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 WHA3ᵀ, 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 WHA3ᵀ had a high similarity to Pacificimonas flava JLT2015ᵀ (95.80%) and 94.79% to Pacificimonas aurantium JLT2012ᵀ. Furthermore, the dDDH and ANI value analysis between WHA3ᵀ 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 JLT2015ᵀ and Pacificimonas aurantium JLT2012ᵀ represented in the ranges of higher than 50% and 60%, respectively. Strain WHA3ᵀ contained ubiquinone-10 (Q-10) as the predominant quinone, and the major fatty acids were C₁₆:₁ ω7c and C₁₈:₁ ω7c. 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 WHA3ᵀ was 61.69%. An analysis of the whole-genome sequence in the frame of genome mining strain WHA3ᵀ 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 WHA3ᵀ moderately inhibited the growth of Candida albicans DSM 1665. The polyphasic taxonomic analysis results suggested that strain WHA3ᵀ could be separated from its closest type strains. Strain WHA3ᵀ represents a novel species in the genus Pacificimonas, for which we propose the name Pacificimonaspallium sp. nov., with the type strain WHA3ᵀ (= DSM 111825ᵀ = NCCB 100832ᵀ).