101
|
Yao Y, Sui XH, Zhang XX, Wang ET, Chen WX. Bradyrhizobium erythrophlei sp. nov. and Bradyrhizobium ferriligni sp. nov., isolated from effective nodules of Erythrophleum fordii. Int J Syst Evol Microbiol 2015; 65:1831-1837. [PMID: 25754551 DOI: 10.1099/ijs.0.000183] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six slow-growing rhizobial strains isolated from effective nodules of Erythrophleum fordii were classified into the genus Bradyrhizobiumbased on their 16S rRNA gene sequences. The results of multilocus sequence analysis of recA, glnII and gyrB genes and 16S-23S rRNA intergenic spacer (IGS) sequence phylogeny indicated that the six strains belonged to two novel species, represented by CCBAU 53325T and CCBAU 51502T, which were consistent with the results of DNA-DNA hybridization; CCBAU 53325T had 17.65-25.59 % relatedness and CCBAU 51502T had 22.69-44.58 % relatedness with five closely related type strains, Bradyrhizobium elkanii USDA 76T, B. pachyrhizi LMG 24246T, B. lablabi CCBAU 23086T, B. jicamae LMG 24556T and B. japonicum USDA 6T. In addition, analysis of phenotypic characteristics and fatty acid profiles also distinguished the test strains from defined species of Bradyrhizobium. Two novel species, Bradyrhizobium erythrophlei sp. nov., represented by the type strain CCBAU 53325T ( = HAMBI 3614T = CGMCC 1.13002T = LMG 28425T), and Bradyrhizobium ferriligni sp. nov., represented by the type strain CCBAU 51502T ( = HAMBI 3613T = CGMCC 1.13001T), are proposed to accommodate the strains.
Collapse
Affiliation(s)
- Yao Yao
- State Key Lab for Agro-Biotechnology; Ministry of Agriculture Key Lab of Soil Microbiology; College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Lab for Agro-Biotechnology; Ministry of Agriculture Key Lab of Soil Microbiology; College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xiao Xia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - En Tao Wang
- State Key Lab for Agro-Biotechnology; Ministry of Agriculture Key Lab of Soil Microbiology; College of Biological Sciences, China Agricultural University, Beijing 100193, PR China.,Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México DF, Mexico
| | - Wen Xn Chen
- State Key Lab for Agro-Biotechnology; Ministry of Agriculture Key Lab of Soil Microbiology; College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| |
Collapse
|
102
|
Mousavi SA, Willems A, Nesme X, de Lajudie P, Lindström K. Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Syst Appl Microbiol 2015; 38:84-90. [DOI: 10.1016/j.syapm.2014.12.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/07/2014] [Accepted: 12/12/2014] [Indexed: 01/26/2023]
|
103
|
Sheu SY, Huang HW, Young CC, Chen WM. Rhizobium alvei sp. nov., isolated from a freshwater river. Int J Syst Evol Microbiol 2015; 65:472-478. [DOI: 10.1099/ijs.0.065706-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated TNR-22T was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TNR-22T were facultatively anaerobic, Gram-stain-negative, rod-shaped, motile by a single polar flagellum and formed cream-coloured colonies. Growth occurred at 4–45 °C (optimum, 25–30 °C), with 0–1.0 % (w/v) NaCl (optimum, 0.5 %) and at pH 7.0–8.0 (optimum, pH 7.0). Strain TNR-22T did not form nodules on Macroptilium atropurpureum. The nifH gene encoding denitrogenase reductase was not detected by PCR. The major fatty acids (>10 %) of strain TNR-22T were C18 : 1ω7c and C16 : 0. The DNA G+C content was 60.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an uncharacterized aminoglycolipid and an uncharacterized phospholipid. Comparative analysis of 16S rRNA gene sequences showed that strain TNR-22T constituted a distinct branch within the genus
Rhizobium
, showing the highest level of sequence similarity with
Rhizobium rosettiformans
W3T (96.3 %). Phenotypic characteristics of the novel strain also differed from those of the most closely related species of the genus
Rhizobium
. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain TNR-22T represents a novel species in the genus
Rhizobium
, for which the name Rhizobium alvei sp. nov. is proposed. The type strain is TNR-22T ( = BCRC 80408T = LMG 26895T = KCTC 23919T).
Collapse
Affiliation(s)
- Shih-Yi Sheu
- Department of Marine Biotechnology, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Hsing-Wei Huang
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| | - Chiu-Chung Young
- College of Agriculture and Natural Resources, Department of Soil and Environmental Sciences, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Wen-Ming Chen
- Laboratory of Microbiology, Department of Seafood Science, National Kaohsiung Marine University, No. 142 Hai-Chuan Rd, Nan-Tzu, Kaohsiung City 811, Taiwan, ROC
| |
Collapse
|
104
|
Jiao YS, Yan H, Ji ZJ, Liu YH, Sui XH, Wang ET, Guo BL, Chen WX, Chen WF. Rhizobium sophorae sp. nov. and Rhizobium sophoriradicis sp. nov., nitrogen-fixing rhizobial symbionts of the medicinal legume Sophora flavescens. Int J Syst Evol Microbiol 2015; 65:497-503. [DOI: 10.1099/ijs.0.068916-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five bacterial strains representing 45 isolates originated from root nodules of the medicinal legume Sophora flavescens were defined as two novel groups in the genus
Rhizobium
based on their phylogenetic relationships estimated from 16S rRNA genes and the housekeeping genes recA, glnII and atpD. These groups were distantly related to
Rhizobium leguminosarum
USDA 2370T (95.6 % similarity for group I) and
Rhizobium phaseoli
ATCC 14482T (93.4 % similarity for group II) in multilocus sequence analysis. In DNA–DNA hybridization experiments, the reference strains CCBAU 03386T (group I) and CCBAU 03470T (group II) showed levels of relatedness of 17.9–57.8 and 11.0–42.9 %, respectively, with the type strains of related species. Both strains CCBAU 03386T and CCBAU 03470T contained ubiquinone 10 (Q-10) as the major respiratory quinone and possessed 16 : 0, 18 : 0, 19 : 0 cyclo ω8c, summed feature 8 and summed feature 2 as major fatty acids, but did not contain 20 : 3 ω6,8,12c. Phenotypic features distinguishing both groups from all closely related species of the genus
Rhizobium
were found. Therefore, two novel species, Rhizobium sophorae sp. nov. for group I (type strain CCBAU 03386T = E5T = LMG 27901T = HAMBI 3615T) and Rhizobium sophoriradicis sp. nov. for group II (type strain CCBAU 03470T = C-5-1T = LMG 27898T = HAMBI 3510T), are proposed. Both groups were able to nodulate Phaseolus vulgaris and their hosts of origin (Sophora flavescens) effectively and their nodulation gene nodC was phylogenetically located in the symbiovar phaseoli.
Collapse
Affiliation(s)
- Yin Shan Jiao
- MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
- College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, PR China
- State Key Laboratory of Agrobiotechnology, Beijing 100193, PR China
| | - Hui Yan
- MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
- College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, PR China
- State Key Laboratory of Agrobiotechnology, Beijing 100193, PR China
| | - Zhao Jun Ji
- MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
- College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, PR China
- State Key Laboratory of Agrobiotechnology, Beijing 100193, PR China
| | - Yuan Hui Liu
- MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
- College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, PR China
- State Key Laboratory of Agrobiotechnology, Beijing 100193, PR China
| | - Xin Hua Sui
- MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
- College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, PR China
- State Key Laboratory of Agrobiotechnology, Beijing 100193, PR China
| | - En Tao Wang
- MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
- College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, PR China
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, México
- State Key Laboratory of Agrobiotechnology, Beijing 100193, PR China
| | - Bao Lin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, PR China
| | - Wen Xin Chen
- MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
- College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, PR China
- State Key Laboratory of Agrobiotechnology, Beijing 100193, PR China
| | - Wen Feng Chen
- MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
- College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, PR China
- State Key Laboratory of Agrobiotechnology, Beijing 100193, PR China
| |
Collapse
|
105
|
Kelly S, Sullivan J, Ronson C, Tian R, Bräu L, Munk C, Goodwin L, Han C, Woyke T, Reddy T, Huntemann M, Pati A, Mavromatis K, Markowitz V, Ivanova N, Kyrpides N, Reeve W. Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A. Stand Genomic Sci 2014; 9:6. [PMID: 25780499 PMCID: PMC4334631 DOI: 10.1186/1944-3277-9-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 06/16/2014] [Indexed: 11/10/2022] Open
Abstract
Mesorhizobium loti strain R7A was isolated in 1993 in Lammermoor, Otago, New Zealand from a Lotus corniculatus root nodule and is a reisolate of the inoculant strain ICMP3153 (NZP2238) used at the site. R7A is an aerobic, Gram-negative, non-spore-forming rod. The symbiotic genes in the strain are carried on a 502-kb integrative and conjugative element known as the symbiosis island or ICEMlSym(R7A). M. loti is the microsymbiont of the model legume Lotus japonicus and strain R7A has been used extensively in studies of the plant-microbe interaction. This report reveals that the genome of M. loti strain R7A does not harbor any plasmids and contains a single scaffold of size 6,529,530 bp which encodes 6,323 protein-coding genes and 75 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
Collapse
Affiliation(s)
- Simon Kelly
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - John Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Clive Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Perth, Australia
| | - Lambert Bräu
- School of Life and Environmental Sciences, Deakin University, Melbourne, Australia
| | - Christine Munk
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Cliff Han
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Konstantinos Mavromatis
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, California, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Perth, Australia
| |
Collapse
|
106
|
Reeve W, Sullivan J, Ronson C, Tian R, Bräu L, Davenport K, Goodwin L, Chain P, Woyke T, Lobos E, Huntemann M, Pati A, Mavromatis K, Markowitz V, Ivanova N, Kyrpides N. Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B. Stand Genomic Sci 2014; 9:3. [PMID: 25780496 PMCID: PMC4334104 DOI: 10.1186/1944-3277-9-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 06/16/2014] [Indexed: 11/22/2022] Open
Abstract
Mesorhizobium loti strain R88B was isolated in 1993 in the Rocklands range in Otago, New Zealand from a Lotus corniculatus root nodule. R88B is an aerobic, Gram-negative, non-spore-forming rod. This report reveals the genome of M. loti strain R88B contains a single scaffold of size 7,195,110 bp which encodes 6,950 protein-coding genes and 66 RNA-only encoding genes. This genome does not harbor any plasmids but contains the integrative and conjugative element ICEMlSymR7A, also known as the R7A symbiosis island, acquired by horizontal gene transfer in the field environment from M. loti strain R7A. It also contains a mobilizable genetic element ICEMladhR88B, that encodes a likely adhesin gene which has integrated downstream of ICEMlSymR7A, and three acquired loci that together allow the utilization of the siderophore ferrichrome. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
Collapse
Affiliation(s)
- Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - John Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Clive Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Western Australia, Australia
| | - Lambert Bräu
- School of Life and Environmental Sciences, Deakin University, Victoria, Australia
| | - Karen Davenport
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| |
Collapse
|
107
|
Kelly S, Sullivan J, Ronson C, Tian R, Bräu L, Davenport K, Daligault H, Erkkila T, Goodwin L, Gu W, Munk C, Teshima H, Xu Y, Chain P, Woyke T, Liolios K, Pati A, Mavromatis K, Markowitz V, Ivanova N, Kyrpides N, Reeve W. Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain NZP2037. Stand Genomic Sci 2014; 9:7. [PMID: 25780500 PMCID: PMC4334872 DOI: 10.1186/1944-3277-9-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 06/16/2014] [Indexed: 12/04/2022] Open
Abstract
Mesorhizobium loti strain NZP2037 was isolated in 1961 in Palmerston North, New Zealand from a Lotus divaricatus root nodule. Compared to most other M. loti strains, it has a broad host range and is one of very few M. loti strains able to form effective nodules on the agriculturally important legume Lotus pedunculatus. NZP2037 is an aerobic, Gram negative, non-spore-forming rod. This report reveals that the genome of M. loti strain NZP2037 does not harbor any plasmids and contains a single scaffold of size 7,462,792 bp which encodes 7,318 protein-coding genes and 70 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.
Collapse
Affiliation(s)
- Simon Kelly
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - John Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Clive Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Perth, Australia
| | - Lambert Bräu
- School of Life and Environmental Sciences, Deakin University, Deakin, Victoria, Australia
| | - Karen Davenport
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Hajnalka Daligault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Tracy Erkkila
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Wei Gu
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Christine Munk
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Yan Xu
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA, USA
| | - Konstantinos Mavromatis
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Victor Markowitz
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, Perth, Australia
| |
Collapse
|
108
|
Francini G, Männistö M, Alaoja V, Kytöviita MM. Arbuscular mycorrhizal fungal community divergence within a common host plant in two different soils in a subarctic Aeolian sand area. MYCORRHIZA 2014; 24:539-550. [PMID: 24687606 DOI: 10.1007/s00572-014-0573-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 03/13/2014] [Indexed: 06/03/2023]
Abstract
There is rising awareness that different arbuscular mycorrhizal (AM) fungi have different autoecology and occupy different soil niches and that the benefits they provide to the host plant are dependent on plant-AM fungus combination. However, the role and community composition of AM fungi in succession are not well known and the northern latitudes remain poorly investigated ecosystems. We studied AM fungal communities in the roots of the grass Deschampsia flexuosa in two different, closely located, successional stages in a northern Aeolian sand area. The AM fungal taxa richness in planta was estimated by cloning and sequencing small subunit ribosomal RNA genes. AM colonization, shoot δ (13)C signature, and %N and %C were measured. Soil microbial community structure and AM fungal mycelium abundance were estimated using phospholipid (PLFA) and neutral lipid (NLFA) analyses. The two successional stages were characterized by distinct plant, microbial, and fungal communities. AM fungal species richness was very low in both the early and late successional stages. AM frequency in D. flexuosa roots was higher in the early successional stage than in the late one. The AM fungal taxa retrieved belonged to the genera generally adapted to Arctic or extreme environments. AM fungi seemed to be important in the early stage of the succession, suggesting that AM fungi may help plants to better cope with the harsh environmental conditions, especially in an early successional stage with more extreme environmental fluctuations.
Collapse
Affiliation(s)
- Gaia Francini
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland,
| | | | | | | |
Collapse
|
109
|
Zilli JE, Baraúna AC, da Silva K, De Meyer SE, Farias ENC, Kaminski PE, da Costa IB, Ardley JK, Willems A, Camacho NN, Dourado FDS, O'Hara G. Bradyrhizobium neotropicale sp. nov., isolated from effective nodules of Centrolobium paraense. Int J Syst Evol Microbiol 2014; 64:3950-3957. [PMID: 25205796 DOI: 10.1099/ijs.0.065458-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Root nodule bacteria were isolated from Centrolobium paraense Tul. grown in soils from the Amazon region, State of Roraima (Brazil). 16S rRNA gene sequence analysis of seven strains (BR 10247(T), BR 10296, BR 10297, BR 10298, BR 10299, BR 10300 and BR 10301) placed them in the genus Bradyrhizobium with the closest neighbours being the type strains of Bradyrhizobium paxllaeri (98.8 % similarity), Bradyrhizobium icense (98.8 %), Bradyrhizobium lablabi (98.7 %), Bradyrhizobium jicamae (98.6 %), Bradyrhizobium elkanii (98.6 %), Bradyrhizobium pachyrhizi (98.6 %) and Bradyrhizobium retamae (98.3 %). This high similarity, however, was not confirmed by the intergenic transcribed spacer (ITS) 16S-23S rRNA region sequence analysis nor by multi-locus sequence analysis. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05(T) ( = LMG 24129(T)) to be the most closely related type strain (95.7 % sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [major components being C16 : 0 and summed feature 8 (18 : 1ω6c/18 : 1ω7c)], DNA G+C content, slow growth rate and carbon compound utilization patterns, supported the placement of the novel strains in the genus Bradyrhizobium. Results of DNA-DNA relatedness studies and physiological data (especially carbon source utilization) differentiated the strains from the closest recognized species of the genus Bradyrhizobium. Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) placed the novel species in a new branch within the genus Bradyrhizobium. Based on the current data, these seven strains represent a novel species for which the name Bradyrhizobium neotropicale sp. nov. is proposed. The type strain is BR 10247(T) ( = HAMBI 3599(T)).
Collapse
Affiliation(s)
- Jerri E Zilli
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Alexandre C Baraúna
- Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23890-000, Brazil
| | - Krisle da Silva
- Embrapa Roraima, Rodovia BR 174 km 08, Boa Vista, Roraima 69301-970, Brazil
| | - Sofie E De Meyer
- Laboratory of Microbiology, Department of Biochemistry and Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
| | - Eliane N C Farias
- Embrapa Roraima, Rodovia BR 174 km 08, Boa Vista, Roraima 69301-970, Brazil
| | - Paulo E Kaminski
- Embrapa Roraima, Rodovia BR 174 km 08, Boa Vista, Roraima 69301-970, Brazil
| | - Ismaele B da Costa
- Embrapa Roraima, Rodovia BR 174 km 08, Boa Vista, Roraima 69301-970, Brazil
| | - Julie K Ardley
- Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Natália N Camacho
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Fernanda Dos S Dourado
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Graham O'Hara
- Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
| |
Collapse
|
110
|
Rozahon M, Ismayil N, Hamood B, Erkin R, Abdurahman M, Mamtimin H, Abdukerim M, Lal R, Rahman E. Rhizobium
populi sp. nov., an endophytic bacterium isolated from Populus euphratica. Int J Syst Evol Microbiol 2014; 64:3215-3221. [DOI: 10.1099/ijs.0.061416-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An endophytic bacterium, designated K-38T, was isolated from the storage liquid in the stems of Populus euphratica trees at the ancient Ugan River in Xinjiang, PR China. Strain K-38T was found to be rod-shaped, Gram-stain-negative, aerobic, non-motile and non-spore-forming. Strain K-38T grew at temperatures of 25–37 °C (optimum, 28 °C), at pH 6.0–9.0 (optimum, pH 7.5) and in the presence of 0–3 % (w/v) NaCl with 1 % as the optimum concentration for growth. According to phylogenetic analysis based on 16S rRNA gene sequences, strain K-38T was assigned to the genus
Rhizobium
with highest 16S rRNA gene sequence similarity of 97.2 % to
Rhizobium rosettiformans
W3T, followed by
Rhizobium nepotum
39/7T (96.5 %) and
Rhizobium borbori
DN316T (96.2 %). Phylogenetic analysis of strain K-38T based on the protein coding genes recA, atpD and nifH confirmed (similarities were less than 90 %) it to be a representative of a distinctly delineated species of the genus
Rhizobium
. The DNA G+C content was determined to be 63.5 mol%. DNA–DNA relatedness between K-38T and
R. rosettiformans
W3T was 48.4 %, indicating genetic separation of strain K-38T from the latter strain. The major components of the cellular fatty acids in strain K-38T were revealed to be summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c; 57.2 %), C16 : 0 (13.6 %) and summed feature 2 (comprising C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 1 I and/or unknown ECL 10.928; 11.0 %). Polar lipids of strain K-38T include phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids and two unidentified phospholipids. Q-10 was the major quinone in strain K-38T. Based on phenotypic, chemotaxonomic and phylogenetic properties, strain K-38T represents a novel species of the genus
Rhizobium
, for which the name Rhizobium
populi sp. nov. is proposed. The type strain is K-38T ( = CCTCC AB 2013068T = NRRL B-59990T = JCM 19159T).
Collapse
Affiliation(s)
- Manziram Rozahon
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Nurimangul Ismayil
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Buayshem Hamood
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Raziya Erkin
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Mehfuzem Abdurahman
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Hormathan Mamtimin
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Muhtar Abdukerim
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Erkin Rahman
- College of Life Science and Technology of Xinjiang University, Urumchi, Xinjiang 830046, PR China
| |
Collapse
|
111
|
Suarez C, Ratering S, Geissler-Plaum R, Schnell S. Hartmannibacter diazotrophicus gen. nov., sp. nov., a phosphate-solubilizing and nitrogen-fixing alphaproteobacterium isolated from the rhizosphere of a natural salt-meadow plant. Int J Syst Evol Microbiol 2014; 64:3160-3167. [DOI: 10.1099/ijs.0.064154-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A phosphate-mobilizing, Gram-negative bacterium was isolated from rhizospheric soil of Plantago winteri from a natural salt meadow as part of an investigation of rhizospheric bacteria from salt-resistant plant species and evaluation of their plant-growth-promoting abilities. Cells were rods, motile, strictly aerobic, oxidase-positive and catalase-negative. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain E19T was distinct from other taxa within the class
Alphaproteobacteria
. Strain E19T showed less than 93.5 % 16S rRNA gene sequence similarity with members of the genera
Rhizobium
(≤93.5 %),
Labrenzia
(≤93.1 %),
Stappia
(≤93.1 %),
Aureimonas
(≤93.1 %) and
Mesorhizobium
(≤93.0 %) and was most closely related to
Rhizobium rhizoryzae
(93.5 % 16S rRNA gene sequence similarity to the type strain). The sole respiratory quinone was Q-10, and the polar lipids comprised phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an aminolipid and an unidentified phospholipid. Major fatty acids were C18 : 1ω7c (71.4 %), summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1; 8.3 %), C20 : 0 (7.9 %) and C16 : 0 (6.1 %). The DNA G+C content of strain E19T was 59.9±0.7 mol%. The capacity for nitrogen fixation was confirmed by the presence of the nifH gene and the acetylene reduction assay. On the basis of the results of our polyphasic taxonomic study, the new isolate represents a novel genus and species, for which the name Hartmannibacter diazotrophicus gen. nov., sp. nov. is proposed. The type strain of Hartmannibacter diazotrophicus is E19T ( = LMG 27460T = KACC 17263T).
Collapse
Affiliation(s)
- Christian Suarez
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Stefan Ratering
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Rita Geissler-Plaum
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, IFZ, Justus-Liebig University Giessen, 35392 Giessen, Germany
| |
Collapse
|
112
|
Yu X, Cloutier S, Tambong JT, Bromfield ESP. Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada. Int J Syst Evol Microbiol 2014; 64:3202-3207. [PMID: 24969302 PMCID: PMC4156109 DOI: 10.1099/ijs.0.065540-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Sixteen strains of symbiotic bacteria from root nodules of Glycine max grown in Ottawa, Canada, were previously characterized and placed in a novel group within the genus Bradyrhizobium. To verify their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences that were 99.79 % similar to the closest relative, Bradyrhizobium liaoningense LMG 18230(T). Phylogenetic analysis of concatenated atpD, glnII, recA, gyrB, rpoB and dnaK genes divided the 16 strains into three multilocus sequence types that were placed in a highly supported lineage distinct from named species of the genus Bradyrhizobium consistent with results of DNA-DNA hybridization. Based on analysis of symbiosis gene sequences (nodC and nifH), all novel strains were placed in a phylogenetic group with five species of the genus Bradyrhizobium that nodulate soybeans. The combination of phenotypic characteristics from several tests including carbon and nitrogen source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Novel strain OO99(T) elicits effective nodules on Glycine max, Glycine soja and Macroptilium atropurpureum, partially effective nodules on Desmodium canadense and Vigna unguiculata, and ineffective nodules on Amphicarpaea bracteata and Phaseolus vulgaris. Based on the data presented, we conclude that our strains represent a novel species for which the name Bradyrhizobium ottawaense sp. nov. is proposed, with OO99(T) ( = LMG 26739(T) = HAMBI 3284(T)) as the type strain. The DNA G+C content is 62.6 mol%.
Collapse
Affiliation(s)
- Xiumei Yu
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada
| | - Sylvie Cloutier
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada
| | - James T Tambong
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada
| | - Eden S P Bromfield
- Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada
| |
Collapse
|
113
|
Rhizobium
paranaense sp. nov., an effective N2-fixing symbiont of common bean (Phaseolus vulgaris L.) with broad geographical distribution in Brazil. Int J Syst Evol Microbiol 2014; 64:3222-3229. [DOI: 10.1099/ijs.0.064543-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrogen (N), the nutrient most required for plant growth, is key for good yield of agriculturally important crops. Common bean (Phaseolus vulgaris L.) can benefit from bacteria collectively called rhizobia, which are capable of fixing atmospheric nitrogen (N2) in root nodules and supplying it to the plant. Common bean is amongst the most promiscuous legume hosts; several described species, in addition to putative novel ones have been reported as able to nodulate this legume, although not always effectively in terms of fixing N2. In this study, we present data indicating that Brazilian strains PRF 35T, PRF 54, CPAO 1135 and H 52, currently classified as
Rhizobium tropici
, represent a novel species symbiont of common bean. Morphological, physiological and biochemical properties differentiate these strains from other species of the genus
Rhizobium
, as do BOX-PCR profiles (less than 60 % similarity), multilocus sequence analysis with recA, gyrB and rpoA (less than 96.4 % sequence similarity), DNA–DNA hybridization (less than 50 % DNA–DNA relatedness), and average nucleotide identity of whole genomes (less than 92.8.%). The novel species is effective in nodulating and fixing N2 with P. vulgaris, Leucaena leucocephala and Leucaena esculenta. We propose the name Rhizobium paranaense sp. nov. for this novel taxon, with strain PRF 35T ( = CNPSo 120T = LMG 27577T = IPR-Pv 1249T) as the type strain.
Collapse
|
114
|
da Silva K, De Meyer SE, Rouws LFM, Farias ENC, Dos Santos MAO, O'Hara G, Ardley JK, Willems A, Pitard RM, Zilli JE. Bradyrhizobium ingae sp. nov., isolated from effective nodules of Inga laurina grown in Cerrado soil. Int J Syst Evol Microbiol 2014; 64:3395-3401. [PMID: 25013231 DOI: 10.1099/ijs.0.063727-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Root-nodule bacteria were isolated from Inga laurina (Sw.) Willd. growing in the Cerrado Amazon region, State of Roraima, Brazil. The 16S rRNA gene sequences of six strains (BR 10250(T), BR 10248, BR 10249, BR 10251, BR 10252 and BR 10253) showed low similarities with currently described species of the genus Bradyrhizobium. Phylogenetic analyses of sequences of five housekeeping genes (dnaK, glnII, gyrB, recA and rpoB) revealed Bradyrhizobium iriomotense EK05(T) to be the closest type strain (97.4% sequence similarity or less). Chemotaxonomic data, including fatty acid profiles [with the major components C16:0 and summed feature 8 (C18:1ω6c/C18:1ω7c)], the slow growth rate and carbon compound utilization patterns supported the assignment of our strains to the genus Bradyrhizobium. Results from DNA-DNA hybridizations and physiological traits differentiated our strains from the closest related species of the genus Bradyrhizobium with validly published names. Sequences of symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) grouped together with those of B. iriomotense EK05(T) and Bradyrhizobium sp. strains BR 6610 (used as a commercial inoculant for Inga marginata in Brazil) and TUXTLAS-10 (previously observed in Central America). Based on these data, the six strains represent a novel species, for which the name Bradyrhizobium ingae sp. nov. is proposed. The type strain is BR 10250(T) ( = HAMBI 3600(T)).
Collapse
Affiliation(s)
- Krisle da Silva
- Embrapa Roraima, Rodovia BR 174 km 08, Boa Vista, Roraima 69301-970, Brazil
| | - Sofie E De Meyer
- Laboratory of Microbiology, Department of Biochemistry and Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
| | - Luc F M Rouws
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Eliane N C Farias
- Embrapa Roraima, Rodovia BR 174 km 08, Boa Vista, Roraima 69301-970, Brazil
| | - Marco A O Dos Santos
- Universidade Estadual de Roraima, Rua Sete de Setembro, 231, Canarinho, Boa Vista - Roraima, 69306-530, Brazil
| | - Graham O'Hara
- Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
| | - Julie K Ardley
- Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Rosa Maria Pitard
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Jerri E Zilli
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| |
Collapse
|
115
|
Kittiwongwattana C, Thawai C. Rhizobium
lemnae sp. nov., a bacterial endophyte of Lemna aequinoctialis. Int J Syst Evol Microbiol 2014; 64:2455-2460. [DOI: 10.1099/ijs.0.061622-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Bacterial strain L6-16T was isolated from Lemna aequinoctialis. Cells were Gram-stain-negative, rod-shaped and motile with monopolar flagella. The phylogenetic analysis of its nearly complete 16S rRNA gene sequence revealed that strain L6-16T was a member of the genus
Rhizobium
. Its closest relative was
Rhizobium tarimense
PL-41T with a 16S rRNA gene sequence similarity value of 98.3 %. Sequence similarity analysis of the housekeeping recA and atpD genes showed low levels of sequence similarity (<93.9 %) between strain L6-16T and other species of the genus
Rhizobium
. Strain L6-16T was able to grow between pH 5 and 11 (optimum 7.0) and at temperatures ranging from 20 to 41 °C (optimum 30 °C). It tolerated NaCl up to 1 % (w/v) (optimum 0.5 %). C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8; 79.5 %) were found as predominant cellular fatty acids. The DNA G+C content of strain L6-16T was 58.1 mol% (T
m). Based on low levels of DNA–DNA relatedness, strain L6-16T was distinct from members of phylogenetically related species including
R. tarimense
PL-41T (38.3±0.8 %),
Rhizobium rosettiformans
W3T (6.9±0.4 %) and
Rhizobium pseudoryzae
J3-A127T (12.3±0.6 %). Strain L6-16T was unable to nodulate the roots of Phaseolus vulgaris, and nodC and nifH genes were not detected. The results obtained from phylogenetic analyses, phenotypic characterization and DNA–DNA hybridization indicated that strain L6-16T represents a novel species of the genus
Rhizobium
, for which the name Rhizobium lemnae sp. nov. is proposed. The type strain is L6-16T ( = NBRC 109339T = BCC 55143T).
Collapse
Affiliation(s)
- Chokchai Kittiwongwattana
- Actinobacterial Research Unit, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
- Department of Biology, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Chitti Thawai
- Actinobacterial Research Unit, Faculty of Science, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
- Department of Biology, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| |
Collapse
|
116
|
Durán D, Rey L, Navarro A, Busquets A, Imperial J, Ruiz-Argüeso T. Bradyrhizobium valentinum sp. nov., isolated from effective nodules of Lupinus mariae-josephae, a lupine endemic of basic-lime soils in Eastern Spain. Syst Appl Microbiol 2014; 37:336-41. [DOI: 10.1016/j.syapm.2014.05.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 05/01/2014] [Accepted: 05/02/2014] [Indexed: 11/28/2022]
|
117
|
Jia J, Chen Y, Jiang Y, Tang J, Yang L, Liang C, Jia Z, Zhao L. Visualized analysis of cellular fatty acid profiles of Vibrio parahaemolyticus strains under cold stress. FEMS Microbiol Lett 2014; 357:92-8. [PMID: 24910303 DOI: 10.1111/1574-6968.12498] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/28/2014] [Accepted: 06/02/2014] [Indexed: 12/01/2022] Open
Abstract
Vibrio parahaemolyticus is a common foodborne bacterial pathogen, which survives in cold environments and is sometimes difficult to culture. Fatty acid analysis under cold stress was conducted for several V. parahaemolyticus strains using gas chromatography/mass spectrometry, and the results were compared with those of the controls. All the fatty acid profiles obtained were visualized by multidimensional scaling (MDS) and self-organized map (SOM). It was observed that the fatty acid profiles of V. parahaemolyticus substantially changed under cold stress. The percentage of methyl palmitate remarkably decreased and that of methyl palmitoleate (except for two strains) and methyl oleate increased. These findings demonstrate the role of fatty acids in cold stress. The changes in the fatty acid profiles illustrated by MDS and SOM could differentiate strains under cold stress from the controls and can potentially lead to a method of detecting injured cold-stressed V. parahaemolyticus.
Collapse
Affiliation(s)
- Juntao Jia
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, Qingdao, China
| | | | | | | | | | | | | | | |
Collapse
|
118
|
Durán D, Rey L, Mayo J, Zúñiga-Dávila D, Imperial J, Ruiz-Argüeso T, Martínez-Romero E, Ormeño-Orrillo E. Bradyrhizobium paxllaeri sp. nov. and Bradyrhizobium icense sp. nov., nitrogen-fixing rhizobial symbionts of Lima bean (Phaseolus lunatus L.) in Peru. Int J Syst Evol Microbiol 2014; 64:2072-2078. [DOI: 10.1099/ijs.0.060426-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A group of strains isolated from root nodules of Phaseolus lunatus (Lima bean) in Peru were characterized by genotypic, genomic and phenotypic methods. All strains possessed identical 16S rRNA gene sequences that were 99.9 % identical to that of
Bradyrhizobium lablabi
CCBAU 23086T. Despite having identical 16S rRNA gene sequences, the Phaseolus lunatus strains could be divided into two clades by sequence analysis of recA, atpD, glnII, dnaK and gyrB genes. The genome sequence of a representative of each clade was obtained and compared to the genomes of closely related species of the genus
Bradyrhizobium
. Average nucleotide identity values below the species circumscription threshold were obtained when comparing the two clades to each other (88.6 %) and with all type strains of the genus
Bradyrhizobium
(≤92.9 %). Phenotypes distinguishing both clades from all described and closely related species of the genus
Bradyrhizobium
were found. On the basis of the results obtained, two novel species, Bradyrhizobium paxllaeri sp. nov. (type strain LMTR 21T = DSM 18454T = HAMBI 2911T) and Bradyrhizobium icense sp. nov. (type strain LMTR 13T = HAMBI 3584T = CECT 8509T = CNPSo 2583T), are proposed to accommodate the uncovered clades of Phaseolus lunatus bradyrhizobia. These species share highly related but distinct nifH and nodC symbiosis genes.
Collapse
Affiliation(s)
- David Durán
- Departamento de Biotecnología (ETS de Ingenieros Agrónomos) and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Spain
| | - Luis Rey
- Departamento de Biotecnología (ETS de Ingenieros Agrónomos) and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Spain
| | - Juan Mayo
- Laboratorio de Ecología Microbiana y Biotecnología ‘Marino Tabusso’, Universidad Nacional Agraria La Molina, Peru
| | - Doris Zúñiga-Dávila
- Laboratorio de Ecología Microbiana y Biotecnología ‘Marino Tabusso’, Universidad Nacional Agraria La Molina, Peru
| | - Juan Imperial
- Departamento de Biotecnología (ETS de Ingenieros Agrónomos) and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Spain
| | - Tomás Ruiz-Argüeso
- Departamento de Biotecnología (ETS de Ingenieros Agrónomos) and Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid, Spain
| | | | | |
Collapse
|
119
|
Paulucci NS, Dardanelli MS, García de Lema M. Biochemical and molecular evidence of a Δ9 fatty acid desaturase from Ensifer meliloti 1021. Microbiol Res 2014; 169:463-8. [DOI: 10.1016/j.micres.2013.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 07/23/2013] [Accepted: 08/10/2013] [Indexed: 11/16/2022]
|
120
|
Wang J, Tóth K, Tanaka K, Nguyen CT, Yan Z, Brechenmacher L, Dahmen J, Chen M, Thelen JJ, Qiu L, Stacey G. A soybean acyl carrier protein, GmACP, is important for root nodule symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:415-23. [PMID: 24400939 DOI: 10.1094/mpmi-09-13-0269-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Legumes (members of family Fabaceae) establish a symbiotic relationship with nitrogen-fixing soil bacteria (rhizobia) to overcome nitrogen source limitation. Single root hair epidermal cells serve as the entry point for bacteria to infect the host root, leading to development of a new organ, the nodule, which the bacteria colonize. In the present study, the putative role of a soybean acyl carrier protein (ACP), GmACP (Glyma18g47950), was examined in nodulation. ACP represent an essential cofactor protein in fatty acid biosynthesis. Phylogenetic analysis of plant ACP protein sequences showed that GmACP was classified in a legume-specific clade. Quantitative reverse-transcription polymerase chain reaction analysis demonstrated that GmACP was expressed in all soybean tissues but showed higher transcript accumulation in nodule tissue. RNA interference-mediated gene silencing of GmACP resulted in a significant reduction in nodule numbers on soybean transgenic roots. Fluorescent protein-labeled GmACP was localized to plastids in planta, the site of de novo fatty acid biosynthesis in plants. Analysis of the fatty acid content of root tissue silenced for GmACP expression, as determined by gas chromatography-mass spectrometry, showed an approximately 22% reduction, specifically in palmitic and stearic acid. Taken together, our data provide evidence that GmACP plays an important role in nodulation.
Collapse
|
121
|
Silva FV, De Meyer SE, Simões-Araújo JL, Barbé TDC, Xavier GR, O'Hara G, Ardley JK, Rumjanek NG, Willems A, Zilli JE. Bradyrhizobium manausense sp. nov., isolated from effective nodules of Vigna unguiculata grown in Brazilian Amazonian rainforest soils. Int J Syst Evol Microbiol 2014; 64:2358-2363. [PMID: 24744018 DOI: 10.1099/ijs.0.061259-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Root nodule bacteria were trapped within cowpea (Vigna unguiculata) in soils with different cultivation histories collected from the Amazonian rainforest in northern Brazil. Analysis of the 16S rRNA gene sequences of six strains (BR 3351(T), BR 3307, BR 3310, BR 3315, BR 3323 BR and BR 3361) isolated from cowpea nodules showed that they formed a distinct group within the genus Bradyrhizobium, which was separate from previously identified type strains. Phylogenetic analyses of three housekeeping genes (glnII, recA and rpoB) revealed that Bradyrhizobium huanghuaihaiense CCBAU 23303(T) was the most closely related type strain (96% sequence similarity or lower). Chemotaxonomic data, including fatty acid profiles (predominant fatty acids being C16 : 0 and summed feature 8), the slow growth rate and carbon compound utilization patterns supported the assignment of the strains to the genus Bradyrhizobium. The results of DNA-DNA hybridizations, antibiotic resistance and physiological tests differentiated these novel strains from the most closely related species of the genus Bradyrhizobium with validly published names. Symbiosis-related genes for nodulation (nodC) and nitrogen fixation (nifH) grouped the novel strains of the genus Bradyrhizobium together with Bradyrhizobium iriomotense strain EK05(T), with 94% and 96% sequence similarity, respectively. Based on these data, these six strains represent a novel species for which the name Brabyrhizobium manausense sp. nov. (BR 3351(T) = HAMBI 3596(T)), is proposed.
Collapse
Affiliation(s)
- Flavia V Silva
- Departamento de Ciências, Universidade do Estado do Rio de Janeiro, Rua Dr. Francisco Portela, 1470, São Gonçalo, Rio de Janeiro 24435-000, Brazil
| | - Sofie E De Meyer
- Laboratory of Microbiology, Department of Biochemistry and Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium.,Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
| | - Jean L Simões-Araújo
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Tatiane da Costa Barbé
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Gustavo R Xavier
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Graham O'Hara
- Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
| | - Julie K Ardley
- Centre for Rhizobium Studies, Murdoch University, 90 South Street, Murdoch 6150, Western Australia, Australia
| | - Norma G Rumjanek
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Jerri E Zilli
- Embrapa Agrobiologia, Rodovia BR 465 km 07, Seropédica, Rio de Janeiro 23891-000, Brazil
| |
Collapse
|
122
|
Lu JK, Dou YJ, Zhu YJ, Wang SK, Sui XH, Kang LH. Bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from Acacia melanoxylon R. Br. nodules. Int J Syst Evol Microbiol 2014; 64:1900-1905. [PMID: 24585376 PMCID: PMC4051118 DOI: 10.1099/ijs.0.056564-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three slow-growing rhizobial strains, designated RITF806T, RITF807 and RITF211, isolated from root nodules of Acacia melanoxylon grown in Ganzhou city, Jiangxi Province, China, had been previously defined, based on amplified 16S rRNA gene restriction analysis, as a novel group within the genus Bradyrhizobium. To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. According to 16S rRNA gene sequence analysis, the isolates formed a group that was closely related to ‘Bradyrhizobium rifense’ CTAW71, with a similarity value of 99.9 %. In phylogenetic analyses of the housekeeping and symbiotic gene sequences, the three strains formed a distinct lineage within the genus Bradyrhizobium, which was consistent with the results of DNA–DNA hybridization. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related species of the genus Bradyrhizobium, indicating that these three strains constituted a novel group distinct from any recognized species of the genus Bradyrhizobium. Based on the data obtained in this study, we conclude that our strains represent a novel species of the genus Bradyrhizobium, for which the name Bradyrhizobium ganzhouense sp. nov. is proposed, with RITF806T ( = CCBAU 101088T = JCM 19881T) as the type strain. The DNA G+C content of strain RITF806T is 64.6 mol% (Tm).
Collapse
Affiliation(s)
- Jun Kun Lu
- Research Institute of Tropical Forestry, Guangzhou 510520, PR China
| | - Ya Jing Dou
- Research Institute of Tropical Forestry, Guangzhou 510520, PR China
| | - Ya Jie Zhu
- Research Institute of Tropical Forestry, Guangzhou 510520, PR China
| | - Sheng Kun Wang
- Research Institute of Tropical Forestry, Guangzhou 510520, PR China
| | - Xin Hua Sui
- State Key Laboratories for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Li Hua Kang
- Research Institute of Tropical Forestry, Guangzhou 510520, PR China
| |
Collapse
|
123
|
Mousavi SA, Österman J, Wahlberg N, Nesme X, Lavire C, Vial L, Paulin L, de Lajudie P, Lindström K. Phylogeny of the Rhizobium-Allorhizobium-Agrobacterium clade supports the delineation of Neorhizobium gen. nov. Syst Appl Microbiol 2014; 37:208-15. [PMID: 24581678 DOI: 10.1016/j.syapm.2013.12.007] [Citation(s) in RCA: 133] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 12/14/2013] [Accepted: 12/16/2013] [Indexed: 10/25/2022]
Abstract
The genera Agrobacterium, Allorhizobium, and Rhizobium belong to the family Rhizobiaceae. However, the placement of a phytopathogenic group of bacteria, the genus Agrobacterium, among the nitrogen-fixing bacteria and the unclear position of Rhizobium galegae have caused controversy in previous taxonomic studies. To resolve uncertainties in the taxonomy and nomenclature within this family, the phylogenetic relationships of generic members of Rhizobiaceae were studied, but with particular emphasis on the taxa included in Agrobacterium and the "R. galegae complex" (R. galegae and related taxa), using multilocus sequence analysis (MLSA) of six protein-coding housekeeping genes among 114 rhizobial and agrobacterial taxa. The results showed that R. galegae, R. vignae, R. huautlense, and R. alkalisoli formed a separate clade that clearly represented a new genus, for which the name Neorhizobium is proposed. Agrobacterium was shown to represent a separate cluster of mainly pathogenic taxa of the family Rhizobiaceae. A. vitis grouped with Allorhizobium, distinct from Agrobacterium, and should be reclassified as Allorhizobium vitis, whereas Rhizobium rhizogenes was considered to be the proper name for former Agrobacterium rhizogenes. This phylogenetic study further indicated that the taxonomic status of several taxa could be resolved by the creation of more novel genera.
Collapse
Affiliation(s)
- Seyed Abdollah Mousavi
- University of Helsinki, Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Biocentre 1, Viikinkaari 9, P.O. Box 56, Helsinki FIN-00014, Finland.
| | - Janina Österman
- University of Helsinki, Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Biocentre 1, Viikinkaari 9, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Niklas Wahlberg
- University of Turku, Laboratory of Genetics, Department of Biology, 20014 Turku, Finland
| | - Xavier Nesme
- University of Lyon, Université Lyon1, Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, 16 rue R. Dubois, F-69622 Villeurbanne Cedex, France
| | - Céline Lavire
- University of Lyon, Université Lyon1, Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, 16 rue R. Dubois, F-69622 Villeurbanne Cedex, France
| | - Ludovic Vial
- University of Lyon, Université Lyon1, Ecologie Microbienne, UMR CNRS 5557/USC INRA 1364, 16 rue R. Dubois, F-69622 Villeurbanne Cedex, France
| | - Lars Paulin
- University of Helsinki, Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, Viikinkaari 4, P.O. Box 56, Helsinki FIN-00014, Finland
| | - Philippe de Lajudie
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, Campus de Baillarguet TA A-82/J, 34398 Montpellier Cédex 5, France
| | - Kristina Lindström
- University of Helsinki, Division of Microbiology and Biotechnology, Department of Food and Environmental Sciences, Biocentre 1, Viikinkaari 9, P.O. Box 56, Helsinki FIN-00014, Finland; University of Helsinki, Department of Environmental Sciences, Viikinkaari 2a, P.O. Box 65, Helsinki FIN-00014, Finland
| |
Collapse
|
124
|
Zhang XX, Tang X, Sheirdil RA, Sun L, Ma XT. Rhizobium rhizoryzae sp. nov., isolated from rice roots. Int J Syst Evol Microbiol 2014; 64:1373-1377. [PMID: 24449787 DOI: 10.1099/ijs.0.056325-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (J3-AN59(T) and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59(T) and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus Rhizobium, and they were most closely related to Rhizobium tarimense ACCC 06128(T) (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59(T) and J3-N84 and those of recognized species of the genus Rhizobium were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59(T) and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA-DNA relatedness value between J3-AN59(T) and J3-N84 was 89 %, and strain J3-AN59(T) showed 9 % DNA-DNA relatedness to R. tarimense ACCC 06128(T), the most closely related strain. Based on this evidence, we found that J3-AN59(T) and J3-N84 represent a novel species in the genus Rhizobium and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59(T) ( = ACCC 05916(T) = KCTC 23652(T)).
Collapse
Affiliation(s)
- Xiao-Xia Zhang
- Key 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
| | - Xue Tang
- Key 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
| | - Rizwan Ali Sheirdil
- Department of Soil Science and Soil Water Conservation, PMAS Arid Agriculture University, Rawalpindi, Pakistan.,Key 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
| | - Lei Sun
- College of Life Sciences, Hebei University, Baoding 071002, PR China
| | - Xiao-Tong Ma
- Key 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
| |
Collapse
|
125
|
Modulation in fatty acid composition influences salinity stress tolerance in Frankia strains. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0775-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
126
|
Dall’Agnol RF, Ribeiro RA, Ormeño-Orrillo E, Rogel MA, Delamuta JRM, Andrade DS, Martínez-Romero E, Hungria M. Rhizobium
freirei sp. nov., a symbiont of Phaseolus vulgaris that is very effective at fixing nitrogen. Int J Syst Evol Microbiol 2013; 63:4167-4173. [DOI: 10.1099/ijs.0.052928-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Common bean (Phaseolus vulgaris L.) can establish symbiotic associations with several
Rhizobium
species; however, the effectiveness of most strains at fixing nitrogen under field conditions is very low. PRF 81T is a very effective strain, usually referred to as
Rhizobium tropici
and used successfully in thousands of doses of commercial inoculants for the common bean crop in Brazil; it has shown high rates of nitrogen fixation in all areas representative of the crop in the country. Here, we present results that indicate that PRF 81T, although it belongs to the ‘
R. tropici
group’, which includes 10
Rhizobium
species,
R. tropici
,
R. leucaenae
,
R. lusitanum
,
R. multihospitium
,
R. miluonense
,
R. hainanense
,
R. calliandrae
,
R. mayense
,
R. jaguaris
and
R. rhizogenes
, represents a novel species. Several morpho-physiological traits differentiated PRF 81T from related species. Differences were also confirmed in the analysis of rep-PCR (sharing less than 45 % similarity with the other species), MLSA with recA, atpD and rpoB genes, and DNA–DNA hybridization. The novel species, for which we propose the name
Rhizobium
freirei sp. nov., is able to establish effective root nodule symbioses with Phaseolus vulgaris, Leucaena leucocephala, Leucaena esculenta, Crotalaria juncea and Macroptilium atropurpureum. The type strain is PRF 81T ( = CNPSo 122T = SEMIA 4080T = IPR-Pv81T = WDCM 440T).
Collapse
Affiliation(s)
- Rebeca Fuzinatto Dall’Agnol
- Universidade Estadual de Londrina, Dept of Biochemistry and Biotechnology, C.P. 6001, 86051-990 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- Universidade Estadual de Londrina, Dept of Microbiology, C.P. 60001, 86051-990 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Ernesto Ormeño-Orrillo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Marco Antonio Rogel
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jakeline Renata Marçon Delamuta
- Universidade Estadual de Londrina, Dept of Microbiology, C.P. 60001, 86051-990 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | | | | | - Mariangela Hungria
- Universidade Estadual de Londrina, Dept of Microbiology, C.P. 60001, 86051-990 Londrina, Paraná, Brazil
- Universidade Estadual de Londrina, Dept of Biochemistry and Biotechnology, C.P. 6001, 86051-990 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| |
Collapse
|
127
|
Wang YC, Wang F, Hou BC, Wang ET, Chen WF, Sui XH, Chen WX, Li Y, Zhang YB. Proposal of Ensifer psoraleae sp. nov., Ensifer sesbaniae sp. nov., Ensifer morelense comb. nov. and Ensifer americanum comb. nov. Syst Appl Microbiol 2013; 36:467-73. [DOI: 10.1016/j.syapm.2013.05.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
128
|
Rhizobium
paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis). Int J Syst Evol Microbiol 2013; 63:3823-3828. [DOI: 10.1099/ijs.0.051888-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, rod-shaped bacterium was isolated and designated strain L6-8T during a study of endophytic bacterial communities in lesser duckweed (Lemna aequinoctialis). Cells of strain L6-8T were motile with peritrichous flagella. The analysis of the nearly complete 16S rRNA gene sequence indicated that strain L6-8T was phylogenetically related to species of the genus
Rhizobium
. Its closest relatives were
Rhizobium borbori
DN316T (97.6 %),
Rhizobium oryzae
Alt 505T (97.3 %) and
Rhizobium pseudoryzae
J3-A127T (97.0 %). The sequence similarity analysis of housekeeping genes recA, glnII, atpD and gyrB showed low levels of sequence similarity (<91.5 %) between strain L6-8T and other species of the genus
Rhizobium
with validly published names. The pH range for growth was 4.0–9.0 (optimum 6.0–7.0), and the temperature range for growth was 20–45 °C (optimum 30 °C). Strain L6-8T tolerated NaCl up to 2 % (w/v) (optimum 1 % NaCl). The predominant components of cellular fatty acids were C19 : 0 cyclo ω8c (31.32 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 25.39 %) and C16 : 0 (12.03 %). The DNA G+C content of strain L6-8T was 60.4 mol% (T
m). nodC and nifH were not amplified in strain L6-8T. DNA–DNA relatedness between strain L6-8T and
R. borbori
DN316T,
R. oryzae
Alt505T and
R. pseudoryzae
J3-A127T was between 11.2 and 18.3 %. Based on the sequence similarity analyses, phenotypic, biochemical and physiological characteristics and DNA–DNA hybridization, strain L6-8T could be readily distinguished from its closest relatives and represents a novel species of the genus
Rhizobium
, for which the name
Rhizobium
paknamense sp. nov. is proposed. The type strain is L6-8T ( = NBRC 109338T = BCC 55142T).
Collapse
|
129
|
Xu YJ, Ho WE, Xu F, Wen T, Ong CN. Exploratory investigation reveals parallel alteration of plasma fatty acids and eicosanoids in coronary artery disease patients. Prostaglandins Other Lipid Mediat 2013; 106:29-36. [PMID: 24007966 DOI: 10.1016/j.prostaglandins.2013.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 12/23/2022]
Abstract
Fatty acids and eicosanoids are two important classes of signaling lipid molecules involved in the pathogenesis of cardiovascular diseases. To investigate the physiological functions and interplay between fatty acids and eicosanoids in coronary artery disease (CAD) patients, we developed an analytical approach for parallel quantitative analysis of plasma fatty acids and eicosanoids, using gas chromatography-tandem mass spectrometry (GC-MS/MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this study, 26 fatty acids and 12 eicosanoids were confidently detected in 12 patients with confirmed coronary artery disease and 11 healthy subjects. Pattern recognition analysis (principal components analysis, orthogonal partial least-square discriminate analysis, and hierarchical clustering analysis) demonstrated that the plasma lipid profile of fatty acids and eicosanoids enabled robust discrimination of CAD patients versus healthy subjects. Significant differences in six fatty acids and five eicosanoids were noted among CAD patients and healthy subjects. The development of cardiovascular disease-induced metabolic change of fatty acids and eicosanoids, such as eicosapentaenoic acid, docosahexaenoic acid, arachidonic acid, hydroxyeicosatetraenoic acids and hydroxyoctadecadienoic acid, were consistent with previous isolated observations. Moderate-strong correlations between three plasma fatty acids and three eicosanoids from arachidonic acid metabolism were also observed. In brief, findings from this exploratory study offered a new insight on the roles of various bioactive lipid molecules in the development of coronary artery disease biomarkers.
Collapse
Affiliation(s)
- Yong-Jiang Xu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Key Laboratory of Insect Development and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Science, Chinese Academy of Sciences, Shanghai, People's Republic of China.
| | | | | | | | | |
Collapse
|
130
|
Delamuta JRM, Ribeiro RA, Ormeño-Orrillo E, Melo IS, Martínez-Romero E, Hungria M. Polyphasic evidence supporting the reclassification of
Bradyrhizobium japonicum
group Ia strains as
Bradyrhizobium
diazoefficiens sp. nov. Int J Syst Evol Microbiol 2013; 63:3342-3351. [DOI: 10.1099/ijs.0.049130-0] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bradyrhizobium japonicum
was described from soybean root-nodule bacterial isolates. Since its description, several studies have revealed heterogeneities among rhizobia assigned to this species. Strains assigned to
B. japonicum
group Ia have been isolated in several countries, and many of them are outstanding soybean symbionts used in inoculants worldwide, but they have also been isolated from other legume hosts. Here, we summarize published studies that indicate that group Ia strains are different from the
B. japonicum
type strain USDA 6T and closely related strains, and present new morphophysiological, genotypic and genomic evidence to support their reclassification into a novel species, for which the name
Bradyrhizobium
diazoefficiens sp. nov. is proposed. The type strain of the novel species is the well-studied strain USDA 110T ( = IAM 13628T = CCRC 13528T = NRRL B-4361T = NRRL B-4450T = TAL 102T = BCRC 13528T = JCM 10833T = TISTR 339T = SEMIA 5032T = 3I1B110T = ACCC 15034T = CCT 4249T = NBRC 14792T = R-12974T = CNPSo 46T).
Collapse
Affiliation(s)
- Jakeline Renata Marçon Delamuta
- Universidade Estadual de Londrina, Dept of Microbiology, C.P. 60001, 86051-990 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- Universidade Estadual de Londrina, Dept of Microbiology, C.P. 60001, 86051-990 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Ernesto Ormeño-Orrillo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | | | - Mariangela Hungria
- Universidade Estadual de Londrina, Dept of Microbiology, C.P. 60001, 86051-990 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| |
Collapse
|
131
|
Zhou S, Li Q, Jiang H, Lindström K, Zhang X. Mesorhizobium
sangaii sp. nov., isolated from the root nodules of Astragalus luteolus and Astragalus ernestii. Int J Syst Evol Microbiol 2013; 63:2794-2799. [DOI: 10.1099/ijs.0.044685-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Our previous published data indicated that the two rhizobial strains SCAU7T and SCAU27, which were isolated from the root nodules of Astragalus luteolus and Astragalus ernestii respectively, in Sichuan Province, China, might be novel species of the genus
Mesorhizobium
. Their exact taxonomic position was determined in the present study by using polyphasic approaches. Comparative analysis of nearly full-length 16S rRNA gene sequences showed that these strains belonged to the genus
Mesorhizobium
, with
Mesorhizobium ciceri
USDA 3383T,
Mesorhizobium loti
NZP 2213T,
Mesorhizobium shangrilense
CCBAU 65327T and
Mesorhizobium australicum
WSM2073T as the closest neighbours (>99 % 16S rRNA gene sequence similarity). Phylogenies of the housekeeping genes atpD and recA confirmed their distinct position, showing low similarity with respect to those of
M. loti
LMG 6125T (96.5 % and 92.3 % similarity respectively),
M. ciceri
USDA 3383T (96.8 % and 93.3 % similarity, respectively),
M. shangrilense
CCBAU 65327T (96.5 % and 92.7 % similarity, respectively) and
M. australicum
WSM2073T (95.4 % and 90.6 % similarity, respectively). The DNA–DNA relatedness values between strain SCAU7T and strain SCAU27 were 83.0 %, showing that they belong to the same species. The DNA–DNA relatedness values of SCAU7T with
M. loti
NZP 2213T,
M. ciceri
USDA 3383T and
M. shangrilense
CCBAU 65327T were 41.1 %, 48.8 % and 23.4 %, respectively, clearly indicating that strain SCAU7T represents a novel species. A series of phenotypic and genotypic tests and comparison of cellular fatty acids indicated that the novel group of isolates was distinct from previously described species. Therefore, we propose that strains SCAU7T and SCAU27 represent a novel species of the genus
Mesorhizobium
,
Mesorhizobium
sangaii sp. nov., with strain SCAU7T ( = HAMBI 3318T = ACCC 13218T) as the type strain.
Collapse
Affiliation(s)
- Shen Zhou
- Department of Resources and Environment, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Qiongfang Li
- College of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621000, Sichuan, PR China
| | - Huaming Jiang
- Department of Resources and Environment, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Kristina Lindström
- Department of Applied Chemistry and Microbiology, University of Helsinki, Helsinki FIN-00014, Finland
| | - Xiaoping Zhang
- Department of Resources and Environment, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| |
Collapse
|
132
|
Rhizobium pongamiae sp. nov. from root nodules of Pongamia pinnata. BIOMED RESEARCH INTERNATIONAL 2013; 2013:165198. [PMID: 24078904 PMCID: PMC3783817 DOI: 10.1155/2013/165198] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 06/06/2013] [Indexed: 11/17/2022]
Abstract
Pongamia pinnata has an added advantage of N2-fixing ability and tolerance to stress conditions as compared with other biodiesel crops. It harbours “rhizobia” as an endophytic bacterial community on its root nodules. A gram-negative, nonmotile, fast-growing, rod-shaped, bacterial strain VKLR-01T was isolated from root nodules of Pongamia that grew optimal at 28°C, pH 7.0 in presence of 2% NaCl. Isolate VKLR-01 exhibits higher tolerance to the prevailing adverse conditions, for example, salt stress, elevated temperatures and alkalinity. Strain VKLR-01T has the major cellular fatty acid as C18:1
ω7c (65.92%). Strain VKLR-01T was found to be a nitrogen fixer using the acetylene reduction assay and PCR detection of a nifH gene. On the basis of phenotypic, phylogenetic distinctiveness and molecular data (16S rRNA, recA, and atpD gene sequences, G + C content, DNA-DNA hybridization etc.), strain VKLR-01T = (MTCC 10513T = MSCL 1015T) is considered to represent a novel species of the genus Rhizobium for which the name Rhizobium pongamiae sp. nov. is proposed. Rhizobium pongamiae may possess specific traits that can be transferred to other rhizobia through biotechnological tools and can be directly used as inoculants for reclamation of wasteland; hence, they are very important from both economic and environmental prospects.
Collapse
|
133
|
Determination of fatty acid methyl esters by GC–triple quadrupole MS using electron and chemical ionization. Bioanalysis 2013; 5:1527-43. [DOI: 10.4155/bio.13.112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: The main objective of this study was to explore the potential use of electron ionization (EI) and chemical ionization (CI) techniques in fatty acid measurement. MS/MS, together with main fragment ions in EI and positive CI of 37 fatty acid methyl esters (FAMEs), were investigated using a triple quadrupole mass spectrometer. Results: Our results demonstrated that several diagnostic ions of FAMEs could be confirmed using EI. On the other hand, the characteristic fragmentation patterns and probable pathway of FAMEs could be deduced from the collision-induced dissociation mass spectra when using positive CI. Owing to its capability in using the specific ions of fatty acids for selected ion monitoring and SRM, CI is considered to be more suitable for fatty acid quantitative analysis. Based on these features, a systematic strategy was then developed to integrate these fragments for GC–MS/MS for the determination of fatty acids. Conclusion: This approach offers a rapid and accurate method for measuring a wide spectrum of fatty acids.
Collapse
|
134
|
Zheng WT, Li Y, Wang R, Sui XH, Zhang XX, Zhang JJ, Wang ET, Chen WX. Mesorhizobium qingshengii sp. nov., isolated from effective nodules of Astragalus sinicus. Int J Syst Evol Microbiol 2013; 63:2002-2007. [DOI: 10.1099/ijs.0.044362-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In a study on the diversity of rhizobia isolated from root nodules of Astragalus sinicus, five strains showed identical 16S rRNA gene sequences. They were related most closely to the type strains of
Mesorhizobium loti
,
Mesorhizobium shangrilense
,
Mesorhizobium ciceri
and
Mesorhizobium australicum
, with sequence similarities of 99.6–99.8 %. A polyphasic approach, including 16S–23S intergenic spacer (IGS) RFLP, comparative sequence analysis of 16S rRNA, atpD, glnII and recA genes, DNA–DNA hybridization and phenotypic tests, clustered the five isolates into a coherent group distinct from all recognized
Mesorhizobium
species. Except for strain CCBAU 33446, from which no symbiotic gene was detected, the four remaining strains shared identical nifH and nodC gene sequences and nodulated with Astragalus sinicus. In addition, these five strains showed similar but different fingerprints in IGS-RFLP and BOX-repeat-based PCR, indicating that they were not clones of the same strain. They were also distinguished from recognized
Mesorhizobium
species by several phenotypic features and fatty acid profiles. Based upon all the results, we suggest that the five strains represent a novel species for which the name Mesorhizobium qingshengii sp. nov. is proposed. The type strain is CCBAU 33460T ( = CGMCC 1.12097T = LMG 26793T = HAMBI 3277T). The DNA G+C content of the type strain is 59.52 mol% (T
m).
Collapse
Affiliation(s)
- Wen Tao Zheng
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Ying Li
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Rui Wang
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Xin Hua Sui
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Xiao Xia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Jun Jie Zhang
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México DF, Mexico
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| | - Wen Xin Chen
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, PR China
| |
Collapse
|
135
|
Paulucci N, Medeot D, Woelke M, Dardanelli M, de Lema M. Monounsaturated fatty acid aerobic synthesis in Bradyrhizobium
TAL1000 peanut-nodulating is affected by temperature. J Appl Microbiol 2013; 114:1457-67. [DOI: 10.1111/jam.12155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 12/21/2012] [Accepted: 01/04/2013] [Indexed: 11/29/2022]
Affiliation(s)
- N.S. Paulucci
- Departamento de Biología Molecular; Facultad de Ciencias Exactas; Físico-Químicas y Naturales; Universidad Nacional de Río Cuarto; Río Cuarto Córdoba Argentina
| | - D.B. Medeot
- Departamento de Biología Molecular; Facultad de Ciencias Exactas; Físico-Químicas y Naturales; Universidad Nacional de Río Cuarto; Río Cuarto Córdoba Argentina
| | - M. Woelke
- Departamento de Biología Molecular; Facultad de Ciencias Exactas; Físico-Químicas y Naturales; Universidad Nacional de Río Cuarto; Río Cuarto Córdoba Argentina
| | - M.S. Dardanelli
- Departamento de Biología Molecular; Facultad de Ciencias Exactas; Físico-Químicas y Naturales; Universidad Nacional de Río Cuarto; Río Cuarto Córdoba Argentina
| | - M.G. de Lema
- Departamento de Biología Molecular; Facultad de Ciencias Exactas; Físico-Químicas y Naturales; Universidad Nacional de Río Cuarto; Río Cuarto Córdoba Argentina
| |
Collapse
|
136
|
Bradyrhizobium arachidis sp. nov., isolated from effective nodules of Arachis hypogaea grown in China. Syst Appl Microbiol 2013; 36:101-5. [DOI: 10.1016/j.syapm.2012.10.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 10/10/2012] [Accepted: 10/11/2012] [Indexed: 11/20/2022]
|
137
|
Wang YC, Wang F, Hou BC, Wang ET, Chen WF, Sui XH, Chen WX, Li Y, Zhang YB. WITHDRAWN: Ensifer psoraleae sp. nov. and Ensifer sesbaniae sp. nov., isolated from the root nodules of Psoralea corylifolia, Sesbania cannabina and other legumes. Syst Appl Microbiol 2013:S0723-2020(13)00011-8. [PMID: 23453021 DOI: 10.1016/j.syapm.2013.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 11/21/2022]
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
Collapse
Affiliation(s)
- Yuan Chun Wang
- State Key Lab for Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | | | | | | | | | | | | | | | | |
Collapse
|
138
|
Wang JY, Wang R, Zhang YM, Liu HC, Chen WF, Wang ET, Sui XH, Chen WX. Bradyrhizobium daqingense sp. nov., isolated from soybean nodules. Int J Syst Evol Microbiol 2013; 63:616-624. [PMID: 22544787 DOI: 10.1099/ijs.0.034280-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thirteen slow-growing rhizobial strains isolated from root nodules of soybean (Glycine max L.) grown in Daqing city in China were classified in the genus Bradyrhizobium based on 16S rRNA gene sequence analysis. Multilocus sequence analysis of IGS, atpD, glnII and recA genes revealed that the isolates represented a novel clade in this genus. DNA-DNA relatedness lower than 42.5 % between the representative strain CCBAU 15774(T) and the type strains of the closely related species Bradyrhizobium liaoningense USDA 3622(T), Bradyrhizobium yuanmingense CCBAU 10071(T) and Bradyrhizobium betae LMG 21987(T), further confirmed that this group represented a novel species. CCBAU 15774(T) shared seven cellular fatty acids with the three above-mentioned species, but the fatty acids 15 : 0 iso and summed feature 5 (18 : 2ω6,9c and/or 18 : 0 anteiso) were unique for this strain. The respiratory quinone in CCBAU 15774(T) was ubiquinone-10 and the cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, cardiolipin and unknown aminolipid, polar lipid and phospholipid. In addition, some phenotypic features could be used to differentiate the novel group from the related species. On basis of these results, we propose the name Bradyrhizobium daqingense sp. nov., with CCBAU 15774(T) ( = LMG 26137(T) = HAMBI 3184(T) = CGMCC 1.10947(T)) as the type strain. The DNA G+C content of the type strain is 61.2 mol% (T(m)).
Collapse
Affiliation(s)
- Jing Yu Wang
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Rui Wang
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yan Ming Zhang
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Hong Can Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen Feng Chen
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México DF, Mexico
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Xin Chen
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| |
Collapse
|
139
|
Kaiya S, Rubaba O, Yoshida N, Yamada T, Hiraishi A. Characterization of Rhizobium naphthalenivorans sp. nov. with special emphasis on aromatic compound degradation and multilocus sequence analysis of housekeeping genes. J GEN APPL MICROBIOL 2012; 58:211-24. [PMID: 22878739 DOI: 10.2323/jgam.58.211] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Three strains of aerobic chemoorganotrophic naphthalene-degrading bacteria (designated TSY03b(T), TSY04, and TSW01) isolated from sediment of a polychlorinated-dioxin-transforming microcosm were characterized. These strains had Gram-negative-stained, rod-shaped cells measuring 0.6‒0.9 μm in width and 1.2‒3.0 μm in length and were motile by means of peritrichous flagella. Naphthalene was utilized as the sole carbon and energy source, and the transcription of a putative aromatic-ring hydroxylating gene was inducible by naphthalene. The major component of cellular fatty acids was summed feature 8 (C18:1ω7c and/or C18:1ω6c), and significant proportions of C18:0 and C19:0 cyclo ω8cis were also found. The major respiratory quinone was ubiquinone-10. The G+C content of the DNA was 60.3‒60.9 mol%. Phylogenetic analyses by studying sequence information on the housekeeping atpD, dnaK, glnII, gyrB, and recA genes as well as on 16S rRNA genes and the 16S-23S rDNA internal transcribed spacer region revealed that the strains grouped with members of the genus Rhizobium, with Rhizobium selenitireducens as their closest relative but formed a distinct lineage at the species level. This was confirmed by genomic DNA-DNA hybridization studies. These phenotypic, genotypic, and phylogenetic data strongly suggest that our isolates should be classified under a novel species of the genus Rhizobium. Thus, we propose the name Rhizobium naphthalenivorans sp. nov. to accommodate the novel isolates. The type strain is TSY03b(T) (= NBRC 107585T = KCTC 23252T).
Collapse
Affiliation(s)
- Shinichi Kaiya
- Department of Environmental and Life Sciences, Toyohashi University of Technology, Toyohashi 4418580, Japan
| | | | | | | | | |
Collapse
|
140
|
Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota A. Thermovum composti gen. nov., sp. nov., an alphaproteobacterium from compost. Int J Syst Evol Microbiol 2012; 62:2991-2996. [DOI: 10.1099/ijs.0.037812-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive thermophilic bacterium, designated strain Nis3T, was isolated from compost. The strain grew at 23–57 °C (optimum, 50 °C); no growth was observed below 15 or above 60 °C. The pH range for growth was 5.9–8.8 (optimum, 7.0); no growth was observed below pH 5.4 or above pH 9.3. The DNA G+C content of strain Nis3T was 63.4 mol%. The dominant quinone type was ubiquinone Q-10. The major fatty acids were C18 : 1ω7c, C19 : 0ω8c cyclo and C18 : 0. The polar lipids comprised phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol, phosphatidylmonomethylethanolamine, an unknown glycolipid and a ninhydrin-positive phospholipid. 16S rRNA gene sequence analysis assigned this bacterium to the family
Phyllobacteriaceae
in the
Alphaproteobacteria
but it shared less than 95.2 % sequence similarity with other members of the family. The chemotaxonomic and phenotypic characteristics of strain Nis3T differed in some respects from those of members of the family
Phyllobacteriaceae
. Therefore, strain Nis3T is considered to represent a novel species of a new genus in the family
Phyllobacteriaceae
, for which the name Thermovum composti gen. nov., sp. nov. is proposed. The type strain is Nis3T ( = JCM 17863T = KCTC 23707T).
Collapse
Affiliation(s)
- Shuhei Yabe
- Hazaka Plant Research Center, Kennan Eisei Kogyo Co. Ltd, 44 Aza-Inariyama, Oaza-Ashitate, Murata-cho, Shibata-gun, Miyagi 989-1311, Japan
| | - Yoshifumi Aiba
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yasuteru Sakai
- Hazaka Plant Research Center, Kennan Eisei Kogyo Co. Ltd, 44 Aza-Inariyama, Oaza-Ashitate, Murata-cho, Shibata-gun, Miyagi 989-1311, Japan
| | - Masaru Hazaka
- Hazaka Plant Research Center, Kennan Eisei Kogyo Co. Ltd, 44 Aza-Inariyama, Oaza-Ashitate, Murata-cho, Shibata-gun, Miyagi 989-1311, Japan
| | - Akira Yokota
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi Bunkyo-ku, Tokyo 113-0032, Japan
| |
Collapse
|
141
|
Rhizobium qilianshanense sp. nov., a novel species isolated from root nodule of Oxytropis ochrocephala Bunge in China. Antonie van Leeuwenhoek 2012; 103:559-65. [DOI: 10.1007/s10482-012-9840-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 10/22/2012] [Indexed: 10/27/2022]
|
142
|
Patel U, Sinha S. Rhizobia species: A Boon for "Plant Genetic Engineering". Indian J Microbiol 2012; 51:521-7. [PMID: 23024417 DOI: 10.1007/s12088-011-0149-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 10/05/2009] [Indexed: 10/18/2022] Open
Abstract
Since past three decades new discoveries in plant genetic engineering have shown remarkable potentials for crop improvement. Agrobacterium Ti plasmid based DNA transfer is no longer the only efficient way of introducing agronomically important genes into plants. Recent studies have explored a novel plant genetic engineering tool, Rhizobia sp., as an alternative to Agrobacterium, thereby expanding the choice of bacterial species in agricultural plant biotechnology. Rhizobia sp. serve as an open license source with no major restrictions in plant biotechnology and help broaden the spectrum for plant biotechnologists with respect to the use of gene transfer vehicles in plants. New efficient transgenic plants can be produced by transferring genes of interest using binary vector carrying Rhizobia sp. Studies focusing on the interactions of Rhizobia sp. with their hosts, for stable and transient transformation and expression of genes, could help in the development of an adequate gene transfer vehicle. Along with being biologically beneficial, it may also bring a new means for fast economic development of transgenic plants, thus giving rise to a new era in plant biotechnology, viz. "Rhizobia mediated transformation technology."
Collapse
Affiliation(s)
- Urmi Patel
- Institute of Science, Nirma University, Sarkhej-Gandhinagar Highway, Ahmedabad, 382481 Gujarat India
| | | |
Collapse
|
143
|
Rhizobium cauense sp. nov., isolated from root nodules of the herbaceous legume Kummerowia stipulacea grown in campus lawn soil. Syst Appl Microbiol 2012; 35:415-20. [DOI: 10.1016/j.syapm.2012.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 07/28/2012] [Accepted: 08/10/2012] [Indexed: 11/19/2022]
|
144
|
Zhao CT, Wang ET, Zhang YM, Chen WF, Sui XH, Chen WX, Liu HC, Zhang XX. Mesorhizobium silamurunense sp. nov., isolated from root nodules of Astragalus species. Int J Syst Evol Microbiol 2012; 62:2180-2186. [DOI: 10.1099/ijs.0.031229-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four rhizobial strains representing a previously defined novel group in the genus
Mesorhizobium
and isolated from Astragalus species in China were further characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that these Gram-negative bacteria belonged to the genus
Mesorhizobium
, with
Mesorhizobium plurifarium
LMG 11892T as the closest neighbour sharing a sequence similarity of 99.8 %. Comparative sequence analysis of the atpD, recA, glnII, rpoB, nodC and nifH genes, SDS-PAGE of whole-cell soluble proteins, DNA–DNA hybridization, fatty acid profiles and a series of phenotypic and physiological tests differentitated the novel group from all recognized species of the genus
Mesorhizobium
. Based on the data obtained in the present and previous studies, this group represents a novel species within the genus
Mesorhizobium
, for which the name Mesorhizobium silamurunense sp. nov. is proposed. The type strain is CCBAU 01550T ( = HAMBI 3029T = LMG 24822T), and could form effective nodules on Astragalus membranaceus, Astragalus adsurgens and Caragana intermedia, and ineffective nodules on Phaseolus vulgaris in cross-nodulation tests.
Collapse
Affiliation(s)
- Chun Tian Zhao
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
- State Key Laboratories for AgroBiotechnology/Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México DF 11340, México
| | - Yan Ming Zhang
- State Key Laboratories for AgroBiotechnology/Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Feng Chen
- State Key Laboratories for AgroBiotechnology/Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Laboratories for AgroBiotechnology/Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Xin Chen
- State Key Laboratories for AgroBiotechnology/Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Hong Can Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xiao Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| |
Collapse
|
145
|
Degefu T, Wolde-Meskel E, Liu B, Cleenwerck I, Willems A, Frostegård Å. Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees. Int J Syst Evol Microbiol 2012; 63:1746-1753. [PMID: 22941297 DOI: 10.1099/ijs.0.044032-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 18 strains, representing members of the genus Mesorhizobium, obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours Mesorhizobium plurifarium, Mesorhizobium amorphae, Mesorhizobium septentrionale and Mesorhizobium huakuii was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the atpD and glnII genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus Mesorhizobium. The DNA-DNA relatedness between the representative strains of genospecies I-III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov. The isolates AC39a(T) ( = LMG 26966(T) = HAMBI 3295(T)), AC99b(T) ( = LMG 26968(T) = HAMBI 3301(T)) and AC98c(T) ( = LMG 26967(T) = HAMBI 3306(T)) are proposed as type strains for the respective novel species.
Collapse
Affiliation(s)
- Tulu Degefu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Endalkachew Wolde-Meskel
- School of Plant and Horticultural Sciences, Hawassa University, PO Box 5, Hawassa, Ethiopia.,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Binbin Liu
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Anne Willems
- Laboratory of Microbiology (WE10), Ghent University, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Åsa Frostegård
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| |
Collapse
|
146
|
Bibi F, Chung EJ, Khan A, Jeon CO, Chung YR. Rhizobium halophytocola sp. nov., isolated from the root of a coastal dune plant. Int J Syst Evol Microbiol 2012; 62:1997-2003. [DOI: 10.1099/ijs.0.029488-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study of endophytic bacteria from coastal dune plants, a bacterial strain, designated YC6881T, was isolated from the root of Rosa rugosa collected from the coastal dune areas of Namhae Island, Korea. The bacterium was found to be Gram-staining-negative, motile, halophilic and heterotrophic with a single polar flagellum. Strain YC6881T grew at temperatures of 4–37 °C (optimum, 28–32 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0), and at NaCl concentrations in the range of 0–7.5 % (w/v) (optimum, 4–5 % NaCl). Strain YC6881T was catalase- and oxidase-positive and negative for nitrate reduction. According to phylogenetic analysis using 16S rRNA gene sequences, strain YC6881T belonged to the genus
Rhizobium
and showed the highest 16S rRNA gene sequence similarity of 96.9 % to
Rhizobium rosettiformans
, followed by
Rhizobium borbori
(96.3 %),
Rhizobium radiobacter
(96.1 %),
Rhizobium daejeonense
(95.9 %),
Rhizobium larrymoorei
(95.6 %) and
Rhizobium giardinii
(95.4 %). Phylogenetic analysis of strain YC6881T by recA, atpD, glnII and 16S–23S intergenic spacer (IGS) sequences all confirmed the phylogenetic arrangements obtained by using 16S rRNA gene sequences. Cross-nodulation tests showed that strain YC6881T was a symbiotic bacterium that nodulated Vigna unguiculata and Pisum sativum. The major components of the cellular fatty acids were C18 : 1ω7c (53.7 %), C19 : 0 cyclo ω8c (12.6 %) and C12 : 0 (8.1 %). The DNA G+C content was 52.8 mol%. Phenotypic and physiological tests with respect to carbon source utilization, antibiotic resistance, growth conditions, phylogenetic analyses of housekeeping genes recA, atpD and glnII, and fatty acid composition could be used to discriminate strain YC6881T from other species of the genus
Rhizobium
in the same sublineage. Based on the results obtained in this study, strain YC6881T is considered to represent a novel species of the genus
Rhizobium
, for which the name Rhizobium halophytocola sp. nov. is proposed. The type strain is YC6881T ( = KACC 13775T = DSM 21600T).
Collapse
Affiliation(s)
- Fehmida Bibi
- Division of Applied Life Science (BK 21), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Eu Jin Chung
- JGreen Inc., Department of Research & Development, Changnyeong 635-806, Republic of Korea
| | - Ajmal Khan
- Division of Applied Life Science (BK 21), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Young Ryun Chung
- Division of Applied Life Science (BK 21), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 660-701, Republic of Korea
| |
Collapse
|
147
|
Zhang YM, Li Y, Chen WF, Wang ET, Sui XH, Li QQ, Zhang YZ, Zhou YG, Chen WX. Bradyrhizobium huanghuaihaiense sp. nov., an effective symbiotic bacterium isolated from soybean (Glycine max L.) nodules. Int J Syst Evol Microbiol 2012; 62:1951-1957. [PMID: 22003042 DOI: 10.1099/ijs.0.034546-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In a survey of the biodiversity and biogeography of rhizobia associated with soybean (Glycine max L.) in different sites of the Northern (Huang-Huai-Hai) Plain of China, ten strains were defined as representing a novel genomic species in the genus of Bradyrhizobium. They were distinguished from defined species in restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene and the 16S-23S rRNA gene intergenic spacer (IGS). In BOX-PCR, these strains presented two patterns that shared 94% similarity, demonstrating that they were a homogenous group with limited diversity. In phylogenetic analyses of the 16S rRNA gene, IGS and housekeeping gene sequences, four representative strains formed a distant lineage within the genus Bradyrhizobium, which was consistent with the results of DNA-DNA hybridization. The strains of this novel group formed effective nodules with G. max, Glycine soja and Vigna unguiculata in cross-nodulation tests and harboured symbiotic genes (nodC and nifH) identical to those of reference strains of Bradyrhizobium japonicum, Bradyrhizobium liaoningense and 'Bradyrhizobium daqingense' originating from soybean, implying that the novel group may have obtained these symbiotic genes by lateral gene transfer. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related Bradyrhizobium species, demonstrating that the novel group is distinct phenotypically from other Bradyrhizobium species. Based upon the data obtained, these strains are proposed to represent a novel species, Bradyrhizobium huanghuaihaiense sp. nov., with CCBAU 23303(T) ( = LMG 26136(T) = CGMCC 1.10948(T) = HAMBI 3180(T)) as the type strain. The DNA G+C content of strain CCBAU 23303(T) is 61.5 mol% (T(m)).
Collapse
Affiliation(s)
- Yan Ming Zhang
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Ying Li
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Feng Chen
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México Distrito Federal, Mexico
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Qin Qin Li
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yun Zeng Zhang
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yu Guang Zhou
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| |
Collapse
|
148
|
Ibragimova MY, Salafutdinov II, Sahin F, Zhdanov RI. Biomarkers of Bacillus subtilis total lipids FAME profile under various temperatures and growth phases. DOKL BIOCHEM BIOPHYS 2012; 443:109-12. [PMID: 22562637 DOI: 10.1134/s1607672912020135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Indexed: 11/22/2022]
Affiliation(s)
- M Y Ibragimova
- Kazan (Volga) Federal University, ul. Kremlevskaya 18, Kazan, 420008 Tatarstan, Russia
| | | | | | | |
Collapse
|
149
|
Yao LJ, Shen YY, Zhan JP, Xu W, Cui GL, Wei GH. Rhizobium taibaishanense sp. nov., isolated from a root nodule of Kummerowia striata. Int J Syst Evol Microbiol 2012; 62:335-341. [DOI: 10.1099/ijs.0.029108-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study of the diversity and phylogeny of rhizobia in the root nodules of Kummerowia striata grown in north-western China, four strains were classified in the genus Rhizobium on the basis of their 16S rRNA gene sequences. The 16S rRNA gene sequences of three of these strains were identical and that of the other strain, which was the only one isolated in Yangling, differed from the others by just 1 bp. The16S rRNA gene sequences of the four strains showed a mean similarity of 99.3 % with the most closely related, recognized species, Rhizobium vitis. The corresponding recA and glnA gene sequences showed similarities with established species of Rhizobium of less than 86.5 % and less than 89.6 %, respectively. These low similarities indicated that the four strains represented a novel species of the genus Rhizobium. The strains were also found to be distinguishable from the closest related, established species (R. vitis) by rep-PCR DNA fingerprinting, analysis of cellular fatty acid profiles and from the results of a series of phenotypic tests. The level of DNA–DNA relatedness between the representative strain CCNWSX 0483T and Rhizobium vitis IAM 14140T was only 40.13 %. Therefore, a novel species, Rhizobium taibaishanense sp. nov., is proposed, with strain CCNWSX 0483T ( = ACCC 14971T = HAMBI 3214T) as the type strain. In nodulation and pathogenicity tests, none of the four strains of Rhizobium taibaishanense sp. nov. was able to induce any nodule or tumour formation on plants. As no amplicons were detected when DNA from the strains was run in PCR with primers for the detection of nodA, nifH and virC gene sequences, the strains probably do not carry sym or vir genes.
Collapse
Affiliation(s)
- Li Juan Yao
- College of Life Sciences, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling Shaanxi 712100, PR China
| | - Yao Yao Shen
- College of Life Sciences, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling Shaanxi 712100, PR China
| | - Jun Peng Zhan
- College of Life Sciences, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling Shaanxi 712100, PR China
| | - Wei Xu
- College of Life Sciences, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling Shaanxi 712100, PR China
| | - Guang Ling Cui
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Xinjiang Production and Construction Group, Alar Xinjiang 843300, PR China
- College of Life Sciences, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Northwest A & F University, Yangling Shaanxi 712100, PR China
| | | |
Collapse
|
150
|
Zhang JJ, Liu TY, Chen WF, Wang ET, Sui XH, Zhang XX, Li Y, Li Y, Chen WX. Mesorhizobium muleiense sp. nov., nodulating with Cicer arietinum L. Int J Syst Evol Microbiol 2012; 62:2737-2742. [PMID: 22228663 DOI: 10.1099/ijs.0.038265-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three chickpea rhizobial strains (CCBAU 83963(T), CCBAU 83939 and CCBAU 83908), which were identified previously as representing a distinctive genospecies, were further studied here and compared taxonomically with related species in the genus Mesorhizobium. Results from SDS-PAGE of whole-cell soluble proteins revealed differences from closely related recognized species of the genus Mesorhizobium. Levels of DNA-DNA relatedness were 15.28-50.97% between strain CCBAU 83963(T) and the type strains of recognized Mesorhizobium species (except for Mesorhizobium thiogangeticum). Strain CCBAU 83963(T) contained fatty acids characteristic of members of the genus Mesorhizobium, but it possessed high concentrations of C(19:0) cyclo ω8c and iso-C(17:0). Strain CCBAU 83963(T) had phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol as major polar lipids, and an ornithine-containing lipid, phosphatidyl-N-dimethylethanolamine and cardiolipin as minor components. Nodulation tests demonstrated the distinct symbiotic character of strain CCBAU 83963(T); only Cicer arietinum, its host plant, could be invaded to form effective nitrogen-fixing nodules. The narrow spectrum of utilization of sole carbon sources, lower resistance to antibiotics, and NaCl, pH and temperature growth ranges differentiated these novel rhizobia from recognized species of the genus Mesorhizobium. Based on the data presented, the three novel rhizobial strains are considered to represent a novel species of the genus Mesorhizobium, for which the name Mesorhizobium muleiense sp. nov. is proposed. The type strain is CCBAU 83963(T) (=HAMBI 3264(T)=CGMCC 1.11022(T)).
Collapse
Affiliation(s)
- Jun Jie Zhang
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Tian Yan Liu
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Feng Chen
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México DF 11340, México.,State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xiao Xia Zhang
- Agricultural Cultural Collection of China, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100080, PR China
| | - Yán Li
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yàn Li
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology and Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| |
Collapse
|