1
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Goossens P, Spooren J, Baremans KCM, Andel A, Lapin D, Echobardo N, Pieterse CMJ, Van den Ackerveken G, Berendsen RL. Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana. Nat Microbiol 2023; 8:2349-2364. [PMID: 37973867 DOI: 10.1038/s41564-023-01502-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/13/2023] [Indexed: 11/19/2023]
Abstract
Hyaloperonospora arabidopsidis (Hpa) is an obligately biotrophic downy mildew that is routinely cultured on Arabidopsis thaliana hosts that harbour complex microbiomes. We hypothesized that the culturing procedure proliferates Hpa-associated microbiota (HAM) in addition to the pathogen and exploited this model system to investigate which microorganisms consistently associate with Hpa. Using amplicon sequencing, we found nine bacterial sequence variants that are shared between at least three out of four Hpa cultures in the Netherlands and Germany and comprise 34% of the phyllosphere community of the infected plants. Whole-genome sequencing showed that representative HAM bacterial isolates from these distinct Hpa cultures are isogenic and that an additional seven published Hpa metagenomes contain numerous sequences of the HAM. Although we showed that HAM benefit from Hpa infection, HAM negatively affect Hpa spore formation. Moreover, we show that pathogen-infected plants can selectively recruit HAM to both their roots and shoots and form a soil-borne infection-associated microbiome that helps resist the pathogen. Understanding the mechanisms by which infection-associated microbiomes are formed might enable breeding of crop varieties that select for protective microbiomes.
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Affiliation(s)
- Pim Goossens
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
| | - Jelle Spooren
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
| | - Kim C M Baremans
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
| | - Annemiek Andel
- Translational Plant Biology, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
| | - Dmitry Lapin
- Translational Plant Biology, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
- Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Nakisa Echobardo
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
| | - Guido Van den Ackerveken
- Translational Plant Biology, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, the Netherlands.
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2
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Wang Y, Yuan S, Shao C, Zhu W, Xiao D, Zhang C, Hou X, Li Y. BcOPR3 Mediates Defense Responses to Biotrophic and Necrotrophic Pathogens in Arabidopsis and Non-heading Chinese Cabbage. PHYTOPATHOLOGY 2022; 112:2523-2537. [PMID: 35852468 DOI: 10.1094/phyto-02-22-0049-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In plants, the salicylic acid (SA) and jasmonic acid (JA) signaling pathways usually mediate the defense response to biotrophic and necrotrophic pathogens, respectively. Our previous work showed that after non-heading Chinese cabbage (NHCC) was infected with the biotrophic pathogen Hyaloperonospora parasitica, expression of the JA biosynthetic gene BcOPR3 is induced; however, its molecular mechanism remains unclear. Here, we overexpressed BcOPR3 in Arabidopsis and silenced BcOPR3 in NHCC001 plants to study the defensive role of BcOPR3 in plants against pathogen invasion. The results showed that overexpression of BcOPR3 increased the susceptibility of Arabidopsis to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) but enhanced its resistance to Botrytis cinerea. BcOPR3-silenced NHCC001 plants with a 50% reduction in BcOPR3 expression increased their resistance to downy mildew by reducing the hyphal density and spores of H. parasitica. In addition, BcOPR3-partly silenced NHCC001 plants were also resistant to B. cinerea, which could be the result of a synergistic effect of JA and SA. These findings indicate a complicated role of BcOPR3 in the mediating defense responses to biotrophic and necrotrophic pathogens.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuilin Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Cen Shao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Weitong Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Changwei Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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3
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Orf I, Tenenboim H, Omranian N, Nikoloski Z, Fernie AR, Lisec J, Brotman Y, Bromke MA. Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession. Int J Mol Sci 2022; 23:ijms232012087. [PMID: 36292941 PMCID: PMC9603445 DOI: 10.3390/ijms232012087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/06/2022] [Accepted: 10/08/2022] [Indexed: 11/24/2022] Open
Abstract
Accessions of one plant species may show significantly different levels of susceptibility to stresses. The Arabidopsis thaliana accessions Col-0 and C24 differ significantly in their resistance to the pathogen Pseudomonas syringae pv. tomato (Pst). To help unravel the underlying mechanisms contributing to this naturally occurring variance in resistance to Pst, we analyzed changes in transcripts and compounds from primary and secondary metabolism of Col-0 and C24 at different time points after infection with Pst. Our results show that the differences in the resistance of Col-0 and C24 mainly involve mechanisms of salicylic-acid-dependent systemic acquired resistance, while responses of jasmonic-acid-dependent mechanisms are shared between the two accessions. In addition, arginine metabolism and differential activity of the biosynthesis pathways of aliphatic glucosinolates and indole glucosinolates may also contribute to the resistance. Thus, this study highlights the difference in the defense response strategies utilized by different genotypes.
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Affiliation(s)
- Isabel Orf
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Hezi Tenenboim
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Nooshin Omranian
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Zoran Nikoloski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Jan Lisec
- Department of Analytical Chemistry, Federal Institute for Materials Research and Testing, Richard-Willstätter-Straße 11, 12489 Berlin, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Correspondence: (Y.B.); (M.A.B.)
| | - Mariusz A. Bromke
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, ul. Chałubińskiego 10, 50-367 Wrocław, Poland
- Correspondence: (Y.B.); (M.A.B.)
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4
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Peng Z, He Y, Parajuli S, You Q, Wang W, Bhattarai K, Palmateer AJ, Deng Z. Integration of early disease-resistance phenotyping, histological characterization, and transcriptome sequencing reveals insights into downy mildew resistance in impatiens. HORTICULTURE RESEARCH 2021; 8:108. [PMID: 33931631 PMCID: PMC8087834 DOI: 10.1038/s41438-021-00543-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/11/2021] [Accepted: 03/22/2021] [Indexed: 05/11/2023]
Abstract
Downy mildew (DM), caused by obligate parasitic oomycetes, is a destructive disease for a wide range of crops worldwide. Recent outbreaks of impatiens downy mildew (IDM) in many countries have caused huge economic losses. A system to reveal plant-pathogen interactions in the early stage of infection and quickly assess resistance/susceptibility of plants to DM is desired. In this study, we established an early and rapid system to achieve these goals using impatiens as a model. Thirty-two cultivars of Impatiens walleriana and I. hawkeri were evaluated for their responses to IDM at cotyledon, first/second pair of true leaf, and mature plant stages. All I. walleriana cultivars were highly susceptible to IDM. While all I. hawkeri cultivars were resistant to IDM starting at the first true leaf stage, many (14/16) were susceptible to IDM at the cotyledon stage. Two cultivars showed resistance even at the cotyledon stage. Histological characterization showed that the resistance mechanism of the I. hawkeri cultivars resembles that in grapevine and type II resistance in sunflower. By integrating full-length transcriptome sequencing (Iso-Seq) and RNA-Seq, we constructed the first reference transcriptome for Impatiens comprised of 48,758 sequences with an N50 length of 2060 bp. Comparative transcriptome and qRT-PCR analyses revealed strong candidate genes for IDM resistance, including three resistance genes orthologous to the sunflower gene RGC203, a potential candidate associated with DM resistance. Our approach of integrating early disease-resistance phenotyping, histological characterization, and transcriptome analysis lay a solid foundation to improve DM resistance in impatiens and may provide a model for other crops.
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Affiliation(s)
- Ze Peng
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Yanhong He
- Visiting scholar at University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Saroj Parajuli
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Qian You
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Weining Wang
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Krishna Bhattarai
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA
| | - Aaron J Palmateer
- University of Florida, IFAS, Department of Plant Pathology, Tropical Research and Education Center, 18905 S.W. 280th Street, Homestead, FL, 33031, USA
- Bayer Environmental Science US, 5000 Centregreen Way, Cary, NC, 27513, USA
| | - Zhanao Deng
- University of Florida, IFAS, Department of Environmental Horticulture, Gulf Coast Research and Education Center, 14625 County Road 672, Wimauma, FL, 33598, USA.
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5
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Trapet PL, Verbon EH, Bosma RR, Voordendag K, Van Pelt JA, Pieterse CMJ. Mechanisms underlying iron deficiency-induced resistance against pathogens with different lifestyles. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2231-2241. [PMID: 33188427 DOI: 10.1093/jxb/eraa535] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/10/2020] [Indexed: 05/10/2023]
Abstract
Iron (Fe) is a poorly available mineral nutrient which affects the outcome of many cross-kingdom interactions. In Arabidopsis thaliana, Fe starvation limits infection by necrotrophic pathogens. Here, we report that Fe deficiency also reduces disease caused by the hemi-biotrophic bacterium Pseudomonas syringae and the biotrophic oomycete Hyaloperonospora arabidopsidis, indicating that Fe deficiency-induced resistance is effective against pathogens with different lifestyles. Furthermore, we show that Fe deficiency-induced resistance is not caused by withholding Fe from the pathogen but is a plant-mediated defense response that requires activity of ethylene and salicylic acid. Because rhizobacteria-induced systemic resistance (ISR) is associated with a transient up-regulation of the Fe deficiency response, we tested whether Fe deficiency-induced resistance and ISR are similarly regulated. However, Fe deficiency-induced resistance functions independently of the ISR regulators MYB72 and BGLU42, indicating that both types of induced resistance are regulated in a different manner. Mutants opt3 and frd1, which display misregulated Fe homeostasis under Fe-sufficient conditions, show disease resistance levels comparable with those of Fe-starved wild-type plants. Our results suggest that disturbance of Fe homeostasis, through Fe starvation stress or other non-homeostatic conditions, is sufficient to prime the plant immune system for enhanced defense.
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Affiliation(s)
- Pauline L Trapet
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan, CH Utrecht, The Netherlands
| | - Eline H Verbon
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan, CH Utrecht, The Netherlands
| | - Renda R Bosma
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan, CH Utrecht, The Netherlands
| | - Kirsten Voordendag
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan, CH Utrecht, The Netherlands
| | - Johan A Van Pelt
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan, CH Utrecht, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan, CH Utrecht, The Netherlands
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6
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Völz R, Park JY, Kim S, Park SY, Harris W, Chung H, Lee YH. The rice/maize pathogen Cochliobolus spp. infect and reproduce on Arabidopsis revealing differences in defensive phytohormone function between monocots and dicots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:412-429. [PMID: 32168401 DOI: 10.1111/tpj.14743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/11/2020] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
The fungal genus Cochliobolus describes necrotrophic pathogens that give rise to significant losses on rice, wheat, and maize. Revealing plant mechanisms of non-host resistance (NHR) against Cochliobolus will help to uncover strategies that can be exploited in engineered cereals. Therefore, we developed a heterogeneous pathosystem and studied the ability of Cochliobolus to infect dicotyledons. We report here that C. miyabeanus and C. heterostrophus infect Arabidopsis accessions and produce functional conidia, thereby demonstrating the ability to accept Brassica spp. as host plants. Some ecotypes exhibited a high susceptibility, whereas others hindered the necrotrophic disease progression of the Cochliobolus strains. Natural variation in NHR among the tested Arabidopsis accessions can advance the identification of genetic loci that prime the plant's defence repertoire. We found that applied phytotoxin-containing conidial fluid extracts of C. miyabeanus caused necrotic lesions on rice leaves but provoked only minor irritations on Arabidopsis. This result implies that C. miyabeanus phytotoxins are insufficiently adapted to promote dicot colonization, which corresponds to a retarded infection progression. Previous studies on rice demonstrated that ethylene (ET) promotes C. miyabeanus infection, whereas salicylic acid (SA) and jasmonic acid (JA) exert a minor function. However, in Arabidopsis, we revealed that the genetic disruption of the ET and JA signalling pathways compromises basal resistance against Cochliobolus, whereas SA biosynthesis mutants showed a reduced susceptibility. Our results refer to the synergistic action of ET/JA and indicate distinct defence systems between Arabidopsis and rice to confine Cochliobolus propagation. Moreover, this heterogeneous pathosystem may help to reveal mechanisms of NHR and associated defensive genes against Cochliobolus infection.
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Affiliation(s)
- Ronny Völz
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
| | - Ju-Young Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
- R&D Institute, YUHAN Inc., Yongin, 17084, Korea
| | - Soonok Kim
- Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 22689, Korea
| | - Sook-Young Park
- Department of Plant Medicine, Suncheon National University, Suncheon, 57922, Korea
| | - William Harris
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Hyunjung Chung
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Yong-Hwan Lee
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul, 08826, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
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7
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Ferguson J, Meyer R, Edwards K, Humphry M, Brendel O, Bechtold U. Accelerated flowering time reduces lifetime water use without penalizing reproductive performance in Arabidopsis. PLANT, CELL & ENVIRONMENT 2019; 42:1847-1867. [PMID: 30707443 PMCID: PMC6563486 DOI: 10.1111/pce.13527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 01/14/2019] [Indexed: 05/30/2023]
Abstract
Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf-level water-use efficiency (WUE). In Arabidopsis, little is known about the variation of whole-plant water use (PWU) and whole-plant WUE (transpiration efficiency). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large-scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water use and drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water-use strategies, namely, C24 (low PWU) and Col-0 (high PWU). Subsequent quantitative trait loci mapping and validation through near-isogenic lines identified two causal quantitative trait loci, which showed that a combination of weak and nonfunctional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water use due to their control of flowering time. Crucially, we observed that reducing flowering time and consequently water use did not penalize reproductive performance, as such water productivity (seed produced per unit of water transpired) improved. Natural polymorphisms of FRI and FLC have previously been elucidated as key determinants of natural variation in intrinsic WUE (δ13 C). However, in the genetic backgrounds tested here, drought tolerance traits, stomatal conductance, δ13 C. and rosette water use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining lifetime PWU but not always leaf-level traits.
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Affiliation(s)
- John N. Ferguson
- School of Biological SciencesUniversity of EssexColchesterUK
- Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Rhonda C. Meyer
- Department of Molecular GeneticsLeibniz Institute of Plant Genetics and Crop Plant Research (IPK) GaterslebenSeelandGermany
| | - Kieron D. Edwards
- Sibelius Natural Products Health Wellness and FitnessOxfordUK
- Advanced Technologies CambridgeCambridgeUK
| | - Matt Humphry
- Advanced Technologies CambridgeCambridgeUK
- Quantitative GeneticsBritish American TobaccoCambridgeUK
| | - Oliver Brendel
- Université de LorraineAgroParisTech, INRA, SilvaNancyFrance
| | - Ulrike Bechtold
- School of Biological SciencesUniversity of EssexColchesterUK
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8
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Bechtold U, Ferguson JN, Mullineaux PM. To defend or to grow: lessons from Arabidopsis C24. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2809-2821. [PMID: 29562306 DOI: 10.1093/jxb/ery106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 03/13/2018] [Indexed: 06/08/2023]
Abstract
The emergence of Arabidopsis as a model species and the availability of genetic and genomic resources have resulted in the identification and detailed characterization of abiotic stress signalling pathways. However, this has led only to limited success in engineering abiotic stress tolerance in crops. This is because there needs to be a deeper understanding of how to combine resistances to a range of stresses with growth and productivity. The natural variation and genomic resources of Arabidopsis thaliana (Arabidopsis) are a great asset to understand the mechanisms of multiple stress tolerances. One natural variant in Arabidopsis is the accession C24, and here we provide an overview of the increasing research interest in this accession. C24 is highlighted as a source of tolerance for multiple abiotic and biotic stresses, and a key accession to understand the basis of basal immunity to infection, high water use efficiency, and water productivity. Multiple biochemical, physiological, and phenological mechanisms have been attributed to these traits in C24, and none of them constrains productivity. Based on the uniqueness of C24, we postulate that the use of variation derived from natural selection in undomesticated species provides opportunities to better understand how complex environmental stress tolerances and resource use efficiency are co-ordinated.
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Affiliation(s)
- Ulrike Bechtold
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, UK
| | - John N Ferguson
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Philip M Mullineaux
- University of Essex, School of Biological Sciences, Wivenhoe Park, Colchester, UK
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9
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Berendsen RL, Vismans G, Yu K, Song Y, de Jonge R, Burgman WP, Burmølle M, Herschend J, Bakker PAHM, Pieterse CMJ. Disease-induced assemblage of a plant-beneficial bacterial consortium. ISME JOURNAL 2018. [PMID: 29520025 PMCID: PMC5956071 DOI: 10.1038/s41396-018-0093-1] [Citation(s) in RCA: 378] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Disease suppressive soils typically develop after a disease outbreak due to the subsequent assembly of protective microbiota in the rhizosphere. The role of the plant immune system in the assemblage of a protective rhizosphere microbiome is largely unknown. In this study, we demonstrate that Arabidopsis thaliana specifically promotes three bacterial species in the rhizosphere upon foliar defense activation by the downy mildew pathogen Hyaloperonospora arabidopsidis. The promoted bacteria were isolated and found to interact synergistically in biofilm formation in vitro. Although separately these bacteria did not affect the plant significantly, together they induced systemic resistance against downy mildew and promoted growth of the plant. Moreover, we show that the soil-mediated legacy of a primary population of downy mildew infected plants confers enhanced protection against this pathogen in a second population of plants growing in the same soil. Together our results indicate that plants can adjust their root microbiome upon pathogen infection and specifically recruit a group of disease resistance-inducing and growth-promoting beneficial microbes, therewith potentially maximizing the chance of survival of their offspring that will grow in the same soil.
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Affiliation(s)
- Roeland L Berendsen
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Gilles Vismans
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Ke Yu
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Yang Song
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Jiangsu Provincial Coordinated Research Center for Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 927, 9052, Ghent, Belgium
| | - Wilco P Burgman
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, København, Denmark
| | - Jakob Herschend
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, København, Denmark
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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10
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Ferguson JN, Humphry M, Lawson T, Brendel O, Bechtold U. Natural variation of life-history traits, water use, and drought responses in Arabidopsis. PLANT DIRECT 2018; 2:e00035. [PMID: 31245683 PMCID: PMC6508493 DOI: 10.1002/pld3.35] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 11/20/2017] [Accepted: 12/12/2017] [Indexed: 05/17/2023]
Abstract
The ability of plants to acquire and use water is critical in determining life-history traits such as growth, flowering, and allocation of biomass into reproduction. In this context, a combination of functionally linked traits is essential for plants to respond to environmental changes in a coordinated fashion to maximize resource use efficiency. We analyzed different water-use traits in Arabidopsis ecotypes to identify functionally linked traits that determine water use and plant growth performance. Water-use traits measured were (i) leaf-level water-use efficiency (WUE i ) to evaluate the amount of CO 2 fixed relative to water loss per leaf area and (ii) short-term plant water use at the vegetative stage (VWU) as a measure of whole-plant transpiration. Previously observed phenotypic variance in VWU, WUE i and life-history parameters, highlighted C24 as a valuable ecotype that combined drought tolerance, preferential reproductive biomass allocation, high WUE i , and reduced water use. We therefore screened 35 Arabidopsis ecotypes for these parameters, in order to assess whether the phenotypic combinations observed in C24 existed more widely within Arabidopsis ecotypes. All parameters were measured on a short dehydration cycle. A segmented regression analysis was carried out to evaluate the plasticity of the drought response and identified the breakpoint as a reliable measure of drought sensitivity. VWU was largely dependent on rosette area, but importantly the drought sensitivity and plasticity measures were independent of the transpiring leaf surface. A breakpoint at high rSWC indicated a more drought-sensitive plant that closed stomata early during the dehydration cycle and consequently showed stronger plasticity in leaf-level WUE i parameters. None of the sensitivity, plasticity, or water-use measurements were able to predict the overall growth performance; however, there was a general trade-off between vegetative and reproductive biomass. PCA and hierarchical clustering revealed that C24 was unique among the 35 ecotypes in uniting all the beneficial water use and stress tolerance traits, while also maintaining above average plant growth. We propose that a short dehydration cycle, measuring drought sensitivity and VWU is a fast and reliable screen for plant water use and drought response strategies.
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Affiliation(s)
- John N. Ferguson
- School of Biological SciencesUniversity of EssexColchesterUK
- Present address:
Institute for Genomic BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Matt Humphry
- Advanced Technologies CambridgeCambridge Science ParkCambridgeUK
- Present address:
British American TobaccoCambridge Science ParkCambridgeUK
| | - Tracy Lawson
- School of Biological SciencesUniversity of EssexColchesterUK
| | | | - Ulrike Bechtold
- School of Biological SciencesUniversity of EssexColchesterUK
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11
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Slow erosion of a quantitative apple resistance to Venturia inaequalis based on an isolate-specific Quantitative Trait Locus. INFECTION GENETICS AND EVOLUTION 2016; 44:541-548. [DOI: 10.1016/j.meegid.2016.07.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/10/2016] [Accepted: 07/13/2016] [Indexed: 11/18/2022]
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12
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Copeland C, Ao K, Huang Y, Tong M, Li X. The Evolutionarily Conserved E3 Ubiquitin Ligase AtCHIP Contributes to Plant Immunity. FRONTIERS IN PLANT SCIENCE 2016; 7:309. [PMID: 27014328 PMCID: PMC4791365 DOI: 10.3389/fpls.2016.00309] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 02/29/2016] [Indexed: 05/24/2023]
Abstract
Plants possess a sophisticated immune system to recognize and respond to microbial threats in their environment. The level of immune signaling must be tightly regulated so that immune responses can be quickly activated in the presence of pathogens, while avoiding autoimmunity. HSP90s, along with their diverse array of co-chaperones, forms chaperone complexes that have been shown to play both positive and negative roles in regulating the accumulation of immune receptors and regulators. In this study, we examined the role of AtCHIP, an evolutionarily conserved E3 ligase that was known to interact with chaperones including HSP90s in multicellular organisms including fruit fly, Caenorhabditis elegans, plants and human. Atchip knockout mutants display enhanced disease susceptibility to a virulent oomycete pathogen, and overexpression of AtCHIP causes enhanced disease resistance at low temperature. Although CHIP was reported to target HSP90 for ubiquitination and degradation, accumulation of HSP90.3 was not affected in Atchip plants. In addition, protein accumulation of nucleotide-binding, leucine-rich repeat domain immune receptor (NLR) SNC1 is not altered in Atchip mutant. Thus, while AtCHIP plays a role in immunity, it does not seem to regulate the turnover of HSP90 or SNC1. Further investigation is needed in order to determine the exact mechanism behind AtCHIP's role in regulating plant immune responses.
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Affiliation(s)
- Charles Copeland
- Michael Smith Laboratories, University of British ColumbiaVancouver, BC, Canada
- Department of Botany, University of British ColumbiaVancouver, BC, Canada
| | - Kevin Ao
- Michael Smith Laboratories, University of British ColumbiaVancouver, BC, Canada
- Department of Botany, University of British ColumbiaVancouver, BC, Canada
| | - Yan Huang
- Michael Smith Laboratories, University of British ColumbiaVancouver, BC, Canada
- Department of Botany, University of British ColumbiaVancouver, BC, Canada
| | - Meixuizi Tong
- Michael Smith Laboratories, University of British ColumbiaVancouver, BC, Canada
- Department of Botany, University of British ColumbiaVancouver, BC, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British ColumbiaVancouver, BC, Canada
- Department of Botany, University of British ColumbiaVancouver, BC, Canada
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13
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Anderson RG, McDowell JM. A PCR assay for the quantification of growth of the oomycete pathogen Hyaloperonospora arabidopsidis in Arabidopsis thaliana. MOLECULAR PLANT PATHOLOGY 2015; 16:893-898. [PMID: 25676785 PMCID: PMC6638379 DOI: 10.1111/mpp.12247] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The accurate quantification of disease severity is important for the assessment of host-pathogen interactions in laboratory or field settings. The interaction between Arabidopsis thaliana and its naturally occurring downy mildew pathogen, Hyaloperonospora arabidopsidis (Hpa), is a widely used reference pathosystem for plant-oomycete interactions. Current methods for the assessment of disease severity in the Arabidopsis-Hpa interaction rely on measurements at the terminal stage of pathogen development; namely, visual counts of spore-producing structures or the quantification of spore production with a haemocytometer. These assays are useful, but do not offer sensitivity for the robust quantification of small changes in virulence or the accurate quantification of pathogen growth prior to the reproductive stage. Here, we describe a quantitative real-time polymerase chain reaction (qPCR) assay for the monitoring of Hpa growth in planta. The protocol is rapid, inexpensive and can robustly distinguish small changes in virulence. We used this assay to investigate the dynamics of early Hpa mycelial growth and to demonstrate the proof of concept that this assay could be used in screens for novel oomycete growth inhibitors.
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Affiliation(s)
- Ryan G Anderson
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA, 24061-0329, USA
| | - John M McDowell
- Department of Plant Pathology, Physiology and Weed Science, Virginia Tech, Blacksburg, VA, 24061-0329, USA
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14
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Miller M, Song Q, Shi X, Juenger TE, Chen ZJ. Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis. Nat Commun 2015; 6:7453. [PMID: 26154604 DOI: 10.1038/ncomms8453] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 05/11/2015] [Indexed: 11/09/2022] Open
Abstract
The genetic distance between hybridizing parents affects heterosis; however, the mechanisms for this remain unclear. Here we report that this genetic distance correlates with natural variation and epigenetic regulation of circadian clock-mediated stress responses. In intraspecific hybrids of Arabidopsis thaliana, genome-wide expression of many biotic and abiotic stress-responsive genes is diurnally repressed and this correlates with biomass heterosis and biomass quantitative trait loci. Expression differences of selected stress-responsive genes among diverse ecotypes are predictive of heterosis in their hybrids. Stress-responsive genes are repressed in the hybrids under normal conditions but are induced to mid-parent or higher levels under stress at certain times of the day, potentially balancing the tradeoff between stress responses and growth. Consistent with this hypothesis, repression of two candidate stress-responsive genes increases growth vigour. Our findings may therefore provide new criteria for effectively selecting parents to produce high- or low-yield hybrids.
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Affiliation(s)
- Marisa Miller
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Qingxin Song
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaoli Shi
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Thomas E Juenger
- Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Z Jeffrey Chen
- 1] Departments of Molecular Biosciences and of Integrative Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA [2] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
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15
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Xu E, Vaahtera L, Hõrak H, Hincha DK, Heyer AG, Brosché M. Quantitative trait loci mapping and transcriptome analysis reveal candidate genes regulating the response to ozone in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2015; 38:1418-33. [PMID: 25496229 DOI: 10.1111/pce.12499] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
As multifaceted molecules, reactive oxygen species (ROS) are known to accumulate in response to various stresses. Ozone (O3 ) is an air pollutant with detrimental effect on plants and O3 can also be used as a tool to study the role of ROS in signalling. Genetic variation of O3 sensitivity in different Arabidopsis accessions highlights the complex genetic architecture of plant responses to ROS. To investigate the genetic basis of O3 sensitivity, a recombinant inbred line (RIL) population between two Arabidopsis accessions with distinct O3 sensitivity, C24 (O3 tolerant) and Te (O3 sensitive) was used for quantitative trait loci (QTL) mapping. Through analysis of QTL mapping combined with transcriptome changes in response to O3 , we identified three causal QTLs and several potential candidate genes regulating the response to O3 . Based on gene expression data, water loss and stomatal conductance measurement, we found that a combination of relatively low stomatal conductance and constitutive activation of salicylic acid (SA)-mediated defence signalling were responsible for the O3 tolerance in C24. Application of exogenous SA prior to O3 exposure can mimic the constitutive SA signalling in C24 and could attenuate O3 -induced leaf damage in the sensitive Arabidopsis accessions Te and Cvi-0.
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Affiliation(s)
- Enjun Xu
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, FI-00014, Finland
| | - Lauri Vaahtera
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, FI-00014, Finland
| | - Hanna Hõrak
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
| | - Dirk K Hincha
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam, D-14476, Germany
| | - Arnd G Heyer
- Department of Plant Biotechnology, Institute of Biology, University of Stuttgart, Stuttgart, D-70569, Germany
| | - Mikael Brosché
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, FI-00014, Finland
- Institute of Technology, University of Tartu, Tartu, 50411, Estonia
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Gao D, Appiano M, Huibers RP, Loonen AEHM, Visser RGF, Wolters AMA, Bai Y. Natural loss-of-function mutation of EDR1 conferring resistance to tomato powdery mildew in Arabidopsis thaliana accession C24. MOLECULAR PLANT PATHOLOGY 2015; 16:71-82. [PMID: 24925473 PMCID: PMC6638503 DOI: 10.1111/mpp.12165] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
To screen for potentially novel types of resistance to tomato powdery mildew Oidium neolycopersici, a disease assay was performed on 123 Arabidopsis thaliana accessions. Forty accessions were fully resistant, and one, C24, was analysed in detail. By quantitative trait locus (QTL) analysis of an F2 population derived from C24 × Sha (susceptible accession), two QTLs associated with resistance were identified in C24. Fine mapping of QTL-1 on chromosome 1 delimited the region to an interval of 58 kb encompassing 15 candidate genes. One of these was Enhanced Disease Resistance 1 (EDR1). Evaluation of the previously obtained edr1 mutant of Arabidopsis accession Col-0, which was identified because of its resistance to powdery mildew Golovinomyces cichoracearum, showed that it also displayed resistance to O. neolycopersici. Sequencing of EDR1 in our C24 germplasm (referred to as C24-W) revealed two missing nucleotides in the second exon of EDR1 resulting in a premature stop codon. Remarkably, C24 obtained from other laboratories does not contain the EDR1 mutation. To verify the identity of C24-W, a DNA region containing a single nucleotide polymorphism (SNP) unique to C24 was sequenced showing that C24-W contains the C24-specific nucleotide. C24-W showed enhanced resistance to O. neolycopersici compared with C24 not containing the edr1 mutation. Furthermore, C24-W displayed a dwarf phenotype, which was not associated with the mutation in EDR1 and was not caused by the differential accumulation of pathogenesis-related genes. In conclusion, we identified a natural edr1 mutant in the background of C24.
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Affiliation(s)
- Dongli Gao
- Wageningen UR Plant Breeding, Wageningen University, Research Centre, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
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Lapin D, Van den Ackerveken G. Susceptibility to plant disease: more than a failure of host immunity. TRENDS IN PLANT SCIENCE 2013; 18:546-54. [PMID: 23790254 DOI: 10.1016/j.tplants.2013.05.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/15/2013] [Accepted: 05/21/2013] [Indexed: 05/23/2023]
Abstract
Susceptibility to infectious diseases caused by pathogens affects most plants in their natural habitat and leads to yield losses in agriculture. However, plants are not helpless because their immune system can deal with the vast majority of attackers. Nevertheless, adapted pathogens are able to circumvent or avert host immunity making plants susceptible to these uninvited guests. In addition to the failure of the plant immune system, there are other host processes that contribute to plant disease susceptibility. In this review, we discuss recent studies that show the active role played by the host in supporting disease, focusing mainly on biotrophic stages of infection. Plants attract pathogens, enable their entry and accommodation, and facilitate nutrient provision.
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Affiliation(s)
- Dmitry Lapin
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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