title: Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches.
abstract: The selection of microbes by enrichment on plant biomass has been proposed as an efficient way to develop new strategies for lignocellulose saccharification. Here, we report an in-depth analysis of soil-derived microbial consortia that were trained to degrade once-used wheat straw (WS1-M), switchgrass (SG-M) and corn stover (CS-M) under aerobic and mesophilic conditions. Molecular fingerprintings, bacterial 16S ribosomal RNA (rRNA) gene amplicon sequencing and metagenomic analyses showed that the three microbial consortia were taxonomically distinct. Based on the taxonomic affiliation of protein-encoding sequences, members of the Bacteroidetes (e.g. Chryseobacterium, Weeksella, Flavobacterium and Sphingobacterium) were preferentially selected on WS1-M, whereas SG-M and CS-M favoured members of the Proteobacteria (e.g. Caulobacter, Brevundimonas, Stenotrophomonas and Xanthomonas). The highest degradation rates of lignin (~59 %) were observed with SG-M, whereas CS-M showed a high consumption of cellulose and hemicellulose. Analyses of the carbohydrate-active enzymes in the three microbial consortia showed the dominance of glycosyl hydrolases (e.g. of families GH3, GH43, GH13, GH10, GH29, GH28, GH16, GH4 and GH92). In addition, proteins of families AA6, AA10 and AA2 were detected. Analysis of secreted protein fractions (metasecretome) for each selected microbial consortium mainly showed the presence of enzymes able to degrade arabinan, arabinoxylan, xylan, β-glucan, galactomannan and rhamnogalacturonan. Notably, these metasecretomes contain enzymes that enable us to produce oligosaccharides directly from wheat straw, sugarcane bagasse and willow. Thus, the underlying microbial consortia constitute valuable resources for the production of enzyme cocktails for the efficient saccharification of plant biomass.
authors.affiliation: Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands. d.j.jimenez.avella@rug.nl.
authors.forename: Diego Javier
authors.initials: DJ
authors.lastname: Jiménez
authors.affiliation: Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Maria Julia
authors.initials: MJ
authors.lastname: de Lima Brossi
authors.affiliation: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Copenhagen, Denmark.
authors.forename: Julia
authors.initials: J
authors.lastname: Schückel
authors.affiliation: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Copenhagen, Denmark.
authors.forename: Stjepan Krešimir
authors.initials: SK
authors.lastname: Kračun
authors.affiliation: Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C 1871, Copenhagen, Denmark.
authors.forename: William George Tycho
authors.initials: WG
authors.lastname: Willats
authors.affiliation: Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Jan Dirk
authors.initials: JD
authors.lastname: van Elsas
mesh_terms: D000332:Aerobiosis; D001419:Bacteria / Q000145:classification* / Q000201:enzymology / Q000235:genetics; D001711:Biotransformation; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D004798:Enzymes / Q000378:metabolism; D008031:Lignin / Q000378:metabolism*; D056186:Metagenomics; D059013:Microbial Consortia; D008897:Panicum / Q000737:chemistry; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D014908:Triticum / Q000737:chemistry; D003313:Zea mays / Q000737:chemistry
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D004798:Enzymes; D012336:RNA, Ribosomal, 16S; C036909:lignocellulose; D008031:Lignin
keywords: Enzyme cocktails; Metagenomics; Metasecretome; Microbial consortia; Plant biomass