Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression

Daly, Paul; van Munster, Jolanda M.; Kokolski, Matthew; Sang, Fei; Blythe, Martin J.; Malla, Sunir; Velasco de Castro Oliveira, Juliana; Goldman, Gustavo H.; Archer, David B.

Abstract

Gaining new knowledge through fungal monoculture responses to lignocellulose is a widely used approach that can lead to better cocktails for lignocellulose saccharification (the enzymatic release of sugars which are subsequently used to make biofuels). However, responses in lignocellulose mixed cultures are rarely studied in the same detail even though in nature fungi often degrade lignocellulose as mixed communities.

Using a dual RNA-seq approach, we describe the first study of the transcriptional responses of wild-type strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw.

Based on quantification of species-specific rRNA, a set of conditions was identified where mixed cultures could be sampled so as to obtain sufficient RNA-seq reads for analysis from each species. The number of differentially-expressed genes varied from a couple of thousand to fewer than one hundred. The proportion of carbohydrate active enzyme (CAZy) encoding transcripts was lower in the majority of the mixed cultures compared to the respective straw monocultures. A small subset of P. chrysogenum CAZy genes showed five to ten-fold significantly increased transcript abundance in a two-species mixed culture with T. reesei. However, a substantial number of T. reesei CAZy transcripts showed reduced abundance in mixed cultures. The highly induced genes in mixed cultures indicated that fungal antagonism was a major part of the mixed cultures. In line with this, secondary metabolite producing gene clusters showed increased transcript abundance in mixed cultures and also mixed cultures with T. reesei led to a decrease in the mycelial biomass of A. niger. Significantly higher monomeric sugar release from straw was only measured using a minority of the mixed culture filtrates and there was no overall improvement.

This study demonstrates fungal interaction with changes in transcripts, enzyme activities and biomass in the mixed cultures and whilst there were minor beneficial effects for CAZy transcripts and activities, the competitive interaction between T. reesei and the other fungi was the most prominent feature of this study.

Citation

Daly, P., van Munster, J. M., Kokolski, M., Sang, F., Blythe, M. J., Malla, S., Velasco de Castro Oliveira, J., Goldman, G. H., & Archer, D. B. (2017). Transcriptomic responses of mixed cultures of ascomycete fungi to lignocellulose using dual RNA-seq reveal inter-species antagonism and limited beneficial effects on CAZyme expression. Fungal Genetics and Biology, 102, https://doi.org/10.1016/j.fgb.2016.04.005

• Journal Article Type: Article
• Acceptance Date: Apr 29, 2016
• Online Publication Date: May 2, 2017
• Publication Date: May 1, 2017
• Deposit Date: May 30, 2017
• Publicly Available Date: May 30, 2017
• Journal: Fungal Genetics and Biology
• Print ISSN: 1087-1845
• Electronic ISSN: 1096-0937
• Publisher: Elsevier
• Peer Reviewed: Peer Reviewed
• Volume: 102
• DOI: https://doi.org/10.1016/j.fgb.2016.04.005
• Keywords: Aspergillus niger; Trichoderma reesei; Penicillium chrysogenum; Lignocellulose; Mixed cultures; Dual RNA-seq; Competition
• Public URL: https://nottingham-repository.worktribe.com/output/969106
• Publisher URL: http://www.sciencedirect.com/science/article/pii/S1087184516300457
• Contract Date: May 30, 2017