JUAN Jiaxiang, XIAO Tingting, WANG Qian, SONG Xiaoxia, SHEN Xinfen, GAO Fei, CHEN Mingjie, HUANG Jianchun
In order to elucidate microbial populations in Agaricus bisporus culture substrate during the composting process and to predict their metabolic functions, substrates at 3 different composting stages were determined for their cellulose, hemicellulose and lignin contents, and analyzed for their microbial populations using primers specific to V3V4 of 16S rRNA to construct a gene library through PCR and the QIIME software to analyze the library. The sequences in the library were first removed for sequence redundancy and categorized into different operational taxonomic units (OTU). Then each sample were calculated for Chao1, ACE, Shannon, and Simpson index, and analyzed for microbial population at the phylum and the genus level, respectively. Using the software R, the number of OTU shared by different samples were calculated. The microbial composition at the genus level in each sample was presented as a column figure. Using the online Galaxy platform, relative abundance matrices at the genus level were subjected to LEfSe analysis, and both unweighted UniFrac matrices were subjected to nonmetric multidimensional scaling (NMDS) analysis. Using the software PICRUSt, the metabolic functions of the microbes in the samples were predicted by aligning the sequences of the samples to a microbial reference gene database with already known metabolic function. The results showed that both cellulose and hemicellulose decreased as the number of composting times increased, and lignin content was the highest in the phase II culture substrate. There were 419 OTUs shared by all 3 composting substrates. There were 420, 761 and 750 OTUs specific to the phase I, II and III composting substrate, respectively. Compared to the phase I composting substrate, the phase II and the phase III composting substrates had greater microbial diversity and abundance. At the phylum level, all 3 composting substrates contained a great abundance of DeinococcusThermus, Chloroflexi, Proteobacteria, Firmicutes and Acfinobacteria. The dominant genus in the phase I composting substrate was Thermus. Genus Pseudoxanthomonas and Thermobifida were dominant in the phase II composting substrate. Genus Pseudoxanthomonas and Truepera were dominant in the phase III composting substrate. The phase I microbial community was significantly different from that of the phase II and the phase III; and the phase II and the phase III composting substrates had highly similar microbial communities. For all 3 phases, the first two predicted metabolic pathway were amino acid and carbohydrate metabolism.
