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 Pacifi...
Published in: | Diversity |
---|---|
Main Authors: | , , , , |
Format: | Text |
Language: | English |
Published: |
Multidisciplinary Digital Publishing Institute
2022
|
Subjects: | |
Online Access: | https://doi.org/10.3390/d14030181 |
id |
ftmdpi:oai:mdpi.com:/1424-2818/14/3/181/ |
---|---|
record_format |
openpolar |
spelling |
ftmdpi:oai:mdpi.com:/1424-2818/14/3/181/ 2023-08-20T04:06:02+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 agris 2022-02-28 application/pdf https://doi.org/10.3390/d14030181 EN eng Multidisciplinary Digital Publishing Institute https://dx.doi.org/10.3390/d14030181 https://creativecommons.org/licenses/by/4.0/ Diversity; Volume 14; Issue 3; Pages: 181 pacific oyster Crassostrea gigas one-carbon metabolism genome mining TonB-dependent transporters Pacificimonas Text 2022 ftmdpi https://doi.org/10.3390/d14030181 2023-08-01T04:19:30Z 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). Text Crassostrea gigas Pacific oyster MDPI Open Access Publishing Pacific Diversity 14 3 181 |
institution |
Open Polar |
collection |
MDPI Open Access Publishing |
op_collection_id |
ftmdpi |
language |
English |
topic |
pacific oyster Crassostrea gigas one-carbon metabolism genome mining TonB-dependent transporters Pacificimonas |
spellingShingle |
pacific oyster Crassostrea gigas one-carbon metabolism genome mining TonB-dependent transporters Pacificimonas 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 |
description |
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). |
format |
Text |
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 |
Multidisciplinary Digital Publishing Institute |
publishDate |
2022 |
url |
https://doi.org/10.3390/d14030181 |
op_coverage |
agris |
geographic |
Pacific |
geographic_facet |
Pacific |
genre |
Crassostrea gigas Pacific oyster |
genre_facet |
Crassostrea gigas Pacific oyster |
op_source |
Diversity; Volume 14; Issue 3; Pages: 181 |
op_relation |
https://dx.doi.org/10.3390/d14030181 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/d14030181 |
container_title |
Diversity |
container_volume |
14 |
container_issue |
3 |
container_start_page |
181 |
_version_ |
1774716937622781952 |