Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics

Abstract

The mechanisms by which specific anaerobic microorganisms remain firmly attached to lignocellulosic material, allowing them to efficiently decompose organic matter, have yet to be elucidated. To circumvent this issue, 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 a 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 in the engineered ecosystem. Moreover, a composite bioinformatic analysis using multiple databases for functional annotation revealed that uncultured members of the and follow diverse metabolic strategies for polysaccharide degradation. The structure of cellulosome in species can differ depending on the number and functional roles of carbohydrate-binding modules. In contrast, members of the are able to adhere to 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. This 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 and Even though structural elements of cellulosome were restricted to species, our study identified a putative mechanism in species for biomass decomposition, which is based on a gene cluster responsible for cellulose degradation, disaccharide cleavage to glucose, and transport to cytoplasm.

New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

“…To improve the understanding of highly diverse and interconnected networks of AD microbiomes, several studies focused on the taxonomic and functional characterization of microbial communities originating from laboratory-scale biogas reactors [8][9][10][11][12][13][14][15][16][17] as well as from full-scale biogas plants [18][19][20][21][22][23] trying to connect microbiome compositions to prevailing process parameters [4,24]. Other studies focused on the identification of the functional roles of particular species isolated from AD systems [25][26][27].…”

Carbohydrate Hydrolytic Potential and Redundancy of an Anaerobic Digestion Microbiome Exposed to Acidosis, as Uncovered by Metagenomics

“…CAZymes are very important to the success of microbes in AD reactors fed with vegetal substrate as they are involved in the digestion of complex polysaccharides, which are particularly abundant in this environment (17). Here, we showed the usefulness of the complementary Hotpep analysis to the dbCAN-mediated CAZyme-coding gene discovery and classification.…”

“…CAZyme-coding genes can be expressed separately in bacterial genomes or they can form operons of coexpressed genes, e.g., cellulosomes in Firmicutes or polysaccharide-utilization loci (PULs) in Bacteroidetes . While cellulosomes have been given large scientific attention in the past (17, 18), PULs were much less investigated (17, 19). PULs are defined as gene clusters encoding cell envelope-associated enzymes that allow Bacteroidetes to bind to and degrade a specific polysaccharide and to import the released oligosaccharides inside the cell (20, 21).…”

CuBi-MeAn Customized Pipeline for Metagenomic Data Analysis

“…These shortcomings in gene centric approaches in metagenomic studies led to the development of the genome-centric concept which has revealed the functional properties of individual genomes, leading to a more detailed comprehension of the microbial interactions occurring in the microbiome (Kougias, Campanaro et al 2018). While, gene-centric approaches focus on to the function of individual genes and correlating it to the biochemical activities of the system, genome-centric approaches decipher the complexity of the genome by considering the genes functions and interplay within a genome.…”