Temperature-Induced Annual Variation in Microbial Community Changes and Resulting Metabolome Shifts in a Controlled Fermentation System

Abstract

We are rapidly increasing our understanding on the spatial distribution of microbial communities. However, microbial functioning, as well as temporal differences and mechanisms causing microbial community shifts, remains comparably little explored. Here, using Chinese liquor fermentation as a model system containing a low microbial diversity, we studied temporal changes in microbial community structure and functioning. For that, we used high-throughput sequencing to analyze the composition of bacteria and fungi and analyzed the microbially derived metabolome throughout the fermentation process in all four seasons in both 2018 and 2019. We show that microbial communities and the metabolome changed throughout the fermentation process in each of the four seasons, with metabolome diversity increasing throughout the fermentation process. Across seasons, bacterial and fungal communities as well as the metabolome driven by 10 indicator microorganisms and six metabolites varied even more. Daily average temperature in the external surroundings was the primary determinant of the observed temporal microbial community and metabolome changes. Collectively, our work reveals critical insights into patterns and processes determining temporal changes of microbial community composition and functioning. We highlight the importance of linking taxonomic to functional changes in microbial ecology to enable predictions of human-relevant applications. IMPORTANCE We used Chinese liquor fermentation as a model system to show that microbiome composition changes more dramatically across seasons than throughout the fermentation process within seasons. These changes translate to differences in the metabolome as the ultimate functional outcome of microbial activity, suggesting that temporal changes in microbiome composition are translating into functional changes. This result is striking as it suggests that microbial functioning, despite controlled conditions in the fermentors, fluctuates over season along with external temperature differences, which threatens a reproducible food taste. As such, we believe that our study provides a stepping-stone into novel taxonomy-functional studies that promote future work in other systems and that also is relevant in applied settings to better control surrounding conditions in food production.

Deciphering Succession and Assembly Patterns of Microbial Communities in a Two-Stage Solid-State Fermentation System

“…As individual microorganisms have different adaptability to environmental pH, it has been reported that pH has a great influence on the composition of microorganisms in many natural ecosystems ( 33 – 35 ). It has also been found that temperature affects the functional microbial community structure in the brewing process of liquor in both the short ( 23 ) and long term ( 17 ). Meanwhile, most bacteria rely on reducing sugar produced by fungal degradation of starch as a carbon source for proliferation and metabolism in the liquor brewing ecosystem ( 36 ).…”

“…The flavor compounds in fermented foods were key components determining consumer preference and control targets in food fermentation production ( 60 ). These flavor compounds are often metabolized by complex microbial communities; therefore, flavor compounds vary with changes in microbial communities ( 17 ). Despite the fact that two groups shared similar compositions of functional microbial communities in the fermentation stage, metabolites of grains and fresh liquor still exhibited differences between the two groups (Fig.…”

“…Environmental microorganisms thus could play an important role in shaping the microbial composition in fermented food microbial ecosystems ( 13 , 14 ). These characteristics make fermented food an ideal in situ model for analyzing the temporal succession of microbial composition ( 13 , 15 – 17 ). Additionally, the flavor compounds metabolized by the microbial community determine the quality of fermented foods.…”

Gradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing Data

“…1A ]) were added to the same sample at different concentrations to construct the concentration gradient (approximately 10 4 , 10 5 , 10 6 , 10 7 , and 10 8 copies g −1 ). The concentrations were chosen based on previous studies on the microbial concentration ranges (10 3 to 10 9 copies g −1 ) in the Chinese liquor solid-state fermentation ecosystem ( 19 – 21 ) ( Fig. 1B ).…”

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

“…It is possibly very difficult to completely eliminate some players in the community [ 34 ], but it is hypothesised that when there is no stationary phase, the community will mainly consist of fast growers, while at constant low nutrient levels, the community will consist of mainly slow-growing survivors, like it was observed in lactic acid fermentations [ 114 ]. Temperature regimes also affect the core microbiome composition and therefore, overall community composition and functional state [ 115 ]. Another crucial factor is nutrient availability: nutrient limitation /caloric restriction may lead to fixation of specific strains/microorganisms, such as nitrogen-fixing and cellulose producing bacteria in kombucha fermentation, of which domination might not be beneficial when media is rich in nutrients [ 116 , 117 ].…”