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Jibril SM, Yan W, Wang Y, Zhu X, Yunying Z, Wu J, Wang L, Zhang L, Li C. Highly diverse microbial community of regenerated seedlings reveals the high capacity of the bulb in lily, Lilium brownii. Front Microbiol 2024; 15:1387870. [PMID: 38903799 PMCID: PMC11188333 DOI: 10.3389/fmicb.2024.1387870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Lily bulbs, which have both nutrient storage and reproductive functions, are a representative group of plants for studying the maintenance and transfer of plant-associated microbiomes. In this study, a comparison of the microbial composition of bulbs and their regenerated seedlings cultured under aseptic conditions, as well as subcultured seedlings that succeeded five times, was examined by amplicon sequencing. A total of 62 bacterial taxa and 56 fungal taxa were found to be transferred to the 5th generation in seedlings, which are the core microbiome of lily. After the regeneration of seedlings from bulbs, there was a significant increase in the number of detectable microbial species, and after 1, 3, and 5 successive generations, there was a decrease in the number of detectable species. Interestingly, some "new" microorganisms appeared in each generation of samples; for instance, 167 and 168 bacterial operational taxonomic units (OTUs) in the 3rd and 5th generations of seedlings that were not detected in either bulbs or seedlings of the previous two generations. These results suggest that bulbs can maintain a high diversity of microorganisms, including some with ultra-low abundance, and have a high transfer capacity to tuck shoots through continuous subculture. The diversity and maintenance of the microbiome can provide the necessary microbial reservoir support for regenerating seedlings. This habit of maintaining low abundance and high diversity may be biologically and ecologically critical for maintaining microbiome stability and function due to the sequestration nature of the plant.
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Affiliation(s)
- Sauban Musa Jibril
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Wu Yan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Xishen Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Zhou Yunying
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Jie Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Ling Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Limin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Chengyun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
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Chen X, He C, Zhang Q, Bayakmetov S, Wang X. Modularized Design and Construction of Tunable Microbial Consortia with Flexible Topologies. ACS Synth Biol 2024; 13:183-194. [PMID: 38166159 PMCID: PMC10805104 DOI: 10.1021/acssynbio.3c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/04/2024]
Abstract
Complex and fluid bacterial community compositions are critical to diversity, stability, and function. However, quantitative and mechanistic descriptions of the dynamics of such compositions are still lacking. Here, we develop a modularized design framework that allows for bottom-up construction and the study of synthetic bacterial consortia with different topologies. We showcase the microbial consortia design and building process by constructing amensalism and competition consortia using only genetic circuit modules to engineer different strains to form the community. Functions of modules and hosting strains are validated and quantified to calibrate dynamic parameters, which are then directly fed into a full mechanistic model to accurately predict consortia composition dynamics for both amensalism and competition without further fitting. More importantly, such quantitative understanding successfully identifies the experimental conditions to achieve coexistence composition dynamics. These results illustrate the process of both computationally and experimentally building up bacteria consortia complexity and hence achieve robust control of such fluid systems.
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Affiliation(s)
- Xingwen Chen
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Changhan He
- Department
of Mathematics, University of California
Irvine, Irvine, California 92697, United States
| | - Qi Zhang
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Samat Bayakmetov
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
| | - Xiao Wang
- School
of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States
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3
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Guardiola-Márquez CE, López-Mena ER, Segura-Jiménez ME, Gutierrez-Marmolejo I, Flores-Matzumiya MA, Mora-Godínez S, Hernández-Brenes C, Jacobo-Velázquez DA. Development and Evaluation of Zinc and Iron Nanoparticles Functionalized with Plant Growth-Promoting Rhizobacteria (PGPR) and Microalgae for Their Application as Bio-Nanofertilizers. PLANTS (BASEL, SWITZERLAND) 2023; 12:3657. [PMID: 37896120 PMCID: PMC10609697 DOI: 10.3390/plants12203657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/16/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023]
Abstract
Micronutrient deficiencies are widespread and growing global concerns. Nanoscale nutrients present higher absorption rates and improved nutrient availability and nutrient use efficiency. Co-application of nanofertilizers (NFs) with biological agents or organic compounds increases NF biocompatibility, stability, and efficacy. This study aimed to develop and evaluate zinc and iron bio-nanofertilizers formulated with plant growth-promoting rhizobacteria (PGPR) and microalgae. Nanoparticles (NPs) were synthesized with the co-precipitation method and functionalized with Pseudomonas species and Spirulina platensis preparation. NPs were characterized and evaluated on seed germination, soil microbial growth, and early plant response under seedbed conditions. NPs corresponded to zinc oxide (ZnO; 77 nm) and maghemite (γ-Fe2O3; 68 nm). Functionalized nanoparticles showed larger sizes, around 145-233 nm. The seedling vigor index of tomato and maize was significantly increased (32.9-46.1%) by bacteria-functionalized ZnO- and γ-Fe2O3-NPs at 75 ppm. NFs at 250 and 75 ppm significantly increased bacterial growth. NFs also improved early plant growth by increasing plant height (14-44%), leaf diameter (22-47%), and fresh weight (46-119%) in broccoli and radish, which were mainly influenced by bacteria capped ZnO- and γ-Fe2O3-NPs at 250 ppm. Beneficial effects on plant growth can be attributed to the synergistic interaction of the biological components and the zinc and iron NPs in the bio-nanofertilizers.
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Affiliation(s)
- Carlos Esteban Guardiola-Márquez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Guadalajara, Ave. General Ramon Corona 2514, Zapopan 45138, Mexico; (C.E.G.-M.)
| | - Edgar R. López-Mena
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Guadalajara, Ave. General Ramon Corona 2514, Zapopan 45138, Mexico; (C.E.G.-M.)
| | - M. Eugenia Segura-Jiménez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Guadalajara, Ave. General Ramon Corona 2514, Zapopan 45138, Mexico; (C.E.G.-M.)
| | - Isaac Gutierrez-Marmolejo
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Mexico
| | - Manuel A. Flores-Matzumiya
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Guadalajara, Ave. General Ramon Corona 2514, Zapopan 45138, Mexico; (C.E.G.-M.)
| | - Shirley Mora-Godínez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute for Obesity Research, Ave. General Ramon Corona 2514, Zapopan 45201, Mexico
| | - Carmen Hernández-Brenes
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey 64849, Mexico
- Tecnologico de Monterrey, Institute for Obesity Research, Ave. General Ramon Corona 2514, Zapopan 45201, Mexico
| | - Daniel A. Jacobo-Velázquez
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, Campus Guadalajara, Ave. General Ramon Corona 2514, Zapopan 45138, Mexico; (C.E.G.-M.)
- Tecnologico de Monterrey, Institute for Obesity Research, Ave. General Ramon Corona 2514, Zapopan 45201, Mexico
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Guardiola-Márquez CE, Santos-Ramírez MT, Figueroa-Montes ML, Valencia-de los Cobos EO, Stamatis-Félix IJ, Navarro-López DE, Jacobo-Velázquez DA. Identification and Characterization of Beneficial Soil Microbial Strains for the Formulation of Biofertilizers Based on Native Plant Growth-Promoting Microorganisms Isolated from Northern Mexico. PLANTS (BASEL, SWITZERLAND) 2023; 12:3262. [PMID: 37765426 PMCID: PMC10537599 DOI: 10.3390/plants12183262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Plant growth-promoting microorganisms (PGPM) benefit plant health by enhancing plant nutrient-use efficiency and protecting plants against biotic and abiotic stresses. This study aimed to isolate and characterize autochthonous PGPM from important agri-food crops and nonagricultural plants to formulate biofertilizers. Native microorganisms were isolated and evaluated for PGP traits (K, P, and Zn solubilization, N2-fixation, NH3-, IAA and siderophore production, and antifungal activity against Fusarium oxysporum). Isolates were tested on radish and broccoli seedlings, evaluating 19 individual isolates and 12 microbial consortia. Potential bacteria were identified through DNA sequencing. In total, 798 bacteria and 209 fungi were isolated. Isolates showed higher mineral solubilization activity than other mechanisms; 399 bacteria and 156 fungi presented mineral solubilization. Bacteria were relevant for nitrogen fixation, siderophore, IAA (29-176 mg/L), and ammonia production, while fungi for Fusarium growth inhibition (40-69%). Twenty-four bacteria and eighteen fungi were selected for their PGP traits. Bacteria had significantly (ANOVA, p < 0.05) better effects on plants than fungi; treatments improved plant height (23.06-51.32%), leaf diameter (25.43-82.91%), and fresh weight (54.18-85.45%) in both crops. Most potential species belonged to Pseudomonas, Pantoea, Serratia, and Rahnella genera. This work validated a high-throughput approach to screening hundreds of rhizospheric microorganisms with PGP potential isolated from rhizospheric samples.
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Affiliation(s)
- Carlos Esteban Guardiola-Márquez
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
| | - María Teresa Santos-Ramírez
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
| | - Melina Lizeth Figueroa-Montes
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
| | | | - Iván Jesús Stamatis-Félix
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
| | - Diego E. Navarro-López
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
| | - Daniel A. Jacobo-Velázquez
- Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Ave. General Ramon Corona 2514, Zapopan 45138, Jalisco, Mexico; (C.E.G.-M.)
- Tecnologico de Monterrey, Institute for Obesity Research, Av. General Ramon Corona 2514, Zapopan 45201, Jalisco, Mexico
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Carreiras J, Cruz-Silva A, Fonseca B, Carvalho RC, Cunha JP, Proença Pereira J, Paiva-Silva C, A. Santos S, Janeiro Sequeira R, Mateos-Naranjo E, Rodríguez-Llorente ID, Pajuelo E, Redondo-Gómez S, Matos AR, Mesa-Marín J, Figueiredo A, Duarte B. Improving Grapevine Heat Stress Resilience with Marine Plant Growth-Promoting Rhizobacteria Consortia. Microorganisms 2023; 11:microorganisms11040856. [PMID: 37110279 PMCID: PMC10141645 DOI: 10.3390/microorganisms11040856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/15/2023] [Accepted: 03/25/2023] [Indexed: 03/30/2023] Open
Abstract
Amid climate change, heatwave events are expected to increase in frequency and severity. As a result, yield losses in viticulture due to heatwave stress have increased over the years. As one of the most important crops in the world, an eco-friendly stress mitigation strategy is greatly needed. The present work aims to evaluate the physiological fitness improvement by two marine plant growth-promoting rhizobacteria consortia in Vitis vinifera cv. Antão Vaz under heatwave conditions. To assess the potential biophysical and biochemical thermal stress feedback amelioration, photochemical traits, pigment and fatty acid profiles, and osmotic and oxidative stress biomarkers were analysed. Bioaugmented grapevines exposed to heatwave stress presented a significantly enhanced photoprotection capability and higher thermo-stability, exhibiting a significantly lower dissipation energy flux than the non-inoculated plants. Additionally, one of the rhizobacterial consortia tested improved light-harvesting capabilities by increasing reaction centre availability and preserving photosynthetic efficiency. Rhizobacteria inoculation expressed an osmoprotectant promotion, revealed by the lower osmolyte concentration while maintaining leaf turgidity. Improved antioxidant mechanisms and membrane stability resulted in lowered lipid peroxidation product formation when compared to non-inoculated plants. Although the consortia were found to differ significantly in their effectiveness, these findings demonstrate that bioaugmentation induced significant heatwave stress tolerance and mitigation. This study revealed the promising usage of marine PGPR consortia to promote plant fitness and minimize heatwave impacts in grapevines.
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Miranda-Carrazco A, Chávez-López C, Ramírez-Villanueva DA, Dendooven L. Bacteria in (vermi)composted organic wastes mostly survive when applied to an arable soil cultivated with wheat (Triticum sp. L.). ENVIRONMENTAL MONITORING AND ASSESSMENT 2022; 194:363. [PMID: 35419663 DOI: 10.1007/s10661-022-09996-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Composting and vermicomposting are an environmentally friendly way to reduce pathogens in organic wastes and generate a valuable product that provides nutrients for crops. However, how the bacterial community structure changes during these different processes and if the bacteria applied with the (vermi)composted products survive in an arable cultivated soil is still largely unknown. In this study, we monitored how the bacterial community structure changed during conditioning, composting with and without Eisenia fetida, and when the end-product was applied to arable soil cultivated with wheat Triticum sp. L. The organic wastes used were biosolid, cow manure, and a mixture of both. Large changes occurred in the relative abundance of some of the most abundant bacterial genera during conditioning, but the changes were much smaller during composting or vermicomposting. The bacterial community structure was significantly different in the organic wastes during conditioning and (vermi)composting but adding E. fetida had no significant effect on it. Changes in the relative abundance of the bacterial groups in the (vermi)composted waste applied to the arable soil cultivated with wheat were small, suggesting that most survived even after 140 days. As such, applying (vermi)composted organic wastes not only adds nutrients to a crop but also contributes to the survival of plant growth-promoting bacteria found in the (vermi)compost. However, putative human pathogens found in the biosolid also survived in the arable soil, and their relative abundance remained high but mixing the biosolid with cow manure reduced that risk. It was found that applying (vermi)composted organic wastes to an arable soil not only provides plant nutrients and adds bacteria with plant growth-promoting capacities, but some putative pathogens also survived.
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Affiliation(s)
- Alejandra Miranda-Carrazco
- Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, Cinvestav, Mexico City, Mexico
| | - Claudia Chávez-López
- Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, Cinvestav, Mexico City, Mexico
| | | | - Luc Dendooven
- Laboratory of Soil Ecology, Department of Biotechnology and Bioengineering, Cinvestav, Mexico City, Mexico.
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Gómez-Godínez LJ, Martínez-Romero E, Banuelos J, Arteaga-Garibay RI. Tools and challenges to exploit microbial communities in agriculture. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100062. [PMID: 34841352 PMCID: PMC8610360 DOI: 10.1016/j.crmicr.2021.100062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Plants contain diverse microbial communities. The associated microorganisms confer advantages to the host plant, which include growth promotion, nutrient absorption, stress tolerance, and pathogen and disease resistance. In this review, we explore how agriculture is implementing the use of microbial inoculants (single species or consortia) to improve crop yields, and discuss current strategies to study plant-associated microorganisms and how their diversity varies under unconventional agriculture. It is predicted that microbial inoculation will continue to be used in agriculture.
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Affiliation(s)
- Lorena Jacqueline Gómez-Godínez
- Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos. Instituto Nacional de Investigación Forestales, Agrícolas y Pecuarios. Boulevard de la Biodiversidad 400, Rancho las Cruces, C.P. 47600. Tepatitlán de Morelos, Jalisco, México
| | - Esperanza Martínez-Romero
- Centro de Ciencias genómicas, Universidad Nacional Autónoma de México Campus Morelos, Cuernavaca, Morelos México
| | - Jacob Banuelos
- Laboratorio de Organismos Benéficos, Facultad de Ciencias Agrícolas, Universidad Veracruzana. Circuito Aguirre Beltrán SN, Col. Universitaria, CP 91000, Xalapa, Veracruz, México
| | - Ramón I. Arteaga-Garibay
- Laboratorio de Recursos Genéticos Microbianos, Centro Nacional de Recursos Genéticos. Instituto Nacional de Investigación Forestales, Agrícolas y Pecuarios. Boulevard de la Biodiversidad 400, Rancho las Cruces, C.P. 47600. Tepatitlán de Morelos, Jalisco, México
- Corresponding authors.
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