Genome-scale phylogeny and comparative genomics of the fungal order Sordariales.

The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa.

Breathing can be dangerous: Opportunistic fungal pathogens and the diverse community of the small mammal lung mycobiome.

Human lung mycobiome studies typically sample bronchoalveolar lavage or sputum, potentially overlooking fungi embedded in tissues. Employing ultra-frozen lung tissues from biorepositories, we obtained fungal ribosomal RNA ITS2 sequences from 199 small mammals across 39 species. We documented diverse fungi, including common environmental fungi such as and , associates of the human mycobiome such as and , and others specifically adapted for lungs (, , and ).

Genomic Analysis of Diverse Members of the Fungal Genus Reveals Novel Lineages, Unique Genome Content and a Potential Bacterial Associate.

The genus represents an enigmatic group of fungi important in agriculture and widely distributed in natural arid ecosystems. Of the nine described species, two ( and ) are important pathogens on the roots of members of Cucurbitaceae in agricultural settings. The remaining seven species are capable of colonizing roots from a diverse host range without causing obvious disease symptoms.

First Analysis of Human Isolates from New Mexico and the Southwest Four Corners Region: Implications for the Distributions of and and Human Groups at Risk.

Coccidioidomycosis (Valley Fever) is a disease caused by species of . The disease is endemic to arid regions of the Southwestern US and while most common in CA and AZ is also present in NM. We present the first genetic analysis of clinical isolates from NM.

Diversity of thermophilic and thermotolerant fungi in corn grain.

Corn bins in the midwestern United States can reach temperatures up to 52 C. High temperatures combined with sufficient moisture and humidity in bins provide the perfect environment to promote the growth of thermophilic and thermotolerant fungi. In this article, we characterize for the first time thermophilic and thermotolerant fungi in corn grain bins using culture-based methods and pyrosequencing techniques.

Experimental drought reduces genetic diversity in the grassland foundation species Bouteloua eriopoda.

Understanding the resistance and resilience of foundation plant species to climate change is a critical issue because the loss of these species would fundamentally reshape communities and ecosystem processes. High levels of population genetic diversity may buffer foundation species against climate disruptions, but the strong selective pressures associated with climatic shifts may also rapidly reduce such diversity. We characterized genetic diversity and its responsiveness to experimental drought in the foundation plant, black grama grass (Bouteloua eriopoda), which dominates many western North American grasslands and shrublands.

Diverse members of the Xylariales lack canonical mating-type regions.

A survey of genomes reported here for 10 isolates of Monosporascus species and an additional 25 genomes from other members of the Xylariales (representing 15 genera) available in public databases indicated that genes typically associated with MAT1-1 (mat A) or MAT1-2 (mat a) mating types are absent or have diverged greatly relative to counterparts in other Pezizomycotina. This was particularly surprising for isolates known to be homothallic, given that homothallic members of the Pezizomycotina typically possess a MAT1-1-1 (mat A-1) gene and one or both of two other closely-linked mating-type genes, MAT1-1-2 (mat A-2) and MAT1-1-3 (mat A-3), in addition to MAT1-2-1 (mat a-1). We failed to detect candidate genes for either MAT1-1-1 or MAT1-1-2 in any member of the Xylariales.

Genetics of mating in members of the Chaetomiaceae as revealed by experimental and genomic characterization of reproduction in Myceliophthora heterothallica.

Members of the Chaetomiaceae are among the most studied fungi in industry and among the most reported in investigations of biomass degradation in both natural and laboratory settings. The family is recognized for production of carbohydrate-active enzymes and antibiotics. Thermophilic species are of special interest for their abilities to produce thermally stable enzymes and to be grown under conditions that are unsuitable for potential contaminant microorganisms.

Lignin-modifying processes in the rhizosphere of arid land grasses.

Genes associated with elevated oxidative enzyme activities in arid systems have not been well characterized. To link measured oxidative activities with specific enzymes, we assembled protein-coding reads from the rhizospheres (RHZ) of two arid land grasses. Targeted gene scans for open reading frames, encoding genes potentially involved in lignin modification, resulted in 127 distinct assembly products.

Mycothermus thermophilus gen. et comb. nov., a new home for the itinerant thermophile Scytalidium thermophilum (Torula thermophila).

Thermophilic fungi have received substantial attention in industry for their potential to produce thermostable enzymes and as production platforms tolerant of high temperature. Studies exploring the ecology and biosystematics of thermophilic fungi have lagged behind studies in applied biology. The species commonly known as Scytalidium thermophilum (Chaetomiaceae) is one of the most frequently encountered organisms in surveys of thermophilic fungi.

Antimicrobial activity of cationic conjugated polyelectrolytes and oligomers against Saccharomyces cerevisiae vegetative cells and ascospores.

The antifungal activities of poly(phenylene ethynylene) (PPE)-based cationic conjugated polyelectrolytes (CPEs) and oligo-phenylene ethynylenes (OPEs) were investigated using Saccharomyces cerevisiae (S. cerevisiae) as a model pathogen. The effect of the CPE and OPE materials on the vegetative cells and ascospores were tested in the dark or with UV-irradiation.

Thermophilic fungi in an aridland ecosystem.

We report a comprehensive multi-year study of thermophilic fungi at the Sevilleta National Wildlife Refuge in central New Mexico. Recovery of thermophilic fungi from soils showed seasonal fluctuations, with greater abundance correlating with spring and summer precipitation peaks. In addition to grassland soils, we obtained and characterized isolates from grassland and riparian litter, herbivore dung and biological soil crusts.

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris.

Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi.

Massive changes in genome architecture accompany the transition to self-fertility in the filamentous fungus Neurospora tetrasperma.

A large region of suppressed recombination surrounds the sex-determining locus of the self-fertile fungus Neurospora tetrasperma. This region encompasses nearly one-fifth of the N. tetrasperma genome and suppression of recombination is necessary for self-fertility.

Diversity and distribution of soil fungal communities in a semiarid grassland.

The fungal loop model of semiarid ecosystems integrates microtopographic structures and pulse dynamics with key microbial processes. However limited data exist about the composition and structure of fungal communities in these ecosystems. The goal of this study was to characterize diversity and structure of soil fungal communities in a semiarid grassland.

Shifting fungal endophyte communities colonize Bouteloua gracilis: effect of host tissue and geographical distribution.

Communities of root-associated fungi (RAF) commonly have been studied under the auspices of arbuscular mycorrhizal fungi (AMF) or ectomycorrhizal fungi. However many studies now indicate that other groups of endophytic RAF, including dark septate endophytes (DSE) are more abundant in some plants and environments. The common forage grass, Bouteloua gracilis, was used as a model to examine whether RAF also colonize different organs within the same plant and to compare RAF communities from sites across North America, spanning the latitudinal range of B.

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).

The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes.

Novel root fungal consortium associated with a dominant desert grass.

The broad distribution and high colonization rates of plant roots by a variety of endophytic fungi suggest that these symbionts have an important role in the function of ecosystems. Semiarid and arid lands cover more than one-third of the terrestrial ecosystems on Earth. However, a limited number of studies have been conducted to characterize root-associated fungal communities in semiarid grasslands.

Ancestral polymorphism and linkage disequilibrium at the het-6 region in pseudohomothallic Neurospora tetrasperma.

In species of Neurospora, non-self recognition is mediated by at least 11 heterokaryon (het) incompatibility loci. Previously, we identified ancient allelic variation at het-c in pseudohomothallic N. tetrasperma, which confirmed outcrossing in this species.

Neurospora in temperate forests of western North America.

The fungal genus Neurospora has a distinguished history as a laboratory model in genetics and biochemistry. The most recent milestone in this history has been the sequencing of the genome of the best known species, N. crassa.

Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves.

Lechuguilla Cave is an ancient, deep, oligotrophic subterranean environment that contains an abundance of low-density ferromanganese deposits, the origin of which is uncertain. To assess the possibility that biotic factors may be involved in the production of these deposits and to investigate the nature of the microbial community in these materials, we carried out culture-independent, small subunit ribosomal RNA (SSU rRNA) sequence-based studies from two sites and from manganese and iron enrichment cultures inoculated with ferromanganese deposits from Lechuguilla and Spider Caves. Sequence analysis showed the presence of some organisms whose closest relatives are known iron- and manganese-oxidizing/reducing bacteria, including Hyphomicrobium, Pedomicrobium, Leptospirillum, Stenotrophomonas and Pantoea.

Variation among natural isolates of Neurospora on small spatial scales.

Although species of Neurospora are among the most studied model organisms in genetics and biochemistry, basic questions remain with respect to their ecology and population biology. In this study, we sought to clarify relationships among individuals over a small spatial scale, toward assessing both local variation and mode of colonization. Isolates of Neurospora were collected after fires in the Florida Everglades (May 1999), where abundant colonies appeared on diverse plants, including grasses and woody shrubs.

The genome sequence of the filamentous fungus Neurospora crassa.

Neurospora crassa is a central organism in the history of twentieth-century genetics, biochemistry and molecular biology. Here, we report a high-quality draft sequence of the N. crassa genome.