New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences

Lange, Lene; Barrett, Kristian; Meyer, Anne S.

doi:10.3390/jof7030207

Cited by 12 publications

(4 citation statements)

References 55 publications

(75 reference statements)

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“…Compared to EcM fungi, the role of DSE fungi in soil organic matter decomposition is less known. Dark septate endophytes may be relatively efficient degraders of organic matter due to their expanded repertoire of CAZymes, including plant cell wall degrading enzymes 62 , 63 . We found that DSE colonization positively associated with soil fungal CAZyme diversity and influenced their composition.…”

Section: Discussionmentioning

confidence: 99%

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Netherway,

Bengtsson,

Buegger

et al. 2024

Nat Commun

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Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi and root endophytes. Here, we explore the role of fungal root symbionts as predictors of the soil and root-associated microbiomes of widespread broad-leaved trees across a European latitudinal gradient. Our results suggest that, alongside factors such as climate, soil, and vegetation properties, root colonization by ectomycorrhizal, arbuscular mycorrhizal, and dark septate endophytic fungi also shapes tree-associated microbiomes. Notably, the structure of root and soil microbiomes across our sites is more strongly and consistently associated with dark septate endophyte colonization than with mycorrhizal colonization and many abiotic factors. Root colonization by dark septate endophytes also has a consistent negative association with the relative abundance and diversity of nutrient cycling genes. Our study not only indicates that root-symbiotic interactions are an important factor structuring soil communities and functions in forest ecosystems, but also that the hitherto less studied dark septate endophytes are likely to be central players in these interactions.

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Section: Discussionmentioning

confidence: 99%

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Netherway,

Bengtsson,

Buegger

et al. 2024

Nat Commun

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“…The increase in sequence read proportions of fungi in the basidiomycete genus Mycena (order Agaricales) toward summer in petioles from both the healthy and diseased stand is noteworthy. For basidiomycetes, some species of Mycena have an astonishingly potent carbohydrate active enzyme portfolio on all plant cell wall components (Lange et al, 2021), something that may enable plasticity in feeding on different cell wall carbohydrates according to substrate properties and phase of decomposition.…”

Section: Discussionmentioning

confidence: 99%

Fungal succession in decomposing ash leaves colonized by the ash dieback pathogen Hymenoscyphus fraxineus or its harmless relative Hymenoscyphus albidus

et al. 2023

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IntroductionThe ascomycete Hymenoscyphus fraxineus, originating from Asia, is currently threatening common ash (Fraxinus excelsior) in Europe, massive ascospore production from the saprotrophic phase being a key determinant of its invasiveness.MethodsTo consider whether fungal diversity and succession in decomposing leaf litter are affected by this invader, we used ITS-1 metabarcoding to profile changes in fungal community composition during overwintering. The subjected ash leaf petioles, collected from a diseased forest and a healthy ash stand hosting the harmless ash endophyte Hymenoscyphus albidus, were incubated in the forest floor of the diseased stand between October 2017 and June 2018 and harvested at 2–3-month intervals.ResultsTotal fungal DNA level showed a 3-fold increase during overwintering as estimated by FungiQuant qPCR. Petioles from the healthy site showed pronounced changes during overwintering; ascomycetes of the class Dothideomycetes were predominant after leaf shed, but the basidiomycete genus Mycena (class Agaricomycetes) became predominant by April, whereas H. albidus showed low prevalence. Petioles from the diseased site showed little change during overwintering; H. fraxineus was predominant, while Mycena spp. showed increased read proportion by June.DiscussionThe low species richness and evenness in petioles from the diseased site in comparison to petioles from the healthy site were obviously related to tremendous infection pressure of H. fraxineus in diseased forests. Changes in leaf litter quality, owing to accumulation of host defense phenolics in the pathogen challenged leaves, and strong saprophytic competence of H. fraxineus are other factors that probably influence fungal succession. For additional comparison, we examined fungal community structure in petioles collected in the healthy stand in August 2013 and showing H. albidus ascomata. This species was similarly predominant in these petioles as H. fraxineus was in petioles from the diseased site, suggesting that both fungi have similar suppressive effects on fungal richness in petiole/rachis segments they have secured for completion of their life cycle. However, the ability of H. fraxineus to secure the entire leaf nerve system in diseased forests, in opposite to H. albidus, impacts the general diversity and successional trajectory of fungi in decomposing ash petioles.

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“…Non-pathogenic Diaporthe species have been recognized as plant growth promoters ( Vázquez de Aldana et al, 2021 ; da Silva Santos et al, 2022 ; Toghueo et al, 2022 ), and biocontrol agents ( Marak et al, 2002 ; Dos Santos et al, 2016 ; Dini-Andreote, 2020 ; Abramczyk et al, 2022 ). From an industrial and pharmaceutical point of view, they are well-known producers of enzymes ( Lange et al, 2021 ; Baluyot et al, 2022 ) and secondary metabolites exhibiting a wide range of activities including antimicrobial, antiviral, antioxidant, anti-inflammatory and anticancer ( Chepkirui and Stadler, 2017 ; Xu et al, 2021 ). Therefore, studies aiming to analyze and better characterize Diaporthe species are of interest, particularly to fully comprehend not only their role as ubiquitous species in nature, but also their potential as metabolite producers, plant growth promoters, biocontrol agents, or for control measures in case of potential pathogenicity.…”

Section: Introductionmentioning

confidence: 99%

Diaporthe species associated with the maritime grass Festuca rubra subsp. pruinosa

Toghueo

Aldana²,

Zabalgogeazcoa³

2023

Front. Microbiol.

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Festuca rubra subsp. pruinosa is a perennial grass growing in sea cliffs where plants are highly exposed to salinity and marine winds, and often grow in rock fissures where soil is absent. Diaporthe species are one of the most abundant components of the root microbiome of this grass and several Diaporthe isolates have been found to produce beneficial effects in their host and other plant species of agronomic importance. In this study, 22 strains of Diaporthe isolated as endophytes from roots of Festuca rubra subsp. pruinosa were characterized by molecular, morphological, and biochemical analyses. Sequences of the nuclear ribosomal internal transcribed spacers (ITS), translation elongation factor 1-α (TEF1), beta-tubulin (TUB), histone-3 (HIS), and calmodulin (CAL) genes were analyzed to identify the isolates. A multi-locus phylogenetic analysis of the combined five gene regions led to the identification of two new species named Diaporthe atlantica and Diaporthe iberica. Diaporthe atlantica is the most abundant Diaporthe species in its host plant, and Diaporthe iberica was also isolated from Celtica gigantea, another grass species growing in semiarid inland habitats. An in vitro biochemical characterization showed that all cultures of D. atlantica produced indole-3-acetic acid and ammonium, and the strains of D. iberica produced indole 3-acetic acid, ammonium, siderophores, and cellulase. Diaporthe atlantica is closely related to D. sclerotioides, a pathogen of cucurbits, and caused a growth reduction when inoculated in cucumber, melon, and watermelon.

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New Method for Identifying Fungal Kingdom Enzyme Hotspots from Genome Sequences

Cited by 12 publications

References 55 publications

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Fungal succession in decomposing ash leaves colonized by the ash dieback pathogen Hymenoscyphus fraxineus or its harmless relative Hymenoscyphus albidus

Diaporthe species associated with the maritime grass Festuca rubra subsp. pruinosa

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