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Summary: Wildfires drastically impact the soil environment, altering the soil organic matter, forming pyrolyzed compounds, and markedly reducing the diversity of microorganisms. Pyrophilous fungi, especially the species from the orders Pezizales and Agaricales, are fire‐responsive fungal colonizers of post‐fire soil that have historically been found fruiting on burned soil and thus may encode mechanisms of processing these compounds in their genomes.Pyrophilous fungi are diverse. In this work, we explored this diversity and sequenced six new genomes of pyrophilous Pezizales fungi isolated after the 2013 Rim Fire near Yosemite Park in California, USA: Pyronema domesticum, Pyronema omphalodes, Tricharina praecox, Geopyxis carbonaria, Morchella snyderi, and Peziza echinospora.A comparative genomics analysis revealed the enrichment of gene families involved in responses to stress and the degradation of pyrolyzed organic matter. In addition, we found that both protein sequence lengths and G + C content in the third base of codons (GC3) in pyrophilous fungi fall between those in mesophilic/nonpyrophilous and thermophilic fungi.A comparative transcriptome analysis of P. domesticum under two conditions – growing on charcoal, and during sexual development – identified modules of genes that are co‐expressed in the charcoal and light‐induced sexual development conditions. In addition, environmental sensors such as transcription factors STE12, LreA, LreB, VosA, and EsdC were upregulated in the charcoal condition.Taken together, these results highlight genomic adaptations of pyrophilous fungi and indicate a potential connection between charcoal tolerance and fruiting body formation in P. domesticum. [ABSTRACT FROM AUTHOR]

Summary: Forest fires generate a large amount of carbon that remains resident on the site as dead and partially 'pyrolysed' (i.e. burnt) material that has long residency times and constitutes a significant pool in fire‐prone ecosystems. In addition, fire‐induced hydrophobic soil layers, caused by condensation of pyrolysed waxes and lipids, increase post‐fire erosion and can lead to long‐term productivity losses. A small set of pyrophilous fungi dominate post‐fire soils and are likely to be involved with the degradation of all these compounds, yet almost nothing is currently known about what these fungi do or the metabolic processes they employ. In this study, we sequenced and analysed genomes from fungi isolated after Rim fire near Yosemite National Park in 2013 and showed the enrichment/expansion of CAZymes and families known to be involved in fruiting body initiation when compared to other basidiomycete fungi. We found gene families potentially involved in the degradation of the hydrophobic layer and pyrolysed organic matter, such as hydrophobic surface binding proteins, laccases (AA1_1), xylanases (GH10, GH11), fatty acid desaturases and tannases. Thus, pyrophilous fungi are important actors to restate the soil's functional capabilities. [ABSTRACT FROM AUTHOR]

We have designed a pyrocosm to enable fine-scale dissection of post-fire soil microbial communities. Using it we show that the peak soil temperature achieved at a given depth occurs hours after the fire is out, lingers near this peak for a significant time, and is accurately predicted by soil depth and the mass of charcoal burned. Flash fuels that produce no large coals were found to have a negligible soil heating effect. Coupling this system with Illumina MiSeq sequencing of the control and post-fire soil we show that we can stimulate a rapid, massive response by Pyronema, a well-known genus of pyrophilous fungus, within two weeks of a test fire. This specific stimulation occurs in a background of many other fungal taxa that do not change noticeably with the fire, although there is an overall reduction in richness and evenness. We introduce a thermo-chemical gradient model to summarize the way that heat, soil depth and altered soil chemistry interact to create a predictable, depth-structured habitat for microbes in post-fire soils. Coupling this model with the temperature relationships found in the pyrocosms, we predict that the width of a survivable "goldilocks zone", which achieves temperatures that select for postfire-adapted microbes, will stay relatively constant across a range of fuel loads. In addition we predict that a larger necromass zone, containing labile carbon and nutrients from recently heat-killed organisms, will increase in size rapidly with addition of fuel and then remain nearly constant in size over a broad range of fuel loads. The simplicity of this experimental system, coupled with the availability of a set of sequenced, assembled and annotated genomes of pyrophilous fungi, offers a powerful tool for dissecting the ecology of post-fire microbial communities. [ABSTRACT FROM AUTHOR]

The draft genome, morphological description, and phylogenetic placement of Coniella lustricola sp. nov. (Schizoparmeaceae) are provided. The species was isolated from submerged detritus in a fen at Black Moshannon State Park, Pennsylvania, USA and differs from all other Coniella species by having ellipsoid to fusoid, inequilateral conidia that are rounded on one end and truncate or obtuse on the other end, with a length to width ratio of 2.8. The draft genome is 36.56 Mbp and consists of 870 contigs on 634 scaffolds (L50 = 0.14 Mb, N50 = 76 scaffolds), with 0.5% of the scaffold length in gaps. It contains 11,317 predicted gene models, including predicted genes for cellulose, hemicellulose, and xylan degradation, as well as predicted regions encoding for amylase, laccase, and tannase enzymes. Many members of the Schizoparmeaceae are plant pathogens of agricultural crops. This draft genome represents the first sequenced Coniella genome and will be a valuable tool for comparisons among pathogenic Coniella species. [ABSTRACT FROM AUTHOR]

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild. Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild. [ABSTRACT FROM AUTHOR]