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McLaughlin S, Himmighofen P, Khan SA, Siffert A, Robert CAM, Sasse J. Root Exudation: An In-Depth Experimental Guide. PLANT, CELL & ENVIRONMENT 2025; 48:3052-3065. [PMID: 39676732 DOI: 10.1111/pce.15311] [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: 12/22/2023] [Accepted: 11/15/2024] [Indexed: 12/17/2024]
Abstract
Plants exude a wide variety of compounds into the rhizosphere, modulating soil functioning and diversity. The number of studies investigating exudation has exponentially increased over the past decades. Yet, the high inter-study variability of the results is slowing down our understanding of root-soil interactions. This variability is partly due to the absence of harmonized methodologies to collect and characterize exudation. Here, we discuss how various experimental aspects influence exudation profiles by performing a literature review, and we suggest best practices for different experimental setups. We discuss state-of-the-art of spatially resolved exudate collection, collection in controlled versus field conditions and plant growth setups ranging from hydroponics to soil. We highlight the importance of preparing experimental blanks, in situ versus ex situ exudate collection, various collection media and timing of collection, exudate storage and processing and analytical considerations. We summarize best practices for experimental setup and reporting of parameters in an easily accessible table format to facilitate discussion of best practices in the field. An increased standardization in the field together with the systematic studies suggested will improve our knowledge of how plant exudation shapes interactions with organisms in soil.
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Affiliation(s)
- Sarah McLaughlin
- Institute of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Paul Himmighofen
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Sheharyar A Khan
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Alexandra Siffert
- Institute of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | | | - Joëlle Sasse
- Institute of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
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de Haas BR, Oburger E, Van Labeke MC, Dhooghe E, Geelen D. Light and substrate composition control root exudation rates at the initial stages of soilless lettuce cultivation. SCIENTIA HORTICULTURAE 2025; 341:114006. [PMID: 39990249 PMCID: PMC11845566 DOI: 10.1016/j.scienta.2025.114006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 01/13/2025] [Accepted: 02/04/2025] [Indexed: 02/25/2025]
Abstract
Plant root exudation is an inherent metabolic process that enhances various functions of the root system like the mobilization of nutrients and interactions with surrounding microbial communities. In soilless crop production, roots are temporally submerged in a nutrient solution affecting the root exudation process. In this study, we asked whether root exudation in soilless cultures is affected by culturing method and substrate composition, important factors determining the root microbial ecosystem. Exploration of different growth conditions revealed that the effect of light quality depended on the substrate used. The impact of light quality and substrate was assessed by growing soilless lettuce in 100 % red light (660 nm), 100 % blue light (450 nm), and white light (full-light spectrum) in deep flow culture, or in 100 % perlite, 100 % potting soil, or mixtures of both growing media. Root exudates were collected at different time points after transplanting. The root exudation rate declined with plant age in all culturing conditions, underscoring its importance during the early stages of development. The total carbon root exudation rate was influenced by light conditions and substrate composition at the earliest timepoint of the culture but not at later growth stages. The total carbohydrate exudation rate was significantly higher under pure blue and red light compared to white light. The impact of light depended on the presence of perlite in the substrate. The total phenolic compound exudation rate was most strongly influenced by the substrate composition and reached the highest level in either pure potting soil or pure perlite. Light and growing media influence the exudation rate at the early stage, suggesting that exudation is an adaptive process of the soilless lettuce culture.
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Affiliation(s)
- Brechtje R. de Haas
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Eva Oburger
- BOKU, University of Natural Resources and Life Sciences, Institute of Soil Research, 3430 Tulln an der Donau, Austria
| | - Marie-Christine Van Labeke
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Emmy Dhooghe
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Danny Geelen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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Schwalm H, Staudinger C, Hajirezaei MR, Mundschenk E, Golestanifard A, Holz M, Wissuwa M, Oburger E. Root exudation patterns of contrasting rice (Oryza sativa L.) lines in response to P limitation. PLANTA 2024; 260:123. [PMID: 39441370 PMCID: PMC11499414 DOI: 10.1007/s00425-024-04556-2] [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: 07/17/2024] [Accepted: 10/14/2024] [Indexed: 10/25/2024]
Abstract
MAIN CONCLUSION Rice exudation patterns changed in response to P deficiency. Higher exudation rates were associated with lower biomass production. Total carboxylate exudation rates mostly decreased under P-limiting conditions. Within the rhizosphere, root exudates are believed to play an important role in plant phosphorus (P) acquisition. This could be particularly beneficial in upland rice production where P is often limited. However, knowledge gaps remain on how P deficiency shapes quality and quantity of root exudation in upland rice genotypes. We therefore investigated growth, plant P uptake, and root exudation patterns of two rice genotypes differing in P efficiency in semi-hydroponics at two P levels (low P = 1 µM, adequate P = 100 µM). Root exudates were collected hydroponically 28 and 40 days after germination to analyze total carbon (C), carbohydrates, amino acids, phenolic compounds spectrophotometrically and carboxylates using a targeted LC-MS approach. Despite their reported role in P solubilization, we observed that carboxylate exudation rates per unit root surface area were not increased under P deficiency. In contrast, exudation rates of total C, carbohydrates, amino acids and phenolics were mostly enhanced in response to low P supply. Overall, higher exudation rates were associated with lower biomass production in the P-inefficient genotype Nerica4, whereas the larger root system with lower C investment (per unit root surface area) in root exudates of the P-efficient DJ123 allowed for better plant growth under P deficiency. Our results reveal new insights into genotype-specific resource allocation in rice under P-limiting conditions that warrant follow-up research including more genotypes.
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Affiliation(s)
- Henning Schwalm
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, 3430, Tulln an der Donau, Vienna, Austria
| | - Christiana Staudinger
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, 3430, Tulln an der Donau, Vienna, Austria
- Department of Crop Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences, 3430, Tulln an der Donau, Vienna, Austria
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gartersleben, Germany
| | - Eva Mundschenk
- Group of Isotope Biogeochemistry and Gas Fluxes, Leibniz Centre for Agricultural Landscape Research (ZALF) e.V., Müncheberg, Germany
| | - Alireza Golestanifard
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, 3430, Tulln an der Donau, Vienna, Austria
| | - Maire Holz
- Group of Isotope Biogeochemistry and Gas Fluxes, Leibniz Centre for Agricultural Landscape Research (ZALF) e.V., Müncheberg, Germany
| | - Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | - Eva Oburger
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, 3430, Tulln an der Donau, Vienna, Austria.
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Meshram S, Adhikari TB. Microbiome-Mediated Strategies to Manage Major Soil-Borne Diseases of Tomato. PLANTS (BASEL, SWITZERLAND) 2024; 13:364. [PMID: 38337897 PMCID: PMC10856849 DOI: 10.3390/plants13030364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024]
Abstract
The tomato (Solanum lycopersicum L.) is consumed globally as a fresh vegetable due to its high nutritional value and antioxidant properties. However, soil-borne diseases can severely limit tomato production. These diseases, such as bacterial wilt (BW), Fusarium wilt (FW), Verticillium wilt (VW), and root-knot nematodes (RKN), can significantly reduce the yield and quality of tomatoes. Using agrochemicals to combat these diseases can lead to chemical residues, pesticide resistance, and environmental pollution. Unfortunately, resistant varieties are not yet available. Therefore, we must find alternative strategies to protect tomatoes from these soil-borne diseases. One of the most promising solutions is harnessing microbial communities that can suppress disease and promote plant growth and immunity. Recent omics technologies and next-generation sequencing advances can help us develop microbiome-based strategies to mitigate tomato soil-borne diseases. This review emphasizes the importance of interdisciplinary approaches to understanding the utilization of beneficial microbiomes to mitigate soil-borne diseases and improve crop productivity.
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Affiliation(s)
- Shweta Meshram
- Department of Plant Pathology, Lovely Professional University, Phagwara 144402, India;
| | - Tika B. Adhikari
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
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Santangeli M, Steininger-Mairinger T, Vetterlein D, Hann S, Oburger E. Maize (Zea mays L.) root exudation profiles change in quality and quantity during plant development - A field study. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111896. [PMID: 37838155 DOI: 10.1016/j.plantsci.2023.111896] [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: 07/14/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023]
Abstract
Deciphering root exudate composition of soil-grown plants is considered a crucial step to better understand plant-soil-microbe interactions affecting plant growth performance. In this study, two genotypes of Zea mays L. (WT, rth3) differing in root hair elongation were grown in the field in two substrates (sand, loam) in custom-made, perforated columns inserted into the field plots. Root exudates were collected at different plant developmental stages (BBCH 14, 19, 59, 83) using a soil-hydroponic-hybrid exudation sampling approach. Exudates were characterized by LC-MS based non-targeted metabolomics, as well as by photometric assays targeting total dissolved organic carbon, soluble carbohydrates, proteins, amino acids, and phenolics. Results showed that plant developmental stage was the main driver shaping both the composition and quantity of exuded compounds. Carbon (C) exudation per plant increased with increasing biomass production over time, while C exudation rate per cm² root surface area h-1 decreased with plant maturity. Furthermore, exudation rates were higher in the substrate with lower nutrient mobility (i.e., loam). Surprisingly, we observed higher exudation rates in the root hairless rth3 mutant compared to the root hair-forming WT sibling, though exudate metabolite composition remained similar. Our results highlight the impact of plant developmental stage on the plant-soil-microbe interplay.
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Affiliation(s)
- Michael Santangeli
- University of Natural Resources and Life Sciences, Vienna, Department of Forest and Soil Science, Institute of Soil Research, 3430 Tulln an der Donau, Austria; University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, 1190 Vienna, Austria
| | - Teresa Steininger-Mairinger
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, 1190 Vienna, Austria
| | - Doris Vetterlein
- Department of Soil System Science, UFZ, 06120 Halle/Saale, Germany; Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Stephan Hann
- University of Natural Resources and Life Sciences, Vienna, Department of Chemistry, Institute of Analytical Chemistry, 1190 Vienna, Austria
| | - Eva Oburger
- University of Natural Resources and Life Sciences, Vienna, Department of Forest and Soil Science, Institute of Soil Research, 3430 Tulln an der Donau, Austria.
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Salem MA, Wang JY, Al-Babili S. Metabolomics of plant root exudates: From sample preparation to data analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:1062982. [PMID: 36561464 PMCID: PMC9763704 DOI: 10.3389/fpls.2022.1062982] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Plants release a set of chemical compounds, called exudates, into the rhizosphere, under normal conditions and in response to environmental stimuli and surrounding soil organisms. Plant root exudates play indispensable roles in inhibiting the growth of harmful microorganisms, while also promoting the growth of beneficial microbes and attracting symbiotic partners. Root exudates contain a complex array of primary and specialized metabolites. Some of these chemicals are only found in certain plant species for shaping the microbial community in the rhizosphere. Comprehensive understanding of plant root exudates has numerous applications from basic sciences to enhancing crop yield, production of stress-tolerant crops, and phytoremediation. This review summarizes the metabolomics workflow for determining the composition of root exudates, from sample preparation to data acquisition and analysis. We also discuss recent advances in the existing analytical methods and future perspectives of metabolite analysis.
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Affiliation(s)
- Mohamed A. Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University, Menoufia, Egypt
| | - Jian You Wang
- The BioActives Lab, Center for Desert Agriculture, Biological and Environment Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Salim Al-Babili
- The BioActives Lab, Center for Desert Agriculture, Biological and Environment Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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