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Nicotra D, Ghadamgahi F, Ghosh S, Anzalone A, Dimaria G, Mosca A, Massimino ME, Vetukuri RR, Catara V. Genomic insights and biocontrol potential of ten bacterial strains from the tomato core microbiome. FRONTIERS IN PLANT SCIENCE 2024; 15:1437947. [PMID: 39253574 PMCID: PMC11381245 DOI: 10.3389/fpls.2024.1437947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/05/2024] [Indexed: 09/11/2024]
Abstract
Introduction Despite their adverse environmental effects, modern agriculture relies heavily on agrochemicals to manage diseases and pests and enhance plant growth and productivity. Some of these functions could instead be fulfilled by endophytes from the plant microbiota, which have diverse activities beneficial for plant growth and health. Methods We therefore used a microbiome-guided top-down approach to select ten bacterial strains from different taxa in the core microbiome of tomato plants in the production chain for evaluation as potential bioinoculants. High-quality genomes for each strain were obtained using Oxford Nanopore long-read and Illumina short-read sequencing, enabling the dissection of their genetic makeup to identify phyto-beneficial traits. Results Bacterial strains included both taxa commonly used as biofertilizers and biocontrol agents (i.e. Pseudomonas and Bacillus) as well as the less studied genera Leclercia, Chryseobacterium, Glutamicibacter, and Paenarthorbacter. When inoculated in the tomato rhizosphere, these strains promoted plant growth and reduced the severity of Fusarium Crown and Root Rot and Bacterial Spot infections. Genome analysis yielded a comprehensive inventory of genes from each strain related to processes including colonization, biofertilization, phytohormones, and plant signaling. Traits directly relevant to fertilization including phosphate solubilization and acquisition of nitrogen and iron were also identified. Moreover, the strains carried several functional genes putatively involved in abiotic stress alleviation and biotic stress management, traits that indirectly foster plant health and growth. Discussion This study employs a top-down approach to identify new plant growth-promoting rhizobacteria (PGPRs), offering an alternative to the conventional bottom-up strategy. This method goes beyond the traditional screening of the strains and thus can expand the range of potential bioinoculants available for market application, paving the way to the use of new still underexplored genera.
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Affiliation(s)
- Daniele Nicotra
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Farideh Ghadamgahi
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Samrat Ghosh
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Alice Anzalone
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Giulio Dimaria
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Alexandros Mosca
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Maria Elena Massimino
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Ramesh Raju Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
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Seo H, Kim JH, Lee SM, Lee SW. The Plant-Associated Flavobacterium: A Hidden Helper for Improving Plant Health. THE PLANT PATHOLOGY JOURNAL 2024; 40:251-260. [PMID: 38835296 PMCID: PMC11162857 DOI: 10.5423/ppj.rw.01.2024.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 04/01/2024] [Accepted: 04/06/2024] [Indexed: 06/06/2024]
Abstract
Flavobacterium is a genus within the phylum Bacteroidota that remains relatively unexplored. Recent analyses of plant microbiota have identified the phylum Bacteroidota as a major bacterial group in the plant rhizosphere. While Flavobacterium species within the phylum Bacteroidota have been recognized as pathogens in the aquatic habitats, microbiome analysis and the characterization of novel Flavobacterium species have indicated the great diversity and potential of their presence in various environments. Many Flavobacterium species have positively contribute to plant health and development, including growth promotion, disease control, and tolerance to abiotic stress. Despite the well-described beneficial interactions of the Flavobacterium species with plants, the molecular mechanisms and bacterial determinants underlying these interactions remain unclear. To broaden our understanding of the genus Flavobacterium's role in plant health, we review the recent studies focusing on their ecological niche, functional roles, and determinants in plant-beneficial interactions. Additionally, this review discusses putative mechanisms explaining the interactions between plants and Flavobacterium. We have also introduced the importance of future research on Flavobacterium spp. and its potential applications in agriculture.
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Affiliation(s)
- Hyojun Seo
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea
| | - Ju Hui Kim
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea
| | - Sang-Moo Lee
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea
- Institute of Agricultural Life Sciences, Dong-A University, Busan 49315, Korea
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Gutierrez Yanez D, Testen AL, Peduto Hand F. Evaluation of Anaerobic Soil Disinfestation to Reduce Soilborne Diseases in Soilless and Soil-Based Substrates for Specialty Cut Flower Production. PLANT DISEASE 2024; 108:908-919. [PMID: 37814515 DOI: 10.1094/pdis-05-23-0857-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Anaerobic soil disinfestation (ASD) is a nonchemical soil treatment where an easily decomposable carbon source is incorporated into soil, which is then irrigated to saturation and tarped to create anaerobic conditions, which prompts shifts in the soil microbiota from aerobes to anaerobes. ASD has been tested successfully for soilborne disease management in a variety of cropping systems but has not been sufficiently investigated in ornamentals. In this study, ASD was evaluated in soil-based and soilless substrates commonly used in specialty cut flower production using two model pathosystems: Rhizoctonia solani-Zinnia elegans and Phytophthora drechsleri-Gerbera jamesonii. Each substrate was mixed with pathogen-infested vermiculite and amended with either wheat bran, tomato pomace, or soybean meal as the carbon source. Amended substrates were incubated at 25°C for 4 weeks and used as growing substrates for the two crops mentioned above, which were monitored weekly for disease development for up to 5 weeks posttransplant. Additional experiments tested the effect of plant age and inoculum concentration in the substrate on ASD efficacy. Results showed that ASD has the potential to be deployed successfully for the control of Rhizoctonia stem rot in both substrates. Conversely, ASD was not effective at controlling Phytophthora crown rot on gerbera daisy in any of the experiments conducted in this study. More research is needed to understand the influence of carbon amendments, inoculum thresholds, and environmental conditions on ASD efficacy.
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Quijia Pillajo J, Chapin LJ, Quiroz-Moreno CD, Altland JE, Jones ML. Nutrient availability and plant phenological stage influence the substrate microbiome in container-grown Impatiens walleriana 'Xtreme Red'. BMC PLANT BIOLOGY 2024; 24:176. [PMID: 38448825 PMCID: PMC10916185 DOI: 10.1186/s12870-024-04854-7] [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: 11/28/2023] [Accepted: 02/22/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND The microbiome plays a fundamental role in plant health and performance. Soil serves as a reservoir of microbial diversity where plants attract microorganisms via root exudates. The soil has an important impact on the composition of the rhizosphere microbiome, but greenhouse ornamental plants are commonly grown in soilless substrates. While soil microbiomes have been extensively studied in traditional agriculture to improve plant performance, health, and sustainability, information about the microbiomes of soilless substrates is still limited. Thus, we conducted an experiment to explore the microbiome of a peat-based substrate used in container production of Impatiens walleriana, a popular greenhouse ornamental plant. We investigated the effects of plant phenological stage and fertilization level on the substrate microbiome. RESULTS Impatiens plants grown under low fertilization rates were smaller and produced more flowers than plants grown under optimum and high fertilization. The top five bacterial phyla present in the substrate were Proteobacteria, Actinobacteria, Bacteriodota, Verrucomicrobiota, and Planctomycetota. We found a total of 2,535 amplicon sequence variants (ASV) grouped into 299 genera. The substrate core microbiome was represented by only 1.8% (48) of the identified ASV. The microbiome community composition was influenced by plant phenological stage and fertilizer levels. Phenological stage exhibited a stronger influence on microbiome composition than fertilizer levels. Differential abundance analysis using DESeq2 identified more ASVs significantly affected (enriched or depleted) in the high fertilizer levels at flowering. As observed for community composition, the effect of plant phenological stage on microbial community function was stronger than fertilizer level. Phenological stage and fertilizer treatments did not affect alpha-diversity in the substrate. CONCLUSIONS In container-grown ornamental plants, the substrate serves as the main microbial reservoir for the plant, and the plant and agricultural inputs (fertilization) modulate the microbial community structure and function of the substrate. The differences observed in substrate microbiome composition across plant phenological stage were explained by pH, total organic carbon (TOC) and fluoride, and across fertilizer levels by pH and phosphate (PO4). Our project provides an initial diversity profile of the bacteria occurring in soilless substrates, an underexplored source of microbial diversity.
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Affiliation(s)
- Juan Quijia Pillajo
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, 44691, USA
| | - Laura J Chapin
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, 44691, USA
| | - Cristian D Quiroz-Moreno
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH, 43210, USA
| | - James E Altland
- Application Technology Research Unit, United States Department of Agriculture (USDA)-Agricultural Research Service, Wooster, OH, 44691, USA
| | - Michelle L Jones
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, 44691, USA.
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Saeed F, Hashmi MH, Aksoy E, Demirel U, Bakhsh A. Identification and characterization of RNA polymerase II (RNAP) C-Terminal domain phosphatase-like 3 (SlCPL3) in tomato under biotic stress. Mol Biol Rep 2023; 50:6783-6793. [PMID: 37392286 DOI: 10.1007/s11033-023-08564-5] [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: 12/14/2022] [Accepted: 05/31/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND Bacterial diseases are a huge threat to the production of tomatoes. During infection intervals, pathogens affect biochemical, oxidant and molecular properties of tomato. Therefore, it is necessary to study the antioxidant enzymes, oxidation state and genes involved during bacterial infection in tomato. METHODS AND RESULTS Different bioinformatic analyses were performed to conduct homology, gene promoter analysis and determined protein structure. Antioxidant, MDA and H2O2 response was measured in Falcon, Rio grande and Sazlica tomato cultivars. In this study, RNA Polymerase II (RNAP) C-Terminal Domain Phosphatase-like 3 (SlCPL-3) gene was identified and characterized. It contained 11 exons, and encoded for two protein domains i.e., CPDCs and BRCT. SOPMA and Phyre2, online bioinformatic tools were used to predict secondary structure. For the identification of protein pockets CASTp web-based tool was used. Netphos and Pondr was used for prediction of phosphorylation sites and protein disordered regions. Promoter analysis revealed that the SlCPL-3 is involved in defense-related mechanisms. We further amplified two different regions of SlCPL-3 and sequenced them. It showed homology respective to the reference tomato genome. Our results showed that SlCPL-3 gene was triggered during bacterial stress. SlCPL-3 expression was upregulated in response to bacterial stress during different time intervals. Rio grande showed a high level of SICPL-3 gene expression after 72 hpi. Biochemical and gene expression analysis showed that under biotic stress Rio grande cultivar is more sensitive to Pst DC 3000 bacteria. CONCLUSION This study lays a solid foundation for the functional characterization of SlCPL-3 gene in tomato cultivars. All these findings would be beneficial for further analysis of SlCPL-3 gene and may be helpful for the development of resilient tomato cultivars.
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Affiliation(s)
- Faisal Saeed
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240, Nigde, Turkey
| | - Muneeb Hassan Hashmi
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240, Nigde, Turkey
| | - Emre Aksoy
- Dept. of Biological Sciences, Middle East Technical University, 06800, Cankaya, Ankara, Turkey
| | - Ufuk Demirel
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240, Nigde, Turkey
| | - Allah Bakhsh
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240, Nigde, Turkey.
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
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Resendiz-Nava CN, Alonso-Onofre F, Silva-Rojas HV, Rebollar-Alviter A, Rivera-Pastrana DM, Stasiewicz MJ, Nava GM, Mercado-Silva EM. Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System. Microorganisms 2023; 11:1633. [PMID: 37512805 PMCID: PMC10383152 DOI: 10.3390/microorganisms11071633] [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: 05/18/2023] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
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 (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, 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 Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. 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.
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Affiliation(s)
- Carolina N Resendiz-Nava
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | | | - Hilda V Silva-Rojas
- Posgrado en Recursos Geneticos y Productividad, Produccion de Semillas, Colegio de Postgraduados, Km 36.5 Carretera Mexico-Texcoco, Texcoco 56264, Mexico
| | - Angel Rebollar-Alviter
- Centro Regional Morelia, Universidad Autonoma de Chapingo, Morelia 58170, Michoacan, Mexico
| | - Dulce M Rivera-Pastrana
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | - Matthew J Stasiewicz
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 1302W Pennsylvania Ave, Urbana, IL 61801, USA
| | - Gerardo M Nava
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
| | - Edmundo M Mercado-Silva
- Facultad de Quimica, Universidad Autonoma de Queretaro, Cerro de las Campanas S/N, Queretaro 76010, Queretaro, Mexico
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A Potential Application of Pseudomonas psychrotolerans IALR632 for Lettuce Growth Promotion in Hydroponics. Microorganisms 2023; 11:microorganisms11020376. [PMID: 36838341 PMCID: PMC9962264 DOI: 10.3390/microorganisms11020376] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Controlled environment agriculture hydroponic systems grow plants year-round without restriction from outside environmental conditions. In order to further improve crop yield, plant growth-promoting bacteria were tested on hydroponically grown lettuce (Lactuca sativa) plants. From our bacterial endophyte library, we found one bacterium, Pseudomonas psychrotolerans IALR632, that is promising in promoting lettuce growth in multiple hydroponic systems. When Green Oakleaf lettuce seeds were inoculated with IALR632 during germination, IALR632 significantly increased lateral root development by 164%. When germinated seedlings were inoculated with IALR632 and then transplanted to different hydroponic systems, shoot and root fresh weights of Green Oakleaf increased by 55.3% and 17.2% in a nutrient film technique (NFT) system in the greenhouse, 13.5% and 13.8% in an indoor vertical NFT system, and 15.3% and 13.6% in a deep water cultivation (DWC) system, respectively. IALR632 also significantly increased shoot fresh weights of Rex by 33.9%, Red Oakleaf by 21.0%, Red Sweet Crisp by 15.2%, and Nancy by 29.9%, as well as Red Rosie by 8.6% (no significant difference). Inoculation of IALR632-GFP and subsequent analysis by confocal microscopy demonstrated the endophytic nature and translocation from roots to shoots. The results indicate that P. psychrotolerans IALR632 has a potential application in hydroponically grown lettuce plants.
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Stegelmeier AA, Rose DM, Joris BR, Glick BR. The Use of PGPB to Promote Plant Hydroponic Growth. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202783. [PMID: 36297807 PMCID: PMC9611108 DOI: 10.3390/plants11202783] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 05/13/2023]
Abstract
Improvements to the world's food supply chain are needed to ensure sufficient food is produced to meet increasing population demands. Growing food in soilless hydroponic systems constitutes a promising strategy, as this method utilizes significantly less water than conventional agriculture, can be situated in urban areas, and can be stacked vertically to increase yields per acre. However, further research is needed to optimize crop yields in these systems. One method to increase hydroponic plant yields involves adding plant growth-promoting bacteria (PGPB) into these systems. PGPB are organisms that can significantly increase crop yields via a wide range of mechanisms, including stress reduction, increases in nutrient uptake, plant hormone modulation, and biocontrol. The aim of this review is to provide critical information for researchers on the current state of the use of PGPB in hydroponics so that meaningful advances can be made. An overview of the history and types of hydroponic systems is provided, followed by an overview of known PGPB mechanisms. Finally, examples of PGPB research that has been conducted in hydroponic systems are described. Amalgamating the current state of knowledge should ensure that future experiments can be designed to effectively transition results from the lab to the farm/producer, and the consumer.
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Affiliation(s)
- Ashley A. Stegelmeier
- Ceragen Inc., 151 Charles St W, Suite 199, Kitchener, ON N2G 1H6, Canada
- Correspondence: author:
| | - Danielle M. Rose
- Ceragen Inc., 151 Charles St W, Suite 199, Kitchener, ON N2G 1H6, Canada
| | - Benjamin R. Joris
- Ceragen Inc., 151 Charles St W, Suite 199, Kitchener, ON N2G 1H6, Canada
| | - Bernard R. Glick
- Department of Biology, University of Waterloo, 200 University Avenue West, Waterloo, ON N2L 3G1, Canada
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