Improving Instructional Fitness Requires Change.

Transmission of information has benefitted from a breathtaking level of innovation and change over the past 20 years; however, instructional methods within colleges and universities have been slow to change. In the article, we present a novel framework to structure conversations that encourage innovation, change, and improvement in our system of higher education, in general, and our system of biology education, specifically. In particular, we propose that a conceptual model based on evolutionary landscapes in which fitness is replaced by educational effectiveness would encourage educational improvement by helping to visualize the multidimensional nature of education and learning, acknowledge the complexity and dynamism of the educational landscape, encourage collaboration, and stimulate experimental thinking about how new approaches and methodology could take various fields associated with learning, to more universal fitness optima. The framework also would encourage development and implementation of new techniques and persistence through less efficient or effective valleys of death.

Streptomyces buecherae sp. nov., an actinomycete isolated from multiple bat species.

A putative novel clade within the genus Streptomyces was discovered following antifungal screening against Pseudogymnoascus destructans, the causative agent of white-nose syndrome, and described using multi-locus sequencing analysis. Swabs from both the cave myotis bat (Myotis velifer) and the Brazilian free-tailed bat (Tadarida brasiliensis) in southern New Mexico bore isolates AC536, AC541T and AC563, which were characterised using phylogenetic, morphological, and phenotypic analyses. Multi-locus sequence analysis positions AC541T with neighbors Streptomyces rubidus (NRRL B-24619T), Streptomyces guanduensis (NRRL B-24617T), and Streptomyces yeochonensis (NRRL B-24245T). A complete genome of the type strain was assembled to determine its taxonomy and secondary metabolite potential. ANI comparisons between all closely related types strains are shown to be well below the 95-96% species delineation. DNA-DNA relatedness between AC541T and its nearest neighbors ranged between 23.7 and 24.1% confirming novelty. Approximately 1.49 Mb or 17.76% of the whole genome is devoted to natural product biosynthesis. The DNA G + C content of the genomic DNA of the type strain is 73.13 mol %. Micromorphology depicts ovoid spores with smooth surfaces in flexuous chains. Strains presented an ivory to yellow hue on most ISP media except inorganic salts-starch agar (ISP4) and can grow on D-glucose, mannitol, and D-fructose, but exhibited little to no growth on L-arabinose, sucrose, D-xylose, inositol, L-rhamnose, D-raffinose, and cellulose. This clade possesses the capability to grow from 10 to 45 °C and 12.5% (w/v) NaCl. There was strain growth variation in pH, but all isolates thrive at alkaline levels. Based on our polyphasic study of AC541T, the strain warrants the assignment to a novel species, for which the name Streptomyces buecherae sp. nov. is proposed. The type strain is AC541T (= JCM 34263T, = ATCC TSD201T).

Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis.

BACKGROUND: The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in soil stability, plant biomass decomposition, and endophytic interactions with plants. They may also form symbiotic associations with biocrust components or be latent saprotrophs or pathogens that live on plant tissues. However, their functional potential in arid soils, where organic matter, nutrients and water are very low or only periodically available, is poorly characterized. RESULTS: Five Ascomycota fungi were isolated from different soil crust microhabitats and rhizosphere soils around the native bunchgrass Pleuraphis jamesii in an arid grassland near Moab, UT, USA. Putative genera were Coniochaeta, isolated from lichen biocrust, Embellisia from cyanobacteria biocrust, Chaetomium from below lichen biocrust, Phoma from a moss microhabitat, and Aspergillus from the soil. The fungi were grown in replicate cultures on different carbon sources (chitin, native bunchgrass or pine wood) relevant to plant biomass and soil carbon sources. Secretomes produced by the fungi on each substrate were characterized. Results demonstrate that these fungi likely interact with primary producers (biocrust or plants) by secreting a wide range of proteins that facilitate symbiotic associations. Each of the fungal isolates secreted enzymes that degrade plant biomass, small secreted effector proteins, and proteins involved in either beneficial plant interactions or virulence. Aspergillus and Phoma expressed more plant biomass degrading enzymes when grown in grass- and pine-containing cultures than in chitin. Coniochaeta and Embellisia expressed similar numbers of these enzymes under all conditions, while Chaetomium secreted more of these enzymes in grass-containing cultures. CONCLUSIONS: This study of Ascomycota genomes and secretomes provides important insights about the lifestyles and the roles that Ascomycota fungi likely play in arid grassland, ecosystems. However, the exact nature of those interactions, whether any or all of the isolates are true endophytes, latent saprotrophs or opportunistic phytopathogens, will be the topic of future studies.

Streptomyces corynorhini sp. nov., isolated from Townsend's big-eared bats (Corynorhinus townsendii).

Four bacterial strains, with the capability of inhibiting Pseudogymnoascus destructans, the causative agent of white-nose syndrome, were isolated from male Townsend's big-eared bats (Corynorhinus townsendii, Family: Vespertilionidae) in New Mexico. Isolates AC161, AC162, AC208, and AC230T were characterised as a novel clade using morphological, phenotypic and phylogenetic analysis. A draft genome of the type strain was completed to determine its taxonomy and secondary metabolite biosynthetic potential. Multi-locus sequence analysis nests AC230T with neighbours Streptomyces scopuliridis (NRRL B-24574T), Streptomyces lushanensis (NRRL B-24994T), Streptomyces odonnellii (NRRL B-24891T) and Streptomyces niveus (NRRL 2466T). Further phylogenetic analysis showed the MLSA distances between AC230T and its near neighbours are much greater than the generally accepted threshold (> 0.007) for bacterial species delineation. DNA-DNA relatedness between AC230T and its near neighbours ranged between 25.7 ± 2.1 and 29.9 ± 2.4%. The DNA G+C content of the genomic DNA of the type strain is 71.7 mol%. Isolate AC230T presents a white to ivory hue on most ISP media and its micromorphology exhibits ovoid spores with smooth surfaces in flexuous chains. Based on our study of AC230T, the strain warrants the assignment to a novel species, for which the name Streptomyces corynorhini sp. nov. is proposed. The type strain is AC230T (= JCM 33171T, = ATCC TSD155T).

Microscopic characterization of orchid mycorrhizal fungi: Scleroderma as a putative novel orchid mycorrhizal fungus of Vanilla in different crop systems.

Vanilla is an orchid of economic importance widely cultivated in tropical regions and native to Mexico. We sampled three species of Vanilla (V. planifolia, V. pompona, and V. insignis) in different crop systems. We studied the effect of crop system on the abundance, type of fungi, and quality of pelotons found in the roots using light and electron microscopy and direct sequencing of mycorrhizal structures. Fungi were identified directly from pelotons obtained from terrestrial roots of vanilla plants in the flowering stage. Root samples were collected from plants in crop systems located in the Totonacapan area in Mexico (states of Puebla and Veracruz). DNA was extracted directly from 40 pelotons and amplified using ITS rRNA sequencing. Peloton-like structures were observed, presenting a combination of active pelotons characterized by abundant hyphal coils and pelotons in various stages of degradation. The most active pelotons were observed in crop systems throughout living tutors (host tree) in comparison with roots collected from dead or artificial tutors. Fungi identified directly from pelotons included Scleroderma areolatum, a common ectomycorrhizal fungus that has not been reported as a mycorrhizal symbiont in orchids. Direct amplification of pelotons also yielded common plant pathogens, including Fusarium and Pyrenophora seminiperda, especially in those sites with low colonization rates, and where large numbers of degraded pelotons were observed. This research reports for the first time the potential colonization of Vanilla by Scleroderma, as a putative orchid mycorrhizal symbiont in four sites in Mexico and the influence of crop system on mycorrhizal colonization on this orchid.

Western Bats as a Reservoir of Novel Streptomyces Species with Antifungal Activity.

At least two-thirds of commercial antibiotics today are derived from Actinobacteria, more specifically from the genus Streptomyces Antibiotic resistance and new emerging diseases pose great challenges in the field of microbiology. Cave systems, in which actinobacteria are ubiquitous and abundant, represent new opportunities for the discovery of novel bacterial species and the study of their interactions with emergent pathogens. White-nose syndrome is an invasive bat disease caused by the fungus Pseudogymnoascus destructans, which has killed more than six million bats in the last 7 years. In this study, we isolated naturally occurring actinobacteria from white-nose syndrome (WNS)-free bats from five cave systems and surface locations in the vicinity in New Mexico and Arizona, USA. We sequenced the 16S rRNA region and tested 632 isolates from 12 different bat species using a bilayer plate method to evaluate antifungal activity. Thirty-six actinobacteria inhibited or stopped the growth of P. destructans, with 32 (88.9%) actinobacteria belonging to the genus Streptomyces Isolates in the genera Rhodococcus, Streptosporangium, Luteipulveratus, and Nocardiopsis also showed inhibition. Twenty-five of the isolates with antifungal activity against P. destructans represent 15 novel Streptomyces spp. based on multilocus sequence analysis. Our results suggest that bats in western North America caves possess novel bacterial microbiota with the potential to inhibit P. destructansIMPORTANCE This study reports the largest collection of actinobacteria from bats with activity against Pseudogymnoascus destructans, the fungal causative agent of white-nose syndrome. Using multigene analysis, we discovered 15 potential novel species. This research demonstrates that bats and caves may serve as a rich reservoir for novel Streptomyces species with antimicrobial bioactive compounds.

Bifiguratus adelaidae, gen. et sp. nov., a new member of Mucoromycotina in endophytic and soil-dwelling habitats.

Illumina amplicon sequencing of soil in a temperate pine forest in the southeastern United States detected an abundant, nitrogen (N)-responsive fungal genotype of unknown phylogenetic affiliation. Two isolates with ribosomal sequences consistent with that genotype were subsequently obtained. Examination of records in GenBank revealed that a genetically similar fungus had been isolated previously as an endophyte of moss in a pine forest in the southwestern United States. The three isolates were characterized using morphological, genomic, and multilocus molecular data (18S, internal transcribed spacer [ITS], and 28S rRNA sequences). Phylogenetic and maximum likelihood phylogenomic reconstructions revealed that the taxon represents a novel lineage in Mucoromycotina, only preceded by Calcarisporiella, the earliest diverging lineage in the subphylum. Sequences for the novel taxon are frequently detected in environmental sequencing studies, and it is currently part of UNITE's dynamic list of most wanted fungi. The fungus is dimorphic, grows best at room temperature, and is associated with a wide variety of bacteria. Here, a new monotypic genus, Bifiguratus, is proposed, typified by Bifiguratus adelaidae.

Ribosomal Database Project: data and tools for high throughput rRNA analysis.

Ribosomal Database Project (RDP; http://rdp.cme.msu.edu/) provides the research community with aligned and annotated rRNA gene sequence data, along with tools to allow researchers to analyze their own rRNA gene sequences in the RDP framework. RDP data and tools are utilized in fields as diverse as human health, microbial ecology, environmental microbiology, nucleic acid chemistry, taxonomy and phylogenetics. In addition to aligned and annotated collections of bacterial and archaeal small subunit rRNA genes, RDP now includes a collection of fungal large subunit rRNA genes. RDP tools, including Classifier and Aligner, have been updated to work with this new fungal collection. The use of high-throughput sequencing to characterize environmental microbial populations has exploded in the past several years, and as sequence technologies have improved, the sizes of environmental datasets have increased. With release 11, RDP is providing an expanded set of tools to facilitate analysis of high-throughput data, including both single-stranded and paired-end reads. In addition, most tools are now available as open source packages for download and local use by researchers with high-volume needs or who would like to develop custom analysis pipelines.

Ribosomal RNA gene detection and targeted culture of novel nitrogen-responsive fungal taxa from temperate pine forest soil.

Soil fungal communities are responsible for carbon and nitrogen (N) cycling. The high complexity of the soil fungal community and the high proportion of taxonomically unidentifiable sequences confound ecological interpretations in field studies because physiological information is lacking for many organisms known only by their rRNA sequences. This situation forces experimental comparisons to be made at broader taxonomic racks where functions become difficult to infer. The objective of this study was to determine OTU (operational taxonomic units) level responses of the soil fungal community to N enrichment in a temperate pine forest experiment and to use the sequencing data to guide culture efforts of novel N-responsive fungal taxa. Replicate samples from four soil horizons (up to 10 cm depth) were obtained from ambient, enriched CO2 and N-fertilization plots. Through a fungal large subunit rRNA gene (LSU) sequencing survey, we identified two novel fungal clades that were abundant in our soil sampling (representing up to 27% of the sequences in some samples) and responsive to changes in soil N. The two N-responsive taxa with no predicted taxonomic association were targeted for isolation and culturing from specific soil samples where their sequences were abundant. Representatives of both OTUs were successfully cultured using a filtration approach. One taxon (OTU6) was most closely related to Saccharomycotina; the second taxon (OTU69) was most closely related to Mucoromycotina. Both taxa likely represent novel species. This study shows how observation of specific OTUs level responses to altered N status in a large rRNA gene field survey provided the impetus to design targeted culture approaches for isolation of novel N-responsive fungal taxa.

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences.

Fungi are key organisms in many ecological processes and communities. Rapid and low cost surveys of the fungal members of a community can be undertaken by isolating and sequencing a taxonomically informative genomic region, such as the ITS (internal transcribed spacer), from DNA extracted from a metagenomic sample, and then classifying these sequences to determine which organisms are present. This paper announces the availability of the Warcup ITS training set and shows how it can be used with the Ribosomal Database Project (RDP) Bayesian Classifier to rapidly and accurately identify fungi using ITS sequences. The classifications can be down to species level and use conventional literature-based mycological nomenclature and taxonomic assignments.

Sequence-based classification and identification of Fungi.

Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable validPUBLICation of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources.

Root-associated fungal community response to drought-associated changes in vegetation community.

Recent droughts in southwestern USA have led to large-scale mortality of piñon (Pinus edulis) in piñon-juniper woodlands. Piñon mortality alters soil moisture, nutrient and carbon availability, which could affect the root-associated fungal (RAF) communities and therefore the fitness of the remaining plants. We collected fine root samples at a piñon-juniper woodland and a juniper savannah site in central New Mexico. Roots were collected from piñon and juniper (Juniperus monosperma) trees whose nearest neighbors were live piñon, live juniper or dead piñon. RAF communities were analyzed by 454 pyrosequencing of the universal fungal ITS region. The most common taxa were Hypocreales and Chaetothyriales. More than 10% of ITS sequences could not be assigned taxonomy at the phylum level. Two of the unclassified OTUs significantly differed between savanna and woodland, had few like sequences in GenBank and formed new fungal clades with other unclassified RAF from arid plants, highlighting how little study has been done on the RAF of arid ecosystems. Plant host or neighbor did not affect RAF community composition. However, there was a significant difference between RAF communities from woodland vs. savanna, indicating that abiotic factors such as temperature and aridity might be more important in structuring these RAF communities than biotic factors such as plant host or neighbor identity. Ectomycorrhizal fungi (EM) were present in juniper as well as piñon in the woodland site, in contrast with previous research, but did not occur in juniper savanna, suggesting a potential shared EM network with juniper. RAF richness was lower in hosts that were neighbors of the opposite host. This may indicate competitive exclusion between fungi from different hosts. Characterizing these communities and their responses to environment and plant neighborhood is a step toward understanding the effects of drought on a biome that spans 19,000,000 ha of southwestern USA.

From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition.

We compared the classification accuracy of two sections of the fungal internal transcribed spacer (ITS) region, individually and combined, and the 5' section (about 600 bp) of the large-subunit rRNA (LSU), using a naive Bayesian classifier and BLASTN. A hand-curated ITS-LSU training set of 1,091 sequences and a larger training set of 8,967 ITS region sequences were used. Of the factors evaluated, database composition and quality had the largest effect on classification accuracy, followed by fragment size and use of a bootstrap cutoff to improve classification confidence. The naive Bayesian classifier and BLASTN gave similar results at higher taxonomic levels, but the classifier was faster and more accurate at the genus level when a bootstrap cutoff was used. All of the ITS and LSU sections performed well (>97.7% accuracy) at higher taxonomic ranks from kingdom to family, and differences between them were small at the genus level (within 0.66 to 1.23%). When full-length sequence sections were used, the LSU outperformed the ITS1 and ITS2 fragments at the genus level, but the ITS1 and ITS2 showed higher accuracy when smaller fragment sizes of the same length and a 50% bootstrap cutoff were used. In a comparison using the larger ITS training set, ITS1 and ITS2 had very similar accuracy classification for fragments between 100 and 200 bp. Collectively, the results show that any of the ITS or LSU sections we tested provided comparable classification accuracy to the genus level and underscore the need for larger and more diverse classification training sets.

Nitrogen deposition alters plant-fungal relationships: linking belowground dynamics to aboveground vegetation change.

Nitrogen (N) deposition rates are increasing globally due to anthropogenic activities. Plant community responses to N are often attributed to altered competitive interactions between plants, but may also be a result of microbial responses to N, particularly root-associated fungi (RAF), which are known to affect plant fitness. In response to N, Deschampsia cespitosa, a codominant plant in the alpine tundra at Niwot Ridge (CO), increases in abundance, while Geum rossii, its principal competitor, declines. Importantly, G. rossii declines with N even in the absence of its competitor. We examined whether contrasting host responses to N are associated with altered plant-fungal symbioses, and whether the effects of N are distinct from effects of altered plant competition on RAF, using 454 pyrosequencing. Host RAF communities were distinct (only 9.4% of OTUs overlapped). N increased RAF diversity in G. rossii, but decreased it in D. cespitosa. D. cespitosa RAF communities were more responsive to N than G. rossii RAF communities, perhaps indicating a flexible microbial community aids host adaptation to nutrient enrichment. Effects of removing D. cespitosa were distinct from effects of N on G. rossii RAF, and D. cespitosa presence reversed RAF diversity response to N. The most dominant G. rossii RAF order, Helotiales, was the most affected by N, declining from 83% to 60% of sequences, perhaps indicating a loss of mutualists under N enrichment. These results highlight the potential importance of belowground microbial dynamics in plant responses to N deposition.

Psychrophilic and psychrotolerant fungi on bats and the presence of Geomyces spp. on bat wings prior to the arrival of white nose syndrome.

Since 2006, Geomyces destructans, the causative agent of white nose syndrome (WNS), has killed over 5.7 million bats in North America. The current hypothesis suggests that this novel fungus is an invasive species from Europe, but little is known about the diversity within the genus Geomyces and its distribution on bats in the United States. We documented the psychrophilic and psychrotolerant fungal flora of hibernating bats prior to the arrival of WNS using culture-based techniques. A total of 149 cultures, which were obtained from 30 bats in five bat hibernacula located in four caves and one mine, were sequenced for the entire internal transcribed spacer (ITS) nuclear ribosomal DNA (nrDNA) region. Approximately 53 operational taxonomic units (OTUs) at 97% similarity were recovered from bat wings, with the community dominated by fungi within the genera Cladosporium, Fusarium, Geomyces, Mortierella, Penicillium, and Trichosporon. Eleven Geomyces isolates were obtained and placed in at least seven distinct Geomyces clades based on maximum-likelihood phylogenetic analyses. Temperature experiments revealed that all Geomyces strains isolated are psychrotolerant, unlike G. destructans, which is a true psychrophile. Our results confirm that a large diversity of fungi, including several Geomyces isolates, occurs on bats prior to the arrival of WNS. Most of these isolates were obtained from damaged wings. Additional studies need to be conducted to determine potential ecological roles of these abundant Geomyces strains isolated from bats.

Pleoardoris graminearum, gen. et sp. nov., a new member of Pleosporales from North American Plains, its biogeography and effects on a foundation grass species.

Diverse fungi colonize plant roots worldwide and include species from many orders of the phylum Ascomycota. These fungi include taxa with dark septate hyphae that colonize grass roots and may modulate plant responses to stress. We describe a novel group of fungal isolates and evaluate their effects on the grass Bouteloua gracilis in vitro. We isolated fungi from roots of six native grasses from 24 sites spanning replicated latitudinal gradients in the south-central US grasslands and characterized isolates phylogenetically using a genome analysis. We analyzed 14 isolates representing a novel clade within the family Montagnulaceae (order Pleosporales), here typified as Pleoardoris graminearum, closely related to the genera Didymocrea and Bimuria. This novel species produces asexual, light brown pycnidium-like conidioma, hyaline hyphae, and chlamydospores when cultured on quinoa and kiwicha agar. To evaluate its effects on B. gracilis, seeds were inoculated with one of three isolates (DS304, DS334, and DS1613) and incubated at 25 C for 20 d. We also tested the effect of volatile organic compounds (VOCs) produced by the same isolates on B. gracilis root and stem lengths. Isolates had variable effects on plant growth. One isolate increased B. gracilis root length up to 34% compared with uninoculated controls. VOCs produced by two isolates increased root and stem lengths (P < 0.05) compared with controls. Internal transcribed spacer ITS2 metabarcode data revealed that P. graminearum is distributed across a wide range of sites in North America (22 of 24 sites sampled), and its relative abundance is influenced by host species identity and latitude. Host species identity and site were the most important factors determining P. graminearum relative abundance in drought experiments at the Extreme Drought in the Grasslands Experiment (EDGE) sites. Variable responses of B. gracilis to inoculation highlight the potential importance of nonmycorrhizal root-associated fungi on plant survival in arid ecosystems.

Accurate, rapid taxonomic classification of fungal large-subunit rRNA genes.

Taxonomic and phylogenetic fingerprinting based on sequence analysis of gene fragments from the large-subunit rRNA (LSU) gene or the internal transcribed spacer (ITS) region is becoming an integral part of fungal classification. The lack of an accurate and robust classification tool trained by a validated sequence database for taxonomic placement of fungal LSU genes is a severe limitation in taxonomic analysis of fungal isolates or large data sets obtained from environmental surveys. Using a hand-curated set of 8,506 fungal LSU gene fragments, we determined the performance characteristics of a naïve Bayesian classifier across multiple taxonomic levels and compared the classifier performance to that of a sequence similarity-based (BLASTN) approach. The naïve Bayesian classifier was computationally more rapid (>460-fold with our system) than the BLASTN approach, and it provided equal or superior classification accuracy. Classifier accuracies were compared using sequence fragments of 100 bp and 400 bp and two different PCR primer anchor points to mimic sequence read lengths commonly obtained using current high-throughput sequencing technologies. Accuracy was higher with 400-bp sequence reads than with 100-bp reads. It was also significantly affected by sequence location across the 1,400-bp test region. The highest accuracy was obtained across either the D1 or D2 variable region. The naïve Bayesian classifier provides an effective and rapid means to classify fungal LSU sequences from large environmental surveys. The training set and tool are publicly available through the Ribosomal Database Project.

Soil fungal cellobiohydrolase I gene (cbhI) composition and expression in a loblolly pine plantation under conditions of elevated atmospheric CO2 and nitrogen fertilization.

The simultaneous increase of atmospheric CO(2) and nitrogen (N) deposition to terrestrial ecosystems is predicted to alter plant productivity and, consequently, to change the amount and quality of above- and belowground carbon entering forest soils. It is not known how such changes will impact the composition and function of soil fungal communities that play a key role in degrading complex carbon. We sequenced the fungal cellobiohydrolase I gene (cbhI) from soil DNA and cDNA to compare the richness and composition of resident and expressed cbhI genes at a U.S. Department of Energy free air-carbon dioxide enrichment (FACE) site (NC), which had been exposed to elevated atmospheric CO(2) and/or N fertilization treatment for several years. Our results provide evidence that the richness and composition of the cellulolytic fungi surveyed in this study were distinct in the DNA- and cDNA-based gene surveys and were dominated by Basidiomycota that have low or no representation in public databases. The surveys did not detect differences in richness or phylum-level composition of cbhI-containing, cellulolytic fungi that correlated with elevated CO(2) or N fertilization at the time of sampling.

Darksidea phi, sp. nov., a dark septate root-associated fungus in foundation grasses in North American Great Plains.

Darksidea is a common genus of dark septate fungi-a group of ascomycetes in semiarid regions. A survey reported D. alpha and a distinct Darksidea lineage as abundant root-associated fungi of foundational grasses in North America. Fungi were isolated, and metabarcode data were obtained from sequencing of fungal communities of grass roots in the United States. During a comprehensive investigation of the Darksidea lineage, we carried out polyphasic taxonomy, genomic characterization, and identification of host associations, geographic distribution, and environmental factors that correlate with its abundance. For molecular phylogenetic studies, seven loci were sequenced. Isolates of the distinct Darksidea had variable colony morphology. No sexual reproductive structures were detected, but chlamydospores were frequently observed. The complete genome of an isolate of the lineage was sequenced with a size of 52.3 Mb including 14 707 gene models. Based on morphology and phylogenetic analysis, we propose the novel species Darksidea phi, sp. nov. Metabarcoding data showed that D. phi distribution and relative abundance were not limited to semiarid regions or a specific grass species, suggesting low host specificity among graminoids. This new species, D. phi, expands the distribution of the genus in the United States beyond prior reports from arid regions.

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. The effect of long-term nitrogen fertilization on fungi also was evaluated. Samples of rhizosphere (soil surrounding plant roots) and biological soil crust (BSC) were collected in central New Mexico, USA. DNA was amplified from the samples with fungal specific primers. Twelve clone libraries were generated with a total of 307 (78 operational taxonomic units, OTUs) and 324 sequences (67 OTUs) for BSC and rhizosphere respectively. Approximately 40% of soil OTUs were considered novel (less than 97% identity when compared to other sequences in NCBI using BLAST). The dominant organisms were dark-septate (melanized fungi) ascomycetes belonging to Pleosporales. Effects of N enrichment on fungi were not evident at the community level; however the abundance of unique sequences, sampling intensity and temporal variations may be uncovering the effect of N in composition and diversity of fungal communities. The fungal communities of rhizosphere soil and BSC overlapped substantially in composition, with a Jaccard abundance similarity index of 0.75. Further analyses are required to explore possible functions of the dominant species colonizing zones of semiarid grassland soils.