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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.
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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.)
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Muñoz-Torres P, Huanca-Mamani W, Cárdenas-Ninasivincha S, Aguilar Y, Quezada A, Bugueño F. Plant Growth-Promoting and Herbicidal Bacteria as Potential Bio-Based Solutions for Agriculture in Desertic Regions. PLANTS (BASEL, SWITZERLAND) 2024; 14:9. [PMID: 39795269 PMCID: PMC11723097 DOI: 10.3390/plants14010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2024] [Revised: 12/18/2024] [Accepted: 12/20/2024] [Indexed: 01/13/2025]
Abstract
The region of Arica and Parinacota hosts unexplored remote sites with unique characteristics suitable for developing novel agricultural bioproducts. Notable locations include Jurasi Hot Springs, Polloquere Hot Springs, and Amuyo Lagoons, featuring open pools fed by thermal mountain springs. These geothermal sites harbor bacteria with plant growth-promoting activities, particularly interesting to the strains J19, TP22, A20, and A3. These bacteria possess in vitro plant growth-promoting traits, the ability to produce hydrolytic enzymes, and the capacity to inhibit phytopathogenic fungi. Moreover, they can tolerate different concentrations of NaCl and boron, making them suitable for developing new agricultural bioproducts for arid environments. The bacterial strains A3 and A20 have a positive effect on the growth of the aerial part of tomato plants (increased stem length, fresh and dry weight), with a significant increment in proline concentration and chlorophyll A and B content under saline conditions. Meanwhile, the strains J19 and TP22 exhibit herbicidal activity against Cenchrus echinatus by reducing root elongation and germination of the weed. These strains possess plant growth-promoting traits and improve plant resistance to salinity stress. They are promising candidates for developing innovative bio-based agricultural products suited to arid and semi-arid regions.
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Affiliation(s)
- Patricio Muñoz-Torres
- Laboratory of Plant Pathology and Bioproducts, Faculty of Agronomic Sciences, University of Tarapacá, Av. General Velásquez 1775, Arica 1000000, Chile; (W.H.-M.); (S.C.-N.); (Y.A.); (A.Q.); (F.B.)
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Yu J, Yang S, Zhang X, Liu X, Tang X, Wang L, Chen J, Luo H, Liu C, Song C. Integrating metagenomics and culturomics to uncover the soil bacterial community in Asparagus cochinchinensis cultivation. Front Microbiol 2024; 15:1467864. [PMID: 39697658 PMCID: PMC11652531 DOI: 10.3389/fmicb.2024.1467864] [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: 07/21/2024] [Accepted: 11/20/2024] [Indexed: 12/20/2024] Open
Abstract
Asparagus cochinchinensis is a medicinal plant in China, which has gained attention owing its protective effect in human health. However, there are seldom studies to systematically reveal the rhizosphere bacterial community of A. cochinchinensis. In this study, we employed metagenomics and culturomics to analyze the bacterial community composition and diversity in continuous rhizosphere soil of A. cochinchinensis. Meanwhile, we assessed the effect of soil physicochemical properties on the bacterial community. Results showed that the most abundant TAXA is a taxon belonging to the family Streptomycetaceae, the genus Mycobacterium and the species Oligotropha carboxidovorans. The bacterial communities across various areas were similar. Significant differences of exchangeable magnesium and available phosphorus level were observed between three groups. Furthermore, bacterial community structure correlated closely with soil physicochemical properties. Additionally, a total of 103 strains were isolated and identified, representing 28 species. Based on this study, the rhizosphere bacterial community of A. cochinchinensis might influence its growth and development. The rhizosphere strains were isolated and their function request further investigation. This study firstly revealed the bacterial community in the A. cochinchinensis rhizosphere soil, providing valuable references for its quality improvement in practical cultivation process.
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Affiliation(s)
- Jingsheng Yu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shuai Yang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoyong Zhang
- Traditional Chinese Medicine Health Industry Promotion Center of Dongxing District, Neijiang, China
- Neijiang Dongxing District Bureau of Health, Neijiang, China
| | - Xiongwei Liu
- Traditional Chinese Medicine Health Industry Promotion Center of Dongxing District, Neijiang, China
- Committee of Education, Science, Culture and Health of Dongxing District, Neijiang, China
| | - Xuebo Tang
- Traditional Chinese Medicine Health Industry Promotion Center of Dongxing District, Neijiang, China
| | - Liuyan Wang
- Traditional Chinese Medicine Health Industry Promotion Center of Dongxing District, Neijiang, China
| | - Jinglan Chen
- Traditional Chinese Medicine Health Industry Promotion Center of Dongxing District, Neijiang, China
| | - Huimin Luo
- Traditional Chinese Medicine Health Industry Promotion Center of Dongxing District, Neijiang, China
| | - Changmin Liu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Azarnoosh R, Yarahmadi F, Keshavarz-Tohid V, Rajabpour A. Isolation and identification of rhizospheric pseudomonads with insecticidal effects from various crops in Khuzestan Province, Iran. J Invertebr Pathol 2024; 204:108099. [PMID: 38556196 DOI: 10.1016/j.jip.2024.108099] [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: 02/20/2024] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024]
Abstract
Pseudomonas bacteria include a variety of species with distinct characteristics. Some species within this genus are known for their ability to stimulate plant growth. Recently, the potential of these bacteria in controlling insect pests has been documented. In this study, 58 bacterial isolates were purified from rhizospheres of wheat, broad bean and canola that were collected from different fields of Khuzestan province in south-west of Iran. With biochemical tests 19 non plant pathogenic pseudomonads strains were detected and their lethal effects on the eggs and larvae of Ephestia keuhniella as an important pest that infests stored products, were evaluated under laboratory conditions. For the bioassays, two concentrations of each strain were administered, and the 5th instar larvae and eggs of the pest were subjected to treatment. Mortality rates were recorded after 24 h. The results showed that all isolated Pseudomonad strains of this study had insecticidal effects against eggs and larvae of E. keuhniella. The strains AWI1, AWI2, AWI7, ABI12, ABI15 and ABI16 displayed the highest mortality rate (91.1 %, 86.2 %, 82.3 %, 84.2, 90.5 % and 90.5 %, respectively). Molecular identification and phylogeny tree according to 16 s rRNA sequencing clarified that AWI1, AWI2 belong to P. plecoglossicida, AWI5 belongs to P. lini, ABI12, ABI15 and ABI16 belong to P. taiwanensis. Moreover, the bacterial efficacy at a suspension concentration of 0.5 OD (80 %) was significantly greater than that at a concentration of 0.2 OD (63.33 %). No significant difference was detected in the response of the pest larvae or eggs to the different strains. Furthermore, olfactory trials revealed that the female parasitoid wasp Habrabracon hebetor actively avoided the infection of the treated larvae by the strains. These findings have practical implications for the development of microbiological pest control strategies.
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Affiliation(s)
- Roghayeh Azarnoosh
- Department of Plant Protection, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Bavi, Khuzestan Province, Iran
| | - Fatemeh Yarahmadi
- Department of Plant Protection, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Bavi, Khuzestan Province, Iran.
| | - Vahid Keshavarz-Tohid
- Department of Plant Protection, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Bavi, Khuzestan Province, Iran.
| | - Ali Rajabpour
- Department of Plant Protection, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Bavi, Khuzestan Province, Iran
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Muñoz-Torres P, Márquez SL, Sepúlveda-Chavera G, Cárdenas-Ninasivincha S, Arismendi-Macuer M, Huanca-Mamani W, Aguilar Y, Quezada A, Bugueño F. Isolation and Identification of Bacteria from Three Geothermal Sites of the Atacama Desert and Their Plant-Beneficial Characteristics. Microorganisms 2023; 11:2635. [PMID: 38004648 PMCID: PMC10672901 DOI: 10.3390/microorganisms11112635] [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: 09/21/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
The Region of Arica and Parinacota (Atacama Desert) offers several unexplored remote sites with unique characteristics that would allow for the formulation of new bioproducts for agriculture. Among them, Jurasi Hot Springs, Polloquere Hot Springs, and Amuyo Lagoons represent a group of open pools fed by thermal water springing from the mountains. Their microbiomes remain unspecified, providing a unique opportunity to characterize the endemic community of these sites and develop new bioproducts for sustainable agriculture. Bacteria were isolated from the sediments of these geothermal sites and characterized by sequencing the 16S rRNA gene, microbiological characterization, and agricultural functional characterization. A total of 57 bacteria were isolated from three geothermal sites north of the Atacama Desert. The sequence analysis showed that the isolates belong to several bacterial genera, including Pantoea, Bacillus, and Pseudomonas, among others. The functional characterization revealed the presence of PGP traits, hydrolytic enzymes, and biocontrol activity against phytopathogenic fungi. These bacteria possess the potential to develop new biobased products for agriculture in arid conditions.
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Affiliation(s)
- Patricio Muñoz-Torres
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Av. General Velásquez 1775, Arica 1000000, Chile; (G.S.-C.); (S.C.-N.); (M.A.-M.); (W.H.-M.); (Y.A.); (A.Q.); (F.B.)
| | - Sebastián L. Márquez
- Fundación Científica y Cultural Biociencia, José Domingo Cañas, 2280 Ñuñoa, Santiago 7750132, Chile;
| | - Germán Sepúlveda-Chavera
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Av. General Velásquez 1775, Arica 1000000, Chile; (G.S.-C.); (S.C.-N.); (M.A.-M.); (W.H.-M.); (Y.A.); (A.Q.); (F.B.)
| | - Steffany Cárdenas-Ninasivincha
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Av. General Velásquez 1775, Arica 1000000, Chile; (G.S.-C.); (S.C.-N.); (M.A.-M.); (W.H.-M.); (Y.A.); (A.Q.); (F.B.)
| | - Mabel Arismendi-Macuer
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Av. General Velásquez 1775, Arica 1000000, Chile; (G.S.-C.); (S.C.-N.); (M.A.-M.); (W.H.-M.); (Y.A.); (A.Q.); (F.B.)
| | - Wilson Huanca-Mamani
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Av. General Velásquez 1775, Arica 1000000, Chile; (G.S.-C.); (S.C.-N.); (M.A.-M.); (W.H.-M.); (Y.A.); (A.Q.); (F.B.)
| | - Yola Aguilar
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Av. General Velásquez 1775, Arica 1000000, Chile; (G.S.-C.); (S.C.-N.); (M.A.-M.); (W.H.-M.); (Y.A.); (A.Q.); (F.B.)
| | - Antonio Quezada
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Av. General Velásquez 1775, Arica 1000000, Chile; (G.S.-C.); (S.C.-N.); (M.A.-M.); (W.H.-M.); (Y.A.); (A.Q.); (F.B.)
| | - Franco Bugueño
- Laboratorio de Patología Vegetal y Bioproductos, Facultad de Ciencias Agronómicas, Universidad de Tarapacá, Av. General Velásquez 1775, Arica 1000000, Chile; (G.S.-C.); (S.C.-N.); (M.A.-M.); (W.H.-M.); (Y.A.); (A.Q.); (F.B.)
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Gupta S, Pandey S, Sharma S. Decoding the Plant Growth Promotion and Antagonistic Potential of Bacterial Endophytes From Ocimum sanctum Linn. Against Root Rot Pathogen Fusarium oxysporum in Pisum sativum. FRONTIERS IN PLANT SCIENCE 2022; 13:813686. [PMID: 35237287 PMCID: PMC8884270 DOI: 10.3389/fpls.2022.813686] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
The present study demonstrates plant growth promotion and induction of systemic resistance in pea (Pisum sativum) plant against Fusarium oxysporum f.sp. pisi by two bacterial endophytes, Pseudomonas aeruginosa OS_12 and Aneurinibacillus aneurinilyticus OS_25 isolated from leaves of Ocimum sanctum Linn. The endophytes were evaluated for their antagonistic potential against three phytopathogens Rhizoctonia solani, F. oxysporum f. sp. pisi, and Pythium aphanidermatum by dual culture assay. Maximum inhibition of F. oxysporum f. sp. pisi was observed by strains OS_12 and OS_25 among all root rot pathogens. Scanning electron microscopy of dual culture indicated hyphal distortion and destruction in the case of F. oxysporum f. sp. pisi. Further, volatile organic compounds (VOCs) were identified by gas chromatography-mass spectrometry (GC-MS). The GC-MS detected eight bioactive compounds from hexane extracts for instance, Dodecanoic acid, Tetra decanoic acid, L-ascorbic acid, Trans-13-Octadecanoic acid, Octadecanoic acid. Both the endophytes exhibited multifarious plant growth promoting traits such as indole acetic production (30-33 μg IAA ml-1), phosphate solubilization, and siderophore and ammonia production. Pot trials were conducted to assess the efficacy of endophytes in field conditions. A significant reduction in disease mortality rate and enhancement of growth parameters was observed in pea plants treated with consortium of endophytes OS_12 and OS_25 challenged with F. oxysporum f.sp. pisi infection. The endophytic strains elicited induced systemic resistance (ISR) in pathogen challenged pea plants by enhancing activities of Phenylalanine ammonia lyase (PAL), peroxidase (PO), polyphenol oxidase (PPO), ascorbate oxidase (AO), catalase (CAT) and total phenolic content. The endophytes reduced the oxidative stress as revealed by decrease in malondialdehyde (MDA) content and subsequently, lipid peroxidation in host plant leaves. Robust root colonization of pea seedlings by endophytes was observed by scanning electron microscopy (SEM) and fluorescence microscopy. Thus, plant growth promoting endophytic P. aeruginosa and A. aneurinilyticus can be further exploited through bio-formulations for sustainable protection of crops against root rot diseases as bio-control agents.
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Affiliation(s)
- Shikha Gupta
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India
| | - Sangeeta Pandey
- Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, Noida, India
| | - Satyawati Sharma
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, India
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