Cultivating oyster mushrooms (Pleurotus ostreatus), a typical primary decomposer of lignocellulose, on a short composting substrate is a novel procedure which possesses energy conserves, reduced the chance of infection by competitive species, shorter production duration and achieved high production efficiency. However, the microbiome and microbial metabolic functions in the composting substrate during the mushroom cropping is unknown. In the present study, the contents of hemicellulose, cellulose and lignin and the activities of protease, laccase and cellulase were evaluated in the corncob short composting substrate from before oyster mushroom spawning to first flush fructification; meanwhile the changes in the microbiome and microbial metabolic functions were surveyed by using metagenomic sequencing. Results showed that the hemicellulose, cellulose and lignin in the short composting substrate were decomposed of 42.76, 34.01, and 30.18%, respectively, during the oyster mushroom cropping process. In addition, the contents of hemicellulose, cellulose and lignin in the composting substrate were reduced rapidly and negatively correlated with the abundance of the Actinobacteria phylum. The activities of protease, laccase and cellulase fastly increased in the period of before oyster mushroom spawning to full colonization and were positively correlated to the abundance of Actinobacteria phylum. The total abundance of bacteria domain gradually decreased by only approximately 15%, while the abundance of Actinobacteria phylum increased by 68% and was positively correlated with that of oyster mushroom. The abundance of oyster mushroom increased by 50 times from spawning to first flush fructification. The dominant genera, all in the order of Actinomycetales, were Cellulosimicrobium, Mycobacterium, Streptomyces and Saccharomonospora. The total abundance of genes with functions annotated in the Clusters of Orthologous Groups of proteins (COG) for Bacteria and Archaea and Kyoto Encyclopedia of Genes and Genomes (KEGG) database for all three life domains was positively correlated.The three metabolic pathways for carbohydrates, amino acids and energy were the primary enrichment pathways in KEGG pathway, accounting for more than 30% of all pathways, during the mushroom cropping in which the glycine metabolic pathway, carbon fixation pathways in prokaryotes and methane metabolism were all dominated by bacteria. The genes of cellulolytic enzymes, hemicellulolytic enzymes, laccase, chitinolytic enzymes, peptidoglycanlytic enzymes and ammonia assimilation enzymes with abundances from 0.28 to 0.24%, 0.05 to 0.02%, 0.02 to 0.01%, 0.14 to 0.08%, 0.39 to 0.16%, and 0.13 to 0.12% during the mushroom cropping identified in the Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (eggNOG) database for all three life domains were all aligned to COG database. These results indicated that bacteria, especially Actinomycetales, were the main metabolism participants in the short composting substrate during the oyster mushroom cropping. The relationship between oyster mushrooms and bacteria was cooperative, Actinomycetales were oyster mushroom growth promoting bacteria (OMGPB).

Oyster mushrooms (Pleurotus ostreatus) are one of the most commonly grown edible mushrooms using compost, which contains high concentrations of ammonia. In this study, inoculation of the oyster mushroom culture substrate with ammonia-assimilating bacterium Enterobacter sp. B12, either before or after composting, reduced the ammonia nitrogen content, increased the total nitrogen content of the compost, and enhanced the mushroom yield. Co-cultivation with P. ostreatus mycelia on potato dextrose agar (PDA) plates containing 200 mM NH₄⁺, B12 reduced reactive oxygen species (ROS) accumulation in the mycelia and downregulated the expression of the ROS-generating enzymes NADPH oxidase A (NOXA) and the stress hormone ethylene synthase 1-aminocyclopropane-1-carboxylate oxidase (ACO). It also downregulated the expression of the ammonia-assimilating related genes in the mycelia, such as glutamate dehydrogenase (GDH), glutamate synthase (GOGAT), glutamine synthetase (GS), ammonia transporter protein (AMT), and amino acid transporter protein (AAT), while upregulating its own ammonia-assimilation genes. These findings suggest that the mechanism by which B12 promoted oyster mushroom growth was that B12 assimilated ammonia, alleviated ammonia stress, mitigated ROS accumulation in the mycelia, and supplied ammonia and amino acids to the mycelia. To our knowledge, ammonia-assimilating bacteria are a novel type of mushroom growth promoter (MGP).