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

Journal Article · 12 December 2019 · BMC Genomics

DOI: https://doi.org/10.1186/s12864-019-6358-x · OSTI ID:1618577

Challacombe, Jean Faust  ^[1]; Hesse, Cedar N. ^[2]; Bramer, Lisa M.  ^[3]; McCue, Lee Ann  ^[3]; Lipton, Mary S. ^[3]; Purvine, Samuel O.  ^[3]; Nicora, Carrie D.  ^[3]; Gallegos-Graves, Laverne A. ^[1]; Porras-Alfaro, Andrea ^[4]; Kuske, Cheryl Rae  ^[1]

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1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States); US Dept. of Agriculture (USDA)., Corvallis, OR (United States). Agricultural Research Service (ARS)
3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
4. Western Illinois Univ., Macomb, IL (United States)

The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in soil stability, plant biomass decomposition, and endophytic interactions with plants. They may also form symbiotic associations with biocrust components or be latent saprotrophs or pathogens that live on plant tissues. However, their functional potential in arid soils, where organic matter, nutrients and water are very low or only periodically available, is poorly characterized. Five Ascomycota fungi were isolated from different soil crust microhabitats and rhizosphere soils around the native bunchgrass Pleuraphis jamesii in an arid grassland near Moab, UT, USA. Putative genera were Coniochaeta, isolated from lichen biocrust, Embellisia from cyanobacteria biocrust, Chaetomium from below lichen biocrust, Phoma from a moss microhabitat, and Aspergillus from the soil. The fungi were grown in replicate cultures on different carbon sources (chitin, native bunchgrass or pine wood) relevant to plant biomass and soil carbon sources. Secretomes produced by the fungi on each substrate were characterized. Results demonstrate that these fungi likely interact with primary producers (biocrust or plants) by secreting a wide range of proteins that facilitate symbiotic associations. Each of the fungal isolates secreted enzymes that degrade plant biomass, small secreted effector proteins, and proteins involved in either beneficial plant interactions or virulence. Aspergillus and Phoma expressed more plant biomass degrading enzymes when grown in grass- and pine-containing cultures than in chitin. Coniochaeta and Embellisia expressed similar numbers of these enzymes under all conditions, while Chaetomium secreted more of these enzymes in grass-containing cultures. This study of Ascomycota genomes and secretomes provides important insights about the lifestyles and the roles that Ascomycota fungi likely play in arid grassland, ecosystems. However, the exact nature of those interactions, whether any or all of the isolates are true endophytes, latent saprotrophs or opportunistic phytopathogens, will be the topic of future studies.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE National Nuclear Security Administration (NNSA)
• Grant/Contract Number: AC05-76RL01830; 89233218CNA000001
• OSTI ID: 1618577
• Alternate ID(s): OSTI ID: 1580512; OSTI ID: 1603981; OSTI ID: 1634951
• Report Number(s): PNNL-SA-140986; LA-UR-16-29573; LA-UR-19-20737; LA-UR-18-25519
• Journal Information: BMC Genomics, Vol. 20, Issue 1; ISSN 1471-2164
• Publisher: SpringerCopyright Statement
• Country of Publication: United States
• Language: English