Microbiome analysis of sugarcane juices and biofilms from Louisiana raw sugar factories

Authors: Qi, Yunci; Bruni, Gillian; Klasson, K Thomas

Submitted to: Microbiology Spectrum
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/20/2023
Publication Date: 5/10/2023
Citation: Qi, Y., Bruni, G.O., Klasson, K.T. 2023. Microbiome analysis of sugarcane juices and biofilms from Louisiana raw sugar factories. Microbiology Spectrum. 11(3). Article e04345-22. https://doi.org/10.1128/spectrum.04345-22.
DOI: https://doi.org/10.1128/spectrum.04345-22

Interpretive Summary: During post-harvest processing of sugarcane for raw sugar, microbial activity results in sucrose loss and production of problematic polymers that cause economic losses and operational challenges. Amplicon-based sequencing is a powerful tool for profiling the microbial community present in complex environmental samples due to having higher throughput and not depending on culturing microbes. Historically, sugarcane juice spoilage has been blamed on Leuconostoc mesenteroides, but today it is well understood that environmental microbiomes contain many diverse species. So far little is known about the complete composition of bacterial and fungal communities responsible for post-harvest sucrose losses and problematic exopolysaccharide production during sugarcane processing. In this work we collected sugarcane crusher and mixed juices as well as biofilms from Louisiana raw sugarcane factories. The microorganisms present in these samples were different between crusher juice, mixed juice, and biofilms. The microbial composition also changed between different factories and dates of sampling. Overall, the results revealed a much more diverse microbiome than previously defined by traditional low throughput, culture-based isolation techniques. This study is the first to use amplicon-based profiling of microbes in sugarcane juices and biofilms at raw sugarcane factories and will help to contextualize microbial contamination problems in raw sugarcane factories and help to guide future studies on biocontrol measures aimed at inhibiting sucrose losses and operational challenges. Practically, these studies could eventually help to reduce costs and improve overall profits for the sugar industry.

Technical Abstract: During post-harvest processing of sugarcane for raw sugar, microbial activity results in sucrose loss and undesirable exopolysaccharide (EPS) production. Historically, culture-based approaches have focused on the bacterium Leuconostoc mesenteroides as the main contributor to both processes. In the present study, high-throughput amplicon-based sequence profiling, a powerful tool for comprehensively unraveling the microbial composition of environmental samples, was applied to samples from sugarcane post-harvest processing streams collected at three Louisiana raw sugarcane factories, including crusher juices, mixed juices, and biofilms. Microbial profiling of the bacterial and fungal microbiomes by 16S V4 and ITS1 sequences, respectively, identified 789 bacterial ASVs and 1210 fungal ASVs. These results revealed a more diverse microbiome than previously observed in traditional isolation-based studies conducted on samples from raw sugarcane factories. Additionally, we found that biofilms are composed of a much smaller number of microorganisms. Furthermore, flask cultures inoculated with the same samples demonstrated differences in the rate of sucrose consumption, as well as the production of exopolysaccharides and other organic acids.