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

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 cult...

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Main Authors:	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.
Format:	Article
Language:	English
Published:	Elsevier 2017
Online Access:	http://eprints.nottingham.ac.uk/43272/ http://eprints.nottingham.ac.uk/43272/ http://eprints.nottingham.ac.uk/43272/ http://eprints.nottingham.ac.uk/43272/1/Dalyetal2017.pdf

id	nottingham-43272
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spelling	nottingham-432722017-10-13T00:16:22Z http://eprints.nottingham.ac.uk/43272/ 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. 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. Elsevier 2017-05 Article PeerReviewed application/pdf en cc_by http://eprints.nottingham.ac.uk/43272/1/Dalyetal2017.pdf Daly, Paul and van Munster, Jolanda M. and Kokolski, Matthew and Sang, Fei and Blythe, Martin J. and Malla, Sunir and Velasco de Castro Oliveira, Juliana and Goldman, Gustavo H. and Archer, David 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 . pp. 4-21. ISSN 1096-0937 http://www.sciencedirect.com/science/article/pii/S1087184516300457 doi:10.1016/j.fgb.2016.04.005 doi:10.1016/j.fgb.2016.04.005
repository_type	Digital Repository
institution_category	Local University
institution	University of Nottingham Malaysia Campus
building	Nottingham Research Data Repository
collection	Online Access
language	English
description	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.
format	Article
author	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.
spellingShingle	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. 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
author_facet	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.
author_sort	Daly, Paul
title	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
title_short	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
title_full	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
title_fullStr	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
title_full_unstemmed	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
title_sort	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
publisher	Elsevier
publishDate	2017
url	http://eprints.nottingham.ac.uk/43272/ http://eprints.nottingham.ac.uk/43272/ http://eprints.nottingham.ac.uk/43272/ http://eprints.nottingham.ac.uk/43272/1/Dalyetal2017.pdf
first_indexed	2018-09-06T13:25:08Z
last_indexed	2018-09-06T13:25:08Z
_version_	1610864717955334144

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

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