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Xu L, Wei HM, Sun YN, Wu Q, Gao XY, Shen B, Sun JQ. Halomonas rhizosphaerae sp. nov. and Halomonas kalidii sp. nov., two novel moderate halophilic phenolic acid-degrading species isolated from saline soil. Syst Appl Microbiol 2024; 47:126488. [PMID: 38278082 DOI: 10.1016/j.syapm.2024.126488] [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] [Received: 09/18/2023] [Revised: 01/01/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024]
Abstract
Four vanillic acid-degrading bacterial strains, named LR5S13T, LR5S20, and M4R5S39T and LN1S58, were isolated from Kalidium cuspidatum rhizosphere and bulk soils, respectively. Phylogenetic analysis based on 16S rRNA gene as well as core genome revealed that LR5S13T and LR5S20 clustered closely with each other and with Halomonas ventosae Al12T, and that the two strains shared the highest similarities (both 99.3 %) with H. ventosae Al12T, in contrast, M4R5S39T and LN1S58 clustered together and with Halomonas heilongjiangensis 9-2T, and the two strains shared the highest similarities (99.4 and 99.2 %, respectively) with H. heilongjiangensis 9-2T. The average nucleotides identities based on BLAST (ANIb) and digital DNA-DNA hybridization (dDDH) values of strains LR5S13T to LR5S20, and M4R5S39T to LN1S58, were both higher than the threshold values for delineation of a species. The ANIb and dDDH values of the four strains to their closely relatives were lower than the threshold values. All four strains take phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids, Summed Feature 8, Summed Feature 3, and C16:0 as the major fatty acids. Based on the phylogenetic and phenotypic results, the four strains should be classified as two novel Halomonas species. Therefore, Halomonas rhizosphaerae sp. nov. (type strain LR5S13T = KCTC 8016T = CGMCC 1.62049T) and Halomonas kalidii (type strain M4R5S39T = KCTC 8015T = CGMCC 1.62047T) are proposed. The geographical distribution analysis based on 16S rRNA gene revealed that the two novel species are widely distributed across the globe, specifically in highly saline habits, especially in Central and Eastern Asia.
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Affiliation(s)
- Lian Xu
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China; Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Hua-Mei Wei
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Ye-Nan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Qi Wu
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Xiao-Yan Gao
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Biao Shen
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China.
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Ding WJ, Xu L, Zhao Y, Sun JQ. Aquibacillus rhizosphaerae sp. nov., an Indole Acetic Acid (IAA)-producing Halotolerant Bacterium Isolated from the Rhizosphere Soil of Kalidium cuspidatum. Curr Microbiol 2023; 80:404. [PMID: 37930394 DOI: 10.1007/s00284-023-03543-2] [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: 07/05/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
A bacterium (named strain LR5S19T) was isolated from the rhizosphere soil of the halophyte Kalidium cuspidatum in Baotou, Inner Mongolia, China. Strain LR5S19T was Gram-stain-positive, motile with a polar flagellum, rod shaped, and spore forming at the terminal position in swollen sporangia, and it grew at 10-40 ℃ (optimum 30 ℃), pH 6.0-9.0 (optimum pH 7.0), and in the presence of 1.0-15.0% (w/v) NaCl (optimum 2.0%). The phylogenetic analysis of the 16S rRNA gene showed that strain LR5S19T shared the highest similarity (96.7%) with A. koreensis JCM 12387T, followed by A. kalidii HU2P27T (96.2%), A. sediminis BH258T (96.1%), and 'A. salsiterrae' 3ASR75-54T (96.0%). The ANIb, AAI and dDDH values between strain LR5S19T and its closely related type strains were 69.3-73.8%, 65.4-72.4% and 19.2-20.3%, respectively. The major polar lipids in strain LR5S19T consisted of diphosphatidylglycerol, phosphatidylglycerol, and three unidentified phospholipids, while MK-7 was the major respiratory quinone. The major fatty acids of the strain were anteiso-C15:0 and iso-C15:0. Based on phylogenomic and phenotypic results, strain LR5S19T should be classified as a novel species within the genus Aquibacillus, for which Aquibacillus rhizosphaerae sp. nov. is proposed. The type strain is LR5S19T (= CGMCC 1.62028T = KCTC 43434T). The comparative genomic analysis revealed that all eight members of Aquibacillus could utilize D-glucose via the glycolysis-gluconeogenesis pathway or the pentose phosphate pathway and use the tricarboxylic acid cycle as the metabolic center. The potassium ion transport proteins and compatible solute synthesis pathways in all the members likely also help them cope with hypersaline environments.
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Affiliation(s)
- Wen-Jing Ding
- Laboratory for Microbial Resources, Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Lian Xu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yang Zhao
- Laboratory for Microbial Resources, Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, Department of Environmental Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China.
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Shang J, Xu L, Yang R, Zhao Y, Tang SK, Sun JQ. Halomonas alkalisoli sp. nov., a novel haloalkalophilic species from saline-alkaline soil, and reclassification of Halomonas daqingensis Wu et al. 2008 as a later heterotypic synonym of Halomonas desiderata Berendes et al. 1996. Syst Appl Microbiol 2022; 45:126351. [PMID: 35905572 DOI: 10.1016/j.syapm.2022.126351] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 10/17/2022]
Abstract
Two Gram-stain-negative, strictly aerobic, moderately halophilic, non-spore-forming and rod-shaped bacteria, designated M5N1S17T and M5N1S15, were isolated from saline soil in Baotou, China. A phylogenetic analysis based on 16S rRNA gene sequences showed that the two strains clustered closely with Halomonas montanilacus PYC7WT and shared 99.1 and 99.3% sequence similarities, respectively. The average nucleotide identity based on BLAST (ANIb) and MUMmer (ANIm) values of the two strains with each other were 95.5% and 96.7%, respectively, while the ANIb and ANIm values between the two strains and 15 closer Halomonas species were 74.8-91.3% and 84.1-92.6%, respectively. The major polar lipids of M5N1S17T are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and an unidentified phospholipid. The major polar lipids of M5N1S15 are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids, and an unidentified lipid. The predominant ubiquinone in the two strains is Q-9. The major fatty acids of the two strains are C18:1ω6c and/or C18:1ω7c, C16:0, and C16:1ω7c and/or C16:1ω6c. Based on phylogenetic, phenotypic, and physiological results, strains M5N1S17T and M5N1S15 should be identified as a novel species of the genus Halomonas, for which Halomonas alkalisoli sp. nov. is proposed. The type strain is M5N1S17T (= CGMCC 1.19023T = KCTC 92130T). The phylogenetic trees showed that Halomonas daqingensis CGMCC 1.6443T clustered tightly with Halomonas desiderata FB2T, and the two strains shared >98.0% of ANI values with each other. Therefore, we propose the reclassification of H. daqingensis Wu et al. 2008 as a later heterotypic synonym of H. desiderata Berendes et al. 1996.
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Affiliation(s)
- Jia Shang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Lian Xu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Rui Yang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Yang Zhao
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Shu-Kun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, and Key Laboratory for Microbial Resources of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming 650091, PR China.
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China.
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Xu L, Shang J, Tian J, Sun JQ, Shen B. Ruania suaedae sp. nov. and Ruania halotolerans sp. nov., two actinobacteria isolated from saline soil, and reclassification of Haloactinobacterium kanbiaonis as Occultella kanbiaonis comb. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005443] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-positive, non-motile, strictly aerobic, yellow-coloured, rod-shaped bacterial strains, designated LR1S40T and M4N3S171T, were isolated from rhizosphere and bulk saline soil of Suaeda salsa collected in Inner Mongolia, China. Phylogenetic trees based on 16S rRNA gene and whole genome sequences showed that the two strains clustered tightly with strains of the genus
Ruania
. Strains LR1S40T and M4N3S171T had 95.5% 16S rRNA gene similarity to each other, and strain LR1S40T had 98.8, 98.7, 97.4 and <97.0% similarity to
Ruania alkalisoli
RN3S43T,
Ruania rhizosphaerae
LNNU 22110T,
Ruania alba
YIM 93306T and all other current type strains, while strain M4N3S171T had 98.6 and <97.0% similarity to
R. alba
YIM 93306T, and all other current type strains, respectively. The average nucleotide identity based on blast (ANIb) and digital DNA–DNA hybridization (dDDH) values of LR1S40T and M4N3S171T with each other and to the other type strains of
Ruania
were well below the threshold values (95% for ANIb, 70% for dDDH) for differentiating a species. Diphosphatidylglycerol and phosphatidylglycerol were the major polar lipids in both strains. The predominant menaquinone in both strains was both MK-8. The genome of strain LR1S40T consisted of a 3557440 bp circular chromosome, with a G+C content of 71.1 mol%, while the genome of strain M4N3S171T consisted of 4270413 bp, with a G+C content of 67.6 mol%. The phylogenetic, physiological and phenotypic characteristics allowed discrimination of the two strains from their relatives. The names Ruania suaedae sp. nov. [type strain LR1S40T (=CGMCC 1.19028T=KCTC 49726T)] and Ruania halotolerans sp. nov. [type strain M4N3S171T (=CGMCC 1. 19142T=KCTC 49727T)] are therefore proposed. During the publication of
Haloactinobacterium kanbiaonis
,
Haloactinobacterium glacieicola
(type strain T3246-1T), which was selected as the reference strain for the identification of
H. kanbiaonis
, was reclassified as
Occultella glacieicola
. The two phylogenetic trees showed that
H. kanbiaonis
HY164T tightly clustered with
Occultella aeris
F300T, and had the highest 16S rRNA gene similarity (99.8%) to
O. aeris
F300T. Based on the phylogenetic analysis and the publication record,
Haloactinobacterium kanbiaonis
should be reclassified as Occultella kanbiaonis comb. nov.
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Affiliation(s)
- Lian Xu
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Jia Shang
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Jing Tian
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Biao Shen
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, PR China
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Huang XX, Xu L, Shang J, Sun JQ. Marinilactibacillus kalidii sp. nov., an Indole Acetic Acid-Producing Endophyte Isolated from a Shoot of Halophyte Kalidium cuspidatum. Curr Microbiol 2022; 79:198. [PMID: 35595934 DOI: 10.1007/s00284-022-02894-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 05/03/2022] [Indexed: 12/01/2022]
Abstract
A Gram-stain-positive, facultatively anaerobic, non-sporulating, motile with single polar flagellum, rod-shaped, indole-3-acetic acid (IAA)-producing bacterium, named M4U5P12T, was isolated from a shoot of Kalidium cuspidatum, Inner Mongolia, China. Strain M4U5P12T grew at pH 6.0-11.0 (optimum 7.5), 4-40 °C (optimum 25 °C), and in the presence of 0-15% (w/v) NaCl (optimum 4%). Positive for catalase, urease, methyl red (M.R.) reaction, and hydrolysis of starch; and negative for oxidase, Voges-Proskauer (V-P) test, and hydrolysis of cellulose. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequences both revealed that it clustered with Marinilactibacillus piezotolerans JCM 12337T (99.3%) and Marinilactibacillus psychrotolerans M13-2T (99.1%). The dDDH and ANIb values of strain M4U5P12T to M. piezotolerans DSM 16108T and M. psychrotolerans M13-2T were 19.3 and 18.9%, and 74.3 and 74.0%, respectively. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, and two unidentified lipids. The major fatty acids were C16:0, C18:1 ω9c, C16:1 ω9c, and C15:1 ω5c. The genomic DNA G + C content was 37.3%. On the basis of physiological, phenotypic, and phylogenetic characteristics, strain M4U5P12T should be classified as a novel species. Therefore, Marinilactibacillus kalidii sp. nov. is proposed, and the type strain is M4U5P12T (= CGMCC 1.17696T = KCTC 43247T).
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Affiliation(s)
- Xiao-Xian Huang
- Laboratory for Microbial Resources, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, People's Republic of China
| | - Lian Xu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Jia Shang
- Laboratory for Microbial Resources, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, People's Republic of China
| | - Ji-Quan Sun
- Laboratory for Microbial Resources, Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, People's Republic of China.
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Comparative genome characterization of Echinicola marina sp. nov., isolated from deep-sea sediment provide insight into carotenoid biosynthetic gene cluster evolution. Sci Rep 2021; 11:24188. [PMID: 34921217 PMCID: PMC8683446 DOI: 10.1038/s41598-021-03683-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/02/2021] [Indexed: 11/23/2022] Open
Abstract
Echinicola, carotenoid-pigmented bacteria, are isolated from various hypersaline environments. Carotenoid accumulation in response to salt stress can stabilize the cell membrane in order to survive. A pink-colored strain SCS 3-6 was isolated from the deep-sea sediment of the South China Sea. Growth was found to occur at 10-45 °C. The strain could tolerate 10% (w/v) NaCl concentration and grow at pH 5-9. The complete genome of SCS 3-6 comprises 5053 putative genes with a total 5,693,670 bp and an average G + C content of 40.11 mol%. The 16S rRNA gene sequence analysis indicated that strain SCS 3-6 was affiliated with the genus Echinicola, with the closely strains were Echinicola arenosa CAU 1574T (98.29%)and Echinicola shivajiensis AK12T (97.98%). For Echinicola species with available genome sequences, pairwise comparisons for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) revealed ANIb values from 70.77 to 74.71%, ANIm values from 82.72 to 88.88%, and DDH values from 18.00 to 23.40%. To identify their genomic features, we compared their genomes with those of other Echinicola species. Phylogenetic analysis showed that strain SCS 3-6 formed a monophyletic clade. Genomic analysis revealed that strain SCS 3-6 possessed a complete synthetic pathway of carotenoid and speculated that the production was astaxanthin. Based on phenotypic and genotypic analyses in this study, strain SCS 3-6 is considered to represent a novel species of the genus Echinicola for which the name Echinicola marina sp. nov. is proposed. The type strain is SCS 3-6T (= GDMCC 1.2220T = JCM 34403T).
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Huang XX, Xu L, Sun JQ. Gracilibacillus suaedae sp. nov., an indole acetic acid-producing endophyte isolated from a root of Suaeda salsa. Int J Syst Evol Microbiol 2021; 71. [PMID: 34878379 DOI: 10.1099/ijsem.0.005140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, facultatively anaerobic, spore-forming, motile with unipolar biflagella, rod-shaped, indole acetic acid-producing bacterium, named LD4P30T, was isolated from a root of Suaeda salsa collected in Inner Mongolia, northern China. Strain LD4P30T grew at pH 6.0-11.0 (optimum, pH 7.0), 10-40 °C (35 °C) and in the presence of 1-15% (w/v) NaCl (5%). The strain was positive for oxidase and negative for catalase. The major cellular fatty acids of strain LD4P30T were iso-C15:0, C15:1 ω5c and anteiso-C15:0; the major polar lipids were diphosphatidylglycerol and phosphatidylglycerol; and menaquinone-7 was the only respiratory quinone. The genomic DNA G+C content was 36.7 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain LD4P30T clustered with Gracilibacillus thailandensis TP2-8T, Gracilibacillus saliphilus YIM 91119T and Gracilibacillus lacisalsi BH312T, and showed 99.0, 98.9, 98.0 and <97.7% 16S rRNA gene similarity to G. thailandensis TP2-8T, G. saliphilus YIM 91119T, G. lacisalsi BH312T and all other current type strains, respectively. The digital DNA-DNA hybridization and average nucleotide identity based on blast values between strain LD4P30T and G. saliphilus YIM 91119T, G. thailandensis TP2-8T and G. lacisalsi BH312T were 44.9, 44.7 and 44.4%, and 91.1, 91.0 and 90.8%, respectively. Based on its phenotypic, physiological and phylogenetic characteristics, strain LD4P30T represents a novel species, for which the name Gracilibacillus suaedae is proposed. The type strain is LD4P30T (=CGMCC 1.17697T=KCTC 82375T).
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Affiliation(s)
- Xiao-Xian Huang
- Lab for Microbial Resources, Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Ji-Quan Sun
- Lab for Microbial Resources, Inner Mongolia Key Laboratory of Environmental Pollution Prevention and Waste Resource Recycle & Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, PR China
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Baek J, Weerawongwiwat V, Kim JH, Yoon JH, Lee JS, Sukhoom A, Kim W. Echinicola arenosa sp. nov., isolated from marine sand. Arch Microbiol 2021; 203:5675-5681. [PMID: 34463811 DOI: 10.1007/s00203-021-02553-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 12/29/2022]
Abstract
A novel bacterium, designated CAU 1574T, was isolated from marine sand. Cells were Gram stain negative, aerobic, gliding and rod shaped. Growth was observed at 20-37 °C (optimum, 30 °C), a pH of 5.5-10.0 (optimum, 8.0), and 0-3.0% (w/v) NaCl concentrations (optimum, 1%). Based on the results of 16S rRNA gene sequence analyses, strain CAU 1574T belonged to the genus Echinicola, and showed the highest similarity to Echinicola shivajiensis JCM 17847T (97.5%). Phylogenomic analysis based on consisting of 92 core genes extracted from the genome sequences showed that strain CAU 1574T was affiliated with species in the genus Echinicola. The average nucleotide identity (ANI), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values between strain CAU 1574T and the closely related species were below the cut-off values of 95-96, 90, and 70%, respectively used for species demarcation. The chemotaxonomic data of CAU 1574T were as follows: major isoprenoid quinone, MK-7; predominant polar lipids, phosphatidylethanolamine, two unidentified aminophospholipids and two unidentified lipids; major fatty acids, iso-C15:0, summed feature 3 (C16:1 ω6c/C16:1 ω7c). The 5.4 Mb genome included 20 contigs and 4237 protein-coding genes with a 39.8 mol% G + C content. Based on the phylogenetic, phenotypic, and physiological result, strain CAU 1574T represents a novel species of this genus Echinicola, for which the name Echinicola arenosa sp. nov. is proposed. The type strain is CAU 1574T (= KCTC 82410T = MCCC 1K05669T).
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Affiliation(s)
- Jihye Baek
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Veeraya Weerawongwiwat
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jong-Hwa Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Jung-Sook Lee
- Korea Research Institute of Bioscience and Biotechnology, Korean Collection for Type Cultures, Jeongeup, Republic of Korea
| | - Ampaitip Sukhoom
- Faculty of Science, Division of Biological Science, Prince of Songkla University, Songkhla, Thailand
| | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, Seoul, Republic of Korea.
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Echinicola salinicaeni sp. nov., a novel bacterium isolated from saltern mud. Antonie van Leeuwenhoek 2021; 114:1915-1924. [PMID: 34480253 DOI: 10.1007/s10482-021-01650-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
A novel gram-negative, aerobic, pink, motile, gliding, rod-shaped bacterium, designated P51T, was isolated from saline silt samples in Yantai, China. It was able to grow at 4-42 °C (optimum 33 °C), pH 4.0-9.0 (optimum 7.0), and in 0-11.0% NaCl (optimum 4.0%, w/v). It grew at 4 °C, which was lower than the minimum temperature for related strains. The genome consisted of 4111 genes with a total length of 5 139 782 bp. The 16S rRNA gene sequence analysis indicated that strain P51T was a member of the genus Echinicola and most closely related to 'Echinicola shivajiensis'. A genome analysis identified genes encoding proteins associated with carbon source utilisation, and the carotenoid biosynthesis and β-lactam resistance pathways. Strain P51T shared an average nucleotide identity value below 84.7%, an average amino acid identity value between 70.8 and 89.3%, and a digital DNA-DNA hybridisation identity of between 17.9-28.2% with closely related type strains within the genus Echinicola. The sole menaquinone was MK-7, and the major fatty acids were iso-C15:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c), summed feature 4 (anteiso-C17:1 B and/or iso-C17:1 I), and summed feature 9 (iso-C17:1ω9c and/or 10-methyl C16:0). The polar lipids included one phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, three unidentified aminolipids, and one unknown lipid. The phenotypic, chemotaxonomic, and phylogenetic analyses suggest that strain P51T is a novel species of the genus Echinicola, for which the name Echinicola salinicaeni sp. nov. is proposed. The type strain was P51T (KCTC 82513T = MCCC 1K04413T).
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Song L, Liu H, Huang Y, Dai X, Zhou Y. Pararhodonellum marinum gen. nov., sp. nov., isolated from deep-sea sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 34427552 DOI: 10.1099/ijsem.0.004966] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, non-motile bacterial strain, designated SW124T, was isolated from a deep-sea sediment sample collected from the Indian Ocean. SW124T was aerobic and catalase-positive. The strain grew at 4-40 °C (optimum, 30 °C), at pH 5.0-8.6 (optimum, pH 7.0) and in the presence of 0.5-9.5 % (w/v) NaCl (optimum, 3.0%). The results of comparative analyses of the 16S rRNA gene sequence indicated that SW124T was grouped in the vicinity of the genus Rhodonellum in the family Cyclobacteriaceae. The quinone system contained menaquinone MK-7. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). SW124T contained phosphatidylethanolamine (PE) as the major polar lipid. The genomic DNA G+C content of SW124T was 41.7 mol%. On the basis of its phenotypic characteristics and phylogenetic data, we propose that strain SW124T (=CGMCC 1.16171T=KCTC 82235T) represents a novel species of a novel genus, with the name Pararhodonellum marinum gen. nov., sp. nov.
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Affiliation(s)
- Lei Song
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hongcan Liu
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Yuguang Zhou
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
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Sun JQ, Yiayeng PE, Xu L, Huang XX, Li Y. Ruania alkalisoli sp. nov., Isolated from Saline-Alkaline Soil. Curr Microbiol 2021; 78:3285-3291. [PMID: 34164698 DOI: 10.1007/s00284-021-02579-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 06/15/2021] [Indexed: 11/29/2022]
Abstract
A Gram-positive, strictly aerobic, ivory-colored, rod-shaped bacterial strain, designated RN3S43T, was isolated from saline-alkaline soil, in Tumd Right Banner, Inner Mongolia, China. Strain RN3S43T grew at 10-40 °C (optimum 30 °C), pH 6.0-10.0 (optimum pH 9.0), and 0-12.5% NaCl (optimum 2-4%). It was positive to oxidase, catalase, urease, and nitrate reductase. The methyl red and Voges-Proskauer tests were negative. The phylogenetic trees based on the 16S rRNA gene sequences and genome both showed that strain RN3S43T clustered with Ruania alba YIM 93306 T and shared 95.5% and < 95.0% of 16S rRNA gene similarities with R. alba YIM 93306 T and all the other type strains. MK-8 was the major respiratory quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and an unidentified lipid were the major polar lipids. The major fatty acids were anteiso-C15:0 and iso-C15:0. The genome consisted of a 4,448,708-bp circular chromosome, with a G+C content of 68.2%, predicting 3,911 coding sequence genes, 44 tRNA genes and two rRNA operons. The average nucleotide identity (ANI), amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) values of strain RN3S43T to R. alba YIM 93306T were 79.0%, 79.2%, and 23.4%, respectively. The results of phylogenetic, physiological, and phenotypic tests allowed the discrimination of strain RN3S43T from its phylogenetic relatives. Ruania alkalisoli sp. nov. is therefore proposed, and the type strain is RN3S43T (=CGMCC 1.18652T = KCTC 49471T).
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Affiliation(s)
- Ji-Quan Sun
- Department of Environment Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China.
| | - Pa Eryang Yiayeng
- Department of Environment Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao-Xian Huang
- Department of Environment Engineering, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010021, PR China
| | - Yan Li
- Institute of Environment and Ecology & Institute of Environmental Health and Ecological Security, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
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