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Open AccessArticle

Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone

1
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, P. Bag X20, Hatfield 0028, Pretoria 0002, South Africa
2
Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, P. Bag X20, Hatfield 0028, Pretoria 0002, South Africa
3
AG Geobotanik, Ruhr-Universität Bochum, Gebäude ND 1/150, Universitätsstraße 150, 44780 Bochum, Germany
*
Authors to whom correspondence should be addressed.
Microorganisms 2019, 7(10), 375; https://doi.org/10.3390/microorganisms7100375
Received: 12 July 2019 / Revised: 6 August 2019 / Accepted: 9 August 2019 / Published: 20 September 2019
(This article belongs to the Special Issue Ecology and Genomics of Forest Fungi and Their Interactions)
Fungi represent a common and diverse part of the microbial communities that associate with plants. They also commonly colonise various plant parts asymptomatically. The molecular mechanisms of these interactions are, however, poorly understood. In this study we use transcriptomic data from Eucalyptus grandis, to demonstrate that RNA-seq data are a neglected source of information to study fungal–host interactions, by exploring the fungal transcripts they inevitably contain. We identified fungal transcripts from E. grandis data based on their sequence dissimilarity to the E. grandis genome and predicted biological functions. Taxonomic classifications identified, amongst other fungi, many well-known pathogenic fungal taxa in the asymptomatic tissue of E. grandis. The comparison of a clone of E. grandis resistant to Chrysoporthe austroafricana with a susceptible clone revealed a significant difference in the number of fungal transcripts, while the number of fungal taxa was not substantially affected. Classifications of transcripts based on their respective biological functions showed that the fungal communities of the two E. grandis clones associate with fundamental biological processes, with some notable differences. To shield the greater host defence machinery in the resistant E. grandis clone, fungi produce more secondary metabolites, whereas the environment for fungi associated with the susceptible E. grandis clone is more conducive for building fungal cellular structures and biomass growth. Secreted proteins included carbohydrate active enzymes that potentially are involved in fungal–plant and fungal–microbe interactions. While plant transcriptome datasets cannot replace the need for designed experiments to probe plant–microbe interactions at a molecular level, they clearly hold potential to add to the understanding of the diversity of plant–microbe interactions. View Full-Text
Keywords: asymptomatic plant infection; plant–fungus interaction; plant–microbe interaction; secreted proteins; metatranscriptomics; CAZymes; pathogen–host interaction asymptomatic plant infection; plant–fungus interaction; plant–microbe interaction; secreted proteins; metatranscriptomics; CAZymes; pathogen–host interaction
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Messal, M.; Slippers, B.; Naidoo, S.; Bezuidt, O.; Kemler, M. Active Fungal Communities in Asymptomatic Eucalyptus grandis Stems Differ between a Susceptible and Resistant Clone. Microorganisms 2019, 7, 375.

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