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Veremeichik GN, Gorpenchenko TY, Rusapetova TV, Brodovskaya EV, Tchernoded GK, Bulgakov DV, Shkryl YN, Bulgakov VP. Auxin-dependent regulation of growth via rolB-induced modulation of the ROS metabolism in the long-term cultivated pRiA4-transformed Rubiacordifolia L. calli. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107932. [PMID: 37557016 DOI: 10.1016/j.plaphy.2023.107932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/07/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023]
Abstract
Gene transfer from Agrobacterium to plants is the best studied example of horizontal gene transfer (HGT) between prokaryotes and eukaryotes. The rol genes of A. rhizogenes (Rhizobium rhizogenes) provide uncontrolled root growth, or "hairy root" syndrome, the main diagnostic feature. In the present study, we investigated the stable pRiA4-transformed callus culture of Rubia cordifolia L. While untransformed callus cultures need PGRs (plant growth regulators) as an obligatory supplement, pRiA4 calli is able to achieve long-term PGR-free cultivation. For the first time, we described the pRiA4-transformed callus cultures' PGR-dependent ROS status, growth, and specialized metabolism. As we have shown, expression of the rolA and rolB but not the rolC genes is contradictory in a PGR-dependent manner. Moreover, a PGR-free pRiA4 transformed cell line is characterised as more anthraquinone (AQ) productive than an untransformed cell culture. These findings pertain to actual plant biotechnology: it could be the solution to troubles in choosing the best PGR combination for the cultivation of some rare, medicinal, and woody plants; wild-type Ri-plants and tissue cultures may become freed from legal controls on genetically modified organisms in the future. We propose possible PGR-dependent relationships between rolA and rolB as well as ROS signalling targets. The present study highlighted the high importance of the rolA gene in the regulation of combined rol gene effects and the large knowledge gap in rolA action.
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Affiliation(s)
- Galina N Veremeichik
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia.
| | - Tatiana Y Gorpenchenko
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Tatiana V Rusapetova
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Evgenia V Brodovskaya
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Galina K Tchernoded
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Dmitry V Bulgakov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Yurii N Shkryl
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
| | - Victor P Bulgakov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia
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Núñez-Cano J, Romera FJ, Prieto P, García MJ, Sevillano-Caño J, Agustí-Brisach C, Pérez-Vicente R, Ramos J, Lucena C. Effect of the Nonpathogenic Strain Fusarium oxysporum FO12 on Fe Acquisition in Rice ( Oryza sativa L.) Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3145. [PMID: 37687390 PMCID: PMC10489696 DOI: 10.3390/plants12173145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
Rice (Oryza sativa L.) is a very important cereal worldwide, since it is the staple food for more than half of the world's population. Iron (Fe) deficiency is among the most important agronomical concerns in calcareous soils where rice plants may suffer from this deficiency. Current production systems are based on the use of high-yielding varieties and the application of large quantities of agrochemicals, which can cause major environmental problems. The use of beneficial rhizosphere microorganisms is considered a relevant sustainable alternative to synthetic fertilizers. The main goal of this study was to determine the ability of the nonpathogenic strain Fusarium oxysporum FO12 to induce Fe-deficiency responses in rice plants and its effects on plant growth and Fe chlorosis. Experiments were carried out under hydroponic system conditions. Our results show that the root inoculation of rice plants with FO12 promotes the production of phytosiderophores and plant growth while reducing Fe chlorosis symptoms after several days of cultivation. Moreover, Fe-related genes are upregulated by FO12 at certain times in inoculated plants regardless of Fe conditions. This microorganism also colonizes root cortical tissues. In conclusion, FO12 enhances Fe-deficiency responses in rice plants, achieves growth promotion, and reduces Fe chlorosis symptoms.
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Affiliation(s)
- Jorge Núñez-Cano
- Departamento de Agronomía (Unit of Excellence ‘María de Maeztu’ 2020-24), Edificio Celestino Mutis (C-4), Campus de Excelencia Internacional Agroalimentario de Rabanales (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain; (J.N.-C.); (F.J.R.); (M.J.G.); (J.S.-C.); (C.A.-B.)
| | - Francisco J. Romera
- Departamento de Agronomía (Unit of Excellence ‘María de Maeztu’ 2020-24), Edificio Celestino Mutis (C-4), Campus de Excelencia Internacional Agroalimentario de Rabanales (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain; (J.N.-C.); (F.J.R.); (M.J.G.); (J.S.-C.); (C.A.-B.)
| | - Pilar Prieto
- Departamento de Mejora Genética, Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), 14004 Córdoba, Spain;
| | - María J. García
- Departamento de Agronomía (Unit of Excellence ‘María de Maeztu’ 2020-24), Edificio Celestino Mutis (C-4), Campus de Excelencia Internacional Agroalimentario de Rabanales (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain; (J.N.-C.); (F.J.R.); (M.J.G.); (J.S.-C.); (C.A.-B.)
| | - Jesús Sevillano-Caño
- Departamento de Agronomía (Unit of Excellence ‘María de Maeztu’ 2020-24), Edificio Celestino Mutis (C-4), Campus de Excelencia Internacional Agroalimentario de Rabanales (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain; (J.N.-C.); (F.J.R.); (M.J.G.); (J.S.-C.); (C.A.-B.)
| | - Carlos Agustí-Brisach
- Departamento de Agronomía (Unit of Excellence ‘María de Maeztu’ 2020-24), Edificio Celestino Mutis (C-4), Campus de Excelencia Internacional Agroalimentario de Rabanales (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain; (J.N.-C.); (F.J.R.); (M.J.G.); (J.S.-C.); (C.A.-B.)
| | - Rafael Pérez-Vicente
- Departamento de Botánica, Ecología y Fisiología Vegetal, Edificio Celestino Mutis (C-4), Campus de Excelencia Internacional Agroalimentario de Rabanales (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain;
| | - José Ramos
- Departamento de Química Agrícola, Edafología y Microbiología, Edificio Severo Ochoa (C-6), Campus de Excelencia Internacional Agroalimentario de Rabanales (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain;
| | - Carlos Lucena
- Departamento de Agronomía (Unit of Excellence ‘María de Maeztu’ 2020-24), Edificio Celestino Mutis (C-4), Campus de Excelencia Internacional Agroalimentario de Rabanales (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain; (J.N.-C.); (F.J.R.); (M.J.G.); (J.S.-C.); (C.A.-B.)
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Almeida A, Favero BT, Dong L, Cárdenas PD, Saenz-Mata J, Lütken H, Bak S. Lessons learned from metabolic engineering in hairy roots: Transcriptome and metabolic profile changes caused by Rhizobium-mediated plant transformation in Cucurbitaceae species. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107797. [PMID: 37302255 DOI: 10.1016/j.plaphy.2023.107797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 06/13/2023]
Abstract
Cucurbitaceae species are used in traditional medicine around the world. Cucurbitacins are highly oxygenated triterpenoids found in Cucurbitaceae species and exhibit potent anticancer activity alone and in combination with other existing chemotherapeutic drugs. Therefore, increasing production of these specialized metabolites is of great relevance. We recently showed that hairy roots of Cucurbita pepo can be used as a platform for metabolic engineering of cucurbitacins to modify their structure and increase their production. To study the changes in cucurbitacin accumulation upon formation of hairy roots, an empty vector (EV) control and Cucurbitacin inducing bHLH transcription factor 1 (CpCUCbH1)-overexpressing hairy roots of C. pepo were compared to untransformed (WT) roots. Whilst CpCUCbH1-overexpression increased production of cucurbitacins I and B by 5-fold, and cucurbitacin E by 3-fold when compared to EV lines, this increase was not significantly different when compared to WT roots. This indicated that Rhizobium rhizogenes transformation lowered the cucurbitacins levels in hairy roots, but that increasing expression of cucurbitacin biosynthetic genes by CpCUCbH1-overexpression restored cucurbitacin production to WT levels. Subsequent metabolomic and RNA-seq analysis indicated that the metabolic profile and transcriptome of hairy roots was significantly changed when compared to WT roots. Interestingly, it was observed that 11% of the differentially expressed genes were transcription factors. It was noteworthy that the majority of transcripts showing highest Pearson correlation coefficients to the Rhizobium rhizogenes genes rolB, rolC and ORF13a, were predicted to be transcription factors. In summary, hairy roots are an excellent platform for metabolic engineering of plant specialized metabolites, but these extensive transcriptome and metabolic profile changes should be considered in subsequent studies.
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Affiliation(s)
- Aldo Almeida
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark.
| | - Bruno Trevenzoli Favero
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Lemeng Dong
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, Netherlands
| | - Pablo D Cárdenas
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Jorge Saenz-Mata
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad s/n, 35010, Gómez Palacio, Durango, Mexico
| | - Henrik Lütken
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Søren Bak
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark.
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Hooykaas PJJ. The Ti Plasmid, Driver of Agrobacterium Pathogenesis. PHYTOPATHOLOGY 2023; 113:594-604. [PMID: 37098885 DOI: 10.1094/phyto-11-22-0432-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The phytopathogenic bacterium Agrobacterium tumefaciens causes crown gall disease in plants, characterized by the formation of tumor-like galls where wounds were present. Nowadays, however, the bacterium and its Ti (tumor-inducing) plasmid is better known as an effective vector for the genetic manipulation of plants and fungi. In this review, I will briefly summarize some of the major discoveries that have led to this bacterium now playing such a prominent role worldwide in plant and fungal research at universities and research institutes and in agricultural biotechnology for the production of genetically modified crops. I will then delve a little deeper into some aspects of Agrobacterium biology and discuss the diversity among agrobacteria and the taxonomic position of these bacteria, the diversity in Ti plasmids, the molecular mechanism used by the bacteria to transform plants, and the discovery of protein translocation from the bacteria to host cells as an essential feature of Agrobacterium-mediated transformation.
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5
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Beneficial effect on the soil microenvironment of Trichoderma applied after fumigation for cucumber production. PLoS One 2022; 17:e0266347. [PMID: 35917326 PMCID: PMC9345367 DOI: 10.1371/journal.pone.0266347] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/19/2022] [Indexed: 11/19/2022] Open
Abstract
Biocontrol agents applied after fumigation play an important role to the soil microenvironment. We studied the effect of Trichoderma applied after dimethyl disulfide (DMDS) plus chloropicrin (PIC) fumigation on the cucumber growth, soil physicochemical properties, enzyme activity, taxonomic diversity, and yield through laboratory and field experiments. The results confirmed that Trichoderma applied after fumigation significantly improved soil physicochemical properties, cucumber growth, soil-borne pathogens, and soil enzyme activity. Genetic analysis indicated that Trichoderma applied after fumigation significantly increased the relative abundance of Pseudomonas, Humicola and Chaetomium, and significantly decreased the relative abundance of the pathogens Fusarium spp. and Gibberella spp., which may help to control pathogens and enhanced the ecological functions of the soil. Moreover, Trichoderma applied after fumigation obviously improved cucumber yield (up to 35.6%), and increased relative efficacy of soil-borne pathogens (up to 99%) and root-knot nematodes (up to 96%). Especially, we found that Trichoderma applied after fumigation increased the relative abundance of some beneficial microorganisms (such as Sodiomyces and Rhizophlyctis) that can optimize soil microbiome. It is worth noting that with the decline in the impact of the fumigant, these beneficial microorganisms still maintain a higher abundance when the cucumber plants were uprooted. Importantly, we found one tested biocontrol agent Trichoderma 267 identified and stored in our laboratory not only improved cucumber growth, reduced soil-borne diseases in late cucumber growth stages but also optimized micro-ecological environment which may have good application prospect and help to keep environmental healthy and sustainable development.
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Chamkhi I, El Omari N, Balahbib A, El Menyiy N, Benali T, Ghoulam C. Is the rhizosphere a source of applicable multi-beneficial microorganisms for plant enhancement? Saudi J Biol Sci 2022; 29:1246-1259. [PMID: 35241967 PMCID: PMC8864493 DOI: 10.1016/j.sjbs.2021.09.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/12/2021] [Accepted: 09/13/2021] [Indexed: 01/08/2023] Open
Abstract
The plant faces different pedological and climatic challenges that influence its growth and enhancement. While, plant-microbes interactions throught the rhizosphere offer several privileges to this hotspot in the service of plant, by attracting multi-beneficial mutualistic and symbiotic microorganisms as plant growth-promoting bacteria (PGPB), archaea, mycorrhizal fungi, endophytic fungi, and others…). Currently, numerous investigations showed the beneficial effects of these microbes on growth and plant health. Indeed, rhizospheric microorganisms offer to host plants the essential assimilable nutrients, stimulate the growth and development of host plants, and induce antibiotics production. They also attributed to host plants numerous phenotypes involved in the increase the resistance to abiotic and biotic stresses. The investigations and the studies on the rhizosphere can offer a way to find a biological and sustainable solution to confront these environmental problems. Therefore, the interactions between microbes and plants may lead to interesting biotechnological applications on plant improvement and the adaptation in different climates to obtain a biological sustainable agricultures without the use of chemical fertilizers.
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Key Words
- AMF, Arbuscular Mycorrhizal Fungi
- AOA, Ammonia-Oxidizing Archaea
- BMV, Brome Mosaic Virus
- C, Carbon
- CMV, Cucumber mosaic virus
- LDH, Layered double hydroxides
- MF, Mycorrhizal fungi
- Microorganisms
- P, Phosphorus
- PAL, L-Phenylalanine Ammonia Lyase
- PCA, Phenazine-1-Carboxylic Acid
- PGPR, Plant Growth-Promoting Rhizobacteria
- POX, Peroxidase
- PPO, Polyphenol Oxidase
- Plant growth promoting microbes
- Plant-microbes interactions
- Rhizosphere
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Affiliation(s)
- Imane Chamkhi
- Geo-Biodiversity and Natural Patrimony Laboratory (GeoBio), Geophysics, Natural Patrimony Research Center (GEOPAC), Scientific Institute, Mohammed V University in Rabat, Morocco.,University Mohammed VI Polytechnic, Agrobiosciences Program, Lot 660, Hay Moulay Rachid, Benguerir, Morocco
| | - Nasreddine El Omari
- Laboratory of Histology, Embryology, and Cytogenetic, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Morocco
| | - Abdelaali Balahbib
- Laboratory of Zoology and General Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
| | - Naoual El Menyiy
- Faculty of Science, University Sidi Mohamed Ben Abdellah, Fez, Morocco
| | - Taoufiq Benali
- Environment and Health Team, Polydisciplinary Faculty of Safi, Cadi Ayyad University, Safi, Morocco
| | - Cherki Ghoulam
- University Mohammed VI Polytechnic, Agrobiosciences Program, Lot 660, Hay Moulay Rachid, Benguerir, Morocco.,Cadi Ayyad University, Faculty of Sciences and Techniques, PO Box 549, Gueliz, Marrakech,Morocco
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Bourigault Y, Rodrigues S, Crépin A, Chane A, Taupin L, Bouteiller M, Dupont C, Merieau A, Konto-Ghiorghi Y, Boukerb AM, Turner M, Hamon C, Dufour A, Barbey C, Latour X. Biocontrol of Biofilm Formation: Jamming of Sessile-Associated Rhizobial Communication by Rhodococcal Quorum-Quenching. Int J Mol Sci 2021; 22:ijms22158241. [PMID: 34361010 PMCID: PMC8347015 DOI: 10.3390/ijms22158241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Abstract
Biofilms are complex structures formed by a community of microbes adhering to a surface and/or to each other through the secretion of an adhesive and protective matrix. The establishment of these structures requires a coordination of action between microorganisms through powerful communication systems such as quorum-sensing. Therefore, auxiliary bacteria capable of interfering with these means of communication could be used to prevent biofilm formation and development. The phytopathogen Rhizobium rhizogenes, which causes hairy root disease and forms large biofilms in hydroponic crops, and the biocontrol agent Rhodococcus erythropolis R138 were used for this study. Changes in biofilm biovolume and structure, as well as interactions between rhizobia and rhodococci, were monitored by confocal laser scanning microscopy with appropriate fluorescent biosensors. We obtained direct visual evidence of an exchange of signals between rhizobia and the jamming of this communication by Rhodococcus within the biofilm. Signaling molecules were characterized as long chain (C14) N-acyl-homoserine lactones. The role of the Qsd quorum-quenching pathway in biofilm alteration was confirmed with an R. erythropolis mutant unable to produce the QsdA lactonase, and by expression of the qsdA gene in a heterologous host, Escherichia coli. Finally, Rhizobium biofilm formation was similarly inhibited by a purified extract of QsdA enzyme.
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Affiliation(s)
- Yvann Bourigault
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Sophie Rodrigues
- Laboratoire de Biotechnologie et Chimie Marines, LBCM IUEM, EA 3884, Université de Bretagne-Sud, F-56100 Lorient, France; (S.R.); (L.T.); (A.D.)
| | - Alexandre Crépin
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, F-86073 Poitiers, France;
| | - Andrea Chane
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
| | - Laure Taupin
- Laboratoire de Biotechnologie et Chimie Marines, LBCM IUEM, EA 3884, Université de Bretagne-Sud, F-56100 Lorient, France; (S.R.); (L.T.); (A.D.)
| | - Mathilde Bouteiller
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Charly Dupont
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Annabelle Merieau
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Yoan Konto-Ghiorghi
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Amine M. Boukerb
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
| | - Marie Turner
- Vegenov, F-29250 Saint-Pol-de-Léon, France; (M.T.); (C.H.)
- Biocontrol Consortium, F-75007 Paris, France
| | - Céline Hamon
- Vegenov, F-29250 Saint-Pol-de-Léon, France; (M.T.); (C.H.)
| | - Alain Dufour
- Laboratoire de Biotechnologie et Chimie Marines, LBCM IUEM, EA 3884, Université de Bretagne-Sud, F-56100 Lorient, France; (S.R.); (L.T.); (A.D.)
| | - Corinne Barbey
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
| | - Xavier Latour
- Laboratory of Microbiology Signals and Microenvironment (LMSM EA 4312), University of Rouen Normandy, F-27000 Evreux, France; (Y.B.); (A.C.); (M.B.); (C.D.); (A.M.); (Y.K.-G.); (A.M.B.); (C.B.)
- Research Federations NORVEGE Fed4277 & NORSEVE, Normandy University, F-76821 Mont-Saint-Aignan, France
- Biocontrol Consortium, F-75007 Paris, France
- Correspondence: ; +33-235-146-000
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Chen WF, Wang ET, Ji ZJ, Zhang JJ. Recent development and new insight of diversification and symbiosis specificity of legume rhizobia: mechanism and application. J Appl Microbiol 2021; 131:553-563. [PMID: 33300250 DOI: 10.1111/jam.14960] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022]
Abstract
Currently, symbiotic rhizobia (sl., rhizobium) refer to the soil bacteria in α- and β-Proteobacteria that can induce root and/or stem nodules on some legumes and a few of nonlegumes. In the nodules, rhizobia convert the inert dinitrogen gas (N2 ) into ammonia (NH3 ) and supply them as nitrogen nutrient to the host plant. In general, this symbiotic association presents specificity between rhizobial and leguminous species, and most of the rhizobia use lipochitooligosaccharides, so called Nod factor (NF), for cooperating with their host plant to initiate the formation of nodule primordium and to inhibit the plant immunity. Besides NF, effectors secreted by type III secretion system (T3SS), exopolysaccharides and many microbe-associated molecular patterns in the rhizobia also play important roles in nodulation and immunity response between rhizobia and legumes. However, the promiscuous hosts like Glycine max and Sophora flavescens can nodulate with various rhizobial species harbouring diverse symbiosis genes in different soils, meaning that the nodulation specificity/efficiency might be mainly determined by the host plants and regulated by the soil conditions in a certain cases. Based on previous studies on rhizobial application, we propose a '1+n-N' model to promote the function of symbiotic nitrogen fixation (SNF) in agricultural practice, where '1' refers to appreciate rhizobium; '+n' means the addition of multiple trace elements and PGPR bacteria; and '-N' implies the reduction of chemical nitrogen fertilizer. Finally, open questions in the SNF field are raised to future think deeply and researches.
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Affiliation(s)
- W F Chen
- State Key Laboratory of Agrobiotechnology, Beijing, P. R. China.,College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, P. R. China
| | - E T Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, D.F, México
| | - Z J Ji
- College of Life Science and Food Engineering, Horqin Plant Stress Biology Research Institute, Inner Mongolia University for the Nationalities, Tongliao, Inner Mongolia, P. R. China
| | - J J Zhang
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou, Henan Province, P. R. China.,Henan Key Laboratory of Cold Chain Food Quality and Safety Control, Henan Province, P. R. China.,Collaborative Innovation Center for Food Production and Safety of Henan Province, Zhengzhou, Henan Province, P. R. China
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9
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Ramírez MDA, España M, Sekimoto H, Okazaki S, Yokoyama T, Ohkama-Ohtsu N. Genetic Diversity and Characterization of Symbiotic Bacteria Isolated from Endemic Phaseolus Cultivars Located in Contrasting Agroecosystems in Venezuela. Microbes Environ 2021; 36:ME20157. [PMID: 34092740 PMCID: PMC8209454 DOI: 10.1264/jsme2.me20157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/26/2021] [Indexed: 11/12/2022] Open
Abstract
Phaseolus vulgaris is a grain cultivated in vast areas of different countries. It is an excellent alternative to the other legumes in the Venezuelan diet and is of great agronomic interest due to its resistance to soil acidity, drought, and high temperatures. Phaseolus establishes symbiosis primarily with Rhizobium and Ensifer species in most countries, and this rhizobia-legume interaction has been studied in Asia, Africa, and the Americas. However, there is currently no evidence to show that rhizobia nodulate the endemic cultivars of P. vulgaris in Venezuela. Therefore, we herein investigated the phylogenetic diversity of plant growth-promoting and N2-fixing nodulating bacteria isolated from the root nodules of P. vulgaris cultivars in a different agroecosystem in Venezuela. In comparisons with other countries, higher diversity was found in isolates from P. vulgaris nodules, ranging from α- and β-proteobacteria. Some isolates belonging to several new phylogenetic lineages within Bradyrhizobium, Ensifer, and Mesorhizobium species were also specifically isolated at some topographical regions. Additionally, some isolates exhibited tolerance to high temperature, acidity, alkaline pH, salinity stress, and high Al levels; some of these characteristics may be related to the origin of the isolates. Some isolates showed high tolerance to Al toxicity as well as strong plant growth-promoting and antifungal activities, thereby providing a promising agricultural resource for inoculating crops.
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Affiliation(s)
- María Daniela Artigas Ramírez
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, 870 Uehara, Yaeyama, Taketomi, Okinawa, 907–1541, Japan
- Institute of Global Innovation Research and Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo, 183–8538, Japan
| | | | - Hitoshi Sekimoto
- Faculty of Agriculture, Utsunomiya University, Utsunomiya 321–8505, Japan
| | - Shin Okazaki
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo, 183–8538, Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo, 183–8538, Japan
- Faculty of Food and Agricultural Science, Fukushima University, Kanayagawa 1, Fukushima city, Fukushima, 960–1296, Japan
| | - Naoko Ohkama-Ohtsu
- Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo, 183–8538, Japan
- Institute of Global Innovation Research and Institute of Agriculture, Tokyo University of Agriculture and Technology (TUAT), Saiwai-cho 3–5–8, Fuchu, Tokyo, 183–8538, Japan
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De Saeger J, Park J, Chung HS, Hernalsteens JP, Van Lijsebettens M, Inzé D, Van Montagu M, Depuydt S. Agrobacterium strains and strain improvement: Present and outlook. Biotechnol Adv 2020; 53:107677. [PMID: 33290822 DOI: 10.1016/j.biotechadv.2020.107677] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 11/03/2020] [Accepted: 11/28/2020] [Indexed: 12/12/2022]
Abstract
Almost 40 years ago the first transgenic plant was generated through Agrobacterium tumefaciens-mediated transformation, which, until now, remains the method of choice for gene delivery into plants. Ever since, optimized Agrobacterium strains have been developed with additional (genetic) modifications that were mostly aimed at enhancing the transformation efficiency, although an optimized strain also exists that reduces unwanted plasmid recombination. As a result, a collection of very useful strains has been created to transform a wide variety of plant species, but has also led to a confusing Agrobacterium strain nomenclature. The latter is often misleading for choosing the best-suited strain for one's transformation purposes. To overcome this issue, we provide a complete overview of the strain classification. We also indicate different strain modifications and their purposes, as well as the obtained results with regard to the transformation process sensu largo. Furthermore, we propose additional improvements of the Agrobacterium-mediated transformation process and consider several worthwhile modifications, for instance, by circumventing a defense response in planta. In this regard, we will discuss pattern-triggered immunity, pathogen-associated molecular pattern detection, hormone homeostasis and signaling, and reactive oxygen species in relationship to Agrobacterium transformation. We will also explore alterations that increase agrobacterial transformation efficiency, reduce plasmid recombination, and improve biocontainment. Finally, we recommend the use of a modular system to best utilize the available knowledge for successful plant transformation.
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Affiliation(s)
- Jonas De Saeger
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jihae Park
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Marine Sciences, Incheon National University, Incheon 406-840, South Korea
| | - Hoo Sun Chung
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | | | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Stephen Depuydt
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon 406-840, South Korea; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.
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11
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Suleiman MK, Quoreshi AM, Bhat NR, Manuvel AJ, Sivadasan MT. Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N2-fixation potential. PLoS One 2019; 14:e0220679. [PMID: 31877136 PMCID: PMC6932743 DOI: 10.1371/journal.pone.0220679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 11/19/2019] [Indexed: 12/31/2022] Open
Abstract
Kuwait is a semi-arid region with soils that are relatively nitrogen-poor. Thus, biological nitrogen fixation is an important natural process in which N2-fixing bacteria (diazotrophs) convert atmospheric nitrogen into plant-usable forms such as ammonium and nitrate. Currently, there is limited information on free-living and root-associated nitrogen-fixing bacteria and their potential to fix nitrogen and aid natural plant communities in the Kuwait desert. In this study, free living N2-fixing diazotrophs were enriched and isolated from the rhizosphere soil associated with three native keystone plant species; Rhanterium epapposum, Farsetia aegyptia, and Haloxylon salicornicum. Root-associated bacteria were isolated from the root nodules of Vachellia pachyceras. The result showed that the strains were clustered in five groups represented by class: γ-proteobacteria, and α-proteobacteria; phyla: Actinobacteria being the most dominant, followed by phyla: Firmicutes, and class: β-proteobacteria. This study initially identified 50 nitrogen-fixers by16S rRNA gene sequencing, of which 78% were confirmed to be nitrogen-fixers using the acetylene reduction assay. Among the nitrogen fixers identified, the genus Rhizobium was predominant in the rhizosphere soil of R. epapposum and H. salicornicum, whereas Pseudomonas was predominant in the rhizosphere soil of F. aegyptia, The species Agrobacterium tumefaciens was mainly found to be dominant among the root nodules of V. pachyceras and followed by Cellulomonas, Bacillus, and Pseudomonas genera as root-associated bacteria. The variety of diazotrophs revealed in this study, signifying the enormous importance of free-living and root-associated bacteria in extreme conditions and suggesting potential ecological importance of diazotrophs in arid ecosystem. To our knowledge, this study is the first to use culture-based isolation, molecular identification, and evaluation of N2-fixing ability to detail diazotroph diversity in Kuwaiti desert soils.
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Affiliation(s)
- M. K. Suleiman
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - A. M. Quoreshi
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
- * E-mail:
| | - N. R. Bhat
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - A. J. Manuvel
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - M. T. Sivadasan
- Desert Agriculture and Ecosystems Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
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12
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Kang W, Xu L, Jiang Z, Shi S. Genetic diversity and symbiotic efficiency difference of endophytic rhizobia of Medicago sativa. Can J Microbiol 2018; 65:68-83. [PMID: 30273494 DOI: 10.1139/cjm-2018-0158] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Research on rhizobium diversity has paved the way for diversification of rhizobial germplasm resources. Seventy-three endophytic bacterial isolates were collected from seven tissues of five alfalfa cultivars in three geographic locations in Gansu, China. Restriction fragment length polymorphism (RFLP) fingerprinting of 16S rRNA and analysis of concatenated sequence of three housekeeping genes (atpD, glnII, and recA) and two symbiotic genes (nodC and nifH) were used for strain identification. Results showed that the endophytic strains were genetically diverse at different taxonomic levels, and Ensifer meliloti (31) and Agrobacterium radiobacter (12) are common Medicago sativa endophytic bacteria in Gansu, China. The nifH genes (97%-98% sequence identity) of E. meliloti strains were more diverse than the nodC genes (99%-100% sequence identity), even though the strains evolved from a common ancestor. The degree of dispersion of symbiotic phenotypes of E. meliloti strains on M. sativa 'Gannong No. 3', 'Gannong No. 9', and 'Qingshui' was much less than that on M. sativa 'Longzhong' and 'WL168HQ'. This suggested that the symbiotic efficiency of E. meliloti strains on the former three alfalfa cultivars was similar but on the latter two was discrepant. Their symbiotic efficiency differed primarily according to alfalfa cultivars and, to a lesser extent, to the tested strains, indicating the difference in the sensitivity of different alfalfa cultivars to rhizobial strains.
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Affiliation(s)
- Wenjuan Kang
- a College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, P.R. China
| | - Lin Xu
- b College of Agriculture and Biotechnology, Hexi University, Zhangye 734000, P.R. China
| | - Zhehao Jiang
- a College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, P.R. China
| | - Shangli Shi
- a College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, P.R. China.,c Key Laboratory of Grassland Ecosystem of Ministry of Education, Lanzhou 730070, P.R. China
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13
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Kishi LT, Fernandes CC, Omori WP, Campanharo JC, Lemos EGDM. Reclassification of the taxonomic status of SEMIA3007 isolated in Mexico B-11A Mex as Rhizobium leguminosarum bv. viceae by bioinformatic tools. BMC Microbiol 2016; 16:260. [PMID: 27814683 PMCID: PMC5097390 DOI: 10.1186/s12866-016-0882-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 10/28/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Evidence based on genomic sequences is extremely important to confirm the phylogenetic relationships within the Rhizobium group. SEMIA3007 was analyzed within the Mesorhizobium groups to define the underlying causes of taxonomic identification. We previously used biochemical tests and phenotypic taxonomic methods to identify bacteria, which can lead to erroneous classification. An improved understanding of bacterial strains such as the Mesorhizobium genus would increase our knowledge of classification and evolution of these species. RESULTS In this study, we sequenced the complete genome of SEMIA3007 and compared it with five other Mesorhizobium and two Rhizobium genomes. The genomes of isolated SEMIA3007 showed several orthologs with M. huakuii, M. erdmanii and M. loti. We identified SEMIA3007 as a Mesorhizobium by comparing the 16S rRNA gene and the complete genome. CONCLUSION Our ortholog, 16S rRNA gene and average nucleotide identity values (ANI) analysis all demonstrate SEMIA3007 is not Rhizobium leguminosarum bv. viceae. The results of the phylogenetic analysis clearly show SEMIA3007 is part of the Mesorhizobium group and suggest a reclassification is warranted.
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Affiliation(s)
- Luciano Takeshi Kishi
- Departamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Planta – LBMP, UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900 Jaboticabal, SP Brazil
| | - Camila Cesário Fernandes
- Departamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Planta – LBMP, UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900 Jaboticabal, SP Brazil
| | - Wellington Pine Omori
- Departamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Planta – LBMP, UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900 Jaboticabal, SP Brazil
| | - João Carlos Campanharo
- Departamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Planta – LBMP, UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900 Jaboticabal, SP Brazil
| | - Eliana Gertrudes de Macedo Lemos
- Departamento de Tecnologia, Laboratório de Bioquímica de Microrganismos e Planta – LBMP, UNESP - Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Via de Acesso Prof. Paulo Donato Castellane s/n, 14884-900 Jaboticabal, SP Brazil
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14
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Remigi P, Zhu J, Young JPW, Masson-Boivin C. Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts. Trends Microbiol 2015; 24:63-75. [PMID: 26612499 DOI: 10.1016/j.tim.2015.10.007] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/08/2015] [Accepted: 10/22/2015] [Indexed: 10/22/2022]
Abstract
Bacterial accessory genes are genomic symbionts with an evolutionary history and future that is different from that of their hosts. Packages of accessory genes move from strain to strain and confer important adaptations, such as interaction with eukaryotes. The ability to fix nitrogen with legumes is a remarkable example of a complex trait spread by horizontal transfer of a few key symbiotic genes, converting soil bacteria into legume symbionts. Rhizobia belong to hundreds of species restricted to a dozen genera of the Alphaproteobacteria and Betaproteobacteria, suggesting infrequent successful transfer between genera but frequent successful transfer within genera. Here we review the genetic and environmental conditions and selective forces that have shaped evolution of this complex symbiotic trait.
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Affiliation(s)
- Philippe Remigi
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France; New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Jun Zhu
- Department of Microbiology, Nanjing Agricultural University, Nanjing, China; Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Catherine Masson-Boivin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France.
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15
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Kumar N, Lad G, Giuntini E, Kaye ME, Udomwong P, Shamsani NJ, Young JPW, Bailly X. Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biol 2015; 5:140133. [PMID: 25589577 PMCID: PMC4313370 DOI: 10.1098/rsob.140133] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Biological species may remain distinct because of genetic isolation or ecological adaptation, but these two aspects do not always coincide. To establish the nature of the species boundary within a local bacterial population, we characterized a sympatric population of the bacterium Rhizobium leguminosarum by genomic sequencing of 72 isolates. Although all strains have 16S rRNA typical of R. leguminosarum, they fall into five genospecies by the criterion of average nucleotide identity (ANI). Many genes, on plasmids as well as the chromosome, support this division: recombination of core genes has been largely within genospecies. Nevertheless, variation in ecological properties, including symbiotic host range and carbon-source utilization, cuts across these genospecies, so that none of these phenotypes is diagnostic of genospecies. This phenotypic variation is conferred by mobile genes. The genospecies meet the Mayr criteria for biological species in respect of their core genes, but do not correspond to coherent ecological groups, so periodic selection may not be effective in purging variation within them. The population structure is incompatible with traditional ‘polyphasic taxonomy′ that requires bacterial species to have both phylogenetic coherence and distinctive phenotypes. More generally, genomics has revealed that many bacterial species share adaptive modules by horizontal gene transfer, and we envisage a more consistent taxonomic framework that explicitly recognizes this. Significant phenotypes should be recognized as ‘biovars' within species that are defined by core gene phylogeny.
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Affiliation(s)
- Nitin Kumar
- Department of Biology, University of York, York YO10 5DD, UK
| | - Ganesh Lad
- Department of Biology, University of York, York YO10 5DD, UK
| | - Elisa Giuntini
- Department of Biology, University of York, York YO10 5DD, UK
| | - Maria E Kaye
- Department of Biology, University of York, York YO10 5DD, UK
| | | | | | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Xavier Bailly
- Department of Biology, University of York, York YO10 5DD, UK
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16
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Gopalakrishnan S, Sathya A, Vijayabharathi R, Varshney RK, Gowda CLL, Krishnamurthy L. Plant growth promoting rhizobia: challenges and opportunities. 3 Biotech 2015; 5:355-377. [PMID: 28324544 PMCID: PMC4522733 DOI: 10.1007/s13205-014-0241-x] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 07/19/2014] [Indexed: 11/24/2022] Open
Abstract
Modern agriculture faces challenges, such as loss of soil fertility, fluctuating climatic factors and increasing pathogen and pest attacks. Sustainability and environmental safety of agricultural production relies on eco-friendly approaches like biofertilizers, biopesticides and crop residue return. The multiplicity of beneficial effects of microbial inoculants, particularly plant growth promoters (PGP), emphasizes the need for further strengthening the research and their use in modern agriculture. PGP inhabit the rhizosphere for nutrients from plant root exudates. By reaction, they help in (1) increased plant growth through soil nutrient enrichment by nitrogen fixation, phosphate solubilization, siderophore production and phytohormones production (2) increased plant protection by influencing cellulase, protease, lipase and β-1,3 glucanase productions and enhance plant defense by triggering induced systemic resistance through lipopolysaccharides, flagella, homoserine lactones, acetoin and butanediol against pests and pathogens. In addition, the PGP microbes contain useful variation for tolerating abiotic stresses like extremes of temperature, pH, salinity and drought; heavy metal and pesticide pollution. Seeking such tolerant PGP microbes is expected to offer enhanced plant growth and yield even under a combination of stresses. This review summarizes the PGP related research and its benefits, and highlights the benefits of PGP rhizobia belonging to the family Rhizobiaceae, Phyllobacteriaceae and Bradyrhizobiaceae.
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Affiliation(s)
- Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Andhra Pradesh, India
| | - Arumugam Sathya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Andhra Pradesh, India
| | - Rajendran Vijayabharathi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Andhra Pradesh, India
| | - Rajeev Kumar Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Andhra Pradesh, India
| | - C L Laxmipathi Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Andhra Pradesh, India
| | - Lakshmanan Krishnamurthy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, Andhra Pradesh, India.
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Verástegui-Valdés MM, Zhang YJ, Rivera-Orduña FN, Cheng HP, Sui XH, Wang ET. Microsymbionts of Phaseolus vulgaris in acid and alkaline soils of Mexico. Syst Appl Microbiol 2014; 37:605-12. [PMID: 25294010 DOI: 10.1016/j.syapm.2014.08.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 11/18/2022]
Abstract
In order to investigate bean-nodulating rhizobia in different types of soil, 41 nodule isolates from acid and alkaline soils in Mexico were characterized. Based upon the phylogenetic studies of 16S rRNA, atpD, glnII, recA, rpoB, gyrB, nifH and nodC genes, the isolates originating from acid soils were identified as the phaseoli symbiovar of the Rhizobium leguminosarum-like group and Rhizobium grahamii, whereas the isolates from alkaline soils were defined as Ensifer americanum sv. mediterranense and Rhizobium radiobacter. The isolates of "R. leguminosarum" and E. americanum harbored nodC and nifH genes, but the symbiotic genes were not detected in the four isolates of the other two species. It was the first time that "R. leguminosarum" and E. americanum have been reported as bean-nodulating bacteria in Mexico. The high similarity of symbiotic genes in the Rhizobium and Ensifer populations showed that these genes had the same origin and have diversified recently in different rhizobial species. Phenotypic characterization revealed that the "R. leguminosarum" population was more adapted to the acid and low salinity conditions, while the E. americanum population preferred alkaline conditions. The findings of this study have improved the knowledge of the diversity, geographic distribution and evolution of bean-nodulating rhizobia in Mexico.
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Affiliation(s)
- Myrthala M Verástegui-Valdés
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, C.P. 11430, Mexico, D.F., Mexico
| | - Yu Jing Zhang
- State Key Laboratory of Agrobiotechnology and Center of Biomass Engineering, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Flor N Rivera-Orduña
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, C.P. 11430, Mexico, D.F., Mexico
| | - Hai-Ping Cheng
- Biological Sciences Department, Lehman College and Graduate Center, The City University of New York, Bronx, NY, USA
| | - Xing Hua Sui
- State Key Laboratory of Agrobiotechnology and Center of Biomass Engineering, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, C.P. 11430, Mexico, D.F., Mexico.
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18
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Remigi P, Capela D, Clerissi C, Tasse L, Torchet R, Bouchez O, Batut J, Cruveiller S, Rocha EPC, Masson-Boivin C. Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer. PLoS Biol 2014; 12:e1001942. [PMID: 25181317 PMCID: PMC4151985 DOI: 10.1371/journal.pbio.1001942] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 07/25/2014] [Indexed: 11/22/2022] Open
Abstract
Stress-responsive error-prone DNA polymerase genes transferred along with key symbiotic genes ease the evolution of a soil bacterium into a legume endosymbiont by accelerating adaptation of the recipient bacterial genome to its new plant host. Horizontal gene transfer (HGT) is an important mode of adaptation and diversification of prokaryotes and eukaryotes and a major event underlying the emergence of bacterial pathogens and mutualists. Yet it remains unclear how complex phenotypic traits such as the ability to fix nitrogen with legumes have successfully spread over large phylogenetic distances. Here we show, using experimental evolution coupled with whole genome sequencing, that co-transfer of imuABC error-prone DNA polymerase genes with key symbiotic genes accelerates the evolution of a soil bacterium into a legume symbiont. Following introduction of the symbiotic plasmid of Cupriavidus taiwanensis, the Mimosa symbiont, into pathogenic Ralstonia solanacearum we challenged transconjugants to become Mimosa symbionts through serial plant-bacteria co-cultures. We demonstrate that a mutagenesis imuABC cassette encoded on the C. taiwanensis symbiotic plasmid triggered a transient hypermutability stage in R. solanacearum transconjugants that occurred before the cells entered the plant. The generated burst in genetic diversity accelerated symbiotic adaptation of the recipient genome under plant selection pressure, presumably by improving the exploration of the fitness landscape. Finally, we show that plasmid imuABC cassettes are over-represented in rhizobial lineages harboring symbiotic plasmids. Our findings shed light on a mechanism that may have facilitated the dissemination of symbiotic competency among α- and β-proteobacteria in natura and provide evidence for the positive role of environment-induced mutagenesis in the acquisition of a complex lifestyle trait. We speculate that co-transfer of complex phenotypic traits with mutagenesis determinants might frequently enhance the ecological success of HGT. Horizontal gene transfer has an extraordinary impact on microbe evolution and diversification, by allowing exploration of new niches such as higher organisms. This is the case for rhizobia, a group of phylogenetically diverse bacteria that form a nitrogen-fixing symbiotic relationship with most leguminous plants. While these arose through horizontal transfer of symbiotic plasmids, this in itself is usually unproductive, and full expression of the acquired traits needs subsequent remodeling of the genome to ensure the ecological success of the transfer. Here we uncover a mechanism that accelerates the evolution of a soil bacterium into a legume symbiont. We show that key symbiotic genes are co-transferred with genes encoding stress-responsive error-prone DNA polymerases that transiently elevate the mutation rate in the recipient genome. This burst in genetic diversity accelerates the symbiotic evolution process under selection pressure from the host plant. A more widespread involvement of plasmid mutagenesis cassettes in rhizobium evolution is supported by their overrepresentation in rhizobia-containing lineages. Our findings provide evidence for the role of environment-induced mutagenesis in the acquisition of a complex lifestyle trait and predict that co-transfer of complex phenotypic traits with mutagenesis determinants might help successful horizontal gene transfer.
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Affiliation(s)
- Philippe Remigi
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Delphine Capela
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Camille Clerissi
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Léna Tasse
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Rachel Torchet
- CNRS-UMR 8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, Evry, France
| | - Olivier Bouchez
- INRA, UMR1388 Génétique, Physiologie et Systèmes d'Elevage, Castanet-Tolosan, France; GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Jacques Batut
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Stéphane Cruveiller
- CNRS-UMR 8030 and Commissariat à l'Energie Atomique CEA/DSV/IG/Genoscope LABGeM, Evry, France
| | - Eduardo P C Rocha
- CNRS UMR3525, Paris, France; Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
| | - Catherine Masson-Boivin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
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Flores-Félix JD, Carro L, Velázquez E, Valverde Á, Cerda-Castillo E, García-Fraile P, Rivas R. Phyllobacterium endophyticum sp. nov., isolated from nodules of Phaseolus vulgaris. Int J Syst Evol Microbiol 2012; 63:821-826. [PMID: 22611197 DOI: 10.1099/ijs.0.038497-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strain, PEPV15(T), was isolated from a nodule on Phaseolus vulgaris grown in soil in northern Spain. Phylogenetic analyses of 16S rRNA and atpD genes showed that this strain belongs to the genus Phyllobacterium. The most closely related species were, in both cases, Phyllobacterium brassicacearum, Phyllobacterium bourgognense and Phyllobacterium trifolii, the type strains of which gave sequence similarities of 98.9, 98.6 and 98.4 %, respectively, in the 16S rRNA gene and 88.1, 87.5 and 88.7 %, respectively, in the atpD gene. PEPV15(T) contained Q-10 as the major quinone (88 %) and low amounts of Q-9 (12 %). It differed from its closest relatives in its growth in diverse culture conditions and in the assimilation of several carbon sources. The strain was not able to produce nodules in Phaseolus vulgaris. The results of DNA-DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain represents a novel species of the genus Phyllobacterium for which the name Phyllobacterium endophyticum sp. nov. is proposed; the type strain is PEPV15(T) ( = LMG 26470(T) = CECT 7949(T)). An emended description of the genus Phyllobacterium is also provided.
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Affiliation(s)
| | - Lorena Carro
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Encarna Velázquez
- Unidad Asociada Universidad de Salamanca, IRNASA (CSIC), Salamanca, Spain
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Ángel Valverde
- Instituto de Recursos Naturales y Agrobiología, IRNASA CSIC, Salamanca, Spain
- Unidad Asociada Universidad de Salamanca, IRNASA (CSIC), Salamanca, Spain
| | | | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Raúl Rivas
- Unidad Asociada Universidad de Salamanca, IRNASA (CSIC), Salamanca, Spain
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
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López-López A, Rogel-Hernández MA, Barois I, Ortiz Ceballos AI, Martínez J, Ormeño-Orrillo E, Martínez-Romero E. Rhizobium grahamii sp. nov., from nodules of Dalea leporina, Leucaena leucocephala and Clitoria ternatea, and Rhizobium mesoamericanum sp. nov., from nodules of Phaseolus vulgaris, siratro, cowpea and Mimosa pudica. Int J Syst Evol Microbiol 2011; 62:2264-2271. [PMID: 22081714 DOI: 10.1099/ijs.0.033555-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel related Rhizobium species, Rhizobium grahamii sp. nov. and Rhizobium mesoamericanum sp. nov., were identified by a polyphasic approach using DNA-DNA hybridization, whole-genome sequencing and phylogenetic and phenotypic characterization including nodulation of Leucaena leucocephala and Phaseolus vulgaris (bean). As similar bacteria were found in the Los Tuxtlas rainforest in Mexico and in Central America, we suggest the existence of a Mesoamerican microbiological corridor. The type strain of Rhizobium grahamii sp. nov. is CCGE 502(T) (= ATCC BAA-2124(T) = CFN 242(T) = Dal4(T) = HAMBI 3152(T)) and that of Rhizobium mesoamericanum sp. nov. is CCGE 501(T) (= ATCC BAA-2123(T) = HAMBI 3151(T) = CIP 110148(T) = 1847(T)).
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Affiliation(s)
- Aline López-López
- Centro de Ciencias Genómicas, UNAM, Chamilpa 62210, Cuernavaca, Morelos, Mexico
| | | | - Isabelle Barois
- Departamento de Biología de Suelos, Instituto de Ecología AC, AP 63, Veracruz 91000, Xalapa, Mexico
| | | | - Julio Martínez
- Centro de Ciencias Genómicas, UNAM, Chamilpa 62210, Cuernavaca, Morelos, Mexico
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Saïdi S, Mnasri B, Mhamdi R. Diversity of nodule-endophytic agrobacteria-like strains associated with different grain legumes in Tunisia. Syst Appl Microbiol 2011; 34:524-30. [DOI: 10.1016/j.syapm.2011.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/03/2010] [Accepted: 01/03/2011] [Indexed: 11/30/2022]
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22
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Robledo M, Velázquez E, Ramírez-Bahena MH, García-Fraile P, Pérez-Alonso A, Rivas R, Martínez-Molina E, Mateos PF. The celC gene, a new phylogenetic marker useful for taxonomic studies in Rhizobium. Syst Appl Microbiol 2011; 34:393-9. [DOI: 10.1016/j.syapm.2011.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 01/15/2011] [Accepted: 01/17/2011] [Indexed: 11/17/2022]
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23
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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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Evidence of an American origin for symbiosis-related genes in Rhizobium lusitanum. Appl Environ Microbiol 2011; 77:5665-70. [PMID: 21705533 DOI: 10.1128/aem.02017-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Randomly amplified polymorphic DNA (RAPD) analysis was used to investigate the diversity of 179 bean isolates recovered from six field sites in the Arcos de Valdevez region of northwestern Portugal. The isolates were divided into 6 groups based on the fingerprint patterns that were obtained. Representatives for each group were selected for sequence analysis of 4 chromosomal DNA regions. Five of the groups were placed within Rhizobium lusitanum, and the other group was placed within R. tropici type IIA. Therefore, the collection of Portuguese bean isolates was shown to include the two species R. lusitanum and R. tropici. In plant tests, the strains P1-7, P1-1, P1-2, and P1-16 of R. lusitanum nodulated and formed nitrogen-fixing symbioses both with Phaseolus vulgaris and Leucaena leucocephala. A methyltransferase-encoding nodS gene identical with the R. tropici locus that confers wide host range was detected in the strain P1-7 as well as 24 others identified as R. lusitanum. A methyltransferase-encoding nodS gene also was detected in the remaining isolates of R. lusitanum, but in this case the locus was that identified with the narrow-host-range R. etli. Representatives of isolates with the nodS of R. etli formed effective nitrogen-fixing symbioses with P. vulgaris and did not nodulate L. leucocephala. From sequence data of nodS, the R. lusitanum genes for symbiosis were placed within those of either R. tropici or R. etli. These results would support the suggestion that R. lusitanum was the recipient of the genes for symbiosis with beans from both R. tropici and R. etli.
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25
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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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26
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Velázquez E, Palomo JL, Rivas R, Guerra H, Peix A, Trujillo ME, García-Benavides P, Mateos PF, Wabiko H, Martínez-Molina E. Analysis of core genes supports the reclassification of strains Agrobacterium radiobacter K84 and Agrobacterium tumefaciens AKE10 into the species Rhizobium rhizogenes. Syst Appl Microbiol 2010; 33:247-51. [PMID: 20627641 DOI: 10.1016/j.syapm.2010.04.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 04/17/2010] [Accepted: 04/20/2010] [Indexed: 11/18/2022]
Abstract
Some strains of the former genus Agrobacterium have high biotechnological interest and are currently misclassified. Consequently, in this study, the taxonomic status of the non-pathogenic strain Agrobacterium radiobacter K84, used in biological control, and the tumourigenic strain Agrobacterium tumefaciens AKE10, able to regenerate tobacco transgenic plants, was revised. The phylogenetic analysis of the chromosomal genes rrs, atpD and recA showed that they should be reclassified into Rhizobium rhizogenes. The analysis of virulence genes located in the Ti plasmid (pTi) outside T-DNA showed a common phylogenetic origin among strains AKE10, R. rhizogenes 163C and A. tumefaciens (currently R. radiobacter) C58. However, the genes located inside the T-DNA, mainly the 6b gene, of strain AKE10 were phylogenetically close to those of strain 163C but divergent from those of strain C58. Furthermore, the T-DNA of tumourigenic strains from R. rhizogenes conferred on them the ability to regenerate tumour tissue resembling fasciation in tobacco plants. These results showed the existence of a highly mosaic genetic organization in tumourigenic strains of the genus Rhizobium and provided evidence of the involvement of T-DNA from tumourigenic strains of R. rhizogenes in fasciation of Nicotiana leaves. The data further suggested that pathogenic strains of Rhizobium could be good models to analyse bacterial evolution.
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Affiliation(s)
- Encarna Velázquez
- Departamento de Microbiología y Genética, Edificio Departamental de Biología, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain.
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Carvalho FM, Souza RC, Barcellos FG, Hungria M, Vasconcelos ATR. Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales. BMC Microbiol 2010; 10:37. [PMID: 20144182 PMCID: PMC2907836 DOI: 10.1186/1471-2180-10-37] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Accepted: 02/08/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Species belonging to the Rhizobiales are intriguing and extensively researched for including both bacteria with the ability to fix nitrogen when in symbiosis with leguminous plants and pathogenic bacteria to animals and plants. Similarities between the strategies adopted by pathogenic and symbiotic Rhizobiales have been described, as well as high variability related to events of horizontal gene transfer. Although it is well known that chromosomal rearrangements, mutations and horizontal gene transfer influence the dynamics of bacterial genomes, in Rhizobiales, the scenario that determine pathogenic or symbiotic lifestyle are not clear and there are very few studies of comparative genomic between these classes of prokaryotic microorganisms trying to delineate the evolutionary characterization of symbiosis and pathogenesis. RESULTS Non-symbiotic nitrogen-fixing bacteria and bacteria involved in bioremediation closer to symbionts and pathogens in study may assist in the origin and ancestry genes and the gene flow occurring in Rhizobiales. The genomic comparisons of 19 species of Rhizobiales, including nitrogen-fixing, bioremediators and pathogens resulted in 33 common clusters to biological nitrogen fixation and pathogenesis, 15 clusters exclusive to all nitrogen-fixing bacteria and bacteria involved in bioremediation, 13 clusters found in only some nitrogen-fixing and bioremediation bacteria, 01 cluster exclusive to some symbionts, and 01 cluster found only in some pathogens analyzed. In BBH performed to all strains studied, 77 common genes were obtained, 17 of which were related to biological nitrogen fixation and pathogenesis. Phylogenetic reconstructions for Fix, Nif, Nod, Vir, and Trb showed possible horizontal gene transfer events, grouping species of different phenotypes. CONCLUSIONS The presence of symbiotic and virulence genes in both pathogens and symbionts does not seem to be the only determinant factor for lifestyle evolution in these microorganisms, although they may act in common stages of host infection. The phylogenetic analysis for many distinct operons involved in these processes emphasizes the relevance of horizontal gene transfer events in the symbiotic and pathogenic similarity.
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Affiliation(s)
- Fabíola M Carvalho
- Laboratório Nacional de Computação Científica, Laboratório de Bioinformática, Av Getúlio Vargas 333, 25651-075 Petrópolis, Rio de Janeiro, Brazil
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Liu J, Wang ET, Ren DW, Chen WX. Mixture of endophytic Agrobacterium and Sinorhizobium meliloti strains could induce nonspecific nodulation on some woody legumes. Arch Microbiol 2010; 192:229-34. [PMID: 20098981 DOI: 10.1007/s00203-010-0543-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2009] [Revised: 10/01/2009] [Accepted: 01/04/2010] [Indexed: 11/28/2022]
Abstract
Agrobacterium sp. II CCBAU 21244 isolated from root nodules of Wisteria sinensis was verified as an endophytic bacterium by inoculation and reisolation tests. However, inoculation with a mixture of this strain and a Sinorhizobium meliloti strain could induce root nodules on W. sinensis and two other woody legumes, which do not form a symbiosis with S. meliloti alone. Rod-shaped and irregular nodules were found on the inoculated plants, in which the S. meliloti strain was detected in all of the nodules; while the Agrobacterium strain was inside of the rod-shaped nodules, or occupied only the nodule surface of the irregular globe-shaped nodules. These findings revealed novel interactions among the symbiotic bacteria, endophytic bacteria and the legume plants, although the mechanisms are still unknown.
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Affiliation(s)
- Jie Liu
- Department of Bioengineering and Biotechnology, Qingdao University of Science and Technology, 266042 Qingdao, China.
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29
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López-López A, Rosenblueth M, Martínez J, Martínez-Romero E. Rhizobial Symbioses in Tropical Legumes and Non-Legumes. SOIL BIOLOGY 2010. [DOI: 10.1007/978-3-642-05076-3_8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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30
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Rivas R, García-Fraile P, Velázquez E. Taxonomy of Bacteria Nodulating Legumes. Microbiol Insights 2009. [DOI: 10.4137/mbi.s3137] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Over the years, the term “rhizobia” has come to be used for all the bacteria that are capable of nodulation and nitrogen fixation in association with legumes but the taxonomy of rhizobia has changed considerably over the last 30 year. Recently, several non-rhizobial species belonging to alpha and beta subgroup of Proteobacteria have been identified as nitrogen-fixing legume symbionts. Here we provide an overview of the history of the rhizobia and the widespread phylogenetic diversity of nitrogen-fixing legume symbionts.
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Affiliation(s)
- Raúl Rivas
- Departamento de Microbiología y Genética, Laboratorio 209, Edificio Departamental de Biología, Doctores de la Reina s/n, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Laboratorio 209, Edificio Departamental de Biología, Doctores de la Reina s/n, Universidad de Salamanca, 37007 Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Laboratorio 209, Edificio Departamental de Biología, Doctores de la Reina s/n, Universidad de Salamanca, 37007 Salamanca, Spain
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Álvarez-Martínez ER, Valverde Á, Ramírez-Bahena MH, García-Fraile P, Tejedor C, Mateos PF, Santillana N, Zúñiga D, Peix A, Velázquez E. The analysis of core and symbiotic genes of rhizobia nodulating Vicia from different continents reveals their common phylogenetic origin and suggests the distribution of Rhizobium leguminosarum strains together with Vicia seeds. Arch Microbiol 2009; 191:659-68. [DOI: 10.1007/s00203-009-0495-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 05/31/2009] [Accepted: 07/02/2009] [Indexed: 11/30/2022]
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32
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Cummings SP, Gyaneshwar P, Vinuesa P, Farruggia FT, Andrews M, Humphry D, Elliott GN, Nelson A, Orr C, Pettitt D, Shah GR, Santos SR, Krishnan HB, Odee D, Moreira FMS, Sprent JI, Young JPW, James EK. Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia. Environ Microbiol 2009; 11:2510-25. [PMID: 19555380 PMCID: PMC7163632 DOI: 10.1111/j.1462-2920.2009.01975.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Concatenated sequence analysis with 16S rRNA, rpoB and fusA genes identified a bacterial strain (IRBG74) isolated from root nodules of the aquatic legume Sesbania cannabina as a close relative of the plant pathogen Rhizobium radiobacter (syn. Agrobacterium tumefaciens). However, DNA:DNA hybridization with R. radiobacter, R. rubi, R. vitis and R. huautlense gave only 44%, 5%, 8% and 8% similarity respectively, suggesting that IRBG74 is potentially a new species. Additionally, it contained no vir genes and lacked tumour‐forming ability, but harboured a sym‐plasmid containing nifH and nodA genes similar to those in other Sesbania symbionts. Indeed, IRBG74 effectively nodulated S. cannabina and seven other Sesbania spp. that nodulate with Ensifer (Sinorhizobium)/Rhizobium strains with similar nodA genes to IRBG74, but not species that nodulate with Azorhizobium or Mesorhizobium. Light and electron microscopy revealed that IRBG74 infected Sesbania spp. via lateral root junctions under flooded conditions, but via root hairs under non‐flooded conditions. Thus, IRBG74 is the first confirmed legume‐nodulating symbiont from the Rhizobium (Agrobacterium) clade. Cross‐inoculation studies with various Sesbania symbionts showed that S. cannabina could form fully effective symbioses with strains in the genera Rhizobium and Ensifer, only ineffective ones with Azorhizobium strains, and either partially effective (Mesorhizobium huakii) or ineffective (Mesorhizobium plurifarium) symbioses with Mesorhizobium. These data are discussed in terms of the molecular phylogeny of Sesbania and its symbionts.
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Affiliation(s)
- Stephen P Cummings
- School of Applied Sciences, Ellison Building, University of Northumbria, Newcastle-upon-Tyne, UK
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Yim WJ, Poonguzhali S, Madhaiyan M, Palaniappan P, Siddikee MA, Sa T. Characterization of plant-growth promoting diazotrophic bacteria isolated from field grown Chinese cabbage under different fertilization conditions. J Microbiol 2009; 47:147-55. [DOI: 10.1007/s12275-008-0201-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 01/19/2009] [Indexed: 10/20/2022]
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García-Fraile P, Velázquez E, Mateos PF, Martínez-Molina E, Rivas R. Cohnella phaseoli sp. nov., isolated from root nodules of Phaseolus coccineus in Spain, and emended description of the genus Cohnella. Int J Syst Evol Microbiol 2008; 58:1855-9. [PMID: 18676468 DOI: 10.1099/ijs.0.65468-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain designated GSPC1 T was isolated from root nodules of Phaseolus coccineus in Segovia (Spain). The 16S rRNA gene sequence of this strain showed 95.9 and 94.7 % sequence similarity, respectively, with those of the type strains of Cohnella hongkongensis and Cohnella thermotolerans. Strain GSPC1 T presented phenotypic, chemotaxonomic and molecular differences with respect to Cohnella species which indicated that it belonged to a different species. The isolate was a Gram-positive, aerobic, sporulated rod, motile by means of peritrichous flagella. The strain was catalase-positive and showed weak oxidase activity. It grew in the presence of 2 % NaCl. MK-7 was the predominant menaquinone. anteiso-C15:0, iso-C15:0, iso-C16: 0 and C16:0 were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content was 60.3 mol%. The results of this study suggest that isolate GSPC1 T should be classified within a novel Cohnella species, for which the name Cohnella phaseoli sp. nov. is proposed, with strain GSPC1T (=LMG 24086T =DSM 19269T) as the type strain.
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Affiliation(s)
- Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
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36
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Sharma M, Schmid M, Rothballer M, Hause G, Zuccaro A, Imani J, Kämpfer P, Domann E, Schäfer P, Hartmann A, Kogel KH. Detection and identification of bacteria intimately associated with fungi of the order Sebacinales. Cell Microbiol 2008; 10:2235-46. [PMID: 18637023 DOI: 10.1111/j.1462-5822.2008.01202.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Because of their beneficial impact on plants, the highly diverse mycorrhizal fungi grouped in the order Sebacinales lay claim to high ecological and agricultural significance. Here, we describe for the first time associations of Sebacinoid members with bacteria. Using quantitative PCR, denaturating gradient gel electrophoresis and fluorescence in situ hybridization, we detected an intimate association between Piriformospora indica and Rhizobium radiobacter, an alpha-Proteobacterium. The stability of the association, vertical transmission of the bacteria during asexual fungal reproduction and fungal plant colonization was monitored using R. radiobacter-specific primers. Treatment of mycelium or fungal protoplasts with antibiotics highly efficient against the free bacteria failed to cure the fungus. Barley seedlings dip-inoculated with R. radiobacter showed growth promotion and systemic resistance to the powdery mildew fungus Blumeria graminis comparable to P. indica inoculation. By screening additional isolates of the Sebacina vermifera complex, three species-specific associations with bacteria from the genera Paenibacillus, Acinetobacter and Rhodococcus were found. These findings suggest that Sebacinales species regularly undergo complex interactions involving host plants and bacteria reminiscent of other ectomycorrhizal and endomycorrhizal associations.
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Affiliation(s)
- Monica Sharma
- Institute of Phytopathology and Applied Zoology, Research Centre for BioSystems, Land use and Nutrition, Justus-Liebig-University Giessen, D-35392 Giessen, Germany
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37
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Santillana N, Ramírez-Bahena MH, García-Fraile P, Velázquez E, Zúñiga D. Phylogenetic diversity based on rrs, atpD, recA genes and 16S-23S intergenic sequence analyses of rhizobial strains isolated from Vicia faba and Pisum sativum in Peru. Arch Microbiol 2008; 189:239-47. [PMID: 17985116 DOI: 10.1007/s00203-007-0313-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2007] [Revised: 09/05/2007] [Accepted: 10/15/2007] [Indexed: 11/28/2022]
Abstract
In this study 17 isolates from effective nodules of Vicia faba and Pisum sativum var. macrocarpum growing in different soils from Peru were isolated and characterized. The isolates, presenting 11 different RAPD profiles, were distributed in three groups on the basis of their 16S-RFLP patterns. The 16S rRNA gene sequences of strains from 16S-RFLP groups I, II and III were closely related (identities higher than 99.5%) to Rhizobium leguminosarum bv. trifolii DSM 30141 (=ATCC 14480), R. leguminosarum bv. viciae DSM 30132(T) and Rhizobium etli CFN42(T) (=USDA 9032(T)), respectively. The analysis of the 16S-23S intergenic spacer (ITS) and two housekeeping genes, atpD and recA, confirmed the identification of strains from group I, however those from groups II and III were phylogenetically divergent to strains DSM 30132(T) and CFN42(T). These results support the fact that the 16S rRNA gene is not adequate for identification at species level within genus Rhizobium and suggest the existence of putative new species within the phylogenetic group of R. leguminosarum. They also confirm the need of a taxonomic revision of R. leguminosarum since the reference strains of the three biovars included in this study are phylogenetically divergent according to their ITS, atpD and recA gene sequences.
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MESH Headings
- Bacterial Proteins/genetics
- Biodiversity
- Cluster Analysis
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Molecular Sequence Data
- Pisum sativum/microbiology
- Peru
- Phylogeny
- Plant Roots/microbiology
- Polymorphism, Restriction Fragment Length
- RNA, Ribosomal, 16S/genetics
- Random Amplified Polymorphic DNA Technique
- Rhizobium/classification
- Rhizobium/genetics
- Rhizobium/isolation & purification
- Sequence Analysis, DNA
- Sequence Homology
- Vicia faba/microbiology
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Affiliation(s)
- Nery Santillana
- Laboratorio de Ecología Microbiana y Biotecnología Marino Tabusso, Departamento de Biología, Universidad Nacional Agraria La Molina, Lima, Peru
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Zurdo-Piñeiro JL, Rivas R, Trujillo ME, Vizcaíno N, Carrasco JA, Chamber M, Palomares A, Mateos PF, Martínez-Molina E, Velázquez E. Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain. Int J Syst Evol Microbiol 2007; 57:784-788. [PMID: 17392207 DOI: 10.1099/ijs.0.64613-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains named ESC1(T) and ESC5 were isolated from nodules of Cytisus scoparius growing in a Spanish soil. Phylogenetic analysis of the 16S rRNA gene showed that these strains belong to the genus Ochrobactrum, their closest relatives being Ochrobactrum anthropi and Ochrobactrum lupini, with 100 and 99.9 % similarity to the respective type strains. Despite this high similarity, the results of DNA-DNA hybridization, phenotypic tests and fatty acid analyses showed that these strains represent a novel species of genus Ochrobactrum. The DNA-DNA hybridization values were respectively 70, 66 and 55 % with respect to O. lupini LUP21(T), O. anthropi DSM 6882(T) and Ochrobactrum tritici DSM 13340(T). The predominant fatty acids were C(18 : 1)omega7c and C(18 : 1) 2-OH. Strains ESC1(T) and ESC5 were strictly aerobic and were able to reduce nitrate and to hydrolyse aesculin. They produced beta-galactosidase and beta-glucosidase and did not produce urease after 48 h incubation. The G+C content of strain ESC1(T) was 56.4 mol%. Both strains ESC1(T) and ESC5 contained nodD and nifH genes on megaplasmids that were related phylogenetically to those of rhizobial strains nodulating Phaseolus, Leucaena, Trifolium and Lupinus. From the results of this work, we propose that the strains isolated in this study be included in a novel species named Ochrobactrum cytisi sp. nov. The type strain is ESC1(T) (=LMG 22713(T)=CECT 7172(T)).
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Affiliation(s)
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Nieves Vizcaíno
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | | | | | - Antonio Palomares
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, Sevilla, Spain
| | - Pedro F Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | | | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
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Hunter WJ, Kuykendall LD, Manter DK. Rhizobium selenireducens sp. nov.: a selenite-reducing alpha-Proteobacteria isolated from a bioreactor. Curr Microbiol 2007; 55:455-60. [PMID: 17805926 DOI: 10.1007/s00284-007-9020-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2007] [Accepted: 06/21/2007] [Indexed: 10/22/2022]
Abstract
A Gram-negative, nonpigmented bacterium designated strain B1 was isolated from a laboratory bioreactor that reduced selenate to elemental red selenium (Se(0)). 16S rRNA gene-sequence alignment identified the isolate as a Rhizobium sp. belonging to the Rhizobium clade, which includes R. daejeonense, R. giardinii, R. undicola, R. larrymoorei, R. radiobacter, R. rubi, and R. vitis. R. radiobacter and R. rubi are its closest relatives as indicated by 16S rRNA gene-sequence alignments, which differ from strain B1 by 2.6% and 2.8%, respectively. Within this group, strains that show variances > 0.8% to 2.2% have been classified as different species. The major cellular fatty acids present in the B1 strain were C16:0 (1.8%), C18:0 (3.38%), 18:0 3-OH (1.6%), 18:1 omega7c (86.8%), 19:0 cycloomega8c (1.5%), and summed features 2 (3.8%) and 3 (1.2%). The large amount of 18:1 omega7c present is constant with members of this group of bacteria, but the small amounts of 16:0, 19:0 cycloomega8c, and summed feature 3 shows variance from R. radiobacter and R. rubi. The strain's phenotypic and biochemical characteristics are consistent with its placement in this genus.
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Affiliation(s)
- W J Hunter
- United States Department of Agriculture-Agricultural Research Service, 2150-D Centre Avenue, Fort Collins, CO 80526-8119, USA.
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Humphry DR, Andrews M, Santos SR, James EK, Vinogradova LV, Perin L, Reis VM, Cummings SP. Phylogenetic assignment and mechanism of action of a crop growth promoting Rhizobium radiobacter strain used as a biofertiliser on graminaceous crops in Russia. Antonie van Leeuwenhoek 2007; 91:105-13. [PMID: 17013548 DOI: 10.1007/s10482-006-9100-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 06/23/2006] [Indexed: 10/24/2022]
Abstract
The taxonomic position of "Agrobacterium radiobacter strain 204," used in Russia as a cereal crop growth promoting inoculant, was derived by a polyphasic approach. The phenotypic analyses gave very similar biochemical profiles for strain 204, Rhizobium radiobacter NCIMB 9042 (formerly the A. radiobacter type strain) and R. radiobacter NCIMB 13307 (formerly the Agrobacterium tumefaciens type strain). High percentage similarities, above the species separation level, were observed between the 16S rRNA, fusA and rpoB housekeeping gene sequences of these three strains, and the genomic DNA-DNA hybridisation of strain 204 against the type strain of R. radiobacter NCIMB 9042 was over 70%. Strain 204 is not phytopathogenic and it does not fix atmospheric N2 or form a physical association with the roots of barley. Strain 204 culture and culture supernatant stimulated the rate of mobilisation of seed reserves of barley in darkness and promoted its shoot growth in the light. Gibberellic acid (GA) concentration was 1.3 microM but indole acetic acid was undetectable (< 50 nM) in cultures of strain 204. It is concluded that strain 204 is phenotypically and genotypically very similar to the current R. radiobacter type strain and that the mechanism of its effect on growth of cereals is via the production of plant growth promoting substances. GA is likely to play an important role in the strain 204 stimulation of early growth of barley.
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MESH Headings
- Agrobacterium tumefaciens/classification
- Agrobacterium tumefaciens/genetics
- Agrobacterium tumefaciens/physiology
- Bacterial Proteins/genetics
- Bacterial Typing Techniques
- Crops, Agricultural/growth & development
- Crops, Agricultural/microbiology
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA-Directed RNA Polymerases/genetics
- Genes, rRNA
- Gibberellins/biosynthesis
- Hordeum/growth & development
- Hordeum/microbiology
- Indoleacetic Acids/metabolism
- Molecular Sequence Data
- Nitrogen Fixation/genetics
- Nucleic Acid Hybridization
- Oxidoreductases/genetics
- Peptide Elongation Factor G/genetics
- Phylogeny
- Plant Diseases/microbiology
- Plant Shoots/growth & development
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/genetics
- Russia
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Solanum tuberosum/microbiology
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Affiliation(s)
- David R Humphry
- Department of Biology, University of York, P.O. Box 373, University Road, Heslington, York, UK
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Rivas R, Laranjo M, Mateos PF, Oliveira S, Martínez-Molina E, Velázquez E. Strains of Mesorhizobium amorphae and Mesorhizobium tianshanense, carrying symbiotic genes of common chickpea endosymbiotic species, constitute a novel biovar (ciceri) capable of nodulating Cicer arietinum. Lett Appl Microbiol 2007; 44:412-8. [PMID: 17397480 DOI: 10.1111/j.1472-765x.2006.02086.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To identify several strains of Mesorhizobium amorphae and Mesorhizobium tianshanense nodulating Cicer arietinum in Spain and Portugal, and to study the symbiotic genes carried by these strains. METHODS AND RESULTS The sequences of 16S-23S intergenic spacer (ITS), 16S rRNA gene and symbiotic genes nodC and nifH were analysed. According to their 16S rRNA gene and ITS sequences, the strains from this study were identified as M. amorphae and M. tianshanense. The type strains of these species were isolated in China from Glycyrrhiza pallidiflora and Amorpha fruticosa nodules, respectively, and are not capable of nodulating chickpea. These strains carry symbiotic genes, phylogenetically divergent from those of the chickpea isolates, whose nodC and nifH genes showed more than 99% similarity with respect to those from Mesorhizobium ciceri and Mesorhizobium mediterraneum, the two common chickpea nodulating species in Spain and Portugal. CONCLUSIONS The results from this study showed that different symbiotic genes have been acquired by strains from the same species during their coevolution with different legumes in distinct geographical locations. SIGNIFICANCE AND IMPACT OF THE STUDY A new infrasubspecific division named biovar ciceri is proposed within M. amorphae and M. tianshanense to include the strains able to effectively nodulate Cicer arietinum.
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Affiliation(s)
- R Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
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42
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García-Fraile P, Rivas R, Willems A, Peix A, Martens M, Martínez-Molina E, Mateos PF, Velázquez E. Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba. Int J Syst Evol Microbiol 2007; 57:844-848. [PMID: 17392217 DOI: 10.1099/ijs.0.64680-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study of polysaccharide-hydrolysing bacteria present in different plant sources, two strains were isolated from pulverized decaying wood of Populus alba and classified in the genus Rhizobium on basis of their almost complete 16S rRNA gene sequences. Their closest phylogenetic relatives were Rhizobium galegae USDA 4128T and Rhizobium huautlense S02T, with 98.2 and 98.1 % 16S rRNA gene sequence similarity, respectively. recA and atpD sequence analysis showed that these species have less than 88 and 92 % similarity, respectively, to the novel strains. In contrast to their closest phylogenetic relatives, the two strains showed strong cellulase activity on plates containing CM-cellulose as a carbon source. They were also distinguishable from these species on the basis of other phenotypic characteristics. The strains were able to induce ineffective nodules on Medicago sativa and the sequence of their nodD gene was phylogenetically close to that of Ensifer meliloti 1021 (99.6 % similarity). DNA–DNA hybridization values ranged from 10 to 22 % with respect to R. galegae USDA 4128T and 14 to 25 % with respect to R. huautlense S02T, showing that the strains from this study belong to a novel species, for which the name Rhizobium cellulosilyticum sp. nov. is proposed. The type strain is ALA10B2T (=LMG 23642T=DSM 18291T=CECT 7176T).
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Affiliation(s)
| | - Raúl Rivas
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
| | - Anne Willems
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNA-CSIC, Salamanca, Spain
| | - Miet Martens
- Laboratorium voor Microbiologie, Vakgroep Biochemie, Fysiologie en Microbiologie, Universiteit Gent, K. L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | | | - Pedro F Mateos
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
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Valverde A, Igual JM, Peix A, Cervantes E, Velázquez E. Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris. Int J Syst Evol Microbiol 2006; 56:2631-2637. [PMID: 17082403 DOI: 10.1099/ijs.0.64402-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The species Phaseolus vulgaris is a promiscuous legume nodulated by several species of the family Rhizobiaceae. During a study of rhizobia nodulating this legume in Portugal, we isolated several strains that nodulate P. vulgaris effectively and also Macroptilium atropurpureum and Leucaena leucocephala, but they form ineffective nodules in Medicago sativa. According to phylogenetic analysis of the 16S rRNA gene sequence, the strains from this study belong to the genus Rhizobium, with Rhizobium rhizogenes and Rhizobium tropici as the closest related species, with 99.9 and 99.2 % similarity, respectively, between the type strains of these species and strain P1-7T. The nodD and nifH genes carried by strain P1-7T are phylogenetically related to those of other species nodulating Phaseolus. This strain does not carry virulence genes present in the type strain of R. rhizogenes, ATCC 11325T. Analysis of the recA and atpD genes confirms this phylogenetic arrangement, showing low similarity with respect to those of R. rhizogenes ATCC 11325T (91.9 and 94.1 % similarity, respectively) and R. tropici IIB CIAT 899T (90.6 % and 91.8 % similarity, respectively). The intergenic spacer (ITS) of the strains from this study is phylogenetically divergent from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, with 85.9 and 82.8 % similarity, respectively, with respect to strain P1-7T. The tRNA profile and two-primer random amplified polymorphic DNA pattern of strain P1-7T are also different from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T. The strains isolated in this study can be also differentiated from R. rhizogenes and R. tropici by several phenotypic characteristics. The results of DNA–DNA hybridization showed means of 28 and 25 % similarity between strain P1-7T and R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, respectively. All these data showed that the strains isolated in this study belong to a novel species of the genus Rhizobium, for which we propose the name Rhizobium lusitanum sp. nov.; the type strain is P1-7T (=LMG 22705T=CECT 7016T).
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Affiliation(s)
- Angel Valverde
- Departamento de Producción Vegetal, IRNASA-CSIC, Salamanca, Spain
| | - José M Igual
- Departamento de Producción Vegetal, IRNASA-CSIC, Salamanca, Spain
| | - Alvaro Peix
- Departamento de Producción Vegetal, IRNASA-CSIC, Salamanca, Spain
| | - Emilio Cervantes
- Departamento de Producción Vegetal, IRNASA-CSIC, Salamanca, Spain
| | - Encarna Velázquez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Spain
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Young JPW, Crossman LC, Johnston AWB, Thomson NR, Ghazoui ZF, Hull KH, Wexler M, Curson ARJ, Todd JD, Poole PS, Mauchline TH, East AK, Quail MA, Churcher C, Arrowsmith C, Cherevach I, Chillingworth T, Clarke K, Cronin A, Davis P, Fraser A, Hance Z, Hauser H, Jagels K, Moule S, Mungall K, Norbertczak H, Rabbinowitsch E, Sanders M, Simmonds M, Whitehead S, Parkhill J. The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol 2006; 7:R34. [PMID: 16640791 PMCID: PMC1557990 DOI: 10.1186/gb-2006-7-4-r34] [Citation(s) in RCA: 351] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Revised: 02/20/2006] [Accepted: 03/22/2006] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Rhizobium leguminosarum is an alpha-proteobacterial N2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841. RESULTS The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were over-represented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens. CONCLUSION Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.
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Affiliation(s)
| | - Lisa C Crossman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Nicholas R Thomson
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | | | - Margaret Wexler
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Andrew RJ Curson
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Jonathan D Todd
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Philip S Poole
- School of Biological Sciences, University of Reading, Reading, UK
| | - Tim H Mauchline
- School of Biological Sciences, University of Reading, Reading, UK
| | - Alison K East
- School of Biological Sciences, University of Reading, Reading, UK
| | - Michael A Quail
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Carol Churcher
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Claire Arrowsmith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Inna Cherevach
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Tracey Chillingworth
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Kay Clarke
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Ann Cronin
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Paul Davis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Audrey Fraser
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Zahra Hance
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Heidi Hauser
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Kay Jagels
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Sharon Moule
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Karen Mungall
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Halina Norbertczak
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Ester Rabbinowitsch
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Mandy Sanders
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Mark Simmonds
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Sally Whitehead
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
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