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Li M, Perez-Limón S, Ramírez-Flores MR, Barrales-Gamez B, Meraz-Mercado MA, Ziegler G, Baxter I, Olalde-Portugal V, Sawers RJH. Mycorrhizal status and host genotype interact to shape plant nutrition in field grown maize (Zea mays ssp. mays). MYCORRHIZA 2023; 33:345-358. [PMID: 37851276 PMCID: PMC10752836 DOI: 10.1007/s00572-023-01127-3] [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: 05/20/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) establish symbioses with the major cereal crops, providing plants with increased access to nutrients while enhancing their tolerance to toxic heavy metals. However, not all plant varieties benefit equally from this association. In this study, we used quantitative trait loci (QTL) mapping to evaluate the combined effect of host genotypic variation (G) and AMF across 141 genotypes on the concentration of 20 mineral elements in the leaves and grain of field grown maize (Zea mays spp. mays). Our mapping design included selective incorporation of a castor AMF-incompatibility mutation, allowing estimation of AMF, QTL and QTLxAMF effects by comparison of mycorrhizal and non-mycorrhizal plants. Overall, AMF compatibility was associated with higher concentrations of boron (B), copper (Cu), molybdenum (Mo), phosphorus (P), selenium (Se) and zinc (Zn) and lower concentrations of arsenic (As), iron (Fe), magnesium (Mg), manganese (Mn), potassium (K) and strontium (Sr). In addition to effects on individual elements, pairwise correlation matrices for element concentration differed between mycorrhizal and non-mycorrhizal plants. We mapped 22 element QTLs, including 18 associated with QTLxAMF effects that indicate plant genotype-specific differences in the impact of AMF on the host ionome. Although there is considerable interest in AMF as biofertilizers, it remains challenging to estimate the impact of AMF in the field. Our design illustrates an effective approach for field evaluation of AMF effects. Furthermore, we demonstrate the capacity of the ionome to reveal host genotype-specific variation in the impact of AMF on plant nutrition.
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Affiliation(s)
- Meng Li
- Department of Plant Science, The Pennsylvania State University, State College, PA, 16802, USA
| | - Sergio Perez-Limón
- Department of Plant Science, The Pennsylvania State University, State College, PA, 16802, USA
| | - M Rosario Ramírez-Flores
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
- Bioscience Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN, 37830, USA
| | - Benjamín Barrales-Gamez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
- Postgrado en Recursos Genéticos y Productividad-Genética, Campus Montecillo, Colegio de Postgraduados, Montecillo, Texcoco, Edo. de México, 56230, México
| | - Marco Antonio Meraz-Mercado
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
| | - Gregory Ziegler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Víctor Olalde-Portugal
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados (CINVESTAV-IPN), Irapuato, Guanajuato, 36821, México
| | - Ruairidh J H Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA, 16802, USA.
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Pradhan M, Baldwin IT, Pandey SP. Argonaute7 (AGO7) optimizes arbuscular mycorrhizal fungal associations and enhances competitive growth in Nicotiana attenuata. THE NEW PHYTOLOGIST 2023; 240:382-398. [PMID: 37532924 DOI: 10.1111/nph.19155] [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: 03/23/2023] [Accepted: 07/02/2023] [Indexed: 08/04/2023]
Abstract
Plants interact with arbuscular mycorrhizal fungi (AMF) and in doing so, change transcript levels of many miRNAs and their targets. However, the identity of an Argonaute (AGO) that modulates this interaction remains unknown, including in Nicotiana attenuata. We examined how the silencing of NaAGO1/2/4/7/and 10 by RNAi influenced plant-competitive ability under low-P conditions when they interact with AMF. Furthermore, the roles of seven miRNAs, predicted to regulate signaling and phosphate homeostasis, were evaluated by transient overexpression. Only NaAGO7 silencing by RNAi (irAGO7) significantly reduced the competitive ability under P-limited conditions, without changes in leaf or root development, or juvenile-to-adult phase transitions. In plants growing competitively in the glasshouse, irAGO7 roots were over-colonized with AMF, but they accumulated significantly less phosphate and the expression of their AMF-specific transporters was deregulated. Furthermore, the AMF-induced miRNA levels were inversely regulated with the abundance of their target transcripts. miRNA overexpression consistently decreased plant fitness, with four of seven-tested miRNAs reducing mycorrhization rates, and two increasing mycorrhization rates. Overexpression of Na-miR473 and Na-miRNA-PN59 downregulated targets in GA, ethylene, and fatty acid metabolism pathways. We infer that AGO7 optimizes competitive ability and colonization by regulating miRNA levels and signaling pathways during a plant's interaction with AMF.
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Affiliation(s)
- Maitree Pradhan
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Shree P Pandey
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
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Groten K, Yon F, Baldwin IT. Arbuscular mycorrhizal fungi influence the intraspecific competitive ability of plants under field and glasshouse conditions. PLANTA 2023; 258:60. [PMID: 37535207 PMCID: PMC10400695 DOI: 10.1007/s00425-023-04214-z] [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: 03/24/2023] [Accepted: 07/24/2023] [Indexed: 08/04/2023]
Abstract
MAIN CONCLUSION Nicotiana attenuata's capacity to interact with arbuscular mycorrhizal fungi influences its intraspecific competitive ability under field and glasshouse conditions, but not its overall community productivity. Arbuscular mycorrhizal (AM) fungi can alter the nutrient status and growth of plants, and they can also affect plant-plant, plant-herbivore, and plant-pathogen interactions. These AM effects are rarely studied in populations under natural conditions due to the limitation of non-mycorrhizal controls. Here we used a genetic approach, establishing field and glasshouse communities of AM-harboring Nicotiana attenuata empty vector (EV) plants and isogenic plants silenced in calcium- and calmodulin-dependent protein kinase expression (irCCaMK), and unable to establish AM symbioses. Performance and growth were quantified in communities of the same (monocultures) or different genotypes (mixed cultures) and both field and glasshouse experiments returned similar responses. In mixed cultures, AM-harboring EV plants attained greater stalk lengths, shoot and root biomasses, clearly out-competing the AM fungal-deficient irCCaMK plants, while in monocultures, both genotypes grew similarly. Competitive ability was also reflected in reproductive traits: EV plants in mixed cultures outperformed irCCaMK plants. When grown in monocultures, the two genotypes did not differ in reproductive performance, though total leaf N and P contents were significantly lower independent of the community type. Plant productivity in terms of growth and seed production at the community level did not differ, while leaf nutrient content of phosphorus and nitrogen depended on the community type. We infer that AM symbioses drastically increase N. attenuata's competitive ability in mixed communities resulting in increased fitness for the individuals harboring AM without a net gain for the community.
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Affiliation(s)
- Karin Groten
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany.
| | - Felipe Yon
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany
- Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ian T Baldwin
- Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745, Jena, Germany
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You Y, Ray R, Halitschke R, Baldwin G, Baldwin IT. Arbuscular mycorrhizal fungi-indicative blumenol-C-glucosides predict lipid accumulations and fitness in plants grown without competitors. THE NEW PHYTOLOGIST 2023; 238:2159-2174. [PMID: 36866959 DOI: 10.1111/nph.18858] [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: 10/12/2022] [Accepted: 02/20/2023] [Indexed: 05/04/2023]
Abstract
Hydroxy- and carboxyblumenol C-glucosides specifically accumulate in roots and leaves of plants harboring arbuscular mycorrhizal fungi (AMF). To explore blumenol function in AMF relationships, we silenced an early key-gene in blumenol biosynthesis, CCD1 (carotenoid cleavage dioxygenase 1), in the ecological model plant, Nicotiana attenuata, and analyzed whole-plant performance in comparison with control and CCaMK-silenced plants, unable to form AMF associations. Root blumenol accumulations reflected a plant's Darwinian fitness, as estimated by capsule production, and were positively correlated with AMF-specific lipid accumulations in roots, with relationships that changed as plants matured when grown without competitors. When grown with wild-type competitors, transformed plants with decreased photosynthetic capacity or increased carbon flux to roots had blumenol accumulations that predicted plant fitness and genotype trends in AMF-specific lipids, but had similar levels of AMF-specific lipids between competing plants, likely reflecting AMF-networks. We propose that when grown in isolation, blumenol accumulations reflect AMF-specific lipid allocations and plant fitness. When grown with competitors, blumenol accumulations predict fitness outcomes, but not the more complicated AMF-specific lipid accumulations. RNA-seq analysis provided candidates for the final biosynthetic steps of these AMF-indicative blumenol C-glucosides; abrogation of these steps will provide valuable tools for understanding blumenol function in this context-dependent mutualism.
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Affiliation(s)
- Yanrong You
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Rishav Ray
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Gundega Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
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Bennett AE, Groten K. The Costs and Benefits of Plant-Arbuscular Mycorrhizal Fungal Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:649-672. [PMID: 35216519 DOI: 10.1146/annurev-arplant-102820-124504] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The symbiotic interaction between plants and arbuscular mycorrhizal (AM) fungi is often perceived as beneficial for both partners, though a large ecological literature highlights the context dependency of this interaction. Changes in abiotic variables, such as nutrient availability, can drive the interaction along the mutualism-parasitism continuum with variable outcomes for plant growth and fitness. However, AM fungi can benefit plants in more ways than improved phosphorus nutrition and plant growth. For example, AM fungi can promote abiotic and biotic stress tolerance even when considered parasitic from a nutrient provision perspective. Other than being obligate biotrophs, very little is known about the benefits AM fungi gain from plants. In this review, we utilize both molecular biology and ecological approaches to expand our understanding of the plant-AM fungal interaction across disciplines.
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Affiliation(s)
- Alison E Bennett
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio, USA;
| | - Karin Groten
- Max Planck Institute for Chemical Ecology, Jena, Germany;
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Tseng YH, Rouina H, Groten K, Rajani P, Furch ACU, Reichelt M, Baldwin IT, Nataraja KN, Uma Shaanker R, Oelmüller R. An Endophytic Trichoderma Strain Promotes Growth of Its Hosts and Defends Against Pathogen Attack. FRONTIERS IN PLANT SCIENCE 2020; 11:573670. [PMID: 33424876 PMCID: PMC7793846 DOI: 10.3389/fpls.2020.573670] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/02/2020] [Indexed: 05/30/2023]
Abstract
Plants host numerous endophytic microbes which promote plant performance, in particular under stress. A new endophytic fungus was isolated from the leaves of a deciduous wood tree Leucas aspera. Morphological inspection and multilocus phylogeny identified the fungus as a new Trichoderma strain. If applied to Arabidopsis thaliana and Nicotiana attenuata, it mainly colonizes their roots and strongly promotes initial growth of the plants on soil. The fungus grows on high NaCl or mannitol concentrations, and shows predatory capability on the pathogenic fungus Alternaria brassicicola. Colonized Arabidopsis plants tolerate higher salt stress and show lower A. brassicicola spread in roots and shoots, while arbuscular mycorrhiza formation in N. attenuata is not affected by the Trichoderma strain. These beneficial features of the novel Trichoderma strain are important prerequisites for agricultural applications.
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Affiliation(s)
- Yu-Heng Tseng
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Hamid Rouina
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Karin Groten
- Department of Molecular Ecology, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Pijakala Rajani
- School of Ecology and Conservation, University of Agricultural Sciences, Gandhi Krishi Vigyana Kendra (GKVK), Bengaluru, India
| | - Alexandra C. U. Furch
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
| | - Michael Reichelt
- Department of Molecular Ecology, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max-Planck-Institute for Chemical Ecology, Jena, Germany
| | - Karaba N. Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, Gandhi Krishi Vigyana Kendra (GKVK), Bengaluru, India
| | - Ramanan Uma Shaanker
- School of Ecology and Conservation, University of Agricultural Sciences, Gandhi Krishi Vigyana Kendra (GKVK), Bengaluru, India
| | - Ralf Oelmüller
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University Jena, Jena, Germany
- School of Ecology and Conservation, University of Agricultural Sciences, Gandhi Krishi Vigyana Kendra (GKVK), Bengaluru, India
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7
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Fabiańska I, Pesch L, Koebke E, Gerlach N, Bucher M. Neighboring plants divergently modulate effects of loss-of-function in maize mycorrhizal phosphate uptake on host physiology and root fungal microbiota. PLoS One 2020; 15:e0232633. [PMID: 32555651 PMCID: PMC7299352 DOI: 10.1371/journal.pone.0232633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/17/2020] [Indexed: 01/05/2023] Open
Abstract
Maize, a main crop worldwide, establishes a mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi providing nutrients to the roots from soil volumes which are normally not in reach of the non-colonized root. The mycorrhizal phosphate uptake pathway (MPU) spans from extraradical hyphae to root cortex cells housing fungal arbuscules and promotes the supply of phosphate to the mycorrhizal host in exchange for photosynthetic carbon. This symbiotic association with the mycobiont has been shown to affect plant host nutritional status and growth performance. However, whether and how the MPU affects the root microbial community associated with mycorrhizal hosts in association with neighboring plants, remains to be demonstrated. Here the maize germinal Mu transposon insertion mutant pht1;6, defective in mycorrhiza-specific Pi transporter PHT1;6 gene, and wild type B73 (wt) plants were grown in mono- and mixed culture and examined under greenhouse and field conditions. Disruption of the MPU in pht1;6 resulted in strongly diminished growth performance, in reduced P allocation to photosynthetic source leaves, and in imbalances in leaf elemental composition beyond P. At the microbial community level a loss of MPU activity had a minor effect on the root-associated fungal microbiome which was almost fully restricted to AM fungi of the Glomeromycotina. Moreover, while wt grew better in presence of pht1;6, pht1;6 accumulated little biomass irrespective of whether it was grown in mono- or mixed culture and despite of an enhanced fungal colonization of its roots in co-culture with wt. This suggested that a functional MPU is prerequisite to maintain maize growth and that neighboring plants competed for AM fungal Pi in low P soil. Thus future strategies towards improving yield in maize populations on soils with low inputs of P fertilizer could be realized by enhancing MPU at the individual plant level while leaving the root-associated fungal community largely unaffected.
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Affiliation(s)
- Izabela Fabiańska
- Institute for Plant Sciences, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Lina Pesch
- Institute for Plant Sciences, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Eva Koebke
- Institute for Plant Sciences, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Nina Gerlach
- Institute for Plant Sciences, Cologne Biocenter, University of Cologne, Cologne, Germany
| | - Marcel Bucher
- Institute for Plant Sciences, Cologne Biocenter, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, University of Cologne, Cologne, Germany
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McGale E, Valim H, Mittal D, Morales Jimenez J, Halitschke R, Schuman MC, Baldwin IT. Determining the scale at which variation in a single gene changes population yields. eLife 2020; 9:e53517. [PMID: 32057293 PMCID: PMC7136025 DOI: 10.7554/elife.53517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/13/2020] [Indexed: 11/13/2022] Open
Abstract
Plant trait diversity is known to influence population yield, but the scale at which this happens remains unknown: divergent individuals might change yields of immediate neighbors (neighbor scale) or of plants across a population (population scale). We use Nicotiana attenuata plants silenced in mitogen-activated protein kinase 4 (irMPK4) - with low water-use efficiency (WUE) - to study the scale at which water-use traits alter intraspecific population yields. In the field and glasshouse, we observed overyielding in populations with low percentages of irMPK4 plants, unrelated to water-use phenotypes. Paired-plant experiments excluded the occurrence of overyielding effects at the neighbor scale. Experimentally altering field arbuscular mycorrhizal fungal associations by silencing the Sym-pathway gene NaCCaMK did not affect reproductive overyielding, implicating an effect independent of belowground AMF interactions. Additionally, micro-grafting experiments revealed dependence on shoot-expressed MPK4 for N. attenuata to vary its yield per neighbor presence. We find that variation in a single gene, MPK4, is responsible for population overyielding through a mechanism, independent of irMPK4's WUE phenotype, at the aboveground, population scale.
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Affiliation(s)
- Erica McGale
- Department of Molecular Ecology, Max Planck for Chemical EcologyJenaGermany
| | - Henrique Valim
- Department of Molecular Ecology, Max Planck for Chemical EcologyJenaGermany
| | - Deepika Mittal
- Department of Molecular Ecology, Max Planck for Chemical EcologyJenaGermany
| | | | - Rayko Halitschke
- Department of Molecular Ecology, Max Planck for Chemical EcologyJenaGermany
| | - Meredith C Schuman
- Department of Molecular Ecology, Max Planck for Chemical EcologyJenaGermany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck for Chemical EcologyJenaGermany
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Song Y, Wang M, Zeng R, Groten K, Baldwin IT. Priming and filtering of antiherbivore defences among Nicotiana attenuata plants connected by mycorrhizal networks. PLANT, CELL & ENVIRONMENT 2019; 42:2945-2961. [PMID: 31348534 DOI: 10.1111/pce.13626] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 07/14/2019] [Indexed: 06/10/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) establish symbiotic associations with a majority of terrestrial plants to form underground common mycorrhizal networks (CMNs) that connect neighbouring plants. Because Nicotiana attenuata plants do not respond to herbivory-elicited volatiles from neighbours, we used this ecological model system to evaluate if CMNs function in interplant transmission of herbivory-elicited responses. A mesocosm system was designed to establish and remove CMNs linking N. attenuata plants to examine the herbivory-elicited metabolic and hormone responses in CMNs-connected "receiver" plants after the elicitation of "donor" plants by wounding (W) treated with Manduca sexta larval oral secretions (OS). AMF colonization increased constitutive jasmonate (JA and JA-Ile) levels in N. attenuata roots but did not affect well-characterized JAs-regulated defensive metabolites in systemic leaves. Interestingly, larger JAs bursts, and higher levels of several amino acids and particular sectors of hydroxygeranyllinalool diterpene glycoside metabolism were elevated in the leaves of W + OS-elicited "receivers" with CMN connections with "donors" that had been W + OS-elicited 6 hr previously. Our results demonstrate that AMF colonization alone does not enhance systemic defence responses but that sectors of systemic responses in leaves can be primed by CMNs, suggesting that CMNs can transmit and even filter defence signalling among connected plants.
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Affiliation(s)
- Yuanyuan Song
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ming Wang
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Rensen Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Karin Groten
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
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Uroz S, Courty PE, Oger P. Plant Symbionts Are Engineers of the Plant-Associated Microbiome. TRENDS IN PLANT SCIENCE 2019; 24:905-916. [PMID: 31288964 DOI: 10.1016/j.tplants.2019.06.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/03/2019] [Accepted: 06/07/2019] [Indexed: 05/09/2023]
Abstract
Plants interact throughout their lives with environmental microorganisms. These interactions determine plant development, nutrition, and fitness in a dynamic and stressful environment, forming the basis for the holobiont concept in which plants and plant-associated microbes are not considered as independent entities but as a single evolutionary unit. A primary open question concerns whether holobiont structure is shaped by its microbial members or solely by the plant. Current knowledge of plant-microbe interactions argues that the establishment of symbiosis directly and indirectly conditions the plant-associated microbiome. We propose to define the impact of the symbiont on the plant microbiome as the 'symbiosis cascade effect', in which the symbionts and their plant host jointly shape the plant microbiome.
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Affiliation(s)
- Stephane Uroz
- Institut National de la Recherche Agronomique (INRA) Unité Mixte de Recherche (UMR) 1136, Interactions Arbres-Microorganismes, F-54280, Champenoux, France; Université de Lorraine, UMR 1136, Interactions Arbres-Microorganismes, F-54500 Vandoeuvre-lès-, Nancy, France; INRA Unité de Recherche (UR) 1138, Biogéochimie des Écosystèmes Forestiers, F-54280, Champenoux, France.
| | - Pierre Emmanuel Courty
- Agroécologie, Institut National de la Recherche, Agronomique (INRA), AgroSup Dijon, Centre, National de la Recherche Scientifique (CNRS), Université de Bourgogne, INRA, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Phil Oger
- Université de Lyon, Institut National des Sciences Appliquées (INSA) de Lyon, CNRS UMR, 5240, Villeurbanne, France
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Xue L, Almario J, Fabiańska I, Saridis G, Bucher M. Dysfunction in the arbuscular mycorrhizal symbiosis has consistent but small effects on the establishment of the fungal microbiota in Lotus japonicus. THE NEW PHYTOLOGIST 2019; 224:409-420. [PMID: 31125425 PMCID: PMC6773208 DOI: 10.1111/nph.15958] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/15/2019] [Indexed: 05/10/2023]
Abstract
Most land plants establish mutualistic interactions with arbuscular mycorrhizal (AM) fungi. Intracellular accommodation of AM fungal symbionts remodels important host traits like root morphology and nutrient acquisition. How mycorrhizal colonization impacts plant microbiota is unclear. To understand the impact of AM symbiosis on fungal microbiota, ten Lotus japonicus mutants impaired at different stages of AM formation were grown in non-sterile natural soil and their root-associated fungal communities were studied. Plant mutants lacking the capacity to form mature arbuscules (arb- ) exhibited limited growth performance associated with altered phosphorus (P) acquisition and reduction-oxidation (redox) processes. Furthermore, arb- plants assembled moderately but consistently different root-associated fungal microbiota, characterized by the depletion of Glomeromycota and the concomitant enrichment of Ascomycota, including Dactylonectria torresensis. Single and co-inoculation experiments showed a strong reduction of root colonization by D. torresensis in the presence of AM fungus Rhizophagus irregularis, particularly in arbuscule-forming plants. Our results suggest that impairment of central symbiotic functions in AM host plants leads to specific changes in root microbiomes and in tripartite interactions between the host plant, AM and non-AM fungi. This lays the foundation for mechanistic studies on microbe-microbe and microbe-host interactions in AM symbiosis of the model L. japonicus.
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Affiliation(s)
- Li Xue
- Botanical InstituteCologne BiocenterUniversity of Cologne50674CologneGermany
| | - Juliana Almario
- Botanical InstituteCologne BiocenterUniversity of Cologne50674CologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)University of Cologne50674CologneGermany
| | - Izabela Fabiańska
- Botanical InstituteCologne BiocenterUniversity of Cologne50674CologneGermany
| | - Georgios Saridis
- Botanical InstituteCologne BiocenterUniversity of Cologne50674CologneGermany
| | - Marcel Bucher
- Botanical InstituteCologne BiocenterUniversity of Cologne50674CologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)University of Cologne50674CologneGermany
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Pandey P, Wang M, Baldwin IT, Pandey SP, Groten K. Complex regulation of microRNAs in roots of competitively-grown isogenic Nicotiana attenuata plants with different capacities to interact with arbuscular mycorrhizal fungi. BMC Genomics 2018; 19:937. [PMID: 30558527 PMCID: PMC6296096 DOI: 10.1186/s12864-018-5338-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 11/29/2018] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Nicotiana attenuata is an ecological model plant whose 2.57 Gb genome has recently been sequenced and assembled and for which miRNAs and their genomic locations have been identified. To understand how this plant's miRNAs are reconfigured during plant-arbuscular mycorrhizal fungal (AMF) interactions and whether hostplant calcium- and calmodulin dependent protein kinase (CCaMK) expression which regulates the AMF interaction also modulates miRNAs levels and regulation, we performed a large-scale miRNA analysis of this plant-AMF interaction. RESULTS Next generation sequencing of miRNAs in roots of empty vector (EV) N. attenuata plants and an isogenic line silenced in CCaMK expression (irCCaMK) impaired in AMF-interactions grown under competitive conditions with and without AMF inoculum revealed a total of 149 unique miRNAs: 67 conserved and 82 novel ones. The majority of the miRNAs had a length of 21 nucleotides. MiRNA abundances were highly variable ranging from 400 to more than 25,000 reads per million. The miRNA profile of irCCaMK plants impaired in AMF colonization was distinct from fully AMF-functional EV plants grown in the same pot. Six conserved miRNAs were present in all conditions and accumulated differentially depending on treatment and genotype; five (miR6153, miR403a-3p, miR7122a, miR167-5p and miR482d, but not miR399a-3p) showed the highest accumulation in AMF inoculated EV plants compared to inoculated irCCaMK plants. Furthermore, the accumulation patterns of sequence variants of selected conserved miRNAs showed a very distinct pattern related to AMF colonization - one variant of miR473-5p specifically accumulated in AMF-inoculated plants. Also abundances of miR403a-3p, miR171a-3p and one of the sequence variants of miR172a-3p increased in AMF-inoculated EV compared to inoculated irCCaMK plants and to non-inoculated EV plants, while miR399a-3p was most strongly enriched in AMF inoculated irCCaMK plants grown in competition with EV. The analysis of putative targets of selected miRNAs revealed an involvement in P starvation (miR399), phytohormone signaling (Nat-R-PN59, miR172, miR393) and defense (e.g. miR482, miR8667, Nat-R-PN-47). CONCLUSIONS Our study demonstrates (1) a large-scale reprograming of miRNAs induced by AMF colonization and (2) that the impaired AMF signaling due to CCaMK silencing and the resulting reduced competitive ability of irCCaMK plants play a role in modulating signal-dependent miRNA accumulation.
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Affiliation(s)
- Priyanka Pandey
- National Institute of Biomedical Genomics, Kalyani, West Bengal India
| | - Ming Wang
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Shree P. Pandey
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
- Department of Biological Sciences, IISER Kolkata, Mohanpur, Nadia, West Bengal 741246 India
| | - Karin Groten
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
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Wang M, Schäfer M, Li D, Halitschke R, Dong C, McGale E, Paetz C, Song Y, Li S, Dong J, Heiling S, Groten K, Franken P, Bitterlich M, Harrison MJ, Paszkowski U, Baldwin IT. Blumenols as shoot markers of root symbiosis with arbuscular mycorrhizal fungi. eLife 2018; 7:e37093. [PMID: 30152755 PMCID: PMC6156081 DOI: 10.7554/elife.37093] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 08/22/2018] [Indexed: 02/02/2023] Open
Abstract
High-through-put (HTP) screening for functional arbuscular mycorrhizal fungi (AMF)-associations is challenging because roots must be excavated and colonization evaluated by transcript analysis or microscopy. Here we show that specific leaf-metabolites provide broadly applicable accurate proxies of these associations, suitable for HTP-screens. With a combination of untargeted and targeted metabolomics, we show that shoot accumulations of hydroxy- and carboxyblumenol C-glucosides mirror root AMF-colonization in Nicotiana attenuata plants. Genetic/pharmacologic manipulations indicate that these AMF-indicative foliar blumenols are synthesized and transported from roots to shoots. These blumenol-derived foliar markers, found in many di- and monocotyledonous crop and model plants (Solanum lycopersicum, Solanum tuberosum, Hordeum vulgare, Triticum aestivum, Medicago truncatula and Brachypodium distachyon), are not restricted to particular plant-AMF interactions, and are shown to be applicable for field-based QTL mapping of AMF-related genes.
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Affiliation(s)
- Ming Wang
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Martin Schäfer
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Dapeng Li
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Rayko Halitschke
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Chuanfu Dong
- Department of Bioorganic ChemistryMax Planck Institute for Chemical EcologyJenaGermany
| | - Erica McGale
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Christian Paetz
- Research Group Biosynthesis / NMRMax Planck Institute for Chemical EcologyJenaGermany
| | - Yuanyuan Song
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Suhua Li
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Junfu Dong
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Sven Heiling
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Karin Groten
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Philipp Franken
- Leibniz-Institute of Vegetable and Ornamental CropsGrossbeerenGermany
- Institute of BiologyHumboldt Universität zu BerlinBerlinGermany
| | | | | | - Uta Paszkowski
- Department of Plant SciencesUniversity of CambridgeCambridgeUnited Kingdom
| | - Ian T Baldwin
- Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany
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Schuman MC, Baldwin IT. Field studies reveal functions of chemical mediators in plant interactions. Chem Soc Rev 2018; 47:5338-5353. [PMID: 29770376 DOI: 10.1039/c7cs00749c] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Plants are at the trophic base of most ecosystems, embedded in a rich network of ecological interactions in which they evolved. While their limited range and speed of motion precludes animal-typical behavior, plants are accomplished chemists, producing thousands of specialized metabolites which may function to convey information, or even to manipulate the physiology of other organisms. Plants' complex interactions and their underlying mechanisms are typically dissected within the controlled environments of growth chambers and glasshouses, but doing so introduces conditions alien to plants evolved in natural environments, such as being pot-bound, and receiving artificial light with a spectrum very different from sunlight. The mechanistic understanding gained from a reductionist approach provides the tools required to query and manipulate plant interactions in real-world settings. The few tests conducted in natural ecosystems and agricultural fields have highlighted the limitations of studying plant interactions only in artificial environments. Here, we focus on three examples of known or hypothesized chemical mediators of plants' interactions: the volatile phytohormone ethylene (ET), more complex plant volatile blends, and as-yet-unknown mediators transferred by common mycorrhizal networks (CMNs). We highlight how mechanistic knowledge has advanced research in all three areas, and the critical importance of field work if we are to put our understanding of chemical ecology on rigorous experimental and theoretical footing, and demonstrate function.
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Affiliation(s)
- Meredith C Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany.
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15
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Wang M, Wilde J, Baldwin IT, Groten K. Nicotiana attenuata's capacity to interact with arbuscular mycorrhiza alters its competitive ability and elicits major changes in the leaf transcriptome. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:242-261. [PMID: 29087617 DOI: 10.1111/jipb.12609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
To study the local and systemic effects of arbuscular mycorrhizal fungal (AMF) colonization, Nicotiana attenuata plants impaired in their interactions with AMF due to silencing of a calcium- and calmodulin dependent protein kinase (inverted repreat (ir)CCaMK) were grown competitively in pairs with empty vector (EV) plants, with and without two different types of inoculum. When inoculated, EV plants strongly outperformed irCCaMK plants. Foliar transcript profiling revealed that AMF colonization significantly changed gene expression of P-starvation and -transporter genes in irCCaMK plants. The Pht1 family phosphate transporter NaPT5 was not only specifically induced in roots after AMF colonization, but also in leaves of AMF-colonized irCCaMK plants, and in plants grown under low Pi conditions in the absence of AMF. The P-starvation signature of inoculated irCCaMK plants corresponded with increases in selected amino acids and phenolic compounds in leaves. We also found a strong AMF-induced increase in amino acids and phenolic metabolites in roots. Plants impaired in their interactions with AMF clearly have a fitness disadvantage when competing for limited soil nutrients with a fully functional isogenic line. The additional role of the AMF-induced Pht1 family transporter NaPT5 in leaves under P-starvation conditions will require further experiments to fully resolve.
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Affiliation(s)
- Ming Wang
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena 07745, Germany
| | - Julia Wilde
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena 07745, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena 07745, Germany
| | - Karin Groten
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena 07745, Germany
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Poosakkannu A, Nissinen R, Kytöviita MM. Native arbuscular mycorrhizal symbiosis alters foliar bacterial community composition. MYCORRHIZA 2017; 27:801-810. [PMID: 28812152 DOI: 10.1007/s00572-017-0796-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/04/2017] [Indexed: 06/07/2023]
Abstract
The effects of arbuscular mycorrhizal (AM) fungi on plant-associated microbes are poorly known. We tested the hypothesis that colonization by an AM fungus affects microbial species richness and microbial community composition of host plant tissues. We grew the grass, Deschampsia flexuosa in a greenhouse with or without the native AM fungus, Claroideoglomus etunicatum. We divided clonally produced tillers into two parts: one inoculated with AM fungus spores and one without AM fungus inoculation (non-mycorrhizal, NM). We characterized bacterial (16S rRNA gene) and fungal communities (internal transcribed spacer region) in surface-sterilized leaf and root plant compartments. AM fungus inoculation did not affect microbial species richness or diversity indices in leaves or roots, but the AM fungus inoculation significantly affected bacterial community composition in leaves. A total of three OTUs in leaves belonging to the phylum Firmicutes positively responded to the presence of the AM fungus in roots. Another six OTUs belonging to the Proteobacteria (Alpha, Beta, and Gamma) and Bacteroidetes were significantly more abundant in NM plants when compared to AM fungus-inoculated plants. Further, there was a significant correlation between plant dry weight and leaf microbial community compositional shift. Also, there was a significant correlation between leaf bacterial community compositional shift and foliar nitrogen content changes due to AM fungus inoculation. The results suggest that AM fungus colonization in roots has a profound effect on plant physiology that is reflected in leaf bacterial community composition.
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Affiliation(s)
- Anbu Poosakkannu
- Department of Biological and Environmental Science, University of Jyvaskyla, PO Box 35, FI-40014, Jyvaskyla, Finland.
| | - Riitta Nissinen
- Department of Biological and Environmental Science, University of Jyvaskyla, PO Box 35, FI-40014, Jyvaskyla, Finland
| | - Minna-Maarit Kytöviita
- Department of Biological and Environmental Science, University of Jyvaskyla, PO Box 35, FI-40014, Jyvaskyla, Finland
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17
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Santhanam R, Oh Y, Kumar R, Weinhold A, Luu VT, Groten K, Baldwin IT. Specificity of root microbiomes in native-grown Nicotiana attenuata and plant responses to UVB increase Deinococcus colonization. Mol Ecol 2017; 26:2543-2562. [PMID: 28173617 DOI: 10.1111/mec.14049] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/24/2017] [Accepted: 01/29/2017] [Indexed: 01/02/2023]
Abstract
Plants recruit microbial communities from the soil in which they germinate. Our understanding of the recruitment process and the factors affecting it is still limited for most microbial taxa. We analysed several factors potentially affecting root microbiome structure - the importance of geographic location of natural populations, the microbiome of native seeds as putative source of colonization and the effect of a plant's response to UVB exposure on root colonization of highly abundant species. The microbiome of Nicotiana attenuata seeds was determined by a culture-dependent and culture-independent approach, and the root microbiome of natural N. attenuata populations from five different locations was analysed using 454-pyrosequencing. To specifically address the influence of UVB light on root colonization by Deinococcus, a genus abundant and consistently present in N. attenuata roots, transgenic lines impaired in UVB perception (irUVR8) and response (irCHAL) were investigated in a microcosm experiment with/without UVB supplementation using a synthetic bacterial community. The seed microbiome analysis indicated that N. attenuata seeds are sterile. Alpha and beta diversities of native root bacterial communities differed significantly between soil and root, while location had only a significant effect on the fungal but not the bacterial root communities. With UVB supplementation, root colonization of Deinococcus increased in wild type, but decreased in irUVR8 and irCHAL plants compared to nontreated plants. Our results suggest that N. attenuata recruits a core root microbiome exclusively from soil, with fungal root colonization being less selective than bacterial colonization. Root colonization by Deinococcus depends on the plant's response to UVB.
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Affiliation(s)
- Rakesh Santhanam
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
| | - Youngjoo Oh
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
| | - Ramesh Kumar
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
- CSIR - National Institute for Interdisciplinary Science and Technology (NIIST), Industrial Estate Po, Thiruvananthapuram, Kerala, 695019, India
| | - Arne Weinhold
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
| | - Van Thi Luu
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
| | - Karin Groten
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, Jena, 07745, Germany
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18
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Minamisawa K, Imaizumi-Anraku H, Bao Z, Shinoda R, Okubo T, Ikeda S. Are Symbiotic Methanotrophs Key Microbes for N Acquisition in Paddy Rice Root? Microbes Environ 2016; 31:4-10. [PMID: 26960961 PMCID: PMC4791114 DOI: 10.1264/jsme2.me15180] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The relationships between biogeochemical processes and microbial functions in rice (Oryza sativa) paddies have been the focus of a large number of studies. A mechanistic understanding of methane–nitrogen (CH4–N) cycle interactions is a key unresolved issue in research on rice paddies. This minireview is an opinion paper for highlighting the mechanisms underlying the interactions between biogeochemical processes and plant-associated microbes based on recent metagenomic, metaproteomic, and isotope analyses. A rice symbiotic gene, relevant to rhizobial nodulation and mycorrhization in plants, likely accommodates diazotrophic methanotrophs or the associated bacterial community in root tissues under low-N fertilizer management, which may permit rice plants to acquire N via N2 fixation. The amount of N fixed in rice roots was previously estimated to be approximately 12% of plant N based on measurements of 15N natural abundance in a paddy field experiment. Community analyses also indicate that methanotroph populations in rice roots are susceptible to environmental conditions such as the microclimate of rice paddies. Therefore, CH4 oxidation by methanotrophs is a driving force in shaping bacterial communities in rice roots grown in CH4-rich environments. Based on these findings, we propose a hypothesis with unanswered questions to describe the interplay between rice plants, root microbiomes, and their biogeochemical functions (CH4 oxidation and N2 fixation).
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Groten K, Pahari NT, Xu S, Miloradovic van Doorn M, Baldwin IT. Virus-Induced Gene Silencing Using Tobacco Rattle Virus as a Tool to Study the Interaction between Nicotiana attenuata and Rhizophagus irregularis. PLoS One 2015; 10:e0136234. [PMID: 26291081 PMCID: PMC4546398 DOI: 10.1371/journal.pone.0136234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/30/2015] [Indexed: 01/09/2023] Open
Abstract
Most land plants live in a symbiotic association with arbuscular mycorrhizal fungi (AMF) that belong to the phylum Glomeromycota. Although a number of plant genes involved in the plant-AMF interactions have been identified by analyzing mutants, the ability to rapidly manipulate gene expression to study the potential functions of new candidate genes remains unrealized. We analyzed changes in gene expression of wild tobacco roots (Nicotiana attenuata) after infection with mycorrhizal fungi (Rhizophagus irregularis) by serial analysis of gene expression (SuperSAGE) combined with next generation sequencing, and established a virus-induced gene-silencing protocol to study the function of candidate genes in the interaction. From 92,434 SuperSAGE Tag sequences, 32,808 (35%) matched with our in-house Nicotiana attenuata transcriptome database and 3,698 (4%) matched to Rhizophagus genes. In total, 11,194 Tags showed a significant change in expression (p<0.05, >2-fold change) after infection. When comparing the functions of highly up-regulated annotated Tags in this study with those of two previous large-scale gene expression studies, 18 gene functions were found to be up-regulated in all three studies mainly playing roles related to phytohormone metabolism, catabolism and defense. To validate the function of identified candidate genes, we used the technique of virus-induced gene silencing (VIGS) to silence the expression of three putative N. attenuata genes: germin-like protein, indole-3-acetic acid-amido synthetase GH3.9 and, as a proof-of-principle, calcium and calmodulin-dependent protein kinase (CCaMK). The silencing of the three plant genes in roots was successful, but only CCaMK silencing had a significant effect on the interaction with R. irregularis. Interestingly, when a highly activated inoculum was used for plant inoculation, the effect of CCaMK silencing on fungal colonization was masked, probably due to trans-complementation. This study demonstrates that large-scale gene expression studies across different species induce of a core set of genes of similar functions. However, additional factors seem to influence the overall pattern of gene expression, resulting in high variability among independent studies with different hosts. We conclude that VIGS is a powerful tool with which to investigate the function of genes involved in plant-AMF interactions but that inoculum strength can strongly influence the outcome of the interaction.
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Affiliation(s)
- Karin Groten
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Nabin T. Pahari
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Shuqing Xu
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Maja Miloradovic van Doorn
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany
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