Abstract
BackgroundDegradation of pectin in lignocellulosic materials is one of the key steps for biofuel production. Biological hydrolysis of pectin, i.e., degradation by pectinolytic microbes and enzymes, is an attractive paradigm because of its obvious advantages, such as environmentally friendly procedures, low in energy demand for lignin removal, and the possibility to be integrated in consolidated process. In this study, a metagenomics sequence-guided strategy coupled with enrichment culture technique was used to facilitate targeted discovery of pectinolytic microbes and enzymes. An apple pomace-adapted compost (APAC) habitat was constructed to boost the enrichment of pectinolytic microorganisms.ResultsAnalyses of 16S rDNA high-throughput sequencing revealed that microbial communities changed dramatically during composting with some bacterial populations being greatly enriched. Metagenomics data showed that apple pomace-adapted compost microbial community (APACMC) was dominated by Proteobacteria and Bacteroidetes. Functional analysis and carbohydrate-active enzyme profiles confirmed that APACMC had been successfully enriched for the targeted functions. Among the 1756 putative genes encoding pectinolytic enzymes, 129 were predicted as novel (with an identity <30% to any CAZy database entry) and only 1.92% were more than 75% identical with proteins in NCBI environmental database, demonstrating that they have not been observed in previous metagenome projects. Phylogenetic analysis showed that APACMC harbored a broad range of pectinolytic bacteria and many of them were previously unrecognized.ConclusionsThe immensely diverse pectinolytic microbes and enzymes found in our study will expand the arsenal of proficient degraders and enzymes for lignocellulosic biofuel production. Our study provides a powerful approach for targeted mining microbes and enzymes in numerous industries.
Highlights
Degradation of pectin in lignocellulosic materials is one of the key steps for biofuel production
Pectin embeds in the cellulose–hemicellulose network of the cell wall and regulates intercellular adhesion like glues [16]. It is the complex matrix of pectin that masks cellulose and/or hemicellulose through hydrogen bonding interactions [53], and blocks their accessibility to degradative enzymes [8], resulting in plant biomass that is less susceptible to degradation and more recalcitrant to deconstruction [23]
The results showed that apple pomace-adapted compost microbial community (APACMC) harbored a total of 9274 different carbohydrate-active enzymes (CAZymes) genes, which distributed heterogeneously among glycoside hydrolases (GHs, 35.6%), glycosyltransferases (GTs, 26.9%), carbohydrate esterases (CEs, 17.5%), carbohydrate-binding modules (CBMs, 13.3%), auxiliary activities (AAs, 4.6%), and polysaccharide lyases (PLs, 2.1%) (Additional file 6: Table S4)
Summary
Degradation of pectin in lignocellulosic materials is one of the key steps for biofuel production. Lignocellulosic biofuel, which derived from the most abundant renewable organic material on Pectin is one of the plant cell wall components. Pectin embeds in the cellulose–hemicellulose network of the cell wall and regulates intercellular adhesion like glues [16]. It is the complex matrix of pectin that masks cellulose and/or hemicellulose through hydrogen bonding interactions [53], and blocks their accessibility to degradative enzymes [8], resulting in plant biomass that is less susceptible to degradation and more recalcitrant to deconstruction [23]. The reduction of bulk percentage of pectin through genetic manipulation or enzymatic means has been proved to reduce the recalcitrance and accelerate the lignocellulose saccharification of herbaceous plants [23], Arabidopsis [12], switchgrass [8], and woody biomass [3, 4]
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