An Integrated Metagenomics/Metaproteomics Investigation of the Microbial Communities and Enzymes in Solid-state Fermentation of Pu-erh tea.

Ming Zhao,Dong-Lian Zhang,Jin-Qiong Wan,Wen-Xia Yuan,Ying-Hong Pan,Shuang-Mei Duan,Ben-Ying Liu,Xiao-Qin Su,Yan Ma

doi:10.1038/srep10117

Abstract

Microbial enzymes during solid-state fermentation (SSF), which play important roles in the food, chemical, pharmaceutical and environmental fields, remain relatively unknown. In this work, the microbial communities and enzymes in SSF of Pu-erh tea, a well-known traditional Chinese tea, were investigated by integrated metagenomics/metaproteomics approach. The dominant bacteria and fungi were identified as Proteobacteria (48.42%) and Aspergillus (94.98%), through pyrosequencing-based analyses of the bacterial 16S and fungal 18S rRNA genes, respectively. In total, 335 proteins with at least two unique peptides were identified and classified into 28 Biological Processes and 35 Molecular Function categories using a metaproteomics analysis. The integration of metagenomics and metaproteomics data demonstrated that Aspergillus was dominant fungus and major host of identified proteins (50.45%). Enzymes involved in the degradation of the plant cell wall were identified and associated with the soft-rotting of tea leaves. Peroxiredoxins, catalase and peroxidases were associated with the oxidation of catechins. In conclusion, this work greatly advances our understanding of the SSF of Pu-erh tea and provides a powerful tool for studying SSF mechanisms, especially in relation to the microbial communities present.

Highlights

Solid-state fermentation (SSF) is defined as a fermentation process in which microorganisms grow on solid materials without the presence, or in the near-absence, of free liquid[1]
The sample collected on day 21 was selected for further metagenomics and metaproteomics analyses
The content of CAF was slight increased (P > 0.05). This change in the chemical compounds during solid-state fermentation (SSF) of Pu-erh tea was in accord with previous reports[34]

Summary

Introduction

Solid-state fermentation (SSF) is defined as a fermentation process in which microorganisms grow on solid materials without the presence, or in the near-absence, of free liquid[1]. Culture-independent molecular techniques, such as denaturing gradient gel electrophoresis (DGGE), temporal temperature gradient gel electrophoresis (TTGE), single stranded con formation polymorphism (SSCP), real-time quantitative PCR (qPCR), the construction and analysis of 16S rRNA gene libraries, terminal restriction fragment length polymorphism (TRFLP) and generation sequencing (NGS) techniques, have been widely used to analyze the microbiota of food fermentation, including the SSF process, increasing our knowledge of microbial diversity, population structure and dynamics[13,14,15] These studies were based on the analysis of 16S rRNA gene sequences, which provides useful information on microbial composition; the microbial enzymes still remain unknown. As far as we know, there are little reports on the microbial enzymes during the SSF of Pu-erh tea

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