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Thapa A, Hasan MR, Kabir AH. Transcriptional reprogramming and microbiome dynamics in garden pea exposed to high pH stress during vegetative stage. PLANTA 2025; 261:83. [PMID: 40059228 DOI: 10.1007/s00425-025-04656-7] [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: 12/09/2024] [Accepted: 02/20/2025] [Indexed: 03/29/2025]
Abstract
MAIN CONCLUSION High soil pH induces the upregulation of genes involved in oxidative stress and nutrient transport, while the enrichment of beneficial microbes (Variovorax, Chaetomium, and Pseudomonas) highlights their potential role in promoting stress adaptation. High soil pH severely impacts plant growth and productivity, yet the transcriptomic changes and microbial dynamics underlying stress adaptation in garden pea (Pisum sativum ssp. hortense) remain unclear. This study demonstrates that high soil pH leads to stunted growth, reduced biomass, impaired photosynthesis, and nutrient status in garden pea. Further, disruption in key nitrogen-fixing bacteria (Rhizobium indicum, R. leguminosarum, and R. redzepovicii), along with the downregulation of NifA and NifD genes and upregulation of NifH in nodules highlights the critical role of micronutrient balance in legume-microbe symbiosis and a compensatory response to maintain nitrogen status. RNA seq analysis revealed extensive transcriptional reprogramming in roots, characterized by the upregulation of oxidative stress response genes (e.g., oxidoreductase and glutathione transferase activities, metal ion transporters) and the downregulation of genes related to ammonia-lyase activity and ion binding, reflecting broader disruptions in nutrient homeostasis. KEGG pathway analysis identified enrichment of MAPK signaling pathway, likely interacting with other pathways associated with stress tolerance, metabolic adjustment, and structural reorganization as part of adaptive responses to high pH. Root microbiome analysis showed significant enrichment of Variovorax, Shinella, and Chaetomium, suggesting host-driven recruitment under high pH stress. Stable genera, such as Pseudomonas, Novosphingobium, Mycobacterium, Herbaspirillum, and Paecilomyces, displayed resilience to stress conditions, potentially forming core microbiome components for adaptation to high pH. In a targeted study, inoculation of plants with an enriched microbiome, particularly C. globosum, under high pH conditions improved growth parameters and increased the abundance of Stenotrophomonas and Pseudomonas in the roots. It suggests that these bacterial genera may act as helper microbes to C. globosum, collectively promoting stress resilience in pea plants suffering from high pH. These findings provide a foundation for microbiome-aided breeding programs and the development of microbial consortia to enhance the adaptation of pea plants to high pH conditions.
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Affiliation(s)
- Asha Thapa
- School of Sciences, University of Louisiana at Monroe, Monroe, LA, 71209, USA
| | - Md Rokibul Hasan
- School of Sciences, University of Louisiana at Monroe, Monroe, LA, 71209, USA
| | - Ahmad H Kabir
- School of Sciences, University of Louisiana at Monroe, Monroe, LA, 71209, USA.
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Hami A, El Attar I, Mghazli N, Ennajeh S, Ait-Ouakrim EH, Bennis M, Oulghazi S, Badaoui B, Aurag J, Sbabou L, Taha K. Enhancing drought tolerance in Pisum sativum and Vicia faba through interspecific interactions with a mixed inoculum of Rhizobium laguerreae and non-host beneficial rhizobacteria. FRONTIERS IN PLANT SCIENCE 2025; 16:1528923. [PMID: 40078631 PMCID: PMC11898328 DOI: 10.3389/fpls.2025.1528923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Accepted: 02/06/2025] [Indexed: 03/14/2025]
Abstract
Introduction Harnessing plant growth-promoting rhizobia presents a sustainable and cost-effective method to enhance crop performance, particularly under drought stress. This study evaluates the variability of plant growth-promoting (PGP) traits among three strains of Rhizobium laguerreae LMR575, LMR571, and LMR655, and two native PGP strains Bacillus LMR698 and Enterobacter aerogenes LMR696. The primary objective was to assess the host range specificity of these strains and their effectiveness in improving drought tolerance in three legume species: Pisum sativum, Vicia faba, and Phaseolus vulgaris. Methods In-vitro experiments were conducted to assess the PGP traits of the selected strains, including phosphate solubilization, indole-3-acetic acid (IAA) production, and siderophore production. Greenhouse trials were also performed using a mixed inoculum of performing strains to evaluate their effects on plant physiological and biochemical traits under drought conditions. Results Significant variability in PGP traits was observed among the strains. R. laguerreae LMR655 exhibited the highest phosphate solubilization (113.85 mg mL-1 PO4 2-), while R. laguerreae LMR571 produced the highest IAA concentration (25.37 mg mL-1). E. aerogenes LMR696 demonstrated 82% siderophore production. Symbiotic interactions varied, with R. laguerreae LMR571 and LMR655 forming associations with P. sativum and V. faba, but none establishing compatibility with P. vulgaris. Greenhouse experiments showed that a mixed inoculum of R. laguerreae LMR571, LMR655, and E. aerogenes LMR696 significantly improved proline, total soluble sugars, proteins, and chlorophyll content under drought stress, with V. faba showing the strongest response. Discussion These findings highlight the importance of strain selection based on host specificity and PGP potential. The enhanced drought tolerance observed suggests that tailored microbial inoculants can improve legume resilience in water-limited environments. This study provides valuable insights for optimizing bioinoculant formulations to enhance crop performance under drought stress.
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Affiliation(s)
- Asma Hami
- Microbiology and Molecular Biology Team, of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Imane El Attar
- Microbiology and Molecular Biology Team, of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- AgroBioscience Program, University Mohammed VI Polytechnic (UM6P), Benguerir, Morocco
| | - Najoua Mghazli
- Microbiology and Molecular Biology Team, of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- Institut de Recherche en Mines et Environnement, Université du Québec en Abitibi-Témiscamingue, Rouyn-Noranda, QC, Canada
| | - Salah Ennajeh
- Microbiology and Molecular Biology Team, of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - El Houcine Ait-Ouakrim
- Microbiology and Molecular Biology Team, of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Meryeme Bennis
- Microbiology and Molecular Biology Team, of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- AgroBioscience Program, University Mohammed VI Polytechnic (UM6P), Benguerir, Morocco
| | - Said Oulghazi
- Biodiversity, Ecology and Genome Laboratory of Zoology and General Biology, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Bouabid Badaoui
- Biodiversity, Ecology and Genome Laboratory of Zoology and General Biology, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
- African Sustainable Agriculture Research Institute (ASARI), Mohammed VI Polytechnic University (UM6P), Laayoune, Morocco
| | - Jamal Aurag
- Microbiology and Molecular Biology Team, of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Laila Sbabou
- Microbiology and Molecular Biology Team, of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Kaoutar Taha
- Microbiology and Molecular Biology Team, of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University, Rabat, Morocco
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Yu T, Wu X, Song Y, Lv H, Zhang G, Tang W, Zheng Z, Wang X, Gu Y, Zhou X, Li J, Tian S, Hou X, Chen Q, Xin D, Ni H. Isolation and Identification of Salinity-Tolerant Rhizobia and Nodulation Phenotype Analysis in Different Soybean Germplasms. Curr Issues Mol Biol 2024; 46:3342-3352. [PMID: 38666939 PMCID: PMC11049135 DOI: 10.3390/cimb46040209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/01/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Increasing the soybean-planting area and increasing the soybean yield per unit area are two effective solutions to improve the overall soybean yield. Northeast China has a large saline soil area, and if soybeans could be grown there with the help of isolated saline-tolerant rhizobia, the soybean cultivation area in China could be effectively expanded. In this study, soybeans were planted in soils at different latitudes in China, and four strains of rhizobia were isolated and identified from the soybean nodules. According to the latitudes of the soil-sampling sites from high to low, the four isolated strains were identified as HLNEAU1, HLNEAU2, HLNEAU3, and HLNEAU4. In this study, the isolated strains were identified for their resistances, and their acid and saline tolerances and nitrogen fixation capacities were preliminarily identified. Ten representative soybean germplasm resources in Northeast China were inoculated with these four strains, and the compatibilities of these four rhizobium strains with the soybean germplasm resources were analyzed. All four isolates were able to establish different extents of compatibility with 10 soybean resources. Hefeng 50 had good compatibility with the four isolated strains, while Suinong 14 showed the best compatibility with HLNEAU2. The isolated rhizobacteria could successfully establish symbiosis with the soybeans, but host specificity was also present. This study was a preliminary exploration of the use of salinity-tolerant rhizobacteria to help the soybean nitrogen fixation in saline soils in order to increase the soybean acreage, and it provides a valuable theoretical basis for the application of saline-tolerant rhizobia.
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Affiliation(s)
- Tong Yu
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Xiaodong Wu
- Heilongjiang Green Food Science Research Institute, Harbin 150000, China;
| | - Yunshan Song
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Hao Lv
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Guoqing Zhang
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Weinan Tang
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Zefeng Zheng
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Xiaohan Wang
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Yumeng Gu
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Xin Zhou
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Jianlin Li
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Siyi Tian
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Xiuming Hou
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Qingshan Chen
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Dawei Xin
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
| | - Hejia Ni
- Key Laboratory of Soybean Biology of the Chinese Ministry of Education, Key Laboratory of Soybean Biology and Breeding, Genetics of Chinese Agriculture Ministry, College of Agriculture, Northeast Agricultural University, Harbin 150036, China; (T.Y.); (Y.S.); (H.L.); (G.Z.); (W.T.); (Z.Z.); (X.W.); (Y.G.); (X.Z.); (J.L.); (S.T.); (X.H.); (Q.C.)
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