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.
Highlights
Lignocellulose is an abundant raw material that has the potential to be a cost-effective source of liquid biofuels
Using a dual RNA-seq approach, we describe the first study of the transcriptional responses of wildtype strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw
We explored the interactions of wild-type strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw using a range of approaches including dual RNA-seq
Summary
Lignocellulose is an abundant raw material that has the potential to be a cost-effective source of liquid biofuels. A key limitation of the process is the saccharification stage which requires costly enzymes (Klein-Marcuschamer et al, 2012). The enzymes required are lignocellulose degrading carbohydrate active enzymes (CAZymes) which include cellulases, hemicellulases and accessory activities (van den Brink and de Vries, 2011). Part of the rationale for using mixed cultures to degrade lignocellulose is that different fungal species can be found in the same lignocellulose-containing ecological niche such as a hollow tree stump (Tian et al, 2010) or leaves (Das et al, 2007). The inter-species fungal interaction are most likely to be based on antagonism and competition (Boddy, 2000) cooperative interactions are possible that could benefit the saccharification of lignocellulose. We explored the interactions of wild-type strains of Aspergillus niger, Trichoderma reesei and Penicillium chrysogenum in two and three mixed species shake-flask cultures with wheat straw using a range of approaches including dual RNA-seq
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