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Liu Y, Huang W, Wang Q, Ma C, Chang Y, Su J. Research on the targeted improvement of the yield of a new VB 12-producing strain, Ensifer adhaerens S305, based on genomic and transcriptomic analysis. BMC Biotechnol 2023; 23:53. [PMID: 38082291 PMCID: PMC10712150 DOI: 10.1186/s12896-023-00824-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Vitamin B12 (VB12) has a wide range of applications and high economic value. In this study, a new strain with high VB12 production potential, Ensifer adhaerens S305, was identified in sewage. Because E. adhaerens strains have become the main strains for VB12 production via fermentation in recent years, the directional modification of the S305 strain to obtain a strain suitable for the industrial production of VB12 has great potential and commercial value. RESULTS 16S rRNA and genome-wide phylogenetic tree analysis combined with average nucleotide identity (ANI) analysis showed that the high-yielding VB12 strain was a E. adhaerens strain and that its VB12 synthesis pathway genes were highly similar to related genes of strains of this and other species, including E. adhaerens Casida A, Pseudomonas denitrificans SC 510, and E. adhaerens Corn53. High-pressure liquid chromatography (HPLC) results indicated that the VB12 yields of the S305 strain were more than double those of the Casida A strain under different medium components. Multiple genes with significantly upregulated and downregulated transcription were identified by comparing the transcription intensity of different genes through transcriptome sequencing. KEGG enrichment analysis of the porphyrin metabolism pathway identified 9 significantly upregulated and downregulated differentially expressed genes (DEGs) in the VB12 synthesis pathway, including 7 transcriptionally upregulated genes (cobA, cobT, hemA, cobJ, cobN, cobR, and cobP) that were episomally overexpressed in the Casida A strain. The results showed that the VB12 yield of the overexpressed strain was higher than that of the wild-type strain. Notably, the strains overexpressing the cobA and cobT genes exhibited the most significant increases in VB12 yield, i.e., 31.4% and 24.8%, respectively. The VB12 yield of the S305 strain in shake-flask culture was improved from 176.6 ± 8.21 mg/L to 245.6 ± 4.36 mg/L by integrating the cobA and cobT genes into the strain. CONCLUSION Phylogenetic tree and ANI analysis showed that the Ensifer and Sinorhizobium strains were quite different at the genome level; the overexpression and integrated expression of significantly upregulated genes in the VB12 synthesis pathway could increase the yield of VB12, further improving the VB12 yield of the E. adhaerens S305 strain.
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Affiliation(s)
- Yongheng Liu
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China
| | - Wei Huang
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China
| | - Qi Wang
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China
| | - Cilang Ma
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China
| | - Yongyong Chang
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China
| | - Jianyu Su
- School of Life Science, Ningxia University, Xixia District, No. 539, Helan Moutain-West Road, Yinchuan, 750021, Ningxia, China.
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Romanenko L, Otstavnykh N, Tanaka N, Kurilenko V, Svetashev V, Tekutyeva L, Mikhailov V, Isaeva M. Characterization and Genomic Analysis of Fererhizobium litorale gen. nov., sp. nov., Isolated from the Sandy Sediments of the Sea of Japan Seashore. Microorganisms 2023; 11:2385. [PMID: 37894043 PMCID: PMC10609224 DOI: 10.3390/microorganisms11102385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The taxonomic status of two gram-negative, whitish-pigmented motile bacteria KMM 9576T and KMM 9553 isolated from a sandy sediment sample from the Sea of Japan seashore was defined. Phylogenetic analysis revealed that strains KMM 9576T and KMM 9553 represent a distinct lineage within the family Rhizobiaceae, sharing 100% 16S rRNA sequence similarity and 99.5% average nucleotide identity (ANI) to each other. The strains showed the highest 16S rRNA sequence similarities of 97.4% to Sinorhizobium garamanticum LMG 24692T, 96.9% to Ensifer adhaerens NBRC 100388T, and 96.8% to Pararhizobium giardinii NBRC 107135T. The ANI values between strain KMM 9576T and Ensifer adhaerens NBRC 100388T, Sinorhizobium fredii USDA 205T, Pararhizobium giardinii NBRC 107135T, and Rhizobium leguminosarum NBRC 14778T were 79.9%, 79.6%, 79.4%, and 79.2%, respectively. The highest core-proteome average amino acid identity (cpAAI) values of 82.1% and 83.1% were estimated between strain KMM 9576T and Rhizobium leguminosarum NBRC 14778T and 'Rhizobium album' NS-104, respectively. The DNA GC contents were calculated from a genome sequence to be 61.5% (KMM 9576T) and 61.4% (KMM 9553). Both strains contained the major ubiquinone Q-10 and C18:1ω7c as the dominant fatty acid followed by 11-methyl C18:1ω7c and C19:0 cyclo, and polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, and two unidentified phospholipids. Based on phylogenetic and phylogenomic analyses, and phenotypic characterization, strains KMM 9576T and KMM 9553 are concluded to represent a novel genus and species, for which the name Fererhizobium litorale gen. nov., sp. nov. is proposed. The type strain of the type species is strain KMM 9576T (=NRIC 0957T).
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Affiliation(s)
- Lyudmila Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Nadezhda Otstavnykh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan;
| | - Valeriya Kurilenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Vasily Svetashev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Street 17, Vladivostok 690041, Russia;
| | - Liudmila Tekutyeva
- ARNIKA, Territory of PDA Nadezhdinskaya, Centralnaya St. 42, Volno-Nadezhdinskoye, Primorsky krai, Vladivostok 692481, Russia;
| | - Valery Mikhailov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
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Kuzmanović N, Fagorzi C, Mengoni A, Lassalle F, diCenzo GC. Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation. Int J Syst Evol Microbiol 2022; 72. [PMID: 35238735 PMCID: PMC9558580 DOI: 10.1099/ijsem.0.005243] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The alphaproteobacterial family
Rhizobiaceae
is highly diverse, with 168 species with validly published names classified into 17 genera with validly published names. Most named genera in this family are delineated based on genomic relatedness and phylogenetic relationships, but some historically named genera show inconsistent distribution and phylogenetic breadth. The most problematic is
Rhizobium
, which is notorious for being highly paraphyletic, as most newly described species in the family are assigned to this genus without consideration of their proximity to existing genera, or the need to create novel genera. Moreover, many
Rhizobiaceae
genera lack synapomorphic traits that would give them biological and ecological significance. We propose a common framework for genus delimitation within the family
Rhizobiaceae
, wherein genera are defined as monophyletic groups in a core-genome gene phylogeny, that are separated from related species using a pairwise core-proteome average amino acid identity (cpAAI) threshold of approximately 86 %. We further propose that additional genomic or phenotypic evidence can justify division of species into separate genera even if they share greater than 86 % cpAAI. Applying this framework, we propose to reclassify
Rhizobium rhizosphaerae
and
Rhizobium oryzae
into Xaviernesmea gen. nov. Data is also provided to support the formation of Peteryoungia aggregata comb. nov., Endobacterium yantingense comb. nov., Neorhizobium petrolearium comb. nov., Pararhizobium arenae comb. nov., Pseudorhizobium tarimense comb. nov. and Mycoplana azooxidifex comb. nov. Lastly, we present arguments that the unification of the genera
Ensifer
and
Sinorhizobium
in Opinion 84 of the Judicial Commission is no longer justified by current genomic and phenotypic data. Despite pairwise cpAAI values for all
Ensifer
species and all
Sinorhizobium
species being >86 %, additional genomic and phenotypic data suggest that they significantly differ in their biology and ecology. We therefore propose emended descriptions of
Ensifer
and
Sinorhizobium
, which we argue should be considered as separate genera.
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Affiliation(s)
- Nemanja Kuzmanović
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants (JKI), Institute for Plant Protection in Horticulture and Forests, Braunschweig, Germany
| | - Camilla Fagorzi
- Department of Biology, University of Florence, Florence, Italy
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Florent Lassalle
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - George C diCenzo
- Department of Biology, Queen's University, Kingston, Ontario, Canada
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El-Batanony NH, Castellano-Hinojosa A, Correa-Galeote D, Bedmar EJ. Phylogenetic diversity of bacterial strains from root nodules of legumes grown wild in Egypt. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Rejili M, BenAbderrahim MA, Mars M, Sherrier JD. Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties. FEMS Microbiol Lett 2020; 367:5838745. [DOI: 10.1093/femsle/fnaa084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/17/2020] [Indexed: 11/13/2022] Open
Abstract
ABSTRACT
Phylogenetically diverse rhizobial strains endemic to Tunisia were isolated from symbiotic nodules of Lotus creticus, growing in different arid extremophile geographical regions of Tunisia, and speciated using multiloci-phylogenetic analysis as Neorhizobium huautlense (LCK33, LCK35, LCO42 and LCO49), Ensifer numidicus (LCD22, LCD25, LCK22 and LCK25), Ensifer meliloti (LCK8, LCK9 and LCK12) and Mesorhizobium camelthorni (LCD11, LCD13, LCD31 and LCD33). In addition, phylogenetic analyses revealed eight additional strains with previously undescribed chromosomal lineages within the genera Ensifer (LCF5, LCF6 and LCF8),Rhizobium (LCF11, LCF12 and LCF14) and Mesorhizobium (LCF16 and LCF19). Analysis using the nodC gene identified five symbiovar groups, four of which were already known. The remaining group composed of two strains (LCD11 and LCD33) represented a new symbiovar of Mesorhizobium camelthorni, which we propose designating as sv. hedysari. Interestingly, we report that soil properties drive and structure the symbiosis of L. creticus and its rhizobia.
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Affiliation(s)
- Mokhtar Rejili
- Research Laboratory Biodiversity & Valorization of Arid Areas Bioressources (BVBAA) - Faculty of Sciences of Gabes, Erriadh-Zrig, 6072-Tunisia
| | - Mohamed Ali BenAbderrahim
- Laboratoire d'Aridocultures et des Cultures Oasiennes, Institut des Régions Arides, 6051 Gabès, Tunisia
| | - Mohamed Mars
- Research Laboratory Biodiversity & Valorization of Arid Areas Bioressources (BVBAA) - Faculty of Sciences of Gabes, Erriadh-Zrig, 6072-Tunisia
| | - Janine Darla Sherrier
- Department of Crop & Soil Sciences, University of Georgia, 3111 Miller Plant Sci, 120 Carlton St., Athens, GA 30602, USA
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Soares R, Trejo J, Lorite MJ, Figueira E, Sanjuán J, Videira e Castro I. Diversity, Phylogeny and Plant Growth Promotion Traits of Nodule Associated Bacteria Isolated from Lotus parviflorus. Microorganisms 2020; 8:microorganisms8040499. [PMID: 32244524 PMCID: PMC7232477 DOI: 10.3390/microorganisms8040499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/18/2020] [Accepted: 03/30/2020] [Indexed: 11/18/2022] Open
Abstract
Lotus spp. are widely used as a forage to improve pastures, and inoculation with elite rhizobial strains is a common practice in many countries. However, only a few Lotus species have been studied in the context of plant-rhizobia interactions. In this study, forty highly diverse bacterial strains were isolated from root nodules of wild Lotus parviflorus plants growing in two field locations in Portugal. However, only 10% of these isolates could nodulate one or more legume hosts tested, whereas 90% were thought to be opportunistic nodule associated bacteria. Phylogenetic studies place the nodulating isolates within the Bradyrhizobium genus, which is closely related to B. canariense and other Bradyrhizobium sp. strains isolated from genistoid legumes and Ornithopus spp. Symbiotic nodC and nifH gene phylogenies were fully consistent with the taxonomic assignment and host range. The non-nodulating bacteria isolated were alpha- (Rhizobium/Agrobacterium), beta- (Massilia) and gamma-proteobacteria (Pseudomonas, Lysobacter, Luteibacter, Stenotrophomonas and Rahnella), as well as some bacteroidetes from genera Sphingobacterium and Mucilaginibacter. Some of these nodule-associated bacteria expressed plant growth promotion (PGP) traits, such as production of lytic enzymes, antagonistic activity against phytopathogens, phosphate solubilization, or siderophore production. This argues for a potential beneficial role of these L. parviflorus nodule-associated bacteria.
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Affiliation(s)
- Ricardo Soares
- Laboratório de Microbiologia do Solo, UEISSAFSV, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (R.S.); (J.T.)
- Laboratório de Bioquímica Inorgânica e RMN, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Jesús Trejo
- Laboratório de Microbiologia do Solo, UEISSAFSV, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (R.S.); (J.T.)
| | - Maria J. Lorite
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, E-18160 Granada, Spain; (M.L.); (J.S.)
| | - Etelvina Figueira
- Departamento de Biologia & CESAM, Universidade de Aveiro, 3810-193 Aveiro, Portugal;
| | - Juan Sanjuán
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, E-18160 Granada, Spain; (M.L.); (J.S.)
| | - Isabel Videira e Castro
- Laboratório de Microbiologia do Solo, UEISSAFSV, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV, I.P.), 2780-159 Oeiras, Portugal; (R.S.); (J.T.)
- Correspondence:
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Novel putative Mesorhizobium and Ensifer genomospecies together with a novel symbiovar psoraleae nodulate legumes of agronomic interest grown in Tunisia. Syst Appl Microbiol 2020; 43:126067. [PMID: 32005490 DOI: 10.1016/j.syapm.2020.126067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 12/08/2019] [Accepted: 12/10/2019] [Indexed: 11/22/2022]
Abstract
Forty rhizobial strains were isolated from Lotus creticus, L. pusillus and Bituminaria bituminosa endemic to Tunisia, and they belonged to the Mesorhizobium and Ensifer genera based on 16S rDNA sequence phylogeny. According to the concatenated recA and glnII sequence-based phylogeny, four Bituminaria isolates Pb5, Pb12, Pb8 and Pb17 formed a monophyletic group with Mesorhizobium chacoense ICMP14587T, whereas four other strains Pb1, Pb6, Pb13 and Pb15 formed two separate lineages within the Ensifer genus. Among the L. pusillus strains, Lpus9 and Lpus10 showed a 96% identical nucleotide with Ensifer meliloti CCBAU83493T; whereas six other strains could belong to previously undescribed Mesorhizobium and Ensifer species. For L. creticus strains, Lcus37, Lcus39 and Lcus44 showed 98% sequence identity with Ensifer aridi JNVU TP6, and Lcus42 shared a 96% identical nucleotide with Ensifer meliloti CCBAU83493T; whereas another four strains were divergent from all the described Ensifer and Mesorhizobium species. The analysis of the nodC gene-based phylogeny identified four symbiovar groups; Mesorhizobium sp. sv. anthyllidis (Lpus3 and Lpus11 from L. pusillus, Lcus43 from L. creticus), Ensifer medicae sv. meliloti (four strains from L. creticus and two strains from L. pusillus), E. meliloti sv. meliloti (four from L. creticus, four from L. pusillus and four from B. bituminosa). In addition, four B. bituminosa strains (Pb5, Pb8, Pb12, and Pb17) displayed a distinctive nodC sequence distant from those of other symbiovars described to date. According to their symbiotic gene sequences and host range, the B. bituminosa symbionts (Pb5, Pb8, Pb12 and Pb17) would represent a new symbiovar of M. chacoense for which sv. psoraleae is proposed.
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Zhao T, Cheng K, Cao YH, Ouwehand AC, Jiao CF, Yao S. Identification and Antibiotic Resistance Assessment of Ensifer adhaerens YX1, a Vitamin B 12 -Producing Strain Used as a Food and Feed Additive. J Food Sci 2019; 84:2925-2931. [PMID: 31546283 DOI: 10.1111/1750-3841.14804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 11/29/2022]
Abstract
This study provides phenotypic and molecular analyses of the antibiotic resistance of Ensifer adhaerens strain YX1 (CICC 11008s), a strain that was identified using a polyphasic taxonomy approach. The antibiotic resistance profile of E. adhaerens YX1 was assessed using the Clinical & Laboratory Standards Inst. (CLSI) method. The strain was susceptible to ciprofloxacin, levofloxacin, norfloxacin, ofloxacin, gentamicin, tobramycin, chloramphenicol, tetracycline, imipenem, and ceftazidime, and resistant to kanamycin, streptomycin, fosfomycin, and nitrofurantoin. The antibiotic resistance genes nsfA, nsfB, fosA, aph, and aadA1 were not detected in E. adhaerens YX1 via PCR using gene-specific primers. Subsequently, the genome sequence of E. adhaerens was screened for antibiotic genes. Although no antibiotic resistance genes were identified using the ResFinder database, five genes copies of one resistance gene, adeF, were detected using the Comprehensive Antibiotic Resistance Database (CARD). The results of this study will be useful for understanding the phenotypic and genotypic aspects of E. adhaerens antibiotic resistance. No safety issues were identified for E. adhaerens YX1 in terms of antibiotic resistance. Performing similar studies will be conducive to the safety assessment and control of the use of E. adhaerens in the food and feed industry. PRACTICAL APPLICATION: Few relevant reports are currently available regarding antibiotic resistance assessments or other safety evaluations for Ensifer adhaerens. Because of a lack of relevant information on the safety of this bacterium, including the genetic basis of antibiotic resistance in the production strain, it has not been recommended for use in the "qualified presumption of safety" (QPS) list and subsequent updated lists. The current study shows no safety issue of E. adhaerens YX1 in terms of its antibiotic resistance. These results are important as they provide an initial basis for an understanding of the antibiotic resistance/susceptibility of E. adhaerens YX1 (CICC 11008s), which produces vitamin B12 and is widely used in the food and feed industry.
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Affiliation(s)
- Ting Zhao
- China National Research Inst. of Food & Fermentation Industries Co., Ltd, China Center of Industrial Culture Collection, Building 6, No. 24 Yard, Jiuxianqiao Middle Road, Chaoyang District, Beijing, 100015, China
| | - Kun Cheng
- China National Research Inst. of Food & Fermentation Industries Co., Ltd, China Center of Industrial Culture Collection, Building 6, No. 24 Yard, Jiuxianqiao Middle Road, Chaoyang District, Beijing, 100015, China
| | - Yan-Hua Cao
- China National Research Inst. of Food & Fermentation Industries Co., Ltd, China Center of Industrial Culture Collection, Building 6, No. 24 Yard, Jiuxianqiao Middle Road, Chaoyang District, Beijing, 100015, China
| | - Arthur C Ouwehand
- DuPont Nutrition & Health, Sokeritehtaantie 20, 02460, Kantvik, Finland
| | - Cui-Feng Jiao
- Hebei Yuxing Bio-engineering Co., Ltd., Xicheng District, Ningjin, Xingtai, Heibei, 055550, China
| | - Su Yao
- China National Research Inst. of Food & Fermentation Industries Co., Ltd, China Center of Industrial Culture Collection, Building 6, No. 24 Yard, Jiuxianqiao Middle Road, Chaoyang District, Beijing, 100015, China
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de Lajudie PM, Andrews M, Ardley J, Eardly B, Jumas-Bilak E, Kuzmanović N, Lassalle F, Lindström K, Mhamdi R, Martínez-Romero E, Moulin L, Mousavi SA, Nesme X, Peix A, Puławska J, Steenkamp E, Stępkowski T, Tian CF, Vinuesa P, Wei G, Willems A, Zilli J, Young P. Minimal standards for the description of new genera and species of rhizobia and agrobacteria. Int J Syst Evol Microbiol 2019; 69:1852-1863. [PMID: 31140963 DOI: 10.1099/ijsem.0.003426] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Herein the members of the Subcommittee on Taxonomy of Rhizobia and Agrobacteria of the International Committee on Systematics of Prokaryotes review recent developments in rhizobial and agrobacterial taxonomy and propose updated minimal standards for the description of new species (and genera) in these groups. The essential requirements (minimal standards) for description of a new species are (1) a genome sequence of at least the proposed type strain and (2) evidence for differentiation from other species based on genome sequence comparisons. It is also recommended that (3) genetic variation within the species is documented with sequence data from several clearly different strains and (4) phenotypic features are described, and their variation documented with data from a relevant set of representative strains. Furthermore, it is encouraged that information is provided on (5) nodulation or pathogenicity phenotypes, as appropriate, with relevant gene sequences. These guidelines supplement the current rules of general bacterial taxonomy, which require (6) a name that conforms to the International Code of Nomenclature of Prokaryotes, (7) validation of the name by publication either directly in the International Journal of Systematic and Evolutionary Microbiology or in a validation list when published elsewhere, and (8) deposition of the type strain in two international culture collections in separate countries.
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Affiliation(s)
| | - Mitchell Andrews
- 2Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln 7647, New Zealand
| | - Julie Ardley
- 3School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia
| | | | - Estelle Jumas-Bilak
- 5UMR 5569, Department of Microbiology, Faculty of Pharmacy, University of Montpellier, France
| | - Nemanja Kuzmanović
- 6Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104 Braunschweig, Germany
| | - Florent Lassalle
- 7Department of Infectious Disease Epidemiology - MRC Centre for Outbreak Analysis and Modelling, St Mary's Hospital, Praed Street, London W2 1NY, UK
| | - Kristina Lindström
- 8Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Ridha Mhamdi
- 9Centre of Biotechnology of Borj-Cedria, BP 901 Hammam-lif 2050, Tunisia
| | - Esperanza Martínez-Romero
- 10Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Lionel Moulin
- 11IRD, CIRAD, University of Montpellier, IPME, Montpellier, France
| | - Seyed Abdollah Mousavi
- 8Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki FI-00014, Finland
| | - Xavier Nesme
- 12LEM, UCBL, CNRS, INRA, Univ Lyon, Villeurbanne, France
| | - Alvaro Peix
- 13Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, c/Cordel de Merinas 40-52, 37008 Salamanca, Spain
| | - Joanna Puławska
- 14Department of Phytopathology, Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100 Skierniewice, Poland
| | - Emma Steenkamp
- 15Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria 0002, South Africa
| | - Tomasz Stępkowski
- 16Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Chang-Fu Tian
- 17State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, College of Biological Sciences, China Agricultural University, 100193, Beijing, PR China
| | - Pablo Vinuesa
- 10Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
| | - Gehong Wei
- 18Northwest A&F University, Yangling, Shaanxi, PR China
| | - Anne Willems
- 19Department Biochemistry and Microbiology, Lab. Microbiology, Ghent University, Belgium
| | - Jerri Zilli
- 20Embrapa Agrobiologia, BR 465 km 07, Seropédica, Rio de Janeiro, Brazil, 23891-000, Brazil
| | - Peter Young
- 21Department of Biology, University of York, York YO10 5DD, UK
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10
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Lorite MJ, Estrella MJ, Escaray FJ, Sannazzaro A, Videira e Castro IM, Monza J, Sanjuán J, León-Barrios M. The Rhizobia- Lotus Symbioses: Deeply Specific and Widely Diverse. Front Microbiol 2018; 9:2055. [PMID: 30258414 PMCID: PMC6144797 DOI: 10.3389/fmicb.2018.02055] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/13/2018] [Indexed: 11/13/2022] Open
Abstract
The symbiosis between Lotus and rhizobia has been long considered very specific and only two bacterial species were recognized as the microsymbionts of Lotus: Mesorhizobium loti was considered the typical rhizobia for the L. corniculatus complex, whereas Bradyrhizobium sp. (Lotus) was the symbiont for L. uliginosus and related species. As discussed in this review, this situation has dramatically changed during the last 15 years, with the characterization of nodule bacteria from worldwide geographical locations and from previously unexplored Lotus spp. Current data support that the Lotus rhizobia are dispersed amongst nearly 20 species in five genera (Mesorhizobium, Bradyrhizobium, Rhizobium, Ensifer, and Aminobacter). As a consequence, M. loti could be regarded an infrequent symbiont of Lotus, and several plant-bacteria compatibility groups can be envisaged. Despite the great progress achieved with the model L. japonicus in understanding the establishment and functionality of the symbiosis, the genetic and biochemical bases governing the stringent host-bacteria compatibility pairships within the genus Lotus await to be uncovered. Several Lotus spp. are grown for forage, and inoculation with rhizobia is a common practice in various countries. However, the great diversity of the Lotus rhizobia is likely squandered, as only few bacterial strains are used as inoculants for Lotus pastures in very different geographical locations, with a great variety of edaphic and climatic conditions. The agroecological potential of the genus Lotus can not be fully harnessed without acknowledging the great diversity of rhizobia-Lotus interactions, along with a better understanding of the specific plant and bacterial requirements for optimal symbiotic nitrogen fixation under increasingly constrained environmental conditions.
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Affiliation(s)
- María J. Lorite
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - María J. Estrella
- Instituto Tecnológico de Chascomús, IIB-INTECH, UNSAM-CONICET, Chascomús, Argentina
| | - Francisco J. Escaray
- Instituto Tecnológico de Chascomús, IIB-INTECH, UNSAM-CONICET, Chascomús, Argentina
| | - Analía Sannazzaro
- Instituto Tecnológico de Chascomús, IIB-INTECH, UNSAM-CONICET, Chascomús, Argentina
| | | | - Jorge Monza
- Facultad de Agronomia, Universidad de la República, Montevideo, Uruguay
| | - Juan Sanjuán
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de la Laguna, Santa Cruz de Tenerife, Spain
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11
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Dekak A, Chabi R, Menasria T, Benhizia Y. Phenotypic characterization of rhizobia nodulating legumes Genista microcephala and Argyrolobium uniflorum growing under arid conditions. J Adv Res 2018; 14:35-42. [PMID: 30009051 PMCID: PMC6041434 DOI: 10.1016/j.jare.2018.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 01/14/2023] Open
Abstract
A phenotypic characterization of thirteen root nodule bacteria recovered from wild legumes (Genista microcephala and Argyrolobium uniflorum) growing in arid eco-climate zones (Northeastern Algeria) was conducted using analysis of sixty-six phenotypic traits (carbohydrate and nitrogen assimilation, vitamin requirements, growth temperature, salinity/pH tolerance and enzyme production). Furthermore, SDS-PAGE profiles of total cell protein, antibiotic susceptibility and heavy metal resistance were performed. The results showed that the isolates can grow at pH 4 to 10, salt concentration (0–5%) and temperature up to 45 °C. The rhizobia associated with Genista microcephala and Argyrolobium uniflorum were able to produce different hydrolytic enzymes including cellulose, pectinase and urease, with remarkable tolerance to toxic metals such as zinc, lead, copper, and mercury. Numerical analysis of the phenotypic characteristics revealed that the rhizobial isolates formed four main distinct groups showing high levels of similarity with Gammaproteobacteria. The salt tolerant and heavy metals resistance patterns found among the indigenous rhizobial strains are reflecting the environmental stresses pressure and make the strains good candidates for plant successful inoculation in arid areas.
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Affiliation(s)
- Ahmed Dekak
- Department of Biological Sciences, Faculty of Exact Sciences and Natural and Life Sciences, University of Tebessa, Tebessa 12002, Algeria.,Department of Microbiology, Faculty of Natural and Life Sciences, University of Constantine I, Constantine 25000, Algeria
| | - Rabah Chabi
- Department of Microbiology, Faculty of Natural and Life Sciences, University of Constantine I, Constantine 25000, Algeria
| | - Taha Menasria
- Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Tebessa, Tebessa 12002, Algeria
| | - Yacine Benhizia
- Department of Microbiology, Faculty of Natural and Life Sciences, University of Constantine I, Constantine 25000, Algeria
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12
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Stępkowski T, Banasiewicz J, Granada CE, Andrews M, Passaglia LMP. Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae. Genes (Basel) 2018. [PMID: 29538303 PMCID: PMC5867884 DOI: 10.3390/genes9030163] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes. This indicates that the capacity for nodulation of Genisteae spp. has evolved independently in various symbiotic gene clades, and that it has not been a long-multi-step process. The exception is Bradyrhizobium Clade II, which unlike other clades comprises strains that are specialized in nodulation of Genisteae, but also Loteae spp. Presumably, Clade II represents an example of long-lasting co-evolution of bradyrhizobial symbionts with their legume hosts.
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Affiliation(s)
- Tomasz Stępkowski
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Joanna Banasiewicz
- Autonomous Department of Microbial Biology, Faculty of Agriculture and Biology, Warsaw University of Life Sciences (SGGW), Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Camille E Granada
- Universidade do Vale do Taquari-UNIVATES, Rua Avelino Tallini, 171, 95900-000 Lajeado, RS, Brazil.
| | - Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 84, Lincoln 7647, New Zealand.
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul. Av. Bento Gonçalves, 9500, Caixa Postal 15.053, 91501-970 Porto Alegre, RS, Brazil.
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13
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Osman WAM, van Berkum P, León-Barrios M, Velázquez E, Elia P, Tian R, Ardley J, Gollagher M, Seshadri R, Reddy TBK, Ivanova N, Woyke T, Pati A, Markowitz V, Baeshen MN, Baeshen NN, Kyrpides N, Reeve W. High-quality draft genome sequence of Ensifer meliloti Mlalz-1, a microsymbiont of Medicago laciniata (L.) miller collected in Lanzarote, Canary Islands, Spain. Stand Genomic Sci 2017; 12:58. [PMID: 28975015 PMCID: PMC5613336 DOI: 10.1186/s40793-017-0270-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 09/14/2017] [Indexed: 11/26/2022] Open
Abstract
10.1601/nm.1335 Mlalz-1 (INSDC = ATZD00000000) is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing nodule of Medicago laciniata (L.) Miller from a soil sample collected near the town of Guatiza on the island of Lanzarote, the Canary Islands, Spain. This strain nodulates and forms an effective symbiosis with the highly specific host M. laciniata. This rhizobial genome was sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) sequencing project. Here the features of 10.1601/nm.1335 Mlalz-1 are described, together with high-quality permanent draft genome sequence information and annotation. The 6,664,116 bp high-quality draft genome is arranged in 99 scaffolds of 100 contigs, containing 6314 protein-coding genes and 74 RNA-only encoding genes. Strain Mlalz-1 is closely related to 10.1601/nm.1335 10.1601/strainfinder?urlappend=%3Fid%3DIAM+12611 T, 10.1601/nm.1334 A 321T and 10.1601/nm.17831 10.1601/strainfinder?urlappend=%3Fid%3DORS+1407 T, based on 16S rRNA gene sequences. gANI values of ≥98.1% support the classification of strain Mlalz-1 as 10.1601/nm.1335. Nodulation of M. laciniata requires a specific nodC allele, and the nodC gene of strain Mlalz-1 shares ≥98% sequence identity with nodC of M. laciniata-nodulating 10.1601/nm.1328 strains, but ≤93% with nodC of 10.1601/nm.1328 strains that nodulate other Medicago species. Strain Mlalz-1 is unique among sequenced 10.1601/nm.1335 strains in possessing genes encoding components of a T2SS and in having two versions of the adaptive acid tolerance response lpiA-acvB operon. In 10.1601/nm.1334 strain 10.1601/strainfinder?urlappend=%3Fid%3DWSM+419, lpiA is essential for enhancing survival in lethal acid conditions. The second copy of the lpiA-acvB operon of strain Mlalz-1 has highest sequence identity (> 96%) with that of 10.1601/nm.1334 strains, which suggests genetic recombination between strain Mlalz-1 and 10.1601/nm.1334 and the horizontal gene transfer of lpiA-acvB.
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Affiliation(s)
| | - Peter van Berkum
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, Tenerife, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genetica and Instituto Hispanoluso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Salamanca, Spain
| | - Patrick Elia
- U.S. Department of Agriculture, Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, 10300 Baltimore Avenue, Bldg. 006, Beltsville, MD 20705 USA
| | - Rui Tian
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Julie Ardley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA Australia
| | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Amrita Pati
- 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
| | - Mohamed N. Baeshen
- Department of Biology, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia
| | | | | | - Wayne Reeve
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA Australia
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14
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Biogeography of a Novel Ensifer meliloti Clade Associated with the Australian Legume Trigonella suavissima. Appl Environ Microbiol 2017; 83:AEM.03446-16. [PMID: 28283520 DOI: 10.1128/aem.03446-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/02/2017] [Indexed: 11/20/2022] Open
Abstract
Here, we describe a novel clade within Ensifer meliloti and consider how geographic and ecological isolation contributed to the limited distribution of this group. Members of the genus Ensifer are best known for their ability to form nitrogen-fixing symbioses with forage legumes of three related genera, Medicago L., Melilotus Mill., and Trigonella L., which are members of the tribe Trifolieae. These legumes have a natural distribution extending from the Mediterranean Basin through western Asia, where there is an unsurpassed number of species belonging to these genera. Trigonella suavissima L. is unusual in that it is the only species in the tribe Trifolieae that is native to Australia. We compared the genetic diversity and taxonomic placement of rhizobia nodulating T. suavissima with those of members of an Ensifer reference collection. Our goal was to determine if the T. suavissima rhizobial strains, like their plant host, are naturally limited to the Australian continent. We used multilocus sequence analysis to estimate the genetic relatedness of 56 T. suavissima symbionts to 28 Ensifer reference strains. Sequence data were partitioned according to the replicons in which the loci are located. The results were used to construct replicon-specific phylogenetic trees. In both the chromosomal and chromid trees, the Australian strains formed a distinct clade within E. meliloti The strains also shared few alleles with Ensifer reference strains from other continents. Carbon source utilization assays revealed that the strains are also unusual in their ability to utilize 2-oxoglutarate as a sole carbon source. A strategy was outlined for locating similar strains elsewhere.IMPORTANCE In this study, we employed a biogeographical approach to investigate the origins of a symbiotic relationship between an Australian legume and its nitrogen-fixing rhizobia. The question of the ancestral origins of these symbionts is based on the observation that the legume host is not closely related to other native Australian legumes. Previous research has shown that the legume host Trigonella suavissima is instead closely related to legumes native to the Mediterranean Basin and western Asia, suggesting that it may have been introduced in Australia from those regions. This led to the question of whether its rhizobia may have been introduced as well. In this study, we were unable to find persuasive evidence supporting this hypothesis. Instead, our results suggest either that the T. suavissima rhizobia are native to Australia or that our methods for locating their close relatives elsewhere are inadequate. A strategy to investigate the latter alternative is proposed.
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15
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Chen WH, Yang SH, Li ZH, Zhang XX, Sui XH, Wang ET, Chen WX, Chen WF. Ensifer shofinae sp. nov., a novel rhizobial species isolated from root nodules of soybean (Glycine max). Syst Appl Microbiol 2017; 40:144-149. [PMID: 28209394 DOI: 10.1016/j.syapm.2017.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/09/2016] [Accepted: 01/04/2017] [Indexed: 10/20/2022]
Abstract
Two bacterial strains isolated from root nodules of soybean were characterized phylogenetically as members of a distinct group in the genus Ensifer based on 16S rRNA gene comparisons. They were also verified as a separated group by the concatenated sequence analyses of recA, atpD and glnII (with similarities ≤93.9% to the type strains for defined species), and by the average nucleotide identities (ANI) between the whole genome sequence of the representative strain CCBAU 251167T and those of the closely related strains in Ensifer glycinis and Ensifer fredii (90.5% and 90.3%, respectively). Phylogeny of symbiotic genes (nodC and nifH) grouped these two strains together with some soybean-nodulating strains of E. fredii, E. glycinis and Ensifer sojae. Nodulation tests indicated that the representative strain CCBAU 251167T could form root nodules with capability of nitrogen fixing on its host plant and Glycine soja, Cajanus cajan, Vigna unguiculata, Phaseolus vulgaris and Astragalus membranaceus, and it formed ineffective nodules on Leucaena leucocephala. Strain CCBAU 251167T contained fatty acids 18:1 ω9c, 18:0 iso and 20:0, differing from other related strains. Utilization of l-threonine and d-serine as carbon source, growth at pH 6.0 and intolerance of 1% (w/v) NaCl distinguished strain CCBAU 251167T from other type strains of the related species. The genome size of CCBAU 251167T was 6.2Mbp, comprising 7,581 predicted genes with DNA G+C content of 59.9mol% and 970 unique genes. Therefore, a novel species, Ensifer shofinae sp. nov., is proposed, with CCBAU 251167T (=ACCC 19939T=LMG 29645T) as type strain.
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Affiliation(s)
- Wen Hao Chen
- State Key Laboratory of Agro-Biotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology; Beijing 100193, PR China; Engineering Research Centre of Plant Growth Regulators, Ministry of Education; College of Agronomy and Biotechnology, China Agricultural University; Beijing 100193, PR China; College of Life Science & Food Engineering, Yibin University, Yibin 644000, Sichuan Province, PR China
| | - Sheng Hui Yang
- State Key Laboratory of Agro-Biotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology; Beijing 100193, PR China; Shandong Shofine Seed Technology Co. Ltd., Jiaxiang 272400, PR China
| | - Zhao Hu Li
- Engineering Research Centre of Plant Growth Regulators, Ministry of Education; College of Agronomy and Biotechnology, China Agricultural University; Beijing 100193, PR China
| | - 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
| | - Xin Hua Sui
- State Key Laboratory of Agro-Biotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology; Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, Mexico.
| | - Wen Xin Chen
- State Key Laboratory of Agro-Biotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology; Beijing 100193, PR China
| | - Wen Feng Chen
- State Key Laboratory of Agro-Biotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology; Beijing 100193, PR China.
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16
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Andrews M, Andrews ME. Specificity in Legume-Rhizobia Symbioses. Int J Mol Sci 2017; 18:E705. [PMID: 28346361 PMCID: PMC5412291 DOI: 10.3390/ijms18040705] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 03/19/2017] [Accepted: 03/21/2017] [Indexed: 11/24/2022] Open
Abstract
Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils. Strain-specific legume rhizobia symbioses can develop in particular habitats.
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Affiliation(s)
- Mitchell Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
| | - Morag E Andrews
- Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, New Zealand.
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17
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León-Barrios M, Pérez-Yépez J, Dorta P, Garrido A, Jiménez C. Alkalinity of Lanzarote soils is a factor shaping rhizobial populations with Sinorhizobium meliloti being the predominant microsymbiont of Lotus lancerottensis. Syst Appl Microbiol 2017; 40:171-178. [PMID: 28216096 DOI: 10.1016/j.syapm.2016.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/15/2016] [Accepted: 12/18/2016] [Indexed: 10/20/2022]
Abstract
Lotus lancerottensis is an endemic species that grows widely throughout Lanzarote Island (Canary Is.). Characterization of 48 strains isolated from root nodules of plants growing in soils from eleven locations on the island showed that 38 isolates (79.1%) belonged to the species Sinorhizobium meliloti, whereas only six belonged to Mesorhizobium sp., the more common microsymbionts for the Lotus. Other genotypes containing only one isolate were classified as Pararhizobium sp., Sinorhizobium sp., Phyllobacterium sp. and Bradyrhizobium-like. Strains of S. meliloti were distributed along the island and, in most of the localities they were exclusive or major microsymbionts of L. lancerottensis. Phylogeny of the nodulation nodC gene placed the S. meliloti strains within symbiovar lancerottense and the mesorhizobial strains with the symbiovar loti. Although strains from both symbiovars produced effective N2-fixing nodules, S. meliloti symbiovar lancerottense was clearly the predominant microsymbiont of L. lancerottensis. This fact correlated with the better adaptation of strains of this species to the alkaline soils of Lanzarote, as in vitro characterization showed that while the mesorhizobial strains were inhibited by alkaline pH, S. meliloti strains grew well at pH 9.
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Affiliation(s)
- Milagros León-Barrios
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain.
| | - Juan Pérez-Yépez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
| | - Paola Dorta
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
| | - Ana Garrido
- Granja Agrícola Experimental, Área de Agricultura y Ganadería, Cabildo de Lanzarote, Canary Islands, Spain
| | - Concepción Jiménez
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, 38200 La Laguna, Tenerife, Canary Islands, Spain
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18
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Li Y, Yan J, Yu B, Wang ET, Li X, Yan H, Liu W, Xie Z. Ensifer alkalisoli sp. nov. isolated from root nodules of Sesbania cannabina grown in saline–alkaline soils. Int J Syst Evol Microbiol 2016; 66:5294-5300. [DOI: 10.1099/ijsem.0.001510] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yan Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - Jun Yan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, PR China
| | - Bing Yu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Mexico City, D.F., México
| | - Xiangyue Li
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - Hui Yan
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, PR China
| | - Wei Liu
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
| | - Zhihong Xie
- Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 264003 Yantai, PR China
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19
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Shamseldin A, Abdelkhalek A, Sadowsky MJ. Recent changes to the classification of symbiotic, nitrogen-fixing, legume-associating bacteria: a review. Symbiosis 2016. [DOI: 10.1007/s13199-016-0462-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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Yan H, Yan J, Sui XH, Wang ET, Chen WX, Zhang XX, Chen WF. Ensifer glycinis sp. nov., a rhizobial species associated with species of the genus Glycine. Int J Syst Evol Microbiol 2016; 66:2910-2916. [PMID: 27125987 DOI: 10.1099/ijsem.0.001120] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Rhizobial strains from root nodules of Astragalus mongholicus and soybean (Glycine max) were characterized phylogenetically as members of the genus Ensifer (formerly named Sinorhizobium), based on 16S rRNA gene sequence comparisons. Results based upon concatenated sequence analysis of three housekeeping genes (recA, atpD and glnII, ≤ 93.8 % similarities to known species) and average nucleotide identity (ANI) values of whole genome sequence comparisons (ranging from 89.6 % to 83.4 % to Ensifer fredii and Ensifer saheli, respectively) indicated the distinct positions of these novel strains within the genus Ensifer. Phylogeny of symbiotic genes (nodC and nifH) of three novel strains clustered them with rhizobial species Ensifer fredii and Ensifer sojae, both isolated from nodules of Glycine max. Cross-nodulation tests showed that the representative strain CCBAU 23380T could form root nodules with nitrogen fixation capability on Glycine soja, Albizia julibrissin, Vigna unguiculata and Cajanus cajan, but failed to nodulate Astragalus mongholicus, its original host legume. Strain CCBAU 23380T formed inefficient nodules on G. max, and it did not contain 18 : 0, 18 : 1ω7c 11-methyl or summed feature 1 fatty acids, which differed from other related strains. Failure to utilize malonic acid as a carbon source distinguished strain CCBAU 23380T from the type strains of related species. The genome size of CCBAU 23380T was 6.0 Mbp, comprising 5624 predicted genes with DNA G+C content of 62.4 mol%. Based on the results above, a novel species, Ensifer glycinis sp. nov., is proposed, with CCBAU 23380T (=LMG 29231T =HAMBI 3645T) as the type strain.
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Affiliation(s)
- Hui Yan
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
| | - Jun Yan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, PR China
| | - Xin Hua Sui
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
| | - En Tao Wang
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México D. F. 11340, Mexico
| | - Wen Xin Chen
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
| | - 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
| | - Wen Feng Chen
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China
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21
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Beukes CW, Stępkowski T, Venter SN, Cłapa T, Phalane FL, le Roux MM, Steenkamp ET. Crotalarieae and Genisteae of the South African Great Escarpment are nodulated by novel Bradyrhizobium species with unique and diverse symbiotic loci. Mol Phylogenet Evol 2016; 100:206-218. [DOI: 10.1016/j.ympev.2016.04.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 12/21/2022]
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22
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Sami D, Mokhtar R, Peter M, Mohamed M. Rhizobium leguminosarum symbiovar trifolii, Ensifer numidicus and Mesorhizobium amorphae symbiovar ciceri (or Mesorhizobium loti) are new endosymbiotic bacteria of Lens culinaris Medik. FEMS Microbiol Ecol 2016; 92:fiw118. [PMID: 27267929 DOI: 10.1093/femsec/fiw118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2016] [Indexed: 11/13/2022] Open
Abstract
A total of 142 rhizobial bacteria were isolated from root nodules of Lens culinaris Medik endemic to Tunisia and they belonged to the species Rhizobium leguminosarum, and for the first time to Ensifer and Mesorhizobium, genera never previously described as microsymbionts of lentil. Phenotypically, our results indicate that L. culinaris Medik strains showed heterogenic responses to the different phenotypic features and they effectively nodulated their original host. Based on the concatenation of the 16S rRNA with relevant housekeeping genes (glnA, recA, dnaK), rhizobia that nodulate lentil belonged almost exclusively to the known R. leguminosarum sv. viciae. Interestingly, R. leguminosarum sv. trifolii, Ensifer numidicus (10 isolates) and Mesorhizobium amorphae (or M. loti) (9 isolates) isolates species, not considered, up to now, as a natural symbiont of lentil are reported. The E. numidicus and M. amorphae (or M. loti) strains induced fixing nodules on Medicago sativa and Cicer arietinum host plants, respectively. Symbiotic gene phylogenies showed that the E. numidicus, new symbiont of lentil, markedly diverged from strains of R. leguminosarum, the usual symbionts of lentil, and converged to the symbiovar meliloti so far described within E. meliloti Indeed, the nodC and nodA genes from the M. amorphae showed more than 99% similarity with respect to those from M. mediterraneum, the common chickpea nodulating species, and would be included in the new infrasubspecific division named M. amorphae symbiovar ciceri, or to M. loti, related to the strains able to effectively nodulate C. arietinum host plant. On the basis of these data, R. leguminosarum sv. trifolii (type strain LBg3 (T)), M. loti or M. amorphae sv. ciceri (type strain LB4 (T)) and E. numidicus (type strain LBi2 (T)) are proposed as new symbionts of L. culinaris Medik.
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Affiliation(s)
- Dhaoui Sami
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
| | - Rejili Mokhtar
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
| | - Mergaert Peter
- Institute for IntegrativeBiology of the Cell, Centre National de la Recherche Scientifique, Avenue de la Terrasse Bât. 34, 91198 Gif-sur-Yvette, France
| | - Mars Mohamed
- Research Unit Biodiversity & Valorization of Arid Areas Bioressources, Faculty of Sciences of Gabès, Erriadh-Zrig, Gabes 6072, Tunisia
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Chaïch K, Bekki A, Bouras N, Holtz MD, Soussou S, Mauré L, Brunel B, de Lajudie P, Cleyet-Marel JC. Rhizobial diversity associated with the spontaneous legume Genista saharae in the northeastern Algerian Sahara. Symbiosis 2016. [DOI: 10.1007/s13199-016-0414-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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24
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Gnat S, Małek W, Oleńska E, Wdowiak-Wróbel S, Kalita M, Rogalski J, Wójcik M. Multilocus sequence analysis supports the taxonomic position of Astragalus glycyphyllos symbionts based on DNA–DNA hybridization. Int J Syst Evol Microbiol 2016; 66:1906-1912. [DOI: 10.1099/ijsem.0.000862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Sebastian Gnat
- Department of Veterinary Microbiology, University of Life Sciences, 13 Akademicka st., 20-950 Lublin, Poland
| | - Wanda Małek
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Ewa Oleńska
- Department of Genetics and Evolution, University of Bialystok, 1J Ciolkowskiego st., 15-245 Bialystok, Poland
| | - Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Michał Kalita
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Jerzy Rogalski
- Department of Biochemistry, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
| | - Magdalena Wójcik
- Department of Genetics and Microbiology, University of Maria Curie-Sklodowska, 19 Akademicka st., 20-033 Lublin, Poland
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25
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Phenotypic and genotypic characterization of root nodules rhizobia of Medicago littoralis Rhode and Melilotus indicus (L.) All. growing in the Oasis of Touggourt, Oued Righ Valley, in the Algerian Sahara. Symbiosis 2015. [DOI: 10.1007/s13199-015-0336-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Mhamdi R, Ardley J, Tian R, Seshadri R, Reddy T, Pati A, Woyke T, Markowitz V, Ivanova N, Kyrpides N, Reeve W. High-quality permanent draft genome sequence of Ensifer meliloti strain 4H41, an effective salt- and drought-tolerant microsymbiont of Phaseolus vulgaris. Stand Genomic Sci 2015; 10:34. [PMID: 26380038 PMCID: PMC4571125 DOI: 10.1186/s40793-015-0005-1] [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: 02/18/2015] [Accepted: 04/15/2015] [Indexed: 11/10/2022] Open
Abstract
Ensifer meliloti 4H41 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of common bean (Phaseolus vulgaris). Strain 4H41 was isolated in 2002 from root nodules of P. vulgaris grown in South Tunisia from the oasis of Rjim-Maatoug. Strain 4H41 is salt- and drought-tolerant and highly effective at fixing nitrogen with P. vulgaris. Here we describe the features of E. meliloti 4H41, together with genome sequence information and its annotation. The 6,795,637 bp high-quality permanent draft genome is arranged into 47 scaffolds of 47 contigs containing 6,350 protein-coding genes and 72 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.
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Affiliation(s)
- Ridha Mhamdi
- Laboratory of Legumes, Centre of Biotechnology of Borj-Cedria, BP 901, Hammam-Lif, 2050 Tunisia
| | - Julie Ardley
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia
| | - Rui Tian
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia
| | | | - T.B.K. Reddy
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, CA USA
| | - Tanja Woyke
- 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, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Wayne Reeve
- Centre for Rhizobium Studies, Murdoch University, Murdoch, WA Australia
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27
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Riah N, Béna G, Djekoun A, Heulin K, de Lajudie P, Laguerre G. Genotypic and symbiotic diversity of Rhizobium populations associated with cultivated lentil and pea in sub-humid and semi-arid regions of Eastern Algeria. Syst Appl Microbiol 2014; 37:368-75. [PMID: 24582507 DOI: 10.1016/j.syapm.2013.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/27/2013] [Accepted: 12/04/2013] [Indexed: 11/19/2022]
Abstract
The genetic structure of rhizobia nodulating pea and lentil in Algeria, Northern Africa was determined. A total of 237 isolates were obtained from root nodules collected on lentil (Lens culinaris), proteaginous and forage pea (Pisum sativum) growing in two eco-climatic zones, sub-humid and semi-arid, in Eastern Algeria. They were characterised by PCR-restriction fragment length polymorphism (RFLP) of the 16S-23S rRNA intergenic region (IGS), and the nodD-F symbiotic region. The combination of these haplotypes allowed the isolates to be clustered into 26 distinct genotypes, and all isolates were classified as Rhizobium leguminosarum. Symbiotic marker variation (nodD-F) was low but with the predominance of one nod haplotype (g), which had been recovered previously at a high frequency in Europe. Sequence analysis of the IGS further confirmed its high variability in the studied strains. An AMOVA analysis showed highly significant differentiation in the IGS haplotype distribution between populations from both eco-climatic zones. This differentiation was reflected by differences in dominant genotype frequencies. Conversely, no host plant effect was detected. The nodD gene sequence-based phylogeny suggested that symbiotic gene diversity in pea and lentil nodulating rhizobial populations in Algeria was low compared to that reported elsewhere in the world.
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MESH Headings
- Algeria
- Bacterial Proteins/genetics
- Cluster Analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Intergenic/chemistry
- DNA, Intergenic/genetics
- Genetic Variation
- Haplotypes
- Lens Plant/microbiology
- Molecular Sequence Data
- Pisum sativum/microbiology
- Phylogeny
- Plant Roots/microbiology
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Rhizobium leguminosarum/classification
- Rhizobium leguminosarum/genetics
- Rhizobium leguminosarum/physiology
- Sequence Analysis, DNA
- Symbiosis
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Affiliation(s)
- Nassira Riah
- Laboratoire de Génétique, Biochimie et Biotechnologies Végétalesm, Faculté des Sciences de la Nature, Université Constantine 1, Route Ain El Bey 25000, Algeria; IRD - INRA LSTM, Tropical and Mediterranean Symbiosis Laboratory, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Gilles Béna
- IRD - INRA LSTM, Tropical and Mediterranean Symbiosis Laboratory, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France.
| | - Abdelhamid Djekoun
- Laboratoire de Génétique, Biochimie et Biotechnologies Végétalesm, Faculté des Sciences de la Nature, Université Constantine 1, Route Ain El Bey 25000, Algeria
| | - Karine Heulin
- IRD - INRA LSTM, Tropical and Mediterranean Symbiosis Laboratory, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Philippe de Lajudie
- IRD - INRA LSTM, Tropical and Mediterranean Symbiosis Laboratory, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
| | - Gisèle Laguerre
- IRD - INRA LSTM, Tropical and Mediterranean Symbiosis Laboratory, Campus International de Baillarguet, TA A-82/J, 34398 Montpellier Cedex 5, France
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28
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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]
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29
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Rejii M, Mahdhi M, Domínguez-Núñez JA, Mars M. The phenotypic, phylogenetic and symbiotic characterization of rhizobia nodulating Lotus sp. in Tunisian arid soils. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0670-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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30
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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.
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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
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Phylogenetic multilocus sequence analysis identifies seven novel
Ensifer
genospecies isolated from a less-well-explored biogeographical region in East Africa. Int J Syst Evol Microbiol 2012; 62:2286-2295. [DOI: 10.1099/ijs.0.039230-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The diversity of 71 rhizobial strains belonging to the genus
Ensifer
, isolated from root nodules of woody legumes growing in southern Ethiopia, was studied using multilocus sequence analysis (MLSA) and phenotypic approaches. Phylogenetic analyses based on core genes revealed that 43 strains were clustered in seven distinct and consistent positions (genospecies I–VII), while another 25 strains were also distinct but were discrepant in their placement on the different gene trees. The remaining three strains occupied the same phylogenetic branches as defined
Ensifer
species and thus were not distinct. Irrespective of their chromosomal background, the majority of the test strains were highly related with respect to their nifH and nodC gene sequences, suggesting that these symbionts might have acquired these genes recently from a common origin. On the nifH phylogenetic tree, the branch containing the test strains and reference species isolated from woody legumes in Africa was clearly separate from those isolated outside the continent, suggesting that these symbionts have a long history of separate evolution within
Ensifer
for this gene. A cross-inoculation study showed that our strains were capable of eliciting effective nodulation on the homologous host and on other host species. This suggests a potential to improve nitrogen fixation by selecting for broad-host-range inoculants. Our study confirms the presence of a wide diversity of
Ensifer
in East Africa and, while contributing to the general knowledge of the biodiversity within the genus, also highlights the need to focus on previously less-well-explored biogeographical regions to unravel as-yet-unidentified rhizobial resources.
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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.
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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
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Ramírez-Bahena MH, Hernández M, Peix Á, Velázquez E, León-Barrios M. Mesorhizobial strains nodulating Anagyris latifolia and Lotus berthelotii in Tamadaya ravine (Tenerife, Canary Islands) are two symbiovars of the same species, Mesorhizobium tamadayense sp. nov. Syst Appl Microbiol 2012; 35:334-41. [DOI: 10.1016/j.syapm.2012.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 04/25/2012] [Accepted: 05/06/2012] [Indexed: 10/28/2022]
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35
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Fterich A, Mahdhi M, Lafuente A, Pajuelo E, Caviedes MA, Rodriguez-Llorente ID, Mars M. Taxonomic and symbiotic diversity of bacteria isolated from nodules of Acacia tortilis subsp. raddiana in arid soils of Tunisia. Can J Microbiol 2012; 58:738-51. [PMID: 22616625 DOI: 10.1139/w2012-048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A collection of rhizobia isolated from Acacia tortilis subsp. raddiana nodules from various arid soils in Tunisia was analyzed for their diversity at both taxonomic and symbiotic levels. The isolates were found to be phenotypically diverse. The majority of the isolates tolerated 3% NaCl and grew at 40 °C. Genetic characterization emphasized that most of the strains (42/50) belong to the genus Ensifer, particularly the species Ensifer meliloti, Ensifer garamanticus, and Ensifer numidicus. Symbiotic properties of isolates showed diversity in their capacity to nodulate their host plant and to fix atmospheric nitrogen. The most effective isolates were closely related to E. garamanticus. Nodulation tests showed that 3 strains belonging to Mesorhizobium genus failed to renodulate their host plant, which is surprising for symbiotic rhizobia. Furthermore, our results support the presence of non-nodulating endophytic bacteria belonging to the Acinetobacter genus in legume nodules.
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Affiliation(s)
- A Fterich
- Laboratoire de biotechnologies végétales appliquées à l'amélioration des cultures, Faculté des sciences de Gabès, Université de Gabès, Cité Erriadh, Zrig 6072 Gabès, Tunisia
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Phylogeny and genetic diversity of native rhizobia nodulating common bean (Phaseolus vulgaris L.) in Ethiopia. Syst Appl Microbiol 2012; 35:120-31. [DOI: 10.1016/j.syapm.2011.11.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/22/2011] [Accepted: 11/24/2011] [Indexed: 11/24/2022]
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37
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Lorite MJ, Videira e Castro I, Muñoz S, Sanjuán J. Phylogenetic relationship of Lotus uliginosus symbionts with bradyrhizobia nodulating genistoid legumes. FEMS Microbiol Ecol 2012; 79:454-64. [PMID: 22092879 DOI: 10.1111/j.1574-6941.2011.01230.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 10/13/2011] [Accepted: 10/14/2011] [Indexed: 11/26/2022] Open
Abstract
Lotus species are legumes with potential for pastures in soils with low-fertility and environmental constraints. The aim of this work was to characterize bacteria that establish efficient nitrogen-fixing symbiosis with the forage species Lotus uliginosus. A total of 39 isolates were obtained from nodules of L. uliginosus naturally growing in two different locations of Portugal. Molecular identification of the isolates plus the commercial inoculant strain NZP2039 was performed by REP-PCR, 16S rRNA RFLP, and 16S rRNA, glnII and recA sequence analyses. Limited genetic diversity was found among the L. uliginosus symbionts, which showed a close phylogenetic relationship with the species Bradyrhizobium japonicum. The symbiotic nifH, nodA and nodC gene sequences were closely related with the corresponding genes of various Bradyrhizobium strains isolated from Lupinus and other genistoid legumes and therefore were phylogenetically separated from other Lotus spp. rhizobia. The L. uliginosus bradyrhizobia were able to nodulate and fix nitrogen in association with L. uliginosus, could nodulate Lotus corniculatus with generally poor nitrogen-fixing efficiency, formed nonfixing nodules in Lotus tenuis and Lupinus luteus roots and were unable to nodulate Glycine soja or Glycine max. Thus, L. uliginosus rhizobia seem closely related to B. japonicum biovar genistearum strains.
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Affiliation(s)
- María J Lorite
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, CSIC, Granada, Spain
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38
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Scientific Opinion on the maintenance of the list of QPS biological agents intentionally added to food and feed (2011 update). EFSA J 2011. [DOI: 10.2903/j.efsa.2011.2497] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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39
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Margaret I, Becker A, Blom J, Bonilla I, Goesmann A, Göttfert M, Lloret J, Mittard-Runte V, Rückert C, Ruiz-Sainz JE, Vinardell JM, Weidner S. Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean. J Biotechnol 2011; 155:11-9. [PMID: 21458507 DOI: 10.1016/j.jbiotec.2011.03.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 03/11/2011] [Accepted: 03/22/2011] [Indexed: 10/18/2022]
Abstract
Glycine max (soybean) plants can be nodulated by fast-growing rhizobial strains of the genus Sinorhizobium as well as by slow-growing strains clustered in the genus Bradyrhizobium. Fast-growing rhizobia strains with different soybean cultivar specificities have been isolated from Chinese soils and from other geographical regions. Most of these strains have been clustered into the species Sinorhizobium fredii. The S. fredii strain HH103 was isolated from soils of Hubei province, Central China and was first described in 1985. This strain is capable to nodulate American and Asiatic soybean cultivars and many other different legumes and is so far the best studied fast-growing soybean-nodulating strain. Additionally to the chromosome S. fredii HH103 carries five indigenous plasmids. The largest plasmid (pSfrHH103e) harbours genes for the production of diverse surface polysaccharides, such as exopolysaccharides (EPS), lipopolysaccharides (LPS), and capsular polysaccharides (KPS). The second largest plasmid (pSfrHH103d) is a typical symbiotic plasmid (pSym), carrying nodulation and nitrogen fixation genes. The present mini review focuses on symbiotic properties of S. fredii HH103, in particular on nodulation and surface polysaccharides aspects. The model strain S. fredii HH103 was chosen for genomic sequencing, which is currently in progress. First analyses of the draft genome sequence revealed an extensive synteny between the chromosomes of S. fredii HH103 and Rhizobium sp. NGR234.
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Affiliation(s)
- Isabel Margaret
- Departamento de Microbiología, Universidad de Sevilla, Sevilla, Spain
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Djedidi S, Yokoyama T, Ohkama-Ohtsu N, Risal CP, Abdelly C, Sekimoto H. Stress tolerance and symbiotic and phylogenic features of root nodule bacteria associated with Medicago species in different bioclimatic regions of Tunisia. Microbes Environ 2011; 26:36-45. [PMID: 21487201 DOI: 10.1264/jsme2.me10138] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Thirty two rhizobial isolates were obtained from different bioclimatic regions of Tunisia using as trap plants, Medicago sativa, Medicago ciliaris, Medicago polymorpha and Medicago minima. To study their diversity and characterize them in relation to Mediterranean conditions, abiotic stress resistance, symbiotic properties and genetic diversity in terms of 16S rRNA and nodA sequences were assessed. Five isolates from M. sativa, three from M. ciliaris and three from M. minima could grow at 45°C. Only two isolates from M. sativa grew at 4% NaCl. The most stress tolerant isolates were obtained from arid soils. A phylogenetic analysis of 16S rRNA genes revealed 29 isolates to be closely related to Ensifer including one (Pl.3-9) that showed a 16S rRNA sequence similar to that of Ensifer meliloti and nodA sequence similar to that of Ensifer medicae. However, three isolates were categorized into Agrobacterium containing the nodA of Ensifer. Furthermore, these isolates developed nodules on original hosts. The results for the four isolates suggest horizontal gene transfer between the species.
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Affiliation(s)
- Salem Djedidi
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, 3–5–8 Saiwai-cho, Fuchu, Tokyo 183–8509, Japan
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41
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Ferreira L, Sánchez-Juanes F, García-Fraile P, Rivas R, Mateos PF, Martínez-Molina E, González-Buitrago JM, Velázquez E. MALDI-TOF mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family Rhizobiaceae. PLoS One 2011; 6:e20223. [PMID: 21655291 PMCID: PMC3105015 DOI: 10.1371/journal.pone.0020223] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/21/2011] [Indexed: 11/19/2022] Open
Abstract
Family Rhizobiaceae includes fast growing bacteria currently arranged into three genera, Rhizobium, Ensifer and Shinella, that contain pathogenic, symbiotic and saprophytic species. The identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae. In this work we evaluated the suitability of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for this purpose. Firstly, we evaluated the capability of this methodology to differentiate among species of family Rhizobiaceae including those closely related and then we extended the database of MALDI Biotyper 2.0 including the type strains of 56 species from genera Rhizobium, Ensifer and Shinella. Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences. The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.
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Affiliation(s)
- Laura Ferreira
- Unidad de Investigación, Hospital Universitario de Salamanca, Salamanca, Spain
| | | | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Pedro F. Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | | | - José Manuel González-Buitrago
- Unidad de Investigación, Hospital Universitario de Salamanca, Salamanca, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- * E-mail:
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Fterich A, Mahdhi M, Caviedes MA, Pajuelo E, Rivas R, Rodriguez-Llorente ID, Mars M. Characterization of root-nodulating bacteria associated to Prosopis farcta growing in the arid regions of Tunisia. Arch Microbiol 2011; 193:385-97. [PMID: 21359955 DOI: 10.1007/s00203-011-0683-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/02/2011] [Accepted: 02/04/2011] [Indexed: 10/18/2022]
Abstract
Diversity of 50 bacterial isolates recovered from root nodules of Prosopis farcta grown in different arid soils in Tunisia, was investigated. Characterization of isolates was assessed using a polyphasic approach including phenotypic characteristics, 16S rRNA gene PCR--RFLP and sequencing, nodA gene sequencing and MLSA. It was found that most of isolates are tolerant to high temperature (40°C) and salinity (3%). Genetic characterization emphasizes that isolates were assigned to the genus Ensifer (80%), Mesorhizobium (4%) and non-nodulating endophytic bacteria (16%). Forty isolates belonging to the genus Ensifer were affiliated to Ensifer meliloti, Ensifer xinjiangense/Ensifer fredii and Ensifer numidicus species. Two isolates belonged to the genus Mesorhizobium. Eight isolates failing to renodulate their host plant were endophytic bacteria and belonged to Bacillus, Paenibacillus and Acinetobacter genera. Symbiotic properties of nodulating isolates showed a diversity in their capacity to infect their host plant and fix atmospheric nitrogen. Isolate PG29 identified as Ensifer meliloti was the most effective one. Ability of Prosopis farcta to establish symbiosis with rhizobial species confers an important advantage for this species to be used in reforestation programs. This study offered the first systematic information about the diversity of microsymbionts nodulating Prosopis farcta in the arid regions of Tunisia.
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Affiliation(s)
- A Fterich
- Laboratoire de Biotechnologies Végétales Appliquées à l'Amélioration des Cultures, Faculté des Sciences de Gabès, Université de Gabes, Cité Erriadh Zrig, 6072, Gabès, Tunisia
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Young JM. Sinorhizobium versus Ensifer: may a taxonomy subcommittee of the ICSP contradict the Judicial Commission? Int J Syst Evol Microbiol 2010; 60:1711-1713. [DOI: 10.1099/ijs.0.025163-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In response to a Request for an Opinion, the Judicial Commission (Opinion 84) confirmed the earlier synonym, Ensifer, as the correct name for the genus better known as Sinorhizobium. The Judicial Commission considered that this decision would not cause sufficient confusion to justify the conservation of the latter name. The Subcommittee on the Taxonomy of Agrobacterium and Rhizobium of the International Committee on Systematics of Prokaryotes (ICSP) publicly disagreed with this conclusion. Was it justified in doing this?
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Affiliation(s)
- J. M. Young
- Landcare Research, Auckland, Private Bag 92170, New Zealand
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