Co-occurrence among three divergent plant-castrating fungi in the same Silene host species

Genetic Independence of Naturally Correlated Variation in Resistance to Endemic and Novel Pathogens

The emergence of new diseases is an urgent concern, but hosts can also vary in resistance to pathogens that are novel to them, facilitating evolutionary rescue. However, little is known about the genetic source for polymorphic resistance to novel pathogens or its relationship to defences against endemic diseases. With anther-smut disease from wild plant populations, we used selection experiments and genetic analyses to show that resistances to novel and endemic pathogens are genetically independent, despite being positively correlated in nature. Moreover, novel-pathogen resistance presented a much simpler genetic basis and more rapid response to selection. We demonstrate that polymorphic resistance to a newly introduced disease is genetically determined and not an extension of defences against the related endemic pathogen, challenging the conventional view of nonhost resistance.

High diversity, close genetic relatedness, and favorable living conditions benefit species co-occurrence of gut microbiota in Brandt's vole

Introduction

Revealing factors and mechanisms in determining species co-existence are crucial to community ecology, but studies using gut microbiota data are still lacking.

Methods

Using gut microbiota data of 556 Brandt's voles from 37 treatments in eight experiments, we examined the relationship of species co-occurrence of gut microbiota in Brandt's voles (Lasiopodomys brandtii) with genetic distance (or genetic relatedness), community diversity, and several environmental variables.

Results

We found that the species co-occurrence index (a larger index indicates a higher co-occurrence probability) of gut microbiota in Brandt's voles was negatively associated with the genetic distance between paired ASVs and the number of cohabitating voles in the experimental space (a larger number represents more crowding social stress), but positively with Shannon diversity index, grass diets (representing natural foods), and non-physical contact within an experimental space (representing less stress).

Discussion

Our study demonstrated that high diversity, close genetic relatedness, and favorable living conditions would benefit species co-occurrence of gut microbiota in hosts. Our results provide novel insights into factors and mechanisms that shape the community structure and function of gut microbiota and highlight the significance of preserving the biodiversity of gut microbiota.

Quantitative disease resistance in wild Silene vulgaris to its endemic pathogen Microbotryum silenes-inflatae

The evolution of disease resistances is an expected feature of plant-pathogen systems, but whether the genetics of this trait most often produces qualitative or quantitative phenotypic variation is a significant gap in our understanding of natural populations. These two forms of resistance variation are often associated with differences in number of underlying loci, the specificities of host-pathogen coevolution, as well as contrasting mechanisms of preventing or slowing the infection process. Anther-smut disease is a commonly studied model for disease of wild species, where infection has severe fitness impacts, and prior studies have suggested resistance variation in several host species. However, because the outcome of exposing the individual host to this pathogen is binary (healthy or diseased), resistance has been previously measured at the family level, as the proportion of siblings that become diseased. This leaves uncertain whether among-family variation reflects contrasting ratios of segregating discrete phenotypes or continuous trait variation among individuals. In the host Silene vulgaris, plants were replicated by vegetative propagation in order to quantify the infection rates of the individual genotype with the endemic anther-smut pathogen, Microbotryum silenes-inflatae. The variance among field-collected families for disease resistance was significant, while there was unimodal continuous variation in resistance among genotypes. Using crosses between genotypes within ranked resistance quartiles, the offspring infection rate was predicted by the parental resistance values. While the potential remains in this system for resistance genes having major effects, as there were suggestions of such qualitative resistance in a prior study, here the quantitative disease resistance to the endemic anther-smut pathogen is indicated for S. vulgaris. The variation in natural populations and strong heritability of the trait, combined with severe fitness consequences of anther-smut disease, suggests that resistance in these host populations is highly capable of responding to disease-induced selection.

Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex

Sex chromosomes often carry large nonrecombining regions that can extend progressively over time, generating evolutionary strata of sequence divergence. However, some sex chromosomes display an incomplete suppression of recombination. Large genomic regions without recombination and evolutionary strata have also been documented around fungal mating-type loci, but have been studied in only a few fungal systems. In the model fungus Podospora anserina (Ascomycota, Sordariomycetes), the reference S strain lacks recombination across a 0.8-Mb region around the mating-type locus. The lack of recombination in this region ensures that nuclei of opposite mating types are packaged into a single ascospore (pseudohomothallic lifecycle). We found evidence for a lack of recombination around the mating-type locus in the genomes of ten P. anserina strains and six closely related pseudohomothallic Podospora species. Importantly, the size of the nonrecombining region differed between strains and species, as indicated by the heterozygosity levels around the mating-type locus and experimental selfing. The nonrecombining region is probably labile and polymorphic, differing in size and precise location within and between species, resulting in occasional, but infrequent, recombination at a given base pair. This view is also supported by the low divergence between mating types, and the lack of strong linkage disequilibrium, chromosomal rearrangements, transspecific polymorphism and genomic degeneration. We found a pattern suggestive of evolutionary strata in P. pseudocomata. The observed heterozygosity levels indicate low but nonnull outcrossing rates in nature in these pseudohomothallic fungi. This study adds to our understanding of mating-type chromosome evolution and its relationship to mating systems.

Resistance Correlations Influence Infection by Foreign Pathogens

AbstractReciprocal selection promotes the specificity of host-pathogen associations and resistance polymorphisms in response to disease. However, plants and animals also vary in response to pathogen species not previously encountered in nature, with potential effects on new disease emergence. Using anther smut disease, we show that resistance (measured as infection rates) to foreign pathogens can be correlated with standing variation in resistance to an endemic pathogen. In Silene vulgaris, genetic variation in resistance to its endemic anther smut pathogen correlated positively with resistance variation to an anther smut pathogen from another host, but the relationship was negative between anther smut and a necrotrophic pathogen. We present models describing the genetic basis for assessing resistance relationships between endemic and foreign pathogens and for quantifying infection probabilities on foreign pathogen introduction. We show that even when the foreign pathogen has a lower average infection ability than the endemic pathogen, infection outcomes are determined by the sign and strength of the regression of the host's genetic variation in infection rates by a foreign pathogen on variation in infection rates by an endemic pathogen as well as by resistance allele frequencies. Given that preinvasion equilibria of resistance are determined by factors including resistance costs, we show that protection against foreign pathogens afforded by positively correlated resistances can be lessened or even result in elevated infection risk at the population level, depending on local dynamics. Therefore, a pathogen's emergence potential could be influenced not only by its average infection rate but also by resistance variation resulting from prior selection imposed by endemic diseases.

The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks

Here we review how evolving species concepts have been applied to understand yeast diversity. Initially, a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells, and growth profiles. Later the biological species concept was added, which applied data from mating experiments. Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology, leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA. At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy, including yeasts, because various studies revealed a relatively good correlation between the biological species concept and sequence divergence. The application of genome information is becoming increasingly common, and we strongly recommend the use of complete, rather than draft genomes to improve our understanding of species and their genome and genetic dynamics. Complete genomes allow in-depth comparisons on the evolvability of genomes and, consequently, of the species to which they belong. Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts. Note that hybrids may greatly differ in their post-hybridization development. Future in-depth studies, initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes, such as hybridization.

Empirical Support for the Pattern of Competitive Exclusion between Insect Parasitic Fungi

Fungal entomopathogens are largely facultative parasites and play an important role in controlling the density of insect populations in nature. A few species of these fungi have been used for biocontrol of insect pests. The pattern of the entomopathogen competition for insect individuals is still elusive. Here, we report the empirical competition for hosts or niches between the inter- and intra-species of the entomopathogens Metarhizium robertsii and Beauveria bassiana. It was found that the synergistic effect of coinfection on virulence increase was not evident, and the insects were largely killed and mycosed by M. robertsii independent of its initial co-inoculation dosage and infection order. For example, >90% dead insects were mycosed by M. robertsii even after immersion in a spore suspension with a mixture ratio of 9:1 for B. bassiana versus M. robertsii. The results thus support the pattern of competitive exclusion between insect pathogenic fungi that occurred from outside to inside the insect hosts. Even being inferior to compete for insects, B. bassiana could outcompete M. robertsii during co-culturing in liquid medium. It was also found that the one-sided mycosis of insects occurred during coinfection with different genotypic strains of either fungi. However, parasexual recombination was evident to take place between the compatible strains after coinfection. The data of this study can help explain the phenomena of the exclusive mycosis of insect individuals, but co-occurrence of entomopathogens in the fields, and suggest that the synergistic effect is questionable regarding the mixed use of fungal parasites for insect pest control.

Floral fungal-bacterial community structure and co-occurrence patterns in four sympatric island plant species

Flowers' fungal and bacterial communities can exert great impacts on host plant wellness and reproductive success-both directly and indirectly through species interactions. However, information about community structure and co-occurrence patterns in floral microbiome remains scarce. Here, using culture-independent methods, we investigated fungal and bacterial communities associated with stamens and pistils of four plant species (Scaevola taccada, Ipomoea cairica, Ipomoea pes-caprae, and Mussaenda kwangtungensis) growing together under the same environment conditions in an island located in South China. Plant species identity significantly influenced community composition of floral fungi but not bacteria. Stamen and pistil microbiomes did not differ in community composition, but differed in co-occurrence network topological features. Compared with the stamen network, pistil counterpart had fewer links between bacteria and fungi and showed more modular but less concentrated and connected structure. In addition, degree distribution of microbial network in each host species and each microhabitat (stamen or pistil) followed a significant power-law pattern. These results enhance our understanding in the assembly principles and ecological interactions of floral microbial communities.

The smut fungi of Greenland

The first taxonomic treatment of the smut fungi in Greenland is provided. A total of 43 species in 11 genera are treated and illustrated by photographs of sori, microphotographs of spores in LM and SEM, and distribution maps. Two species, Anthracoidea pseudofoetidae and Urocystis tothii, are recorded as new from North America. Thirteen species, Anthracoidea altera, A. capillaris, A. limosa, A. liroi, A. pseudofoetidae, A. scirpoideae, A. turfosa, Microbotryum lagerheimii, M. stellariae, Schizonella elynae, Stegocintractia luzulae, Urocystis fischeri, and U. tothii, are reported for the first time from Greenland. Three new fungus-host combinations, Anthracoidea capillaris on Carex boecheriana, Anthracoidea pseudofoetidae on Carex maritima, and Urocystis tothii on Juncus biglumis, are given. Five plant species are reported as new hosts of smut fungi in Greenland, namely, Carex nigra for Anthracoidea heterospora, C. canescens for Anthracoidea karii, C. fuliginosa subsp. misandra for Anthracoidea misandrae, C. maritima for Orphanomyces arcticus, and C. fuliginosa subsp. misandra for Schizonella melanogramma. Three species, Microbotryum violaceum s. str. (recorded as 'Ustilago violacea'), Urocystis anemones, and U. junci, which were previously reported from Greenland, are considered wrongly identified. Additional distribution records are given for 12 species from Greenland: Anthracoidea bigelowii, A. caricis, A. elynae, A. lindebergiae, A. misandrae, A. nardinae, A. rupestris, A. scirpi, Schizonella melanogramma, Stegocintractia hyperborea, Urocystis agropyri, and U. sorosporioides. The most numerous distribution groups are the following: circumpolar-alpine and Arctic-alpine species - 14; circumboreal-polar species - 10; and circumpolar and Arctic species - 6. The most widely distributed smut fungi in Greenland were Anthracoidea bigelowii, A. elynae, Microbotryum bistortarum, and M. vinosum. Most species were found in the High Arctic zone (29 species), while from the Low Arctic zone and the Subarctic zone, 26 and 19 species were known, respectively. Ten species, Anthracoidea bigelowii, A. capillaris, A. elynae, Microbotryum bistortarum, M. koenigiae, M. pustulatum, M. silenes-acaulis, M. vinosum, Schizonella elynae, and Urocystis sorosporioides, were recorded from all three zones. Only plants belonging to six families, Cyperaceae, Poaceae, Juncaceae, Ranunculaceae, Caryophyllaceae, and Polygonaceae, out of a total of 55 in the flora of Greenland, hosted smut fungi. Cyperaceae was the plant family with most host species (23). Carex was the genus with the highest number of host species (22). The total number of the host plants (45 species) was 8.5 % out of a total of 532 vascular plants in the flora of Greenland. A new combination in Carex, C. macroprophylla subsp. subfilifolia, is proposed for Kobresia filifolia subsp. subfilifolia.

Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics

Anther-smut fungi provide a powerful system to study host-pathogen specialization and coevolution, with hundreds of Microbotryum species specialized on diverse Caryophyllaceae plants, castrating their hosts through manipulation of the hosts' reproductive organs to facilitate disease transmission. Microbotryum fungi have exceptional genomic characteristics, including dimorphic mating-type chromosomes, that make this genus anexcellent model for studying the evolution of mating systems and their influence on population genetics structure and adaptive potential. Important insights into adaptation, coevolution, host specialization, and mating system evolution have been gained using anther-smut fungi, with new insights made possible by the recent advent of genomic approaches. We illustrate with Microbotryum case studies how using a combination of comparative genomics, population genomics, and transcriptomics approaches enables the integration of different evolutionary perspectives across different timescales. We also highlight current challenges and suggest future studies that will contribute to advancing our understanding of the mechanisms underlying adaptive processes in populations of fungal pathogens.

Convergent recombination cessation between mating-type genes and centromeres in selfing anther-smut fungi

The degree of selfing has major impacts on adaptability and is often controlled by molecular mechanisms determining mating compatibility. Changes in compatibility systems are therefore important evolutionary events, but their underlying genomic mechanisms are often poorly understood. Fungi display frequent shifts in compatibility systems, and their small genomes facilitate elucidation of the mechanisms involved. In particular, linkage between the pre- and postmating compatibility loci has evolved repeatedly, increasing the odds of gamete compatibility under selfing. Here, we studied the mating-type chromosomes of two anther-smut fungi with unlinked mating-type loci despite a self-fertilization mating system. Segregation analyses and comparisons of high-quality genome assemblies revealed that these two species displayed linkage between mating-type loci and their respective centromeres. This arrangement renders the same improved odds of gamete compatibility as direct linkage of the two mating-type loci under the automictic mating (intratetrad selfing) of anther-smut fungi. Recombination cessation was found associated with a large inversion in only one of the four linkage events. The lack of trans-specific polymorphism at genes located in nonrecombining regions and linkage date estimates indicated that the events of recombination cessation occurred independently in the two sister species. Our study shows that natural selection can repeatedly lead to similar genomic patterns and phenotypes, and that different evolutionary paths can lead to distinct yet equally beneficial responses to selection. Our study further highlights that automixis and gene linkage to centromeres have important genetic and evolutionary consequences, while being poorly recognized despite being present in a broad range of taxa.

Sympatry and interference of divergent Microbotryum pathogen species

The impact of infectious diseases in natural ecosystems is strongly influenced by the degree of pathogen specialization and by the local assemblies of potential host species. This study investigated anther-smut disease, caused by fungi in the genus Microbotryum, among natural populations of plants in the Caryophyllaceae. A broad geographic survey focused on sites of the disease on multiple host species in sympatry. Analysis of molecular identities for the pathogens revealed that sympatric disease was most often due to co-occurrence of distinct, host-specific anther-smut fungi, rather than localized cross-species disease transmission. Flowers from sympatric populations showed that the Microbotryum spores were frequently moved between host species. Experimental inoculations to simulate cross-species exposure to the pathogens in these plant communities showed that the anther-smut pathogen was less able to cause disease on its regular host when following exposure of the plants to incompatible pathogens from another host species. These results indicate that multi-host/multi-pathogen communities are common in this system and they involve a previously hidden mechanism of interference between Microbotryum fungi, which likely affects both pathogen and host distributions.

Multiple infections, relatedness and virulence in the anther-smut fungus castrating Saponaria plants

Multiple infections (co-occurrence of multiple pathogen genotypes within an individual host) can have important impacts on diseases. Relatedness among pathogens can affect the likelihood of multiple infections and their consequences through kin selection. Previous studies on the castrating anther-smut fungus Microbotryum lychnidis-dioicae have shown that multiple infections occur in its host plant Silene latifolia. Relatedness was high among fungal genotypes within plants, which could result from competitive exclusion between unrelated fungal genotypes, from population structure or from interactions between plant and fungal genotypes for infection ability. Here, we aimed at disentangling these hypotheses using M. saponariae and its host Saponaria officinalis, both experimentally tractable for these questions. By analysing populations using microsatellite markers, we also found frequent occurrence of multiple infections and high relatedness among strains within host plants. Infections resulting from experimental inoculations in the greenhouse also revealed high relatedness among strains co-infecting host plants, even in clonally replicated plant genotypes, indicating that high relatedness within plants did not result merely from plant x fungus interactions or population structure. Furthermore, hyphal growth in vitro was affected by the presence of a competitor growing nearby and by its genetic similarity, although this latter effect was strain-dependent. Altogether, our results support the hypothesis that relatedness-dependent competitive exclusion occurs in Microbotryum fungi within plants. These microorganisms can thus respond to competitors and to their level of relatedness.