Profiling the community structure of pit clay during aging process with the combination of relative and absolute quantitative approaches

Abstract:

[Objective] Based on the traditional relative quantitative method, the microbial community in pit clay with different cellar ages was investigated by using the absolute quantitative method with addition of an internal standard at the DNA extraction step. [Methods] According to the relative and absolute quantitative results, the microbial community and physicochemical factors of pit clay were profiled by using Clostridium acetobutylicum as an internal standard through 16S rRNA gene high-throughput sequencing. [Results] With the increase of cellular age, the diversity of microbial community in pit clay increased, and the relative abundances of representative genera such as Caproiciproducens, Methanobacterium, Methanosarcina, and Syntrophomonas significantly increased. By using the absolute quantitative approach, the biomass in the aged pit clay was 600 times and 28 times as much to that in the new pit clay and the aging pit clay, respectively. Compared with the relative quantification, on the contrary, the absolute abundance of Lactobacillus in aged pit clay did not decrease rather than increase during the aging process, with 20 times as that in new pit clay. The absolute abundance of Caproiciproducens in aged pit clay was 25000 times as much to that in new pit clay. Moreover, the absolute abundances of other functional microorganisms such as Methanobacterium, Methanosarcina, Methanobrevibacter and Syntrophomonas also increased across the aging process. The absolute abundance analysis indicates that the aging process of pit clay is a process with increased diversity as well as biomass of microbial community, contributing to lactate depletion and thus maintaining the stability of pit clay microbiota. [Conclusion] With the combination of relative and absolute quantitative approaches, the dynamic changes of species members in microbial community were profiled during the pit clay aging process. This study will help to provide a new quantitative and causal correlation analysis method to decipher the composition and function of pit clay microbiome.