Deciphering the intra- and inter-kingdom networks of microbiota in the pit mud of Chinese strong-flavor liquor

Abstract

Microbes have central roles in the pit mud (PM) ecosystems and flavor formation, yet specific ecological interactions and keystone taxa among these taxa are largely unknown. Here, we used network analyses to explore the PM microbial intra- and inter-kingdom networks based on Illumina MiSeq sequencing data. The results showed that Firmicutes (mainly Caproiciproducens, Lactobacillus and Bacillus), Ascomycota (mainly Thermoascus, Eurotium and Aspergillus) and Euryarchaeota (mainly Methanobacterium, Methanosarcina, Methanobrevibacter and Methanocorpusculum) were the most dominant taxa detected in PM microbiota. The complexity of PM bacterial networks was much higher than that of fungal and archaeal networks, the hubs were mainly derived from bacteria rather than fungi and archaea in each inter-kingdom network, and the positive correlations dominated in bacterial (>75%), fungal (>90%) and inter-kingdom (>80%) networks. In addition, Mantel test showed that PM properties, especially pH, humic acid, available P and organic matter, were closely correlated with compositional structure of microbial communities and their main ecological clusters. The findings will contribute to a better understanding of PM microbiome structure and the ecological rules guiding community assembly, and have important implications for manipulating microbial resources and controlling PM environmental factors for pit management and sustainable brewing.