Microbial diversity and dominant bacteria causing spoilage during storage and processing of the Antarctic krill, Euphausia superba

The Antarctic region is known for its ecological conditions and the presence of some of the rarest microorganisms on earth. Antarctic krill rapidly degrades while at rest or during transport due to high-activity enzymes in its flesh or from microbes. In this study, we analyzed the microbial diversity of the Antarctic krill, Euphausia superba, and identified the dominant bacteria that cause spoilage during storage and transport using culture-independent high-throughput sequencing and microbial pure culture methods. Antarctic krill samples were incubated at temperatures of 0 °C, 4 °C, 16 °C, and 25 °C to determine the microbial diversity and abundance in decaying marine krill samples. Metagenome high-throughput sequencing indicated that, under incubation at 4 °C and 0 °C for 24 h, the microbial diversity of the Antarctic krill samples was high, with high species richness of microbes adapted to the low-temperature environment, as indicated by the overwhelming dominance of Enterococcus and Bacillus. On the other hand, Psychrobacter became the dominant bacteria at storage temperatures of 16 °C and 25 °C. Quantitative PCR results demonstrated that the microbial copy number increased as the temperature increased from 0 to 25 °C, and the quantity of bacteria was much greater than that of fungi under the same storage conditions. Microbial pure culture methods demonstrated that Psychrobacter was the dominant genus at each incubation temperature after 24 h of storage. Psychrobacter sp. and Psychrobacter-like strains isolated from the Antarctic krill samples exhibited protease activity. Our laboratory results indicated that Psychrobacter was the primary cause of spoilage of the Antarctic krill, E. superba. The results from ITS rDNA fungal sequencing showed that unclassified Saccharomycetes were the predominant microbes in all the Antarctic krill samples.