Multi-omic directed discovery of cellulosomes, polysaccharide utilization loci, and lignocellulases from an enriched rumen anaerobic consortium.
Tomazetto G, Pimentel AC, Wibberg D, Dixon N, Squina FM. Multi-omic directed discovery of cellulosomes, polysaccharide utilization loci, and lignocellulases from an enriched rumen anaerobic consortium. Applied and environmental microbiology. 2020.Lignocellulose is one of the most abundant renewable carbon sources, representing an alternative to petroleum for the production of fuel and chemicals. Nonetheless, the lignocellulose saccharification process, to release sugars for downstream applications, is one of the most crucial challenging economic factors. The synergism required among the various carbohydrate-active enzymes (CAZymes) for efficient lignocellulose breakdown is often not satisfactorily achieved with an enzyme mixture from a single strain. To overcome this challenge enrichment strategies can be applied to develop microbial communities with an efficient CAZymes arsenal, incorporating complementary and synergistic properties, to improve lignocellulose deconstruction. We report a comprehensive and deep analysis of an enriched rumen anaerobic consortium (ERAC) established on sugarcane bagasse (SB). The lignocellulolytic abilities of ERAC were confirmed by analyzing the depolymerization of bagasse by scanning electron microscopy, enzymatic assays, and mass spectrometry. Taxonomic analysis based on 16S sequencing elucidated the community enrichment process, which was marked by a higher abundance of Firmicutes and Synergistetes species. Shotgun metagenomic sequencing of ERAC disclosed 41 metagenome-assembled genomes (MAGs), harboring cellulosomes and polysaccharide utilization loci (PULs), along with a high diversity of CAZymes. The majority of the CAZymes predicted (60 % of the total) shared less than 90 % amino acid identity compared to sequences found in public databases. Additionally, a clostridial MAG identified in this study produces proteins during consortia development with scaffoldin domains and CAZymes appended to dockerin modules, thus representing a novel cellulosome-producing microorganism.IMPORTANCE The lignocellulolytic ERAC displays a unique set of plant polysaccharide degrading enzymes (with multimodular characteristics), cellulosomal complexes, and PULs. The MAGs described herein represent an expansion of the genetic content of rumen bacterial genomes dedicated to plant polysaccharides degradation, therefore providing a valuable resource for the development of biocatalytic toolbox strategies to be applied towards lignocellulose-based biorefineries. Copyright © 2020 American Society for Microbiology