<i>Pacificimonas pallium</i> sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster <i>Crassostrea gigas</i> in Germany, and Prediction of One-Carbon Metabolism
A yellow bacterium from marine agar, strain WHA3<sup>T</sup>, was isolated from the mantel of the Pacific oysters <i>Crassostrea gigas</i> in the Wilhelmshaven Sea in northern Germany. Based on the 16S rRNA gene sequence, strain WHA3<sup>T</sup> had a high similar...
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MDPI AG
2022-02-01
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| author | Hani Pira Chandra Risdian Mathias Müsken Peter J. Schupp Joachim Wink |
| author_facet | Hani Pira Chandra Risdian Mathias Müsken Peter J. Schupp Joachim Wink |
| author_sort | Hani Pira |
| collection | DOAJ |
| description | A yellow bacterium from marine agar, strain WHA3<sup>T</sup>, was isolated from the mantel of the Pacific oysters <i>Crassostrea gigas</i> in the Wilhelmshaven Sea in northern Germany. Based on the 16S rRNA gene sequence, strain WHA3<sup>T</sup> had a high similarity to <i>Pacificimonas flava</i> JLT2015<sup>T</sup> (95.80%) and 94.79% <i>to Pacificimonas aurantium</i> JLT2012<sup>T</sup>. Furthermore, the dDDH and ANI value analysis between WHA3<sup>T</sup> 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 <i>Pacificimonas flava</i> JLT2015<sup>T</sup> and <i>Pacificimonas aurantium</i> JLT2012<sup>T</sup> represented in the ranges of higher than 50% and 60%, respectively. Strain WHA3<sup>T</sup> contained ubiquinone-10 (Q-10) as the predominant quinone, and the major fatty acids were C<sub>16:1</sub> ω7c and C<sub>18:1</sub> 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 WHA3<sup>T</sup> was 61.69%. An analysis of the whole-genome sequence in the frame of genome mining strain WHA3<sup>T</sup> 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<sup>T</sup> moderately inhibited the growth of <i>Candida albicans</i> DSM 1665. The polyphasic taxonomic analysis results suggested that strain WHA3<sup>T</sup> could be separated from its closest type strains. Strain WHA3<sup>T</sup> represents a novel species in the genus <i>Pacificimonas</i>, for which we propose the name <i>Pacificimonas</i><i>pallium</i> sp. nov., with the type strain WHA3<sup>T</sup> (= DSM 111825<sup>T</sup> = NCCB 100832<sup>T</sup>). |
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| spelling | doaj.art-7559fd86dc484ae1ace2f8f8b0f46cfd2023-11-24T00:57:14ZengMDPI AGDiversity1424-28182022-02-0114318110.3390/d14030181<i>Pacificimonas pallium</i> sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster <i>Crassostrea gigas</i> in Germany, and Prediction of One-Carbon MetabolismHani Pira0Chandra Risdian1Mathias Müsken2Peter J. Schupp3Joachim Wink4Microbial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, GermanyMicrobial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, GermanyCentral Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, GermanyInstitute for Chemistry and Biology of the Marine Environment, Oldenburg University, 26129 Oldenburg, GermanyMicrobial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, GermanyA yellow bacterium from marine agar, strain WHA3<sup>T</sup>, was isolated from the mantel of the Pacific oysters <i>Crassostrea gigas</i> in the Wilhelmshaven Sea in northern Germany. Based on the 16S rRNA gene sequence, strain WHA3<sup>T</sup> had a high similarity to <i>Pacificimonas flava</i> JLT2015<sup>T</sup> (95.80%) and 94.79% <i>to Pacificimonas aurantium</i> JLT2012<sup>T</sup>. Furthermore, the dDDH and ANI value analysis between WHA3<sup>T</sup> 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 <i>Pacificimonas flava</i> JLT2015<sup>T</sup> and <i>Pacificimonas aurantium</i> JLT2012<sup>T</sup> represented in the ranges of higher than 50% and 60%, respectively. Strain WHA3<sup>T</sup> contained ubiquinone-10 (Q-10) as the predominant quinone, and the major fatty acids were C<sub>16:1</sub> ω7c and C<sub>18:1</sub> 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 WHA3<sup>T</sup> was 61.69%. An analysis of the whole-genome sequence in the frame of genome mining strain WHA3<sup>T</sup> 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<sup>T</sup> moderately inhibited the growth of <i>Candida albicans</i> DSM 1665. The polyphasic taxonomic analysis results suggested that strain WHA3<sup>T</sup> could be separated from its closest type strains. Strain WHA3<sup>T</sup> represents a novel species in the genus <i>Pacificimonas</i>, for which we propose the name <i>Pacificimonas</i><i>pallium</i> sp. nov., with the type strain WHA3<sup>T</sup> (= DSM 111825<sup>T</sup> = NCCB 100832<sup>T</sup>).https://www.mdpi.com/1424-2818/14/3/181pacific oyster <i>Crassostrea gigas</i>one-carbon metabolismgenome miningTonB-dependent transporters<i>Pacificimonas</i> |
| spellingShingle | Hani Pira Chandra Risdian Mathias Müsken Peter J. Schupp Joachim Wink <i>Pacificimonas pallium</i> sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster <i>Crassostrea gigas</i> in Germany, and Prediction of One-Carbon Metabolism Diversity pacific oyster <i>Crassostrea gigas</i> one-carbon metabolism genome mining TonB-dependent transporters <i>Pacificimonas</i> |
| title | <i>Pacificimonas pallium</i> sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster <i>Crassostrea gigas</i> in Germany, and Prediction of One-Carbon Metabolism |
| title_full | <i>Pacificimonas pallium</i> sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster <i>Crassostrea gigas</i> in Germany, and Prediction of One-Carbon Metabolism |
| title_fullStr | <i>Pacificimonas pallium</i> sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster <i>Crassostrea gigas</i> in Germany, and Prediction of One-Carbon Metabolism |
| title_full_unstemmed | <i>Pacificimonas pallium</i> sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster <i>Crassostrea gigas</i> in Germany, and Prediction of One-Carbon Metabolism |
| title_short | <i>Pacificimonas pallium</i> sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster <i>Crassostrea gigas</i> in Germany, and Prediction of One-Carbon Metabolism |
| title_sort | i pacificimonas pallium i sp nov an isolated bacterium from the mantle of pacific oyster i crassostrea gigas i in germany and prediction of one carbon metabolism |
| topic | pacific oyster <i>Crassostrea gigas</i> one-carbon metabolism genome mining TonB-dependent transporters <i>Pacificimonas</i> |
| url | https://www.mdpi.com/1424-2818/14/3/181 |
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