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The emerald ash borer (EAB) is an exotic forest pest that has killed millions of ash trees in the United States and Canada, resulting in an ecological disaster and billions of dollars in economic losses of urban landscape and forest trees. The beetle was first detected in Michigan in 2002 and has spread through much of the Eastern and Midwestern U.S., reaching Minnesota in 2009. Since then, it has spread across the state and poses a great risk to the more than 1 billion ash trees in Minnesota. The larval stage of EAB creates wounds on trees as they feed on the inner bark, causing disruption of water and sap flow that results in tree death. The fungal community associated with EAB larval galleries is poorly understood and the role these fungi may play in tree death is not known. This study describes fungi isolated from EAB larval galleries sampled throughout the main geographic areas of Minnesota where ash is affected by EAB. Fungal cultures were identified by extracting genomic DNA and sequencing the ITS region of the rDNA. Results from 1126 isolates reveal a diverse assemblage of fungi and three functional guilds comprised of canker pathogens, wood decay, and entomopathogenic fungi. The most common canker-associated genera were Cytospora followed by Phaeoacremonium, Paraconiothyrium, Coniothyrium, Nectria, Diplodia, and Botryosphaeria. Fungi in the Basidiomycota were nearly all wood decay causing fungi and many were species of pioneer colonizing genera including Sistotrema, Irpex, Peniophora, Phlebia and Ganoderma. Some of these fungi seriously affect urban trees, having the potential to cause rapid wood decay resulting in hazardous tree situations. Several entomopathogenic genera with the potential for biological control of EAB were also isolated from galleries. Purpureocillium was the most commonly isolated genus, followed by Beauveria, Clonostachys, Lecanicillium, Akanthomyces, Cordyceps, Microcera, Tolypocladium, and Pochonia. The results identify important fungal functional guilds that are occupying a new niche in ash trees resulting from EAB and include fungi that may accelerate decline in tree health, increase hazard tree situations, or may provide options for biological control of this destructive invasive insect., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Background: Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes, found in fungi and bacteria, which biosynthesize peptides without the aid of ribosomes. Although their metabolite products have been the subject of intense investigation due to their life-saving roles as medicinals and injurious roles as mycotoxins and virulence factors, little is known of the phylogenetic relationships of the corresponding NRPSs or whether they can be ranked into subgroups of common function. We identified genes (NPS) encoding NRPS and NRPS-like proteins in 38 fungal genomes and undertook phylogenomic analyses in order to identify fungal NRPS subfamilies, assess taxonomic distribution, evaluate levels of conservation across subfamilies, and address mechanisms of evolution of multimodular NRPSs. We also characterized relationships of fungal NRPSs, a representative sampling of bacterial NRPSs, and related adenylating enzymes, including alpha-aminoadipate reductases (AARs) involved in lysine biosynthesis in fungi., Results: Phylogenomic analysis identified nine major subfamilies of fungal NRPSs which fell into two main groups: one corresponds to NPS genes encoding primarily mono/bi-modular enzymes which grouped with bacterial NRPSs and the other includes genes encoding primarily multimodular and exclusively fungal NRPSs. AARs shared a closer phylogenetic relationship to NRPSs than to other acyl-adenylating enzymes. Phylogenetic analyses and taxonomic distribution suggest that several mono/bi-modular subfamilies arose either prior to, or early in, the evolution of fungi, while two multimodular groups appear restricted to and expanded in fungi. The older mono/bi-modular subfamilies show conserved domain architectures suggestive of functional conservation, while multimodular NRPSs, particularly those unique to euascomycetes, show a diversity of architectures and of genetic mechanisms generating this diversity., Conclusions: This work is the first to characterize subfamilies of fungal NRPSs. Our analyses suggest that mono/bi-modular NRPSs have more ancient origins and more conserved domain architectures than most multimodular NRPSs. It also demonstrates that the alpha-aminoadipate reductases involved in lysine biosynthesis in fungi are closely related to mono/bi-modular NRPSs. Several groups of mono/bi-modular NRPS metabolites are predicted to play more pivotal roles in cellular metabolism than products of multimodular NRPSs. In contrast, multimodular subfamilies of NRPSs are of more recent origin, are restricted to fungi, show less stable domain architectures, and biosynthesize metabolites which perform more niche-specific functions than mono/bi-modular NRPS products. The euascomycete-only NRPS subfamily, in particular, shows evidence for extensive gain and loss of domains suggestive of the contribution of domain duplication and loss in responding to niche-specific pressures.

Background: Most filamentous ascomycete fungi produce high affinity iron chelators called siderophores, biosynthesized nonribosomally by multimodular adenylating enzymes called nonribosomal peptide synthetases (NRPSs). While genes encoding the majority of NRPSs are intermittently distributed across the fungal kingdom, those encoding ferrichrome synthetase NRPSs, responsible for biosynthesis of ferrichrome siderophores, are conserved, which offers an opportunity to trace their evolution and the genesis of their multimodular domain architecture. Furthermore, since the chemistry of many ferrichromes is known, the biochemical and structural 'rules' guiding NRPS substrate choice can be addressed using protein structural modeling and evolutionary approaches., Results: A search of forty-nine complete fungal genome sequences revealed that, with the exception of Schizosaccharomyces pombe, none of the yeast, chytrid, or zygomycete genomes contained a candidate ferrichrome synthetase. In contrast, all filamentous ascomycetes queried contained at least one, while presence and numbers in basidiomycetes varied. Genes encoding ferrichrome synthetases were monophyletic when analyzed with other NRPSs. Phylogenetic analyses provided support for an ancestral duplication event resulting in two main lineages. They also supported the proposed hypothesis that ferrichrome synthetases derive from an ancestral hexamodular gene, likely created by tandem duplication of complete NRPS modules. Recurrent losses of individual domains or complete modules from this ancestral gene best explain the diversity of extant domain architectures observed. Key residues and regions in the adenylation domain pocket involved in substrate choice and for binding the amino and carboxy termini of the substrate were identified., Conclusion: Iron-chelating ferrichrome synthetases appear restricted to fission yeast, filamentous ascomycetes, and basidiomycetes and fall into two main lineages. Phylogenetic analyses suggest that loss of domains or modules led to evolution of iterative biosynthetic mechanisms that allow flexibility in biosynthesis of the ferrichrome product. The 10 amino acid NRPS code, proposed earlier, failed when we tried to infer substrate preference. Instead, our analyses point to several regions of the binding pocket important in substrate choice and suggest that two positions of the code are involved in substrate anchoring, not substrate choice.

Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or "specialized" metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.

Since the discovery of the Pleurocordyceps/ "Polycephalomyces" clade unaffiliated with the clades of Clavicipitaceae s. str., Ophiocordycipitaceae, and Cordycipitaceae of clavicipitaceous fungi, some taxa have been published and more fungal material relevant to the group have become available for further study. Here, a multigene phylogeny using nrSSU, nrLSU, tef1, rpb1, and rpb2 was constructed with some of the recently discovered additional taxa using maximum likelihood and Bayesian analyses (BI) to test and refine the current phylogenetic framework for Cordyceps s. lat. and other clavicipitaceous fungi. In addition to the well supported major Pleurocordyceps/"Polycephalomyces" clade revealed previously, another clade with newly added taxa referred to as "Polycephalomyces formosus‐like" from Japan was found to be sister to the Pleurocordyceps/"Polycephalomyces" clade. Extensive investigation revealed that strains named "P. formosus‐like" grouped in this new clade and do indeed represent the true P. formosus and that species previously included in the genus Polycephalomyces required a new generic name. Based on the phylogenetic analyses and morphological characteristics, including both sexual and asexual morphs when available, the new generic name Pleurocordyceps is introduced and relevant new combinations are made. A newly designated lectotype and a supporting epitype for P. formosus is selected and the circumscription of Polycephalomyces is discussed. [ABSTRACT FROM AUTHOR]

The soybean cyst nematode (SCN) is the most important pest on soybean, a major crop worldwide. The SCN is considered both parasitic and pathogenic as it derives nutrition from the host and manipulates host physiology to do so. Currently, there are no commercially available chemicals that are specific, environmentally safe and cost effective to control SCN levels. Crop rotation, use of host resistance and other cultural practices remain the main management strategies. The need for bioprospecting other methods of controlling SCN is paramount, and fungi show promise in that respect. Several studies have evaluated fungi and fungal products as biocontrol options against plant-parasitic nematodes. This review discusses fungal genera isolated from the SCN with potential for use as biocontrol agents and the effects of their secondary metabolites on various stages of SCN development. The review also summarizes efforts to control SCN using soil amendments that could potentially impact fungal communities in the soil. [ABSTRACT FROM AUTHOR]

The fungus Cochliobolus miyabeanus causes severe leaf spot disease on rice (Oryza sativa) and two North American specialty crops, American wildrice (Zizania palustris) and switchgrass (Panicum virgatum). Despite the importance of C. miyabeanus as a disease-causing agent in wildrice, little is known about either the mechanisms of pathogenicity or host defense responses. To start bridging these gaps, the genome of C. miyabeanus strain TG12bL2 was shotgun sequenced using Illumina technology. The genome assembly consists of 31.79 Mbp in 2,378 scaffolds with an N50 = 74,921. It contains 11,000 predicted genes of which 94.5% were annotated. Approximately 10% of total gene number is expected to be secreted. The C. miyabeanus genome is rich in carbohydrate active enzymes, and harbors 187 small secreted peptides (SSPs) and some fungal effector homologs. Detoxification systems were represented by a variety of enzymes that could offer protection against plant defense compounds. The non-ribosomal peptide synthetases and polyketide synthases (PKS) present were common to other Cochliobolus species. Additionally, the fungal transcriptome was analyzed at 48 hours after inoculation in planta. A total of 10,674 genes were found to be expressed, some of which are known to be involved in pathogenicity or response to host defenses including hydrophobins, cutinase, cell wall degrading enzymes, enzymes related to reactive oxygen species scavenging, PKS, detoxification systems, SSPs, and a known fungal effector. This work will facilitate future research on C. miyabeanus pathogen-associated molecular patterns and effectors, and in the identification of their corresponding wildrice defense mechanisms. [ABSTRACT FROM AUTHOR]

Fungi produce a myriad of secondary metabolites, compounds that are not required for basic cellular processes, but are thought to be central to ecological functions. Genomic sequencing of fungi has revealed a greater diversity of secondary metabolism than previously realized, including novel taxonomic distributions of known compounds and uncharacterized gene clusters in well-studied organisms. Here we provide an overview of the major groups of metabolites, their ecological functions, the genetic systems that produce them, and the patterns and processes associated with evolutionary diversification of secondary metabolism in plant-associated filamentous ascomycetes. [ABSTRACT FROM AUTHOR]

Abstract: An exhaustive characterization of the set of non-ribosomal peptide synthetase (NRPS) genes of the corn pathogen, Cochliobolus heterostrophus, and the small molecule peptides produced by the enzymes they encode, has been undertaken to ascertain the role of the peptide metabolites in the fungal cell. To date, the NRPS method of peptide biosynthesis has been described for filamentous ascomycete fungi (and to a limited extent, for basidiomycete fungi) and for bacteria, only. In addition to structural diversity, non-ribosomal peptides have a broad spectrum of biological activities, many are useful in medicine, agriculture, industry, and biological research. However, to suggest that inter-organismal activities is their primary function is likely incorrect; in fact, the physiological significance of these peptides to the producing fungi is largely unknown. We document that NRPS enzymes are purveyors of small molecules for both basal metabolism and for specialized environmental niches and that some are conserved, but most are not. [Copyright &y& Elsevier]

Fungal biological control of soybean cyst nematodes (SCN) is an important component of integrated pest management for soybean. However, very few fungal biological control agents are available in the market. In this study, we have screened fungi previously isolated from SCN cysts over 3 years from a long-term crop rotation field experiment for their ability to antagonize SCN using (i) parasitism, (ii) egg hatch inhibition, and (iii) J2 mortality. We evaluated egg parasitism using an invitro egg parasitism bioassays and scored parasitism using the egg parasitic index (EPI) and fluorescent microscopy. The ability of these fungi to produce metabolites causing egg hatch inhibition and J2 mortality was assessed in bioassays using filter-sterilized culture filtrates. We identified 10 high-performing isolates each for egg parasitism and toxicity toward SCN eggs and J2s and repeated the tests after storage for 1 year of cryopreservation at -80°C to validate the durability of biocontrol potential of the chosen 20 isolates. Although the parasitic ability changed slightly for the majority of strains after cryopreservation, they still scored 5/10 on EPI scales. There were no differences in the ability of fungi to produce antinemic metabolites after cryopreservation. [ABSTRACT FROM AUTHOR]

• Twenty fungi screened in planta against SCN. • Three isolates showed high biocontrol efficacy. • One Purpureocillium sp. controlled performed as well as commercial biologicals at lower dosage. The soybean cyst nematode (SCN; Heterodera glycines) is the most economically consequential pathogen of soybeans worldwide. Although biological control of SCN was proposed decades ago, only a few products are available on the market. Mining for new fungal biological control organisms and evaluating their potential to enhance integrated management of SCN is crucial. In this study, we evaluated 20 candidate biological control organisms in vivo that were selected out of a culturable mycobiome of over 5000 isolates based on their performance in in vitro assays. Of these isolates, labelled A through T, we identified three isolates, one Ilyonectria sp. (D), and two Purpureocillium sp. isolates (E and T), that significantly reduced SCN reproduction on a susceptible soybean variety (Sturdy) inoculated with both high and low levels of SCN eggs, compared to an untreated control, in a growth chamber cone-tainer assay. In a greenhouse pot assay, Purpureocillium isolates E and T also controlled nematode reproduction better than an untreated control and performed on par with the commercial fungal biological control agent, MeloCon® WG, which was applied at 41-fold higher concentration. In a second greenhouse assay, with higher nematode numbers, only isolate E performed as well as MeloCon® WG. This research identified promising candidate biological control agents of SCN that are as or more effective than existing products at much lower spore inoculation levels. [ABSTRACT FROM AUTHOR]

Fungi decompose woody debris, an important carbon pool in forests. Fungal community structure is expected to vary according to the wood species, habitats and extent of abiotic disturbance, which have consequences for carbon cycling in tropical forests. Here we examined the effects of fungal diversity and composition on woody debris decomposition rates and sought potential mechanisms to explain an observed lack of difference in decomposition rates across a disturbance gradient in a tropical montane rainforest in Xishuangbanna, SW China. We measured wood specific gravity (WSG) loss from 280 logs of Litsea cubeba and Castanopsis mekongensis over 3 years and monitored fungal communities from 418 samples using next-generation sequencing after 0, 18 and 36 months field exposure. Wood species and termite presence determined changes in fungal diversity through time. Overall there was a peak in fungal diversity at 18 mo, suggesting an initial period of colonization followed by a period of increasingly competitive interactions leading to decreased diversity. Litsea logs, which had relatively low initial WSG and thinner bark, harbored higher fungal diversity. Shared fungal OTUs between wood species peaked at 18 mo (~50%). However, fungal diversity was not a significant predictor of WSG loss. An effect of habitat on fungal community composition suggests that functional replacement explains the similar decay rates across the disturbance gradient. In addition, the proportions of saprotroph and white-rot fungi increased through time regardless of wood species. Termite presence reduced WSG loss, but the effect was mediated via the abundance of soft rot fungi. Our results suggest that changes in functional traits, rather than fungal species diversity, may better explain variation in WSG loss. Future studies should investigate roles of fungal functional traits and rot types, particularly those of Ascomycete fungi, whose roles in wood decay are still poorly characterized. • We investigated fungal community dynamics in decomposing wood in a tropical ecosystem. • Fungal communities varied with habitat without changing wood decay rates. • Saprotroph abundance increase through time and positively affected wood decay rates. • Termites, woody species and exposure time mediate wood decay via soft-rot abundance. • Major fungal functional trait dynamics will improve biogeochemical model accuracy. [ABSTRACT FROM AUTHOR]