera without hyphae, Harpochytrium and Oedogoniomyces. A likelihood ancestral state reconstruction indicated that hyphae arose independently within the Monoblepharidomycetes lineage and in at least two other lineages. Cytological differences among monoblepharidalean and other fungal hyphae are consistent with these convergent origins.

Changes in N:P Supply Ratios Affect the Ecological Stoichiometry of a Toxic Cyanobacterium and Its Fungal Parasite

Human activities have dramatically altered nutrient fluxes from the landscape into receiving waters. As a result, not only the concentration of nutrients in surface waters has increased, but also their elemental ratios have changed. Such shifts in resource supply ratios will alter autotroph stoichiometry, which may in turn have consequences for higher trophic levels, including parasites. Here, we hypothesize that parasite elemental composition will follow changes in the stoichiometry of its host, and that its reproductive success will decrease with host nutrient limitation. We tested this hypothesis by following the response of a host–parasite system to changes in nitrogen (N) and phosphorus (P) supply in a controlled laboratory experiment. To this end, we exposed a fungal parasite (the chytrid Rhizophydium megarrhizum) to its host (the freshwater cyanobacterium Planktothrix rubescens) under control, low N:P and high N:P conditions. Host N:P followed treatment conditions, with a decreased N:P ratio under low N:P supply, and an increased N:P ratio under high N:P supply, as compared to the control. Shifts in host N:P stoichiometry were reflected in the parasite stoichiometry. Furthermore, at low N:P supply, host intracellular microcystin concentration was lowered as compared to high N:P supply. In contrast to our hypothesis, zoospore production decreased at low N:P and increased at high N:P ratio as compared to the control. These findings suggest that fungal parasites have a relatively high N, but low P requirement. Furthermore, zoospore elemental content, and thereby presumably their size, decreased at high N:P ratios. From these results we hypothesize that fungal parasites may exhibit a trade-off between zoospore size and production. Since zooplankton can graze on chytrid zoospores, changes in parasite production, stoichiometry and cell size may have implications for aquatic food web dynamics.

Survey of Early-Diverging Lineages of Fungi Reveals Abundant and Diverse Mycoviruses

Viruses are key drivers of evolution and ecosystem function and are increasingly recognized as symbionts of fungi. Fungi in early-diverging lineages are widespread, ecologically important, and comprise the majority of the phylogenetic diversity of the kingdom. Viruses infecting early-diverging lineages of fungi have been almost entirely unstudied. In this study, we screened fungi for viruses by two alternative approaches: a classic culture-based method and by transcriptome-mining. The results of our large-scale survey demonstrate that early-diverging lineages have higher infection rates than have been previously reported in other fungal taxa and that laboratory strains worldwide are host to infections, the implications of which are unknown. The function and diversity of mycoviruses found in these basal fungal lineages will help guide future studies into mycovirus origins and their evolutionary ramifications and ecological impacts.

Mycoviruses are widespread and purportedly common throughout the fungal kingdom, although most are known from hosts in the two most recently diverged phyla, Ascomycota and Basidiomycota, together called Dikarya. To augment our knowledge of mycovirus prevalence and diversity in underexplored fungi, we conducted a large-scale survey of fungi in the earlier-diverging lineages, using both culture-based and transcriptome-mining approaches to search for RNA viruses. In total, 21.6% of 333 isolates were positive for RNA mycoviruses. This is a greater proportion than expected based on previous taxonomically broad mycovirus surveys and is suggestive of a strong phylogenetic component to mycoviral infection. Our newly found viral sequences are diverse, composed of double-stranded RNA, positive-sense single-stranded RNA (ssRNA), and negative-sense ssRNA genomes and include novel lineages lacking representation in the public databases. These identified viruses could be classified into 2 orders, 5 families, and 5 genera; however, half of the viruses remain taxonomically unassigned. Further, we identified a lineage of virus-like sequences in the genomes of members of Phycomycetaceae and Mortierellales that appear to be novel genes derived from integration of a viral RNA-dependent RNA polymerase gene. The two screening methods largely agreed in their detection of viruses; thus, we suggest that the culture-based assay is a cost-effective means to quickly assess whether a laboratory culture is virally infected. This study used culture collections and publicly available transcriptomes to demonstrate that mycoviruses are abundant in laboratory cultures of early-diverging fungal lineages. The function and diversity of mycoviruses found here will help guide future studies into mycovirus origins and ecological functions.

New insights into the evolutionary history of Fungi from a 407 Ma Blastocladiomycota fossil showing a complex hyphal thallus

Zoosporic fungi are key saprotrophs and parasites of plants, animals and other fungi, playing important roles in ecosystems. They comprise at least three phyla, of which two, Chytridiomycota and Blastocladiomycota, developed a range of thallus morphologies including branching hyphae. Here we describe Retesporangicus lyonii gen. et sp. nov., an exceptionally well preserved fossil, which is the earliest known to produce multiple sporangia on an expanded hyphal network. To better characterize the fungus we develop a new method to render surfaces from image stacks generated by confocal laser scanning microscopy. Here, the method helps to reveal thallus structure. Comparisons with cultures of living species and character state reconstructions analysed against recent molecular phylogenies of 24 modern zoosporic fungi indicate an affinity with Blastocladiomycota. We argue that in zoosporic fungi, kinds of filaments such as hyphae, rhizoids and rhizomycelium are developmentally similar structures adapted for varied functions including nutrient absorption and anchorage. The fossil is the earliest known type to develop hyphae which likely served as a saprotrophic adaptation to patchy resource availability. Evidence from the Rhynie chert provides our earliest insights into the biology of fungi and their roles in the environment. It demonstrates that zoosporic fungi were already diverse in 407 million-year-old terrestrial ecosystems.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.

Diversity and Hidden Host Specificity of Chytrids Infecting Colonial Volvocacean Algae

Chytrids are zoosporic fungi that play an important, but yet understudied, ecological role in aquatic ecosystems. Many chytrid species have been morphologically described as parasites on phytoplankton. However, the majority of them have rarely been isolated and lack DNA sequence data. In this study we isolated and cultivated three parasitic chytrids, infecting a common volvocacean host species, Yamagishiella unicocca. To identify the chytrids, we characterized morphology and life cycle, and analyzed phylogenetic relationships based on 18S and 28S rDNA genes. Host range and specificity of the chytrids was determined by cross-infection assays with host strains, characterized by rbcL and ITS markers. We were able to confirm the identity of two chytrid strains as Endocoenobium eudorinae Ingold and Dangeardia mamillata Schröder and described the third chytrid strain as Algomyces stechlinensis gen. et sp. nov. The three chytrids were assigned to novel and phylogenetically distant clades within the phylum Chytridiomycota, each exhibiting different host specificities. By integrating morphological and molecular data of both the parasitic chytrids and their respective host species, we unveiled cryptic host-parasite associations. This study highlights that a high prevalence of (pseudo)cryptic diversity requires molecular characterization of both phytoplankton host and parasitic chytrid to accurately identify and compare host range and specificity, and to study phytoplankton-chytrid interactions in general.

The linear mitochondrial genome of the quarantine chytrid Synchytrium endobioticum; insights into the evolution and recent history of an obligate biotrophic plant pathogen

BACKGROUND

Chytridiomycota species (chytrids) belong to a basal lineage in the fungal kingdom. Inhabiting terrestrial and aquatic environments, most are free-living saprophytes but several species cause important diseases: e.g. Batrachochytrium dendrobatidis, responsible for worldwide amphibian decline; and Synchytrium endobioticum, causing potato wart disease. S. endobioticum has an obligate biotrophic lifestyle and isolates can be further characterized as pathotypes based on their virulence on a differential set of potato cultivars. Quarantine measures have been implemented globally to control the disease and prevent its spread. We used a comparative approach using chytrid mitogenomes to determine taxonomical relationships and to gain insights into the evolution and recent history of introductions of this plant pathogen.

RESULTS

We assembled and annotated the complete mitochondrial genome of 30 S. endobioticum isolates and generated mitochondrial genomes for five additional chytrid species. The mitochondrial genome of S. endobioticum is linear with terminal inverted repeats which was validated by tailing and PCR amplifying the telomeric ends. Surprisingly, no conservation in organisation and orientation of mitochondrial genes was observed among the Chytridiomycota except for S. endobioticum and its sister species Synchytrium microbalum. However, the mitochondrial genome of S. microbalum is circular and comprises only a third of the 72.9 Kbp found for S. endobioticum suggesting recent linearization and expansion. Four mitochondrial lineages were identified in the S. endobioticum mitochondrial genomes. Several pathotypes occur in different lineages, suggesting that these have emerged independently. In addition, variations for polymorphic sites in the mitochondrial genome of individual isolates were observed demonstrating that S. endobioticum isolates represent a community of different genotypes. Such communities were shown to be complex and stable over time, but we also demonstrate that the use of semi-resistant potato cultivars triggers a rapid shift in the mitochondrial haplotype associated with increased virulence.

CONCLUSIONS

Mitochondrial genomic variation shows that S. endobioticum has been introduced into Europe multiple times, that several pathotypes emerged multiple times, and that isolates represent communities of different genotypes. Our study represents the most comprehensive dataset of chytrid mitogenomes, which provides new insights into the extraordinary dynamics and evolution of mitochondrial genomes involving linearization, expansion and reshuffling.

Characterization of the Mycobiome of the Seagrass, Zostera marina, Reveals Putative Associations With Marine Chytrids

Seagrasses are globally distributed marine flowering plants that are foundation species in coastal ecosystems. Seagrass beds play essential roles as habitats and hatcheries, in nutrient cycling, and in protecting the coastline from erosion. Although many studies have focused on seagrass ecology, only a limited number have investigated their associated fungi. In terrestrial systems, fungi can have beneficial and detrimental effects on plant fitness. However, not much is known about marine fungi and even less is known about seagrass associated fungi. Here we used culture-independent sequencing of the ribosomal internal transcribed spacer (ITS) region to characterize the taxonomic diversity of fungi associated with the seagrass, Zostera marina. We sampled from two Z. marina beds in Bodega Bay over three time points to investigate fungal diversity within and between plants. Our results indicate that there are many fungal taxa for which a taxonomic assignment cannot be made living on and inside Z. marina leaves, roots and rhizomes and that these plant tissues harbor distinct fungal communities. We also identified differences in the abundances of the orders, Glomerellales, Agaricales and Malasseziales, between seagrass tissues. The most prevalent ITS amplicon sequence variants (ASVs) associated with Z. marina tissues could not initially be confidently assigned to a fungal phylum, but shared significant sequence similarity with Chytridiomycota and Aphelidomycota. To obtain a more definitive taxonomic classification of the most abundant ASV associated with Z. marina leaves, we used PCR with one primer targeting a unique region of this ASV's ITS2 and a second primer targeting fungal 28S rRNA genes to amplify part of the 28S rRNA gene region corresponding to this ASV. Sequencing and phylogenetic analysis of the resulting partial 28S rRNA gene revealed that the organism that this ASV comes from is a member of Novel Clade SW-I in the order Lobulomycetales in the phylum Chytridiomycota. This clade includes known parasites of freshwater diatoms and algae and it is possible this chytrid is directly infecting Z. marina leaf tissues. This work highlights a need for further studies focusing on marine fungi and the potential importance of these understudied communities to the larger seagrass ecosystem.

Taxonomic revision of the genus Zygorhizidium: Zygorhizidiales and Zygophlyctidales ord. nov. (Chytridiomycetes, Chytridiomycota)

During the last decade, the classification system of chytrids has dramatically changed based on zoospore ultrastructure and molecular phylogeny. In contrast to well-studied saprotrophic chytrids, most parasitic chytrids have thus far been only morphologically described by light microscopy, hence they hold great potential for filling some of the existing gaps in the current classification of chytrids. The genus Zygorhizidium is characterized by an operculate zoosporangium and a resting spore formed as a result of sexual reproduction in which a male thallus and female thallus fuse via a conjugation tube. All described species of Zygorhizidium are parasites of algae and their taxonomic positions remain to be resolved. Here, we examined morphology, zoospore ultrastructure, host specificity, and molecular phylogeny of seven cultures of Zygorhizidium spp. Based on thallus morphology and host specificity, one culture was identified as Z. willei parasitic on zygnematophycean green algae, whereas the others were identified as parasites of diatoms, Z. asterionellae on Asterionella, Z. melosirae on Aulacoseira, and Z. planktonicum on Ulnaria (formerly Synedra). According to phylogenetic analysis, Zygorhizidium was separated into two distinct order-level novel lineages; one lineage was composed singly of Z. willei, which is the type species of the genus, and the other included the three species of diatom parasites. Zoospore ultrastructural observation revealed that the two lineages can be distinguished from each other and both possess unique characters among the known orders within the Chytridiomycetes. Based on these results, we accommodate the three diatom parasites, Z. asterionellae, Z. melosirae, and Z. planktonicum in the distinct genus Zygophlyctis, and propose two new orders: Zygorhizidiales and Zygophlyctidales.

Rediscovering Zygorhizidium affluens Canter: Molecular Taxonomy, Infectious Cycle, and Cryopreservation of a Chytrid Infecting the Bloom-Forming Diatom Asterionella formosa

Parasitic Chytridiomycota (chytrids) are ecologically significant in various aquatic ecosystems, notably through their roles in controlling bloom-forming phytoplankton populations and in facilitating the transfer of nutrients from inedible algae to higher trophic levels. The diversity and study of these obligate parasites, while critical to understand the interactions between pathogens and their hosts in the environment, have been hindered by challenges inherent to their isolation and stable long-term maintenance under laboratory conditions. Here, we isolated an obligate chytrid parasite (CCAP 4086/1) on the freshwater bloom-forming diatom Asterionella formosa and characterized its infectious cycle under controlled conditions. Phylogenetic analyses based on 18S, 5.8S, and 28S ribosomal DNAs (rDNAs) revealed that this strain belongs to the recently described clade SW-I within the Lobulomycetales. All morphological features observed agree with the description of the known Asterionella parasite Zygorhizidium affluens Canter. We thus provide a phylogenetic placement for this chytrid and present a robust and simple assay that assesses both the infection success and the viability of the host. We also validate a cryopreservation method for stable and cost-effective long-term storage and demonstrate its recovery after thawing. All the above-mentioned tools establish a new gold standard for the isolation and long-term preservation of parasitic aquatic chytrids, thus opening new perspectives to investigate the diversity of these organisms and their physiology in a controlled laboratory environment.IMPORTANCE Despite their ecological relevance, parasitic aquatic chytrids are understudied, especially due to the challenges associated with their isolation and maintenance in culture. Here we isolated and established a culture of a chytrid parasite infecting the bloom-forming freshwater diatom Asterionella formosa The chytrid morphology suggests that it corresponds to the Asterionella parasite known as Zygorhizidium affluens The phylogenetic reconstruction in the present study supports the hypothesis that our Z. affluens isolate belongs to the order Lobulomycetales and clusters within the novel clade SW-I. We also validate a cryopreservation method for stable and cost-effective long-term storage of parasitic chytrids of phytoplankton. The establishment of a monoclonal pathosystem in culture and its successful cryopreservation opens the way to further investigate this ecologically relevant parasitic interaction.

Identification and characterization of GH11 xylanase and GH43 xylosidase from the chytridiomycetous fungus, Rhizophlyctis rosea

The early-lineage, aerobic, zoosporic fungi from the Chytridiomycota constitute less than 1% of the described fungi and can use diverse sources of nutrition from plant or animal products. One of the ancestral sources of fungal nutrition could be products following enzymatic degradation of plant material. However, carbohydrate-active enzymes from these ancient fungi have been less studied. A GH11 xylanase (RrXyn11A) (EC 3.2.1.8) and a GH43 xylosidase (RrXyl43A) (EC 3.2.1.37) were identified from an early-lineage aerobic zoosporic fungus, Rhizophlyctis rosea NBRC 105426. Both genes were heterologously expressed in Pichia pastoris and the recombinant enzymes were purified and characterized. The optimal pH for recombinant RrXyn11A and RrXyl43A was pH 7. RrXyn11A had high stability over a wide range of pH (4–8) and temperature (25–70 °C). RrXyn11A also showed high substrate specificity on both azurine-cross-linked (AZCL) arabinoxylan and AZCL xylan. RrXyl43A had β-xylosidase and minor α-l-arabinofuranosidase activity. This enzyme showed low product inhibition and retained 51% activity in the presence of 100 mM xylose. A combination of RrXyn11A and RrXyl43A exhibited significantly higher hydrolytic and polymer degradation capability and xylose release on wheat bran and beechwood xylan compared to treatment with commercial enzymes. This study was the first to heterologously express and characterize the GH11 xylanase (RrXyn11A) and GH43 xylosidase (RrXyl43A) from the ancient fungus, R. rosea. Meanwhile, this study also demonstrated that the enzymes from the ancient fungus R. rosea can be easily handled and heterologously expressed in Pichia, which presents a promising path to a new source of enzymes for biomass degradation.

Chytrid mycoparasitism of entomophthoralean azygospores

Mycoparasitism - when one fungus parasitizes another - has been reported to affect Beauveria bassiana and mycorrhizal fungi in the field. However, mycoparasitism of any fungi in the Order Entomophthorales has never been reported before now. The majority of entomophthoralean species persist as resting spores (either zygospores or azygospores) in the environment and dormant entomophthoralean resting spores (whether formed as zygospores or azygospores) are thought to be especially well adapted for survival over long periods due to their thick double walls. Entomophthoralean resting spores can accumulate in the soil as large reservoirs of inoculum which can facilitate the onset and development of epizootics. We report parasitism of azygospores of the gypsy moth pathogen Entomophaga maimaiga caged in soil from southern Ohio by the chytrid fungus Gaertneriomyces semiglobifer. G. semiglobifer had previously been isolated from soil samples from North America, Europe and Australia or horse manure from Virginia. After isolation and identification of G. semiglobifer, azygospores of E. maimaiga exposed to zoospores of G. semiglobifer exhibited high levels of mycoparasitism and G. semiglobifer was subsequently reisolated from mycoparasitized resting spores. We discuss the importance of this finding to the epizootiology of insect diseases caused by entomophthoralean fungi.

Parallels in amphibian and bat declines from pathogenic fungi

Pathogenic fungi have substantial effects on global biodiversity, and 2 emerging pathogenic species—the chytridiomycete Batrachochytrium dendrobatidis, which causes chytridiomycosis in amphibians, and the ascomycete Geomyces destructans, which causes white-nose syndrome in hibernating bats—are implicated in the widespread decline of their vertebrate hosts. We synthesized current knowledge for chytridiomycosis and white-nose syndrome regarding disease emergence, environmental reservoirs, life history characteristics of the host, and host–pathogen interactions. We found striking similarities between these aspects of chytridiomycosis and white-nose syndrome, and the research that we review and propose should help guide management of future emerging fungal diseases.

The Synchytrium endobioticum AvrSen1 Triggers a Hypersensitive Response in Sen1 Potatoes While Natural Variants Evade Detection

Synchytrium endobioticum is an obligate biotrophic fungus of division Chytridiomycota. It causes potato wart disease, has a worldwide quarantine status and is included on the Health and Human Services and United States Department of Agriculture Select Agent list. S. endobioticum isolates are grouped in pathotypes based on their ability to evade host resistance in a set of differential potato varieties. Thus far, 39 pathotypes are reported. A single dominant gene (Sen1) governs pathotype 1 (D1) resistance and we anticipated that the underlying molecular model would involve a pathogen effector (AvrSen1) that is recognized by the host. The S. endobioticum-specific secretome of 14 isolates representing six different pathotypes was screened for effectors specifically present in pathotype 1 (D1) isolates but absent in others. We identified a single AvrSen1 candidate. Expression of this candidate in potato Sen1 plants showed a specific hypersensitive response (HR), which cosegregated with the Sen1 resistance in potato populations. No HR was obtained with truncated genes found in pathotypes that evaded recognition by Sen1. These findings established that our candidate gene was indeed Avrsen1. The S. endobioticum AvrSen1 is a single-copy gene and encodes a 376-amino-acid protein without predicted function or functional domains, and is the first effector gene identified in Chytridiomycota, an extremely diverse yet underrepresented basal lineage of fungi.

Basal Parasitic Fungi in Marine Food Webs-A Mystery Yet to Unravel

Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research.

Quaeritorhiza haematococci is a new species of parasitic chytrid of the commercially grown alga, Haematococcus pluvialis

Aquaculture companies grow the green alga Haematococcus pluvialis (Chlorophyta) to extract the carotenoid astaxanthin to sell, which is used as human and animal dietary supplements. We were requested to identify an unknown pathogen of H. pluvialis from an alga growing facility in the southwestern United States. To identify this zoosporic fungus and determine its phylogenetic placement among other chytrids, we isolated it into pure culture, photographed its morphology and zoospore ultrastructure, and sequenced and analyzed portions of nuc rDNA 18S and 28S genes. The organism belongs in the Chytridiomycota, but a comparison of rDNA with available representatives of the phylum did not convincingly place it in any described order. The unique zoospore ultrastructure supports its indeterminate ordinal position, and the morphology, as determined by light microscopy, did not match any described species. Consequently, we have placed this chytrid in the new genus, Quaeritorhiza, and described it as the new species Q. haematococci in the family Quaeritorhizaceae but otherwise incertae sedis in the Chytridiomycetes. This new taxon is important because it increases the known diversity of Chytridiomycota and the organism has the ability to disrupt agricultural production of an algal monoculture.

Actin guides filamentous rhizoid growth and morphogenesis in the zoosporic fungus Chytriomyces hyalinus

The advantage of filamentous growth to the fungal lifestyle is so great that it arose multiple times. Most zoosporic fungi from phylum Chytridiomycota exhibit a monocentric thallus form consisting of anucleate filamentous rhizoids that anchor reproductive sporangia to substrata and absorb nutrients. Actin function during polarized growth and cytokinesis is well documented across eukaryotes, but its role in sculpting nonhyphal, nonyeast fungal cells is unknown. We sought to provide a basis for comparing actin organization among major fungal lineages and to investigate the effects of actin disruption on morphogenesis in a monocentric thallus. Using fluorescence microscopy, we observed fixed, rhodamine phalloidin-stained actin in chemically fixed Chytriomyces hyalinus, exemplifying monocentric thallus development within the diverse, zoosporic phylum Chytridiomycota. We also compared rhizoid lengths and rhizoid branching of thalli incubated with the actin inhibitor latrunculin B to determine the effects of actin disruption on morphology. Actin was concentrated at the tips of growing rhizoids. Actin cables typically formed cortical, parallel arrays in hyphae, but in mature sporangia they were concentrated in a funnel-shaped array in the central region. Thalli treated with latrunculin B had shorter rhizoids with fewer branches than controls. In both hyphae and monocentric thalli, actin localization coincides with active, polarized growth and cytokinesis. Specific actin localization patterns are largely shared between monocentric species but differ significantly from patterns observed in hyphae. Actin integrity is critical for sustaining filamentous growth in all fungi.

Borealophlyctis nickersoniae, a new species in Rhizophlyctidales

Zoospore ultrastructural characters combined with molecular phylogenetic hypotheses have been used to revise the taxonomy of zoosporic true fungi. An example is the reclassification of Rhizophlyctis rosea-like fungal strains into four new families and three new genera within the order Rhizophlyctidales. One genus was Borealophlyctis, which included a Canadian isolate, DAOMC 229843. A recent survey of chytrid diversity in Alabama (USA) yielded additional strains (WJD 170, WJD 171) in the Borealophlyctis lineage. With light and transmission-electron microscopy we examined strains DAOMC 229843, WJD 170 and WJD 171. We also analyzed partial nuc 28S rDNA D1-D3 domains (28S) and nuc rDNA region encompassing the internal transcribed spacers 1 and 2 and 5.8S (ITS) sequences to determine the phylogenetic placement of the strains within Rhizophlyctidales. Based on molecular divergence and morphological differences from the type Borealophlyctis paxensis, we recognize DAOMC 229843, WJD 170 and WJD 171 as representatives of the new species Borealophlyctis nickersoniae.

Cilium axoneme internalization and degradation in chytrid fungi

Loss of the cilium is important for cell cycle progression and certain developmental transitions. Chytrid fungi are a group of basal fungi that have retained centrioles and cilia, and they can disassemble their cilia via axoneme internalization as part of the transition from free-swimming spores to sessile sporangia. While this type of cilium disassembly has been observed in many single-celled eukaryotes, it has not been well characterized because it is not observed in common model organisms. To better characterize cilium disassembly via axoneme internalization, we focused on chytrids Rhizoclosmatium globosum and Spizellomyces punctatus to represent two lineages of chytrids with different motility characteristics. Our results show that each chytrid species can reel in its axoneme into the cell body along its cortex on the order of minutes, while S. punctatus has additional faster ciliary compartment loss and lash-around mechanisms. S. punctatus retraction can also occur away from the cell cortex and is partially actin dependent. Post-internalization, the tubulin of the axoneme is degraded in both chytrids over the course of about 2 hr. Axoneme disassembly and axonemal tubulin degradation are both partially proteasome dependent. Overall, chytrid cilium disassembly is a fast process that separates axoneme internalization and degradation.

Synchytrium endobioticum, the potato wart disease pathogen

Potato wart disease is considered one of the most important quarantine pests for cultivated potato and is caused by the obligate biotrophic chytrid fungus Synchytrium endobioticum. This review integrates observations from early potato wart research and recent molecular, genetic, and genomic studies of the pathogen and its host potato. Taxonomy, epidemiology, pathology, and formation of new pathotypes are discussed, and a model for molecular S. endobioticum-potato interaction is proposed.

TAXONOMY

Currently classified as kingdom: Fungi, phylum: Chytridiomycota, class: Chytridiomycetes, order: Chytridiales, family: Synchytriaceae, genus: Synchytrium, species: Synchytrium endobioticum, there is strong molecular support for Synchytriaceae to be transferred to the order Synchytriales.

HOSTS AND DISEASE SYMPTOMS

Solanum tuberosum is the main host for S. endobioticum but other solanaceous species have been reported as alternative hosts. It is not known if these alternative hosts play a role in the survival of the pathogen in (borders of) infested fields. Disease symptoms on potato tubers are characterized by the warty cauliflower-like malformations that are the result of cell enlargement and cell multiplication induced by the pathogen. Meristematic tissue on tubers, stolons, eyes, sprouts, and inflorescences can be infected while the potato root system seems to be immune.

PATHOTYPES

For S. endobioticum over 40 pathotypes, which are defined as groups of isolates with a similar response to a set of differential potato varieties, are described. Pathotypes 1(D1), 2(G1), 6(O1), and 18(T1) are currently regarded to be most widespread. However, with the current differential set other pathogen diversity largely remains undetected.

PATHOGEN-HOST INTERACTION

A single effector has been described for S. endobioticum (AvrSen1), which is recognized by the potato Sen1 resistance gene product. This is also the first effector that has been described in Chytridiomycota, showing that in this fungal division resistance also fits the gene-for-gene concept. Although significant progress was made in the last decade in mapping wart disease resistance loci, not all resistances present in potato breeding germplasm could be identified. The use of resistant varieties plays an essential role in disease management.

Mycoplankton Biome Structure and Assemblage Processes Differ Along a Transect From the Elbe River Down to the River Plume and the Adjacent Marine Waters

Rivers are transport systems and supply adjacent ecosystems with nutrients. They also serve human well-being, for example as a source of food. Microorganism biodiversity is an important parameter for the ecological balance of river ecosystems. Despite the knowledge that fungi are key players in freshwater nutrient cycling and food webs, data on planktonic fungi of streams with higher stream order are scarce. This study aims to fill this knowledge gap by a fungi-specific 18S ribosomal RNA (rRNA) gene tag sequencing approach, investigating mycoplankton diversity in the Elbe River along a transect from shallow freshwater, to the estuary and river plume down to the adjacent marine waters (sections of seventh stream order number). Using multivariate analyses and the quantitative process estimates (QPEs) method, questions (i) of how mycoplankton communities as part of the river continuum change along the transect, (ii) what factors, spatial and environmental, play a role, and (iii) what assembly processes, such as selection or dispersion, operate along the transect, were addressed. The partitioning of mycoplankton communities into three significant distant biomes was mainly driven by local environmental conditions that were partly under spatial control. The assembly processes underlying the biomes also differed significantly. Thus, variable selection dominated the upstream sections, while undominated processes like ecological drift dominated the sections close to the river mouth and beyond. Dispersal played a minor role. The results suggest that the ecological versatility of the mycoplankton communities changes along the transect as response, for example, to a drastic change from an autotrophic to a heterotrophic system caused by an abrupt increase in the river depth. Furthermore, a significant salinity-dependent occurrence of diverse basal fungal groups was observed, with no clade found exclusively in marine waters. These results provide an important framework to help understand patterns of riverine mycoplankton communities and serve as basis for a further in-depth work so that fungi, as an important ecological organism group, can be integrated into models of, e.g., usage-balance considerations of rivers.

Polyrhizophydium stewartii, the first known rhizomycelial genus and species in the Rhizophydiales, is closely related to Batrachochytrium

Molecular and ultrastructural investigations of the Chytridiomycota during the last 20 years have led to the separation of new orders, including the Rhizophydiales. Most species in this order are morphologically similar, possessing monocentric, eucarpic, spherical thalli. Here, based on analysis of nuc 18S and 28S rDNA, we add the new genus and species Polyrhizophydium stewartii to the order. This saprobe of moribund aquatic plant leaves is the first known rhizomycelial species in the order. In our molecular phylogeny, P. stewartii groups with the amphibian pathogens Batrachochytriuim dendrobatidis and B. salamandrivorans, making it of particular interest to investigators studying evolutionary pathways associated with host-switching and morphological adaptation.

New species of aquatic chytrids from Oman

Oman is a desert country in the south of the Middle East. Springs and other water sources that harbor aquatic organisms can be separated by hundreds of kilometers. In Oct 2019, we isolated four freshwater aquatic fungi (Chytridiomycota) from benthic detritus baited with pine pollen on a general nutrient medium near Salalah, Oman. Database queries of nuc 28S rRNA (28S) and internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) revealed that one of these strains was Dinochytrium kinnereticum, a recently described algal pathogen from the Sea of Galilee. The other three strains had low molecular identity to available ITS sequences. These unknown strains varied in size and released endogenously swarming zoospores through papillae from mature zoosporangia. Zoospore ultrastructure was consistent with described species in the Rhizophydiales, and molecular phylogenetic results grouped these three strains into a clade in the genus Rhizophydium. We circumscribe these three strains as a sp. nov., thereby expanding the diversity within Rhizophydium described as the new species R. jobii. In doing so, we provide the first report of Chytridiomycota from Oman.

Fate of hepatotoxin microcystin during infection of cyanobacteria by fungal chytrid parasites

Chytrid parasites are increasingly recognized as ubiquitous and potent control agents of phytoplankton, including bloom-forming toxigenic cyanobacteria. In order to explore the fate of the cyanobacterial toxin microcystins (MCs) and assess potential upregulation of their production under parasite attack, a laboratory experiment was conducted to evaluate short- and long-term variation in extracellular and intracellular MC in the cyanobacteria Planktothrix agardhii and P. rubescens, both under chytrid infection and in the presence of lysates of previously infected cyanobacteria. MCs release under parasite infection was limited and not different to uninfected cyanobacteria, with extracellular toxin shares never exceeding 10%, substantially below those caused by mechanical lysis induced by a cold-shock. Intracellular MC contents in P. rubescens under infection were not significantly different from uninfected controls, whereas infected P. agardhii showed a 1.5-fold increase in intracellular MC concentrations, but this was detected within the first 48 hours after parasite inoculation and not later, indicating no substantial MC upregulation in cells being infected. The presence of lysates of previously infected cyanobacteria did not elicit higher intracellular MC contents in exposed cyanobacteria, speaking against a putative upregulation of toxin production induced via quorum sensing in response to parasite attack. These results indicate that chytrid epidemics can constitute a bloom decay mechanism that is not accompanied by massive release of toxins into the medium.