Genomic insights into high-yield carotenoid production from renewable resources in radiation-resistant Deinococcus...

The environmental impacts of climate change highlight the need for sustainable bioprocesses using low-cost feedstocks. Microbial fermentation offers an eco-friendly method to produce value-added compounds from renewable resources. Deinoxanthin, a unique carotenoid pigment produced by radiation-resistant bacteria, Deinococcus, has pharmaceutical and food industry applications. However, most microorganisms preferentially utilize glucose as their primary carbon source, limiting their capacity to ferment byproducts or waste-derived resources effectively. Here, we hypothesized that identifying microbial hosts capable of metabolizing a broader range of nutrients could improve fermentation efficiency. Through whole-genome sequencing, we identified that D. yunweiensis KCTC3955 possesses multiple nutrient transporters and is capable of efficiently utilizing glycerol and various nitrogen sources for carotenoid production. Using one-factor-at-a-time and response surface methodologies, we optimized conditions with glycerol, achieving a 4.45-fold increase in carotenoid yield. Notably, key biosynthetic genes (dxr, idi, ispF, ispH, and cruF) were highly up-regulated under mixed nutrient conditions. Fed-batch fermentation with mixed renewable resources such as glycerol and corn steep liquor reached 23.22 mg/L carotenoid production and 15.48 mg/L/day productivity after 36 h, representing over 11- and 15-fold improvements compared to non-optimized conditions. These results highlight D. yunweiensis KCTC3955 as a strong candidate for carotenoid production from mixed renewable substrates.