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1. Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus

   https://doi.org/10.1128/spectrum.03980-23  

   Steenwyk, Jacob L; Balamurugan, Charu; Raja, Huzefa A; Gonçalves, Carla; Li, Ningxiao; Martin, Frank; Berman, Judith; Oberlies, Nicholas H; Gibbons, John G; Goldman, Gustavo H; et al (April 2024, Microbiology Spectrum)

   Alanio, Alexandre (Ed.)

   ABSTRACT Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genusAspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific forAspergillusand provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genusAspergillus. Our evolutionary genomic analyses revealed that nearly 8% of publicly availableAspergillusgenomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases. 

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2. Airborne DNA reveals predictable spatial and seasonal dynamics of fungi

   https://doi.org/10.1038/s41586-024-07658-9  

   Abrego, Nerea; Furneaux, Brendan; Hardwick, Bess; Somervuo, Panu; Palorinne, Isabella; Aguilar-Trigueros, Carlos A; Andrew, Nigel R; Babiy, Ulyana V; Bao, Tan; Bazzano, Gisela; et al (July 2024, Nature)

   Abstract Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions^1,2. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sampling of fungal spores³. The vast majority of operational taxonomic units were detected within only one climatic zone, and the spatiotemporal patterns of species richness and community composition were mostly explained by annual mean air temperature. Tropical regions hosted the highest fungal diversity except for lichenized, ericoid mycorrhizal and ectomycorrhizal fungi, which reached their peak diversity in temperate regions. The sensitivity in climatic responses was associated with phylogenetic relatedness, suggesting that large-scale distributions of some fungal groups are partially constrained by their ancestral niche. There was a strong phylogenetic signal in seasonal sensitivity, suggesting that some groups of fungi have retained their ancestral trait of sporulating for only a short period. Overall, our results show that the hyperdiverse kingdom of fungi follows globally highly predictable spatial and temporal dynamics, with seasonality in both species richness and community composition increasing with latitude. Our study reports patterns resembling those described for other major groups of organisms, thus making a major contribution to the long-standing debate on whether organisms with a microbial lifestyle follow the global biodiversity paradigms known for macroorganisms^4,5. 

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3. Niche modelling predicts that soil fungi occupy a precarious climate in boreal forests

   https://doi.org/10.1111/geb.13684  

   Qin, Clara; Pellitier, Peter T.; Van Nuland, Michael E.; Peay, Kabir G.; Zhu, Kai (April 2023, Global Ecology and Biogeography)

   Abstract AimEfforts to predict the responses of soil fungal communities to climate change are hindered by limited information on how fungal niches are distributed across environmental hyperspace. We predict the climate sensitivity of North American soil fungal assemblage composition by modelling the ecological niches of several thousand fungal species. LocationOne hundred and thirteen sites in the United States and Canada spanning all biomes except tropical rain forest. Major Taxa StudiedFungi. Time Period2011–2018. MethodsWe combine internal transcribed spacer (ITS) sequences from two continental‐scale sampling networks in North America and cluster them into operational taxonomic units (OTUs) at 97% similarity. Using climate and soil data, we fit ecological niche models (ENMs) based on logistic ridge regression for all OTUs present in at least 10 sites (n = 8597). To describe the compositional turnover of soil fungal assemblages over climatic gradients, we introduce a novel niche‐based metric of climate sensitivity, the Sørensen climate sensitivity index. Finally, we map climate sensitivity across North America. ResultsENMs have a mean out‐of‐sample predictive accuracy of 73.8%, with temperature variables being strong predictors of fungal distributions. Soil fungal climate niches clump together across environmental space, which suggests common physiological limits and predicts abrupt changes in composition with respect to changes in climate. Soil fungi in North American climates are more likely to be limited by cold and dry conditions than by warm and wet conditions, and ectomycorrhizal fungi generally tolerate colder temperatures than saprotrophic fungi. Sørensen climate sensitivity exhibits a multimodal distribution across environmental space, with a peak in climates corresponding to boreal forests. Main ConclusionsThe boreal forest occupies an especially precarious region of environmental space for the composition of soil fungal assemblages in North America, as even small degrees of warming could trigger large compositional changes characterized mainly by an influx of warm‐adapted species. 

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4. Environmental and host plant effects on taxonomic and phylogenetic diversity of root fungal endophytes

   https://doi.org/10.1093/femsle/fnaf030  

   Farrer, Emily_C; Kulick, Nelle_K; Birnbaum, Christina; Halbrook, Susannah; Bumby, Caitlin_R; Willis, Claire (March 2025, FEMS Microbiology Letters)

   Abstract Nearly all plants are colonized by fungal endophytes, and a growing body of work shows that both environment and host species shape plant-associated fungal communities. However, few studies place their work in a phylogenetic context to understand endophyte community assembly through an evolutionary lens. Here, we investigated environmental and host effects on root endophyte assemblages in coastal Louisiana marshes. We isolated and sequenced culturable fungal endophytes from roots of three to four dominant plant species from each of three sites of varying salinity. We assessed taxonomic diversity and composition as well as phylogenetic diversity (mean phylogenetic distance, MPD) and phylogenetic composition (based on MPD). When we analyzed plant hosts present across the entire gradient, we found that the effect of the environment on phylogenetic diversity (as measured by MPD) was host dependent and suggested phylogenetic clustering in some circumstances. We found that both environment and host plant affected taxonomic composition of fungal endophytes, but only host plant affected phylogenetic composition, suggesting different host plants selected for fungal taxa drawn from distinct phylogenetic clades, whereas environmental assemblages were drawn from similar clades. Our study demonstrates that including phylogenetic, as well as taxonomic, community metrics can provide a deeper understanding of community assembly in endophytes. 

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5. Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

   https://doi.org/10.1093/gigascience/giz006  

   Krehenwinkel, Henrik; Pomerantz, Aaron; Henderson, James_B; Kennedy, Susan_R; Lim, Jun_Ying; Swamy, Varun; Shoobridge, Juan_Diego; Graham, Natalie; Patel, Nipam_H; Gillespie, Rosemary_G; et al (March 2019, GigaScience)

   Abstract BackgroundIn light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on short amplicon sequences, which yield accurate identification of biological entities in a community but provide limited phylogenetic resolution across broad taxonomic scales. However, the phylogenetic structure of communities is an essential component of biodiversity. Consequently, a barcoding approach is required that unites robust taxonomic assignment power and high phylogenetic utility. A possible solution is offered by sequencing long ribosomal DNA (rDNA) amplicons on the MinION platform (Oxford Nanopore Technologies). FindingsUsing a dataset of various animal and plant species, with a focus on arthropods, we assemble a pipeline for long rDNA barcode analysis and introduce a new software (MiniBar) to demultiplex dual indexed Nanopore reads. We find excellent phylogenetic and taxonomic resolution offered by long rDNA sequences across broad taxonomic scales. We highlight the simplicity of our approach by field barcoding with a miniaturized, mobile laboratory in a remote rainforest. We also test the utility of long rDNA amplicons for analysis of community diversity through metabarcoding and find that they recover highly skewed diversity estimates. ConclusionsSequencing dual indexed, long rDNA amplicons on the MinION platform is a straightforward, cost-effective, portable, and universal approach for eukaryote DNA barcoding. Although bulk community analyses using long-amplicon approaches may introduce biases, the long rDNA amplicons approach signifies a powerful tool for enabling the accurate recovery of taxonomic and phylogenetic diversity across biological communities. 

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