Abstract
Based on the premise that plant biomass can be efficiently degraded by mixed microbial cultures and/or enzymes, we here applied a targeted metagenomics-based approach to explore the metabolic potential of two forest soil-derived lignocellulolytic microbial consortia, denoted RWS and TWS (bred on wheat straw). Using the metagenomes of three selected batches of two experimental systems, about 1.2 Gb of sequence was generated. Comparative analyses revealed an overrepresentation of predicted carbohydrate transporters (ABC, TonB and phosphotransferases), two-component sensing systems and β-glucosidases/galactosidases in the two consortia as compared to the forest soil inoculum. Additionally, “profiling” of carbohydrate-active enzymes showed significant enrichments of several genes encoding glycosyl hydrolases of families GH2, GH43, GH92 and GH95. Sequence analyses revealed these to be most strongly affiliated to genes present on the genomes of Sphingobacterium, Bacteroides, Flavobacterium and Pedobacter spp. Assembly of the RWS and TWS metagenomes generated 16,536 and 15,902 contigs of ≥10 Kb, respectively. Thirteen contigs, containing 39 glycosyl hydrolase genes, constitute novel (hemi)cellulose utilization loci with affiliation to sequences primarily found in the Bacteroidetes. Overall, this study provides deep insight in the plant polysaccharide degrading capabilities of microbial consortia bred from forest soil, highlighting their biotechnological potential.
Highlights
Abundances that are appropriate for efficient biodegradation are predicted to be obtained at each time point in the process
In the “Carbohydrate-Active Enzyme database” (CAZy), enzymes that hydrolyze diverse carbohydrates are classified into different glycosyl hydrolases (GH) families on the basis of their amino acid sequences[15]
Enrichments of the GH65 family, sugar transporters (ABC systems), oxidoreductases and [Fe-S] binding proteins were found in the Fe-amended consortia
Summary
Abundances that are appropriate for efficient biodegradation are predicted to be obtained at each time point in the process. A “matured” consortium presumably contains all of the microbial members that have been, or are, important for the biodegradative process Based on such assumptions, analyses of such matured consortia via metagenomics[10,11] offer exciting possibilities to foster our understanding of the biodegradative process. Enrichments of the GH65 family, sugar transporters (ABC systems), oxidoreductases and [Fe-S] binding proteins were found in the Fe-amended consortia Both studies did not address the levels of enrichment of such genes as compared to the microbial source nor did they analyze the genetic backgrounds of the identified GH-encoding genes. We obtained two microbial consortia from forest soil by sequential transfers on i) untreated and ii) heat-treated wheat straw Both consortia grew efficiently in each step and showed (hemi) cellulolytic enzymatic activities in the extracellular fractions[24,25]. They give insight into the metabolic potential present in the resulting microbial consortia, opening up possibilities for further ecological and biotechnological studies
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