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.
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.
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: Paul.Daly@nottingham.ac.uk.
authors.forename: Paul
authors.initials: P
authors.lastname: Daly
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: Jolanda.van_Munster@nottingham.ac.uk.
authors.forename: Jolanda M
authors.initials: JM
authors.lastname: van Munster
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: Matt.Kokolski@nottingham.ac.uk.
authors.forename: Matthew
authors.initials: M
authors.lastname: Kokolski
authors.affiliation: Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK. Electronic address: Fei.Sang@nottingham.ac.uk.
authors.forename: Fei
authors.initials: F
authors.lastname: Sang
authors.affiliation: Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK. Electronic address: Martin.Blythe@nottingham.ac.uk.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Blythe
authors.affiliation: Deep Seq, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK. Electronic address: Sunir.Malla@nottingham.ac.uk.
authors.forename: Sunir
authors.initials: S
authors.lastname: Malla
authors.affiliation: Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Rua Giuseppe Máximo Scolfaro 10000, Campinas, São Paulo 13083-100, Brazil. Electronic address: Juliana.Velasco@bioetanol.org.br.
authors.forename: Juliana
authors.initials: J
authors.lastname: Velasco de Castro Oliveira
authors.affiliation: Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Avenida do Café, Ribeirão Preto, São Paulo 14040-903, Brazil. Electronic address: GGoldman@usp.br.
authors.forename: Gustavo H
authors.initials: GH
authors.lastname: Goldman
authors.affiliation: School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. Electronic address: David.Archer@nottingham.ac.uk.
authors.forename: David B
authors.initials: DB
authors.lastname: Archer
mesh_terms: D000898:Antibiosis; D001203:Ascomycota / Q000201:enzymology* / Q000235:genetics*; D001234:Aspergillus niger / Q000201:enzymology / Q000235:genetics; D018533:Biomass; D050260:Carbohydrate Metabolism; D018920:Coculture Techniques; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D006867:Hydrolases / Q000235:genetics* / Q000378:metabolism; D008031:Lignin / Q000378:metabolism*; D010408:Penicillium chrysogenum / Q000187:drug effects / Q000201:enzymology / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D014242:Trichoderma / Q000201:enzymology / Q000235:genetics
chemical_list: D005656:Fungal Proteins; C036909:lignocellulose; D008031:Lignin; D006867:Hydrolases
keywords: Aspergillus niger; Competition; Dual RNA-seq; Lignocellulose; Mixed cultures; Penicillium chrysogenum; Trichoderma reesei