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 Pa...
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MDPI AG
2022
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ftdoajarticles:oai:doaj.org/article:7559fd86dc484ae1ace2f8f8b0f46cfd 2023-05-15T15:57:54+02:00 Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism Hani Pira Chandra Risdian Mathias Müsken Peter J. Schupp Joachim Wink 2022-02-01T00:00:00Z https://doi.org/10.3390/d14030181 https://doaj.org/article/7559fd86dc484ae1ace2f8f8b0f46cfd EN eng MDPI AG https://www.mdpi.com/1424-2818/14/3/181 https://doaj.org/toc/1424-2818 doi:10.3390/d14030181 1424-2818 https://doaj.org/article/7559fd86dc484ae1ace2f8f8b0f46cfd Diversity, Vol 14, Iss 181, p 181 (2022) pacific oyster Crassostrea gigas one-carbon metabolism genome mining TonB-dependent transporters Pacificimonas Biology (General) QH301-705.5 article 2022 ftdoajarticles https://doi.org/10.3390/d14030181 2022-12-30T19:55:00Z 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 ω7c and C 18:1 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 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 ). Article in Journal/Newspaper Crassostrea gigas Pacific oyster Directory of Open Access Journals: DOAJ Articles Pacific Diversity 14 3 181 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
pacific oyster Crassostrea gigas one-carbon metabolism genome mining TonB-dependent transporters Pacificimonas Biology (General) QH301-705.5 |
spellingShingle |
pacific oyster Crassostrea gigas one-carbon metabolism genome mining TonB-dependent transporters Pacificimonas Biology (General) QH301-705.5 Hani Pira Chandra Risdian Mathias Müsken Peter J. Schupp Joachim Wink Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism |
topic_facet |
pacific oyster Crassostrea gigas one-carbon metabolism genome mining TonB-dependent transporters Pacificimonas Biology (General) QH301-705.5 |
description |
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 ω7c and C 18:1 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 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 ). |
format |
Article in Journal/Newspaper |
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 |
title |
Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism |
title_short |
Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism |
title_full |
Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism |
title_fullStr |
Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism |
title_full_unstemmed |
Pacificimonas pallium sp. nov., an Isolated Bacterium from the Mantle of Pacific Oyster Crassostrea gigas in Germany, and Prediction of One-Carbon Metabolism |
title_sort |
pacificimonas pallium sp. nov., an isolated bacterium from the mantle of pacific oyster crassostrea gigas in germany, and prediction of one-carbon metabolism |
publisher |
MDPI AG |
publishDate |
2022 |
url |
https://doi.org/10.3390/d14030181 https://doaj.org/article/7559fd86dc484ae1ace2f8f8b0f46cfd |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Diversity, Vol 14, Iss 181, p 181 (2022) |
op_relation |
https://www.mdpi.com/1424-2818/14/3/181 https://doaj.org/toc/1424-2818 doi:10.3390/d14030181 1424-2818 https://doaj.org/article/7559fd86dc484ae1ace2f8f8b0f46cfd |
op_doi |
https://doi.org/10.3390/d14030181 |
container_title |
Diversity |
container_volume |
14 |
container_issue |
3 |
container_start_page |
181 |
_version_ |
1766393610156113920 |