Skip to main content

Research Repository

Advanced Search

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.

Authors

Paul Daly

Jolanda M. van Munster

Matthew Kokolski

FEI SANG Fei.Sang@nottingham.ac.uk
Research Fellow

Martin J. Blythe

Sunir Malla

Juliana Velasco de Castro Oliveira

Gustavo H. Goldman

David B. Archer



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., …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 http://eprints.nottingham.ac.uk/id/eprint/43272
Publisher URL http://www.sciencedirect.com/science/article/pii/S1087184516300457
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0

Files

Dalyetal2017.pdf (2.6 Mb)
PDF

Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0





You might also like



Downloadable Citations