|
1
|
Ma J, Peng Q, Chen S, Liu Z, Zhang W, Zhang C, Du X, Sun S, Peng W, Lei Z, Zhang L, Su P, Zhang D, Liu Y. Microbiome Migration from Soil to Leaves in Maize and Rice. Microorganisms 2025; 13:947. [PMID: 40284783 PMCID: PMC12029745 DOI: 10.3390/microorganisms13040947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2025] [Revised: 04/13/2025] [Accepted: 04/15/2025] [Indexed: 04/29/2025] Open
Abstract
The interactions between plants and microbes are essential for enhancing crop productivity. However, the mechanisms underlying host-specific microbiome migration and functional assembly remain poorly understood. In this study, microbiome migration from soil to leaves in rice (Oryza sativa) and maize (Zea mays) was analyzed through 16S rRNA sequencing and phenotypic assessments. When we used the same soil microbiome source to grow rice and maize, microbiota and functional traits were specifically enriched by maize in its phyllosphere and rhizosphere. This indicated that plants can selectively assemble microbiomes from a shared microbiota source. Therefore, 22 strains were isolated from the phyllospheres of rice and maize and used to construct a synthetic microbial community (SynCom). When the soil for rice and maize growth was inoculated with the SynCom, strains belonging to Bacillus were enriched in the maize phyllosphere compared to the rice phyllosphere. Additionally, a strain belonging to Rhizobium was enriched in the maize rhizosphere compared to the rice rhizosphere. These results suggest that plant species influence the migration of microbiota within their respective compartments. Compared with mock inoculation, SynCom inoculation significantly enhanced plant growth. When we compared the microbiomes, strains belonging to Achromobacter, which were assembled by both rice and maize, played a role in enhancing plant growth. Our findings underscore the importance of microbial migration dynamics and functional assembly in leveraging plant-microbe interactions for sustainable agriculture.
Collapse
Affiliation(s)
- Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Qianze Peng
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Silu Chen
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Weixing Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Chi Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Xiaohua Du
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Shue Sun
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Weiye Peng
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Ziling Lei
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Limei Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Pin Su
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Deyong Zhang
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| | - Yong Liu
- Longping Branch, College of Biology, Hunan University, Changsha 410082, China; (J.M.); (S.C.); (Z.L.); (Z.L.); (D.Z.)
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Academy of Agricultural Sciences, Changsha 410125, China; (Q.P.); (W.Z.); (W.P.); (L.Z.)
| |
Collapse
|
|
2
|
Chiba Y, Sasaki M, Masuda S, Shibata A, Shirasu K, Kawaharada Y. A Novel Rhizobium sp. Chiba-1 Strain Exhibits a Host Range for Nodule Symbiosis in Lotus Species. Microbes Environ 2023; 38:ME23056. [PMID: 38044128 PMCID: PMC10728632 DOI: 10.1264/jsme2.me23056] [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: 06/28/2023] [Accepted: 09/16/2023] [Indexed: 12/05/2023] Open
Abstract
Rhizobia are soil bacteria that induce the formation of nodules in the roots of leguminous plants for mutualistic establishment. Although the symbiotic mechanism between Lotus japonicus and its major symbiotic rhizobia, Mesorhizobium loti, has been extensively characterized, our understanding of symbiotic mechanisms, such as host specificity and host ranges, remains limited. In the present study, we isolated a novel Rhizobium strain capable of forming nodules on L. burttii from agricultural soil at Iwate prefecture in Japan. We conducted genomic and host range ana-lyses of various Lotus species. The results obtained revealed that the novel isolated Rhizobium sp. Chiba-1 was closely related to R. leguminosarum and had a wide host range that induced nodule development, including L. burttii and several L. japonicus wild-type accessions. However, L. japonicus Gifu exhibited an incompatible nodule phenotype. We also identified the formation of an epidermal infection threads that was dependent on the Lotus species and independent of nodule organ development. In conclusion, this newly isolated Rhizobium strain displays a distinct nodulation phenotype from Lotus species, and the results obtained herein provide novel insights into the functional mechanisms underlying host specificity and host ranges.
Collapse
Affiliation(s)
- Yuhei Chiba
- United Graduate School of Agricultural Sciences, Iwate University, 3–18–8, Ueda, Morioka, Iwate 020–8550, Japan
| | - Mao Sasaki
- Graduate School of Arts and Sciences, Iwate University, 3–18–8 Ueda, Morioka, Iwate 020–8550, Japan
| | - Sachiko Masuda
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Arisa Shibata
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Yasuyuki Kawaharada
- United Graduate School of Agricultural Sciences, Iwate University, 3–18–8, Ueda, Morioka, Iwate 020–8550, Japan
- Graduate School of Arts and Sciences, Iwate University, 3–18–8 Ueda, Morioka, Iwate 020–8550, Japan
- Department of Plant BioSciences, Faculty of Agriculture, Iwate University, 3–18–8, Ueda, Morioka, 020–8550, Iwate, Japan
| |
Collapse
|
|
3
|
Jiménez-Guerrero I, Medina C, Vinardell JM, Ollero FJ, López-Baena FJ. The Rhizobial Type 3 Secretion System: The Dr. Jekyll and Mr. Hyde in the Rhizobium–Legume Symbiosis. Int J Mol Sci 2022; 23:ijms231911089. [PMID: 36232385 PMCID: PMC9569860 DOI: 10.3390/ijms231911089] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/08/2022] [Accepted: 09/14/2022] [Indexed: 01/14/2023] Open
Abstract
Rhizobia are soil bacteria that can establish a symbiotic association with legumes. As a result, plant nodules are formed on the roots of the host plants where rhizobia differentiate to bacteroids capable of fixing atmospheric nitrogen into ammonia. This ammonia is transferred to the plant in exchange of a carbon source and an appropriate environment for bacterial survival. This process is subjected to a tight regulation with several checkpoints to allow the progression of the infection or its restriction. The type 3 secretion system (T3SS) is a secretory system that injects proteins, called effectors (T3E), directly into the cytoplasm of the host cell, altering host pathways or suppressing host defense responses. This secretion system is not present in all rhizobia but its role in symbiosis is crucial for some symbiotic associations, showing two possible faces as Dr. Jekyll and Mr. Hyde: it can be completely necessary for the formation of nodules, or it can block nodulation in different legume species/cultivars. In this review, we compile all the information currently available about the effects of different rhizobial effectors on plant symbiotic phenotypes. These phenotypes are diverse and highlight the importance of the T3SS in certain rhizobium–legume symbioses.
Collapse
|