Abstract

In 2011, the class Archaeorhizomycetes was described from one cultured species and environmental sequences representing over hundred OTUs as proxies for species. Since then one more species has been cultured and described but estimates based on publically available sequences at the time suggest that the class encompass close to 500 species. Both described representatives of the class have been isolated from surface sterilized root tips of coniferous forest trees. Both grow on various carbon sources and based on pine root colonization experiments they appear to be non-pathogenic. No mycorrhizal structures have yet been observed in colonized roots. Enhanced root growth and branching has been observed in Arabidopsis thaliana when grown with either of the two species. Together these results suggest that both Archaeorhizomyces finlayi and Archaeorhizomyces borealis are facultative root endophytes. But what does this tell us about the un-cultured species in the class?

Analysis of below ground compartment specialisation in A. thaliana grown in natural soils demonstrated that three Archaeorhizomycetes OTUs were significantly enriched in the rhizosphere compartment rather than in endosphere and bulk soil belonged to. Using UNITE species hypothesis we can learn more about the distribution and habitats of these species, while continuing to develop A. thaliana as a model to identify plant host association of un-cultured Archaeorhizomycetes.

There are several challenges in resolving ecological roles of uncultured fungal species. Firstly, the delamination of environmental species itself is crucial but not uncontroversial. Secondly defining and testing ecological roles of non-cultured fungi is challenging. In this presentation I will discuss some approaches taken in my group to disentangle the ecological role of species in Archaeorhizomycetes, including preliminary comparative genome analysis.

Using long amplicon PacBio sequences from soil samples representing three distinct soil layers at a well-studied field site in Sweden we delimitated thirteen distinct groups of sequences and propose that these represent phylogenetically distinct species. One of these being A. finlayi. By comparing the ITS region of the long reads with short read sequences from metabarcoding studies at the site we concluded that species sampling was exhaustive. Based on the distinct chemical characteristics of different soil horizons we propose that these represent different habitats for soil fungi. We analysed distribution of the thirteen species across three soil horizons as a proxy for species specific niche preference. This analysis supported that the phylogenetic species represented ecologically distinct species. Because rare species have few observations only eleven of the species were firmly supported. In accordance with earlier observations A. finlayi was associated with the mineral B horizon and we conclude that closely related species had rather similar distribution. Our approach demonstrates that it is possible to delaminate fungal species using environmental data alone but the absence of type material may limit the relevance of formally naming species based on such data. However, communication and scientific progress in the field of environmental mycology is severely hampered by the lack of names. I think environmental species need names but these should be distinguishable from those associated with biological type material.

Abstract

Current estimation of fungal biodiversity of 1.5 million species is considered a vast underestimate by many scientists because we have a limited understanding of the diversity of fungi living inside plants. Foliar fungal endophytes (FFE) ubiquitously and asymptomatically inhabit the photosynthetic tissues of all plant phyla, but their biodiversity is only beginning to be fully uncovered with recent advances in high-throughput sequencing. Their ecological roles remain elusive without detailed studies of their natural history. Here we intensively sampled diverse plant communities across a latitudinal gradient in North America while focusing specifically on evergreen pine hosts and their host-specific endophytes. We utilize a collection of cultures in conjunction with high-throughput sequencing to examine previously unexplored patterns of host specificity that help estimate regional diversity and assign potential ecological roles to host-specific endophytic species. We test hypotheses that consider climate and plant-host specialization as causative mechanisms of FFE species diversification with multivariate community and phylogeographic analyses that control for spatial, temporal, and environmental effects previously known to bias species diversity patterns. We show that fungal diversity measured per plant can give qualitatively different biodiversity patterns than when diversity is measured per plant community. Furthermore, we demonstrate how a robust measure of host specificity requires both standardized and intense sampling per plant community. The implications of high host-specificity in the temperate forests and low host-specificity in the tropics on the estimation of alpha, beta and gamma diversity of fungal endophytes will be discussed. Ongoing work will highlight the complementarity of intensively sampling the whole plant community with deep sequencing of single host species to understand the biotic and abiotic influences of fungal endophyte diversification and their ecologies.

Abstract

The agricultural relevance of commensal yeasts inhabiting the phylloplane of leafy green vegetables is still poorly understood. Our current research describing the culturable and total fungal communities associated with Romaine lettuce reported that basidiomycetous yeasts in Sporidiobolales and Tremellales are the most common fungal groups found in this broadly consumed vegetable. We also discovered that a single undescribed species, the sister of Sporobolomyces roseus (S. cfr. roseus), was constantly present in the majority of lettuce plants examined. Here, we present preliminary results of greenhouse experiments designed to evaluate the capabilities of S. cfr. roseus as a bioprotective agent against the establishment of fungal pathogens on Romaine lettuce. All of the experiments were conducted in a BL-2 biosecurity green house, where lettuce seedlings were grown in 12 h photoperiod. First, we demonstrated that S. cfr. roseus is not an inhabitant of lettuce grown under greenhouse conditions. Second, we demonstrated successful colonization of the lettuce phylloplane by S. cfr. roseus and it did not induce any antagonistic immune response in the host. Third, in co-inoculation experiments, we found that the well-known plant pathogen Botrytis cinerea significantly did not induce necrosis on lettuce leaves when seedlings were previously inoculated with S. cfr. roseus. In sum, our results suggested that S. cfr. roseus could be used as a protective agent against the establishment of fungal pathogens on lettuce. The inoculation of commensal red yeasts to leafy green vegetables may also increase the nutritional value of pro-vitamin A, a compound obtained from the digestion of the carotenoid pigments present in vacuoles in the Sporidiobolales yeasts.

Abstract

Moniliophthora roreri is the causal agent of frosty pod rot of cacao (FPR). FPR is a disease that, since the 1950’s, has progressively and severely invaded cacao growing areas from almost all of Latin America but has not yet reached the major world cacao producing regions of Brazil, West Africa and Southeast Asia. This situation makes M. roreri one of the most threatening plant pathogens in the world. The fungus belongs to the Marasmiaceae (Agaricales, Basidiomycota) and no evidence of sexual reproduction has ever been found for this fungus. We have conducted a population genetic study in South America and found that the countries harboring the highest allelic diversity are Colombia and Ecuador, where the first reports of FPR took place. Despite this diversity, thus far we have found that only two clonal lineages appear to be responsible for the majority of invasive FPR. A single clonal lineage is responsible for FPR in Peru and Bolivia, while invasion of this disease throughout Central America, Mexico and Jamaica, was accomplished by another clonal lineage. The factors that contributed to the overall success of these two clones remain unknown, although we have previously determined that they carry separate mating types. In this study, we generated genomic, transcriptomic and comparative culture data to examine the characteristics correlated with the invasive success in this fungus. These and other factors that may explain the overall success of these two clonal lineages will be discussed.

Abstract

Colletotrichum gloeosporioides is an economically important plant fungal pathogen causing substantial yield losses in different host plants. It can infect variety of host plants; however, it is still not clear, whether there is any correlation between certain genotypes of this pathogen with the host. It becomes important to establish such a correlation between genotypes and host specificity, because it may be useful when breeding for resistance or monitoring the sensitivity of fungicides across a collection of well-defined isolates. Therefore, to understand the genetic diversity, host specificity and molecular epidemiology of this fungus, we have developed a novel, high resolution multi-locus microsatellite typing (MLMT) method. Bioinformatic analysis of part of C. gloeosporioides unannotated genome sequence yielded eight potential microsatellite loci, of which five, CG1 (GT)n, CG2 (GT1)n, CG3 (TC)n, CG4 (CT)n, and CG5 (CT1)n were selected for further study based on their universal amplification potential, reproducibility, and repeat number polymorphism. The selected microsatellites were used to analyze 31 strains of C. gloeosporioides isolated from 20 different host plants from India. All microsatellite loci were found to be polymorphic, and the approximate fragment sizes of microsatellite loci CG1, CG2, CG3, CG4, and CG5 were in ranges of 213–241, 197–227, 231–265, 209–275 bp, and 132–188 bp, respectively. Among the 31 isolates, 55 different genotypes were identified. The Simpson’s index of diversity (D) values for the individual locus ranged from 0.79 to 0.92, with the D value of all combined five microsatellite loci being 0.99. Microsatellite data analysis revealed that isolates from Ocimum sanctum, Capsicum annuum (chili pepper), and Mangifera indica (mango) formed distinct clusters, therefore exhibited some level of correlation between certain genotypes and host. The developed MLMT method would be a powerful tool for studying the genetic diversity and any possible genotype-host correlation in C. gloeosporioides.

Abstract

The interaction between orchid and mycorrhizal fungi is undeniably crucial in orchid establishment and recruitment. The ability of orchid mycorrhizal fungi to access soil nutrient sources for their growth is also worth noting. This is not only critical for their own survival in soil, but also contribute to orchid survival and growth and subsequently contribute in determining orchid distribution ranges and population size. One of the fungal genera that many Australian orchids are associated with is Serendipita. Serendipita lineages are widespread across Australia and associate with many genera, both widespread and restricted orchid species. We hypothesise that mycorrhizal fungi from widely and narrowly distributed orchid species will differ in their ability to utilize nutrient sources. Furthermore, we expect fungi from eastern and Western Australia to differ in their nutrient utilizing abilities because of edaphic differences. To effectively test this hypothesis, we tried to determine the diversity of mycorrhizal partners across the orchid’s distribution range (multiple geographical ranges). Therefore, our study approaches multiple geographical ranges that represent orchid biodiversity hotspots in Australia by using Serendipita fungi as a model. Mycorrhizal fungi representing Australian sebacinoid orchid genera were isolated from widely distributed species: Caladenia flava, Caladenia tentaculata, Eriochillus cucullatus, Glossodia major, Elyteranthera brunonis, Cyrtostylis reniformis and Microtis unifolia, and narrowly distributed species: Caladenia atrovespa and Caladenia procera. The accessibility of specific nutrients encompassing carbon sources (monosaccharide, disaccharide, polysaccharide), nitrogen sources (inorganic and organic) and organic phosphorus sources was assessed by comparing dry biomass of orchid mycorrhizal fungi in vitro. The knowledge obtained from this study will improve our understanding of the ecological implications of the differences in nutrient utilisation by orchid mycorrhizal fungi. Furthermore, nutrient utilization patterns of mycorrhizal fungi might shed light on the orchid distribution patterns.