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Novak V, Andeer PF, Bowen BP, Ding Y, Zhalnina K, Hofmockel KS, Tomaka C, Harwood TV, van Winden MCM, Golini AN, Kosina SM, Northen TR. Reproducible growth of Brachypodium in EcoFAB 2.0 reveals that nitrogen form and starvation modulate root exudation. Sci Adv 2024; 10:eadg7888. [PMID: 38170767 PMCID: PMC10776018 DOI: 10.1126/sciadv.adg7888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Understanding plant-microbe interactions requires examination of root exudation under nutrient stress using standardized and reproducible experimental systems. We grew Brachypodium distachyon hydroponically in fabricated ecosystem devices (EcoFAB 2.0) under three inorganic nitrogen forms (nitrate, ammonium, and ammonium nitrate), followed by nitrogen starvation. Analyses of exudates with liquid chromatography-tandem mass spectrometry, biomass, medium pH, and nitrogen uptake showed EcoFAB 2.0's low intratreatment data variability. Furthermore, the three inorganic nitrogen forms caused differential exudation, generalized by abundant amino acids-peptides and alkaloids. Comparatively, nitrogen deficiency decreased nitrogen-containing compounds but increased shikimates-phenylpropanoids. Subsequent bioassays with two shikimates-phenylpropanoids (shikimic and p-coumaric acids) on soil bacteria or Brachypodium seedlings revealed their distinct capacity to regulate both bacterial and plant growth. Our results suggest that (i) Brachypodium alters exudation in response to nitrogen status, which can affect rhizobacterial growth, and (ii) EcoFAB 2.0 is a valuable standardized plant research tool.
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Affiliation(s)
- Vlastimil Novak
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Peter F. Andeer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yezhang Ding
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kateryna Zhalnina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kirsten S. Hofmockel
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Connor Tomaka
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas V. Harwood
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Amber N. Golini
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Suzanne M. Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, 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 Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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3
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McLaughlin S, Zhalnina K, Kosina S, Northen TR, Sasse J. The core metabolome and root exudation dynamics of three phylogenetically distinct plant species. Nat Commun 2023; 14:1649. [PMID: 36964135 PMCID: PMC10039077 DOI: 10.1038/s41467-023-37164-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 03/01/2023] [Indexed: 03/26/2023] Open
Abstract
Root exudates are plant-derived, exported metabolites likely shaping root-associated microbiomes by acting as nutrients and signals. However, root exudation dynamics are unclear and thus also, if changes in exudation are reflected in changes in microbiome structure. Here, we assess commonalities and differences between exudates of different plant species, diurnal exudation dynamics, as well as the accompanying methodological aspects of exudate sampling. We find that exudates should be collected for hours rather than days as many metabolite abundances saturate over time. Plant growth in sterile, nonsterile, or sugar-supplemented environments significantly alters exudate profiles. A comparison of Arabidopsis thaliana, Brachypodium distachyon, and Medicago truncatula shoot, root, and root exudate metabolite profiles reveals clear differences between these species, but also a core metabolome for tissues and exudates. Exudate profiles also exhibit a diurnal signature. These findings add to the methodological and conceptual groundwork for future exudate studies to improve understanding of plant-microbe interactions.
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Affiliation(s)
- Sarah McLaughlin
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA
- Institute for Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Kateryna Zhalnina
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA
| | - Suzanne Kosina
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA
| | - Trent R Northen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA.
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Joelle Sasse
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology, Berkeley, CA, USA.
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Institute for Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
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Salem MA, Wang JY, Al-Babili S. Metabolomics of plant root exudates: From sample preparation to data analysis. Front Plant Sci 2022; 13:1062982. [PMID: 36561464 PMCID: PMC9763704 DOI: 10.3389/fpls.2022.1062982] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [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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5
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Oburger E, Staudinger C, Spiridon A, Benyr V, Aleksza D, Wenzel W, Santangeli M. A quick and simple spectrophotometric method to determine total carbon concentrations in root exudate samples of grass species. Plant Soil 2022; 478:273-281. [PMID: 36277077 PMCID: PMC9579099 DOI: 10.1007/s11104-022-05519-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/23/2022] [Indexed: 06/16/2023]
Abstract
PURPOSE Root exudates are key components driving belowground interaction between plant, microbes and soil. High-end analytical approaches provide advanced insights into exudate metabolite diversity, however, the amount of total carbon (C) released by roots should always be determined as the most basic parameter when characterizing root exudation as it (i) provides quantitative information of C exuded into the surrounding soil and (ii) allows to relate the abundance of individual exudate compounds to total C released. Here we propose a simple and quick, spectrophotometry-based method to quantify total dissolved organic carbon (DOC) concentration in exudation samples that is based on measuring the absorption of a pre-filtered but otherwise untreated exudate sample at 260 nm (DOC260). METHOD Exudate samples collected from different grass genotypes (Zea mays, Oryza sativa, Hordeum vulgare) grown in various experimental settings (soil, hydroponic) were analysed with the DOC260 assay and results were compared with C concentrations obtained by liquid TOC-analyser. CONCLUSION We demonstrated that the DOC260 method allowed for quick and inexpensive measurements of total dissolved organic carbon concentrations in exudate samples from grass species grown under nutrient sufficient as well as under P deficient conditions. Interestingly, DOC260 failed to predict DOC concentrations in exudate samples from plants grown under Zn and Fe deficiency suggesting a strong shift in metabolite composition under micronutrient deficiency. Even though the applicability of the DOC260 method remains to be tested on exudate samples originating from dicots and plants exposed to other environmental stresses (e.g. pathogen attack, heavy metal stress, etc), it will help to increase our understanding of root exudation and related rhizosphere processes in the future.
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Affiliation(s)
- Eva Oburger
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, Tulln, Austria
| | - Christiana Staudinger
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, Tulln, Austria
- Department of Chemistry, Institute of Analytical chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Andreea Spiridon
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, Tulln, Austria
| | - Vera Benyr
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, Tulln, Austria
| | - David Aleksza
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, Tulln, Austria
| | - Walter Wenzel
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, Tulln, Austria
| | - Michael Santangeli
- Department of Forest and Soil Science, Institute of Soil Research, University of Natural Resources and Life Sciences, Tulln, Austria
- Department of Chemistry, Institute of Analytical chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
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6
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Aufrecht J, Khalid M, Walton CL, Tate K, Cahill JF, Retterer ST. Hotspots of root-exuded amino acids are created within a rhizosphere-on-a-chip. Lab Chip 2022; 22:954-963. [PMID: 35089295 DOI: 10.1039/d1lc00705j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The rhizosphere is a challenging ecosystem to study from a systems biology perspective due to its diverse chemical, physical, and biological characteristics. In the past decade, microfluidic platforms (e.g. plant-on-a-chip) have created an alternative way to study whole rhizosphere organisms, like plants and microorganisms, under reduced-complexity conditions. However, in reducing the complexity of the environment, it is possible to inadvertently alter organism phenotype, which biases laboratory data compared to in situ experiments. To build back some of the complexity of the rhizosphere in a fully-defined, parameterized approach we have developed a rhizosphere-on-a-chip platform that mimics the physical structure of soil. We demonstrate, through computational simulation, how this synthetic soil structure can influence the emergence of molecular "hotspots" and "hotmoments" that arise naturally from the plant's exudation of labile carbon compounds. We establish the amenability of the rhizosphere-on-a-chip for long-term culture of Brachypodium distachyon, and experimentally validate the presence of exudate hotspots within the rhizosphere-on-a-chip pore spaces using liquid microjunction surface sampling probe mass spectrometry.
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Affiliation(s)
- Jayde Aufrecht
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - Muneeba Khalid
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Courtney L Walton
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kylee Tate
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
| | - John F Cahill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Scott T Retterer
- Center for Nanophase Materials Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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7
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Frémont A, Sas E, Sarrazin M, Gonzalez E, Brisson J, Pitre FE, Brereton NJB. Phytochelatin and coumarin enrichment in root exudates of arsenic-treated white lupin. Plant Cell Environ 2022; 45:936-954. [PMID: 34392550 DOI: 10.1111/pce.14163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Soil contamination with toxic metalloids, such as arsenic, can represent a substantial human health and environmental risk. Some plants are thought to tolerate soil toxicity using root exudation, however, the nature of this response to arsenic remains largely unknown. Here, white lupin plants were exposed to arsenic in a semi-hydroponic system and their exudates were profiled using untargeted liquid chromatography-tandem mass spectrometry. Arsenic concentrations up to 1 ppm were tolerated and led to the accumulation of 12.9 μg As g-1 dry weight (DW) and 411 μg As g-1 DW in above-ground and belowground tissues, respectively. From 193 exuded metabolites, 34 were significantly differentially abundant due to 1 ppm arsenic, including depletion of glutathione disulphide and enrichment of phytochelatins and coumarins. Significant enrichment of phytochelatins in exudates of arsenic-treated plants was further confirmed using exudate sampling with strict root exclusion. The chemical tolerance toolkit in white lupin included nutrient acquisition metabolites as well as phytochelatins, the major intracellular metal-binding detoxification oligopeptides which have not been previously reported as having an extracellular role. These findings highlight the value of untargeted metabolite profiling approaches to reveal the unexpected and inform strategies to mitigate anthropogenic pollution in soils around the world.
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Affiliation(s)
- Adrien Frémont
- University of Montreal-Institut de Recherche en Biologie Végétale (IRBV), Montreal, Quebec, Canada
| | - Eszter Sas
- University of Montreal-Institut de Recherche en Biologie Végétale (IRBV), Montreal, Quebec, Canada
| | | | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics (C3G)-Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Microbiome Research Platform-McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jacques Brisson
- University of Montreal-Institut de Recherche en Biologie Végétale (IRBV), Montreal, Quebec, Canada
| | - Frédéric Emmanuel Pitre
- University of Montreal-Institut de Recherche en Biologie Végétale (IRBV), Montreal, Quebec, Canada
- Montreal Botanical Garden, Montreal, Quebec, Canada
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8
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Zhang X, Liu S, Jiang Z, Wu Y, Huang X. Gradient of microbial communities around seagrass roots was mediated by sediment grain size. Ecosphere 2022. [DOI: 10.1002/ecs2.3942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Xia Zhang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Songlin Liu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
- Key Laboratory of Tropical Marine Biotechnology of Hainan Province Sanya Institute of Oceanology, SCSIO Sanya China
| | - Zhijian Jiang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Yunchao Wu
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
| | - Xiaoping Huang
- Key Laboratory of Tropical Marine Bio‐resources and Ecology South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou China
- Southern Marine Science and Engineering Guangdong Laboratory Guangzhou China
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9
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Ma KW, Ordon J, Schulze-Lefert P. Gnotobiotic Plant Systems for Reconstitution and Functional Studies of the Root Microbiota. Curr Protoc 2022; 2:e362. [PMID: 35120282 DOI: 10.1002/cpz1.362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Healthy plants host a multi-kingdom community of microbes, which is known as the plant microbiota. Amplicon sequencing technologies for microbial genomic markers were a milestone in revealing the taxonomic composition of the microbiota and its variation associated with a plant host in natural environments. However, this method alone does not allow conclusions to be drawn about functions of these microbial assemblages for the plant. The development of culture collections, which recapitulate natural microbial communities in their diversity, and multiple gnotobiotic plant systems therefore represent a breakthrough in plant-microbiota research such that plants can be inoculated with defined communities to study proposed microbiota functions. These systems provided, for the root microbiota, first insights into mechanisms underlying microbial community establishment and contributions of its microbial members to indirect pathogen protection and mineral nutrition of the host. We argue that the choice of a gnotobiotic system for microbiota reconstitution and subsequent functional analysis depends on the particular plant trait that is influenced by the microbiota. We start by discussing the advantages and limitations of using individual gnotobiotic systems and then describe the general procedures for preparing bacterial cultures from the Arabidopsis thaliana At-R-SPHERE culture collection for inoculation and cocultivation in two gnotobiotic plant growth systems using agar and perlite matrix. Additionally, a protocol for inoculation of plants with opportunistic Pseudomonas pathogens is provided. Lastly, we describe a high-throughput system for visual assessment of roots after inoculation with individual mutants of a transposon library generated from a root-derived bacterial commensal. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Preparation of bacterial cultures from At-R-SPHERE Support Protocol 1: Validation of strains by sequencing hypervariable regions of the 16S rRNA gene Basic Protocol 2: Coinoculation of plants grown on an agar matrix with microbial elicitor and a defined microbial community Alternate Protocol: Inoculation of plants cultivated in a perlite-based growth system Support Protocol 2: Surface sterilization of Arabidopsis thaliana seeds Basic Protocol 3: Inoculation using a Pseudomonas opportunistic pathogen Basic Protocol 4: Assessment of commensal-mediated root phenotypes using phytostrips.
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Affiliation(s)
- Ka-Wai Ma
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jana Ordon
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, Germany
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Nakabayashi R, Takeda-Kamiya N, Yamada Y, Mori T, Uzaki M, Nirasawa T, Toyooka K, Saito K. A multimodal metabolomics approach using imaging mass spectrometry and liquid chromatography-tandem mass spectrometry for spatially characterizing monoterpene indole alkaloids secreted from roots. Plant Biotechnol (Tokyo) 2021; 38:305-310. [PMID: 34782816 PMCID: PMC8562582 DOI: 10.5511/plantbiotechnology.21.0504a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/04/2021] [Indexed: 05/12/2023]
Abstract
Plants release specialized (secondary) metabolites from their roots to communicate with other organisms, including soil microorganisms. The spatial behavior of such metabolites around these roots can help us understand roles for the communication; however, currently, they are unclear because soil-based studies are complex. Here, we established a multimodal metabolomics approach using imaging mass spectrometry (IMS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to spatially assign metabolites under laboratory conditions using agar. In a case study using Catharanthus roseus, we showed that 58 nitrogen (N)-containing metabolites are released from the roots into the agar. For the metabolite assignment, we used 15N-labeled and non-labeled LC-MS/MS data, previously reported. Four metabolite ions were identified using authentic standard compounds as derived from monoterpene indole alkaloids (MIAs) such as ajmalicine, catharanthine, serpentine, and yohimbine. An alkaloid network analysis using dot products and spinglass methods characterized five clusters to which the 58 ions belong. The analysis clustered ions from the indolic skeleton-type MIAs to a cluster, suggesting that other communities may represent distinct metabolite groups. For future chemical assignments of the serpentine community, key fragmentation patterns were characterized using the 15N-labeled and non-labeled MS/MS spectra.
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Affiliation(s)
- Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- E-mail: Tel: 81-45-503-9442
| | - Noriko Takeda-Kamiya
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yutaka Yamada
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Mai Uzaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | | | - Kiminori Toyooka
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
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11
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Sugiyama A. Flavonoids and saponins in plant rhizospheres: roles, dynamics, and the potential for agriculture. Biosci Biotechnol Biochem 2021; 85:1919-1931. [PMID: 34113972 DOI: 10.1093/bbb/zbab106] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/04/2021] [Indexed: 01/13/2023]
Abstract
Plants are in constant interaction with a myriad of soil microorganisms in the rhizosphere, an area of soil in close contact with plant roots. Recent research has highlighted the importance of plant-specialized metabolites (PSMs) in shaping and modulating the rhizosphere microbiota; however, the molecular mechanisms underlying the establishment and function of the microbiota mostly remain unaddressed. Flavonoids and saponins are a group of PSMs whose biosynthetic pathways have largely been revealed. Although these PSMs are abundantly secreted into the rhizosphere and exert various functions, the secretion mechanisms have not been clarified. This review summarizes the roles of flavonoids and saponins in the rhizosphere with a special focus on interactions between plants and the rhizosphere microbiota. Furthermore, this review introduces recent advancements in the dynamics of these metabolites in the rhizosphere and indicates potential applications of PSMs for crop production and discusses perspectives in this emerging research field.
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Affiliation(s)
- Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Japan
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12
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Bardhan K, York LM, Hasanuzzaman M, Parekh V, Jena S, Pandya MN. Can smart nutrient applications optimize the plant's hidden half to improve drought resistance? Physiol Plant 2021; 172:1007-1015. [PMID: 33432608 DOI: 10.1111/ppl.13332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/03/2020] [Accepted: 01/08/2021] [Indexed: 05/14/2023]
Abstract
Global agriculture is challenged with achieving sustainable food security while the climate changes and the threat of drought increases. Much of the research attention has focused on above-ground plant responses with an aim to improve drought resistance. The hidden half, that is, the root system belowground, is receiving increasing attention as the interface of the plant with the soil. Because roots are a sensing organ for nutrients and moisture, we speculate that crop root system traits can be managed using smart nutrient application in order to increase drought resistance. Roots are known to be influenced both by their underlying genetics and also by responses to the environment, termed root plasticity. Though very little is known about the combined effect of water and nutrients on root plasticity, we explore the possibilities of root system manipulation by nutrient application. We compare the effects of different water or nutrient levels on root plasticity and its genetic regulation, with a focus on how this may affect drought resistance. We propose four primary mechanisms through which smart nutrient management can optimize root traits for drought resistance: (1) overall plant vigor, (2) increased root allocation, (3) influence specific root traits, and (4) use smart placement and timing to encourage deep rooting. In the longer term, we envision that beneficial root traits, including plasticity, could be bred into efficient varieties and combined with advanced precision management of water and nutrients to achieve agricultural sustainability.
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Affiliation(s)
- Kirti Bardhan
- Department of Basic Sciences and Humanities, Navsari Agricultural University, Navsari, India
| | - Larry M York
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Mirza Hasanuzzaman
- Department of Agronomy, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Vipulkumar Parekh
- Department of Basic Sciences and Humanities, Navsari Agricultural University, Navsari, India
| | - Suchismita Jena
- Department of Fruit Science, Navsari Agricultural University, Navsari, India
| | - Mansi N Pandya
- Department of Genetics and Plant Breeding, Navsari Agricultural University, Navsari, India
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