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

Challacombe, Jean F.; Hesse, Cedar; Bramer, Lisa; McCue, Lee Ann; Lipton, Mary; Purvine, Samuel O.; Nicora, Carrie; Gallegos‐Graves, La Verne; Porras‐Alfaro, Andrea; Kuske, Cheryl R.

doi:10.1186/s12864-019-6358-x

Cited by 144 publications

(74 citation statements)

References 187 publications

(277 reference statements)

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“…In addition, AAO is potentially implicated in lignin modification by acting on lignin-derived phenolic aromatic aldehydes and acids [ 81 , 82 , 83 ]. Enzyme belonging to the AA3 family were previously identified in the secretomes of several basidiomycetes [ 84 , 85 ] and ascomycetes [ 26 , 86 ] during growth on lignin-rich substrates.…”

Section: Resultsmentioning

confidence: 99%

A Putative Lignin Copper Oxidase from Trichoderma reesei

Daou

Bisotto

Haon

et al. 2021

JoF

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The ability of Trichoderma reesei, a fungus widely used for the commercial production of hemicellulases and cellulases, to grow and modify technical soda lignin was investigated. By quantifying fungal genomic DNA, T. reesei showed growth and sporulation in solid and liquid cultures containing lignin alone. The analysis of released soluble lignin and residual insoluble lignin was indicative of enzymatic oxidative conversion of phenolic lignin side chains and the modification of lignin structure by cleaving the β-O-4 linkages. The results also showed that polymerization reactions were taking place. A proteomic analysis conducted to investigate secreted proteins at days 3, 7, and 14 of growth revealed the presence of five auxiliary activity (AA) enzymes in the secretome: AA6, AA9, two AA3 enzymes), and the only copper radical oxidase encoded in the genome of T. reesei. This enzyme was heterologously produced and characterized, and its activity on lignin-derived molecules was investigated. Phylogenetic characterization demonstrated that this enzyme belonged to the AA5_1 family, which includes characterized glyoxal oxidases. However, the enzyme displayed overlapping physicochemical and catalytic properties across the AA5 family. The enzyme was remarkably stable at high pH and oxidized both, alcohols and aldehydes with preference to the alcohol group. It was also active on lignin-derived phenolic molecules as well as simple carbohydrates. HPSEC and LC-MS analyses on the reactions of the produced protein on lignin dimers (SS ββ, SS βO4 and GG β5) uncovered the polymerizing activity of this enzyme, which was accordingly named lignin copper oxidase (TrLOx). Polymers of up 10 units were formed by hydroxy group oxidation and radical formation. The activations of lignin molecules by TrLOx along with the co-secretion of this enzyme with reductases and FAD flavoproteins oxidoreductases during growth on lignin suggest a synergistic mechanism for lignin breakdown.

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Section: Resultsmentioning

confidence: 99%

A Putative Lignin Copper Oxidase from Trichoderma reesei

Daou

Bisotto

Haon

et al. 2021

JoF

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“…However, our result contrasts against a recent global meta-study of >3,000 soil samples, in which climate variables accounted for ~65% of explained variation in soil fungal communities climate variables than are foliar fungi or fungi that reside primarily in soils rather than inside roots. In addition, the apparently wide ecological plasticity of root-associated fungi (Challacombe et al, 2019;Egidi et al, 2019;Porras-Alfaro & Bayman, 2011) may explain why, in contrast to many other organisms, these fungi were less sensitive to climate than to edaphic or host-associated variables. Alternatively, the lack of a classic latitudinal diversity gradient could occur because our gradient did not extend to the tropics as we constrained sampling to coincide with host plant distributions.…”

Section: Discussionmentioning

confidence: 99%

Biogeography of root‐associated fungi in foundation grasses of North American plains

Rudgers

Fox

Porras-Alfaro

et al. 2021

Journal of Biogeography

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Aim: Roots and rhizospheres host diverse microbial communities that can influence the fitness, phenotypes, and environmental tolerances of plants. Documenting the biogeography of these microbiomes can detect the potential for a changing environment to disrupt host-microbe interactions, particularly in cases where microbes buffer hosts against abiotic stressors. We evaluated whether root-associated fungi had poleward declines in diversity, tested whether fungal communities in roots shifted near host plant range edges, and determined the relative importance of environmental and host predictors of root fungal community structure.Location: North American plains grasslands. Taxon: Foundation grasses -Andropogon gerardii, Bouteloua dactyloides, B. eriopoda, B. gracilis, and Schizachyrium scoparium and root fungi. Methods: At each of 24 sites representing three replicate 17°-latitudinal gradients, we collected roots from 12 individuals per species along five transects spaced 10 m apart (40 m × 40 m grid). We used next-generation sequencing of ITS2, direct fungal culturing from roots, and microscopy to survey fungi associated with grass roots. Results: Root-associated fungi did not follow the poleward declines in diversity documented for many animals and plants. Instead, host plant identity had the largest influence on fungal community structure. Edaphic factors outranked climate or host plant traits as correlates of fungal community structure; however, the relative importance of environmental predictors differed among plant species. As sampling approached host species range edges, fungal composition converged in similarity among individual plants of each grass species. Main conclusions: Environmental predictors of root-associated fungi depended strongly on host plant species identity. Biogeographic patterns in fungal composition suggested a homogenizing influence of stressors at host plant range limits. Resultspredict that communities of non-mycorrhizal, root-associated fungi in the North American plains will be more sensitive to future changes in host plant ranges and edaphic factors than to the direct effects of climate.

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“…Ascomycota are important drivers in carbon and nitrogen cycling in arid ecosystems and may have a promoting effect on the composting process due to the ability of stabilizing the soil and decomposing the plant biomass(Challacombe et al . 2019). The P. variotii , B. spectabilis and A. fumigatus were the main species in A1 stage, and the proportion of species in A2 stage is a little messy and mixed with some pathogenic species for some unknown reasons, while in A3 stage the proportion of dominant species back to normal level and the B. spectabilis took a relatively dominant position (Fig.…”

Section: Resultsmentioning

confidence: 99%

Effect of the compound bacterial agent on microbial community of the aerobic compost of food waste

Yang

Feng

et al. 2021

Letters Applied Microbiology

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In our study, we used 16SrRNA and ITS to investigate the microbial community composition and the effect of compound bacterial agent on the microbial community composition in the aerobic composting process of food waste (FW). At the bacterial level, the main phyla of Group A (compost naturally) were Proteobacteria and Firmicutes, and the main species were Pseudomonas_sp._GR7, Bacillus licheniformis and Pediococcus acidilactici. The main phyla of Group B (compost with compound bacterial agent) were Proteobacteria, Firmicutes and Streptophyta, and the main species were Klebsiella pneumoniae, Cronobacter sakazakii, Macrococcus caseolyticus, Enterococcus faecalis, Citrobacter freundii and Bacillus velezensis. It is worth noting that M. caseolyticus may be able to improve the effect of odour which is an important sensory index during aerobic composting. At the fungal level, the main phylum of both Groups A and B was Ascomycota, and the main species of Group A were Paecilomyces variotii, Byssochlamys spectabilis and Aspergillus fumigatus. The main species of Group B were Ogataea polymorpha and Millerozyma farinosa. Finally, the degradation rate of Group B was 81% that was about 15% higher than that of Group A, indicating that the compound bacterial agent could effectively improve the degradation rate and the composting process, while the low abundance of the compound bacterial agent in the composting process might be due to the small initial addition or the inhibition of other bacteria or fungi in the composting process.

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

Cited by 144 publications

References 187 publications

A Putative Lignin Copper Oxidase from Trichoderma reesei

A Putative Lignin Copper Oxidase from Trichoderma reesei

Biogeography of root‐associated fungi in foundation grasses of North American plains

Effect of the compound bacterial agent on microbial community of the aerobic compost of food waste

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