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


RESULTS
The taxonomic affiliation of the metagenomic data showed that EMSD5 was primarily composed of members from the phylaProteobacteria,FirmicutesandBacteroidetes. The carbohydrate-active enzyme (CAZyme) annotation revealed that representatives ofFirmicutesencoded a broad array of enzymes responsible for hemicellulose and cellulose deconstruction. Extracellular metaproteome analysis further pinpointed the specific role and synergistic interaction ofFirmicutespopulations 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 fromFirmicutesduring 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 fromTrichoderma reesei.


CONCLUSIONS
These 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 ofFirmicutesmembers 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.
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China.
Ning
N
Zhu
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China.
Jinshui
J
Yang
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China.
Lei
L
Ji
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China.
Jiawen
J
Liu
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China.
Yi
Y
Yang
State Key Laboratory of Agrobiotechnology, College of Biological Sciences, Beijing, China ; National Energy R & D Center for Non-food Biomass, China Agricultural University, Beijing, 100193 China.
Hongli
H
Yuan
Corn stover; Firmicutes; Hemicellulase; Metagenomics; Metaproteomics; Microbial consortium; Plant biomass; Synergism