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Rahman A, Manci M, Nadon C, Perez IA, Farsamin WF, Lampe MT, Le TH, Torres Martínez L, Weisberg AJ, Chang JH, Sachs JL. Competitive interference among rhizobia reduces benefits to hosts. Curr Biol 2023; 33:2988-3001.e4. [PMID: 37490853 DOI: 10.1016/j.cub.2023.06.081] [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: 01/23/2023] [Revised: 03/31/2023] [Accepted: 06/29/2023] [Indexed: 07/27/2023]
Abstract
The capacity of beneficial microbes to compete for host infection-and the ability of hosts to discriminate among them-introduces evolutionary conflict that is predicted to destabilize mutualism. We investigated fitness outcomes in associations between legumes and their symbiotic rhizobia to characterize fitness impacts of microbial competition. Diverse Bradyrhizobium strains varying in their capacity to fix nitrogen symbiotically with a common host plant, Acmispon strigosus, were tested in full-factorial coinoculation experiments involving 28 pairwise strain combinations. We analyzed the effects of interstrain competition and host discrimination on symbiotic-interaction outcomes by relativizing fitness proxies to clonally infected and uninfected controls. More than one thousand root nodules of coinoculated plants were genotyped to quantify strain occupancy, and the Bradyrhizobium strain genome sequences were analyzed to uncover the genetic bases of interstrain competition outcomes. Strikingly, interstrain competition favored a fast-growing, minimally beneficial rhizobia strain. Host benefits were significantly diminished in coinoculation treatments relative to expectations from clonally inoculated controls, consistent with competitive interference among rhizobia that reduced both nodulation and plant growth. Competition traits appear polygenic, linked with inter-strain allelopathic interactions in the rhizosphere. This study confirms that competition among strains can destabilize mutualism by favoring microbes that are superior in colonizing host tissues but provide minimal benefits to host plants. Moreover, our findings help resolve the paradox that despite efficient host control post infection, legumes nonetheless encounter rhizobia that vary in their nitrogen fixation.
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Affiliation(s)
- Arafat Rahman
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Max Manci
- Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA
| | - Cassandra Nadon
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Ivan A Perez
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Warisha F Farsamin
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Matthew T Lampe
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Tram H Le
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Lorena Torres Martínez
- Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, St. Mary's College of Maryland, St. Mary's City, MD 20686, USA
| | - Alexandra J Weisberg
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Jeff H Chang
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Joel L Sachs
- Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA; Department of Microbiology & Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA; Department of Evolution Ecology & Organismal Biology, University of California, Riverside, Riverside, CA 92521, USA.
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Cervantes L, Miranda-Sánchez F, Torres Tejerizo G, Romero D, Brom S. Plasmid pSfr64a and the symbiotic plasmid pSfr64b of Sinorhizobium fredii GR64 control each other's conjugative transfer through quorum-sensing elements. Plasmid 2019; 106:102443. [PMID: 31689451 DOI: 10.1016/j.plasmid.2019.102443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/29/2019] [Accepted: 09/17/2019] [Indexed: 11/27/2022]
Abstract
Rhizobia are nitrogen-fixing symbionts of plants. Their genomes frequently contain large plasmids, some of which are able to perform conjugative transfer. Plasmid pSfr64a from Sinorhizobium fredii GR64 is a conjugative plasmid, whose transfer is regulated by quorum sensing genes encoded by itself (traR64a, traI64a), in the symbiotic plasmid pSfr64b (traR64b, traI64b), and in the chromosome (ngrI). Also, transfer of pSfr64b requires quorum sensing elements encoded in this plasmid (traR64b, traI64b), in pSfr64a (traR64a), and in the chromosome (ngrI). These results demonstrate that pSfr64a and the symbiotic plasmid depend on each other for conjugative transfer. Plasmid pSfr64a from S. fredii GR64 is unable to transfer from the genomic background of Rhizobium etli CFN42. Our results show that the relaxase of pRet42a is able to process the oriT of pSfr64a, and viceversa, underlining their functional similarity and suggesting that in addition to the external signals, the "cytoplasmic environment" may pose a barrier to plasmid dissemination, even if the plasmids are functional in other aspects.
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Affiliation(s)
- Laura Cervantes
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Fabiola Miranda-Sánchez
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gonzalo Torres Tejerizo
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico; Instituto de Biotecnología y Biología Molecular (IBBM) - CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - David Romero
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.
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Hernández-Tamayo R, Torres-Tejerizo G, Brom S, Romero D. Site-specific bacterial chromosome engineering mediated by IntA integrase from Rhizobium etli. BMC Microbiol 2016; 16:133. [PMID: 27357704 PMCID: PMC4928290 DOI: 10.1186/s12866-016-0755-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/28/2016] [Indexed: 11/24/2022] Open
Abstract
Background The bacterial chromosome may be used to stably maintain foreign DNA in the mega-base range. Integration into the chromosome circumvents issues such as plasmid replication, stability, incompatibility, and copy number variance. The site-specific integrase IntA from Rhizobium etli CFN42 catalyzes a direct recombination between two specific DNA sites: attA and attD (23 bp). This recombination is stable. The aim of this work was to develop a R. etli derivative that may be used as recipient for the integration of foreign DNA in the chromosome, adapting the IntA catalyzed site-specific recombination system. Results To fulfill our aim, we designed a Rhizobium etli CFN42 derivative, containing a “landing pad” (LP) integrated into the chromosome. The LP sector consists of a green fluorescent protein gene under the control of the lacZ promoter and a spectinomycin resistance gene. Between the lacZ promoter and the GFP gene we inserted an IntA attachment site, which does not affect transcription from the lac promoter. Also, a mobilizable donor vector was generated, containing an attA site and a kanamycin resistance gene; to facilitate insertion of foreign DNA, this vector also contains a multicloning site. There are no promoters flanking the multicloning site. A biparental mating protocol was used to transfer the donor vector into the landing pad strain; insertion of the donor vector into the landing pad sector via IntA-mediated attA X attA recombination thereby interrupted the expression of the green fluorescent protein, generating site-specific cointegrants. Cointegrants were easily recognized by screening for antibiotic sensitivity and lack of GFP expression, and were obtained with an efficiency of 6.18 %. Conclusions Integration of foreign DNA in Rhizobium, lacking any similarity with the genome, can be easily achieved by IntA-mediated recombination. This protocol contains the mating and selection procedures for creating and isolating integrants.
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Affiliation(s)
- Rogelio Hernández-Tamayo
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, 62210, Cuernavaca, Morelos, Mexico
| | - Gonzalo Torres-Tejerizo
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, 62210, Cuernavaca, Morelos, Mexico.,Departamento de Ciencias Biológicas, Instituto de Biotecnología y Biología Molecular, UNLP, CCT-La Plata-CONICET, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Susana Brom
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, 62210, Cuernavaca, Morelos, Mexico
| | - David Romero
- Programa de Ingeniería Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Apartado Postal 565-A, 62210, Cuernavaca, Morelos, Mexico.
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