A field to factory study of the microbial flora of sugar beets and factory processing streams utilizing MinION deep sequencing technology.

Abstract

American Crystal Sugar Company (ACSC) factories have experienced periods of high unaccountable sucrose losses with consequent lower than expected recovery.  In addition, physical processing issues have been intermittently encountered such as poor syrup filtration that have no readily identifiable causes.  Increased unaccountable losses have been correlated to increases in volatile fatty acids such as lactic acid, invert sugars, and ethanol in the diffusion juice and subsequent process streams.  Elevated sucrose losses tend to occur when cossette ethanol levels increase along with invert sugars.  The prior described events may or may not present as physical operating issues.  The response to various treatments to manage undesirable microbial activity during the process can vary greatly. In the spring of 2019 PCR work was undertaken to identify microorganisms present in the beets, the soil, and the process streams, with the aim to correlate the presence and abundance of bacterial taxa with beet health and processing issues.  Various classes of microorganisms were identified in both the beets and process streams that included anaerobic and aerobic mesophiles and thermophiles along with aerobic psychrophiles.  98 species were identified that included Leuconostoc, Bacillus, Enterococcus, Pseudomonas, Thermoanaerobacter spp.  In the fall of 2020 work was done with USDA in utilizing deep sequencing of 16S rRNA gene PCR amplicons with the MinION sequencer (Oxford Nanopore Technologies).  Results of the work were presented at the 2021 ASSBT conference.  Work has continued at ACSC utilizing MinION technology.  In 2021 samples from storage piles (from brei) were analyzed in addition to factory processing samples.  Lueconsostoc, Microbacterium, Pantoea, Pseudomonas spp. were identified and quantified.  To date sequencing experiments have demonstrated that there is a great deal of variability in the micro flora found in field and process streams, the populations shift across campaign