Hidden diversity in the non‐caryophyllaceous plant‐parasitic members of Microbotryum (Pucciniomycotina: Microbotryales)

Abstract

Members of the fungal genus Microbotryum are well‐known parasites on eudicotyledonous plant hosts. However, recent studies focused exclusively on Microbotryum species being parasites in the anthers of Caryophyllaceae in which strong host‐specificity was confirmed by molecular analyses. Consequently, species numbers have risen considerably as multi‐host parasites were split up in so‐called cryptic species. We subjected three non‐caryophyllaceous Microbotryum groups to molecular phylogenetic analyses to see whether we would confirm multi‐host morphospecies or if host‐specific cryptic species in these selected groups could be revealed as well (i.e. a group of non‐caryophyllaceous anther smuts, parasites on different Fallopia species, and parasites on Polygonum bistorta and Polygonum vi‐viparum). We applied a multiple analysis strategy to correct for varying alignment effects on a two‐locus dataset (ITS and LSU rDNA). The results obtained by the different approaches are uniform; high host‐specificity exists in the non‐ caryophyllaceous anther smuts, but overlapping host ranges occur in the parasites of Fallopia species. Results for the parasites of Polygonum are similar, with Microbotryum bistortarum being separated into three lineages and M. marginale forming a lineage on P. bistorta which apparently is conspecific with M. bistortarum p.p. Our study shows that phylogenetic patterns within Microbotryum are much more complicated than deduced from morphological observations alone. Even though Microbotryum species are highly host‐specific, it is impossible to identify species based solely on host taxa affiliation. Species status is reinstated for the anther smut on Salvia pratensis.     

Contrasting phylogenetic patterns of anther smuts (Pucciniomycotina: Microbotryum) reflect phylogenetic patterns of their caryophyllaceous hosts

Anther smuts in the genus Microbotryum often show very high host specificity toward their caryophyllaceous hosts, but some of the larger host groups such as Dianthus are crucially undersampled for these parasites so that the question of host specificity cannot be answered conclusively. In this study we sequenced the internal transcribed spacer (ITS) region of members of the Microbotryum dianthorum species complex as well as their Dianthus hosts. We compared phylogenetic trees of these parasites including sequences of anther smuts from other Caryophyllaceae, mainly Silene, with phylogenies of Caryophyllaceae that are known to harbor anther smuts. Additionally we tested whether observed patterns in parasites are due to shared ancestry or if geographic separation is a factor that should be taken into consideration in delimitating species. Parasites on Dianthus showed mainly an arbitrary distribution on Dianthus hosts, whereas parasites on other Caryophyllaceae formed well-supported monophyletic clades that corresponded to restricted host groups. The same pattern was observed in the Caryophyllaceae studied: morphologically described Dianthus species did not correspond well with monophyletic clades based on molecular data, whereas other Caryophyllaceae mainly did. We suggest that these different patterns primarily result from different breeding systems and speciation times between different host groups as well as difficulties in species delimitations in the genus Dianthus.     

Ein Beitrag zur Systematik und Entwicklungsbiologie höherer Pilze: Hefe-Typen der Basidiomyceten. Teil II: Microbotryum-Typ

In this and three further papers 205 yeasts and yeast states of Basidiomycetes and presumed relatives were investigated comparatively on the basis of the carbohydrate (neutral sugars) pattern of purified cell walls, urease-activity, diazonium blue B reaction on the production of extracellular amyloid compounds (EAS), fermentation of carbohydrates, and ubiquinone data. A clustering leading to the Protomyces-, the Microbotryum-, the Ustilago-, the Dacrymyces-, and the Tremella-type became apparent, especially from the qualitative and quantitative cell wall carbohydrate pattern. The different yeast types correspond well with 5S rRNA clusters known from the literature. 31 strains clustering within the Microbotryum-type comprise the phragmobasidial smut fungi of dicotyledonous hosts (Microbotryum. Sphacelotheca), the phragmobasidial Rhodosporidium- and Leucosporidium-species including some anamorph Rhodotorula-species, which lack an oxidative degradation of myo-inositol, the genera Sporobolomyces and Sporidiobolus, the Septobasidiales and some simple septate Auriculariales e.g. Agaricostilbum, Platygloea. Main characteristics of the Microbotryum-type are: 1. The absence of extracellular amyloid compounds. 2. The dominance of mannose and the presence of fucose as cell wall constituents. 3. A positive DBB-reaction and splitting of urea. Four Ustilago species parasitic on dicotyledonous hosts were transfered to Microbotryum (M. scabiosae, M. scorzonerae, M. cordae, M. vinosum) as a consequence from cell wall carbohydrate composition, production of rhodotorulic acid, and 5S rRNA sequence data from the literature. The predominance of mannose in the cell wall — otherwise only known from ascomycetous yeasts –, a type A secondary structure of 5S rRNA, a simple unifactorial mating system in all parasitic smut species suggest that the Microbotryum-type might be ancestral to the Ustilago-type. An evolution of simple (“siphonal”) holobasidia from “pseudotrichal” phragmobasidia will be discussed.     

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.     

Isolation of 44 polymorphic microsatellite loci in three host races of the phytopathogenic fungus Microbotryum violaceum

We report the development of 44 microsatellite markers in three host races of the fungus Microbotryum violaceum, a sexually transmitted disease of the Caryophyllaceae. An enrichment protocol was used to isolate microsatellite loci from three strains, collected, respectively, from the plant species Gypsophila repens, Dianthus sylvestris, and Silene vulgaris. Polymorphism and cross‐amplification were explored with 32 isolates of M. violaceum, collected on 12 different plant species in natural populations.     

Implications of molecular characters for the phylogeny of the Microbotryaceae (Basidiomycota: Urediniomycetes)

Background  

Anther smuts of the basidiomycetous genus Microbotryum on Caryophyllaceae are important model organisms for many biological disciplines. Members of Microbotryum are most commonly found parasitizing the anthers of host plants in the family Caryophyllaceae, however they can also be found on the anthers of members of the Dipsacaceae, Lamiaceae, Lentibulariaceae, and Portulacaceae. Additionally, some members of Microbotryum can be found infecting other organs of mainly Polygonaceae hosts. Based on ITS nrDNA sequences of members of almost all genera in Microbotryaceae, this study aims to resolve the phylogeny of the anther smuts and their relationship to the other members of the family of plant parasites. A multiple analysis strategy was used to correct for the effects of different equally possible ITS sequence alignments on the phylogenetic outcome, which appears to have been neglected in previous studies.     

PERMANENT GENETIC RESOURCES: Isolation of 60 polymorphic microsatellite loci in EST libraries of four sibling species of the phytopathogenic fungal complex Microbotryum

We report the development of 60 microsatellite markers on four species of the fungal complex Microbotryum, causing anther smut of the Caryophyllaceae. Microsatellites were found in four expressed sequence tag (EST) libraries, built from isolates of M. lychnis-dioicae, M. violaceum sensus stricto, M. lagerheimii and M. dianthorum, collected, respectively, from the plants Silene latifolia, S. nutans, S. vulgaris and Dianthus carthusianorum. Intrapopulation polymorphism was investigated using 24 isolates, and cross-amplification was explored using 23 isolates belonging to at least 10 different Microbotryum species. This study provides numerous microsatellite markers for population genetics and mapping studies.     

Studies in Heterobasidiomycetes, Part 31*). On the Anther Smuts of Silene vuigaris (Moench) Garcke

Microbotryum silenes-inflatae (DC) G. Deml & Oberw. and Microbotryum violaceoirregulare (Brandenburger & Schwinn) G. Deml & Oberw., both parasitic in the anthers of Silene vulgaris (Moench) Garcke, are compared by their morphology, karyology, and some cultural characteristics. The infection of their hosts is similar in both species, but causes different sizes of the flowers and different color of the spore mass. The teliospore initials of that smuts are produced in dikaryotic sporogenous hyphae. During gelatinization of the hyphal coat, surface ornamentations on the teliospores are formed. Mature teliospores are monokaryotic, and presumably diploid, reticulate in Microbotryum silenes-inflatae and echinulate in M. violaceo-irregulare. Teliospores of both species germinate without a resting periode. Germination results in a commonly three-celled promycelium, which in M. silenes-inflatae separates from the producing teliospore, while in M. violaceo-irregulare it remains on the teliospore during basidiospore formation. The basidiospores are monokaryotic and propagate by budding. Monokaryotic strains were isolated and characterized by standard yeast identification tests and by some enzymatic activities on solid media. While no differences in the enzymatic activities can be found, the species differ in their utilization of carbon sources.     

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

The competitive exclusion principle postulates that different species can only coexist in sympatry if they occupy distinct ecological niches. The goal of this study was to understand the geographical distribution of three species of Microbotryum anther‐smut fungi that are distantly related but infect the same host plants, the sister species Silene vulgaris and S. uniflora, in Western Europe. We used microsatellite markers to investigate pathogen distribution in relation to host specialization and ecological factors. Microbotryum violaceo‐irregulare was only found on S. vulgaris at high elevations in the Alps. Microbotryum lagerheimii could be subdivided into two genetically differentiated clusters, one on S. uniflora in the UK and the second on S. vulgaris in the Alps and Pyrenees. The most abundant pathogen species, M. silenes‐inflatae, could be subdivided into four genetic clusters, co‐occurring in the Alps, the UK and the Pyrenees, and was found on both S. vulgaris and S. uniflora. All three fungal species had high levels of homozygosity, in agreement with the selfing mating system generally observed in anther‐smut fungi. The three pathogen species and genetic clusters had large range overlaps, but occurred at sites with different elevations, temperatures and precipitation levels. The three Microbotryum species thus do not appear to be maintained by host specialization or geographic allopatry, but instead may occupy different ecological niches in terms of environmental conditions.     

Host‐specific differentiation in the anther smut fungus Microbotryum violaceum as revealed by microsatellites

The anther smut fungus Microbotryum violaceum ( = Ustilago violacea) is a parasite of many species of the Caryophyllaceae. Its host specificity has been debated since early this century, when cross‐inoculation experiments indicated the existence of host‐specific lineages. Recently, on the basis of spore ultrastructure, all presumed host races were lumped within M. violaceum. To measure gene flow among natural populations of anther smuts from different host species, we used microsatellite variation at 5 loci among samples from 8 Silene, 2 Saponaria, 2 Dianthus and 1 Gypsophila species. Most of the 326 M. violaceum samples investigated originated from the Swiss Alps and close surroundings. Microsatellite variation revealed almost perfect isolation among anther smut fungi from different host species. In addition, differentiation was supported by the nonrandom distribution of null alleles among samples from different host species and host genera. Null alleles were most abundant in anther smut samples from non‐Silene hosts. The resolution of genetic differentiation among anther smuts from different host species was highest in those from Silene species. Genetic relationships among samples as indicated by Neighbour‐Joining analysis based on genetic distances are discussed with respect to host phylogeny and host ecology. One sample was identified as Ustilago gausseni because it had verrucose instead of reticulate spores and was collected from Silene italica. Neighbour‐Joining analysis revealed that this sample was similar to the M. violaceum samples from other Silene host species. Therefore, our data question spore morphology as a reliable character for anther smut systematics.     

Finding candidate genes under positive selection in Non‐model species: examples of genes involved in host specialization in pathogens

Numerous genes in diverse organisms have been shown to be under positive selection, especially genes involved in reproduction, adaptation to contrasting environments, hybrid inviability, and host‐pathogen interactions. Looking for genes under positive selection in pathogens has been a priority in efforts to investigate coevolution dynamics and to develop vaccines or drugs. To elucidate the functions involved in host specialization, here we aimed at identifying candidate sequences that could have evolved under positive selection among closely related pathogens specialized on different hosts. For this goal, we sequenced c. 17 000–32 000 ESTs from each of four Microbotryum species, which are fungal pathogens responsible for anther smut disease on host plants in the Caryophyllaceae. Forty‐two of the 372 predicted orthologous genes showed significant signal of positive selection, which represents a good number of candidate genes for further investigation. Sequencing 16 of these genes in 9 additional Microbotryum species confirmed that they have indeed been rapidly evolving in the pathogen species specialized on different hosts. The genes showing significant signals of positive selection were putatively involved in nutrient uptake from the host, secondary metabolite synthesis and secretion, respiration under stressful conditions and stress response, hyphal growth and differentiation, and regulation of expression by other genes. Many of these genes had transmembrane domains and may therefore also be involved in pathogen recognition by the host. Our approach thus revealed fruitful and should be feasible for many non‐model organisms for which candidate genes for diversifying selection are needed.     

Isolates of Microbotryum violaceum from North American host species are phylogenetically distinct from their European host-derived counterparts

Microbotryum violaceum is a basidiomycete that infects the anthers of its Caryophyllaceae host species. Individual fungal isolates are host limited, though they are not morphologically distinct. This study used variable regions of the highly conserved gamma-tubulin, beta-tubulin, and ribosomal RNA-encoding genes to determine the relationships among M. violaceum fungal isolates from different host species and different geographical locations. Phylogenetic trees from intron nucleotide sequences in two protein-coding genes were compared to trees produced from internal transcribed spacers (ITS) of rDNA. Phylogenetic analyses suggested that there are two clades, one from North America and one from Europe. Isolates from both clades grouped according to host species, although in some analyses isolates from closely related host species were placed together. These results are consistent with the view that M. violaceum has experienced cospeciation with its hosts.     

The impact of genome defense on mobile elements in <Emphasis Type="Italic">Microbotryum</Emphasis>

Repeat induced point mutation (RIP), a mechanism causing hypermutation of repetitive DNA sequences in fungi, has been described as a ‘genome defense’ which functions to inactivate mobile elements and inhibit their deleterious effects on genome stability. Here we address the interactions between RIP and transposable elements in the Microbotryum violaceum species complex. Ten strains of M. violaceum, most of which belong to different species of the fungus, were all found to contain intragenomic populations of copia-like retrotransposons. Intragenomic DNA sequence variation among the copia-like elements was analyzed for evidence of RIP. Among species with RIP, there was no significant correlation between the frequency of RIP-induced mutations and inferred transposition rate based on diversity. Two strains of M. violaceum, from two different plant species but belonging to the same fungal lineage, contained copia-like elements with very low diversity, as would result from a high transposition rate, and these were also unique in showing no evidence of the hypermutation patterns indicative of the RIP genome defense. In this species, evidence of RIP was also absent from a Class II helitron-like transposable element. However, unexpectedly the absolute repetitive element load was lower than in other strains.     

Dynamic linkage relationships to the mating‐type locus in automictic fungi of the genus Microbotryum

Regions of the chromosomes determining mating compatibility in some fungi, including Microbotryum lychnidis‐dioicae and Neurospora tetrasperma, exhibit suppressed recombination similar to sex chromosomes in plants and animals, and recent studies have sought to apply basic theories of sex chromosome evolution to fungi. A phylogeny of the MTL1 locus in Microbotryum indicates that it has become part of the nonrecombining regions of the mating‐type chromosomes in multiple independent events, and that recombination may have been subsequently restored in some cases. This illustrates that fungal mating‐type chromosomes can exhibit linkage relationship that are quite dynamic, adding to the list of similarities to animal or plant sex chromosomes. However, fungi such as M. lychnidis‐dioicae and N. tetrasperma exhibit an automictic mating system, for which an alternate theoretical framework exists to explain the evolution of linkage with the mating‐type locus. This study encourages further comparative studies among fungi to evaluate the role of mating systems in determining the evolution of fungal mating‐type chromosomes.     

The great tit (Parus major) – a misclassified ring species

The great tit (Parus major) has been considered to be the most typical example of an avian ring species. The terminal taxa of the ring (major and minor sectors) are supposed to be reproductively isolated in a zone of secondary contact in the middle Amur valley, Siberia. Our study combines molecular markers (cytochrome‐b), bioacoustic analyses and morphological characters to judge the ring species status of the great tit complex. Despite a notable percentage of intermediately coloured birds in the mixed population of middle Amur, a lack of mitochondrial introgression between the major and minor sectors and a small number of true hybrids among voucher specimens from this area suggest at least a partial reproductive barrier between both sectors. In contrast, variation of morphological and especially acoustic characters along the ring‐shaped area and the phylogenetic structure of the P. major group do not match the ring species concept. Bioacoustic and molecular data (cytochrome‐b sequences) reveal two large and closely related subspecies blocks, the sectors major and bokharensis in the Western Palaearctic and central Asia, and the sectors minor and cinereus in the Eastern Palaearctic and South‐east Asia, respectively. The two western sectors diverged only recently (0.5 Mya) and they were separated from the eastern group by Pleistocene events about 1.5 Mya. Songs from allopatric regions of the two subspecies blocks differ distinctly in frequency parameters and element composition. In the area of secondary contact, males of all phenotypes share the same frequency range of song, close to the range of the typical minor song. Hybrids and major males sing mixed repertoires of typical major and minor strophe types as well as mixed strophes. In contrast, phenotypic minor males display only pure minor strophes. Differences in mate choice and mating success based on repertoire size are believed to uphold the reproductive barrier between major and minor birds in the area of sympatry. Taxonomic consequences suggest three separate species in the Parus major complex: Parus major s.s. (including the very closely related bokharensis sector), Parus minor and Parus cinereus. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 86 , 153–174.     

Ecogeographic and genetic evaluation of endemic species in the Maritime Alps: the case of Moehringia lebrunii and M. sedoides (Caryophyllaceae)

Abstract

The Maritime Alps are one of the ‘hot spots’ in the Mediterranean basin. This study investigated two endemic plants, Moehringia lebrunii and Moehringia sedoides (Caryophyllaceae) in order to increase knowledge of the vegetation of this region, and to investigate possible conservation strategies. Ecogeographic surveys and molecular analyses were undertaken. Gene diversity, the Shannon index and G_ST were calculated within and among populations of the two species based on ISSR data. The populations of M. lebrunii had a density ranging between 0.04 and 0.86 individual/m² and a rather low inner genetic variability value. According to IUCN Red List Criteria, the current status of M. lebrunii is Endangered [EN B2ab(ii, iv)]. M. sedoides is an endemic of the SW Alps (not exclusive of the Maritime Alps), and is very abundant within the core of the range. Its range of occurrence is smaller than previously reported; nevertheless, the species is not under threat. This taxon showed a population density ranging between 0.03 and 0.58 individual/m². Genetic variability values revealed a high variation among the species. Only peripheral populations seemed to suffer from their segregated position. Thus, M. sedoides is to be considered Critically Endangered [CR B1ab(i, ii, iii, iv) + 2ab(i, ii, iii, iv)] for Italy according to Regional Guidelines.     

Microbotryum heliospermae, a new anther smut fungus parasitic on Heliosperma pusillum in the mountains of the European Alpine System

The members of the smut genus Microbotryum are pathogens of a wide range of host plant species from nine dicotyledonous families. Within the genus, the species sporulating in anthers of Caryophyllaceae form a monophyletic group that in recent years attracted much interest in various biological studies. The phylogenetic framework developed for species delimitation within Microbotryum revealed that high level host-specificity is a major feature of most caryophyllaceous anther smuts. However, the great number of anther smut specimens on diverse host plant species reported worldwide has still not been included in phylogenetic analyses due to the inaccessibility of recently collected specimens, and thus many species remain still undiscovered. In this study, anther smut specimens on Heliosperma pusillum originating from all main mountain ranges of the European Alpine System were examined using partial rDNA sequence and/or morphological analyses. The investigation revealed that all specimens are morphologically uniform and phylogenetically represent a monophyletic lineage, sister to Microbotryum lagerheimii complex on Atocion rupestre/Silene lacera/Silene vulgaris/Viscaria vulgaris. This lineage cannot be attributed to any of the previously described species, and therefore the smut in anthers of H. pusillum is described and illustrated here as a new species, Microbotryum heliospermae. The species is known from subalpine zone of the Alps, the Carpathians, the Dinaric Alps, and the Pyrenees, inhabiting host plants growing in open spring communities or semihumid mountain meadows.     

Seed morphology in Moehringia L. and its taxonomic significance in comparative studies within the Caryophyllaceae

Seeds of 30 species of Moehringia and 12 representatives of the Caryophyllaceae were examined with the Scanning Electron Microscope. High diversity was found in seed coat micromorphology, and a number of novel morphological features have been observed. Comparison with other representatives of the Caryophyllaceae has provided new insight into the potential taxonomic value of discrete morphological characters. Though many characters appear informative within Moehringia, they are affected by a high level of homoplasy when considered in a wider phylogenetic context. Smooth seed is the common condition in Moehringia, except for Eastern Balkan and Iberian species that maintain a secondary ornamentation of the testa cells resembling the plesiomorphic Caryophyllaceae-type. Five types of strophioles were recognized, in accordance with previous literature. Among these, the strophiole of the Iberian species appears very distinctive and a proper strophiole could not be verified in M. glochidisperma and M. fontqueri.     

Pollution-related changes in diets of two insectivorous passerines

Insectivorous birds living in polluted areas are not only exposed to pollutants but they may also be affected by changes in their invertebrate food. The populations of many invertebrate species are affected by environmental pollution and such changes may lead to differences in the diet of insectivorous birds. We examined nestling food quality (invertebrate composition and heavy metal levels) and breeding performance of two cavity-nesting passerines, the Great tit, Parus major, and the pied flycatcher, Ficedula hypoleuca, in an area with long-term heavy metal pollution by a copper smelter. There were no differences in feeding frequencies or the amount of food that parents provided to their nestlings between polluted and unpolluted sites, but food quality in a polluted area differed from that of the control area in both bird species. P. major took more beetles and variable “flying insects” and less caterpillars (of smaller size) and moths in the polluted area as compared to the unpolluted one. F. hypoleuca ate more beetles and larvae and less moths and spiders in the polluted area. Breeding success of P. major was better when the nestling diet contained a large proportion of caterpillars and the relationship was especially strong in the polluted area. On the contrary, F. hypoleuca broods succeeded equally well with variable diets. Our data suggest that a more opportunistic forager, F. hypoleuca, is less vulnerable to a changing invertebrate composition caused by human environmental impacts than a caterpillar specialist, P. major. In a heavy metal polluted area, F. hypoleuca seems to be more sensitive to a decreased amount of Ca rich food items (e.g. snails) while P. major suffers especially from the lack of carotenoid rich caterpillars. Our results emphasize the importance of secondary environmental changes, like food quality, in addition to direct impacts of pollutants.