Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

Wei, Hui; Tucker, Melvin P.; Baker, John O.; Harris, Michelle N.; Luo, Yuhua; Xu, Qi; Himmel, Michael E.; Ding, Shi You

doi:10.1186/1754-6834-5-20

Cited by 39 publications

(27 citation statements)

References 48 publications

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“…Cellulolytic and ligninolytic microbiota were much less represented. Their counts were found several orders of magnitude below those of other functional groups (counts ranged 10 5 -10 6 cfu g À1 ) and they were mainly detected at final composting stages as it has been previously reported (Wei et al, 2012). In general, microbial evolution profiles were quite similar in both control and inoculated piles, however, significant differences for all microbial groups were found and counts were always higher in the inoculated piles, especially after the first inoculation had been performed (IMES).…”

Section: Evolution Of Functionality Of Microbial Communitiesmentioning

confidence: 53%

Enhanced turnover of organic matter fractions by microbial stimulation during lignocellulosic waste composting

Jurado

Suárez‐Estrella

López

et al. 2015

Bioresource Technology

170

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Section: Evolution Of Functionality Of Microbial Communitiesmentioning

confidence: 53%

Enhanced turnover of organic matter fractions by microbial stimulation during lignocellulosic waste composting

Jurado

Suárez‐Estrella

López

et al. 2015

Bioresource Technology

170

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“…It has been suggested that multiple CBMs may counteract the loss of binding affinity between thermophilic enzymes and their substrates at elevated temperatures [30]. During a typical composting process, compost microbiota experience a thermophilic phase (above 50 °C) for about one week and much longer mesophilic phases (20–50 °C) [6, 31]. It remains to be seen whPaenibacillusether compost-derived microbial consortia employ a similar strategy to enable strong binding to insoluble polysaccharide substrates.…”

Section: Resultsmentioning

confidence: 99%

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

Zhu¹,

Yang²,

Ji³

et al. 2016

Biotechnol Biofuels

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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.

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“…Although fungi are present throughout the composting process, recent studies suggest that thermophilic fungi are much less abundant than bacteria and that fungal biomass degradation activity is limited during the thermophilic phase [32,33]. The present study therefore focused on the prokaryotic population and the DNA extraction protocol used aimed at isolating prokaryotic DNA.…”

Section: Discussionmentioning

confidence: 99%

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures

et al. 2016

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Cost-effective biofuel production from lignocellulosic biomass depends on efficient degradation of the plant cell wall. One of the major obstacles for the development of a cost-efficient process is the lack of resistance of currently used fungal enzymes to harsh conditions such as high temperature. Adapted, thermophilic microbial communities provide a huge reservoir of potentially interesting lignocellulose-degrading enzymes for improvement of the cellulose hydrolysis step. In order to identify such enzymes, a leaf and wood chip compost was enriched on a mixture of thermo-chemically pretreated wheat straw, poplar and Miscanthus under thermophile conditions, but in two different set-ups. Unexpectedly, metagenome sequencing revealed that incubation of the lignocellulosic substrate with compost as inoculum in a suspension culture resulted in an impoverishment of putative cellulase- and hemicellulase-encoding genes. However, mimicking composting conditions without liquid phase yielded a high number and diversity of glycoside hydrolase genes and an enrichment of genes encoding cellulose binding domains. These identified genes were most closely related to species from Actinobacteria, which seem to constitute important players of lignocellulose degradation under the applied conditions. The study highlights that subtle changes in an enrichment set-up can have an important impact on composition and functions of the microcosm. Composting-like conditions were found to be the most successful method for enrichment in species with high biomass degrading capacity.

show abstract

Tracking dynamics of plant biomass composting by changes in substrate structure, microbial community, and enzyme activity

Cited by 39 publications

References 48 publications

Enhanced turnover of organic matter fractions by microbial stimulation during lignocellulosic waste composting

Enhanced turnover of organic matter fractions by microbial stimulation during lignocellulosic waste composting

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

Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures

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