1
|
Xu C, Peng H, Li H, Xie X, Chen S, Dai J, Ren H. Paracoccus actinidiae sp.nov., a novel bacterium isolated from kiwi tree rhizosphere soil. Int J Syst Evol Microbiol 2024; 74. [PMID: 39453831 DOI: 10.1099/ijsem.0.006529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2024] Open
Abstract
Strain M09T was isolated from the rhizoshere of kiwi fruit trees from an orchard located in Fangshan, Beijing, PR China (39° 49' 25.1″ N, 116° 4' 44.5″ E,). It is a short rod-shaped, Gram-stain-negative, facultatively anaerobic bacterium that tests positive for both oxidase and catalase. The strain exhibited growth within the temperature range of 15-45 °C (optimal growth at 30 °C) and the pH range of 4.0-10.0 (optimal growth at pH 7.0) and without NaCl. It also grew in a sodium chloride-free nutrient agar (NA) medium. The results of phylogenetic analysis of the 16S rRNA gene sequences indicated that M09T represents a member of the genus Paracoccus and shares high similarity with Paracoccus everestensis S8-55T (98.46%) and Paracoccus aerius 011410T (97.58%). The average nucleotide identity values between M09T and P. everestensis S8-55T, P. aerius 011410T, Paracoccus marinaquae X HP0099T and Paracoccus fontiphilus MVW-1T were 95.56, 84.51, 79.83 and 83.68%, respectively. The digital DNA-DNA hybridisation values between between M09T and P. everestensis S8-55T, P. aerius 011410T, P. marinaquae X HP0099T and P. fontiphilus MVW-1T were 56.40, 29.30, 21.60 and 28.60%, respectively. The major fatty acids identified were C10 : 0 3-OH (51.8%) and C18 : 1ω7c (35.5%). The major respiratory quinone was Q-10, with Q-8 present as a minor component. Polar lipids were mainly comprised of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE). Genome sequencing revealed that the strain has a DNA G+C content of 64.31 mol%. On the basis of this comprehensive taxonomic characterisation data, M09T represents a novel species within the genus Paracoccus and has been named Paracoccus actinidiae sp. nov. The type strain is designated as M09T (=GDMCC 1.4157T=KCTC 8143T).
Collapse
Affiliation(s)
- Chenqi Xu
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, School of Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Han Peng
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, School of Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - He Li
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, School of Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Xinran Xie
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, School of Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Siwei Chen
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, School of Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Junhao Dai
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, School of Light Industry, Beijing Technology and Business University, Beijing, PR China
| | - Hong Ren
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, School of Light Industry, Beijing Technology and Business University, Beijing, PR China
| |
Collapse
|
2
|
Cui X, Liu Y, Xu Y, Chen T, Zhang S, Wang J, Yang R, Liu G, Zhang W, Zhang G. Paracoccus everestensis sp. nov., a novel bacterium with great antioxidant capacity isolated from the north slope of Mount Everest. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated S8-55T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. The purpose of this study was to describe a novel species and its characteristics, through genome sequencing and analysis of the relationship between the members of the genus
Paracoccus
, and explore the antioxidant capacity of strain S8-55T. The polyphasic study confirmed the affiliation of strain S8-55T with the genus
Paracoccus
. Strain S8-55T was aerobic, Gram-negative and oxidase- and catalase positive. Cells were orange-pigmented, ellipsoid and had no spore formation, no flagella and no motility. Strain S8-55T grow at 10–37 °C, pH 7–11 and without NaCl. Ubiquinone 10 was its predominant respiratory menaquinone. The polar lipids of strain S8-55T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified phospholipid, an unidentified aminolipid and three unidentified lipids. Its major fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c). The G+C content was 64.3 mol%. The phylogenetic analysis based on the 16S rRNA sequence showed that strain S8-55T was closely related to
Paracoccus angustae
E6T (97.9 %),
Paracoccus aerius
011410T (97.9 %) and
Paracoccus hibisci
THG-T2.8T (97.8 %). The average nucleotide identity values among strain S8-55T and
P. angustae
CCTCC AB 2015056T,
P. aerius
KCTC 42845T and
P. hibisci
CCTCC AB 2016181T were 84.1, 84.5 and 76.3 %, respectively. The genome of strain S8-55T contained antioxidant genes such as oxyR, recD, katE, recD and rpoH. Based on its morphological, physiological and chemical taxonomic characteristics, strain S8-55T (=JCM 35 227T=GDMCC 1.3026T) should be classified as a novel species of the genus
Paracoccus
with the proposed name Paracoccus everestensis sp. nov.
Collapse
Affiliation(s)
- Xiaowen Cui
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, Gansu Province, PR China
| | - Yang Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, PR China
| | - Yajie Xu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Songlin Zhang
- College of Geography and Environment Science, Northwest Normal University, Lanzhou 730070, Gansu Province, PR China
| | - Jinxiu Wang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Ruiqi Yang
- College of Urban Environment, Lanzhou City University, Lanzhou 730070, Gansu Province, PR China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, Gansu Province, PR China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, Gansu Province, PR China
| |
Collapse
|
3
|
Kim J, Kim JY, Song HS, Cha IT, Roh SW, Lee SH. Paracoccus jeotgali sp. nov., isolated from Korean salted and fermented shrimp. J Microbiol 2019; 57:444-449. [PMID: 31054135 DOI: 10.1007/s12275-019-8704-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/01/2019] [Accepted: 02/07/2019] [Indexed: 01/14/2023]
Abstract
A Gram-stain-negative and facultatively aerobic bacterium, designated as strain CBA4604T, was isolated from a traditional Korean salted and fermented shrimp food (saeu-jeot). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBA4604T formed a clearly distinct phyletic lineage from closely related species within the genus Paracoccus. Strain CBA4604T was the most closely related to P. koreensis Ch05T (97.5% 16S rRNA gene sequence similarity) and other type strains (≤ 97.0%). The genome comprised a chromosome and two plasmids of 3,299,166 bp with 66.5% G+C content. The DNA-DNA relatedness values between strain CBA4604T and P. koreensis Ch05T, P. alcaliphilus DSM 8512T, and P. stylophorae KTW-16T were 30.5%, 22.9%, and 16.7%, respectively. Cells of the strain were short rod-shaped and oxidase- and catalase-positive. The growth of strain CBA-4604T was observed at 10-40°C (optimum, 37°C), pH 6.0-10.0 (optimum, pH 7.0), and in the presence of 0-8.0% (w/v) NaCl (optimum, 0-2.0%). Strain CBA4604T contained ubiquinone 10 as the sole isoprenoid quinone and summed feature 8 (C18:1ω7c/C18:1ω6c) and C18:0 as the major cellular fatty acids. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phospholipid, an unidentified aminolipid, an unidentified glycolipid, and three unidentified lipids. Based on its phylogenetic, genomic, phenotypic, and chemotaxonomic features, we concluded that strain CBA-4604T represents a novel species in the genus Paracoccus and we propose the name Paracoccus jeotgali sp. nov. The type strain is CBA4604T (= KACC 19579T = JCM 32510T).
Collapse
Affiliation(s)
- Juseok Kim
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.,Division of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Joon Yong Kim
- Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Hye Seon Song
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - In-Tae Cha
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
| | - Se Hee Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea.
| |
Collapse
|
4
|
Wang YS, Yan ZF, Lin P, Gao W, Yi TH. Paracoccus pueri sp. nov., isolated from Pu'er tea. Antonie van Leeuwenhoek 2018; 111:1535-1542. [PMID: 29484518 DOI: 10.1007/s10482-018-1041-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/05/2018] [Indexed: 12/01/2022]
Abstract
A Gram-stain negative, aerobic, short rod-shaped, motile by flagella bacterial strain (THG-N2.35T), was isolated from Pu'er tea. Growth occurred at 10-40 °C (optimum 28 °C), at pH 4-7 (optimum 7) and at 0-5% NaCl (optimum 1%). Based on 16S rRNA gene sequence analysis, the near phylogenetic neighbours of strain THG-N2.35T were identified as Paracoccus hibisci KACC 18632T (99.0%), Paracoccus tibetensis CGMCC 1.8925T (98.7%), Paracoccus beibuensis CGMCC 1.7295T (98.2%), Paracoccus aestuarii KCTC 22049T (98.2%), Paracoccus rhizosphaerae LMG 26205T (98.1%), Paracoccus zeaxanthinifaciens ATCC 21588T (97.1%), Paracoccus marcusii DSM 11574T (97.0%). Levels of similarity between strain THG-N2.35T and other Paracoccus species were lower than 97.0%. DNA-DNA hybridization values between strain THG-N2.35T and P. hibisci KACC 18632T, P. tibetensis CGMCC 1.8925T, P. beibuensis CGMCC 1.7295T, P. aestuarii KCTC 22049T, P. rhizosphaerae LMG 26205T, P. zeaxanthinifaciens ATCC 21588T, P.marcusii DSM 11574T were 47.5% (42.3%, reciprocal analysis), 36.1% (32.3%), 24.7% (22.1%), 19.2% (16.3%), 11.3% (8.8%), 11.1% (10.8%), 6.1% (5.8%), respectively. The DNA G+C content of strain THG-N2.35T was 62.3 mol%. The polar lipids were diphosphatidylglycerol, phosphatidyl-N-methylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The quinone was ubiquinone-10 (Q-10). The major fatty acids were C10:0 3OH, C16:0, C18:0 and C18:1 ω7ϲ. On the basis of the phylogenetic analysis, chemotaxonomic data, physiological characteristics and DNA-DNA hybridization data, strain THG-N2.35T represent a novel species of the genus Paracoccus, for which the name Paracoccus pueri sp. nov. is proposed. The type strain is THG-N2.35T (= KACC 18934T = CCTCC AB 2016177T).
Collapse
Affiliation(s)
- Yu-Shuai Wang
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea
| | - Zheng-Fei Yan
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea
| | - Pei Lin
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea
| | - Wei Gao
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea
| | - Tae-Hoo Yi
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung Hee University Global Campus, 1732 Deokyoungdae-ro, Giheung-gu, Yongin-Si, Gyeonggi-do, 17104, Republic of Korea.
| |
Collapse
|
5
|
Kim YO, Park IS, Park S, Nam BH, Kim DG, Won SM, Yoon JH. Paracoccus alimentarius sp. nov., isolated from a Korean foodstuff, salted pollack. Int J Syst Evol Microbiol 2018; 68:1238-1243. [PMID: 29469691 DOI: 10.1099/ijsem.0.002658] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, non-motile and coccoid or ovoid bacterial strain, designated LB2T, was isolated from a Korean foodstuff, salted pollack. Strain LB2T grew optimally at 25-30 °C, at pH 7.0-8.0 and in the presence of 0-2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain LB2T belonged to the genus Paracoccus, coherently clustering with the type strain of Paracoccus sulfuroxidans. Strain LB2T exhibited 16S rRNA gene sequence similarity values of 98.0 and 97.0 % to the type strains of P. sulfuroxidans and Paracoccus halophilus, respectively, and of less than 96.9 % to the type strains of other Paracoccus species. Strain LB2T contained Q-10 as the predominant ubiquinone. Major fatty acids of strain LB2T were cyclo C19 : 0ω8c, C18 : 1ω7c and C16 : 0 (when grown on MA) or C18 : 1ω7c and C16 : 0 (on TSA). The major polar lipids detected in strain LB2T were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid and one unidentified glycolipid. The DNA G+C content of strain LB2T was 61.4 mol% and its DNA-DNA relatedness values with the type strains of P. sulfuroxidans and P. halophilus were 26 and 18 %, respectively. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain LB2T is separated from recognized Paracoccus species. On the basis of the data presented, strain LB2T is considered to represent a novel species of the genus Paracoccus, for which the name Paracoccus alimentarius sp. nov. is proposed. The type strain is LB2T (=KCTC 62138T=NBRC 113023T).
Collapse
Affiliation(s)
- Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 46083, Republic of Korea
| | - In-Suk Park
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 46083, Republic of Korea
| | - Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon 16419, Republic of Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 46083, Republic of Korea
| | - Dong-Gyun Kim
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 46083, Republic of Korea
| | - Sung-Min Won
- Biotechnology Research Division, National Institute of Fisheries Science (NIFS), Gijang, Busan 46083, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon 16419, Republic of Korea
| |
Collapse
|