Metagenomic insights into the development of microbial communities of straw and leaf composts

Abstract

AbstractThe objects of this study are microbial communities formed on two types of contrasting lignocellulosic biomass. To study them, a long-term experiment was set up and conducted on the decomposition of oat straw and leaf litter using soil as a microbial inoculum. Combined analyses of enzymatic activity and NGS data for 16S rRNA gene amplicon and full metagenome sequencing was applied to study taxonomic, CAZy (Carbohydrate-Active enzymes), and PULs (Polysaccharide Utilization Loci) composition of microbial communities at different stages of decomposition between substrates. using a combination of 16S rRNA gene amplicon and long-read nanopore sequencing. In straw degradation, the microbial community demonstrated higher amylase, protease, catalase, and cellulase activities, while peroxidase, invertase, and polyphenol oxidase were more active in leaf litter. Consistent with this, the metagenome analysis showed that the microbiome of straw compost was enriched in genes for metabolic pathways of simpler compounds. At the same time, there were more genes for aromatic compound degradation pathways in leaf litter compost. We identified 9 MAGs (Metagenome-assembled genomes) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of degradation. MAGs classified as Bacteroidota (Chitinophaga,Ohtaekwangia), and Actinomycetota (Streptomyces) were found in both substrates, while those from Bacillota (Pristimantibacillus) were specific for leaf litter. The most frequent PULs were specialized on xylans and pectins, but not cellulose, suggesting that PUL databases may be lacking PULs for complex substrates.ImportanceOur study explores the microbial communities from natural ecosystems, like soil and lignocellulosic waste, capable of decomposing lignocellulosic substrates. We used a comprehensive approach with chemical analyses of the substrates, amplicon and full-metagenome sequencing data. We have shown that such communities may be a source of identifying the highly effective decomposing species with novel PULs.