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Nitrogen-Fixing Symbiotic Paraburkholderia Species: Current Knowledge and Future Perspectives. NITROGEN 2023. [DOI: 10.3390/nitrogen4010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
A century after the discovery of rhizobia, the first Beta-proteobacteria species (beta-rhizobia) were isolated from legume nodules in South Africa and South America. Since then, numerous species belonging to the Burkholderiaceae family have been isolated. The presence of a highly branching lineage of nodulation genes in beta-rhizobia suggests a long symbiotic history. In this review, we focus on the beta-rhizobial genus Paraburkholderia, which includes two main groups: the South American mimosoid-nodulating Paraburkholderia and the South African predominantly papilionoid-nodulating Paraburkholderia. Here, we discuss the latest knowledge on Paraburkholderia nitrogen-fixing symbionts in each step of the symbiosis, from their survival in the soil, through the first contact with the legumes until the formation of an efficient nitrogen-fixing symbiosis in root nodules. Special attention is given to the strain P. phymatum STM815T that exhibits extraordinary features, such as the ability to: (i) enter into symbiosis with more than 50 legume species, including the agriculturally important common bean, (ii) outcompete other rhizobial species for nodulation of several legumes, and (iii) endure stressful soil conditions (e.g., high salt concentration and low pH) and high temperatures.
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Wulandari D, Tittabutr P, Songwattana P, Piromyou P, Teamtisong K, Boonkerd N, Boonchuen P, Teaumroong N. Symbiosis Contribution of Non-nodulating <i>Bradyrhizobium cosmicum</i> S23321 after Transferal of the Symbiotic Plasmid pDOA9. Microbes Environ 2022; 37. [PMID: 35676049 PMCID: PMC9530727 DOI: 10.1264/jsme2.me22008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The symbiotic properties of rhizobial bacteria are driven by the horizontal gene transfer of symbiotic genes, which are located in symbiosis islands or on plasmids. The symbiotic megaplasmid pDOA9 of Bradyrhizobium sp. DOA9, carrying the nod, nif, fix, and type three secretion system (T3SS) genes, has been conjugatively transferred to different Bradyrhizobium strains. In the present study, non-nodulating B. cosmicum S23321, which shows a close phylogenetic relationship with Bradyrhizobium sp. DOA9, but lacks symbiotic properties, was used to carry pDOA9 (annotated as chimeric S2:pDOA9). The results obtained showed that pDOA9 conferred symbiotic properties on S23321; however, nodulation phenotypes varied among the DOA9, chimeric ORS278:pDOA9, and S2:pDOA9 strains even though they all carried symbiotic pDOA9 plasmid. S23321 appeared to gain symbiotic nodulation from pDOA9 by processing nodulation genes and broadening the host range. The present results also showed the successful formation of active nodules in Arachis hypogaea (Dalbergoid) and Vigna radiata (Millitoid) by chimeric S2:pDOA9, while Crotalaria juncea (Genistoid) and Macroptilium atropurpureum (Millitoid) formed nodule-like structures. The formation of nodules and nodule-like structures occurred in a nod factor-dependent manner because the nod factor-lacking strain (S2:pDOA9ΩnodB) completely abolished nodulation in all legumes tested. Moreover, T3SS carried by S2:pDOA9 exerted negative effects on symbiosis with Crotalaria juncea, which was consistent with the results obtained on DOA9. T3SS exhibited symbiotic compatibility with V. radiata when nodulated by S23321. These outcomes implied that pDOA9 underwent changes during legume evolution that broadened host specificity and the compatibility of nodulation in a manner that was dependent on the chromosomal background of the recipient as well as legume host restrictions.
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Affiliation(s)
- Dyah Wulandari
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Pongpan Songwattana
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological Equipment, Suranaree University of Technology
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology
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Bellés-Sancho P, Lardi M, Liu Y, Hug S, Pinto-Carbó MA, Zamboni N, Pessi G. Paraburkholderia phymatum Homocitrate Synthase NifV Plays a Key Role for Nitrogenase Activity during Symbiosis with Papilionoids and in Free-Living Growth Conditions. Cells 2021; 10:cells10040952. [PMID: 33924023 PMCID: PMC8073898 DOI: 10.3390/cells10040952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 12/29/2022] Open
Abstract
Homocitrate is an essential component of the iron-molybdenum cofactor of nitrogenase, the bacterial enzyme that catalyzes the reduction of dinitrogen (N2) to ammonia. In nitrogen-fixing and nodulating alpha-rhizobia, homocitrate is usually provided to bacteroids in root nodules by their plant host. In contrast, non-nodulating free-living diazotrophs encode the homocitrate synthase (NifV) and reduce N2 in nitrogen-limiting free-living conditions. Paraburkholderia phymatum STM815 is a beta-rhizobial strain, which can enter symbiosis with a broad range of legumes, including papilionoids and mimosoids. In contrast to most alpha-rhizobia, which lack nifV, P. phymatum harbors a copy of nifV on its symbiotic plasmid. We show here that P. phymatum nifV is essential for nitrogenase activity both in root nodules of papilionoid plants and in free-living growth conditions. Notably, nifV was dispensable in nodules of Mimosa pudica despite the fact that the gene was highly expressed during symbiosis with all tested papilionoid and mimosoid plants. A metabolome analysis of papilionoid and mimosoid root nodules infected with the P. phymatum wild-type strain revealed that among the approximately 400 measured metabolites, homocitrate and other metabolites involved in lysine biosynthesis and degradation have accumulated in all plant nodules compared to uninfected roots, suggesting an important role of these metabolites during symbiosis.
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Affiliation(s)
- Paula Bellés-Sancho
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Martina Lardi
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Yilei Liu
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Sebastian Hug
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Marta Adriana Pinto-Carbó
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
| | - Nicola Zamboni
- ETH Zürich, Institute of Molecular Systems Biology, CH-8093 Zürich, Switzerland;
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland; (P.B.-S.); (M.L.); (Y.L.); (S.H.); (M.A.P.-C.)
- Correspondence: ; Tel.: +41-44-63-52904
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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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Greetatorn T, Hashimoto S, Maeda T, Fukudome M, Piromyou P, Teamtisong K, Tittabutr P, Boonkerd N, Kawaguchi M, Uchiumi T, Teaumroong N. Mechanisms of Rice Endophytic Bradyrhizobial Cell Differentiation and Its Role in Nitrogen Fixation. Microbes Environ 2020; 35:ME20049. [PMID: 32727975 PMCID: PMC7511792 DOI: 10.1264/jsme2.me20049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/23/2020] [Indexed: 11/25/2022] Open
Abstract
Bradyrhizobium sp. strain SUTN9-2 is a symbiotic and endophytic diazotrophic bacterium found in legume and rice plants and has the potential to promote growth. The present results revealed that SUTN9-2 underwent cell enlargement, increased its DNA content, and efficiently performed nitrogen fixation in response to rice extract. Some factors in rice extract induced the expression of cell cycle and nitrogen fixation genes. According to differentially expressed genes (DEGs) from the transcriptomic analysis, SUTN9-2 was affected by rice extract and the deletion of the bclA gene. The up-regulated DEGs encoding a class of oxidoreductases, which act with oxygen atoms and may have a role in controlling oxygen at an appropriate level for nitrogenase activity, followed by GroESL chaperonins are required for the function of nitrogenase. These results indicate that following its exposure to rice extract, nitrogen fixation by SUTN9-2 is induced by the collective effects of GroESL and oxidoreductases. The expression of the sensitivity to antimicrobial peptides transporter (sapDF) was also up-regulated, resulting in cell differentiation, even when bclA (sapDF) was mutated. This result implies similarities in the production of defensin-like antimicrobial peptides (DEFs) by rice and nodule-specific cysteine-rich (NCR) peptides in legume plants, which affect bacterial cell differentiation.
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Affiliation(s)
- Teerana Greetatorn
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Shun Hashimoto
- Graduate School of Science and Engineering, Kagoshima University, 890–0065 Kagoshima, Japan
| | - Taro Maeda
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444–8585 Aichi, Japan
| | - Mitsutaka Fukudome
- Graduate School of Science and Engineering, Kagoshima University, 890–0065 Kagoshima, Japan
| | - Pongdet Piromyou
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Kamonluck Teamtisong
- The Center for Scientific and Technological Equipment, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki 444–8585 Aichi, Japan
| | - Toshiki Uchiumi
- Graduate School of Science and Engineering, Kagoshima University, 890–0065 Kagoshima, Japan
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
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