Welcome to IMC 2018 International Mycological Congress
Browsing Over 856 Presentations
Exploring the diversity of secondary metabolite clusters in Dothideomycete fungi
- E. Gluck-Thaler
- K. Bushley
- S. Haridas
- I. Grigoriev
- P. Crous
- J. Spatafora
- J. Slot
Quantifying genotypic diversity is essential for understanding and predicting how organisms adapt to their environment, and in fungi, perhaps no process is as central to adaptation as metabolism. As heterotrophs, fungal growth and survival is necessarily contingent on their ability to extract carbon and energy from a particular niche. Fungi are also adept chemical engineers who synthesize broad arrays of specialized or secondary metabolites (SMs) that shape their interactions with surrounding organisms. For example, many plant pathogens produce toxic SMs to kill their hosts, while plant saprotrophs produce antimicrobial SMs to help them compete for available resources. Although fungi have historically been an important source of economically and medically important SMs (e.g., penicillin), relatively little research has been devoted to studying patterns in the diversity of SMs they produce. Consequently, we lack a comparative framework for understanding both the drivers of fungal metabolic diversity, and the dynamics between metabolic evolution and ecological adaptation. New fungal SM pathways are usually encoded in “gene clusters” made up of neighboring genes in fungal genomes, which facilitates their identification and characterization through whole genome sequencing. Here, we conducted a systematic analysis of SM gene clusters in the largest group of fungi, the Dothideomycetes, in order to evaluate the diversity of their SM gene clusters, and to assess the potential for novel SM discovery within this group. We first developed new bioinformatic algorithms for refining gene cluster prediction that we used to query a database of 101 Dothideomycete genomes. We identified 459 unique types of clusters, of which only 6% produce known SMs, and found that even closely related species harbor distinct SM cluster repertoires. We then used network analyses to identify genes within these clusters that have played an outsized role in the evolution of SM biosynthesis, and whose presence in these clusters can be used to improve future gene cluster detection methods. Next, we used comparative phylogenetic methods to identify clusters with strong signatures of selection that are present in fungal decomposers and pathogens, and that may encode pathways underlying specific plant-associated lifestyles. Finally, based on the phylogenetic distributions of the clusters we detected, we identified specific lineages within the Dothideomycetes that are projected to harbor the greatest diversity of SM clusters, thus providing a valuable roadmap to direct future SM sampling and characterization efforts.
Marine Fungi from India: Range of Substrata
- A. Tuwar
The present paper deals with distribution and substratum range of 217 species of marine fungi (14 Labyrinthulomycetes, 4 Chytridiomycetes, 4 Oomycetes, 143 Ascomycetes, 3 Basidiomycetes and 46 Mitosporic / Asexual fungi) reported so far from the marine waters of India. These fungi were reported as parasites / saprophytes on Animal substrates (16 sp.), saprophytic on intertidal and deep sea sediments (7 sp.), on intertidal woody debris (131 sp.), on decaying algae (17 sp.), saprophytic on salt marsh plants (3 sp.), saprophytic on sea grasses (4 sp.), saprophytic on woody debris of mangroves from intertidal region (165 sp.). Ascospores and conidia of 27 species were recorded in foam samples from sandy beaches. Fungal species (165 sp.) recorded on mangrove substrata forms the largest group after intertidal woody debris (131 sp.). It also shows that most of the fungal species have been recorded from the West coast (154 sp.) after the East coast (152 sp.), Andaman-Nocobar Islands (66 sp.) and Lakshadweep Islands (55 sp.). Maximum number of marine fungi were encountered along the coast of Tamil Nadu state (106 sp.) and followed by Karnataka (100 sp.), Maharashtra (95 sp.), Goa (98 sp.), Kerala (93 sp.), Andhra Pradesh (73 sp.), Gujarat (70 sp.), West Bengal (69 sp.), Orissa (54 sp.), Pondecherry-Mahe (46 sp.), Daman (17 sp.), Diu Island (14 sp.) and Pondecherry (12 sp.). This data will be useful in the compilation of marine fungal biodiversity of India. The taxonomy, morphology and ecology of these fungi are discussed.
Characterization of root fungal endophytes of native and invasive Phragmites australis along a salinity gradient
- M. Gonzalez Mateu
- A. Baldwin
- J. Maul
- S. Yarwood
In the last 150 years an invasive lineage of the wetland plant Phragmites australis has spread aggressively throughout many areas in the United States. Some of the problems associated with the rapid expansion of Phragmites are changes in wetland hydrology, biogeochemistry, reduction of wildlife habitat, and the loss of biodiversity, including a native lineage of the same species Phragmites australis subsp. americanus. Studying the microbiome associated with invasive and native species can lead to new insights into invasive species success, because host microbiome associations can greatly influence plant performance. The objectives of our study were to characterize the fungal endophyte communities associated with native and invasive Phragmites, determine the prevalence of dark septate endophytes (DSE) during the growing season, and examine the role of salinity in fungal root colonization. We identified three sites along a salinity gradient in the Choptank River, an estuary of the Chesapeake Bay (MD, USA), and collected roots from contiguous stands of native and invasive Phragmites every two weeks from June to October. We used microscopy to determine percent colonization of DSE, and Illumina sequencing of the ITS1 region to characterize the root endophyte communities of each lineage. DSE colonization did not vary during the growing season, but the invasive lineage was consistently more colonized than the native. Fungal colonization of invasive Phragmites also increased with salinity. All identified, sequenced OTUs matched the phylum Ascomycota, and the endophyte communities differed between lineages and among sites. In conclusion, invasive and native Phragmites have distinct root endophyte communities that vary across a salinity gradient, and might play a role in aiding the spread of the invasive lineage into higher salinity sites.
Towards a Colorado Mycoflora: Molecular diversity of mushrooms from the Southern Rockies.
- S. Wright
- A. Wilson
- V. Evenson
The diversity of macrofungi across North America is staggering and, traditionally, morphology has been the primary means of identification. While morphology is still considered useful, the advent of cheap and effective DNA sequencing has enhanced the exploration of taxonomic relationships among mushroom forming fungi. Currently, the identities of many North American macrofungi are based on morphological concepts that borrow from Eurasian species. The North American Mycoflora Project was created to test species concepts of the continent’s mushroom forming fungi using DNA sequence data. The North American state of Colorado boasts a wide range of fungal diversity. This project aims to study the specimens vouchered in Vera Evenson’s book “Mushrooms of Colorado and the Southern Rocky Mountains,” and housed in the Sam Mitchel Herbarium of Fungi at Denver Botanic Gardens, in order to produce a regional mycoflora of Colorado and the Southern Rockies. Using ITS sequence data this project intends to expand upon our understanding of the region’s diversity of macrofungi. The results of this project represent the projects first steps, using ITS sequence data of over 100 species Colorado mushrooms and allies, and exploring whether the names traditionally used for the region’s fungi hold up to direct scrutiny.
Response of potato to the black scurf disease pathogen Rhizoctonia solani Kühn AG-3
- R. Grosch
- F. Genzel
- P. Franken
Black scurf disease on potato caused by Rhizoctonia solani AG3 occurs worldwide and is difficult to control. It has been observed that potato cultivars show differences in susceptibility to R. solani AG3. The cultivation of potato cultivars with high resistance level to Rhizoctonia diseases represents an ecological and economic sustainable control strategy. Presently, the degree of resistance is based on symptom assessment in the field, but molecular methods could offer a more effective screening procedure for cultivars with high degree in resistance. We hypothesized that field resistance to black scurf disease in potato cultivars is associated with defense-related gene expression levels and salicylic acid (SA) concentration. In a comparative analysis, the expression levels of common defense-related genes of two cultivars with moderate and high degree in resistance to black scurf disease were studied. Besides RNA accumulation, salicylic acid (SA) concentrations in potato tissues were measured. A higher constitutive expression level of defense-related genes was found in the highly resistant cultivar. A significant increased expression level of these genes upon pathogen infection was only observed in the moderately resistant cultivar. In addition, the constitutively higher expression level correlated with increased amounts of SA compared to the moderately resistant cultivar. R. solani AG3 DNA density reflected differences in resistance. The results indicate that expression levels of defense-related genes and the amount of SA in potato tissues can potentially be used as indicators of potato field resistance to black scurf disease.
Reduction of proteolytic activity in filamentous fungal protein production hosts
- W. De Bonte
- S. Segers-Klaubauf
- A. Ram
- P. Punt
AbstractFungal host strains such as Aspergillus niger, Aspergillus sojae and Trichoderma reesei are used for the production of a wide variety of industrially relevant enzymes. About 80% of all industrial enzymes are derived from filamentous fungi, making these organisms also the hosts of choice for the production of new enzymes and proteins. The presence of unwanted proteolytic activity in filamentous fungi is a major bottleneck for (heterologous) protein production. Despite the accumulation of data by all kinds of -omics techniques, the regulation of protease genes in fungi remains largely unexplored. Dutch DNA Biotech is working on several approaches to tackle this problem in industrial fungal strains. All these approaches are focused on identifying regulatory genes specific for the pathways underlying protease production. Based on strain engineering, using both classical screening and targeted molecular approaches, regulatory mutants are being developed. The research presented here is focussed on three methods to find relevant factors that are involved in the regulation of proteolytic genes. The first method is a positive screenings method for protease mutants, we named SUI selection. SUI selection is a growth based screening method and is much more efficient than activity based screening methods. The second method is the screening of a transcription factor knock out library in Aspergillus niger and Neurospora crassa for mutants with a lower proteolytic activity. The third method involves a multicopy suppressor approach based on strains carrying multiple copies of the major A. niger protease regulator gene, prtT.
The Rhodocybe/Clitopilus clade (Entolomataceae, Agaricomyetes) in the Dominican Republic: a new genus, new species and first reports for Hispaniola
- T. Baroni
- C. Angelini
- S. Bergemann
- D. Lodge
- S. Cantrell
- T. Curtis
AbstractThis report serves as the first ever to outline the diversity of the Rhodocybe/Clitopilus clade for the Dominican Republic. Based on collections made during several expeditions exploring for basidiomycete macrofungi over a span of 20+ years, we now have a reasonable understanding of the biodiversity of these saprotrophic fungi in the Dominican Republic. Diverse ecological habitats were sampled during these studies, ranging from tropical seashore vegetation to the endemic pine covered high peaks in the central mountainous regions. Based on morphological and phylogenetic analyses, we document one new genus, three new species, one new variety, one new combination and four first reports for members of the Rhodocybe/Clitopilus clade on the island of Hispaniola. Images of the new taxa and the three gene phylogenetic data to support these taxonomic conclusions will be presented. A broader biogeographic analysis of the Rhodocybe/Clitopilus clade around the Caribbean region will also be considered.
Genetic and genomic approaches toward understanding the biology of the Korean oak wilt fungus (Raffaelea quercus-mongolicae)
- M. Kim
- J. Stewart
- J. Ibarra Caballero
- N. Klopfenstein
Raffaelea quercus-mongolicae is associated with oak wilt disease in Korea. To date, this ambrosia beetle-vectored fungus has only been found in South Korea, and it is phylogenetically distinct from R. quercivora, which causes a similar oak wilt disease in Japan, and other Raffaelea spp. When this fungus was discovered on a dead Mongolian oak (Quercus mongolica) in 2004, the disease epiphytotic was centered around Seoul and the adjacent Gyeonggi Province; however, it has continued to spread southwards since then. Despite continued expansion of the disease and associated major impacts on forest ecosystems, little genetic and genomic information of R. quercus-mongolicae available for understanding its biology, evaluating pathways of spread, and developing improved disease prediction and management methods. The objectives of this study were to assess genetic diversity and population structure of the Korean oak wilt fungus, R. quercus-mongolicae, using Restriction-site-Associated-DNA sequencing (RAD-seq); sequence the whole genome of R. quercus-mongolicae; and analyze the transcriptome (expressed genes) of R. quercus-mongolicae by RNA sequencing and reference genome-based assembly. Fifty-four isolates of R. quercus-mongolicae were collected from five regions of South Korea. RAD-tag libraries and DNA sequencing were conducted at Floragenex, Inc. (Eugene, OR, USA). The draft genome of R. quercus-mongolicae (KACC44405) was sequenced by Illumina NextSeq and MiSeq systems for paired-end reads and HiSeq2000 for mate-pair reads. Total RNA was extracted from R. quercus-mongolicae (KACC44405) grown under in vitro conditions on two artificial media [potato dextrose agar (PDA) and water agar (WA)]. The mRNA was sequenced using Illumina HiSeq™2000 with a read length of 101 bp. Trimmed sequences were mapped to reference genome. Sequencing the RAD-tag libraries generated 143,696,855 reads using Illumina HiSeq. In total, 179 SNPs were identified among 2,639 RAD loci across the nuclear genome of the 54 R. quercus-mongolicae isolates (0.00080 SNPs per bp). Overall low expected heterozygosity and no apparent population structure were found among South Korean populations R. quercus-mongolicae, which supports the hypothesis that this ambrosia beetle-vectored fungus was introduced to South Korea. The genomic sequence of R. quercus-mongolicae (KACC44405; 27-Mb), along with other Raffaelea spp., will provide valuable resources for comparative genomic analyses and identifying genes that contribute to potential pathogenic relationships between the fungus and host, and potential symbiotic relationships between the fungus and insect vector. After mapping with a reference genome, 7,739 transcripts were identified as the R. quercus-mongolicae transcriptome dataset. The predicted gene products are associated with diverse functions, such as production of ATP for growth, recovery under stressed conditions, fluidity of cell membrane, maintenance of cell membrane, and regulation of fungal virulence. The transcripts that differed significantly in expression levels between PDA and WA media were associated with localization within subcellular components, hydrolase activity, and intrinsic membrane components.
Aureoboletus projectellus - new invasive bolete, rapidly spreading in Europe as an opportunity to study invasions of macromycetes.
- Ł. Istel
- J. Pawłowska
- A. Okrasińska
- Ł. Banasiak
- M. Gorczak
- M. Wrzosek
American bolete Aureoboletus projectellus was reported in Europe in the beginning of the century. At first it was only observed on the Baltic Sea shore. Since 2014 the occurrence range of the species has increased significantly. It now reaches more than 150 km into land and covers eight countries. Main aim of the study was to establish a framework for studying invasion of macrofungus in statu nascendi based on the spread of A.projectellus. A model prepared in MaxEnt was used to estimate distribution of potential niches of A. projectellus in Europe. Comparing model together with data about species distribution in invasive range were combined to predict way of future dispersion and to help to prepare a list of location that should be monitored. Baltic Sea coast line seems to be one of the most suitable area for invasive range. The continuous ring of favorable conditions all around Baltic sea shows that the invasion is unstoppable but can be suitable for studying invasion process. Other disjunctive areas of favorable habitats include Alpine foothills and small remote mountains located on the south of Europe (for example Apennines and Pyrenees). Invasion in remote islands can be probably slowed down or even stopped by preventing the transport of edible fruit bodies or planting pines which is mycorrhizal partner of A. projectellus. Every attempt to stop the spread of invasive fungus is important because A. projectellus can be a threat to domestic/native species of mushrooms (eg, Tricholoma focale or T. apium).
The thread connection between Hotaea weneckii and Dunaliella atacamensis: triggering symbiosis from spiderwebs to in vitro culture
- L. Muggia
- P. Zalar
- A. Azua-Bustos
- N. Gunde Cimerman
Microorganisms have evolved multiple and novel strategies to survive in exreme environments. Iconical examples are lichens, in which the association between fungi and algae enable the symbionts to outcompete in habitats where otherwise the single organisms could not survive. The green algal genus Dunaliella and the black yeast Hortaea are exemplar in being adapted to extremely saline, aquatic environments. Only one single species of the genus Dunaliella, D. atacamensis, is known from subaerial environments. It thrives on spiderwebs on walls at the entrance-twilight transition zones of caves in the Atacama desert (Chile). A closer inspection of the colonies has shown the presence of black yeast cells of Hortaea werneckii between the algal cells. As symbiotic interactions between Dunaliella species and the Hortaea fungi have not been known so far, we performed a series of co-cultivation experiments to test whethere the two symbionts can co-grow in vitro and develop lichen-like symbiotic structures. We set up co-cultures with the axenic strains of Hortaea werneckii isolated from the salterns and Hortaea werneckii isolated from the Chilean spiderwebs together with the salt tolerant Dunaliella salina and the aerial D. atacamensis. We used different growth media and culture approches to trigger the association between the fungi and the algae and documented our observations by light microscopy.
Studies in Floridian boletes
- A. Farid
- A. Franck
- J. Garey
DNA sequencing of macrofungi continually shows that many species are yet to be described and many species belong in different genera than originally thought based on morphology. The boletes are remarkably diverse in Florida, yet very few have been sequenced. Numerous boletes were described my William Alphonso Murrill (1869–1957) and Rolf Singer (1906–1994); the protologues and type specimens of many of these species require critical re-examination to understand their application. We have approached the study of boletes in Florida with field work, herbarium studies, microscopy, and targeting the main phylogenetic loci for fungi (ITS, LSU, TEF1, and RPB), sometimes requiring the design of novel primers for successful amplification. Studies of phylloporoid fungi in Florida revealed one species which requires a new genus, adding another example of the independent gain of gills in boletes. A Tylopilus-like species collected on the University of South Florida campus (Tampa, Florida) likely represents another novel bolete genus. Additional sequencing suggests several species are undescribed, some belong in recently described genera, and other species are newly confirmed for Florida.
Diversity within a single Peronosporaceae sample and implications for phylogenetic studies.
- E. Wallace
- C. Salgado-Salazar
- N. Leblanc
- J. Crouch
Downy mildews are plant diseases caused by a diverse group of diploid organisms in the Oomycota (Peronosporaceae). Over 700 species cause downy mildew diseases. Some of these organisms are thought to affect a wide diversity of plants, but most well-described downy mildew species are delimited by host genus. Downy mildews typically produce foliar lesions but some species are also reported to cause stunting, mottling, and in extreme cases, complete defoliation. The obligate biotrophic nature of downy mildew organisms creates difficulties in maintaining strains of these pathogens for research. This is particularly true for newly emergent or under-studied species where ideal environmental conditions and propagation protocols have not been established. As a result, single-spored isolates are rarely used in molecular phylogenetic studies. Common practices for generating DNA sequences from downy mildew samples involve performing PCR on genomic DNA extracted from sporulating pathogen tissue scraped from the leaf surface, or from excised disease lesions. When nucleotide sequences are generated directly from amplicons via Sanger sequencing technology, forward and reverse sequences are used to generate a consensus sequence, and any conflicting peak calls and double peaks in the chromatogram are indicated with IUPAC nucleotide ambiguity codes. However, by eliminating steps to ensure a single isolate is evaluated in a phylogeny, conclusions may not fully capture diversity of the population in one sample, nor the potential for heterozygosity of nuclear markers. In the current study, diversity within individual samples of Peronospora infecting Monarda didyma and Hyaloperonospora infecting Cleome sp. plants was evaluated using two approaches. DNA was extracted from sporulating leaf lesions, and amplicons of ITS rDNA and cox2 mitochondrial DNA markers were cloned to produce haplotypes, and 7 to 10 inserts were bi-directionally sequenced per sample. Amplicons from the same two markers were also sequenced to a high depth of coverage using next generation sequencing on an Illumina MiSeq to evaluate the level of diversity within individual samples. The resultant data demonstrated that the level of diversity within individual downy mildew samples has the potential to be much greater than what is traditionally captured using direct Sanger sequencing of potentially heterogeneous amplicons. These unaccounted for variant sequences may have substantial impacts on phylogenetic analyses and should be considered when making taxonomic decisions.