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

Abstract

BackgroundMicrobial consortia represent promising candidates for aiding in the development of plant biomass conversion strategies for biofuel production. However, the interaction between different community members and the dynamics of enzyme complements during the lignocellulose deconstruction process remain poorly understood. We present here a comprehensive study on the community structure and enzyme systems of a lignocellulolytic microbial consortium EMSD5 during growth on corn stover, using metagenome sequencing in combination with quantitative metaproteomics.ResultsThe taxonomic affiliation of the metagenomic data showed that EMSD5 was primarily composed of members from the phyla Proteobacteria, Firmicutes and Bacteroidetes. The carbohydrate-active enzyme (CAZyme) annotation revealed that representatives of Firmicutes encoded a broad array of enzymes responsible for hemicellulose and cellulose deconstruction. Extracellular metaproteome analysis further pinpointed the specific role and synergistic interaction of Firmicutes populations in plant polysaccharide breakdown. In particular, a wide range of xylan degradation-related enzymes, including xylanases, β-xylosidases, α-l-arabinofuranosidases, α-glucuronidases and acetyl xylan esterases, were secreted by diverse members from Firmicutes during growth on corn stover. Using label-free quantitative proteomics, we identified the differential secretion pattern of a core subset of enzymes, including xylanases and cellulases with multiple carbohydrate-binding modules (CBMs). In addition, analysis of the coordinate expression patterns indicated that transport proteins and hypothetical proteins may play a role in bacteria processing lignocellulose. Moreover, enzyme preparation from EMSD5 demonstrated synergistic activities in the hydrolysis of pretreated corn stover by commercial cellulases from Trichoderma reesei.ConclusionsThese results demonstrate that the corn stover-adapted microbial consortium EMSD5 harbors a variety of lignocellulolytic anaerobic bacteria and degradative enzymes, especially those implicated in hemicellulose decomposition. The data in this study highlight the pivotal role and cooperative relationship of Firmicutes members in the biodegradation of plant lignocellulose by EMSD5. The differential expression patterns of enzymes reveal the strategy of sequential lignocellulose deconstruction by EMSD5. Our findings provide insights into the mechanism by which consortium members orchestrate their array of enzymes to degrade complex lignocellulosic biomass.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0658-z) contains supplementary material, which is available to authorized users.

Continuous‐cropping tobacco caused variance of chemical properties and structure of bacterial network in soils

“…However, MMs belonging to Acidobacteria , Firmicutes , and Proteobacteria were enriched in the NCC network (Figure b). Species of Firmicutes can degrade hemicellulose and cellulose by producing various enzymes (xylanases, β‐xylosidases, α‐glucuronidases, and acetyl xylan esterases; Zhu et al, ) and inhibit plant pathogens by producing antibiotics (surfactin, iturin, fengycin, etc. ; Qi et al, ).…”

Bringing plant cell wall‐degrading enzymes into the lignocellulosic biorefinery concept

“…Members of the bacterial phyla Proteobacteria , Firmicutes , and Bacteroidetes were found to be prevalent, and each was associated with a metabolic niche within the consortium. Due to greater assignment of (hemi)cellulolytic GHs to members of Firmicutes and Bacteroidetes , it was concluded that such bacteria act mainly on corn stover holocellulose, while Proteobacteria genes were primarily associated with lignin degradation . Similarly, an anaerobic biogas fermenter fed with agricultural wastes was also shown to be populated by Firmicutes and Bacteroidetes , with the former predominating .…”

Low-Cost Cellulase-Hemicellulase Mixture Secreted by Trichoderma harzianum EM0925 with Complete Saccharification Efficacy of Lignocellulose

“…Yang et al [45] reported a degree of synergy of 1.35 for the hydrolysis of delignified corn stover when studying the synergistic effect between a commercial enzyme preparation and a bifunctional enzyme consisting of an acetyl xylan esterase and a α-l-arabinofuranosidase. For glucan conversion of delignified corn stover, Zhu et al [46] found a synergy of 1.96 between a hemicellulase preparation EMSD5 (including xylanases, β-xylosidases, α-l-arabinofuranosidases, α-glucuronidases, and acetyl xylan esterases) and the commercial cellulase from T. reesei. These findings revealed the significant role of glycosidases for efficient lignocellulose degradation.…”

“…These findings revealed the significant role of glycosidases for efficient lignocellulose degradation. Moreover, 9 carbohydrate binding modules (CBMs) were also observed, which could help hydrolyze substrate more effectively [46]. In T. harzianum EM0925 enzyme enzyme cocktail, a LPMO with abundance of 3.23% was found.…”

“…The glucose and xylose concentrations in the filter liquor were determined by HPLC. Acid-insoluble lignin was determined by subtracting the ash content from the solid residue dried at 60 • C. The ash content was determined by heating the solid residue at 575 • C for 12 h. The weight percentages of cellulose, xylan, arabinan, and lignin were calculated according to the method described previously [46].…”