Genome-centric metagenomics revealed the spatial distribution and the diverse metabolic functions of lignocellulose degrading uncultured bacteria

Abstract

The mechanisms by which specific anaerobic microorganisms remain firmly attached to lignocellulosic material allowing them to efficiently decompose the organic matter are far to be elucidated. To circumvent this issue, the microbiomes collected from anaerobic digesters treating pig manure and meadow grass were fractionated to separate the planktonic microbes from those adhered to lignocellulosic substrate. Assembly of shotgun reads followed by binning process recovered 151 population genomes, 80 out of which were completely new and were not previously deposited in any database. Genome coverage allowed the identification of microbial spatial distribution into the engineered ecosystem. Moreover, a composite bioinformatic analysis using multiple databases for functional annotation revealed that uncultured members of Bacteroidetes and Firmicutes follow diverse metabolic strategies for polysaccharide degradation. The structure of cellulosome in Firmicutes can vary depending on the number and functional roles of carbohydrate-binding modules. On contrary, members of Bacteroidetes are able to adhere and degrade lignocellulose due to the presence of multiple carbohydrate-binding family 6 modules in beta-xylosidase and endoglucanase proteins or S-layer homology modules in unknown proteins. This study combines the concept of variability in spatial distribution with genome-centric metagenomics allowing a functional and taxonomical exploration of the biogas microbiome.\n\nImportanceThis work contributes new knowledge about lignocellulose degradation in engineered ecosystems. Specifically, the combination of the spatial distribution of uncultured microbes with genome-centric metagenomics provides novel insights into the metabolic properties of planktonic and firmly attached to plant biomass bacteria. Moreover, the knowledge obtained in this study enabled us to understand the diverse metabolic strategies for polysaccharide degradation in different species of Bacteroidetes and Clostridiales. Even though structural elements of cellulosome were restricted to Clostridiales, our study identified in Bacteroidetes a putative mechanism for biomass decomposition based on a gene cluster responsible for cellulose degradation, disaccharide cleavage to glucose and transport to cytoplasm.