Metasecretome analysis of a lignocellulolytic microbial consortium grown on wheat straw, xylan and xylose

Abstract

BackgroundSynergistic action of different enzymes is required to complete the degradation of plant biomass in order to release sugars which are useful for biorefining. However, the use of single strains is often not efficient, as crucial parts of the required enzymatic machinery can be absent. The use of microbial consortia bred on plant biomass is a way to overcome this hurdle. In these, secreted proteins constitute sources of relevant enzyme cocktails. Extensive analyses of the proteins secreted by effective microbial consortia will contribute to a better understanding of the mechanism of lignocellulose degradation.ResultsHere, we report an analysis of the proteins secreted by a microbial consortium (metasecretome) that was grown on either wheat straw (RWS), xylose or xylan as the carbon sources. Liquid chromatography–tandem mass spectrometry was used to analyze the proteins in the supernatants. Totals of 768 (RWS), 477 (xylose) and 103 (xylan) proteins were identified and taxonomically and functionally classified. In RWS, the proteins were mostly affiliated with Sphingobacterium-like consortium members (~50 %). Specific abundant protein clusters were predicted to be involved in polysaccharide transport and/or sensing (TonB-dependent receptors). In addition, proteins predicted to degrade plant biomass, i.e. endo-1,4-beta-xylanases, alpha-l-arabinofuranosidases and alpha-l-fucosidases, were prominent. In the xylose-driven consortium, most secreted proteins were affiliated with those from Enterobacteriales (mostly Klebsiella species), whereas in the xylan-driven one, they were related to Flavobacterium-like ones. Notably, the metasecretomes of the consortia growing on xylose and xylan contained proteins involved in diverse metabolic functions (e.g. membrane proteins, isomerases, dehydrogenases and oxidoreductases).ConclusionsAn analysis of the metasecretomes of microbial consortia originating from the same source consortium and subsequently bred on three different carbon sources indicated that the major active microorganisms in the three final consortia differed. Importantly, diverse glycosyl hydrolases, predicted to be involved in (hemi)cellulose degradation (e.g. of CAZy families GH3, GH10, GH43, GH51, GH67 and GH95), were identified in the RWS metasecretome. Based on these results, we catalogued the RWS consortium as a true microbial enzyme factory that constitute an excellent source for the production of an efficient enzyme cocktail for the pretreatment of plant biomass.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0387-8) contains supplementary material, which is available to authorized users.

Metagenomic and metaproteomic analyses of a corn stover-adapted microbial consortium EMSD5 reveal its taxonomic and enzymatic basis for degrading lignocellulose

“…In contrast, the extracellular degradation of simple polysaccharide xylan requires much fewer glycoside hydrolases, and xylose completely represses their expression. The differential response to the composition of biomass substrates has also been observed in recent metaproteomic analysis of a wheat straw-adapted consortium [19], but some substantial differences between the two consortia still stood out. The majority of secreted GHs in the presence of wheat straw were involved in the degradation of hemicellulose (GH10, GH43, GH51 and GH95) and α-glucan polysaccharides (GH13), while cellulolytic enzymes mainly comprised GH3 β-glucosidases.…”

“…While metagenome studies inform about the genetic backgrounds of plant biomass degradation by microbial consortia, extracellular metaproteomics provides a more focused picture of the lignocellulolytic apparatus secreted by a microbial consortium under defined conditions. Comparisons of the taxonomic structures and secreted proteins of microbial consortia responsive to substrates with distinct complexity could help to understand their unique enzyme systems [19]. Additionally, such comparative analyses offer the opportunity to explore lignocellulose-depolymerizing mechanisms of microbial consortia and to evaluate their potential applications in industrial biomass conversion.…”

“…Although previous metaproteome studies have revealed much about lignocellulose degradation in microbial consortia, they are limited to the analyses of proteins at a single time point [19, 20]. We hypothesize that in the process of plant biomass deconstruction, variations occur in the microbial consortia with respect to the taxonomic composition, degradative enzyme activities and protein expression levels.…”

Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches

“…2b), similar to previous results (Jiménez et al 2014b), these data suggest that polysaccharides present in wheat straw selected for Bacteroidetes instead of Proteobacteria . Bacteroidetes like Sphingobacterium species can secrete enzymes such as endo-β-1,4-xylanases, α-L-arabinofuranosidases, β-glucosidases, α-glucuronidases and α-L-fucosidases when grown in the presence of wheat straw (Jiménez et al 2015b). Interestingly, organisms belonging to the Enterobacteriales (e.g.…”

Temporal Expression Dynamics of Plant Biomass-Degrading Enzymes by a Synthetic Bacterial Consortium Growing on Sugarcane Bagasse

“…Recently, constructed PB-degrading microbial consortia have proven to be a excellent sources of (hemi)cellulolytic enzyme cocktails ( Park et al, 2012 ; Jiménez et al, 2015b ). A common strategy to obtain these types of consortia is by the dilution-to-stimulation method ( Lee et al, 2013 ).…”