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Dixon MM, Afkairin A, Davis JG, Chitwood-Brown J, Buchanan CM, Ippolito JA, Manter DK, Vivanco JM. Tomato domestication rather than subsequent breeding events reduces microbial associations related to phosphorus recovery. Sci Rep 2024; 14:9934. [PMID: 38689014 PMCID: PMC11061195 DOI: 10.1038/s41598-024-60775-3] [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: 12/21/2023] [Accepted: 04/26/2024] [Indexed: 05/02/2024] Open
Abstract
Legacy phosphorus (P) is a reservoir of sparingly available P, and its recovery could enhance sustainable use of nonrenewable mineral fertilizers. Domestication has affected P acquisition, but it is unknown if subsequent breeding efforts, like the Green Revolution (GR), had a similar effect. We examined how domestication and breeding events altered P acquisition by growing wild, traditional (pre-GR), and modern (post-GR) tomato in soil with legacy P but low bioavailable P. Wild tomatoes, particularly accession LA0716 (Solanum pennellii), heavily cultured rhizosphere P solubilizers, suggesting reliance on microbial associations to acquire P. Wild tomato also had a greater abundance of other putatively beneficial bacteria, including those that produce chelating agents and antibiotic compounds. Although wild tomatoes had a high abundance of these P solubilizers, they had lower relative biomass and greater P stress factor than traditional or modern tomato. Compared to wild tomato, domesticated tomato was more tolerant to P deficiency, and both cultivated groups had a similar rhizosphere bacterial community composition. Ultimately, this study suggests that while domestication changed tomato P recovery by reducing microbial associations, subsequent breeding processes have not further impacted microbial P acquisition mechanisms. Selecting microbial P-related traits that diminished with domestication may therefore increase legacy P solubilization.
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Affiliation(s)
- Mary M Dixon
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Antisar Afkairin
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Jessica G Davis
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jessica Chitwood-Brown
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Cassidy M Buchanan
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - James A Ippolito
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- United States Department of Agriculture-Agricultural Research Service, Soil Management and Sugar Beet Research, Fort Collins, CO, USA
| | - Daniel K Manter
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Jorge M Vivanco
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA.
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Lee Díaz AS, Minchev Z, Raaijmakers JM, Pozo MJ, Garbeva P. Impact of bacterial and fungal inoculants on the resident rhizosphere microbiome and the volatilome of tomato plants under leaf herbivory stress. FEMS Microbiol Ecol 2024; 100:fiad160. [PMID: 38331428 PMCID: PMC10858387 DOI: 10.1093/femsec/fiad160] [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: 01/30/2023] [Revised: 11/16/2023] [Accepted: 02/07/2024] [Indexed: 02/10/2024] Open
Abstract
Various studies have addressed the impact of microbial inoculants on the composition of the resident microbiome. How microbial inoculants impact plant metabolism and interact with the resident rhizobiota under herbivory stress remains elusive. Here, we investigated the impact of two bacterial and two fungal inoculants, inoculated as single species and as a synthetic community, on the rhizosphere microbiome and volatilome of tomato plants (Solanum lycopersicum) comparing nonstress conditions to exposed to leaf herbivory by Spodoptera exigua. Based on amplicon sequencing analysis, rhizobacterial community composition was significantly affected by all four inoculants and the magnitude of this effect was dependent on herbivory stress. Fungal community composition was altered by the microbial inoculants but independent of herbivory stress. The rhizosphere volatilome was impacted by the microbial inoculation and differences between treatments were evened under herbivory stress. Each microbial inoculant caused unique changes in the volatilome of stressed plants but also shared similar responses, in particular the enhanced production of dimethyl disulfide and benzothiazole. In conclusion, the introduction of microbial inoculants in the tomato rhizosphere caused unique as well as common changes in the rhizosphere microbiome and volatilome, but these changes were minor compared to the microbiome changes induced by herbivory stress.
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Affiliation(s)
- Ana Shein Lee Díaz
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Zhivko Minchev
- Department of Soil Microbiology and Symbiotic Systems
, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientfícias (CSIC), Calle Prof. Albareda, 1, 18008, Granada, Spain
| | - Jos M Raaijmakers
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - María José Pozo
- Department of Soil Microbiology and Symbiotic Systems
, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Cientfícias (CSIC), Calle Prof. Albareda, 1, 18008, Granada, Spain
| | - Paolina Garbeva
- Department of Microbial Ecology, The Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
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Adedayo AA, Fadiji AE, Babalola OO. Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum. PeerJ 2023; 11:e15432. [PMID: 37283894 PMCID: PMC10241170 DOI: 10.7717/peerj.15432] [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: 02/16/2023] [Accepted: 04/26/2023] [Indexed: 06/08/2023] Open
Abstract
The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.
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Stanković M. 10th Anniversary of Plants-Recent Advances and Further Perspectives. PLANTS (BASEL, SWITZERLAND) 2023; 12:1696. [PMID: 37111918 PMCID: PMC10145593 DOI: 10.3390/plants12081696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/08/2023] [Indexed: 06/19/2023]
Abstract
Published for the first time in 2012, Plants will celebrate its 10th anniversary [...].
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Affiliation(s)
- Milan Stanković
- Department of Biology and Ecology, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, 34000 Kragujevac, Serbia
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5
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Niza-Costa M, Rodríguez-dos Santos AS, Rebelo-Romão I, Ferrer MV, Sequero López C, Vílchez JI. Geographically Disperse, Culturable Seed-Associated Microbiota in Forage Plants of Alfalfa ( Medicago sativa L.) and Pitch Clover ( Bituminaria bituminosa L.): Characterization of Beneficial Inherited Strains as Plant Stress-Tolerance Enhancers. BIOLOGY 2022; 11:biology11121838. [PMID: 36552347 PMCID: PMC9775229 DOI: 10.3390/biology11121838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Agricultural production is being affected by increasingly harsh conditions caused by climate change. The vast majority of crops suffer growth and yield declines due to a lack of water or intense heat. Hence, commercial legume crops suffer intense losses of production (20-80%). This situation is even more noticeable in plants used as fodder for animals, such as alfalfa and pitch trefoil, since their productivity is linked not only to the number of seeds produced, but also to the vegetative growth of the plant itself. Thus, we decided to study the microbiota associated with their seeds in different locations on the Iberian Peninsula, with the aim of identifying culturable bacteria strains that have adapted to harsh environments and that can be used as biotreatments to improve plant growth and resistance to stress. As potentially inherited microbiota, they may also represent a treatment with medium- and long-term adaptative effects. Hence, isolated strains showed no clear relationship with their geographical sampling location, but had about 50% internal similarity with their model plants. Moreover, out of the 51 strains isolated, about 80% were capable of producing biofilms; around 50% produced mid/high concentrations of auxins and grew notably in ACC medium; only 15% were characterized as xerotolerant, while more than 75% were able to sporulate; and finally, 65% produced siderophores and more than 40% produced compounds to solubilize phosphates. Thus, Paenibacillus amylolyticus BB B2-A, Paenibacillus xylanexedens MS M1-C, Paenibacillus pabuli BB Oeiras A, Stenotrophomonas maltophilia MS M1-B and Enterobacter hormaechei BB B2-C strains were tested as plant bioinoculants in lentil plants (Lens culinaris Medik.), showing promising results as future treatments to improve plant growth under stressful conditions.
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Affiliation(s)
- Marla Niza-Costa
- iPlantMicro Lab, Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, Oeiras, 2784-501 Lisboa, Portugal
| | | | - Inês Rebelo-Romão
- iPlantMicro Lab, Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, Oeiras, 2784-501 Lisboa, Portugal
| | - María Victoria Ferrer
- iPlantMicro Lab, Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, Oeiras, 2784-501 Lisboa, Portugal
| | - Cristina Sequero López
- GeoBioTec, Department of Earth Sciences, NOVA School of Sciences and Technology, Universidade NOVA de Lisboa (Campus de Caparica), 1070-312 Caparica, Portugal
| | - Juan Ignacio Vílchez
- iPlantMicro Lab, Instituto de Tecnologia Química e Biológica (ITQB)-NOVA, Oeiras, 2784-501 Lisboa, Portugal
- Correspondence:
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Impacts of the Green Revolution on Rhizosphere Microbiology Related to Nutrient Acquisition. Appl Microbiol 2022. [DOI: 10.3390/applmicrobiol2040076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The Green Revolution (GR) involved selective breeding of cereals and the use of high fertilizer inputs with the goal of increasing crop yields to alleviate hunger. As a result of both greater use of inorganic fertilizers and the introduction of semi-dwarf cultivars, grain yield increased globally and hunger was alleviated in certain areas of the world. However, these changes in varietal selection and fertilization regimes have impacted soil fertility and the root-associated microbiome. Higher rates of inorganic fertilizer application resulted in reduced rhizosphere microbial diversity, while semi-dwarf varieties displayed a greater abundance of rhizosphere microbes associated with nitrogen utilization. Ultimately, selection for beneficial aboveground traits during the GR led to healthier belowground traits and nutrient uptake capabilities.
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Harutyunyan N, Kushugulova A, Hovhannisyan N, Pepoyan A. One Health Probiotics as Biocontrol Agents: One Health Tomato Probiotics. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11101334. [PMID: 35631758 PMCID: PMC9145216 DOI: 10.3390/plants11101334] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/08/2022] [Accepted: 05/08/2022] [Indexed: 05/06/2023]
Abstract
Tomato (Lycopersicon esculentum) is one of the most popular and valuable vegetables in the world. The most common products of its industrial processing in the food industry are juice, tomato paste, various sauces, canned or sun-dried fruits and powdered products. Tomato fruits are susceptible to bacterial diseases, and bacterial contamination can be a risk factor for the safety of processed tomato products. Developments in bioinformatics allow researchers to discuss target probiotic strains from an existing large number of probiotic strains for any link in the soil-plant-animal-human chain. Based on the literature and knowledge on the "One Health" concept, this study relates to the suggestion of a new term for probiotics: "One Health probiotics", beneficial for the unity of people, animals, and the environment. Strains of Lactiplantibacillus plantarum, having an ability to ferment a broad spectrum of plant carbohydrates, probiotic effects in human, and animal health, as well as being found in dairy products, vegetables, sauerkraut, pickles, some cheeses, fermented sausages, fish products, and rhizospheric soil, might be suggested as one of the probable candidates for "One Health" probiotics (also, for "One Health-tomato" probiotics) for the utilization in agriculture, food processing, and healthcare.
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Affiliation(s)
- Natalya Harutyunyan
- Food Safety and Biotechnology Department, Armenian National Agrarian University, 74 Teryan St., Yerevan 0009, Armenia;
| | - Almagul Kushugulova
- Laboratory of Human Microbiome and Longevity, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, 53 Kabanbay Batyr Ave., Nur-Sultan 010000, Kazakhstan;
| | - Narine Hovhannisyan
- Plant Origin Raw Material Processing Technology Department, Armenian National Agrarian University, 74 Teryan St., Yerevan 0009, Armenia;
| | - Astghik Pepoyan
- Food Safety and Biotechnology Department, Armenian National Agrarian University, 74 Teryan St., Yerevan 0009, Armenia;
- Correspondence: ; Tel.: +374-91-432-493
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Smulders L, Ferrero V, de la Peña E, Pozo MJ, Díaz Pendón JA, Benítez E, López-García Á. Resistance and Not Plant Fruit Traits Determine Root-Associated Bacterial Community Composition along a Domestication Gradient in Tomato. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010043. [PMID: 35009046 PMCID: PMC8747438 DOI: 10.3390/plants11010043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 05/12/2023]
Abstract
Soil bacterial communities are involved in multiple ecosystem services, key in determining plant productivity. Crop domestication and intensive agricultural practices often disrupt species interactions with unknown consequences for rhizosphere microbiomes. This study evaluates whether variation in plant traits along a domestication gradient determines the composition of root-associated bacterial communities; and whether these changes are related to targeted plant traits (e.g., fruit traits) or are side effects of less-often-targeted traits (e.g., resistance) during crop breeding. For this purpose, 18 tomato varieties (wild and modern species) differing in fruit and resistance traits were grown in a field experiment, and their root-associated bacterial communities were characterised. Root-associated bacterial community composition was influenced by plant resistance traits and genotype relatedness. When only considering domesticated tomatoes, the effect of resistance on bacterial OTU composition increases, while the effect due to phylogenetic relatedness decreases. Furthermore, bacterial diversity positively correlated with plant resistance traits. These results suggest that resistance traits not selected during domestication are related to the capacity of tomato varieties to associate with different bacterial groups. Taken together, these results evidence the relationship between plant traits and bacterial communities, pointing out the potential of breeding to affect plant microbiomes.
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Affiliation(s)
- Lisanne Smulders
- Department Enviromental Protection, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain;
- Correspondence:
| | - Victoria Ferrero
- Department of Biodiversity and Environmental Management, Campus de Vegazana s/n, University of León, 24071 León, Spain;
| | - Eduardo de la Peña
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium;
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
| | - María J. Pozo
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
| | - Juan Antonio Díaz Pendón
- Finca Experimental “La Mayora” CSIC, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC), 29750 Málaga, Spain;
| | - Emilio Benítez
- Department Enviromental Protection, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain;
| | - Álvaro López-García
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
- Department Animal Biology, Plant Biology and Ecology, Universidad de Jaén, 23071 Jaén, Spain
- Instituto Interuniversitario de Investigación del Sistema Tierra en Andalucía (IISTA), 18006 Granada, Spain
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