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Feng CY, He HH, Li S, Zheng ZH, Mo YJ, Lian WH, Lu CY, Zhang DY, Li WJ, Dong L. Desertibaculum subflavum gen. nov., sp. nov., a novel member of the family Sneathiellaceae isolated from the Kumtag Desert soil. Antonie Van Leeuwenhoek 2024; 117:108. [PMID: 39080041 DOI: 10.1007/s10482-024-02003-6] [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] [Accepted: 07/15/2024] [Indexed: 10/16/2024]
Abstract
A novel rod-shaped bacterium, designated as strain SYSU D60015T that formed yellowish colonies was isolated from a sandy soil collected from the Kumtag Desert in Xinjiang, China. Cells were Gram-stain-negative, oxidase-positive, catalase-negative and motile with a single polar flagellum. Growth optimum occurred between 28 and 37 °C, pH 7.0 and with 0-0.5% (W/V) NaCl. The predominant cellular fatty acids (> 5%) were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C19:0 cyclo ω8c, C18:1 ω7c 11-methyl and C16:0. The polar lipid profile contained one phosphatidylethanolamine, one diphosphatidylglycerol, one phosphatidylglycerol, one unidentified phospholipid, three unidentified aminolipids, two unidentified aminophospholipids and seven unidentified lipids. The only respiratory quinone was ubiquinone-10. Based on 16S rRNA gene sequence phylogenetic analysis, strain SYSU D60015T was found to form a distinct linage within the family Sneathiellaceae, and had 16S rRNA gene sequence similarities of 90.8% to Taonella mepensis H1T, and 90.2% to Ferrovibrio denitrificans S3T. The genome of SYSU D60015T was 5.66 Mb in size with 68.2% of DNA G + C content. The low digital DNA-DNA hybridization (dDDH, 18.0%), average nucleotide identity (ANI, 77.5%) and amino acid identity (AAI, 56.0%) values between SYSU D60015T and Ferrovibrio terrae K5T indicated that SYSU D60015T might represent a distinct genus. Based on the phylogenetic, phenotypic, chemotaxonomic and genomic data, we propose Desertibaculum subflavum gen. nov., sp. nov. as a novel species of a new genus within the family Sneathiellaceae. The type strain is SYSU D60015T (= NBRC 112952T = CGMCC 1.16256T).
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Affiliation(s)
- Chu-Ying Feng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Huan-Huan He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China
| | - Zhuo-Huan Zheng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Yi-Jun Mo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Wen-Hui Lian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Chun-Yan Lu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
| | - Dong-Ya Zhang
- Microbiome Research Center, Moon (Guangzhou) BiotechLtd., Guangzhou, 510700, People's Republic of China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Key Laboratory of Biodiversity Conservation and Application in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, People's Republic of China.
| | - Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China.
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So Y, Chhetri G, Kim I, Kim J, Park S, Jung Y, Seo T. Neoroseomonas alba sp. nov., Neoroseomonas nitratireducens sp. nov., Paraoseomonas indoligenes sp. nov and Paraoseomonas baculiformis sp. nov., isolated from the rhizosphere of paddy soil. Antonie Van Leeuwenhoek 2023; 116:1009-1022. [PMID: 37587352 DOI: 10.1007/s10482-023-01863-8] [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: 11/10/2022] [Accepted: 07/27/2023] [Indexed: 08/18/2023]
Abstract
Four novel Gram-stain negative bacteria, designated as HAJ6T, PWR1T, SG15T and SSH11T, were isolated from the soil sample of paddy fields from Goyang in the Republic of Korea. The isolated strains were aerobic, short-rod or rod shaped, non-sporulating. They grew optimally at 30 °C, pH 7 and without additional NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that they belong to the genus of Neoroseomonas and Pararoseomonas and closely relate to Neoroseomonas terrae DS-48T (97.5%; HJA6T), Neoroseomonas rubea MO17T (99.4%; PWR1T), Pararoseomonas pecuniae N75T (97.3%; SG15T) and Pararoseomonas rosea 173-96T (97.8%; SSH11T). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of the isolates with the most closely related strains were 72.9-90.9% and 19.1-42.5%, respectively. The major fatty acids in the isolates were C16:0, C19:0 cyclo ω8c, C18:1 2-OH and summed feature 8 (composed of C18:1 ω7c and/or C18:1 ω6c), and the predominant quinone was ubiquinone 10. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and other unidentified polar lipids. Based on the draft genome sequences, the genomic DNA G + C content of HAJ6T, PWR1T, SG15T and SSH11T were 69.5%, 72.0%, 70.8% and 69.7%, respectively. All isolates produced indole-3-acetic acid (IAA), a type of plant growth hormone in the presence of L-tryptophan. Physiological and biochemical tests and 16S rRNA sequence analysis clearly revealed that the isolates were novel species belonging to the genus Neoroseomonas and Pararoseomonas. Their proposed names were as follows: Neoroseomonas alba sp. nov. for strain HJA6T (= KACC 21545T = NBRC 114316T), Neoroseomonas nitratireducens sp. nov. for strain PWR1T (= KCTC 82687T = NBRC 114490T), Pararoseomonas indoligenes sp. nov. for strain SG15T (= KCTC 82686T = NBRC 114481T) and Paraoseomonas baculiformis sp. nov. for strain SSH11T (= KCTC 82685T = NBRC 11482T).
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Affiliation(s)
- Yoonseop So
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Jiyoun Kim
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Sunho Park
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University Seoul, Goyang, 10326, South Korea.
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3
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Jiang ZM, Deng Y, Han XF, Su J, Wang H, Yu LY, Zhang YQ. Geminicoccus flavidas sp. nov. and Geminicoccus harenae sp. nov., two IAA-producing novel rare bacterial species inhabiting desert biological soil crusts. Front Microbiol 2022; 13:1034816. [PMID: 36386637 PMCID: PMC9659566 DOI: 10.3389/fmicb.2022.1034816] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/05/2022] [Indexed: 11/28/2022] Open
Abstract
Two Gram-staining negative strains (CPCC 101082T and CPCC 101083T) were isolated from biological sandy soil crusts samples collected from Badain Jaran desert, China. Both isolates were heterotrophic phototroph, could produce indole-3-acetic acid. The 16S rRNA gene sequences of these two strains were closely related to the members of the family Geminicoccaceae, showing high similarities with Geminicoccus roseus DSM 18922T (96.9%) and Arboricoccus pini B29T1T (90.1%), respectively. In phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 101082T and CPCC 101083T formed a robust distinct clade with Geminicoccus roseus DSM 18922T within the family Geminicoccaceae, which indicated that these two isolates could be classified into the genus Geminicoccus. The growth of strain CPCC 101082T occurred at 15-42°C and pH 4.0-10.0 (optima at 28-37°C and pH 6.0-8.0). The growth of strain CPCC 101083T occurred at 4-45°C and pH 4.0-10.0 (optima at 25-30°C and pH 6.0-8.0). The major cellular fatty acids of CPCC 101082T and CPCC 101083T contained C18:1 ω7c/C18:1 ω6c, cyclo-C19:0 ω8c, and C16:0. Q-10 was detected as the sole respiratory quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified phospholipid and an unidentified aminolipid were tested in the polar lipids profile. The genomes of the two isolates were characterized as about 5.9 Mbp in size with the G + C content of nearly 68%. The IAA-producing encoding genes were predicated in both genomes. The values of average nucleotide identity were 80.6, 81.2 and 92.4% based on a pairwise comparison of the genomes of strains CPCC 101082T and CPCC 101083T and Geminicoccus roseus DSM 18922T, respectively. On the basis of the genotypic, chemotaxonomic and phenotypic characteristics, the strains CPCC 101082T (=NBRC 113513T = KCTC 62853T) and CPCC 101083T (=NBRC 113514T = KCTC 62854T) are proposed to represent two novel species of the genus Geminicoccus with the names Geminicoccus flavidas sp. nov. and Geminicoccus harenae sp. nov.
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Affiliation(s)
- Zhu-Ming Jiang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Dao-di Herb, Beijing, China
| | - Yang Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Dao-di Herb, Beijing, China
| | - Xue-Fei Han
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Dao-di Herb, Beijing, China
| | - Jing Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Hao Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Dao-di Herb, Beijing, China
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Roseomonas rosulenta sp. nov., isolated from rice paddy soil. Arch Microbiol 2022; 204:445. [PMID: 35778570 DOI: 10.1007/s00203-022-03014-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/22/2022] [Indexed: 11/02/2022]
Abstract
Three bacterial isolates, Gram-stain-negative, non-motile, coccobacilli-shaped bacteria, strains OP-27T, OP-5 and OP-30, were isolated from rice paddy soil. Phylogenetic analyses based on 16S rRNA gene sequences revealed that three isolates belonged to the genus Roseomonas, showing the highest sequence similarities to Roseomonas sediminicola FW-3T (98.1%) and Roseomonas lacus TH-G33T (98.0%). The genome size of strain OP-27T was 5.2 Mb in a single contig with DNA G+C content of 71.2%. The genome included 5164 predicted protein-coding genes, as well as 48 tRNA, 4 rRNA and 4 mRNA genes. The average nucleotide identity value between strain OP-27T and type strains of related species of the genus Roseomonas were 81.1-83.1%, and the digital DNA-DNA hybridization values of strain OP-27T and the related strains were 24.6-26.8%, respectively. The DNA-DNA hybridization values between strains OP-27T, OP-5 and OP-30 were 84-100% and its closest relative, Roseomonas sediminicola KACC 16616T was 21.1%. The major fatty acids were C18:1 ω7c, C18:1 2-OH and C16:0 and predominant quinone was Q-10. Based on its distinctive phenotypic, phylogenetic, and chemotaxonomic characteristics, the three strains are considered to represent novel species of the genus Roseomonas, for which the name Roseomonas rosulenta sp. nov. is proposed. The type strain is OP-27T (=KACC 21501T= NBRC 114497T).
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Lee HJ, Whang KS. Roseomonas rubea sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005251] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three pale-red-pigmented, Gram-stain-negative, coccobacilli-shaped, motile and strictly aerobic bacteria, strains MO17T, MO41 and NPKOSM1, were isolated from rice paddy soil. Colonies were circular with entire edges, convex and pale red. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains MO17T, MO41 and NPKOSM1 belonged to the genus
Roseomonas
and were closely related to
Roseomonas sediminicola
FW-3T (98.2 %),
Roseomonas oryzicola
YC6724T (98.0 %),
Roseomonas soli
5N26T (98.0 %),
Roseomonas eburnea
BUT-5T (97.8 %),
Roseomonas alkaliterrae
YIM 78007T (97.7 %),
Roseomonas lacus
TH-G33T (97.6 %) and
Roseomonas terrae
DS-48T (96.8 %). The DNA–DNA hybridization values between strains MO17T, MO41 and NPKOSM1 were 84–92 %, and the values between the three strains and their close phylogenetic relatives were also below 70 %. The major cellular fatty acids were C18 : 1
ω7c, C16 : 0 and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2OH). The predominant respiratory quinone was identified as Q-10. The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and two unknown phospholipids. Based on their distinctive phenotypic, phylogenetic and chemotaxonomic characteristics, the three strains are considered to represent novel species of the genus
Roseomonas
for which the name Roseomonas rubea sp. nov. is proposed. The type strain is MO17T (=KACC 19933T=NBRC 114495T).
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Affiliation(s)
- Hyo-Jin Lee
- Department of Microbial Biotechnology, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
- Department of Microbial Biotechnology, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
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Rai A, Jagadeeshwari U, Deepshikha G, Smita N, Sasikala C, Ramana CV. Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera. Front Microbiol 2021; 12:677842. [PMID: 34484138 PMCID: PMC8414978 DOI: 10.3389/fmicb.2021.677842] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/08/2021] [Indexed: 01/10/2023] Open
Abstract
The genus Roseomonas is a significant group of bacteria which is invariably of great clinical and ecological importance. Previous studies have shown that the genus Roseomonas is polyphyletic in nature. Our present study focused on generating a lucid understanding of the phylogenetic framework for the re-evaluation and reclassification of the genus Roseomonas. Phylogenetic studies based on the 16S rRNA gene and 92 concatenated genes suggested that the genus is heterogeneous, forming seven major groups. Existing Roseomonas species were subjected to an array of genomic, phenotypic, and chemotaxonomic analyses in order to resolve the heterogeneity. Genomic similarity indices (dDDH and ANI) indicated that the members were well-defined at the species level. The Percentage of Conserved Proteins (POCP) and the average Amino Acid Identity (AAI) values between the groups of the genus Roseomonas and other interspersing members of the family Acetobacteraceae were below 65 and 70%, respectively. The pan-genome evaluation depicted that the pan-genome was an open type and the members shared 958 core genes. This claim of reclassification was equally supported by the phenotypic and chemotaxonomic differences between the groups. Thus, in this study, we propose to re-evaluate and reclassify the genus Roseomonas and propose six novel genera as Pararoseomonas gen. nov., Falsiroseomonas gen. nov., Paeniroseomonas gen. nov., Plastoroseomonas gen. nov., Neoroseomonas gen. nov., and Pseudoroseomonas gen. nov.
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Affiliation(s)
- Anusha Rai
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Uppada Jagadeeshwari
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology (IST), Jawaharlal Nehru Technological (JNT) University Hyderabad, Hyderabad, India
| | - Gupta Deepshikha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Nandardhane Smita
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology (IST), Jawaharlal Nehru Technological (JNT) University Hyderabad, Hyderabad, India
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Rat A, Naranjo HD, Lebbe L, Cnockaert M, Krigas N, Grigoriadou K, Maloupa E, Willems A. Roseomonas hellenica sp. nov., isolated from roots of wild-growing Alkanna tinctoria. Syst Appl Microbiol 2021; 44:126206. [PMID: 33945925 DOI: 10.1016/j.syapm.2021.126206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 11/26/2022]
Abstract
Two Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacterial strains (LMG 31523T and LMG 31524) were isolated from roots of wild-growing Alkanna tinctoria plants collected near Thessaloniki, Greece. Analysis of their 16S rRNA gene sequences revealed that they form a separate cluster related to the genus Roseomonas. A comparative whole genome analysis of the two strains and the type strains of related Roseomonas species revealed average nucleotide identity values from 78.84 and 80.32%. The G + C contents of the genomic DNA of strains LMG 31523T and LMG 31524 were 69.69% and 69.74%, respectively. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that the strains LMG 31523T and LMG 31524 represent a novel species of the genus Roseomonas. Genome analysis of the new strains showed a number of genes involved in survival in the rhizosphere environment and in plant colonization and confirmed the endophytic characteristics of LMG 31523T and LMG 31524. Since the strains LMG 31523T and LMG 31524 were isolated from a plant collected in Greece the name Roseomonas hellenica sp. nov. is proposed. The type strain is LMG 31523T (=CECT 30032T).
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Affiliation(s)
- Angélique Rat
- Laboratory of Microbiology, Dept. Biochemistry and Microbiology, Fac. Sciences, Ghent University, Gent, Belgium
| | - Henry D Naranjo
- Laboratory of Microbiology, Dept. Biochemistry and Microbiology, Fac. Sciences, Ghent University, Gent, Belgium
| | - Liesbeth Lebbe
- Laboratory of Microbiology, Dept. Biochemistry and Microbiology, Fac. Sciences, Ghent University, Gent, Belgium
| | - Margo Cnockaert
- Laboratory of Microbiology, Dept. Biochemistry and Microbiology, Fac. Sciences, Ghent University, Gent, Belgium
| | - Nikos Krigas
- Laboratory of Conservation and Evaluation of Native and Floricultural Species, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | - Katerina Grigoriadou
- Laboratory of Conservation and Evaluation of Native and Floricultural Species, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | - Eleni Maloupa
- Laboratory of Conservation and Evaluation of Native and Floricultural Species, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization Demeter, Thessaloniki, Greece
| | - Anne Willems
- Laboratory of Microbiology, Dept. Biochemistry and Microbiology, Fac. Sciences, Ghent University, Gent, Belgium
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Zhao LL, Deng Y, Sun Y, Liu HY, Yu LY, Zhang YQ. Roseomonas vastitatis sp. nov. isolated from Badain Jaran desert in China. Int J Syst Evol Microbiol 2019; 70:1186-1191. [PMID: 31860433 DOI: 10.1099/ijsem.0.003898] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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, coccobacillus-shaped bacterium, designated CPCC 101021T, was isolated from a sandy soil sample collected from Badain Jaran desert, China. Its 16S rRNA gene sequence was closely related to those of members of the genus Roseomonas, showing high similarities with Roseomonas hibiscisoli THG-N2.22T (98.0 %), Roseomonas oryzae KCTC 42542T (97.9 %), Roseomonas rhizosphaerae YW11T (97.9 %) and Roseomonas suffusca S1T (97.8 %). In the phylogenetic tree based on 16S rRNA gene sequences, strain CPCC 101021T formed a distinct subclade with R. oryzae KCTC 42542T within the genus Roseomonas. Growth of the isolate occurred at 15-37 °C and pH 6.0-8.5, with optimal growth at 30 °C and pH 7.0. The major cellular fatty acids were C18 : 1ω7c, summed feature 8 (C16 : 1ω7c/C16 : 1ω6c), summed feature 3 (C16 : 1ω6c/C16 : 1ω7c) and C16 : 0ω6c. Q-10 was detected as the main component in the respiratory quinone system, with Q-9 as a minor component. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid and an unidentified glycolipid were found in the polar lipid profile. The genomic DNA G+C content was 68.7 mol%. The average nucleotide identity was 84.6 % when comparing the draft genome sequences of strain CPCC 101021T with R. oryzae KCTC 42542T. On the basis of genotypic, chemotaxonomic and phenotypic characteristics, strain CPCC 101021T is proposed to represent a novel species of the genus Roseomonas with the name Roseomonas vastitatis sp. nov. Strain CPCC 101021T (=J1A743T=KCTC 62043T) is the type strain of the species.
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Affiliation(s)
- Li-Li Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Yang Deng
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Ye Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Hong-Yu Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
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9
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Jiao S, Wang J, Wei G, Chen W, Lu Y. Dominant role of abundant rather than rare bacterial taxa in maintaining agro-soil microbiomes under environmental disturbances. CHEMOSPHERE 2019; 235:248-259. [PMID: 31260865 DOI: 10.1016/j.chemosphere.2019.06.174] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 06/19/2019] [Accepted: 06/23/2019] [Indexed: 06/09/2023]
Abstract
Elucidating the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances is essential for understanding the biodiversity-stability relationship and maintaining microbial diversity. Here, we explored the response patterns of abundant and rare bacterial taxa to disturbances by invasive plant growth and oil contamination in agricultural soils across a large spatial scale (latitude gradient = 18.62°-46.51°). Our meta-analysis based on existing Illumina sequencing datasets showed that abundant taxa persisted under the disturbances whereas rare taxa were more easily affected, indicating the higher resilience or resistance of abundant taxa to disturbances. The responses of abundant taxa were associated with mean annual temperature at the sampling sites, while rare taxa instead showed stochastic responses. There were significantly negative linear regressions between bacterial α-diversity and community dissimilarities (disturbed vs. undisturbed soils), suggesting stronger resilience or resistance in those bacterial communities with higher α-diversity. This resilience or resistance was mainly associated with the α-diversity of abundant taxa. Our network analysis showed that the disturbances substantially decreased the strength of the connections, loosened the co-occurrence relationships, and reshaped the complex bacterial interactions. In the undisturbed soils, abundant taxa were located in central positions within the network more often than were rare taxa, while these trends were reversed in the disturbed soils. Our results suggest that abundant taxa play a dominant role in the stability and maintenance of agro-soil bacterial communities, while rare taxa could greatly influence local bacterial interactions under environmental disturbances.
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Affiliation(s)
- Shuo Jiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Junman Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weimin Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
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Fang XM, Bai JL, Zhang DW, Su J, Zhao LL, Liu HY, Zhang YQ, Yu LY. Roseomonas globiformis sp. nov., an airborne bacteria isolated from an urban area of Beijing. Int J Syst Evol Microbiol 2018; 68:3301-3306. [PMID: 30152751 DOI: 10.1099/ijsem.0.002985] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel dark pink pigmented bacterium, designated strain CPCC 100847T (deposited with strain code 0113-15), was isolated from the urban air of Beijing, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CPCC 100847T was related to members of the genus Roseomonas and had the highest 16S rRNA gene sequence similarity to Roseomonas aestuarii JC17T (97.5 %). A low level of DNA-DNA relatedness (18.7 %) with its closest type strain R. aestuarii JC17T (KCTC 22692T) proved that strain CPCC 100847T belonged to a unique genomic species. CPCC 100847T had many common characteristics of the genus Roseomonas, but also had a range of cultural, physiological and biochemical characteristics that separated it from related Roseomonas species. Cells were Gram-negative, cocci- to oval-shaped, non-motile, non-endospore-forming and strictly aerobic. The respiratory ubiquinone was Q-10. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified phospholipid. The major fatty acids (>5 %) were C18 : 1ω7c, anteiso-C15 : 0, C16 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The combined genotypic and phenotypic data indicated that the isolate represents a novel species of the genus Roseomonas. The name proposed for this species is Roseomonasglobiformis sp. nov., with CPCC 100847T (=KCTC 52094T) as the type strain. The DNA G+C composition is 65.2 mol%.
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Affiliation(s)
- Xiao-Mei Fang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Jing-Lin Bai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - De-Wu Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Jing Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li-Li Zhao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Hong-Yu Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
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11
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Subhash Y, Lee SS. Roseomonas deserti sp. nov., isolated from crude oil contaminated desert sand. Int J Syst Evol Microbiol 2018; 68:675-680. [PMID: 29388546 DOI: 10.1099/ijsem.0.002565] [Citation(s) in RCA: 10] [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
Two dark pink pigmented bacterial strains (M3T and M11) were isolated from crude oil contaminated desert sand from Kuwait. Both strains were Gram-stain-negative and small-rod to oval-shaped bacteria. Strains M3T and M11 grew at 13-42 °C (optimum, 30-35 °C) and pH 6.5-9.0 (optimum, 7.0-7.5). No additional NaCl was required for the growth of both strains. The genomic DNA G+C content of strains M3T and M11 were 69.5 and 69.0 mol%, respectively. Both strains were closely related and the mean DNA-DNA hybridization value was 92±1 %. 16S rRNA gene sequence comparisons of both strains indicated that they belong to the genus Roseomonas. Strains M3T and M11 had a sequence similarity of 97.3 and 97.4 % with Roseomonas oryzae JC288T, respectively. Both strains had <97 % 16S rRNA gene sequence similarity with other members of the genus Roseomonas. Strain M3T showed 18±2 and 13±2 % reassociation (based on DNA-DNA hybridization) with R. oryzae KCTC 42542T and Roseomonas cervicalis KACC 11686T, respectively. The major cellular fatty acids (>5 %) were identified as C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c and C16 : 0 in both strains. Both strains showed diphosphatidylglycerol, phosphatidylglycerol, phosphatidyl-ethanolamine, phosphatidylcholine and unidentified glycolipid as major polar lipids. Based on distinct phenotypic, genotypic and phylogenetic differences from the previously described taxa, we propose the classification of strains M3T and M11 as representative of a novel species in the genus Roseomonas, for which the name Roseomonas deserti sp. nov. is suggested. The type strain is M3T (=KEMB 2255-459T=JCM 31275T).
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Affiliation(s)
- Y Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do, 16227, Republic of Korea.,Present address: Royal Netherlands Institute for Sea Research (NIOZ), Texel, The Netherlands
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do, 16227, Republic of Korea
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12
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Effect of light wavelength on hot spring microbial mat biodiversity. PLoS One 2018; 13:e0191650. [PMID: 29381713 PMCID: PMC5790269 DOI: 10.1371/journal.pone.0191650] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/09/2018] [Indexed: 11/19/2022] Open
Abstract
Hot spring associated phototrophic microbial mats are purely microbial communities, in which phototrophic bacteria function as primary producers and thus shape the community. The microbial mats at Nakabusa hot springs in Japan harbor diverse photosynthetic bacteria, mainly Thermosynechococcus, Chloroflexus, and Roseiflexus, which use light of different wavelength for energy conversion. The aim of this study was to investigate the effect of the phototrophs on biodiversity and community composition in hot spring microbial mats. For this, we specifically activated the different phototrophs by irradiating the mats with different wavelengths in situ. We used 625, 730, and 890 nm wavelength LEDs alone or in combination and confirmed the hypothesized increase in relative abundance of different phototrophs by 16S rRNA gene sequencing. In addition to the increase of the targeted phototrophs, we studied the effect of the different treatments on chemotrophic members. The specific activation of Thermosynechococcus led to increased abundance of several other bacteria, whereas wavelengths specific to Chloroflexus and Roseiflexus induced a decrease in >50% of the community members as compared to the dark conditions. This suggests that the growth of Thermosynechococcus at the surface layer benefits many community members, whereas less benefit is obtained from an increase in filamentous anoxygenic phototrophs Chloroflexus and Roseiflexus. The increases in relative abundance of chemotrophs under different light conditions suggest a relationship between the two groups. Aerobic chemoheterotrophs such as Thermus sp. and Meiothermus sp. are thought to benefit from aerobic conditions and organic carbon in the form of photosynthates by Thermosynechococcus, while the oxidation of sulfide and production of elemental sulfur by filamentous anoxygenic phototrophs benefit the sulfur-disproportionating Caldimicrobium thiodismutans. In this study, we used an experimental approach under controlled environmental conditions for the analysis of natural microbial communities, which proved to be a powerful tool to study interspecies relationships in the microbiome.
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13
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Yang ZW, Salam N, Hua ZS, Liu BB, Han MX, Fang BZ, Wang D, Xiao M, Hozzein WN, Li WJ. Siccirubricoccus deserti gen. nov., sp. nov., a proteobacterium isolated from a desert sample. Int J Syst Evol Microbiol 2017; 67:4862-4867. [PMID: 28984236 DOI: 10.1099/ijsem.0.002397] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain SYSU D8009T was isolated from a desert sample collected from Saudi Arabia. The taxonomic position of the isolate was investigated by a polyphasic approach. The novel isolate was Gram-stain-negative, non-motile, aerobic and non-spore-forming. It was able to grow at 4-45 °C and pH 4.0-8.0, and exhibited NaCl tolerance of up to 1.5 % (w/v). Strain SYSU D8009T shared the closest 16S rRNA gene sequence similarities with members of the family Acetobacteraceae, with a value of less than 96.0 %. In the phylogenetic dendrograms, the strain clustered with the genera Paracraurococcus, Craurococcus and Crenalkalicoccus within the family Acetobacteraceae but with a distinct lineage, thereby demonstrating that the strain should be classified within the family Acetobacteraceae. The respiratory ubiquinone was found to be Q-10. The polar lipids of the strain comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and four unidentified aminolipids. The predominant cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The genomic DNA G+C content of strain SYSU D8009T was determined to be 71.6 mol%. Based on the results of the phylogenetic analyses and differences in the physiological and biochemical characteristics, strain SYSU D8009T merits representation of a novel species of a new genus within the family Acetobacteraceae, for which the name Siccirubricoccus deserti gen. nov., sp. nov. is proposed. The type strain of Siccirubricoccus deserti sp. nov. is SYSU D8009T (=CGMCC 1.15936T=KCTC 62088T).
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Affiliation(s)
- Zi-Wen Yang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Zheng-Shuang Hua
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Bing-Bing Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Ming-Xian Han
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Bao-Zhu Fang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Dong Wang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Wael N Hozzein
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
- Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi 830011, PR China
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14
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Subhash Y, Lee SS. Roseomonas suffusca sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2017; 67:2390-2396. [PMID: 28714843 DOI: 10.1099/ijsem.0.001966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three light-brown-coloured, Gram-stain-negative, small rod- to oval-shaped, motile bacteria were isolated from lagoon sediments collected from North Carolina, USA. The strains (S1T, AS3 and AS6) grew aerobically at 13-42 °C (optimum, 30-35 °C) and pH 6.5-9.1 (optimum, pH 7.0-7.5). All three strains were positive for catalase and oxidase activity, and no added NaCl was required for growth. C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c, C18 : 1ω7c 11-methyl and C16 : 0 were the predominant fatty acids (>5 %). Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unidentified glycolipid were the major polar lipids. The genomic DNA G+C content of strains S1T, AS3 and AS6 was 70.5, 70.1 and 70.8 mol%, respectively. Strain S1T showed 16S rRNA gene sequence similarity of 99.1 % with Roseomonas rubra S5T, 98.7 % with Roseomonas rhizosphaerae YW11T, 98.5 % with Roseomonas cervicalis E7107T, 97.8 % with Roseomonas aestuarii JC17T, 97.2 % with Roseomonas oryzae JC288T, 97.2 % with Roseomonas ludipueritiae 170/96Tand <97 % with other members of the genus Roseomonas. Strains AS3 and AS6 shared 99.9 % 16S rRNA gene sequence similarity with strain S1T. DNA-DNA hybridization values among strains S1T, AS3 and AS6 were >89 %, while all the three strains showed <56 % relatedness with the most closely related type strains. Distinct phenotypic, genotypic and phylogenetic differences from the previously described taxa support the classification of strain S1T as a representative of a novel species in the genus Roseomonas, for which the name Roseomonas suffusca sp. nov. is proposed. The type strain is S1T (=KEMB 563-465T=JCM 31176T). Strains AS3 and AS6 serve as additional strains of the newly proposed species.
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Affiliation(s)
- Y Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
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15
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Kalam S, Das SN, Basu A, Podile AR. Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere. J Basic Microbiol 2017; 57:376-385. [PMID: 28397264 DOI: 10.1002/jobm.201600588] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 03/01/2017] [Indexed: 11/09/2022]
Abstract
Rhizosphere microbial community has diverse metabolic capabilities and plays a crucial role in maintaining plant health. Oligotrophic plant growth promoting rhizobacteria (PGPR), along with difficult-to-culture microbial fractions, might be involved synergistically in microbe-microbe and plant-microbe interactions in the rhizosphere. Among the difficult-to-culture microbial fractions, Acidobacteria constitutes the most dominant phylum thriving in rhizospheric soils. We selected effective PGPR for tomato and black gram and studied their effect on population densities of acidobacterial members. Three facultatively oligotrophic PGPR were identified through 16S rRNA gene sequencing as Sphingobacterium sp. (P3), Variovorax sp. (P4), and Roseomonas sp. (A2); the latter being a new report of PGPR. In presence of selected PGPR strains, the changes in population densities of Acidobacteria were monitored in metagenomic DNA extracted from bulk and rhizospheric soils of tomato and black gram using real time qPCR. A gradual increase in equivalent cell numbers of Acidobacteria members was observed over time along with a simultaneous increase in plant growth promotion by test PGPR. We report characterization of three effective PGPR strains and their effects on indigenous, underexplored difficult-to-culture phylum-Acidobacteria. We suggest that putative interactions between these two bacterial groups thriving in rhizospheric soils could be beneficial for plant growth.
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Affiliation(s)
- Sadaf Kalam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Subha Narayan Das
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Appa Rao Podile
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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16
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Kim MC, Rim S, Pak S, Ren L, Zhang Y, Chang X, Li X, Fang C, Zheng C, Peng F. Roseomonas arcticisoli sp. nov., isolated from Arctic tundra soil. Int J Syst Evol Microbiol 2016; 66:4057-4064. [DOI: 10.1099/ijsem.0.001310] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Myong Chol Kim
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
- College of Life Sciences, Kim Il Sung University, Pyongyang, Republic of Korea
| | - Songguk Rim
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
- Department of Economic Plant, Wonsan Agricultural University, Wonsan, Republic of Korea
| | - Sehong Pak
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
- College of Life Sciences, Kim Il Sung University, Pyongyang, Republic of Korea
| | - Lvzhi Ren
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Yumin Zhang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xulu Chang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xuhuan Li
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Chengxiang Fang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Congyi Zheng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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17
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Subhash Y, Bang JJ, You TH, Lee SS. Roseomonas rubra sp. nov., isolated from lagoon sediments. Int J Syst Evol Microbiol 2016; 66:3821-3827. [DOI: 10.1099/ijsem.0.001271] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Y. Subhash
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
| | - John J. Bang
- Department of Environmental, Earth and Geospatial Science, North Carolina Central University, Durham, NC 27707, USA
| | - Taek H. You
- Department of Biological Sciences, Campbell University, Buies Creek, NC 27506, USA
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi University, 154-42 Gwanggyosan-ro Yeongtong-gu Suwon-Si, Gyeonggi-Do 16227, Republic of Korea
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18
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Hirose S, Matsuura K, Haruta S. Phylogenetically Diverse Aerobic Anoxygenic Phototrophic Bacteria Isolated from Epilithic Biofilms in Tama River, Japan. Microbes Environ 2016; 31:299-306. [PMID: 27453124 PMCID: PMC5017807 DOI: 10.1264/jsme2.me15209] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The diversity of aerobic anoxygenic phototrophic (AAP) bacteria in freshwater environments, particularly in rivers, has not been examined in as much detail as in ocean environments. In the present study, we investigated the phylogenetic and physiological diversities of AAP bacteria in biofilms that developed on submerged stones in a freshwater river using culture methods. The biofilms collected were homogenized and inoculated on solid media and incubated aerobically in the dark. Sixty-eight red-, pink-, yellow-, orange-, or brown-colored colonies were isolated, and, of these, 28 isolates contained the photosynthetic pigment, bacteriochlorophyll (BChl) a. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates were classified into 14 groups in 8 operational taxonomic units (OTUs) and distributed in the orders Rhodospirillales, Rhodobacterales, and Sphingomonadales of Alphaproteobacteria and in Betaproteobacteria. Physiological analyses confirmed that none of the representative isolates from any of the groups grew under anaerobic phototrophic conditions. Seven isolates in 4 OTUs showed a 16S rRNA gene sequence identity of 98.0% or less with any established species, suggesting the presence of previously undescribed species of AAP bacteria. Six isolates in 2 other OTUs had the closest relatives, which have not been reported to be AAP bacteria. Physiological comparisons among the isolates revealed differences in preferences for nutrient concentrations, BChl contents, and light-harvesting proteins. These results suggest that diverse and previously unknown AAP bacteria inhabit river biofilms.
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Affiliation(s)
- Setsuko Hirose
- Department of Biological Sciences, Tokyo Metropolitan University
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19
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Ming H, Duan YY, Yin YR, Meng XL, Li S, Zhou EM, Huang JR, Nie GX, Li WJ. Crenalkalicoccus roseus gen. nov., sp. nov., a thermophilic bacterium isolated from alkaline hot springs. Int J Syst Evol Microbiol 2016; 66:2319-2326. [DOI: 10.1099/ijsem.0.001029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Hong Ming
- College of Life Sciences and Technology, Xinxiang Medical University, Xinxiang 453003, PR China
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Yan-Yan Duan
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Yi-Rui Yin
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
| | - Xiao-Lin Meng
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Shuai Li
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - En-Min Zhou
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Jian-Rong Huang
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Guo-Xing Nie
- College of Fisheries, Henan Normal University, Xinxiang 453007, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
- Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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20
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Damtab J, Nutaratat P, Boontham W, Srisuk N, Duangmal K, Yurimoto H, Sakai Y, Muramatsu Y, Nakagawa Y. Roseomonas elaeocarpi sp. nov., isolated from olive (Elaeocarpus hygrophilus Kurz.) phyllosphere. Int J Syst Evol Microbiol 2016; 66:474-480. [DOI: 10.1099/ijsem.0.000748] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jenjira Damtab
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Pumin Nutaratat
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Wanatchaporn Boontham
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Nantana Srisuk
- Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Hiroya Yurimoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yasuyoshi Sakai
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuki Muramatsu
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yasuyoshi Nakagawa
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation, 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
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21
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Lee JH, Kim MS, Baik KS, Kim HM, Lee KH, Seong CN. Roseomonas wooponensis sp. nov., isolated from wetland freshwater. Int J Syst Evol Microbiol 2015; 65:4049-4054. [DOI: 10.1099/ijsem.0.000536] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A non-motile, cocobacilli-shaped and pink-pigmented bacterium, designated strain WW53T, was isolated from wetland freshwater (Woopo wetland, Republic of Korea). Cells were Gram-stain-negative, catalase- and oxidase-positive. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c and C16 : 0.The predominant quinone and polyamine were ubiquinone 10 (Q-10) and spermidine, respectively. The DNA G+C content was 71 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine and an unknown aminolipid. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WW53T belongs to the family Acetobacteraceae, and is related to the genus Roseomonas. Strain WW53T was most closely related to Roseomonas stagni HS-69T (95.3 % 16S rRNA gene sequence similarity). Results of a polyphasic taxonomy study suggested that the isolate represents a novel species in the genus Roseomonas, for which the name Roseomonas wooponensis sp. nov. is proposed. The type strain is WW53T ( = KCTC 32534T = JCM 19527T).
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Affiliation(s)
- Ji Hee Lee
- Department of Biology, College of life science and Natural Resources, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Mi Sun Kim
- Department of Biology, College of life science and Natural Resources, Sunchon National University, Suncheon 540-742, Republic of Korea
| | - Keun Sik Baik
- Department of Food Science and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hyang Mi Kim
- Biological Resource Center, KRIBB, Daejeon 305-806, Republic of Korea
| | - Kang Hyun Lee
- Biological Resource Center, KRIBB, Daejeon 305-806, Republic of Korea
| | - Chi Nam Seong
- Department of Biology, College of life science and Natural Resources, Sunchon National University, Suncheon 540-742, Republic of Korea
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Woycheese KM, Meyer-Dombard DR, Cardace D, Argayosa AM, Arcilla CA. Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines). Front Microbiol 2015; 6:44. [PMID: 25745416 PMCID: PMC4333863 DOI: 10.3389/fmicb.2015.00044] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 01/13/2015] [Indexed: 02/01/2023] Open
Abstract
In the Zambales ophiolite range, terrestrial serpentinizing fluid seeps host diverse microbial assemblages. The fluids fall within the profile of Ca2+-OH−-type waters, indicative of active serpentinization, and are low in dissolved inorganic carbon (DIC) (<0.5 ppm). Influx of atmospheric carbon dioxide (CO2) affects the solubility of calcium carbonate as distance from the source increases, triggering the formation of meter-scale travertine terraces. Samples were collected at the source and along the outflow channel to determine subsurface microbial community response to surface exposure. DNA was extracted and submitted for high-throughput 16S rRNA gene sequencing on the Illumina MiSeq platform. Taxonomic assignment of the sequence data indicates that 8.1% of the total sequence reads at the source of the seep affiliate with the genus Methanobacterium. Other major classes detected at the source include anaerobic taxa such as Bacteroidetes (40.7% of total sequence reads) and Firmicutes (19.1% of total reads). Hydrogenophaga spp. increase in relative abundance as redox potential increases. At the carbonate terrace, 45% of sequence reads affiliate with Meiothermus spp. Taxonomic observations and geochemical data suggest that several putative metabolisms may be favorable, including hydrogen oxidation, H2-associated sulfur cycling, methanogenesis, methanotrophy, nitrogen fixation, ammonia oxidation, denitrification, nitrate respiration, methylotrophy, carbon monoxide respiration, and ferrous iron oxidation, based on capabilities of nearest known neighbors. Scanning electron microscopy and energy dispersive X-ray spectroscopy suggest that microbial activity produces chemical and physical traces in the precipitated carbonates forming downstream of the seep's source. These data provide context for future serpentinizing seep ecosystem studies, particularly with regards to tropical biomes.
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Affiliation(s)
- Kristin M Woycheese
- Department of Earth and Environmental Sciences, University of Illinois at Chicago Chicago, IL, USA
| | - D'Arcy R Meyer-Dombard
- Department of Earth and Environmental Sciences, University of Illinois at Chicago Chicago, IL, USA
| | - Dawn Cardace
- Department of Geosciences, University of Rhode Island Kingston, RI, USA
| | - Anacleto M Argayosa
- Institute of Biology, University of the Philippines Diliman Quezon City, Philippines
| | - Carlo A Arcilla
- National Institute of Geological Sciences, University of the Philippines Diliman Quezon City, Philippines
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2014. [DOI: 10.1099/ijs.0.070847-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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