Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System
Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performa...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-06-01
|
| Series: | Microorganisms |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2607/11/7/1633 |
| _version_ | 1797588220886646784 |
|---|---|
| author | Carolina N. Resendiz-Nava Fernando Alonso-Onofre Hilda V. Silva-Rojas Angel Rebollar-Alviter Dulce M. Rivera-Pastrana Matthew J. Stasiewicz Gerardo M. Nava Edmundo M. Mercado-Silva |
| author_facet | Carolina N. Resendiz-Nava Fernando Alonso-Onofre Hilda V. Silva-Rojas Angel Rebollar-Alviter Dulce M. Rivera-Pastrana Matthew J. Stasiewicz Gerardo M. Nava Edmundo M. Mercado-Silva |
| author_sort | Carolina N. Resendiz-Nava |
| collection | DOAJ |
| description | Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (<i>n</i> = 24), root (<i>n =</i> 24), and fruit (<i>n =</i> 24) composite samples were subjected to DNA extraction and high-throughput <i>16S rRNA</i> gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, <i>Bacillaceae</i>, <i>Microbacteriaceae</i>, <i>Nocardioidaceae</i>, <i>Pseudomonadaceae</i>, <i>Rhodobacteraceae</i>, and <i>Sphingomonadaceae</i>, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of <i>Bradyrhizobiaceae</i>, <i>Caulobacteraceae</i>, <i>Chitinophagaceae</i>, <i>Enterobacteriaceae</i>, <i>Erythrobacteraceae</i>, <i>Flavobacteriaceae</i>, <i>Nocardioidaceae</i>, <i>Rhodobacteraceae</i>, and <i>Streptomycetaceae</i>. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs. |
| first_indexed | 2024-03-11T00:49:04Z |
| format | Article |
| id | doaj.art-9bc2e5adcd154463a301bfbe4580b05a |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-11T00:49:04Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-9bc2e5adcd154463a301bfbe4580b05a2023-11-18T20:34:14ZengMDPI AGMicroorganisms2076-26072023-06-01117163310.3390/microorganisms11071633Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture SystemCarolina N. Resendiz-Nava0Fernando Alonso-Onofre1Hilda V. Silva-Rojas2Angel Rebollar-Alviter3Dulce M. Rivera-Pastrana4Matthew J. Stasiewicz5Gerardo M. Nava6Edmundo M. Mercado-Silva7Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, MexicoCentro Universitario CEICKOR, Colon 76299, Queretaro, MexicoPosgrado en Recursos Geneticos y Productividad, Produccion de Semillas, Colegio de Postgraduados, Km 36.5 Carretera Mexico-Texcoco, Texcoco 56264, MexicoCentro Regional Morelia, Universidad Autonoma de Chapingo, Morelia 58170, Michoacan, MexicoFacultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, MexicoDepartment of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 1302W Pennsylvania Ave, Urbana, IL 61801, USAFacultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, MexicoFacultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, MexicoTomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (<i>n</i> = 24), root (<i>n =</i> 24), and fruit (<i>n =</i> 24) composite samples were subjected to DNA extraction and high-throughput <i>16S rRNA</i> gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, <i>Bacillaceae</i>, <i>Microbacteriaceae</i>, <i>Nocardioidaceae</i>, <i>Pseudomonadaceae</i>, <i>Rhodobacteraceae</i>, and <i>Sphingomonadaceae</i>, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of <i>Bradyrhizobiaceae</i>, <i>Caulobacteraceae</i>, <i>Chitinophagaceae</i>, <i>Enterobacteriaceae</i>, <i>Erythrobacteraceae</i>, <i>Flavobacteriaceae</i>, <i>Nocardioidaceae</i>, <i>Rhodobacteraceae</i>, and <i>Streptomycetaceae</i>. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.https://www.mdpi.com/2076-2607/11/7/1633<i>16S rRNA</i>core microbiotaorganicphyllosphererhizospheresoilless |
| spellingShingle | Carolina N. Resendiz-Nava Fernando Alonso-Onofre Hilda V. Silva-Rojas Angel Rebollar-Alviter Dulce M. Rivera-Pastrana Matthew J. Stasiewicz Gerardo M. Nava Edmundo M. Mercado-Silva Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System Microorganisms <i>16S rRNA</i> core microbiota organic phyllosphere rhizosphere soilless |
| title | Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System |
| title_full | Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System |
| title_fullStr | Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System |
| title_full_unstemmed | Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System |
| title_short | Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System |
| title_sort | tomato plant microbiota under conventional and organic fertilization regimes in a soilless culture system |
| topic | <i>16S rRNA</i> core microbiota organic phyllosphere rhizosphere soilless |
| url | https://www.mdpi.com/2076-2607/11/7/1633 |
| work_keys_str_mv | AT carolinanresendiznava tomatoplantmicrobiotaunderconventionalandorganicfertilizationregimesinasoillessculturesystem AT fernandoalonsoonofre tomatoplantmicrobiotaunderconventionalandorganicfertilizationregimesinasoillessculturesystem AT hildavsilvarojas tomatoplantmicrobiotaunderconventionalandorganicfertilizationregimesinasoillessculturesystem AT angelrebollaralviter tomatoplantmicrobiotaunderconventionalandorganicfertilizationregimesinasoillessculturesystem AT dulcemriverapastrana tomatoplantmicrobiotaunderconventionalandorganicfertilizationregimesinasoillessculturesystem AT matthewjstasiewicz tomatoplantmicrobiotaunderconventionalandorganicfertilizationregimesinasoillessculturesystem AT gerardomnava tomatoplantmicrobiotaunderconventionalandorganicfertilizationregimesinasoillessculturesystem AT edmundommercadosilva tomatoplantmicrobiotaunderconventionalandorganicfertilizationregimesinasoillessculturesystem |