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Kawano K, Awano T, Yoshinaga A, Sugiyama J, Sawayama S, Nakagawa S. Paralimibaculum aggregatum gen. nov. sp. nov. and Biformimicrobium ophioploci gen. nov. sp. nov., two novel heterotrophs from brittle star Ophioplocus japonicus. Int J Syst Evol Microbiol 2024; 74. [PMID: 39325648 DOI: 10.1099/ijsem.0.006530] [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: 09/28/2024] Open
Abstract
Two novel Gram-stain-negative, strictly aerobic, halophilic and non-motile bacterial strains, designated NKW23T and NKW57T, were isolated from a brittle star Ophioplocus japonicus collected from a tidal pool in Wakayama, Japan. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that NKW23T represented a member of the family Paracoccaceae, with Limibaculum halophilum CAU 1123T as its closest relative (94.4% sequence identity). NKW57T was identified as representing a member of the family Microbulbiferaceae, with up to 94.9% sequence identity with its closest relatives. Both strains displayed average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values below the species delimitation threshold against their closest relatives. Additionally, amino acid identity (AAI) values of both strains fell below the genus-defining threshold. Phylogenetic trees based on genome sequences indicated that NKW23T formed a novel lineage, branching deeply prior to the divergence of the genera Limibaculum and Thermohalobaculum, with an evolutionary distance (ED) of 0.31-0.32, indicative of genus-level differentiation. NKW57T similarly formed a distinct lineage separate from the species of the genus Microbulbifer. The major respiratory quinones of NKW23T and NKW57T were ubiquinone-10 (Q-10) and Q-8, respectively. The genomic DNA G+C contents of NKW23T and NKW57T were 71.4 and 58.8%, respectively. On the basis of the physiological and phylogenetic characteristics, it was proposed that these strains should be classified as novel species representing two novel genera: Paralimibaculum aggregatum gen. nov., sp. nov., with strain NKW23T (=JCM 36220T=KCTC 8062T) as the type strain, and Biformimicrobium ophioploci gen. nov., sp. nov., with strain NKW57T (=JCM 36221T=KCTC 8063T) as the type strain.
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Affiliation(s)
- Keisuke Kawano
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tatsuya Awano
- Laboratory of Tree Cell Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Arata Yoshinaga
- Laboratory of Tree Cell Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Junji Sugiyama
- Laboratory of Tree Cell Biology, Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-Star), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-Cho, Yokosuka 237-0061, Japan
- Section for Exploration of Life in Extreme Environments, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji-Cho, Okazaki 444-8787, Japan
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Li X, Cai Y, Qiu Q, Wu J, Wang J, Qiu J. Monitoring Ammonium Polyphosphate (APP) Biodegradation by Acinetobacter nosocomialis D-3 Using DAPI. Molecules 2024; 29:2667. [PMID: 38893541 PMCID: PMC11173948 DOI: 10.3390/molecules29112667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Ammonium polyphosphate (APP), a pivotal constituent within environmentally friendly flame retardants, exhibits notable decomposition susceptibility and potentially engenders ecological peril. Consequently, monitoring the APP concentration to ensure product integrity and facilitate the efficacious management of wastewater from production processes is of great significance. A fluorescent assay was devised to swiftly discern APP utilizing 4',6'-diamino-2-phenylindole (DAPI). With increasing APP concentrations, DAPI undergoes intercalation within its structure, emitting pronounced fluorescence. Notably, the flame retardant JLS-PNA220-A, predominantly comprising APP, was employed as the test substrate. Establishing a linear relationship between fluorescence intensity (F-F0) and JLS-PNA220-A concentration yielded the equation y = 76.08x + 463.2 (R2 = 0.9992), with a LOD determined to be 0.853 mg/L. The method was used to assess the degradation capacity of APP-degrading bacteria. Strain D-3 was isolated, and subsequent analysis of its 16S DNA sequence classified it as belonging to the Acinetobacter genus. Acinetobacter nosocomialis D-3 demonstrated superior APP degradation capabilities under pH 7 at 37 °C, with degradation rates exceeding 85% over a four-day cultivation period. It underscores the sensitivity and efficacy of the proposed method for APP detection. Furthermore, Acinetobacter nosocomialis D-3 exhibits promising potential for remediation of residual APP through environmental biodegradation processes.
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Affiliation(s)
- Xiangxiang Li
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yule Cai
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Qiqing Qiu
- Hangzhou JLS Flame Retardants Chemical Co., Ltd., Hangzhou 310011, China
| | - Jiamin Wu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Jing Wang
- Hangzhou JLS Flame Retardants Chemical Co., Ltd., Hangzhou 310011, China
| | - Jieqiong Qiu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
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Deng TH, Zhang Y, Zhang WW, Su Y, Gao JW, Ying JJ, Xu L, Xia XM, Sun C. Marinobacter albus sp. nov., Isolated from Sand Sediment in a Coastal Intertidal Zone. Curr Microbiol 2024; 81:138. [PMID: 38609554 DOI: 10.1007/s00284-024-03676-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
A Gram-stain-negative bacterium with a rod-to-ovoid shape, named strain M216T, was isolated from sand sediment from the coastal intertidal zone of Huludao, Liaoning Province, China. Growth was observed at 8-40 °C (optimal, 30 °C), pH 5.5-9.5 (optimal, pH 6.5) and 0.5-14.0% (w/v) NaCl (optimal, 6%). Strain M216T possessed ubiquinone-9 as its sole respiratory quinone and phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophosphoglycolipid, one unidentified aminophospholipid, two unidentified phosphoglycolipids, three unidentified phospholipids and three unidentified glycolipids as the main polar lipids. C12:0, C16:0, C12:0 3-OH, C16:1 ω9c, C18:1 ω9c and summed features 3 (C16:1 ω7c and/or C16:1 ω6c) were the major fatty acids (> 5%). The 16S rRNA gene sequence of strain M216T exhibited high similarity to those of 'Marinobacter arenosus' CAU 1620T and Marinobacter adhaerens HP15T (99.3% and 98.5%, respectively) and less than 98.5% similarity to those of the other type strains. The ANI and dDDH values between the strain M216T and 'Marinobacter arenosus' CAU 1620T were 87.4% and 33.3%, respectively; these values were the highest among the other type strains but lower than the species threshold. The G+C content of strain M216T was 58.3%. Genomic analysis revealed that strain M216T harbors the major CAZymes of GH13, GH23, GH73, and PL5, which are responsible for polysaccharide degradation and the potential ability to reduce nitrate to ammonia. Through phenotypic, genotypic, and chemotaxonomic analyses, we proposed the name Marinobacter albus sp. nov., a novel species in the genus Marinobacter, with its type strain M216T (= MCCC 1K08600T = KCTC 82894T).
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Affiliation(s)
- Tai-Hang Deng
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Yu Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Wen-Wu Zhang
- Trend Biotech Co., Ltd., Hangzhou, 311121, People's Republic of China
| | - Yue Su
- Trend Biotech Co., Ltd., Hangzhou, 311121, People's Republic of China
| | - Jia-Wei Gao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Jun-Jie Ying
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Lin Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China
| | - Xiao-Ming Xia
- Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, 310012, People's Republic of China
| | - Cong Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China.
- Zhejiang Sci-Tech University Shaoxing Academy of Biomedicine Co., Ltd., Shaoxing, 312369, People's Republic of China.
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Limnobacter parvus sp. nov., a Thiosulfate-Oxidizing Bacterium Isolated from Lake Water. Curr Microbiol 2023; 80:39. [DOI: 10.1007/s00284-022-03128-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/20/2022] [Indexed: 12/23/2022]
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Xue JH, Zhang BN, Zhang F, Liu YY, Wu WJ, Wu ZM, Si Y, Yang PX, Xing X, Zhao LH. Comparative genomic analysis of the genus Marinomonas and taxonomic study of Marinomonas algarum sp. nov., isolated from red algae Gelidium amansii. Arch Microbiol 2022; 204:586. [PMID: 36048288 DOI: 10.1007/s00203-022-03215-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 07/27/2022] [Accepted: 08/22/2022] [Indexed: 11/02/2022]
Abstract
Members of the genus Marinomonas are known for their environmental adaptation and metabolically versatility, with abundant proteins associated with antifreeze, osmotic pressure resistance, carbohydrase and multiple secondary metabolites. Comparative genomic analysis focusing on secondary metabolites and orthologue proteins was conducted with 30 reference genome sequences in the genus Marinomonas. In this study, a Gram-stain-negative, rod-shaped, non-flagellated and strictly aerobic bacterium, designated as strain E8T, was isolated from the red algae (Gelidium amansii) in the coastal of Weihai, China. Optimal growth of the strain E8T was observed at temperatures 25-30 °C, pH 6.5-8.0 and 1-3% (w/v) NaCl. The DNA G + C content was 42.8 mol%. The predominant isoprenoid quinone was Q-8 and the major fatty acids were C16:0, summed feature 3 and summed feature 8. The major polar lipids were phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). Based on data obtained from this polyphasic taxonomic study, strain E8T should be considered as a novel species of the genus Marinomonas, for which the name Marinomonas algarum is proposed. The type strain is E8T (= KCTC 92201T = MCCC 1K07070T).
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Affiliation(s)
- Jian-Heng Xue
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Bei-Ning Zhang
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Feng Zhang
- Weihai Ecological and Environmental Monitoring Center (Weihai Motor Vehicle Emission Monitoring Center), Weihai, 264209, Shandong, People's Republic of China
| | - Ying-Ying Liu
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Wen-Jie Wu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Zhao-Ming Wu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Yue Si
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Peng-Xi Yang
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Xiang Xing
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.
| | - Li-Hua Zhao
- Marine College, Shandong University, Weihai, 264209, Shandong, People's Republic of China.
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Gao Y, Wei Y, Wang P. Marinomonas lutimaris sp. nov., isolated from a tidal flat sediment of the East China Sea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005368] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative bacterial strain, designated as E165T, was isolated from a tidal flat sediment of the East China Sea. Strain E165T grew optimally at pH 6, at 32 °C and with 1–2 % (w/v) NaCl. The 16S rRNA gene sequence similarity results revealed that strain E165T was most closely related to
Marinomonas rhizomae
IVIA-Po-145T,
Marinomonas polaris
CK13T,
Marinomonas foliarum
IVIA-Po-155T,
Marinomonas hwangdonensis
HDW-15T,
Marinomonas pontica
46-16T,
Marinomonas mangrovi
B20-1T and
Marinomonas shanghaiensis
DSL-35T with values of 97.0–98.5 %. The digital DNA–DNA hybridization and average nucleotide identity values between strain E165T and the reference strains were 21.9–34.3 % and 77.6–87.3 %, respectively. The DNA G+C content of the isolate was 42.9 mol%. Strain E165T contained Q-8 as the sole ubiquinone and C16 : 0, summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c) as the major fatty acids. The major polar lipids of strain E165T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, aminolipid and aminophospholipid. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, a novel species, Marinomonas lutimaris sp. nov., is proposed with E165T (=MCCC 1K06241T=KCTC 82809T) as the type strain.
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Affiliation(s)
- Yuxin Gao
- State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, PR China
| | - Yuli Wei
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, PR China
| | - Peng Wang
- State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, PR China
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Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM. Validation List no. 203. Int J Syst Evol Microbiol 2022; 72. [PMID: 35108178 DOI: 10.1099/ijsem.0.005167] [Citation(s) in RCA: 275] [Impact Index Per Article: 137.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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