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

Heiss-Blanquet, Senta; Fayolle-Guichard, Françoise; Lombard, Vincent; Hébert, Agnès; Coutinho, Pedro M.; Groppi, Alexis; Barre, Annick; Henrissat, Bernard

doi:10.1371/journal.pone.0167216

Cited by 11 publications

(10 citation statements)

References 37 publications

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“…Experimental design that uses liquid culturing of compost inoculum could have an effect on fungal growth and hence ligninolytic enzymes expression [ 41 ]. Recent studies showed that the composting conditions without liquid phase were preferable for CAZymes enrichment [ 42 ]. Other factors such as medium composition [ 43 ], temperature, agitation, and inoculum source could also play critical role for suppressing fungal growth.…”

Section: Discussionmentioning

confidence: 99%

Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity

Mello

Alessi

Riaño‐Pachón

et al. 2017

Biotechnol Biofuels

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BackgroundUsing globally abundant crop residues as a carbon source for energy generation and renewable chemicals production stand out as a promising solution to reduce current dependency on fossil fuels. In nature, such as in compost habitats, microbial communities efficiently degrade the available plant biomass using a diverse set of synergistic enzymes. However, deconstruction of lignocellulose remains a challenge for industry due to recalcitrant nature of the substrate and the inefficiency of the enzyme systems available, making the economic production of lignocellulosic biofuels difficult. Metatranscriptomic studies of microbial communities can unveil the metabolic functions employed by lignocellulolytic consortia and identify novel biocatalysts that could improve industrial lignocellulose conversion.ResultsIn this study, a microbial community from compost was grown in minimal medium with sugarcane bagasse sugarcane bagasse as the sole carbon source. Solid-state nuclear magnetic resonance was used to monitor lignocellulose degradation; analysis of metatranscriptomic data led to the selection and functional characterization of several target genes, revealing the first glycoside hydrolase from Carbohydrate Active Enzyme family 11 with exo-1,4-β-xylanase activity. The xylanase crystal structure was resolved at 1.76 Å revealing the structural basis of exo-xylanase activity. Supplementation of a commercial cellulolytic enzyme cocktail with the xylanase showed improvement in Avicel hydrolysis in the presence of inhibitory xylooligomers.ConclusionsThis study demonstrated that composting microbiomes continue to be an excellent source of biotechnologically important enzymes by unveiling the diversity of enzymes involved in in situ lignocellulose degradation.Electronic supplementary materialThe online version of this article (10.1186/s13068-017-0944-4) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity

Mello

Alessi

Riaño‐Pachón

et al. 2017

Biotechnol Biofuels

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“…To characterize the taxonomic structure of the samples, the sequences were then organized into Operational Taxonomic Units (OTUs) at 97% identity using the 'otu' command which implements de novo greedy clustering. OTUs were then classified using the Ribosomal Database Project II classifier (version 11.5) for 16S sequences [28] and the UNITE database (version 7.2) for ITS sequences [29]. Finally, Micca was used to summarize and rarefy the data to compare the taxonomic composition of each sample.…”

Section: Metabarcoding Sequencing Analysismentioning

confidence: 99%

“…Culturing [17][18][19][20][21], metabarcoding, and metagenomics [13,14,[22][23][24][25][26][27] on bagasse pile samples or associated soil has revealed a unique microbial community compared to other lignocellulosic environments and the presence of novel biomass-degrading microbes and enzymes. In addition, composting-like conditions are more efficient than submerged fermentation for enriching organisms with cellulases [28] and presumably other carbohydrate hydrolases. Mello et al, also found that a microbial consortium grown under nutrient limiting conditions on sugarcane bagasse, became more diverse and enriched in lignocellulosedegrading enzymes than the same consortium grown on rich media [29].…”

Section: Introductionmentioning

confidence: 99%

A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile

et al. 2020

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Background: Sugarcane bagasse is a major source of lignocellulosic biomass, yet its economic potential is not fully realised. To add value to bagasse, processing is needed to gain access to the embodied recalcitrant biomaterials. When bagasse is stored in piles in the open for long periods it is colonised by microbes originating from the sugarcane, the soil nearby or spores in the environment. For these microorganisms to proliferate they must digest the bagasse to access carbon for growth. The microbial community in bagasse piles is thus a potential resource for the discovery of useful and novel microbes and industrial enzymes. We used culturing and metabarcoding to understand the diversity of microorganisms found in a uniquely undisturbed bagasse storage pile and screened the cultured organisms for fibre-degrading enzymes. Results: Samples collected from 60 to 80 cm deep in the bagasse pile showed hemicellulose and partial lignin degradation. One hundred and four microbes were cultured from different layers and included a high proportion of oleaginous yeast and biomass-degrading fungi. Overall, 70, 67, 70 and 57% of the microbes showed carboxy-methyl cellulase, xylanase, laccase and peroxidase activity, respectively. These percentages were higher in microbes selectively cultured from deep layers, with all four activities found for 44% of these organisms. Culturing and amplicon sequencing showed that there was less diversity and therefore more selection in the deeper layers, which were dominated by thermophiles and acid tolerant organisms, compared with the top of pile. Amplicon sequencing indicated that novel fungi were present in the pile. Conclusions: A combination of culture-dependent and independent methods was successful in exploring the diversity in the bagasse pile. The variety of species that was found and that are known for biomass degradation shows that the bagasse pile was a valuable selective environment for the identification of new microbes and enzymes with biotechnological potential. In particular, lignin-modifying activities have not been reported previously for many of the species that were identified, suggesting future studies are warranted.

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“…In a few cases, direct comparison of CAZyme profiles has also been performed for enrichment cultures originating from the same source. Examples include soil-derived microbial communities enriched with wheat straw, switchgrass, and corn stover ( Jimenéz et al, 2016 ), and those digesting mixed lignocellulosic substrates in stationary versus submerged and agitated conditions ( Heiss-Blanquet et al, 2016 ; Wang et al, 2016 ). In addition to the influence of enrichment condition, such metagenomic studies highlight the increase in number of CAZyme sequences from families associated with hydrolysis of oligosaccharides and side groups of hemicelluloses and/or pectins (e.g., GH3, GH43).…”

Section: Introductionmentioning

confidence: 99%

Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment

Wong¹,

Wang²,

Couturier³

et al. 2017

Front. Microbiol.

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To identify carbohydrate-active enzymes (CAZymes) that might be particularly relevant for wood fiber processing, we performed a comparative metagenomic analysis of digestive systems from Canadian beaver (Castor canadensis) and North American moose (Alces americanus) following 3 years of enrichment on either microcrystalline cellulose or poplar hydrolysate. In total, 9,386 genes encoding CAZymes and carbohydrate-binding modules (CBMs) were identified, with up to half predicted to originate from Firmicutes, Bacteroidetes, Chloroflexi, and Proteobacteria phyla, and up to 17% from unknown phyla. Both PCA and hierarchical cluster analysis distinguished the annotated glycoside hydrolase (GH) distributions identified herein, from those previously reported for grass-feeding mammals and herbivorous foragers. The CAZyme profile of moose rumen enrichments also differed from a recently reported moose rumen metagenome, most notably by the absence of GH13-appended dockerins. Consistent with substrate-driven convergence, CAZyme profiles from both poplar hydrolysate-fed cultures differed from cellulose-fed cultures, most notably by increased numbers of unique sequences belonging to families GH3, GH5, GH43, GH53, and CE1. Moreover, pairwise comparisons of moose rumen enrichments further revealed higher counts of GH127 and CE15 families in cultures fed with poplar hydrolysate. To expand our scope to lesser known carbohydrate-active proteins, we identified and compared multi-domain proteins comprising both a CBM and domain of unknown function (DUF) as well as proteins with unknown function within the 416 predicted polysaccharide utilization loci (PULs). Interestingly, DUF362, identified in iron–sulfur proteins, was consistently appended to CBM9; on the other hand, proteins with unknown function from PULs shared little identity unless from identical PULs. Overall, this study sheds new light on the lignocellulose degrading capabilities of microbes originating from digestive systems of mammals known for fiber-rich diets, and highlights the value of enrichment to select new CAZymes from metagenome sequences for future biochemical characterization.

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

Cited by 11 publications

References 37 publications

Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity

Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity

A snapshot of microbial diversity and function in an undisturbed sugarcane bagasse pile

Comparative Metagenomics of Cellulose- and Poplar Hydrolysate-Degrading Microcosms from Gut Microflora of the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus) after Long-Term Enrichment

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