A study on prokaryotic communities in fermented skates (Raja pulchra) and isolation of novel marine bacteria

Abstract

Fermented skate is a popular traditional alkaline food in a few countries (e.g. Iceland and Korea). Alkaline fermentation of skate is performed by mainly microbes which are primarily derived from fresh skate and its associated marine environments. Decomposition of urea was a major source of ammonia observed in fermented skates. Quantitative PCR showed that bacterial abundance were much higher than archaeal abundance in both fresh and fermented skates, suggesting that bacteria, not archaea, play an important role in skate fermentation. Bacterial pyrosequencing analysis revealed that fresh skate was predominated by Psychrobacter- and Carnobacterium-like sequences, whereas 4 ℃-and 14 ℃-fermented skates were predominated by Atopostipes- and Myroides-like sequences, respectively. The most distinguishing feature of this study was that the order Lactobacillales were dominant in fresh and fermented skates. The order Lactobacillales is a major group of lactic acid bacteria (LAB), responsible for acidic fermentation. Probably, LAB is important in alkaline fermented seafood. Urease and arginine deiminase activity tests suggested that genera Pychrobacter and Carnobacterium play important roles in alkali fermentation of skate. Out of 211 isolated stains, 24 isolates were identified as putatively novel strains based on 16S rRNA gene similarity. Interestingly, about 42% (n=10) of the putatively novel strains belonged to order Lactobacillales, indicating that skates might be a useful source for finding novel marine LAB.