Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism

A yellow bacterium from marine agar, strain WHA3(T), was isolated from the mantel of the Pacific oysters Crassostrea gigas in the Wilhelmshaven Sea in northern Germany. Based on the 16S rRNA gene sequence, strain WHA3(T) had a high similarity to Pacificimonas flava JLT2015(T) (95.80%) and 94.79% to Pacificimonas aurantium JLT2012(T). Furthermore, the dDDH and ANI value analysis between WHA3(T) and other closest type strains were lower than 70% and 95%, respectively. The percentage of conserved proteins (POCP) and the average amino acid identity (AAI) value against Pacificimonas flava JLT2015(T) and Pacificimonas aurantium JLT2012(T) represented in the ranges of higher than 50% and 60%, respectively. Strain WHA3(T) contained ubiquinone-10 (Q-10) as the predominant quinone, and the major fatty acids were C-16:1 omega 7c and C-18:1 omega 7c. Granules of polyhydroxyalkanoates (PHAs) were absent. The main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, several sphingoglycolipids, an unknown phospholipid, an unknown glycolipid, and an unknown polar lipid. The polyamines contained spermidine and spermine. The DNA G + C content of strain WHA3(T) was 61.69%. An analysis of the whole-genome sequence in the frame of genome mining strain WHA3(T) predicted the presence of genomes for one-carbon metabolism, TonB-dependent transporters, vitamin B12 transporter, iron siderophore receptor protein, and other genes, some of which play important roles against restricted nutrient sources. The extract of strain WHA3(T) moderately inhibited the growth of Candida albicans DSM 1665. The polyphasic taxonomic analysis results suggested that strain WHA3(T) could be separated from its closest type strains. Strain WHA3(T) represents a novel species in the genus Pacificimonas, for which we propose the name Pacificimonas pallium sp. nov., with the type strain WHA3(T) (= DSM 111825(T) = NCCB 100832(T)).