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Xu Y, Liu B, Jiao N, Liu J, Chen F. New evidence supports the prophage origin of RcGTA. Appl Environ Microbiol 2024:e0043424. [PMID: 39189727 DOI: 10.1128/aem.00434-24] [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: 03/06/2024] [Accepted: 08/11/2024] [Indexed: 08/28/2024] Open
Abstract
Gene transfer agents (GTAs) are phage-like entities that package and transfer random host genome fragments between prokaryotes. RcGTA, produced by Rhodobacter capsulatus, is hypothesized to originate from a prophage ancestor. Most of the evidence supporting this hypothesis came from the finding of RcGTA-like genes in phages. More than 75% of the RcGTA genes have a phage homolog. However, only a few RcGTA homologs have been identified in a (pro)phage genome, leaving the hypothesis that GTAs evolved from prophages through gene loss with only weak evidence. We herein report the discovery of an inducible prophage (vB_MseS-P1) from a Mesorhizobium sediminum strain that contains the largest number (12) of RcGTA homologs found in a phage genome to date. We also identified three putative prophages and two prophage remnants harboring 12-14 RcGTA homologs in a Methylobacterium nodulans strain. The protein remote homology detection also revealed more RcGTA homologs from other phages than we previously thought. Moreover, the head-tail gene architecture of these newly discovered prophage-related elements closely resembles that of RcGTA. Furthermore, vB_MseS-P1 virions have structural proteins similar to RcGTA particles. Close phylogenetic relationships between certain prophage genes and RcGTA-like genes in Alphaproteobacteria further support the shared ancestry between RcGTA and prophages. Our findings provide new relatively direct evidence of the origin of RcGTA from a prophage progenitor.IMPORTANCEGTAs are important genetic elements in certain groups of bacteria and contribute to the genetic diversification, evolution, and ecological adaptation of bacteria. RcGTA, a common type of GTA, is known to package and transfer random fragments of the bacterial genome to recipient cells. However, the origin of RcGTA is still elusive. It has been hypothesized that RcGTA evolved from a prophage ancestor through gene loss. However, the few RcGTA homologs identified in a (pro)phage genome leave the hypothesis lacking direct evidence. This study uncovers the presence of a large number of RcGTA homologs in an inducible prophage and several putative prophages. The similar head-tail gene architecture and structural protein compositions of these newly discovered prophage-related elements and RcGTA further demonstrate an unprecedentedly observed close evolutionary relationship between prophages and RcGTA. Together, our findings provide more direct evidence supporting the origin of RcGTA from prophage.
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Affiliation(s)
- Yongle Xu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission Technology, Shandong University, Qingdao, China
| | - Binbin Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Nianzhi Jiao
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission Technology, Shandong University, Qingdao, China
| | - Jihua Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
- Qingdao Key Laboratory of Ocean Carbon Sequestration and Negative Emission Technology, Shandong University, Qingdao, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
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2
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Jiang F, Hao X, Li D, Zhu X, Huang J, Lai Q, Wang J, Wang L, Shao Z. Aquibium pacificus sp. nov., a Novel Mixotrophic Bacterium from Bathypelagic Seawater in the Western Pacific Ocean. Microorganisms 2024; 12:1584. [PMID: 39203426 PMCID: PMC11356281 DOI: 10.3390/microorganisms12081584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Revised: 07/28/2024] [Accepted: 08/01/2024] [Indexed: 09/03/2024] Open
Abstract
A novel Gram-stain-negative, facultatively anaerobic, and mixotrophic bacterium, designated as strain LZ166T, was isolated from the bathypelagic seawater in the western Pacific Ocean. The cells were short rod-shaped, oxidase- and catalase-positive, and motile by means of lateral flagella. The growth of strain LZ166T was observed at 10-45 °C (optimum 34-37 °C), at pH 5-10 (optimum 6-8), and in the presence of 0-5% NaCl (optimum 1-3%). A phylogenetic analysis based on the 16S rRNA gene showed that strain LZ166T shared the highest similarity (98.58%) with Aquibium oceanicum B7T and formed a distinct branch within the Aquibium genus. The genomic characterization, including average nucleotide identity (ANI, 90.73-76.79%), average amino identity (AAI, 88.50-79.03%), and digital DNA-DNA hybridization (dDDH, 36.1-22.2%) values between LZ166T and other species within the Aquibium genus, further substantiated its novelty. The genome of strain LZ166T was 6,119,659 bp in size with a 64.7 mol% DNA G+C content. The predominant fatty acid was summed feature 8 (C18:1ω7c and/or C18:1ω6c). The major polar lipids identified were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), glycolipid (GL), and phosphatidylglycerol (PG), with ubiquinone-10 (Q-10) as the predominant respiratory quinone. The genomic annotation indicated the presence of genes for a diverse metabolic profile, including pathways for carbon fixation via the Calvin-Benson-Bassham cycle and inorganic sulfur oxidation. Based on the polyphasic taxonomic results, strain LZ166T represented a novel species of the genus Aquibium, for which the name Aquibium pacificus sp. nov. is proposed, with the type strain LZ166T (=MCCC M28807T = KACC 23148T = KCTC 82889T).
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Affiliation(s)
- Fan Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xun Hao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Ding Li
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Xuying Zhu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Jiamei Huang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Jianning Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Liping Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of PR China, Xiamen 361102, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen 361102, China
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
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3
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Kim M, Kim W, Park Y, Jung J, Park W. Lineage-specific evolution of Aquibium, a close relative of Mesorhizobium, during habitat adaptation. Appl Environ Microbiol 2024; 90:e0209123. [PMID: 38412007 PMCID: PMC10952388 DOI: 10.1128/aem.02091-23] [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: 11/17/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
The novel genus Aquibium that lacks nitrogenase was recently reclassified from the Mesorhizobium genus. The genomes of Aquibium species isolated from water were smaller and had higher GC contents than those of Mesorhizobium species. Six Mesorhizobium species lacking nitrogenase were found to exhibit low similarity in the average nucleotide identity values to the other 24 Mesorhizobium species. Therefore, they were classified as the non-N2-fixing Mesorhizobium lineage (N-ML), an evolutionary intermediate species. The results of our phylogenomic analyses and the loss of Rhizobiales-specific fur/mur indicated that Mesorhizobium species may have evolved from Aquibium species through an ecological transition. Halotolerant and alkali-resistant Aquibium and Mesorhizobium microcysteis belonging to N-ML possessed many tripartite ATP-independent periplasmic transporter and sodium/proton antiporter subunits composed of seven genes (mrpABCDEFG). These genes were not present in the N2-fixing Mesorhizobium lineage (ML), suggesting that genes acquired for adaptation to highly saline and alkaline environments were lost during the evolution of ML as the habitat changed to soil. Land-to-water habitat changes in Aquibium species, close relatives of Mesorhizobium species, could have influenced their genomic evolution by the gain and loss of genes. Our study indicated that lineage-specific evolution could have played a significant role in shaping their genome architecture and conferring their ability to thrive in different habitats.IMPORTANCEPhylogenetic analyses revealed that the Aquibium lineage (AL) and non-N2-fixing Mesorhizobium lineage (N-ML) were monophyletically grouped into distinct clusters separate from the N2-fixing Mesorhizobium lineage (ML). The N-ML, an evolutionary intermediate species having characteristics of both ancestral and descendant species, could provide a genomic snapshot of the genetic changes that occur during adaptation. Genomic analyses of AL, N-ML, and ML revealed that changes in the levels of genes related to transporters, chemotaxis, and nitrogen fixation likely reflect adaptations to different environmental conditions. Our study sheds light on the complex and dynamic nature of the evolution of rhizobia in response to changes in their environment and highlights the crucial role of genomic analysis in understanding these processes.
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Affiliation(s)
- Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Yerim Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
| | - Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul, South Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, South Korea
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4
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Khanal A, Han SR, Lee JH, Oh TJ. Comparative Genome Analysis of Polar Mesorhizobium sp. PAMC28654 to Gain Insight into Tolerance to Salinity and Trace Element Stress. Microorganisms 2024; 12:120. [PMID: 38257947 PMCID: PMC10820077 DOI: 10.3390/microorganisms12010120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
In this study, Mesorhizobium sp. PAMC28654 was isolated from a soil sample collected from the polar region of Uganda. Whole-genome sequencing and comparative genomics were performed to better understand the genomic features necessary for Mesorhizobium sp. PAMC28654 to survive and thrive in extreme conditions and stresses. Additionally, diverse sequence analysis tools were employed for genomic investigation. The results of the analysis were then validated using wet-lab experiments. Genome analysis showed trace elements' resistant proteins (CopC, CopD, CzcD, and Acr3), exopolysaccharide (EPS)-producing proteins (ExoF and ExoQ), and nitrogen metabolic proteins (NarG, NarH, and NarI). The strain was positive for nitrate reduction. It was tolerant to 100 mM NaCl at 15 °C and 25 °C temperatures and resistant to multiple trace elements (up to 1 mM CuSO4·5H2O, 2 mM CoCl2·6H2O, 1 mM ZnSO4·7H2O, 0.05 mM Cd(NO3)2·4H2O, and 100 mM Na2HAsO4·7H2O at 15 °C and 0.25 mM CuSO4·5H2O, 2 mM CoCl2·6H2O, 0.5 mM ZnSO4·7H2O, 0.01 mM Cd(NO3)2·4H2O, and 100 mM Na2HAsO4·7H2O at 25 °C). This research contributes to our understanding of bacteria's ability to survive abiotic stresses. The isolated strain can be a potential candidate for implementation for environmental and agricultural purposes.
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Affiliation(s)
- Anamika Khanal
- Genome-Based Bio-IT Convergence Institute, Asan 31460, Republic of Korea; (A.K.); (S.-R.H.)
- Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program, SunMoon University, Asan 31460, Republic of Korea
| | - So-Ra Han
- Genome-Based Bio-IT Convergence Institute, Asan 31460, Republic of Korea; (A.K.); (S.-R.H.)
- Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program, SunMoon University, Asan 31460, Republic of Korea
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 31460, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Materials, Korea Polar Research Institute, Incheon 21990, Republic of Korea;
| | - Tae-Jin Oh
- Genome-Based Bio-IT Convergence Institute, Asan 31460, Republic of Korea; (A.K.); (S.-R.H.)
- Bio Big Data-Based Chungnam Smart Clean Research Leader Training Program, SunMoon University, Asan 31460, Republic of Korea
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 31460, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan 31460, Republic of Korea
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5
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Kim I, Chhetri G, So Y, Park S, Jung Y, Woo H, Seo T. Mesorhizobium liriopis sp. nov., isolated from the fermented fruit of Liriope platyphylla a medicinal plant. Int J Syst Evol Microbiol 2023; 73. [PMID: 37801075 DOI: 10.1099/ijsem.0.006086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023] Open
Abstract
A facultative anaerobic and Gram-negative strain, designated RP14T, was isolated from the fruit of Liriope platyphylla fermented for 60 days at 25°C. Strain RP14T showed 98.0 % 16S rRNA similarity to Mesorhizobium huakuii IFO 15243T, but in the phylogenetic tree, Mesorhizobium terrae NIBRBAC000500504T was its closest neighbour. The average nucleotide identity and digital DNA-DNA hybridization values between strain RP14T and 15 genomes of type strains of Mesorhizobium, were 73.8-74.4% and 16.4-20.2 %, respectively, which were lower than the recommended thresholds for species delineation. The strain grew at 25-32°C (optimum, 28°C), at pH 7.0-12.0 (optimum, pH 9.0) and with 0-2% NaCl (optimum, 0 %; w/v). Cells of strain RP14T were catalase-positive, oxidase-negative, rod-shaped and formed yellow-coloured colonies. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major fatty acid were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The DNA G+C content was 62.8 mol%. Based on polyphasic evidence, we propose Mesorhizobium liriopis sp. nov as a novel species within the genus Mesorhizobium. The type strain is RP14T (=KACC 22720T=TBRC 16341T).
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Affiliation(s)
- Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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6
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Aquibium microcysteis gen. nov., sp. nov., isolated from a Microcystis aeruginosa culture and reclassification of Mesorhizobium carbonis as Aquibium carbonis comb. nov. and Mesorhizobium oceanicum as Aquibium oceanicum comb. nov. Int J Syst Evol Microbiol 2022. [DOI: 10.1099/ijsem.0.005230 10.1099/ijsem.0.005230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A novel bacterial strain, NIBR3T, was isolated from a
Microcystis aeruginosa
culture. Strain NIBR3T was characterized as Gram-negative, rod-shaped, catalase- and oxidase-positive, and aerobic. The 16S rRNA gene sequence analysis showed that strain NIBR3T was most closely related to
Mesorhizobium carbonis
B2.3T (=KCTC 52461),
Mesorhizobium oceanicum
B7T (=KCTC 42783) and
Mesorhizobium qingshengii
CCBAU 33460T (=HAMBI 3277), at 98.7, 97.2 and 97.2% similarity, respectively. Our phylogenetic analyses revealed that three strains [strain NIBR3T with the previously reported two
Mesorhizobium
species (
M. carbonis
B2.3T and
M. oceanicum
B7T)] formed a distinct cluster from other
Mesorhizobium
type strains. The average nucleotide identity of strain NIBR3T relative to
M. carbonis
B2.3T
, M. oceanicum B7T, and
M. qingshengii
CCBAU 33460T was found to be 84.3, 79.4 and 75.8 %, with average amino-acid identities of 85.1, 74.8 and 64.3 %, and digital DNA–DNA hybridization values of 27.6, 22.6 and 20.7 %, respectively. The genome size and genomic DNA G+C content of NIBR3T were 6.1 Mbp and 67.9 mol%, respectively. Growth of strain NIBR3T was observed at 23–45 °C (optimum, 33 °C), at pH 6–11 (optimum, 8) and in the presence of 0–4 % (w/v) NaCl (optimum, 0 %). The major polar lipids in this novel strain were phosphatidylethanolamine, phosphatidylcholine and phosphatidylmethylethanolamine. The predominant respiratory quinone was Q-10. Summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) was the most abundant cellular fatty acid in strain NIBR3T. Based on genotypic characteristics using our genomic data, strain NIBR3T was identified as a member of new genus, Aquibium gen. nov., with the two aforementioned stains. The type strain f the novel species, Aquibium microcysteis sp. nov., is NIBR3T (=KACC 22092T=HAMBI 3738T). We also reclassified
Mesorhizobium carbonis
and
M. oceanicum
as Aquibium carbonis comb. nov. and A. oceanicum comb. nov., respectively.
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Kim M, Kim W, Park W. Aquibium microcysteis gen. nov., sp. nov., isolated from a Microcystis aeruginosa culture and reclassification of Mesorhizobium carbonis as Aquibium carbonis comb. nov. and Mesorhizobium oceanicum as Aquibium oceanicum comb. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005230] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterial strain, NIBR3T, was isolated from a
Microcystis aeruginosa
culture. Strain NIBR3T was characterized as Gram-negative, rod-shaped, catalase- and oxidase-positive, and aerobic. The 16S rRNA gene sequence analysis showed that strain NIBR3T was most closely related to
Mesorhizobium carbonis
B2.3T (=KCTC 52461),
Mesorhizobium oceanicum
B7T (=KCTC 42783) and
Mesorhizobium qingshengii
CCBAU 33460T (=HAMBI 3277), at 98.7, 97.2 and 97.2% similarity, respectively. Our phylogenetic analyses revealed that three strains [strain NIBR3T with the previously reported two
Mesorhizobium
species (
M. carbonis
B2.3T and
M. oceanicum
B7T)] formed a distinct cluster from other
Mesorhizobium
type strains. The average nucleotide identity of strain NIBR3T relative to
M. carbonis
B2.3T
, M. oceanicum B7T, and
M. qingshengii
CCBAU 33460T was found to be 84.3, 79.4 and 75.8 %, with average amino-acid identities of 85.1, 74.8 and 64.3 %, and digital DNA–DNA hybridization values of 27.6, 22.6 and 20.7 %, respectively. The genome size and genomic DNA G+C content of NIBR3T were 6.1 Mbp and 67.9 mol%, respectively. Growth of strain NIBR3T was observed at 23–45 °C (optimum, 33 °C), at pH 6–11 (optimum, 8) and in the presence of 0–4 % (w/v) NaCl (optimum, 0 %). The major polar lipids in this novel strain were phosphatidylethanolamine, phosphatidylcholine and phosphatidylmethylethanolamine. The predominant respiratory quinone was Q-10. Summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) was the most abundant cellular fatty acid in strain NIBR3T. Based on genotypic characteristics using our genomic data, strain NIBR3T was identified as a member of new genus, Aquibium gen. nov., with the two aforementioned stains. The type strain f the novel species, Aquibium microcysteis sp. nov., is NIBR3T (=KACC 22092T=HAMBI 3738T). We also reclassified
Mesorhizobium carbonis
and
M. oceanicum
as Aquibium carbonis comb. nov. and A. oceanicum comb. nov., respectively.
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Affiliation(s)
- Minkyung Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Wonjae Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
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Mesorhizobium xinjiangense sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia. Arch Microbiol 2021; 204:29. [PMID: 34921611 DOI: 10.1007/s00203-021-02686-9] [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: 09/07/2021] [Revised: 10/14/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
A beige-pigmented, Gram-strain-negative, aerobic, rod-shaped, non-flagellated and non-gliding bacterium, designated strain lm94T, was isolated from rhizosphere soil of Alhagi sparsifolia obtained from Alar city, located in Xinjiang province, China. Growth occurred at 20-45 °C (optimum, 37 °C), in the presence of 0-6% (w/v) NaCl (optimum, 0-1%) and at pH 6.0-9.5 (optimum, pH 7.0-7.5). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain lm94T belonged to the genus Mesorhizobium, with highest sequence similarity to Mesorhizobium wenxiniae WYCCWR 10195T (96.6%). Genome sequencing revealed a genome size of 5 256 375 bp and a G + C content of 63.6 mol%. The average nucleotide identity value and the digital DNA-DNA hybridization value between strain lm94T and M. wenxiniae LMG 30254T were 75.0% and 20.0%, respectively. The major respiratory quinone was Q-10. The major fatty acids were C19:0 cyclo ω8c and Summed Feature 8 (C18:1 ω6c and/or C18:1 ω7c) and its polar lipids consisted of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), unidentified phospholipid (PL), phosphatidylcholine (PC), diphosphatidylglycerol (DPG), unidentified aminolipid (AL), unknown glycolipid (GL), unidentified aminophospholipid (APL2) and unidentified polar lipid (L1 and L2). On the basis of these data, strain lm94T is considered to represent a novel species of the genus Mesorhizobium, for which the name Mesorhizobium xinjiangense sp. nov. is proposed. The type strain is lm94T (=KCTC 72863T=CCTCC AB2019377T).
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Pedron R, Luchi E, Albiac MA, Di Cagno R, Catorci D, Esposito A, Bianconi I, Losa D, Cristofolini M, Guella G, Jousson O. Mesorhizobium comanense sp. nov., isolated from groundwater. Int J Syst Evol Microbiol 2021; 71. [PMID: 34870580 DOI: 10.1099/ijsem.0.005131] [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
Strain 3P27G6T was isolated from an artesian well connected to the thermal water basin of Comano Terme, Province of Trento, Italy. In phylogenetic analyses based on multilocus sequence analysis, strain 3P27G6T clustered together with Mesorhizobium australicum WSM2073T. Genome sequencing produced a 99.51 % complete genome, with a length of 7 363 057 bp and G+C content of 63.53 mol%, containing 6897 coding sequences, 55 tRNA and three rRNA. Average nucleotide identity analysis revealed that all distances calculated between strain 3P27G6T and the other Mesorhizobium genomes were below 0.9, indicating that strain 3P27G6T represents a new species. Therefore, we propose the name Mesorhizobium comanense sp. nov. with the type strain 3P27G6T (=DSM 110654T=CECT 30067T). Strain 3P27G6T is a Gram-negative, rod-shaped, aerobic bacterium. Growth condition, antibiotic susceptibility, metabolic and fatty acid-methyl esters profiles of the strain were determined. Only few nodulation and nitrogen fixation genes were found in the genome, suggesting that this strain may not be specialized in nodulation or in nitrogen fixation.
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Affiliation(s)
- Renato Pedron
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Elena Luchi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Marta Acin Albiac
- Faculty of Sciences and Technology, Libera Università di Bolzano, 39100 Bolzano, Italy
| | - Raffaella Di Cagno
- Faculty of Sciences and Technology, Libera Università di Bolzano, 39100 Bolzano, Italy
| | - Daniele Catorci
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy.,Department of Physics, University of Trento, 38123 Trento, Italy
| | - Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Irene Bianconi
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | - Davide Losa
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
| | | | - Graziano Guella
- Department of Physics, University of Trento, 38123 Trento, Italy
| | - Olivier Jousson
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, 38123 Trento, Italy
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Jung J, Seo YL, Kim KR, Park HY, Jeon CO. Mesorhizobium microcysteis sp. nov., isolated from a culture of Microcystis aeruginosa. Int J Syst Evol Microbiol 2021; 71. [PMID: 34214029 DOI: 10.1099/ijsem.0.004847] [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
Strain MaA-C15T, a Gram-stain-negative, non-spore-forming and strictly aerobic bacterium, was isolated from a xenic culture of Microcystis aeruginosa in the Republic of Korea. Cells were motile rods showing positive reactions in catalase and oxidase tests. Growth was observed between 15 and 37 °C (optimum, 30 °C), between pH 6.0 and pH 11.0 (optimum, pH 7.5) and in the presence of 0-2.0 % (w/v) NaCl (optimum, 0 %). Strain MaA-C15T contained C16 : 0, 11-methyl-C18 : 1 ω7c, cyclo-C19 : 0 ω8c and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c) as the major cellular fatty acids and ubiquinone-10 as the sole respiratory quinone. Phosphatidylethanolamine, phosphatidylmonomethylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid and three unidentified phospholipids were detected as the major polar lipids. The G+C content of the genomic DNA was 64.1 mol%. Phylogenetic and phylogenomic analyses based on 16S rRNA gene and genome sequences revealed that strain MaA-C15T formed a phyletic lineage with Mesorhizobium sediminum YIM M12096T within the family Phyllobacteriaceae. Strain MaA-C15T was most closely related to Mesorhizobium albiziae DSM 21822T with a 98.2 % 16S rRNA sequence similarity. Average nucleotide identity and in silico DNA-DNA hybridization values between strain MaA-C15T and M. albiziae DSM 21822T were 75.4 and 20.1 %, respectively. Based on the results of phenotypic, chemotaxonomic and molecular analyses, strain MaA-C15T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium microcysteis sp. nov. is proposed. The type strain is MaA-C15T (=KACC 21226T=JCM 33503T).
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Affiliation(s)
- Jaejoon Jung
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ye Lin Seo
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Kyeong Ryeol Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Hye Yoon Park
- National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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Zhao W, Zhu H, Wei F, Zhou D, Li Y, Zhang XX. Investigating the Involvement of Cytoskeletal Proteins MreB and FtsZ in the Origin of Legume-Rhizobial Symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:547-559. [PMID: 33596109 DOI: 10.1094/mpmi-10-20-0299-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rhizobia are rod-shaped bacteria that form nitrogen-fixing root nodules on leguminous plants; however, they don't carry MreB, a key determinant of rod-like cell shape. Here, we introduced an actin-like mreB homolog from a pseudomonad into Mesorhizobium huakuii 7653R (a microsymbiont of Astragalus sinicus L.) and examined the molecular, cellular, and symbiotic phenotypes of the resultant mutant. Exogenous mreB caused an enlarged cell size and slower growth in laboratory medium. However, the mutant formed small, ineffective nodules on A. sinicus (Nod+ Fix-), and rhizobial cells in the infection zone were unable to differentiate into bacteroids. RNA sequencing analysis also revealed minor effects of mreB on global gene expression in free-living cells but larger effects for cells grown in planta. Differentially expressed nodule-specific genes include cell cycle regulators such as the tubulin-like ftsZ1 and ftsZ2. Unlike the ubiquitous FtsZ1, an FtsZ2 homolog was commonly found in Rhizobium, Sinorhizobium, and Mesorhizobium spp. but not in closely related nonsymbiotic species. Bacterial two-hybrid analysis revealed that MreB interacts with FtsZ1 and FtsZ2, which are targeted by the host-derived nodule-specific cysteine-rich peptides. Significantly, MreB mutation D283A disrupted the protein-protein interactions and restored the aforementioned phenotypic defects caused by MreB in M. huakuii. Together, our data indicate that MreB is detrimental for modern rhizobia and its interaction with FtsZ1 and FtsZ2 causes the symbiotic process to cease at the late stage of bacteroid differentiation. These findings led to a hypothesis that loss of mreB in the common ancestor of members of Rhizobiales and subsequent acquisition of ftsZ2 are critical evolutionary steps leading to legume-rhizobial symbiosis.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Wenlong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Huixia Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Feng Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Donglai Zhou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Youguo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Xue-Xian Zhang
- School of Natural and Computational Sciences, Massey University, Auckland 0745, New Zealand
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Gao JL, Xue J, Sun YC, Xue H, Wang ET, Yan H, Tong S, Wang LW, Zhang X, Sun JG. Mesorhizobium rhizophilum sp. nov., a 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from rhizosphere of maize in Northeast China. Antonie van Leeuwenhoek 2020; 113:1179-1189. [PMID: 32468221 DOI: 10.1007/s10482-020-01425-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/02/2020] [Indexed: 11/26/2022]
Abstract
A novel 1-aminocyclopropane-1-carboxylate deaminase producing bacterium, Gram- stain-negative, aerobic, motile, rod-shaped strain designated YM1C-6-2T was isolated from rhizosphere of maize grown in Northeast China. The 16S rRNA gene sequence analysis indicated that strain YM1C-6-2T belongs to the genus Mesorhizobium and is closely related to Mesorhizobium alhagi CCNWXJ12-2T and M. camelthorni CCNWXJ40-4T with sequence similarities of 98.4% and 97.9%, respectively. Multilocus sequence analysis of other housekeeping genes revealed that the new isolates YM1C-6-2T forms a phylogenetically group with some species in the genus Mesorhizobium. The genome size of strain YM1C-6-2T was 5.51 Mb, comprising 5378 predicted genes with a DNA G+C content of 64.5%. The average nucleotide identity and digital DNA-DNA hybridization comparisons between YM1C-6-2T and the most related type strains showed values below the accepted threshold for species discrimination. The major fatty acids of strain YM1C-6-2T were C19:0 cyclo ω8c (47.5%), summed feature 8 (C18:1ω7c and/or C18:1ω6c) (19.5%) and C16:0 (15.1%), which differed from the closely related reference strains in their relative abundance. The major polar lipids consist of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and an unidentified aminophospholipid. The predominant ubiquinone was identified as Quinone 10. Phenotypic and biochemical analysis results indicated that strain YM1C-6-2T can be distinguished from closely related type strains. Based on the above results, strain YM1C-6-2T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium rhizophilum sp. nov. is proposed with YM1C-6-2T (= CGMCC 1.15487T = DSM 101712T) as the type strain.
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Affiliation(s)
- Jun-Lian Gao
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Jing Xue
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Yu-Chen Sun
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Han Xue
- Key Laboratory of State Forestry Administration on Forest Protection, Research Institute of Forest Ecology Environment and Protection, Chinese Academy of Forestry, Beijing, 100091, People's Republic of China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Mexico, DF, Mexico
| | - Hui Yan
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071001, People's Republic of China
| | - Shuai Tong
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Li-Wei Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China
| | - Xiuhai Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry/Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, People's Republic of China.
| | - Jian-Guang Sun
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs/ Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
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Yang X, Jiang Z, Zhang J, Zhou X, Zhang X, Wang L, Yu T, Wang Z, Bei J, Dong B, Dai Z, Yang Q, Chen Z. Mesorhizobium alexandrii sp. nov., isolated from phycosphere microbiota of PSTs-producing marine dinoflagellate Alexandrium minutum amtk4. Antonie Van Leeuwenhoek 2020; 113:907-917. [PMID: 32193664 DOI: 10.1007/s10482-020-01400-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/04/2020] [Indexed: 11/26/2022]
Abstract
An aerobic, Gram-stain-negative, motile and rod-shaped bacterial strain, designated as Z1-4T, was isolated from the phycosphere microbiota of marine dinoflagellate Alexandrium minutum that produces paralytic shellfish poisoning toxins. Phylogenetic analysis based on 16S rRNA gene sequences showed that the new isolate belongs to the genus Mesorhizobium, and it was closely related to Mesorhizobium waimense LMG 28228T and Mesorhizobium amorphae LMG 18977T with both 16S rRNA gene sequence similarities of 97.3%. The values of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) relatedness between strain Z1-4T and its relatives are both well below the thresholds used for the delineation of a new species. A genome-based phylogenetic tree constructed by up-to-date bacterial core gene set (UBCG) indicates that strain Z1-4T forms an independent branch within the genus Mesorhizobium. The respiratory quinone of strain Z1-4T was Q-10. The major fatty acids were similar to other members of the genus Mesorhizobium containing the summed feature 8, C16:0, C19:0cycloω8c, C17:0 and summed feature 3. The polar lipids are phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, five glycolipids and seven unknown polar lipids. The DNA G + C content was determined to be 62.1 mol % based on its genomic sequence. Combined evidences based on the genotypic, chemotaxonomic and phenotypic characteristics clearly indicates that strain Z1-4T represents a novel species of the genus Mesorhizobium, for which the name Mesorhizobium alexandrii sp. nov. is proposed. The type strain is Z1-4T (= KCTC 72512T = CCTCC AB 2019101T).
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Affiliation(s)
- Xi Yang
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Zhiwei Jiang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Jing Zhang
- Comprehensive Technology Service Center of Zhoushan Customs, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Xin Zhou
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Xiaoling Zhang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China
- Key Laboratory of Health Risk Factors for Seafood of Zhejiang Province, Zhoushan Municipal Center for Disease Control and Prevention, Zhoushan, 316021, Zhejiang, People's Republic of China
| | - Lei Wang
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Ting Yu
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Zhilin Wang
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Jinlong Bei
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Bo Dong
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Zhangyan Dai
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China
| | - Qiao Yang
- ABI Group, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316021, Zhejiang, People's Republic of China.
| | - Zhuang Chen
- Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China.
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Fu G, Wang R, Ding J, Qi H, Zhao Z, Chen C, Zhang H, Xue Z, Wang J, Wu M. Micromonospora zhangzhouensis sp. nov., a Novel Actinobacterium Isolated from Mangrove Soil, Exerts a Cytotoxic Activity in vitro. Sci Rep 2020; 10:3889. [PMID: 32127574 PMCID: PMC7054543 DOI: 10.1038/s41598-020-60677-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 02/13/2020] [Indexed: 11/21/2022] Open
Abstract
A new bacterial strain, designated HM134T, was isolated from a sample of soil collected from a Chinese mangrove Avicennia marina forest. Assessed by a polyphasic approach, the taxonomy of strain HM134T was found to be associated with a range of phylogenetic and chemotaxonomic properties consistent with the genus Micromonospora. Phylogenetic analysis based on the 16s rRNA gene sequence indicated that strain HM134T formed a distinct lineage with the most closely related species, including M. rifamycinica AM105T, M. wenchangensis CCTCC AA 2012002T and M. mangrovi 2803GPT1-18T. The ANI values between strain HM134T and the reference strains ranged from 82.6% to 95.2%, which was below the standard criteria for classifying strains as the same species (96.5%). Strain HM134T and related species shared in silico dDDH similarities values below the recommended 70% cut-off for the delineation of species (range from 25.7–62.6%). The DNA G+C content of strain HM134T was 73.2 mol%. Analysis of phylogenetic, genomic, phenotypic and chemotaxonomic characteristics revealed that strain HM134T is considered to represent a novel species of the genus Micromonospora, for which the name M. zhangzhouensis sp. nov. is proposed. The extract of strain HM134T was demonstrated to exhibit cytotoxic activity against the human cancer cell lines HepG2, HCT-116 and A549. Active substance presented in the fermentation broth of strain HM134T was isolated by bioassay-guided analysis and purified afterwards. A new derivative of diterpenoid was identified through electrospray ionizing mass spectrometry (MS) and nuclear magnetic resonance (NMR). The compound showed different cytotoxic activities against cancer cells, with the highest cytotoxicity against HCT-116, corresponding to IC50 value of 38.4 μg/mL.
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Affiliation(s)
- Geyi Fu
- Ocean College, Zhejiang University, Zhoushan, China
| | - Ruijun Wang
- Ocean College, Zhejiang University, Zhoushan, China
| | - Jinglin Ding
- Zhoushan Tourism & Health College, Zhoushan, China
| | - Huan Qi
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China
| | - Zhe Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Can Chen
- Ocean College, Zhejiang University, Zhoushan, China
| | - Hui Zhang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China.,College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China
| | - Zhenglian Xue
- College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China
| | - Jidong Wang
- Zhejiang Key Laboratory of Antifungal Drugs, Zhejiang Hisun Pharmaceutical Co., Ltd., Taizhou, China. .,College of Biochemical Engineering, Anhui Polytechnic University, Wuhu, China.
| | - Min Wu
- Ocean College, Zhejiang University, Zhoushan, China. .,College of Life Sciences, Zhejiang University, Hangzhou, China.
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15
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Fu GY, Yu XY, Yu XD, Zhao Z, Chen C, Wang RJ, Wu M, Zhang XQ. Azoarcus pumilus sp. nov., isolated from seawater in Sanya, China. Int J Syst Evol Microbiol 2019; 69:1459-1464. [PMID: 30882295 DOI: 10.1099/ijsem.0.003341] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ge-yi Fu
- 1Ocean College, Zhejiang University, Zhoushan 316021, PR China
| | - Xiao-yun Yu
- 2Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, 310004, PR China
| | - Xiao-dong Yu
- 3College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhe Zhao
- 3College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Can Chen
- 1Ocean College, Zhejiang University, Zhoushan 316021, PR China
| | - Rui-jun Wang
- 1Ocean College, Zhejiang University, Zhoushan 316021, PR China
| | - Min Wu
- 1Ocean College, Zhejiang University, Zhoushan 316021, PR China
- 3College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xin-qi Zhang
- 4College of Forestry and Biotechnology, Zhejiang Agricultural and Forestry University, Lin’an 311300, PR China
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Mesorhizobium carbonis sp. nov., isolated from coal bed water. Antonie van Leeuwenhoek 2019; 112:1221-1229. [DOI: 10.1007/s10482-019-01254-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 03/04/2019] [Indexed: 12/12/2022]
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Ye Y, Chen C, Ren Y, Wang R, Zhang C, Han S, Ju Z, Zhao Z, Sun C, Wu M. Pseudomonas mangrovi sp. nov., isolated from mangrove soil. Int J Syst Evol Microbiol 2019; 69:377-383. [PMID: 30601113 DOI: 10.1099/ijsem.0.003141] [Citation(s) in RCA: 10] [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, aerobic, non-motile, short-rod-shaped bacterium, designated as strain TC11T, was isolated from rhizosphere soil of mangrove forest (Kandeliaobovata) in Fugong village, Zhangzhou, Fujian, China. Strain TC11T grew at 15-45 °C (optimum, 35 °C), 0-8 % (w/v) NaCl (optimum, 1 %, w/v) and pH 5.5-9.5 (optimum, pH 7.5). Phylogenetic analyses revealed that strain TC11T belonged to a clade of the genus Pseudomonas and showed the highest sequence similarity of 98.4 % to Pseudomonas fluvialis ASS-1T, followed by Pseudomonas oleovorans subsp.oleovorans DSM 1045T (97.9 %), Pseudomonas indoloxydans JCM 14246T (97.7 %), Pseudomonas guguanensis JCM 18416T(97.6 %) and Pseudomonas alcaliphila JCM 10630T (97.5 %) on the basis of their 16S rRNA gene sequences. The DNA G+C content was 64.3 mol%. In silico DNA-DNA hybridization and average nucleotide identity values between strain TC11T and the reference strains were 19-22 % and 72-78 %, respectively. Studies based on the three housekeeping genes, rpoB, gyrB and rpoD, further confirmed that strain TC11T is a novel member of the genus Pseudomonas. The major fatty acids of strain TC11Twere C16 : 0, summed feature 8 (C18 : 1ω6c/C18 : 1ω7c) and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). The sole isoprenoid quinone was Q-9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on the phenotypic, chemotaxonomic and phylogenetic properties, strain TC11T represents a novel species of the genus Pseudomonas, for which the name Pseudomonasmangrovi sp. nov., is proposed. The type strain is TC11T (=KCTC 62159=MCCC 1K03499).
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Affiliation(s)
- Yanghui Ye
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Can Chen
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Yanhu Ren
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Ruijun Wang
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Chongya Zhang
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
| | - Shuaibo Han
- 2College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhao Ju
- 2College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Zhu Zhao
- 2College of Life Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Cong Sun
- 3College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Min Wu
- 1Ocean College, Zhejiang University, Zhoushan 316000, PR China
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Liu L, Liang LX, Zhang XX, Li LB, Sun QW. Mesorhizobium ephedrae sp. nov. isolated from the roots of Ephedra przewalskii in Kumtag desert. Int J Syst Evol Microbiol 2018; 68:3615-3620. [DOI: 10.1099/ijsem.0.003044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lei Liu
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Li-xiong Liang
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Xiao-xia Zhang
- 2Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Lu-bin Li
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
| | - Qi-wu Sun
- 1State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, PR China
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de Lajudie PM, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of rhizobia and agrobacteria Minutes of the closed meeting, Granada, 4 September 2017. Int J Syst Evol Microbiol 2018; 68:3363-3368. [DOI: 10.1099/ijsem.0.002974] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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