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Manantsoa FF, Rakotoarisoa MF, Chaintreuil C, Razakatiana ATE, Gressent F, Pervent M, Bourge M, Andrianandrasana MD, Nouwen N, Randriambanona H, Ramanankierana H, Arrighi JF. Occurrence and diversity of stem nodulation in Aeschynomene and Sesbania legumes from wetlands of Madagascar. Sci Rep 2024; 14:5024. [PMID: 38424094 PMCID: PMC10904833 DOI: 10.1038/s41598-024-55247-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
Legumes have the ability to establish a nitrogen-fixing symbiosis with soil rhizobia that they house in specific organs, the nodules. In most rhizobium-legume interactions, nodulation occurs on the root. However, certain tropical legumes growing in wetlands possess a unique trait: the capacity to form rhizobia-harbouring nodules on the stem. Despite the originality of the stem nodulation process, its occurrence and diversity in waterlogging-tolerant legumes remains underexplored, impeding a comprehensive analysis of its genetics and biology. Here, we aimed at filling this gap by surveying stem nodulation in legume species-rich wetlands of Madagascar. Stem nodulation was readily observed in eight hydrophytic species of the legume genera, Aeschynomene and Sesbania, for which significant variations in stem nodule density and morphology was documented. Among these species, A. evenia, which is used as genetic model to study the rhizobial symbiosis, was found to be frequently stem-nodulated. Two other Aeschynomene species, A. cristata and A. uniflora, were evidenced to display a profuse stem-nodulation as occurs in S. rostrata. These findings extend our knowledge on legumes species that are endowed with stem nodulation and further indicate that A. evenia, A. cristata, A. uniflora and S. rostrata are of special interest for the study of stem nodulation. As such, these legume species represent opportunities to investigate different modalities of the nitrogen-fixing symbiosis and this knowledge could provide cues for the engineering of nitrogen-fixation in non-legume crops.
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Affiliation(s)
- Faustin F Manantsoa
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Marrino F Rakotoarisoa
- Department of Ethnobotany and Botany, National Center for Applied Pharmaceutical Research, Antananarivo 101, Madagascar
| | - Clémence Chaintreuil
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Adamson T E Razakatiana
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Frédéric Gressent
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Marjorie Pervent
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Mickaël Bourge
- Cytometry Facility, Institute for Integrative Biology of the Cell (I2BC), Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, 91198, Gif-Sur-Yvette, France
| | - Martial D Andrianandrasana
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Nico Nouwen
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Jean-François Arrighi
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France.
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Camuel A, Teulet A, Carcagno M, Haq F, Pacquit V, Gully D, Pervent M, Chaintreuil C, Fardoux J, Horta-Araujo N, Okazaki S, Ratu STN, Gueye F, Zilli J, Nouwen N, Arrighi JF, Luo H, Mergaert P, Deslandes L, Giraud E. Widespread Bradyrhizobium distribution of diverse Type III effectors that trigger legume nodulation in the absence of Nod factor. THE ISME JOURNAL 2023; 17:1416-1429. [PMID: 37355742 PMCID: PMC10432411 DOI: 10.1038/s41396-023-01458-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/26/2023]
Abstract
The establishment of the rhizobium-legume symbiosis is generally based on plant perception of Nod factors (NFs) synthesized by the bacteria. However, some Bradyrhizobium strains can nodulate certain legume species, such as Aeschynomene spp. or Glycine max, independently of NFs, and via two different processes that are distinguished by the necessity or not of a type III secretion system (T3SS). ErnA is the first known type III effector (T3E) triggering nodulation in Aeschynomene indica. In this study, a collection of 196 sequenced Bradyrhizobium strains was tested on A. indica. Only strains belonging to the photosynthetic supergroup can develop a NF-T3SS-independent symbiosis, while the ability to use a T3SS-dependent process is found in multiple supergroups. Of these, 14 strains lacking ernA were tested by mutagenesis to identify new T3Es triggering nodulation. We discovered a novel T3E, Sup3, a putative SUMO-protease without similarity to ErnA. Its mutation in Bradyrhizobium strains NAS96.2 and WSM1744 abolishes nodulation and its introduction in an ernA mutant of strain ORS3257 restores nodulation. Moreover, ectopic expression of sup3 in A. indica roots led to the formation of spontaneous nodules. We also report three other new T3Es, Ubi1, Ubi2 and Ubi3, which each contribute to the nodulation capacity of strain LMTR13. These T3Es have no homology to known proteins but share with ErnA three motifs necessary for ErnA activity. Together, our results highlight an unsuspected distribution and diversity of T3Es within the Bradyrhizobium genus that may contribute to their symbiotic efficiency by participating in triggering legume nodulation.
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Affiliation(s)
- Alicia Camuel
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Albin Teulet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- University of Cambridge, Sainsbury Laboratory (SLCU), Cambridge, CB2 1LR, UK
| | - Mélanie Carcagno
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Fazal Haq
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Valérie Pacquit
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Marjorie Pervent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
| | - Natasha Horta-Araujo
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Shin Okazaki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Safirah Tasa Nerves Ratu
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, 183-8509, Japan
| | - Fatou Gueye
- Carrefour International, Bureau Régional Afrique de l'Ouest, Dakar, Sénégal
| | - Jerri Zilli
- Embrapa Agrobiologia, Bairro Ecologia, Seropedica, Rio de Janeiro, Brazil
| | - Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Haiwei Luo
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Laurent Deslandes
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/Institut Agro/INRAE/Université de Montpellier/CIRAD, TA-A82/J- Campus de Baillarguet 34398, Montpellier cedex 5, France.
- PHIM Plant Health Institute, Université de Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France.
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Avontuur JR, Wilken PM, Palmer M, Coetzee MPA, Stępkowski T, Venter SN, Steenkamp ET. Complex evolutionary history of photosynthesis in Bradyrhizobium. Microb Genom 2023; 9:001105. [PMID: 37676703 PMCID: PMC10569730 DOI: 10.1099/mgen.0.001105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Bradyrhizobium comprises a diverse group of bacteria with various lifestyles. Although best known for their nodule-based nitrogen-fixation in symbiosis with legumes, a select group of bradyrhizobia are also capable of photosynthesis. This ability seems to be rare among rhizobia, and its origin and evolution in these bacteria remain a subject of substantial debate. Therefore, our aim here was to investigate the distribution and evolution of photosynthesis in Bradyrhizobium using comparative genomics and representative genomes from closely related taxa in the families Nitrobacteraceae, Methylobacteriaceae, Boseaceae and Paracoccaceae . We identified photosynthesis gene clusters (PGCs) in 25 genomes belonging to three different Bradyrhizobium lineages, notably the so-called Photosynthetic, B. japonicum and B. elkanii supergroups. Also, two different PGC architectures were observed. One of these, PGC1, was present in genomes from the Photosynthetic supergroup and in three genomes from a species in the B. japonicum supergroup. The second cluster, PGC2, was also present in some strains from the B. japonicum supergroup, as well as in those from the B. elkanii supergroup. PGC2 was largely syntenic to the cluster found in Rhodopseudomonas palustris and Tardiphaga . Bayesian ancestral state reconstruction unambiguously showed that the ancestor of Bradyrhizobium lacked a PGC and that it was acquired horizontally by various lineages. Maximum-likelihood phylogenetic analyses of individual photosynthesis genes also suggested multiple acquisitions through horizontal gene transfer, followed by vertical inheritance and gene losses within the different lineages. Overall, our findings add to the existing body of knowledge on Bradyrhizobium ’s evolution and provide a meaningful basis from which to explore how these PGCs and the photosynthesis itself impact the physiology and ecology of these bacteria.
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Affiliation(s)
- Juanita R. Avontuur
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - P. Markus Wilken
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Marike Palmer
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Martin P. A. Coetzee
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Tomasz Stępkowski
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW), Warszawa, Poland
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T. Steenkamp
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Nouwen N, Chaintreuil C, Fardoux J, Giraud E. A glutamate synthase mutant of Bradyrhizobium sp. strain ORS285 is unable to induce nodules on Nod factor-independent Aeschynomene species. Sci Rep 2021; 11:20910. [PMID: 34686745 PMCID: PMC8536739 DOI: 10.1038/s41598-021-00480-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/11/2021] [Indexed: 11/09/2022] Open
Abstract
The Bradyrhizobium sp. strain ORS285 is able to establish a nitrogen-fixing symbiosis with both Nod factor (NF) dependent and NF-independent Aeschynomene species. Here, we have studied the growth characteristics and symbiotic interaction of a glutamate synthase (GOGAT; gltD::Tn5) mutant of Bradyrhizobium ORS285. We show that the ORS285 gltD::Tn5 mutant is unable to use ammonium, nitrate and many amino acids as nitrogen source for growth and is unable to fix nitrogen under free-living conditions. Moreover, on several nitrogen sources, the growth rate of the gltB::Tn5 mutant was faster and/or the production of the carotenoid spirilloxanthin was much higher as compared to the wild-type strain. The absence of GOGAT activity has a drastic impact on the symbiotic interaction with NF-independent Aeschynomene species. With these species, inoculation with the ORS285 gltD::Tn5 mutant does not result in the formation of nodules. In contrast, the ORS285 gltD::Tn5 mutant is capable to induce nodules on NF-dependent Aeschynomene species, but these nodules were ineffective for nitrogen fixation. Interestingly, in NF-dependent and NF-independent Aeschynomene species inoculation with the ORS285 gltD::Tn5 mutant results in browning of the plant tissue at the site of the infection suggesting that the mutant bacteria induce plant defence responses.
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Affiliation(s)
- Nico Nouwen
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/Université de Montpellier/CIRAD - Campus de Baillarguet, Montpellier, France.
| | - Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/Université de Montpellier/CIRAD - Campus de Baillarguet, Montpellier, France
| | - Joel Fardoux
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/Université de Montpellier/CIRAD - Campus de Baillarguet, Montpellier, France
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRAE/Université de Montpellier/CIRAD - Campus de Baillarguet, Montpellier, France
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Bradyrhizobium diazoefficiens USDA110 Nodulation of Aeschynomene afraspera Is Associated with Atypical Terminal Bacteroid Differentiation and Suboptimal Symbiotic Efficiency. mSystems 2021; 6:6/3/e01237-20. [PMID: 33975972 PMCID: PMC8125078 DOI: 10.1128/msystems.01237-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Legume-rhizobium symbiosis is a major ecological process in the nitrogen cycle, responsible for the main input of fixed nitrogen into the biosphere. The efficiency of this symbiosis relies on the coevolution of the partners. Legume plants can form root organs called nodules where they house intracellular symbiotic rhizobium bacteria. Within nodule cells, rhizobia differentiate into bacteroids, which fix nitrogen for the benefit of the plant. Depending on the combination of host plants and rhizobial strains, the output of rhizobium-legume interactions varies from nonfixing associations to symbioses that are highly beneficial for the plant. Bradyrhizobium diazoefficiens USDA110 was isolated as a soybean symbiont, but it can also establish a functional symbiotic interaction with Aeschynomene afraspera. In contrast to soybean, A. afraspera triggers terminal bacteroid differentiation, a process involving bacterial cell elongation, polyploidy, and increased membrane permeability, leading to a loss of bacterial viability while plants increase their symbiotic benefit. A combination of plant metabolomics, bacterial proteomics, and transcriptomics along with cytological analyses were used to study the physiology of USDA110 bacteroids in these two host plants. We show that USDA110 establishes a poorly efficient symbiosis with A. afraspera despite the full activation of the bacterial symbiotic program. We found molecular signatures of high levels of stress in A. afraspera bacteroids, whereas those of terminal bacteroid differentiation were only partially activated. Finally, we show that in A. afraspera, USDA110 bacteroids undergo atypical terminal differentiation hallmarked by the disconnection of the canonical features of this process. This study pinpoints how a rhizobium strain can adapt its physiology to a new host and cope with terminal differentiation when it did not coevolve with such a host. IMPORTANCE Legume-rhizobium symbiosis is a major ecological process in the nitrogen cycle, responsible for the main input of fixed nitrogen into the biosphere. The efficiency of this symbiosis relies on the coevolution of the partners. Some, but not all, legume plants optimize their return on investment in the symbiosis by imposing on their microsymbionts a terminal differentiation program that increases their symbiotic efficiency but imposes a high level of stress and drastically reduces their viability. We combined multi-omics with physiological analyses to show that the symbiotic couple formed by Bradyrhizobium diazoefficiens USDA110 and Aeschynomene afraspera, in which the host and symbiont did not evolve together, is functional but displays a low symbiotic efficiency associated with a disconnection of terminal bacteroid differentiation features.
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de Matos GF, Rouws LFM, Simões-Araújo JL, Baldani JI. Evolution and function of nitrogen fixation gene clusters in sugarcane associated Bradyrhizobium strains. Environ Microbiol 2021; 23:6148-6162. [PMID: 33928743 DOI: 10.1111/1462-2920.15533] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 12/01/2022]
Abstract
Bradyrhizobium spp. are well known to mediate biological nitrogen fixation (BNF) as microsymbionts inhabiting nodules on leguminous plants. However, they may also contribute to plant growth via free-living N2 fixation (FLNF) in association with non-legumes. Notably, several Bradyrhizobium strains from sugarcane roots display FLNF activity. Among them, Bradyrhizobium sacchari is a legume symbiotic species, whereas strains AG48 and M12 are non-symbiotic. In the present study, a phylogenomic approach was applied to study peculiarities of these and other Bradyrhizobium strains with respect to N fixation (nif) gene content in order to reveal genetic features that enable FNLF in Bradyrhizobium spp. All FLNF strains carry an ancestral 'non-symbiotic' nif-gene cluster (NSC). B. sacchari also contains a second 'symbiotic' nif-gene cluster (SC), a characteristic observed in only three of 156 evaluated genomes. B. sacchari stood out and presented a high level of sequence divergence between individual nif-gene homologues and we discuss scenarios for the evolutionary origin of these clusters. The transcript level of NSC nifH gene increased during FLNF, when compared to symbiotic conditions. The data suggest that sugarcane roots harbor diverse Bradyrhizobium spp. that are genetically adapted to a dynamic environment where leguminous and non-leguminous host plants are alternately available.
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Affiliation(s)
- Gustavo Feitosa de Matos
- Curso de Pós-graduação em Fitotecnia, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465 km 7, Seropédica, RJ, 23891-000, Brazil
| | | | | | - José Ivo Baldani
- Embrapa Agrobiologia, Rodovia BR 465 km 7, Seropédica, RJ, 23891-000, Brazil
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7
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Quilbé J, Lamy L, Brottier L, Leleux P, Fardoux J, Rivallan R, Benichou T, Guyonnet R, Becana M, Villar I, Garsmeur O, Hufnagel B, Delteil A, Gully D, Chaintreuil C, Pervent M, Cartieaux F, Bourge M, Valentin N, Martin G, Fontaine L, Droc G, Dereeper A, Farmer A, Libourel C, Nouwen N, Gressent F, Mournet P, D'Hont A, Giraud E, Klopp C, Arrighi JF. Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium-legume symbiosis. Nat Commun 2021; 12:829. [PMID: 33547303 PMCID: PMC7864950 DOI: 10.1038/s41467-021-21094-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023] Open
Abstract
Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding remains limited. To overcome such limitations, we conduct genetic studies of nodulation in Aeschynomene evenia, supported by the development of a genome sequence for A. evenia and transcriptomic resources for 10 additional Aeschynomene spp. Comparative analysis of symbiotic genes substantiates singular mechanisms in the early and late nodulation steps. A forward genetic screen also shows that AeCRK, coding a receptor-like kinase, and the symbiotic signaling genes AePOLLUX, AeCCamK, AeCYCLOPS, AeNSP2, and AeNIN are required to trigger both root and stem nodulation. This work demonstrates the utility of the A. evenia model and provides a cornerstone to unravel mechanisms underlying the rhizobium-legume symbiosis.
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Affiliation(s)
- Johan Quilbé
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Léo Lamy
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Laurent Brottier
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Philippe Leleux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Thomas Benichou
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Rémi Guyonnet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Irene Villar
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Olivier Garsmeur
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Bárbara Hufnagel
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Amandine Delteil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Marjorie Pervent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Fabienne Cartieaux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Mickaël Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nicolas Valentin
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Loïc Fontaine
- BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, F-34398, Montpellier, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Alexis Dereeper
- Institut de Recherche pour le Développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, France
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Cyril Libourel
- LRSV, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Frédéric Gressent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Pierre Mournet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Christophe Klopp
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France.
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8
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Nouwen N, Arrighi JF, Gully D, Giraud E. RibBX of Bradyrhizobium ORS285 Plays an Important Role in Intracellular Persistence in Various Aeschynomene Host Plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:88-99. [PMID: 33226302 DOI: 10.1094/mpmi-07-20-0209-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bradyrhizobium ORS285 forms a nitrogen-fixating symbiosis with both Nod factor (NF)-dependent and NF-independent Aeschynomene spp. The Bradyrhizobium ORS285 ribBA gene encodes for a putative bifunctional enzyme with 3,4-dihydroxybutanone phosphate (3,4-DHBP) synthase and guanosine triphosphate (GTP) cyclohydrolase II activities, catalyzing the initial steps in the riboflavin biosynthesis pathway. In this study, we show that inactivating the ribBA gene does not cause riboflavin auxotrophy under free-living conditions and that, as shown for RibBAs from other bacteria, the GTP cyclohydrolase II domain has no enzymatic activity. For this reason, we have renamed the annotated ribBA as ribBX. Because we were unable to identify other ribBA or ribA and ribB homologs in the genome of Bradyrhizobium ORS285, we hypothesize that the ORS285 strain can use unconventional enzymes or an alternative pathway for the initial steps of riboflavin biosynthesis. Inactivating ribBX has a drastic impact on the interaction of Bradyrhizobium ORS285 with many of the tested Aeschynomene spp. In these Aeschynomene spp., the ORS285 ribBX mutant is able to infect the plant host cells but the intracellular infection is not maintained and the nodules senesce early. This phenotype can be complemented by reintroduction of the 3,4-DHBP synthase domain alone. Our results indicate that, in Bradyrhizobium ORS285, the RibBX protein is not essential for riboflavin biosynthesis under free-living conditions and we hypothesize that its activity is needed to sustain riboflavin biosynthesis under certain symbiotic conditions.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Nico Nouwen
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, SupAgro, INRAE, University of Montpellier, Montpellier, France
| | - Jean-Francois Arrighi
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, SupAgro, INRAE, University of Montpellier, Montpellier, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, SupAgro, INRAE, University of Montpellier, Montpellier, France
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, SupAgro, INRAE, University of Montpellier, Montpellier, France
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9
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Cai W, Ou F, Staehelin C, Dai W. Bradyrhizobium sp. strain ORS278 promotes rice growth and its quorum sensing system is required for optimal root colonization. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:656-666. [PMID: 32929871 DOI: 10.1111/1758-2229.12885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/10/2020] [Indexed: 05/25/2023]
Abstract
Many Gram-negative bacteria communicate by using homoserine lactones (HSLs) as quorum sensing (QS) signals in a cell density-dependent manner. In addition to fatty acyl-HSL (acyl-HSL) signals, certain strains, most of them associated with plants, produce non-canonical aryl-HSLs such as cinnamoyl-HSL. However, the role of aryl-HSL in endophytic associations remained elusive. Bradyrhizobium sp. strain ORS278 possesses a LuxI-LuxR type QS system and produces cinnamoyl-HSL as a QS signal. Here, we report that strain ORS278 promotes growth of domesticated rice (Oryza sativa). QS mutants unable to produce cinnamoyl-HSL exhibited reduced plant-growth promoting activity in comparison to the parent strain ORS278. Likewise, the QS mutants were impaired in their ability to colonize rice roots. These findings suggest that genes controlled by cinnamoyl-HSL play an important role in the association between rice and ORS278. However, biofilm production was not visibly altered in these mutants. In conclusion, our study highlights the importance of aryl-HSLs in endophytic plant-bacteria interactions.
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Affiliation(s)
- Wenjie Cai
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510006, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Fuwen Ou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510006, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
| | - Christian Staehelin
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Bioresources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Weijun Dai
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510006, China
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, 510642, China
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10
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Hashimoto S, Goto K, Pyromyou P, Songwattana P, Greetatorn T, Tittabutr P, Boonkerd N, Teaumroong N, Uchiumi T. Type III Secretion System of Bradyrhizobium sp. SUTN9-2 Obstructs Symbiosis with Lotus spp. Microbes Environ 2020; 35. [PMID: 32611950 PMCID: PMC7511788 DOI: 10.1264/jsme2.me20041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The rhizobial type III secretion system secretes effector proteins into host plant cells, which may either promote or inhibit symbiosis with legumes. We herein demonstrated that the type III secretion system of Bradyrhizobium sp. SUTN9-2 obstructed symbiosis with Lotus japonicus Miyakojima, L. japonicus Gifu, and Lotus burttii. A mutant of SUTN9-2 that is unable to secrete effector proteins showed better nodulation and plant growth promotion than wild-type SUTN9-2 when paired with these Lotus spp. We propose that SUTN9-2 is a useful strain for understanding the mechanisms by which effector proteins obstruct symbiosis between Bradyrhizobium and Lotus spp.
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Affiliation(s)
- Shun Hashimoto
- Graduate School of Science and Engineering, Kagoshima University
| | - Kohki Goto
- Graduate School of Science and Engineering, Kagoshima University
| | - Pongdet Pyromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Teerana Greetatorn
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University
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11
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Aeschynomene indica-Nodulating Rhizobia Lacking Nod Factor Synthesis Genes: Diversity and Evolution in Shandong Peninsula, China. Appl Environ Microbiol 2019; 85:AEM.00782-19. [PMID: 31562167 DOI: 10.1128/aem.00782-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/04/2019] [Indexed: 02/02/2023] Open
Abstract
Aeschynomene indica is a semiaquatic legume that forms both stem and root nodules with rhizobia. Some A. indica rhizobia (AIRs) have been reported to nodulate the host using a Nod factor-independent pathway and possess photosynthetic abilities. To investigate the diversity and community structure of AIRs in China, a total of 300 rhizobial isolates were acquired from the root and stem nodules of A. indica grown at 4 sites in Shandong Peninsula, China. Nineteen representative strains were selected according to their recA phylogeny. With further classification in comparison with reference strains, 10 Bradyrhizobium genospecies were defined based on the 16S rRNA gene phylogeny and multilocus sequence analysis (MLSA) of housekeeping genes (HKGs) recA, atpD, glnII, dnaK, gyrB, and rpoB In addition, 6 genospecies were found only in China. No nodulation gene (nodA, nodB, nodC, or nodZ) was detected in the AIRs isolates by PCR amplification and Southern blotting. Phylogenetic analysis of nifH and the photosynthesis-related gene pufLM revealed their common origins. All representative strains formed root nodules, but only 9 representative strains for 4 genospecies formed stem nodules on A. indica, indicating that the stem nodulation process of A. indica is limited to some strains. The nucleotide diversity and recombination events of the HKGs, as well as nifH and pufLM genes, showed that mutation contributes more than recombination in evolution. The distribution of dominant AIR genospecies was mainly affected by available nitrogen, organic carbon, total nitrogen, and pH. Our study helps to characterize the diversity and evolution of AIRs.IMPORTANCE Aeschynomene indica rhizobia (AIRs) can form both root and stem nodules via Nod factor-independent processes, which distinguishes them from other rhizobia. This study systematically uncovered the diversity and community composition of A. indica rhizobia distributed in eastern China. Our results reclassified all the A. indica rhizobia across the world and represent a useful contribution to evaluating the diversity and distribution of the symbiont. The presence of novel genospecies specifically distributed in China enriched the A. indica rhizobia resources and provided insight into the geographic distribution of rhizobia. The phylogenetic relationship between nifH and pufLM of A. indica rhizobia across the world provides insight into the evolution of their nitrogen fixation and photosynthetic abilities.
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12
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Nouwen N, Gargani D, Giraud E. The Modification of the Flavonoid Naringenin by Bradyrhizobium sp. Strain ORS285 Changes the nod Genes Inducer Function to a Growth Stimulator. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1517-1525. [PMID: 31265361 DOI: 10.1094/mpmi-05-19-0133-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
As inducers of nodulation (nod) genes, flavonoids play an important role in the symbiotic interaction between rhizobia and legumes. However, in addition to the control of expression of nod genes, many other effects of flavonoids on rhizobial cells have been described. Here, we show that the flavonoid naringenin stimulates the growth of the photosynthetic Bradyrhizobium sp. strain ORS285. This growth-stimulating effect was still observed for strain ORS285 with nodD1, nodD2, or the naringenin-degrading fde operon deleted. Phenotypic microarray analysis indicates that in cells grown in the presence of naringenin, the glycerol and fatty acid metabolism is activated. Moreover, electron microscopic and enzymatic analyses show that polyhydroxy alkanoate metabolism is altered in cells grown in the presence of naringenin. Although strain ORS285 was able to degrade naringenin, a fraction was converted into an intensely yellow-colored molecule with an m/z (+) of 363.0716. Further analysis indicates that this molecule is a hydroxylated and O-methylated form of naringenin. In contrast to naringenin, this derivative did not induce nod gene expression, but it did stimulate the growth of strain ORS285. We hypothesize that the growth stimulation and metabolic changes induced by naringenin are part of a mechanism to facilitate the colonization and infection of naringenin-exuding host plants.
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Affiliation(s)
- Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | | | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
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13
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Hashimoto S, Wongdee J, Songwattana P, Greetatorn T, Goto K, Tittabutr P, Boonkerd N, Teaumroong N, Uchiumi T. Homocitrate Synthase Genes of Two Wide-Host-Range Bradyrhizobium Strains are Differently Required for Symbiosis Depending on Host Plants. Microbes Environ 2019; 34:393-401. [PMID: 31597890 PMCID: PMC6934396 DOI: 10.1264/jsme2.me19078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The nifV gene encodes homocitrate synthase, the enzyme that catalyzes the formation of homocitrate, which is essential for arranging the FeMo-cofactor in the catalytic center of nitrogenase. Some host plants, such as Lotus japonicus, supply homocitrate to their symbionts, in this case, Mesorhizobium loti, which lacks nifV. In contrast, Bradyrhizobium ORS285, a symbiont of Aeschynomene cross-inoculation (CI) groups 2 and 3, requires nifV for symbiosis with Aeschynomene species that belong to CI group 3, and some species belonging to CI group 2. However, it currently remains unclear whether rhizobial nifV is required for symbiosis with Aeschynomene species belonging to CI group 1 or with other legumes. We generated nifV-disruption (ΔnifV) mutants of two wide-host-range rhizobia, Bradyrhizobium SUTN9-2 and DOA9, to investigate whether they require nifV for symbiosis. Both ΔnifV mutant strains showed significantly less nitrogenase activity in a free-living state than the respective wild-type strains. The symbiotic phenotypes of SUTN9-2, DOA9, and their ΔnifV mutants were examined with four legumes, Aeschynomene americana, Stylosanthes hamata, Indigofera tinctoria, and Desmodium tortuosum. nifV was required for the efficient symbiosis of SUTN9-2 with A. americana (CI group 1), but not for that of DOA9. SUTN9-2 established symbiosis with all three other legumes; nifV was required for symbiosis with I. tinctoria and D. tortuosum. These results suggest that, in addition to Aeschynomene CI groups 2 and 3, CI group 1 and several other legumes require the rhizobial nifV for symbiosis.
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Affiliation(s)
- Shun Hashimoto
- Graduate School of Science and Engineering, Kagoshima University
| | - Jenjira Wongdee
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Teerana Greetatorn
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Kohki Goto
- Graduate School of Science and Engineering, Kagoshima University
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University
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14
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Bromfield ESP, Cloutier S, Nguyen HDT. Description and complete genome sequence of Bradyrhizobium amphicarpaeae sp. nov., harbouring photosystem and nitrogen-fixation genes. Int J Syst Evol Microbiol 2019; 69:2841-2848. [PMID: 31251718 DOI: 10.1099/ijsem.0.003569] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated 39S1MBT, isolated from a root nodule of a soybean plant that had been inoculated with root-zone soil of Amphicarpaea bracteata (hog peanut) growing in Canada, was previously characterized and placed in a novel lineage within the genus Bradyrhizobium. The taxonomic status of strain 39S1MBT was verified by genomic and phenotypic analyses. Phylogenetic analyses of individual and concatenated protein-encoding gene sequences (atpD, glnII, recA, gyrB and rpoB) placed 39S1MBT in a lineage distinct from named species. Data for sequence similarities of concatenated genes relative to type strains of named species supported the phylogenetic data. Average nucleotide identity values of genome sequences (84.5-91.7 %) were well below the threshold value for bacterial species circumscription. Based on these data, Bradyrhizobium ottawaense OO99T and Bradyrhizobium shewense ERR11T are close relatives of 39S1MBT. The complete genome of 39S1MBT consists of a single 7.04 Mbp chromosome without a symbiosis island; G+C content is 64.7 mol%. Present in the genome are key photosystem and nitrogen-fixation genes, but not nodulation and type III secretion system genes. Sequence analysis of the nitrogen fixation gene, nifH, placed 39S1MBT in a novel lineage distinct from named Bradyrhizobium species. Data for phenotypic tests including growth characteristics and carbon source utilization supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium amphicarpaeae sp. nov. is proposed with 39S1MBT (=LMG 29934T=HAMBI 3680T) as the type strain.
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Affiliation(s)
- Eden S P Bromfield
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
| | - Hai D T Nguyen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario K1A OC6, Canada
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15
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Brottier L, Chaintreuil C, Simion P, Scornavacca C, Rivallan R, Mournet P, Moulin L, Lewis GP, Fardoux J, Brown SC, Gomez-Pacheco M, Bourges M, Hervouet C, Gueye M, Duponnois R, Ramanankierana H, Randriambanona H, Vandrot H, Zabaleta M, DasGupta M, D’Hont A, Giraud E, Arrighi JF. A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses. BMC PLANT BIOLOGY 2018; 18:333. [PMID: 30518342 PMCID: PMC6282307 DOI: 10.1186/s12870-018-1567-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/23/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Among semi-aquatic species of the legume genus Aeschynomene, some have the property of being nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the synthesis of Nod factors. Knowledge of the specificities underlying this Nod-independent symbiosis has been gained from the model legume Aeschynomene evenia but our understanding remains limited due to the lack of comparative genetics with related taxa using a Nod factor-dependent process. To fill this gap, we combined different approaches to perform a thorough comparative analysis in the genus Aeschynomene. RESULTS This study significantly broadened previous taxon sampling, including in allied genera, in order to construct a comprehensive phylogeny. In the phylogenetic tree, five main lineages were delineated, including a novel lineage, the Nod-independent clade and another one containing a polytomy that comprised several Aeschynomene groups and all the allied genera. This phylogeny was matched with data on chromosome number, genome size and low-copy nuclear gene sequences to reveal the diploid species and a polytomy containing mostly polyploid taxa. For these taxa, a single allopolyploid origin was inferred and the putative parental lineages were identified. Finally, nodulation tests with different Bradyrhizobium strains revealed new nodulation behaviours and the diploid species outside of the Nod-independent clade were compared for their experimental tractability and genetic diversity. CONCLUSIONS The extended knowledge of the genetics and biology of the different lineages sheds new light of the evolutionary history of the genus Aeschynomene and they provide a solid framework to exploit efficiently the diversity encountered in Aeschynomene legumes. Notably, our backbone tree contains all the species that are diploid and it clarifies the genetic relationships between the Nod-independent clade and the Nod-dependent lineages. This study enabled the identification of A. americana and A. patula as the most suitable species to undertake a comparative genetic study of the Nod-independent and Nod-dependent symbioses.
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Affiliation(s)
- Laurent Brottier
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Paul Simion
- Institut des Sciences de l’Evolution (ISE-M), Université de Montpellier, CNRS, IRD, EPHE, 34095 Cedex 5 Montpellier, France
| | - Céline Scornavacca
- Institut des Sciences de l’Evolution (ISE-M), Université de Montpellier, CNRS, IRD, EPHE, 34095 Cedex 5 Montpellier, France
| | - Ronan Rivallan
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Pierre Mournet
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Lionel Moulin
- IRD, Interactions Plantes Microorganismes Environnement, UMR IPME, 34394 Montpellier, France
| | - Gwilym P. Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB UK
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Spencer C. Brown
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Mario Gomez-Pacheco
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Mickaël Bourges
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Catherine Hervouet
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Mathieu Gueye
- Laboratoire de Botanique, Institut Fondamental d’Afrique Noire, Ch. A. Diop, BP 206 Dakar, Sénégal
| | - Robin Duponnois
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l’Environnement/Centre National de Recherche sur l’Environnement, 101 Antananarivo, Madagascar
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l’Environnement/Centre National de Recherche sur l’Environnement, 101 Antananarivo, Madagascar
| | - Hervé Vandrot
- IAC, Laboratoire de Botanique et d’Ecologie Végétale Appliquée, UMR AMAP, 98825 Pouembout, Nouvelle-Calédonie France
| | - Maria Zabaleta
- Department of Biochemistry and Microbial Genomics, IIBCE, 11600 Montevideo, Uruguay
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata, 700019 India
| | - Angélique D’Hont
- CIRAD (Centre de Coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France
- AGAP,Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, 34060 Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, 34398 Montpellier, France
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16
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Chaintreuil C, Perrier X, Martin G, Fardoux J, Lewis GP, Brottier L, Rivallan R, Gomez-Pacheco M, Bourges M, Lamy L, Thibaud B, Ramanankierana H, Randriambanona H, Vandrot H, Mournet P, Giraud E, Arrighi JF. Naturally occurring variations in the nod-independent model legume Aeschynomene evenia and relatives: a resource for nodulation genetics. BMC PLANT BIOLOGY 2018; 18:54. [PMID: 29614957 PMCID: PMC5883870 DOI: 10.1186/s12870-018-1260-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 03/06/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Among semi-aquatic species of the legume genus Aeschynomene, some have the unique property of being root and stem-nodulated by photosynthetic Bradyrhizobium lacking the nodABC genes necessary for the production of Nod factors. These species provide an excellent biological system with which to explore the evolution of nodulation in legumes. Among them, Aeschynomene evenia has emerged as a model legume to undertake the genetic dissection of the so-called Nod-independent symbiosis. In addition to the genetic analysis of nodulation on a reference line, natural variation in a germplasm collection could also be surveyed to uncover genetic determinants of nodulation. To this aim, we investigated the patterns of genetic diversity in a collection of 226 Nod-independent Aeschynomene accessions. RESULTS A combination of phylogenetic analyses, comprising ITS and low-copy nuclear genes, along with cytogenetic experiments and artificial hybridizations revealed the richness of the Nod-independent Aeschynomene group with the identification of 13 diploid and 6 polyploid well-differentiated taxa. A set of 54 SSRs was used to further delineate taxon boundaries and to identify different genotypes. Patterns of microsatellite diversity also illuminated the genetic basis of the Aeschynomene taxa that were all found to be predominantly autogamous and with a predicted simple disomic inheritance, two attributes favorable for genetics. In addition, taxa displaying a pronounced genetic diversity, notably A. evenia, A. indica and A. sensitiva, were characterized by a clear geographically-based genetic structure and variations in root and stem nodulation. CONCLUSION A well-characterized germplasm collection now exists as a major genetic resource to thoroughly explore the natural variation of nodulation in response to different bradyrhizobial strains. Symbiotic polymorphisms are expected to be found notably in the induction of nodulation, in nitrogen fixation and also in stem nodulation. Subsequent genetic analysis and locus mapping will pave the way for the identification of the underlying genes through forward or reverse genetics. Such discoveries will significantly contribute to our understanding of the molecular mechanisms underpinning how some Aeschynomene species can be efficiently nodulated in a Nod-independent fashion.
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Affiliation(s)
- Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Xavier Perrier
- CIRAD, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Guillaume Martin
- CIRAD, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Gwilym P. Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Laurent Brottier
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Ronan Rivallan
- CIRAD, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Mario Gomez-Pacheco
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud. Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Mickaël Bourges
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud. Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Léo Lamy
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Béatrice Thibaud
- CIRAD, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l’Environnement/Centre National de Recherche sur l’Environnement, 101 Antananarivo, Madagascar
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l’Environnement/Centre National de Recherche sur l’Environnement, 101 Antananarivo, Madagascar
| | - Hervé Vandrot
- IAC, Laboratoire de Botanique et d’Ecologie Végétale Appliquée, UMR AMAP, 98825 Pouembout, Nouvelle-Calédonie, France
| | - Pierre Mournet
- CIRAD, Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, UMR AGAP, Campus de Lavalette, F-34398 Montpellier, France
- AGAP, Univ. Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR LSTM, Campus International de Baillarguet, F-34398 Montpellier, France
- LSTM, Univ. Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
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17
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Barrière Q, Guefrachi I, Gully D, Lamouche F, Pierre O, Fardoux J, Chaintreuil C, Alunni B, Timchenko T, Giraud E, Mergaert P. Integrated roles of BclA and DD-carboxypeptidase 1 in Bradyrhizobium differentiation within NCR-producing and NCR-lacking root nodules. Sci Rep 2017; 7:9063. [PMID: 28831061 PMCID: PMC5567381 DOI: 10.1038/s41598-017-08830-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/12/2017] [Indexed: 11/09/2022] Open
Abstract
Legumes harbor in their symbiotic nodule organs nitrogen fixing rhizobium bacteria called bacteroids. Some legumes produce Nodule-specific Cysteine-Rich (NCR) peptides in the nodule cells to control the intracellular bacterial population. NCR peptides have antimicrobial activity and drive bacteroids toward terminal differentiation. Other legumes do not produce NCR peptides and their bacteroids are not differentiated. Bradyrhizobia, infecting NCR-producing Aeschynomene plants, require the peptide uptake transporter BclA to cope with the NCR peptides as well as a specific peptidoglycan-modifying DD-carboxypeptidase, DD-CPase1. We show that Bradyrhizobium diazoefficiens strain USDA110 forms undifferentiated bacteroids in NCR-lacking soybean nodules. Unexpectedly, in Aeschynomene afraspera nodules the nitrogen fixing USDA110 bacteroids are hardly differentiated despite the fact that this host produces NCR peptides, suggesting that USDA110 is insensitive to the host peptide effectors and that nitrogen fixation can be uncoupled from differentiation. In agreement with the absence of bacteroid differentiation, USDA110 does not require its bclA gene for nitrogen fixing symbiosis with these two host plants. Furthermore, we show that the BclA and DD-CPase1 act independently in the NCR-induced morphological differentiation of bacteroids. Our results suggest that BclA is required to protect the rhizobia against the NCR stress but not to induce the terminal differentiation pathway.
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Affiliation(s)
- Quentin Barrière
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Ibtissem Guefrachi
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.,Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès University, Erriadh-Zrig, 6072, Gabès, Tunisia.,Université de Pau et des Pays de l'Adour, Pau, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Florian Lamouche
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Olivier Pierre
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.,Institut Sophia AgroBiotech, Sophia-Antipolis, France
| | - Joël Fardoux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Benoît Alunni
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Tatiana Timchenko
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Peter Mergaert
- Institute for Integrative Biology of the Cell, UMR9198, CNRS, Université Paris-Sud, CEA, Gif-sur-Yvette, France.
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18
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The role of rhizobial (NifV) and plant (FEN1) homocitrate synthases in Aeschynomene/photosynthetic Bradyrhizobium symbiosis. Sci Rep 2017; 7:448. [PMID: 28348373 PMCID: PMC5428708 DOI: 10.1038/s41598-017-00559-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 03/03/2017] [Indexed: 11/29/2022] Open
Abstract
In the most studied rhizobium-legume interactions, the host plant supplies the symbiont with homocitrate, an essential co-factor of the nitrogenase enzyme complex, via the expression of a nodule-specific homocitrate synthase FEN1. Photosynthetic bradyrhizobia interacting with Nod factor (NF) dependent and NF-independent Aeschynomene legumes are able to synthesize homocitrate themselves as they contain a nifV gene encoding a homocitrate synthase. Here, we show that in the model strain ORS285, nifV is required for free-living and symbiotic dinitrogen fixation with NF-independent Aeschynomene species. In contrast, in symbiosis with NF-dependent Aeschynomene species, the nifV requirement for efficient nitrogen fixation was found to be host plant dependent. Interestingly, orthologs of FEN1 were found in both NF-dependent and NF-independent Aeschynomene species. However, a high nodule specific induction of FEN1 expression was only observed in A. afraspera, a host plant in which nifV is not required for symbiotic dinitrogen fixation. These data indicate that efficient symbiotic nitrogen fixation in many of the tested Aeschynomene species requires rhizobial homocitrate synthesis. Considering that more than 10% of the fully sequenced rhizobium strains do contain a nifV gene, the Aeschynomene/photosynthetic Bradyrhizobium interaction is likely not the only rhizobium/legume symbiosis where rhizobial nifV expression is required.
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19
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Chaintreuil C, Gully D, Hervouet C, Tittabutr P, Randriambanona H, Brown SC, Lewis GP, Bourge M, Cartieaux F, Boursot M, Ramanankierana H, D'Hont A, Teaumroong N, Giraud E, Arrighi JF. The evolutionary dynamics of ancient and recent polyploidy in the African semiaquatic species of the legume genus Aeschynomene. THE NEW PHYTOLOGIST 2016; 211:1077-1091. [PMID: 27061605 DOI: 10.1111/nph.13956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/04/2016] [Indexed: 06/05/2023]
Abstract
The legume genus Aeschynomene is notable in the ability of certain semiaquatic species to develop nitrogen-fixing stem nodules. These species are distributed in two clades. In the first clade, all the species are characterized by the use of a unique Nod-independent symbiotic process. In the second clade, the species use a Nod-dependent symbiotic process and some of them display a profuse stem nodulation as exemplified in the African Aeschynomene afraspera. To facilitate the molecular analysis of the symbiotic characteristics of such legumes, we took an integrated molecular and cytogenetic approach to track occurrences of polyploidy events and to analyze their impact on the evolution of the African species of Aeschynomene. Our results revealed two rounds of polyploidy: a paleopolyploid event predating the African group and two neopolyploid speciations, along with significant chromosomal variations. Hence, we found that A. afraspera (8x) has inherited the contrasted genomic properties and the stem-nodulation habit of its parental lineages (4x). This study reveals a comprehensive picture of African Aeschynomene diversification. It notably evidences a history that is distinct from the diploid Nod-independent clade, providing clues for the identification of the specific determinants of the Nod-dependent and Nod-independent symbiotic processes, and for comparative analysis of stem nodulation.
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Affiliation(s)
- Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, 34398, Montpellier, France
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l'Environnement/Centre National de Recherche sur l'Environnement, Antananarivo, 101, Madagascar
| | - Spencer C Brown
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91 198, Gif-sur-Yvette, France
| | - Gwilym P Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK
| | - Mickaël Bourge
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91 198, Gif-sur-Yvette, France
| | - Fabienne Cartieaux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Marc Boursot
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l'Environnement/Centre National de Recherche sur l'Environnement, Antananarivo, 101, Madagascar
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, 34398, Montpellier, France
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Jean-François Arrighi
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
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20
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Nouwen N, Fardoux J, Giraud E. NodD1 and NodD2 Are Not Required for the Symbiotic Interaction of Bradyrhizobium ORS285 with Nod-Factor-Independent Aeschynomene Legumes. PLoS One 2016; 11:e0157888. [PMID: 27315080 PMCID: PMC4912097 DOI: 10.1371/journal.pone.0157888] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/06/2016] [Indexed: 11/23/2022] Open
Abstract
Photosynthetic Bradyrhizobium strain ORS285 forms nitrogen-fixing nodules on the roots and stems of tropical aquatic legumes of the Aeschynomene genus. Depending on the Aeschynomene species, this symbiotic interaction does or does not rely on the synthesis of Nod-factors (NFs). However, whether during the interaction of Bradyrhizobium ORS285 with NF-independent Aeschynomene species the nod genes are expressed and if the general regulator NodD plays a symbiotic role is unknown. Expression studies showed that in contrast to the interaction with the NF-dependent Aeschynomene species, A. afraspera, the Bradyrhizobium ORS285 nod genes are not induced upon contact with the NF-independent host plant A. indica. Mutational analysis of the two nodD genes present in ORS285, showed that deletion of nodD1 and nodD2 did not affect the symbiotic interaction between Bradyrhizobium ORS285 and A. indica whereas the deletions had an effect on the symbiotic interaction with A. afraspera plants. In addition, when the expression of nod genes was artificially induced by adding naringenin to the plant growth medium, the nodulation of A. indica by Bradyrhizobium ORS285 is delayed and resulted in lower nodule numbers.
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Affiliation(s)
- Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/ SupAgro/INRA/ UM2 /CIRAD, Montpellier, France
- * E-mail:
| | - Joel Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/ SupAgro/INRA/ UM2 /CIRAD, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/ SupAgro/INRA/ UM2 /CIRAD, Montpellier, France
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21
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Fabre S, Gully D, Poitout A, Patrel D, Arrighi JF, Giraud E, Czernic P, Cartieaux F. Nod Factor-Independent Nodulation in Aeschynomene evenia Required the Common Plant-Microbe Symbiotic Toolkit. PLANT PHYSIOLOGY 2015; 169:2654-64. [PMID: 26446590 PMCID: PMC4677901 DOI: 10.1104/pp.15.01134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/04/2015] [Indexed: 05/06/2023]
Abstract
Nitrogen fixation in the legume-rhizobium symbiosis is a crucial area of research for more sustainable agriculture. Our knowledge of the plant cascade in response to the perception of bacterial Nod factors has increased in recent years. However, the discovery that Nod factors are not involved in the Aeschynomene-Bradyrhizobium spp. interaction suggests that alternative molecular dialogues may exist in the legume family. We evaluated the conservation of the signaling pathway common to other endosymbioses using three candidate genes: Ca(2+)/Calmodulin-Dependent Kinase (CCaMK), which plays a central role in cross signaling between nodule organogenesis and infection processes; and Symbiosis Receptor Kinase (SYMRK) and Histidine Kinase1 (HK1), which act upstream and downstream of CCaMK, respectively. We showed that CCaMK, SYMRK, and HK1 are required for efficient nodulation in Aeschynomene evenia. Our results demonstrate that CCaMK and SYMRK are recruited in Nod factor-independent symbiosis and, hence, may be conserved in all vascular plant endosymbioses described so far.
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Affiliation(s)
- Sandrine Fabre
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Djamel Gully
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Arthur Poitout
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Delphine Patrel
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Jean-François Arrighi
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Eric Giraud
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Pierre Czernic
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
| | - Fabienne Cartieaux
- Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, F-34398 Montpellier cedex 5, France (S.F., D.G., A.P., D.P., J.-F.A., E.G., F.C.);CIRAD, Laboratoire des Interactions Plantes Microorganismes Environnement, Unité Mixte de Recherche Institut de Recherche pour le Développement/Centre de Coopération Internationale en Recherche Agronomique pour le Développement/Université de Montpellier F-34394 Montpellier cedex 5, France (S.F.); andUniversité de Montpellier, F-34095 Montpellier cedex 5, France (A.P., P.C.)
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22
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Guefrachi I, Pierre O, Timchenko T, Alunni B, Barrière Q, Czernic P, Villaécija-Aguilar JA, Verly C, Bourge M, Fardoux J, Mars M, Kondorosi E, Giraud E, Mergaert P. Bradyrhizobium BclA Is a Peptide Transporter Required for Bacterial Differentiation in Symbiosis with Aeschynomene Legumes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:1155-66. [PMID: 26106901 DOI: 10.1094/mpmi-04-15-0094-r] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Nodules of legume plants are highly integrated symbiotic systems shaped by millions of years of evolution. They harbor nitrogen-fixing rhizobium bacteria called bacteroids. Several legume species produce peptides called nodule-specific cysteine-rich (NCR) peptides in the symbiotic nodule cells which house the bacteroids. NCR peptides are related to antimicrobial peptides of innate immunity. They induce the endosymbionts into a differentiated, enlarged, and polyploid state. The bacterial symbionts, on their side, evolved functions for the response to the NCR peptides. Here, we identified the bclA gene of Bradyrhizobium sp. strains ORS278 and ORS285, which is required for the formation of differentiated and functional bacteroids in the nodules of the NCR peptide-producing Aeschynomene legumes. The BclA ABC transporter promotes the import of NCR peptides and provides protection against the antimicrobial activity of these peptides. Moreover, BclA can complement the role of the related BacA transporter of Sinorhizobium meliloti, which has a similar symbiotic function in the interaction with Medicago legumes.
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Affiliation(s)
- Ibtissem Guefrachi
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- 2 Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Olivier Pierre
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Tatiana Timchenko
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Benoît Alunni
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Quentin Barrière
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Pierre Czernic
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | | | - Camille Verly
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Mickaël Bourge
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Joël Fardoux
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Mohamed Mars
- 2 Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Eva Kondorosi
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- 4 Institute of Biochemistry, Hungarian Academy of Sciences, Biological Research Centre, Szeged, Hungary
| | - Eric Giraud
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Peter Mergaert
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
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23
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Czernic P, Gully D, Cartieaux F, Moulin L, Guefrachi I, Patrel D, Pierre O, Fardoux J, Chaintreuil C, Nguyen P, Gressent F, Da Silva C, Poulain J, Wincker P, Rofidal V, Hem S, Barrière Q, Arrighi JF, Mergaert P, Giraud E. Convergent Evolution of Endosymbiont Differentiation in Dalbergioid and Inverted Repeat-Lacking Clade Legumes Mediated by Nodule-Specific Cysteine-Rich Peptides. PLANT PHYSIOLOGY 2015; 169:1254-65. [PMID: 26286718 PMCID: PMC4587450 DOI: 10.1104/pp.15.00584] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 08/17/2015] [Indexed: 05/21/2023]
Abstract
Nutritional symbiotic interactions require the housing of large numbers of microbial symbionts, which produce essential compounds for the growth of the host. In the legume-rhizobium nitrogen-fixing symbiosis, thousands of rhizobium microsymbionts, called bacteroids, are confined intracellularly within highly specialized symbiotic host cells. In Inverted Repeat-Lacking Clade (IRLC) legumes such as Medicago spp., the bacteroids are kept under control by an arsenal of nodule-specific cysteine-rich (NCR) peptides, which induce the bacteria in an irreversible, strongly elongated, and polyploid state. Here, we show that in Aeschynomene spp. legumes belonging to the more ancient Dalbergioid lineage, bacteroids are elongated or spherical depending on the Aeschynomene spp. and that these bacteroids are terminally differentiated and polyploid, similar to bacteroids in IRLC legumes. Transcriptome, in situ hybridization, and proteome analyses demonstrated that the symbiotic cells in the Aeschynomene spp. nodules produce a large diversity of NCR-like peptides, which are transported to the bacteroids. Blocking NCR transport by RNA interference-mediated inactivation of the secretory pathway inhibits bacteroid differentiation. Together, our results support the view that bacteroid differentiation in the Dalbergioid clade, which likely evolved independently from the bacteroid differentiation in the IRLC clade, is based on very similar mechanisms used by IRLC legumes.
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Affiliation(s)
- Pierre Czernic
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Djamel Gully
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Fabienne Cartieaux
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Lionel Moulin
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Ibtissem Guefrachi
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Delphine Patrel
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Olivier Pierre
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Joël Fardoux
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Clémence Chaintreuil
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Phuong Nguyen
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Frédéric Gressent
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Corinne Da Silva
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Julie Poulain
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Patrick Wincker
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Valérie Rofidal
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Sonia Hem
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Quentin Barrière
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Jean-François Arrighi
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Peter Mergaert
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
| | - Eric Giraud
- Université de Montpellier, F-34095 Montpellier cedex 5, France (P.C.);Institut de Recherche pour le Développement, Laboratoire des Symbioses Tropicales et Méditerranéennes, Unité Mixte de Recherche Institut de Recherche pour le Développement/SupAgro/Institut National de la Recherche Agronomique/Université de Montpellier/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Campus International de Baillarguet, 34398 Montpellier cedex 5, France (D.G., F.C., L.M., D.P., J.F., C.C., P.N., F.G., J.-F.A., E.G.);Institute for Integrative Biology of the Cell, Unité Mixte de Recherche 9198, Centre National de la Recherche Scientifique/Université Paris-Sud/Commissariat à l'Energie Atomique, 91198 Gif-sur-Yvette, France (I.G., O.P., Q.B., P.M.);Commissariat à l'Energie Atomique, Direction des Sciences du Vivant, Institut de Génomique, Génoscope, 91000 Evry, France (C.D.S., J.P., P.W.); andLaboratoire de Protéomique Fonctionnelle, Institut National de la Recherche Agronomique, Unité de Recherche 1199, 34060 Montpellier, France (V.R., S.H.)
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The intracellular Scots pine shoot symbiont Methylobacterium extorquens DSM13060 aggregates around the host nucleus and encodes eukaryote-like proteins. mBio 2015; 6:mBio.00039-15. [PMID: 25805725 PMCID: PMC4453540 DOI: 10.1128/mbio.00039-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Endophytes are microbes that inhabit plant tissues without any apparent signs of infection, often fundamentally altering plant phenotypes. While endophytes are typically studied in plant roots, where they colonize the apoplast or dead cells, Methylobacterium extorquens strain DSM13060 is a facultatively intracellular symbiont of the meristematic cells of Scots pine (Pinus sylvestris L.) shoot tips. The bacterium promotes host growth and development without the production of known plant growth-stimulating factors. Our objective was to examine intracellular colonization by M. extorquens DSM13060 of Scots pine and sequence its genome to identify novel molecular mechanisms potentially involved in intracellular colonization and plant growth promotion. Reporter construct analysis of known growth promotion genes demonstrated that these were only weakly active inside the plant or not expressed at all. We found that bacterial cells accumulate near the nucleus in intact, living pine cells, pointing to host nuclear processes as the target of the symbiont’s activity. Genome analysis identified a set of eukaryote-like functions that are common as effectors in intracellular bacterial pathogens, supporting the notion of intracellular bacterial activity. These include ankyrin repeats, transcription factors, and host-defense silencing functions and may be secreted by a recently imported type IV secretion system. Potential factors involved in host growth include three copies of phospholipase A2, an enzyme that is rare in bacteria but implicated in a range of plant cellular processes, and proteins putatively involved in gibberellin biosynthesis. Our results describe a novel endophytic niche and create a foundation for postgenomic studies of a symbiosis with potential applications in forestry and agriculture. All multicellular eukaryotes host communities of essential microbes, but most of these interactions are still poorly understood. In plants, bacterial endophytes are found inside all tissues. M. extorquens DSM13060 occupies an unusual niche inside cells of the dividing shoot tissues of a pine and stimulates seedling growth without producing cytokinin, auxin, or other plant hormones commonly synthesized by plant-associated bacteria. Here, we tracked the bacteria using a fluorescent tag and confocal laser scanning microscopy and found that they localize near the nucleus of the plant cell. This prompted us to sequence the genome and identify proteins that may affect host growth by targeting processes in the host cytoplasm and nucleus. We found many novel genes whose products may modulate plant processes from within the plant cell. Our results open up new avenues to better understand how bacteria assist in plant growth, with broad implications for plant science, forestry, and agriculture.
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Preferential association of endophytic bradyrhizobia with different rice cultivars and its implications for rice endophyte evolution. Appl Environ Microbiol 2015; 81:3049-61. [PMID: 25710371 DOI: 10.1128/aem.04253-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/17/2015] [Indexed: 11/20/2022] Open
Abstract
Plant colonization by bradyrhizobia is found not only in leguminous plants but also in nonleguminous species such as rice. To understand the evolution of the endophytic symbiosis of bradyrhizobia, the effect of the ecosystems of rice plantations on their associations was investigated. Samples were collected from various rice (Oryza sativa) tissues and crop rotational systems. The rice endophytic bradyrhizobia were isolated on the basis of oligotrophic properties, selective medium, and nodulation on siratro (Macroptilium atropurpureum). Six bradyrhizobial strains were obtained exclusively from rice grown in a crop rotational system. The isolates were separated into photosynthetic bradyrhizobia (PB) and nonphotosynthetic bradyrhizobia (non-PB). Thai bradyrhizobial strains promoted rice growth of Thai rice cultivars better than the Japanese bradyrhizobial strains. This implies that the rice cultivars possess characteristics that govern rice-bacterium associations. To examine whether leguminous plants in a rice plantation system support the persistence of rice endophytic bradyrhizobia, isolates were tested for legume nodulation. All PB strains formed symbioses with Aeschynomene indica and Aeschynomene evenia. On the other hand, non-PB strains were able to nodulate Aeschynomene americana, Vigna radiata, and M. atropurpureum but unable to nodulate either A. indica or A. evenia. Interestingly, the nodABC genes of all of these bradyrhizobial strains seem to exhibit low levels of similarity to those of Bradyrhizobium diazoefficiens USDA110 and Bradyrhizobium sp. strain ORS285. From these results, we discuss the evolution of the plant-bradyrhizobium association, including nonlegumes, in terms of photosynthetic lifestyle and nod-independent interactions.
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Berrabah F, Bourcy M, Cayrel A, Eschstruth A, Mondy S, Ratet P, Gourion B. Growth conditions determine the DNF2 requirement for symbiosis. PLoS One 2014; 9:e91866. [PMID: 24632747 PMCID: PMC3954807 DOI: 10.1371/journal.pone.0091866] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 02/17/2014] [Indexed: 11/18/2022] Open
Abstract
Rhizobia and legumes are able to interact in a symbiotic way leading to the development of root nodules. Within nodules, rhizobia fix nitrogen for the benefit of the plant. These interactions are efficient because spectacularly high densities of nitrogen fixing rhizobia are maintained in the plant cells. DNF2, a Medicago truncatula gene has been described as required for nitrogen fixation, bacteroid's persistence and to prevent defense-like reactions in the nodules. This manuscript shows that a Rhizobium mutant unable to differentiate is not sufficient to trigger defense-like reactions in this organ. Furthermore, we show that the requirement of DNF2 for effective symbiosis can be overcome by permissive growth conditions. The dnf2 knockout mutants grown in vitro on agarose or Phytagel as gelling agents are able to produce nodules fixing nitrogen with the same efficiency as the wild-type. However, when agarose medium is supplemented with the plant defense elicitor ulvan, the dnf2 mutant recovers the fix- phenotype. Together, our data show that plant growth conditions impact the gene requirement for symbiotic nitrogen fixation and suggest that they influence the symbiotic suppression of defense reactions in nodules.
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Affiliation(s)
- Fathi Berrabah
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif sur Yvette, France
| | - Marie Bourcy
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif sur Yvette, France
| | - Anne Cayrel
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif sur Yvette, France
| | - Alexis Eschstruth
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif sur Yvette, France
| | - Samuel Mondy
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif sur Yvette, France
| | - Pascal Ratet
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif sur Yvette, France
- * E-mail:
| | - Benjamin Gourion
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, Gif sur Yvette, France
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Arrighi JF, Chaintreuil C, Cartieaux F, Cardi C, Rodier-Goud M, Brown SC, Boursot M, D'Hont A, Dreyfus B, Giraud E. Radiation of the Nod-independent Aeschynomene relies on multiple allopolyploid speciation events. THE NEW PHYTOLOGIST 2014; 201:1457-1468. [PMID: 24237245 DOI: 10.1111/nph.12594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 10/08/2013] [Indexed: 06/02/2023]
Abstract
• The semi-aquatic legumes belonging to the genus Aeschynomene constitute a premium system for investigating the origin and evolution of unusual symbiotic features such as stem nodulation and the presence of a Nod-independent infection process. This latter apparently arose in a single Aeschynomene lineage. But how this unique Nod-independent group then radiated is not yet known. • We have investigated the role of polyploidy in Aeschynomene speciation via a case study of the pantropical A. indica and then extended the analysis to the other Nod-independent species. For this, we combined SSR genotyping, genome characterization through flow cytometry, chromosome counting, FISH and GISH experiments, molecular phylogenies using ITS and single nuclear gene sequences, and artificial hybridizations. • These analyses demonstrate the existence of an A. indica polyploid species complex comprising A. evenia (C. Wright) (2n = 2x = 20), A. indica L. s.s. (2n = 4x = 40) and a new hexaploid form (2n = 6x = 60). This latter contains the two genomes present in the tetraploid (A. evenia and A. scabra) and another unidentified genome. Two other species, A. pratensis and A. virginica, are also shown to be of allopolyploid origin. • This work reveals multiple hybridization/polyploidization events, thus highlighting a prominent role of allopolyploidy in the radiation of the Nod-independent Aeschynomene.
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Affiliation(s)
- Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Fabienne Cartieaux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - C Cardi
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, TA-A 108/03, 34398, Montpellier Cedex 5, France
| | - M Rodier-Goud
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, TA-A 108/03, 34398, Montpellier Cedex 5, France
| | - Spencer C Brown
- CNRS, IBiSA Imagerie Gif et Imagif BioCell, Institut des Sciences du Végétal, UPR 2355, Avenue de la Terrasse, 91198, Gif-sur-Yvette, France
| | - Marc Boursot
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, TA-A 108/03, 34398, Montpellier Cedex 5, France
| | - Bernard Dreyfus
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, TA A-82/J, 34398, Montpellier Cedex 5, France
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Delmotte N, Mondy S, Alunni B, Fardoux J, Chaintreuil C, Vorholt JA, Giraud E, Gourion B. A proteomic approach of bradyrhizobium/aeschynomene root and stem symbioses reveals the importance of the fixA locus for symbiosis. Int J Mol Sci 2014; 15:3660-70. [PMID: 24590127 PMCID: PMC3975360 DOI: 10.3390/ijms15033660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 11/28/2022] Open
Abstract
Rhizobia are soil bacteria that are able to form symbiosis with plant hosts of the legume family. These associations result in the formation of organs, called nodules in which bacteria fix atmospheric nitrogen to the benefit of the plant. Most of our knowledge on the metabolism and the physiology of the bacteria during symbiosis derives from studying roots nodules of terrestrial plants. Here we used a proteomics approach to investigate the bacterial physiology of photosynthetic Bradyrhizobium sp. ORS278 during the symbiotic process with the semi aquatical plant Aeschynomene indica that forms root and stem nodules. We analyzed the proteomes of bacteria extracted from each type of nodule. First, we analyzed the bacteroid proteome at two different time points and found only minor variation between the bacterial proteomes of 2-week- and 3-week-old nodules. High conservation of the bacteroid proteome was also found when comparing stem nodules and root nodules. Among the stem nodule specific proteins were those related to the phototrophic ability of Bradyrhizobium sp. ORS278. Furthermore, we compared our data with those obtained during an extensive genetic screen previously published. The symbiotic role of four candidate genes which corresponding proteins were found massively produced in the nodules but not identified during this screening was examined. Mutant analysis suggested that in addition to the EtfAB system, the fixA locus is required for symbiotic efficiency.
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Affiliation(s)
- Nathanael Delmotte
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
| | - Samuel Mondy
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France.
| | - Benoit Alunni
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France.
| | - Joel Fardoux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France.
| | - Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France.
| | - Julia A Vorholt
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France.
| | - Benjamin Gourion
- Institut des Sciences du Végétal, CNRS, 91198 Gif sur Yvette, France.
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Chaintreuil C, Arrighi JF, Giraud E, Miché L, Moulin L, Dreyfus B, Munive-Hernández JA, Villegas-Hernandez MDC, Béna G. Evolution of symbiosis in the legume genus Aeschynomene. THE NEW PHYTOLOGIST 2013; 200:1247-59. [PMID: 23879229 DOI: 10.1111/nph.12424] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 06/24/2013] [Indexed: 05/22/2023]
Abstract
Legumes in the genus Aeschynomene form nitrogen-fixing root nodules in association with Bradyrhizobium strains. Several aquatic and subaquatic species have the additional capacity to form stem nodules, and some of them can symbiotically interact with specific strains that do not produce the common Nod factors synthesized by all other rhizobia. The question of the emergence and evolution of these nodulation characters has been the subject of recent debate. We conducted a molecular phylogenetic analysis of 38 different Aeschynomene species. The phylogeny was reconstructed with both the chloroplast DNA trnL intron and the nuclear ribosomal DNA ITS/5.8S region. We also tested 28 Aeschynomene species for their capacity to form root and stem nodules by inoculating different rhizobial strains, including nodABC-containing strains (ORS285, USDA110) and a nodABC-lacking strain (ORS278). Maximum likelihood analyses resolved four distinct phylogenetic groups of Aeschynomene. We found that stem nodulation may have evolved several times in the genus, and that all Aeschynomene species using a Nod-independent symbiotic process clustered in the same clade. The phylogenetic approach suggested that Nod-independent nodulation has evolved once in this genus, and should be considered as a derived character, and this result is discussed with regard to previous experimental studies.
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Affiliation(s)
- Clémence Chaintreuil
- IRD/CIRAD/UM2/Supagro, Laboratoire des Symbioses Tropicales et Méditerranéennes, F-34398, Montpellier, France
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30
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Podlešáková K, Fardoux J, Patrel D, Bonaldi K, Novák O, Strnad M, Giraud E, Spíchal L, Nouwen N. Rhizobial synthesized cytokinins contribute to but are not essential for the symbiotic interaction between photosynthetic Bradyrhizobia and Aeschynomene legumes. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2013; 26:1232-8. [PMID: 23777431 DOI: 10.1094/mpmi-03-13-0076-r] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Cytokinins (CK) play an important role in the formation of nitrogen-fixing root nodules. It has been known for years that rhizobia secrete CK in the extracellular medium but whether they play a role in nodule formation is not known. We have examined this question using the photosynthetic Bradyrhizobium sp. strain ORS285 which is able to nodulate Aeschynomene afraspera and A. indica using a Nod-dependent or Nod-independent symbiotic process, respectively. CK profiling showed that the most abundant CK secreted by Bradyrhizobium sp. strain ORS285 are the 2MeS (2-methylthiol) derivatives of trans-zeatin and isopentenyladenine. In their pure form, these CK can activate legume CK receptors in vitro, and their exogenous addition induced nodule-like structures on host plants. Deletion of the miaA gene showed that transfer RNA degradation is the source of CK production in Bradyrhizobium sp. strain ORS285. In nodulation studies performed with A. indica and A. afraspera, the miaA mutant had a 1-day delay in nodulation and nitrogen fixation. Moreover, A. indica plants formed considerably smaller but more abundant nodules when inoculated with the miaA mutant. These data show that CK produced by Bradyrhizobium sp. strain ORS285 are not the key signal triggering nodule formation during the Nod-independent symbiosis but they contribute positively to nodule development in Aeschynomene plants.
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MESH Headings
- Acetylene/metabolism
- Bradyrhizobium/genetics
- Bradyrhizobium/metabolism
- Bradyrhizobium/physiology
- Cytokinins/metabolism
- Cytokinins/pharmacology
- Dose-Response Relationship, Drug
- Ethylenes/metabolism
- Fabaceae/drug effects
- Fabaceae/growth & development
- Fabaceae/metabolism
- Fabaceae/microbiology
- Genes, Reporter
- Nitrogen Fixation
- Nitrogenase
- Phylogeny
- Plant Growth Regulators/metabolism
- Plant Growth Regulators/pharmacology
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plant Root Nodulation
- Plant Roots/drug effects
- Plant Roots/growth & development
- Plant Roots/metabolism
- Plant Roots/microbiology
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Root Nodules, Plant/drug effects
- Root Nodules, Plant/growth & development
- Root Nodules, Plant/metabolism
- Root Nodules, Plant/microbiology
- Sequence Deletion
- Signal Transduction
- Symbiosis
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Isolation of optically targeted single bacteria by application of fluidic force microscopy to aerobic anoxygenic phototrophs from the phyllosphere. Appl Environ Microbiol 2013; 79:4895-905. [PMID: 23770907 DOI: 10.1128/aem.01087-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In their natural environment, bacteria often behave differently than they do under laboratory conditions. To gain insight into the physiology of bacteria in situ, dedicated approaches are required to monitor their adaptations and specific behaviors under environmental conditions. Optical microscopy is crucial for the observation of fundamental characteristics of bacteria, such as cell shape, size, and marker gene expression. Here, fluidic force microscopy (FluidFM) was exploited to isolate optically selected bacteria for subsequent identification and characterization. In this study, bacteriochlorophyll-producing bacteria, which can be visualized due to their characteristic fluorescence in the infrared range, were isolated from leaf washes. Bacterial communities from the phyllosphere were investigated because they harbor genes indicative of aerobic anoxygenic photosynthesis. Our data show that different species of Methylobacterium express their photosystem in planta, and they show a distinct pattern of bacteriochlorophyll production under laboratory conditions that is dependent on supplied carbon sources.
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Arrighi JF, Cartieaux F, Chaintreuil C, Brown S, Boursot M, Giraud E. Genotype delimitation in the Nod-independent model legume Aeschynomene evenia. PLoS One 2013; 8:e63836. [PMID: 23717496 PMCID: PMC3662760 DOI: 10.1371/journal.pone.0063836] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/18/2013] [Indexed: 11/28/2022] Open
Abstract
Research on the nitrogen-fixing symbiosis has been so far focused on two model legumes, Medicago truncatula and Lotus japonicus, which use a sophisticated infection process involving infection thread formation. However, in 25% of the legumes, the bacterial entry occurs more simply in an intercellular fashion. Among them, some semi-aquatic Aeschynomene species present the distinctive feature to form nitrogen-fixing nodules on both roots and stems following elicitation by photosynthetic bradyrhizobia that do not produce Nod factors. This interaction is believed to represent a living testimony of the ancestral state of the rhizobium-legume symbiosis. To decipher the molecular mechanisms of this unique Nod-independent nitrogen-fixing symbiosis, we previously identified A. evenia C. Wright as an appropriate model legume, because it displays all the requisites for molecular and genetic approaches. To advance the use of this new model legume species, here we characterized the intraspecific diversity found in A. evenia. For this, the accessions available in germplasm banks were collected and subjected to morphological investigations, genotyping with RAPD and SSR markers, molecular phylogenies using ITS and single nuclear gene sequences, and cross-compatibility tests. These combined analyses revealed an important intraspecific differentiation that led us to propose a new taxonomic classification for A. evenia comprising two subspecies and four varieties. The A. evenia ssp. evenia contains var. evenia and var. pauciciliata whereas A. evenia ssp. serrulata comprises var. serrulata and var. major. This study provides information to exploit efficiently the diversity encountered in A. evenia and proposes subsp. evenia as the most appropriate subspecies for future projects aimed at identifying plant determinants of the Nod-independent symbiotic process.
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Affiliation(s)
- Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, Montpellier, France
- * E-mail:
| | - Fabienne Cartieaux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Spencer Brown
- Centre national de la recherche scientifique, IBiSA Imagerie Gif et Imagif BioCell, Institut des Sciences du Végétal, UPR 2355, Gif-sur-Yvette, France
| | - Marc Boursot
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Campus International de Baillarguet, Montpellier, France
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Giraud E, Xu L, Chaintreuil C, Gargani D, Gully D, Sadowsky MJ. Photosynthetic Bradyrhizobium sp. strain ORS285 is capable of forming nitrogen-fixing root nodules on soybeans (Glycine max). Appl Environ Microbiol 2013; 79:2459-62. [PMID: 23354704 PMCID: PMC3623219 DOI: 10.1128/aem.03735-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 01/22/2013] [Indexed: 11/20/2022] Open
Abstract
The ability of photosynthetic Bradyrhizobium strains ORS285 and ORS278 to nodulate soybeans was investigated. While the nod gene-deficient ORS278 strain induced bumps only on soybean roots, the nod gene-containing ORS285 strain formed nitrogen-fixing nodules. However, symbiotic efficiencies differed drastically depending on both the soybean genotype used and the culture conditions tested.
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Affiliation(s)
- Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Lei Xu
- BioTechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota, USA
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Daniel Gargani
- CIRAD, UMR BGPI INRA/CIRAD/SUP AGRO, Campus International de Baillarguet, Montpellier, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Michael J. Sadowsky
- BioTechnology Institute and Department of Soil, Water, and Climate, University of Minnesota, St. Paul, Minnesota, USA
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Genome analysis suggests that the soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica. Appl Environ Microbiol 2013; 79:2542-51. [PMID: 23396330 DOI: 10.1128/aem.00009-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agromonas oligotrophica (Bradyrhizobium oligotrophicum) S58(T) is a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. Here, the complete genome sequence of S58 was determined. The S58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1% lacking nodABC genes and the typical symbiosis island. The genome showed a high level of similarity to the genomes of Bradyrhizobium sp. ORS278 and Bradyrhizobium sp. BTAi1, including nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant, Aeschynomene indica, in a Nod factor-independent manner. Although nonsymbiotic (brady)rhizobia are significant components of rhizobial populations in soil, we found that most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nif and fix) with A. indica were well conserved between the ORS278 and S58 genomes. Therefore, we performed inoculation experiments with five A. oligotrophica strains (S58, S42, S55, S72, and S80). Surprisingly, all five strains of A. oligotrophica formed effective nitrogen-fixing nodules on the roots and/or stems of A. indica, with differentiated bacteroids. Nonsymbiotic (brady)rhizobia are known to be significant components of rhizobial populations without a symbiosis island or symbiotic plasmids in soil, but the present results indicate that soil-dwelling A. oligotrophica generally possesses the ability to establish symbiosis with A. indica. Phylogenetic analyses suggest that Nod factor-independent symbiosis with A. indica is a common trait of nodABC- and symbiosis island-lacking strains within the members of the photosynthetic Bradyrhizobium clade, including A. oligotrophica.
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35
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Okubo T, Fukushima S, Minamisawa K. Evolution of Bradyrhizobium-Aeschynomene mutualism: living testimony of the ancient world or highly evolved state? PLANT & CELL PHYSIOLOGY 2012; 53:2000-2007. [PMID: 23161855 DOI: 10.1093/pcp/pcs150] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Until recently it had been well established that the initial step in legume-rhizobia symbioses was flavonoid and Nod factor (NF) signaling. However, NF-independent symbiosis is now known to occur between Bradyrhizobium and some species of Aeschynomene. Since its discovery, this unusual symbiotic system has attracted attention, and efforts have been devoted to revealing the NF-independent symbiotic mechanism, although the molecular mechanisms of nodule initiation still remain to be elucidated. NF-independent symbiosis is also interesting from the perspective of the evolution of legume-rhizobia symbiosis. In this mini-review, we discuss the current literature on the NF-independent symbiotic system in terms of phylogeny of the partners, infection, bacteroid differentiation, nodule structure, photosynthesis, endophytic features and model host plant. We also discuss NF-independent symbiosis, which is generally regarded to be more primitive than NF-dependent symbiosis, because the bacteria invade host plants via 'crack entry'. We propose three possible scenarios concerning the evolution of NF-independent symbiosis, which do not exclude the possibility that the NF-independent system evolved from NF-dependent interactions. Finally, we examine an interesting question on Bradyrhizobium-Aeschynomene mutualism, which is how do they initiate symbiosis without NF. Phylogenetic and genomic analyses of symbiotic and non-symbiotic bradyrhizobia with A. indica may be crucial to address the question, because of the very narrow phylogeny of natural endosymbionts without nod genes compared with other legume-rhizobia symbioses.
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Affiliation(s)
- Takashi Okubo
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, 980-8577 Japan
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36
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Arrighi JF, Cartieaux F, Brown SC, Rodier-Goud M, Boursot M, Fardoux J, Patrel D, Gully D, Fabre S, Chaintreuil C, Giraud E. Aeschynomene evenia, a model plant for studying the molecular genetics of the nod-independent rhizobium-legume symbiosis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:851-861. [PMID: 22475377 DOI: 10.1094/mpmi-02-12-0045-ta] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Research on the nitrogen-fixing symbiosis has been focused, thus far, on two model legumes, Medicago truncatula and Lotus japonicus, which use a sophisticated infection process involving infection thread formation. However, in 25% of the legumes, the bacterial entry occurs more simply in an intercellular fashion. Among them, some Aeschynomene spp. are nodulated by photosynthetic Bradyrhizobium spp. that do not produce Nod factors. This interaction is believed to represent a living testimony of the ancestral state of the rhizobium-legume symbiosis. To decipher the mechanisms of this Nod-independent process, we propose Aeschynomene evenia as a model legume because it presents all the characteristics required for genetic and molecular analysis. It is a short-perennial and autogamous species, with a diploid and relatively small genome (2n=20; 460 Mb/1C). A. evenia 'IRFL6945' is nodulated by the well-characterized photosynthetic Bradyrhizobium sp. strain ORS278 and is efficiently transformed by Agrobacterium rhizogenes. Aeschynomene evenia is genetically homozygous but polymorphic accessions were found. A manual hybridization procedure has been set up, allowing directed crosses. Therefore, it should be relatively straightforward to unravel the molecular determinants of the Nod-independent process in A. evenia. This should shed new light on the evolution of rhizobium-legume symbiosis and could have important agronomic implications.
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Affiliation(s)
- Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France.
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37
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Atamna-Ismaeel N, Finkel O, Glaser F, von Mering C, Vorholt JA, Koblížek M, Belkin S, Béjà O. Bacterial anoxygenic photosynthesis on plant leaf surfaces. ENVIRONMENTAL MICROBIOLOGY REPORTS 2012; 4:209-16. [PMID: 23757275 DOI: 10.1111/j.1758-2229.2011.00323.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The aerial surface of plants, the phyllosphere, is colonized by numerous bacteria displaying diverse metabolic properties that enable their survival in this specific habitat. Recently, we reported on the presence of microbial rhodopsin harbouring bacteria on the top of leaf surfaces. Here, we report on the presence of additional bacterial populations capable of harvesting light as a means of supplementing their metabolic requirements. An analysis of six phyllosphere metagenomes revealed the presence of a diverse community of anoxygenic phototrophic bacteria, including the previously reported methylobacteria, as well as other known and unknown phototrophs. The presence of anoxygenic phototrophic bacteria was also confirmed in situ by infrared epifluorescence microscopy. The microscopic enumeration correlated with estimates based on metagenomic analyses, confirming both the presence and high abundance of these microorganisms in the phyllosphere. Our data suggest that the phyllosphere contains a phylogenetically diverse assemblage of phototrophic species, including some yet undescribed bacterial clades that appear to be phyllosphere-unique.
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Affiliation(s)
- Nof Atamna-Ismaeel
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem 91904, Israel Bioinformatics Knowledge Unit, Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel Faculty of Science, Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland Institute of Microbiology, Department of Phototrophic Microorganisms - ALGATECH, 379 81 Třeboň, Czech Republic
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38
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Okubo T, Tsukui T, Maita H, Okamoto S, Oshima K, Fujisawa T, Saito A, Futamata H, Hattori R, Shimomura Y, Haruta S, Morimoto S, Wang Y, Sakai Y, Hattori M, Aizawa SI, Nagashima KVP, Masuda S, Hattori T, Yamashita A, Bao Z, Hayatsu M, Kajiya-Kanegae H, Yoshinaga I, Sakamoto K, Toyota K, Nakao M, Kohara M, Anda M, Niwa R, Jung-Hwan P, Sameshima-Saito R, Tokuda SI, Yamamoto S, Yamamoto S, Yokoyama T, Akutsu T, Nakamura Y, Nakahira-Yanaka Y, Hoshino YT, Hirakawa H, Mitsui H, Terasawa K, Itakura M, Sato S, Ikeda-Ohtsubo W, Sakakura N, Kaminuma E, Minamisawa K. Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs. Microbes Environ 2012; 27:306-15. [PMID: 22452844 PMCID: PMC4036050 DOI: 10.1264/jsme2.me11321] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 02/28/2012] [Indexed: 11/12/2022] Open
Abstract
Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.
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Affiliation(s)
- Takashi Okubo
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Takahiro Tsukui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Hiroko Maita
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Shinobu Okamoto
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Kenshiro Oshima
- Graduate School of Frontier Sciences, University of Tokyo, 5–1–5, Kashiwa-no-ha, Kashiwa, Chiba 277–8561, Japan
| | - Takatomo Fujisawa
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Akihiro Saito
- Department of Material and Life Science, Faculty of Science and Technology, Shizuoka Institute of Science and Technology 2200–2 Toyosawa, Fukuroi, Shizuoka 437–8555, Japan
| | - Hiroyuki Futamata
- Department of Material Science and Chemical Engineering, Shizuoka University, 3–5–1 Jyohoku, Naka-ku, Hamamatsu, Shizuoka, 432–8561, Japan
| | - Reiko Hattori
- Attic Lab, 1–6–2–401 Komegafukuro, Aobaku, Sendai, Miyagi 980–0813, Japan
| | - Yumi Shimomura
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
| | - Sho Morimoto
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Yong Wang
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Yoriko Sakai
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, University of Tokyo, 5–1–5, Kashiwa-no-ha, Kashiwa, Chiba 277–8561, Japan
| | - Shin-ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima 727–0023, Japan
| | - Kenji V. P. Nagashima
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
| | - Sachiko Masuda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Tsutomu Hattori
- Attic Lab, 1–6–2–401 Komegafukuro, Aobaku, Sendai, Miyagi 980–0813, Japan
| | - Akifumi Yamashita
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Zhihua Bao
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Masahito Hayatsu
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Hiromi Kajiya-Kanegae
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Ikuo Yoshinaga
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Kazunori Sakamoto
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271–8510, Japan
| | - Koki Toyota
- Tokyo University of Agriculture and Technology, 2–24–16, Naka, Koganei, Tokyo 184–8588, Japan
| | - Mitsuteru Nakao
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Mitsuyo Kohara
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Mizue Anda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Rieko Niwa
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Park Jung-Hwan
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Reiko Sameshima-Saito
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422–8529, Japan
| | - Shin-ichi Tokuda
- National Institute of Vegetable and Tea Sciences, National Agriculture and Food Research Organization, 3–1–1 Kannondai, Tsukuba, Ibaraki 305–8666, Japan
| | - Sumiko Yamamoto
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Syuji Yamamoto
- Department of Material Science and Chemical Engineering, Shizuoka University, 3–5–1 Jyohoku, Naka-ku, Hamamatsu, Shizuoka, 432–8561, Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo university of Agriculture and Technology, 3–5–8 Saiwaicho, Fuchu, Tokyo 183–8509, Japan
| | - Tomoko Akutsu
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Yasukazu Nakamura
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Yuka Nakahira-Yanaka
- Graduate School of Life and Environment Sciences, University of Tsukuba, 1–1–1 Ten-noudai, Tsukuba, Ibaraki 305–8572, Japan
| | - Yuko Takada Hoshino
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Hideki Hirakawa
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Kimihiro Terasawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Wakako Ikeda-Ohtsubo
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Natsuko Sakakura
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Eli Kaminuma
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
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International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Agrobacterium and Rhizobium: minutes of the meeting, 7 September 2010, Geneva, Switzerland. Int J Syst Evol Microbiol 2012; 61:3089-3093. [PMID: 22156799 DOI: 10.1099/ijs.0.036913-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Mornico D, Miché L, Béna G, Nouwen N, Verméglio A, Vallenet D, Smith AAT, Giraud E, Médigue C, Moulin L. Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia. Genes (Basel) 2011; 3:35-61. [PMID: 24704842 PMCID: PMC3899966 DOI: 10.3390/genes3010035] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/08/2011] [Accepted: 11/23/2011] [Indexed: 11/30/2022] Open
Abstract
Tropical aquatic species of the legume genus Aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (ND) or a nod gene-independent (NI) pathway to enter into symbiosis with legumes. In this study we used a comparative genomics approach on nine Aeschynomene symbionts representative of their phylogenetic diversity. We produced draft genomes of bradyrhizobial strains representing different phenotypes: five NI photosynthetic strains (STM3809, ORS375, STM3847, STM4509 and STM4523) in addition to the previously sequenced ORS278 and BTAi1 genomes, one photosynthetic strain ORS285 hosting both ND and NI symbiotic systems, and one NI non-photosynthetic strain (STM3843). Comparative genomics allowed us to infer the core, pan and dispensable genomes of Aeschynomene bradyrhizobia, and to detect specific genes and their location in Genomic Islands (GI). Specific gene sets linked to photosynthetic and NI/ND abilities were identified, and are currently being studied in functional analyses.
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Affiliation(s)
- Damien Mornico
- IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France.
| | - Lucie Miché
- IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France.
| | - Gilles Béna
- IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France.
| | - Nico Nouwen
- IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France.
| | - André Verméglio
- Laboratoire de Bioénergétique Cellulaire, CEA Cadarache, DSV, IBEB, 13108 Saint Paul-lez-Durance, France.
| | - David Vallenet
- LABGeM, CEA-Genoscope & CNRS-UMR8030, 91057 Evry, France.
| | | | - Eric Giraud
- IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France.
| | | | - Lionel Moulin
- IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France.
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Renier A, Maillet F, Fardoux J, Poinsot V, Giraud E, Nouwen N. Photosynthetic Bradyrhizobium Sp. strain ORS285 synthesizes 2-O-methylfucosylated lipochitooligosaccharides for nod gene-dependent interaction with Aeschynomene plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1440-7. [PMID: 21864045 DOI: 10.1094/mpmi-05-11-0104] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Bradyrhizobium sp. strain ORS285 is a photosynthetic bacterium that forms nitrogen-fixing nodules on the roots and stems of tropical aquatic legumes of the Aeschynomene genus. The symbiotic interaction of Bradyrhizobium sp. strain ORS285 with certain Aeschynomene spp. depends on the presence of nodulation (nod) genes whereas the interaction with other species is nod gene independent. To study the nod gene-dependent molecular dialogue between Bradyrhizobium sp. strain ORS285 and Aeschynomene spp., we used a nodB-lacZ reporter strain to monitor the nod gene expression with various flavonoids. The flavanones liquiritigenin and naringenin were found to be the strongest inducers of nod gene expression. Chemical analysis of the culture supernatant of cells grown in the presence of naringenin showed that the major Nod factor produced by Bradyrhizobium sp. strain ORS285 is a modified chitin pentasaccharide molecule with a terminal N-C(18:1)-glucosamine and with a 2-O-methyl fucose linked to C-6 of the reducing glucosamine. In this respect, the Bradyrhizobium sp. strain ORS285 Nod factor is the same as the major Nod factor produced by the nonphotosynthetic Bradyrhizobium japonicum USDA110 that nodulates the roots of soybean. This suggests a classic nod gene-dependent molecular dialogue between Bradyrhizobium sp. strain ORS285 and certain Aeschynomene spp. This is supported by the fact that B. japonicum USDA110 is able to form N(2)-fixing nodules on both the roots and stems of Aeschynomene afraspera.
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Affiliation(s)
- Adeline Renier
- Laboratoire des Symbioses Tropicales et Mediterraneennes, UMR IRD, Montpellier, France
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Bonaldi K, Gargani D, Prin Y, Fardoux J, Gully D, Nouwen N, Goormachtig S, Giraud E. Nodulation of Aeschynomene afraspera and A. indica by photosynthetic Bradyrhizobium Sp. strain ORS285: the nod-dependent versus the nod-independent symbiotic interaction. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1359-71. [PMID: 21995799 DOI: 10.1094/mpmi-04-11-0093] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Here, we present a comparative analysis of the nodulation processes of Aeschynomene afraspera and A. indica that differ in their requirement for Nod factors (NF) to initiate symbiosis with photosynthetic bradyrhizobia. The infection process and nodule organogenesis was examined using the green fluorescent protein-labeled Bradyrhizobium sp. strain ORS285 able to nodulate both species. In A. indica, when the NF-independent strategy is used, bacteria penetrated the root intercellularly between axillary root hairs and invaded the subepidermal cortical cells by invagination of the host cell wall. Whereas the first infected cortical cells collapsed, the infected ones immediately beneath kept their integrity and divided repeatedly to form the nodule. In A. afraspera, when the NF-dependent strategy is used, bacteria entered the plant through epidermal fissures generated by the emergence of lateral roots and spread deeper intercellularly in the root cortex, infecting some cortical cells during their progression. Whereas the infected cells of the lower cortical layers divided rapidly to form the nodule, the infected cells of the upper layers gave rise to an outgrowth in which the bacteria remained enclosed in large tubular structures. Together, two distinct modes of infection and nodule organogenesis coexist in Aeschynomene legumes, each displaying original features.
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Affiliation(s)
- Katia Bonaldi
- Laboratoire des Symbioses Tropicales et Mediterraneennes, Montpellier, France
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Gourion B, Delmotte N, Bonaldi K, Nouwen N, Vorholt JA, Giraud E. Bacterial RuBisCO is required for efficient Bradyrhizobium/Aeschynomene symbiosis. PLoS One 2011; 6:e21900. [PMID: 21750740 PMCID: PMC3130060 DOI: 10.1371/journal.pone.0021900] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 06/08/2011] [Indexed: 11/18/2022] Open
Abstract
Rhizobia and legume plants establish symbiotic associations resulting in the formation of organs specialized in nitrogen fixation. In such organs, termed nodules, bacteria differentiate into bacteroids which convert atmospheric nitrogen and supply the plant with organic nitrogen. As a counterpart, bacteroids receive carbon substrates from the plant. This rather simple model of metabolite exchange underlies symbiosis but does not describe the complexity of bacteroids' central metabolism. A previous study using the tropical symbiotic model Aeschynomene indica/photosynthetic Bradyrhizobium sp. ORS278 suggested a role of the bacterial Calvin cycle during the symbiotic process. Herein we investigated the role of two RuBisCO gene clusters of Bradyrhizobium sp. ORS278 during symbiosis. Using gene reporter fusion strains, we showed that cbbL1 but not the paralogous cbbL2 is expressed during symbiosis. Congruently, CbbL1 was detected in bacteroids by proteome analysis. The importance of CbbL1 for symbiotic nitrogen fixation was proven by a reverse genetic approach. Interestingly, despite its symbiotic nitrogen fixation defect, the cbbL1 mutant was not affected in nitrogen fixation activity under free living state. This study demonstrates a critical role for bacterial RuBisCO during a rhizobia/legume symbiotic interaction.
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Affiliation(s)
- Benjamin Gourion
- Laboratoire des Symbioses Tropicales et Méditerranéennes, SupAgro/Institut National de la Recherche Agronomique/Université Montpellier 2/Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier, France.
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Bonaldi K, Gherbi H, Franche C, Bastien G, Fardoux J, Barker D, Giraud E, Cartieaux F. The Nod factor-independent symbiotic signaling pathway: development of Agrobacterium rhizogenes-mediated transformation for the legume Aeschynomene indica. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:1537-44. [PMID: 21039272 DOI: 10.1094/mpmi-06-10-0137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The nitrogen-fixing symbiosis between Aeschynomene indica and photosynthetic bradyrhizobia is the only legume-rhizobium association described to date that does not require lipochito-oligosaccharide Nod factors (NF). To assist in deciphering the molecular basis of this NF-independent interaction, we have developed a protocol for Agrobacterium rhizogenes-mediated transformation of A. indica. The cotransformation frequency (79%), the nodulation efficiency of transgenic roots (90%), and the expression pattern of the 35S Cauliflower mosaic virus promoter in transgenic nodules were all comparable to those obtained for model legumes. We have made use of this tool to monitor the heterologous spatio-temporal expression of the pMtENOD11-β-glucuronidase fusion, a widely used molecular reporter for rhizobial infection and nodulation in both legumes and actinorhizal plants. While MtENOD11 promoter activation was not observed in A. indica roots prior to nodulation, strong reporter-gene expression was observed in the invaded cells of young nodules and in the cell layers bordering the central zone of older nodules. We conclude that pMtENOD11 expression can be used as an infection-related marker in A. indica and that Agrobacterium rhizogenes-mediated root transformation of Aeschynomene spp. will be an invaluable tool for determining the molecular basis of the NF-independent symbiosis.
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Affiliation(s)
- Katia Bonaldi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France
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Bonaldi K, Gourion B, Fardoux J, Hannibal L, Cartieaux F, Boursot M, Vallenet D, Chaintreuil C, Prin Y, Nouwen N, Giraud E. Large-scale transposon mutagenesis of photosynthetic Bradyrhizobium sp. strain ORS278 reveals new genetic loci putatively important for nod-independent symbiosis with Aeschynomene indica. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:760-70. [PMID: 20459315 DOI: 10.1094/mpmi-23-6-0760] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Photosynthetic Bradyrhizobium strains possess the unusual ability to form nitrogen-fixing nodules on a specific group of legumes in the absence of Nod factors. To obtain insight into the bacterial genes involved in this Nod-independent symbiosis, we screened 15,648 Tn5 mutants of Bradyrhizobium sp. strain ORS278 for clones affected in root symbiosis with Aeschynomene indica. From the 268 isolated mutants, 120 mutants were altered in nodule development (Ndv(-)) and 148 mutants were found to be deficient in nitrogen fixation (Fix(-)). More than 50% of the Ndv(-) mutants were found to be altered in purine biosynthesis, strengthening the previous hypothesis of a symbiotic role of a bacterial purine derivative during the Nod-independent symbiosis. The other Ndv(-) mutants were auxotrophic for pyrimidines and amino acids (leucine, glutamate, and lysine) or impaired in genes encoding proteins of unknown function. The Fix(-) mutants were found to be affected in a wide variety of cellular processes, including both novel (n = 56) and previously identified (n = 31) genes important in symbiosis. Among the novel genes identified, several were involved in the Calvin cycle, suggesting that CO(2) fixation could play an important role during this symbiosis.
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Affiliation(s)
- Katia Bonaldi
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR-IRD/SupAgro/INRA/UM2/CIRAD, F-34398 Montpellier, France
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Giraud E, Lavergne J, Verméglio A. Characterization of Bacteriophytochromes from Photosynthetic Bacteria. Methods Enzymol 2010; 471:135-59. [DOI: 10.1016/s0076-6879(10)71009-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Miché L, Moulin L, Chaintreuil C, Contreras-Jimenez JL, Munive-Hernández JA, Del Carmen Villegas-Hernandez M, Crozier F, Béna G. Diversity analyses of Aeschynomene symbionts in Tropical Africa and Central America reveal that nod-independent stem nodulation is not restricted to photosynthetic bradyrhizobia. Environ Microbiol 2009; 12:2152-64. [PMID: 21966910 DOI: 10.1111/j.1462-2920.2009.02090.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tropical aquatic legumes of the genus Aeschynomene are unique in that they can be stem-nodulated by photosynthetic bradyrhizobia. Moreover, a recent study demonstrated that two Aeschynomene indica symbionts lack canonical nod genes, thereby raising questions about the distribution of such atypical symbioses among rhizobial-legume interactions. Population structure and genomic diversity were compared among stem-nodulating bradyrhizobia isolated from various Aeschynomene species of Central America and Tropical Africa. Phylogenetic analyses based on the recA gene and whole-genome amplified fragment length polymorphism (AFLP) fingerprints on 110 bacterial strains highlighted that all the photosynthetic strains form a separate cluster among bradyrhizobia, with no obvious structuring according to their geographical or plant origins. Nod-independent symbiosis was present in all sampling areas and seemed to be linked to Aeschynomene host species. However, it was not strictly dependent on photosynthetic ability, as exemplified by a newly identified cluster of strains that lacked canonical nod genes and efficiently stem-nodulated A. indica, but were not photosynthetic. Interestingly, the phenotypic properties of this new cluster of bacteria were reflected by their phylogenetical position, as being intermediate in distance between classical root-nodulatingBradyrhizobium spp. and photosynthetic ones. This result opens new prospects about stem-nodulating bradyrhizobial evolution.
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48
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Masson-Boivin C, Giraud E, Perret X, Batut J. Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes? Trends Microbiol 2009; 17:458-66. [PMID: 19766492 DOI: 10.1016/j.tim.2009.07.004] [Citation(s) in RCA: 422] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Revised: 07/06/2009] [Accepted: 07/13/2009] [Indexed: 11/27/2022]
Abstract
Rhizobia are phylogenetically disparate alpha- and beta-proteobacteria that have achieved the environmentally essential function of fixing atmospheric nitrogen (N(2)) in symbiosis with legumes. All rhizobia elicit the formation of root - or occasionally stem - nodules, plant organs dedicated to the fixation and assimilation of nitrogen. Bacterial colonization of these nodules culminates in a remarkable case of sustained intracellular infection in plants. Rhizobial phylogenetic diversity raised the question of whether these soil bacteria shared a common core of symbiotic genes. In this article, we review the cumulative evidence from recent genomic and genetic analyses pointing toward an unexpected variety of mechanisms that lead to symbiosis with legumes.
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Affiliation(s)
- Catherine Masson-Boivin
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR CNRS-INRA 2594/441, BP 52627, 31326 Castanet Tolosan Cedex, France.
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Jaubert M, Hannibal L, Fardoux J, Giraud E, Verméglio A. Identification of novel genes putatively involved in the photosystem synthesis of Bradyrhizobium sp. ORS 278. PHOTOSYNTHESIS RESEARCH 2009; 100:97-105. [PMID: 19452262 DOI: 10.1007/s11120-009-9433-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 05/04/2009] [Indexed: 05/27/2023]
Abstract
In aerobic anoxygenic phototrophs, oxygen is required for both the formation of the photosynthetic apparatus and an efficient cyclic electron transfer. Mutants of Bradyrhizobium sp. ORS278 affected in photosystem synthesis were selected by a bacteriochlorophyll fluorescence-based screening. Out of the 9,600 mutants of a random Tn5 insertion library, 50 clones, corresponding to insertions in 28 different genes, present a difference in fluorescence intensity compared to the WT. Besides enzymes and regulators known to be involved in photosystem synthesis, 14 novel components of the photosynthesis control are identified. Among them, two genes, hsIU and hsIV, encode components of a protein degradation complex, probably linked to the renewal of photosystem, an important issue in Bradyrhizobia which have to deal with harmful reactive oxygen species. The presence of homologs in non-photosynthetic bacteria for most of the regulatory genes identified during study suggests that they could be global regulators, as the RegA-RegB system.
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Affiliation(s)
- Marianne Jaubert
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, AGRO-M, INRA, UM2. TA A-82/J, Campus de Baillarguet, 34398, Montpellier Cedex 5, France
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Control of peripheral light-harvesting complex synthesis by a bacteriophytochrome in the aerobic photosynthetic bacterium Bradyrhizobium strain BTAi1. J Bacteriol 2008; 190:5824-31. [PMID: 18606738 DOI: 10.1128/jb.00524-08] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The recent sequence analysis of the photosynthetic and plant-symbiotic Bradyrhizobium sp. strain BTAi1 revealed the unexpected presence of a pucBA operon encoding the apoproteins of peripheral light-harvesting (LH) complexes. This pucBA operon is found close to a bacteriophytochrome gene (BphP3(B BTAi1)) and a two-component transcriptional regulator gene (TF(BTAi1) gene). In this study, we show that BphP3(B BTAi1) acts as a bona fide bacteriophytochrome and controls, according to light conditions, the expression of the pucBA operon found in its vicinity. This light regulatory pathway is very similar to the one previously described for chromo-BphP4(Rp) in Rhodopseudomonas palustris and conducts the synthesis of a peripheral LH complex. This LH complex presents a single absorption band at low temperature, centered at 803 nm. Fluorescence emission analysis of intact cells indicates that this peripheral LH complex does not act as an efficient light antenna. One putative function of this LH complex could be to evacuate excess light energy in order to protect Bradyrhizobium strain BTAi1, an aerobic anoxygenic photosynthetic bacterium, against photooxidative damage during photosynthesis.
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