Complex yeast\u2013bacteria interactions affect the yield of industrial ethanol fermentation

Felipe Senne De Oliveira Lino,Morten Otto Alexander Sommer,Djordje Bajic,Alvaro Sánchez,Jean Celestin Charles Vila

doi:10.1038/s41467-021-21844-7

Felipe Senne De Oliveira Lino, Morten Otto Alexander Sommer + Show 3 more

Open Access

https://doi.org/10.1038/s41467-021-21844-7

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Abstract

Sugarcane ethanol fermentation represents a simple microbial community dominated by S. cerevisiae and co-occurring bacteria with a clearly defined functionality. In this study, we dissect the microbial interactions in sugarcane ethanol fermentation by combinatorically reconstituting every possible combination of species, comprising approximately 80% of the biodiversity in terms of relative abundance. Functional landscape analysis shows that higher-order interactions counterbalance the negative effect of pairwise interactions on ethanol yield. In addition, we find that Lactobacillus amylovorus improves the yeast growth rate and ethanol yield by cross-feeding acetaldehyde, as shown by flux balance analysis and laboratory experiments. Our results suggest that Lactobacillus amylovorus could be considered a beneficial bacterium with the potential to improve sugarcane ethanol fermentation yields by almost 3%. These data highlight the biotechnological importance of comprehensively studying microbial communities and could be extended to other microbial systems with relevance to human health and the environment.

Highlights

Sugarcane ethanol fermentation represents a simple microbial community dominated by S. cerevisiae and co-occurring bacteria with a clearly defined functionality
We constructed a synthetic consortium composed of Lactobacillus amylovorus, Lactobacillus fermentum, Lactobacillus helveticus, Pediococcus claussenii, and Zymomonas mobilis, in addition to the dominant species Saccharomyces cerevisiae, which is responsible for ethanol fermentation (Fig. 1A)
Microbial consortia were incubated for 24 h, after which both cells and media were separated and harvested to analyse community structure via flow cytometry and function via high-pressure liquid chromatography (HPLC) analysis (Fig. 1C, Methods)

Summary

Introduction

Sugarcane ethanol fermentation represents a simple microbial community dominated by S. cerevisiae and co-occurring bacteria with a clearly defined functionality. Our results suggest that Lactobacillus amylovorus could be considered a beneficial bacterium with the potential to improve sugarcane ethanol fermentation yields by almost 3%. These data highlight the biotechnological importance of comprehensively studying microbial communities and could be extended to other microbial systems with relevance to human health and the environment. Microbial communities are shaped and stabilized by the interactions between their constituent members[3] These interactions define the composition, dynamics, and functionality of the microbial community[4]. Synthetic microbial communities represent important tools for studying microbial interactions[7,8,9], as they can be directly manipulated and their responses can be precisely quantified[10,11]. During the last 13 years, bioethanol has been responsible for avoiding the release of more than 500 million tons of CO2 in the atmosphere, and bioethanol replaced >40% of the gasoline consumed in Brazil[16]

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