title: Closely related fungi employ diverse enzymatic strategies to degrade plant biomass.
abstract: BACKGROUND
  Plant biomass is the major substrate for the production of biofuels and biochemicals, as well as food, textiles and other products. It is also the major carbon source for many fungi and enzymes of these fungi are essential for the depolymerization of plant polysaccharides in industrial processes. This is a highly complex process that involves a large number of extracellular enzymes as well as non-hydrolytic proteins, whose production in fungi is controlled by a set of transcriptional regulators. Aspergillus species form one of the best studied fungal genera in this field, and several species are used for the production of commercial enzyme cocktails.
  
  
  RESULTS
  It is often assumed that related fungi use similar enzymatic approaches to degrade plant polysaccharides. In this study we have compared the genomic content and the enzymes produced by eight Aspergilli for the degradation of plant biomass. All tested Aspergilli have a similar genomic potential to degrade plant biomass, with the exception of A. clavatus that has a strongly reduced pectinolytic ability. Despite this similar genomic potential their approaches to degrade plant biomass differ markedly in the overall activities as well as the specific enzymes they employ. While many of the genes have orthologs in (nearly) all tested species, only very few of the corresponding enzymes are produced by all species during growth on wheat bran or sugar beet pulp. In addition, significant differences were observed between the enzyme sets produced on these feedstocks, largely correlating with their polysaccharide composition.
  
  
  CONCLUSIONS
  These data demonstrate that Aspergillus species and possibly also other related fungi employ significantly different approaches to degrade plant biomass. This makes sense from an ecological perspective where mixed populations of fungi together degrade plant biomass. The results of this study indicate that combining the approaches from different species could result in improved enzyme mixtures for industrial applications, in particular saccharification of plant biomass for biofuel production. Such an approach may result in a much better improvement of saccharification efficiency than adding specific enzymes to the mixture of a single fungus, which is currently the most common approach used in biotechnology.
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.|Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Benoit
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.|Megazyme International Ireland, IDA Business Park, Bray, Wicklow Ireland.
authors.forename: Helena
authors.initials: H
authors.lastname: Culleton
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: Miaomiao
authors.initials: M
authors.lastname: Zhou
authors.affiliation: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada.
authors.forename: Marcos
authors.initials: M
authors.lastname: DiFalco
authors.affiliation: Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.|Department of Food Science and Biotechnology, Faculty of Chemistry, National University of México, UNAM, Cd. Universitaria, C.P. 04510 Mexico, DF Mexico.
authors.forename: Guillermo
authors.initials: G
authors.lastname: Aguilar-Osorio
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.|Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Evy
authors.initials: E
authors.lastname: Battaglia
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.|Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Ourdia
authors.initials: O
authors.lastname: Bouzid
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: Carlo P J M
authors.initials: CPJM
authors.lastname: Brouwer
authors.affiliation: Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Hala B O
authors.initials: HBO
authors.lastname: El-Bushari
authors.affiliation: Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, 13288 Marseille, France.|CNRS, UMR7257, Aix-Marseille University, 13288 Marseille, France.
authors.forename: Pedro M
authors.initials: PM
authors.lastname: Coutinho
authors.affiliation: Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Birgit S
authors.initials: BS
authors.lastname: Gruben
authors.affiliation: Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland.
authors.forename: Kristiina S
authors.initials: KS
authors.lastname: Hildén
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: Jos
authors.initials: J
authors.lastname: Houbraken
authors.affiliation: Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland.
authors.forename: Luis Alexis Jiménez
authors.initials: LAJ
authors.lastname: Barboza
authors.affiliation: INRA, UMR1163 de Biotechnologie des Champignons Filamenteux, ESIL, Marseille, France.
authors.forename: Anthony
authors.initials: A
authors.lastname: Levasseur
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: Eline
authors.initials: E
authors.lastname: Majoor
authors.affiliation: Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Viikki Biocenter 1, University of Helsinki, Helsinki, Finland.
authors.forename: Miia R
authors.initials: MR
authors.lastname: Mäkelä
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: Hari-Mander
authors.initials: HM
authors.lastname: Narang
authors.affiliation: Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Blanca
authors.initials: B
authors.lastname: Trejo-Aguilar
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: Joost
authors.initials: J
authors.lastname: van den Brink
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: Patricia A
authors.initials: PA
authors.lastname: vanKuyk
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.
authors.forename: Ad
authors.initials: A
authors.lastname: Wiebenga
authors.affiliation: Megazyme International Ireland, IDA Business Park, Bray, Wicklow Ireland.
authors.forename: Vincent
authors.initials: V
authors.lastname: McKie
authors.affiliation: Megazyme International Ireland, IDA Business Park, Bray, Wicklow Ireland.
authors.forename: Barry
authors.initials: B
authors.lastname: McCleary
authors.affiliation: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada.
authors.forename: Adrian
authors.initials: A
authors.lastname: Tsang
authors.affiliation: Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, 13288 Marseille, France.|INRA, USC 1408 AFMB, 13288 Marseille, France.|Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre and Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.|Microbiology and Kluyver Centre for Genomics of Industrial Fermentation, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: Ronald P
authors.initials: RP
authors.lastname: de Vries
keywords: Aspergillus; Biofuel; Diversity; Enzyme production; Plant biomass degradation; Polysaccharides; Saccharification