1
|
Chroston ECM, Bziuk N, Stauber EJ, Ravindran BM, Hielscher A, Smalla K, Wittstock U. Plant glucosinolate biosynthesis and breakdown pathways shape the rhizosphere bacterial/archaeal community. PLANT, CELL & ENVIRONMENT 2024; 47:2127-2145. [PMID: 38419355 DOI: 10.1111/pce.14870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/12/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
Rhizosphere microbial community assembly results from microbe-microbe-plant interactions mediated by small molecules of plant and microbial origin. Studies with Arabidopsis thaliana have indicated a critical role of glucosinolates in shaping the root and/or rhizosphere microbial community, likely through breakdown products produced by plant or microbial myrosinases inside or outside of the root. Plant nitrile-specifier proteins (NSPs) promote the formation of nitriles at the expense of isothiocyanates upon glucosinolate hydrolysis with unknown consequences for microbial colonisation of roots and rhizosphere. Here, we generated the A. thaliana triple mutant nsp134 devoid of nitrile formation in root homogenates. Using this line and mutants lacking aliphatic or indole glucosinolate biosynthesis pathways or both, we found bacterial/archaeal alpha-diversity of the rhizosphere to be affected only by the ability to produce aliphatic glucosinolates. In contrast, bacterial/archaeal community composition depended on functional root NSPs as well as on pathways of aliphatic and indole glucosinolate biosynthesis. Effects of NSP deficiency were strikingly distinct from those of impaired glucosinolate biosynthesis. Our results demonstrate that rhizosphere microbial community assembly depends on functional pathways of both glucosinolate biosynthesis and breakdown in support of the hypothesis that glucosinolate hydrolysis by myrosinases and NSPs happens before secretion of products to the rhizosphere.
Collapse
Affiliation(s)
- Eleanor C M Chroston
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nina Bziuk
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Einar J Stauber
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Beena M Ravindran
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Annika Hielscher
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kornelia Smalla
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Ute Wittstock
- Institute of Pharmaceutical Biology, Technische Universität Braunschweig, Braunschweig, Germany
| |
Collapse
|
2
|
Sun K, Pan YT, Jiang HJ, Xu JY, Ma CY, Zhou J, Liu Y, Shabala S, Zhang W, Dai CC. Root endophyte-mediated alteration in plant H2O2 homeostasis regulates symbiosis outcome and reshapes the rhizosphere microbiota. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3153-3170. [PMID: 38394357 DOI: 10.1093/jxb/erae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/22/2024] [Indexed: 02/25/2024]
Abstract
Endophytic symbioses between plants and fungi are a dominant feature of many terrestrial ecosystems, yet little is known about the signaling that defines these symbiotic associations. Hydrogen peroxide (H2O2) is recognized as a key signal mediating the plant adaptive response to both biotic and abiotic stresses. However, the role of H2O2 in plant-fungal symbiosis remains elusive. Using a combination of physiological analysis, plant and fungal deletion mutants, and comparative transcriptomics, we reported that various environmental conditions differentially affect the interaction between Arabidopsis and the root endophyte Phomopsis liquidambaris, and link this process to alterations in H2O2 levels and H2O2 fluxes across root tips. We found that enhanced H2O2 efflux leading to a moderate increase in H2O2 levels at the plant-fungal interface is required for maintaining plant-fungal symbiosis. Disturbance of plant H2O2 homeostasis compromises the symbiotic ability of plant roots. Moreover, the fungus-regulated H2O2 dynamics modulate the rhizosphere microbiome by selectively enriching for the phylum Cyanobacteria, with strong antioxidant defenses. Our results demonstrated that the regulation of H2O2 dynamics at the plant-fungal interface affects the symbiotic outcome in response to external conditions and highlight the importance of the root endophyte in reshaping the rhizosphere microbiota.
Collapse
Affiliation(s)
- Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Yi-Tong Pan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Hui-Jun Jiang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Jia-Yan Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Jiayu Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Yunqi Liu
- Zhongguancun Xuyue Non-invasive Micro-test Technology Industrial Alliance, Beijing 10080, China
| | - Sergey Shabala
- School of Biological Science, University of Western Australia, Crawley, WA 60909, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| |
Collapse
|
3
|
Basak AK, Piasecka A, Hucklenbroich J, Türksoy GM, Guan R, Zhang P, Getzke F, Garrido-Oter R, Hacquard S, Strzałka K, Bednarek P, Yamada K, Nakano RT. ER body-resident myrosinases and tryptophan specialized metabolism modulate root microbiota assembly. THE NEW PHYTOLOGIST 2024; 241:329-342. [PMID: 37771245 DOI: 10.1111/nph.19289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 09/13/2023] [Indexed: 09/30/2023]
Abstract
Endoplasmic reticulum (ER) bodies are ER-derived structures that contain a large amount of PYK10 myrosinase, which hydrolyzes tryptophan (Trp)-derived indole glucosinolates (IGs). Given the well-described role of IGs in root-microbe interactions, we hypothesized that ER bodies in roots are important for interaction with soil-borne microbes at the root-soil interface. We used mutants impaired in ER bodies (nai1), ER body-resident myrosinases (pyk10bglu21), IG biosynthesis (myb34/51/122), and Trp specialized metabolism (cyp79b2b3) to profile their root microbiota community in natural soil, evaluate the impact of axenically collected root exudates on soil or synthetic microbial communities, and test their response to fungal endophytes in a mono-association setup. Tested mutants exhibited altered bacterial and fungal communities in rhizoplane and endosphere, respectively. Natural soils and bacterial synthetic communities treated with mutant root exudates exhibited distinctive microbial profiles from those treated with wild-type (WT) exudates. Most tested endophytes severely restricted the growth of cyp79b2b3, a part of which also impaired the growth of pyk10bglu21. Our results suggest that root ER bodies and their resident myrosinases modulate the profile of root-secreted metabolites and thereby influence root-microbiota interactions.
Collapse
Affiliation(s)
- Arpan Kumar Basak
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Krakow, 30-387, Poland
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Anna Piasecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Jana Hucklenbroich
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Gözde Merve Türksoy
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Rui Guan
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Pengfan Zhang
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Felix Getzke
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Ruben Garrido-Oter
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Stephane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Kazimierz Strzałka
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Plant Physiology and Biochemistry, Jagiellonian University, Krakow, 30-387, Poland
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Kenji Yamada
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, 30-387, Poland
| | - Ryohei Thomas Nakano
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| |
Collapse
|
4
|
Mesny F, Hacquard S, Thomma BPHJ. Co-evolution within the plant holobiont drives host performance. EMBO Rep 2023; 24:e57455. [PMID: 37471099 PMCID: PMC10481671 DOI: 10.15252/embr.202357455] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Abstract
Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.
Collapse
Affiliation(s)
- Fantin Mesny
- Institute for Plant SciencesUniversity of CologneCologneGermany
| | - Stéphane Hacquard
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
| | - Bart PHJ Thomma
- Institute for Plant SciencesUniversity of CologneCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
| |
Collapse
|
5
|
Xu ZX, Zhu XM, Yin H, Li B, Chen XJ, Fan XL, Li NQ, Selosse MA, Gao JY, Han JJ. Symbiosis between Dendrobium catenatum protocorms and Serendipita indica involves the plant hypoxia response pathway. PLANT PHYSIOLOGY 2023; 192:2554-2568. [PMID: 36988071 PMCID: PMC10315314 DOI: 10.1093/plphys/kiad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Mycorrhizae are ubiquitous symbioses established between fungi and plant roots. Orchids, in particular, require compatible mycorrhizal fungi for seed germination and protocorm development. Unlike arbuscular mycorrhizal fungi, which have wide host ranges, orchid mycorrhizal fungi are often highly specific to their host orchids. However, the molecular mechanism of orchid mycorrhizal symbiosis is largely unknown compared to that of arbuscular mycorrhizal and rhizobial symbiosis. Here, we report that an endophytic Sebacinales fungus, Serendipita indica, promotes seed germination and the development of protocorms into plantlets in several epiphytic Epidendroideae orchid species (6 species in 2 genera), including Dendrobium catenatum, a critically endangered orchid with high medicinal value. Although plant-pathogen interaction and high meristematic activity can induce the hypoxic response in plants, it has been unclear whether interactions with beneficial fungi, especially mycorrhizal ones, also involve the hypoxic response. By studying the symbiotic relationship between D. catenatum and S. indica, we determined that hypoxia-responsive genes, such as those encoding alcohol dehydrogenase (ADH), are highly induced in symbiotic D. catenatum protocorms. In situ hybridization assay indicated that the ADH gene is predominantly expressed in the basal mycorrhizal region of symbiotic protocorms. Additionally, the ADH inhibitors puerarin and 4-methylpyrazole both decreased S. indica colonization in D. catenatum protocorms. Thus, our study reveals that S. indica is widely compatible with orchids and that ADH and its related hypoxia-responsive pathway are involved in establishing successful symbiotic relationships in germinating orchids.
Collapse
Affiliation(s)
- Zhi-Xiong Xu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Xin-Meng Zhu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Huachun Yin
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Xiao-Jie Chen
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Xu-Li Fan
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Neng-Qi Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Marc-André Selosse
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Institut de Systématique, Évolution, Biodiversité (UMR 7205-CNRS, MNHN, UPMC, EPHE), Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, 75005 Paris, France
- University of Gdańsk, Faculty of Biology, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
- Institut Universitaire de France (IUF), Paris, France
| | - Jiang-Yun Gao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| | - Jia-Jia Han
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650500, China
| |
Collapse
|
6
|
Yang X, Jiang Z, He J, Shen L. iTRAQ-Based Quantitative Proteomics Unveils Protein Dynamics in the Root of Solanum melongena L. under Waterlogging Stress Conditions. Life (Basel) 2023; 13:1399. [PMID: 37374181 DOI: 10.3390/life13061399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Waterlogging poses significant abiotic stress that endangers the survival of plants, including crops. In response, plants dramatically change their physiology to enhance their tolerance to waterlogging, such as proteome reconfiguration. Here, we utilized isobaric tags for the relative and absolute quantitation (iTRAQ)-based protein labeling technique to examine the proteomic changes induced by waterlogging in the roots of Solanum melongena L., a solanaceous plant. The plants were subjected to 6, 12, and 24 h of waterlogging stress at the flowering stage. Of the 4074 identified proteins, compared to the control, the abundance of the proteins increased and decreased in 165 and 78 proteins, respectively, in 6 h of treatments; 219 and 89 proteins, respectively, in 12 h of treatments; and 126 and 127 proteins, respectively, in 24 h of treatments. The majority of these differentially regulated proteins participated in processes such as energy metabolism, amino acid biosynthesis, signal transduction, and nitrogen metabolism. Fructose-bisphosphate aldolase and three alcohol dehydrogenase genes, in particular, were up- or down-regulated in waterlogging-treated Solanum melongena roots, suggesting that some proteins related to anaerobic metabolism (glycolysis and fermentation) may play vital roles in protecting its roots from waterlogging stress to enable long-term survival. Overall, this research not only offers a comprehensive dataset of protein alterations in waterlogged Solanum melongena roots but also insights into the mechanisms by which solanaceous plants adapt to waterlogging stress.
Collapse
Affiliation(s)
- Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Zheng Jiang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jie He
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
7
|
Teulet A, Quan C, Evangelisti E, Wanke A, Yang W, Schornack S. A pathogen effector FOLD diversified in symbiotic fungi. THE NEW PHYTOLOGIST 2023. [PMID: 37257494 DOI: 10.1111/nph.18996] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/27/2023] [Indexed: 06/02/2023]
Abstract
Pathogenic fungi use secreted effector proteins to suppress immunity and support their infection, but effectors have also been reported from fungi that engage in nutritional symbioses with plants. Sequence-based effector comparisons between pathogens and symbiotic arbuscular mycorrhizal (AM) fungi are hampered by the huge diversity of effector sequences even within closely related microbes. To find sequence-divergent but structurally similar effectors shared between symbiotic and pathogenic fungi, we compared secreted protein structure models of the AM fungus Rhizophagus irregularis to known pathogen effectors. We identified proteins with structural similarity to known Fusarium oxysporum f. sp. lycopersici dual domain (FOLD) effectors, which occur in low numbers in several fungal pathogens. Contrastingly, FOLD genes from AM fungi (MycFOLDs) are found in enlarged and diversified gene families with higher levels of positive selection in their C-terminal domains. Our structure model comparison suggests that MycFOLDs are similar to carbohydrate-binding motifs. Different MycFOLD genes are expressed during colonisation of different hosts and MycFOLD-17 transcripts accumulate in plant intracellular arbuscules. The exclusive presence of MycFOLDs across unrelated plant-colonising fungi, their inducible expression, lineage-specific sequence diversification and transcripts in arbuscules suggest that FOLD proteins act as effectors during plant colonisation of symbiotic and pathogenic fungi.
Collapse
Affiliation(s)
- Albin Teulet
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Clément Quan
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | | | - Alan Wanke
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Weibing Yang
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | | |
Collapse
|
8
|
Sehar S, Adil MF, Ma Z, Karim MF, Faizan M, Zaidi SSA, Siddiqui MH, Alamri S, Zhou F, Shamsi IH. Phosphorus and Serendipita indica synergism augments arsenic stress tolerance in rice by regulating secondary metabolism related enzymatic activity and root metabolic patterns. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 256:114866. [PMID: 37023649 DOI: 10.1016/j.ecoenv.2023.114866] [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: 03/03/2023] [Revised: 03/29/2023] [Accepted: 04/01/2023] [Indexed: 06/19/2023]
Abstract
The multifarious problems created by arsenic (As), for collective environment and human health, serve a cogent case for searching integrative agricultural approaches to attain food security. Rice (Oryza sativa L.) acts as a sponge for heavy metal(loid)s accretion, specifically As, due to anaerobic flooded growth conditions facilitating its uptake. Acclaimed for their positive impact on plant growth, development and phosphorus (P) nutrition, 'mycorrhizas' are able to promote stress tolerance. Albeit, the metabolic alterations underlying Serendipita indica (S. indica; S.i) symbiosis-mediated amelioration of As stress along with nutritional management of P are still understudied. By using biochemical, RT-qPCR and LC-MS/MS based untargeted metabolomics approach, rice roots of ZZY-1 and GD-6 colonized by S. indica, which were later treated with As (10 µM) and P (50 µM), were compared with non-colonized roots under the same treatments with a set of control plants. The responses of secondary metabolism related enzymes, especially polyphenol oxidase (PPO) activities in the foliage of ZZY-1 and GD-6 were enhanced 8.5 and 12-fold, respectively, compared to their respective control counterparts. The current study identified 360 cationic and 287 anionic metabolites in rice roots, and the commonly enriched pathway annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was biosynthesis of phenylalanine, tyrosine and tryptophan, which validated the results of biochemical and gene expression analyses associated with secondary metabolic enzymes. Particularly under As+S.i+P comparison, both genotypes exhibited an upregulation of key detoxification and defense related metabolites, including fumaric acid, L-malic acid, choline, 3,4-dihydroxybenzoic acid, to name a few. The results of this study provided the novel insights into the promising role of exogenous P and S. indica in alleviating As stress.
Collapse
Affiliation(s)
- Shafaque Sehar
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Muhammad Faheem Adil
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhengxin Ma
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Muhammad Fazal Karim
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Department of Agronomy, PMAS-Arid Agriculture University Rawalpindi, Rawalpindi 46000, Pakistan
| | - Mohammad Faizan
- Botany Section, School of Sciences, Maulana Azad National Urdu University, Hyderabad 500032, India
| | - Syed Shujaat Ali Zaidi
- Center for Innovation in Brain Science, Department of Neurology, University of Arizona, Tucson, AZ 85719, USA
| | - Manzer H Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Fanrui Zhou
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, China; Key Laboratory of State Forestry and Grassland Administration on Highly Efficient Utilization of Forestry Biomass Resources in Southwest China, College of Material and Chemical Engineering, Southwest Forestry University, Kunming 650224, China
| | - Imran Haider Shamsi
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
| |
Collapse
|
9
|
Biget M, Wang T, Mony C, Xu Q, Lecoq L, Chable V, Theis KR, Ling N, Vandenkoornhuyse P. Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants. iScience 2023; 26:106031. [PMID: 36824281 PMCID: PMC9941212 DOI: 10.1016/j.isci.2023.106031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 09/07/2022] [Accepted: 01/17/2023] [Indexed: 01/25/2023] Open
Abstract
The hologenome concept considers the entity formed by a host and its microbiota, the holobiont, as new level of hierarchical organization subject to neutral and selective forces. We used grafted plants to formally evaluate the hologenome concept. We analyzed the root-endosphere microbiota of two independent watermelon and grapevine plant systems, including ungrafted and reciprocal-grafting combinations. Grafted and ungrafted hosts harbor markedly different microbiota compositions. Furthermore, the results indicate a non-random assembly of bacterial communities inhabiting the root endosphere of chimeric plants with interactive effect of both the rootstock and scion on the recruitment of microorganisms. Because chimeric plants did not have a random microbiota, the null hypothesis that holobionts assemble randomly and hologenome concept is an intellectual construction only can be rejected. The study supports the relevance of hologenome as biological level of organization and opens new avenues for a better fundamental understanding of plants as holobionts.
Collapse
Affiliation(s)
- Marine Biget
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France
| | - Tingting Wang
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France,Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Cendrine Mony
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France
| | - Qicheng Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Lucie Lecoq
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France
| | - Véronique Chable
- UMR BAGAP INRAE, Centre Bretagne-Normandie, Domaine de la Motte, BP35327, 35653 Le Rheu Cedex, France
| | - Kevin R. Theis
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ning Ling
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China,Corresponding author
| | - Philippe Vandenkoornhuyse
- Université de Rennes 1, CNRS, UMR 6553 ECOBIO (écosystèmes, biodiversité, évolution), 35000 Rennes, France,Corresponding author
| |
Collapse
|
10
|
Sharma A, Sinharoy S, Bisht NC. The mysterious non-arbuscular mycorrhizal status of Brassicaceae species. Environ Microbiol 2023; 25:917-930. [PMID: 36655756 DOI: 10.1111/1462-2920.16339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/13/2023] [Indexed: 01/20/2023]
Abstract
The Brassicaceae family is unique in not fostering functional symbiosis with arbuscular mycorrhiza (AM). The family is also special in possessing glucosinolates, a class of secondary metabolites predominantly functioning for plant defence. We have reviewed what effect the glucosinolates of this non-symbiotic host have on AM or vice versa. Isothiocyanates, the toxic degradation product of the glucosinolates, particularly the indolic and benzenic glucosinolates, are known to be involved in the inhibition of AM. Interestingly, AM colonization enhances glucosinolate production in two AM-host in the Brassicales family- Moringa oleifera and Tropaeolum spp. PHOSPHATE STARVATION RESPONSE 1 (PHR1), a central transcription factor that controls phosphate starvation response also activates the glucosinolate biosynthesis in AM non-host Arabidopsis thaliana. Recently, the advances in whole-genome sequencing, enabling extensive ecological microbiome studies have helped unravel the Brassicaceae microbiome, identifying new mutualists that compensate for the loss of AM symbiosis, and reporting cues for some influence of glucosinolates on the microbiome structure. We advocate that glucosinolate is an important candidate in determining the mycorrhizal status of Brassicaceae and has played a major role in its symbiosis-defence trade-off. We also identify key open questions in this area that remain to be addressed in the future.
Collapse
Affiliation(s)
- Aprajita Sharma
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Senjuti Sinharoy
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Naveen C Bisht
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| |
Collapse
|
11
|
Singh G, Agrawal H, Bednarek P. Specialized metabolites as versatile tools in shaping plant-microbe associations. MOLECULAR PLANT 2023; 16:122-144. [PMID: 36503863 DOI: 10.1016/j.molp.2022.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/02/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Plants are rich repository of a large number of chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes including responses against changing abiotic conditions and interactions with various co-existing organisms. One of the strikingly affirmed functions of these specialized metabolites is their involvement in plants' life-long interactions with complex multi-kingdom microbiomes including both beneficial and harmful microorganisms. Recent developments in genomic and molecular biology tools not only help to generate well-curated information about regulatory and structural components of biosynthetic pathways of plant specialized metabolites but also to create and screen mutant lines defective in their synthesis. In this review, we have comprehensively surveyed the function of these specialized metabolites and discussed recent research findings demonstrating the responses of various microbes on tested mutant lines having defective biosynthesis of particular metabolites. In addition, we attempt to provide key clues about the impact of these metabolites on the assembly of the plant microbiome by summarizing the major findings of recent comparative metagenomic analyses of available mutant lines under customized and natural microbial niches. Subsequently, we delineate benchmark initiatives that aim to engineer or manipulate the biosynthetic pathways to produce specialized metabolites in heterologous systems but also to diversify their immune function. While denoting the function of these metabolites, we also discuss the critical bottlenecks associated with understanding and exploiting their function in improving plant adaptation to the environment.
Collapse
Affiliation(s)
- Gopal Singh
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Himani Agrawal
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
| |
Collapse
|
12
|
Kundu A, Vadassery J. Molecular mechanisms of Piriformospora indica mediated growth promotion in plants. PLANT SIGNALING & BEHAVIOR 2022; 17:2096785. [PMID: 35811563 PMCID: PMC9272844 DOI: 10.1080/15592324.2022.2096785] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Piriformospora indica is a root endophyte having a vast host range in plants. Plant growth promotion is a hallmark of the symbiotic interaction of P. indica with its hosts. As a plant growth-promoting microorganism, it is important to know the mechanisms involved in growth induction. Hitherto, multiple reports have demonstrated various molecular mechanisms of P. indica-mediated growth promotion, including protein kinase-mediated pathway, enhanced nutrient uptake and polyamine-mediated growth phytohormone elevation. Here, we briefly present a discussion on the state-of-the-art molecular mechanisms of P. indica-mediated growth promotion in host plants, in order to obtain a future prospect on utilization of this microorganism for sustainable agriculture.
Collapse
Affiliation(s)
- Anish Kundu
- Chemical Ecology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Jyothilakshmi Vadassery
- Chemical Ecology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| |
Collapse
|
13
|
The Impact of Nitrile-Specifier Proteins on Indolic Carbinol and Nitrile Formation in Homogenates of Arabidopsis thaliana. Molecules 2022; 27:molecules27228042. [PMID: 36432142 PMCID: PMC9696369 DOI: 10.3390/molecules27228042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
Glucosinolates, specialized metabolites of the Brassicales including Brassica crops and Arabidopsis thaliana, have attracted considerable interest as chemical defenses and health-promoting compounds. Their biological activities are mostly due to breakdown products formed upon mixing with co-occurring myrosinases and specifier proteins, which can result in multiple products with differing properties, even from a single glucosinolate. Whereas product profiles of aliphatic glucosinolates have frequently been reported, indole glucosinolate breakdown may result in complex mixtures, the analysis of which challenging. The aim of this study was to assess the breakdown of indole glucosinolates in A. thaliana root and rosette homogenates and to test the impact of nitrile-specifier proteins (NSPs) on product profiles. To develop a GC-MS-method for quantification of carbinols and nitriles derived from three prominent indole glucosinolates, we synthesized standards, established derivatization conditions, determined relative response factors and evaluated applicability of the method to plant homogenates. We show that carbinols are more dominant among the detected products in rosette than in root homogenates of wild-type and NSP1- or NSP3-deficient mutants. NSP1 is solely responsible for nitrile formation in rosette homogenates and is the major NSP for indolic nitrile formation in root homogenates, with no contribution from NSP3. These results will contribute to the understanding of the roles of NSPs in plants.
Collapse
|
14
|
Pérez‐Alonso M, Guerrero‐Galán C, González Ortega‐Villaizán A, Ortiz‐García P, Scholz SS, Ramos P, Sakakibara H, Kiba T, Ludwig‐Müller J, Krapp A, Oelmüller R, Vicente‐Carbajosa J, Pollmann S. The calcium sensor CBL7 is required for Serendipita indica-induced growth stimulation in Arabidopsis thaliana, controlling defense against the endophyte and K + homoeostasis in the symbiosis. PLANT, CELL & ENVIRONMENT 2022; 45:3367-3382. [PMID: 35984078 PMCID: PMC9804297 DOI: 10.1111/pce.14420] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/02/2022] [Accepted: 08/07/2022] [Indexed: 06/15/2023]
Abstract
Calcium is an important second messenger in plants. The activation of Ca2+ signalling cascades is critical in the activation of adaptive processes in response to environmental stimuli. Root colonization by the growth promoting endophyte Serendipita indica involves the increase of cytosolic Ca2+ levels in Arabidopsis thaliana. Here, we investigated transcriptional changes in Arabidopsis roots during symbiosis with S. indica. RNA-seq profiling disclosed the induction of Calcineurin B-like 7 (CBL7) during early and later phases of the interaction. Consistently, reverse genetic evidence highlighted the functional relevance of CBL7 and tested the involvement of a CBL7-CBL-interacting protein kinase 13 signalling pathway. The loss-of-function of CBL7 abolished the growth promoting effect and affected root colonization. The transcriptomics analysis of cbl7 revealed the involvement of this Ca2+ sensor in activating plant defense responses. Furthermore, we report on the contribution of CBL7 to potassium transport in Arabidopsis. We analysed K+ contents in wild-type and cbl7 plants and observed a significant increase of K+ in roots of cbl7 plants, while shoot tissues demonstrated K+ depletion. Taken together, our work associates CBL7 with an important role in the mutual interaction between Arabidopsis and S. indica and links CBL7 to K+ transport.
Collapse
Affiliation(s)
- Marta‐Marina Pérez‐Alonso
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA/CSIC)Campus de MontegancedoPozuelo de Alarcón (Madrid)Spain
- Umeå Plant Science CenterUmeå UniversityUmeåSweden
| | - Carmen Guerrero‐Galán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA/CSIC)Campus de MontegancedoPozuelo de Alarcón (Madrid)Spain
| | - Adrián González Ortega‐Villaizán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA/CSIC)Campus de MontegancedoPozuelo de Alarcón (Madrid)Spain
| | - Paloma Ortiz‐García
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA/CSIC)Campus de MontegancedoPozuelo de Alarcón (Madrid)Spain
| | - Sandra S. Scholz
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular BotanyFriedrich‐Schiller‐University JenaJenaGermany
| | - Patricio Ramos
- Centro de Investigación de Estudios Avanzados del MauleUniversidad Católica del MauleTalcaChile
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource ScienceTsurumiYokohamaJapan
- Department of Applied Biosciences, Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaJapan
| | - Takatoshi Kiba
- RIKEN Center for Sustainable Resource ScienceTsurumiYokohamaJapan
- Department of Applied Biosciences, Graduate School of Bioagricultural SciencesNagoya UniversityNagoyaJapan
| | | | - Anne Krapp
- Université Paris‐Saclay, INRAE, AgroParisTechInstitut Jean‐Pierre BourginVersaillesFrance
| | - Ralf Oelmüller
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular BotanyFriedrich‐Schiller‐University JenaJenaGermany
| | - Jesús Vicente‐Carbajosa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA/CSIC)Campus de MontegancedoPozuelo de Alarcón (Madrid)Spain
- Departamento de Biotecnología‐Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de BiosistemasUniversidad Politécnica de Madrid (UPM)MadridSpain
| | - Stephan Pollmann
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA/CSIC)Campus de MontegancedoPozuelo de Alarcón (Madrid)Spain
- Departamento de Biotecnología‐Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de BiosistemasUniversidad Politécnica de Madrid (UPM)MadridSpain
| |
Collapse
|
15
|
Poveda J, Díaz-González S, Díaz-Urbano M, Velasco P, Sacristán S. Fungal endophytes of Brassicaceae: Molecular interactions and crop benefits. FRONTIERS IN PLANT SCIENCE 2022; 13:932288. [PMID: 35991403 PMCID: PMC9390090 DOI: 10.3389/fpls.2022.932288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Brassicaceae family includes an important group of plants of great scientific interest, e.g., the model plant Arabidopsis thaliana, and of economic interest, such as crops of the genus Brassica (Brassica oleracea, Brassica napus, Brassica rapa, etc.). This group of plants is characterized by the synthesis and accumulation in their tissues of secondary metabolites called glucosinolates (GSLs), sulfur-containing compounds mainly involved in plant defense against pathogens and pests. Brassicaceae plants are among the 30% of plant species that cannot establish optimal associations with mycorrhizal hosts (together with other plant families such as Proteaceae, Chenopodiaceae, and Caryophyllaceae), and GSLs could be involved in this evolutionary process of non-interaction. However, this group of plants can establish beneficial interactions with endophytic fungi, which requires a reduction of defensive responses by the host plant and/or an evasion, tolerance, or suppression of plant defenses by the fungus. Although much remains to be known about the mechanisms involved in the Brassicaceae-endophyte fungal interaction, several cases have been described, in which the fungi need to interfere with the GSL synthesis and hydrolysis in the host plant, or even directly degrade GSLs before they are hydrolyzed to antifungal isothiocyanates. Once the Brassicaceae-endophyte fungus symbiosis is formed, the host plant can obtain important benefits from an agricultural point of view, such as plant growth promotion and increase in yield and quality, increased tolerance to abiotic stresses, and direct and indirect control of plant pests and diseases. This review compiles the studies on the interaction between endophytic fungi and Brassicaceae plants, discussing the mechanisms involved in the success of the symbiosis, together with the benefits obtained by these plants. Due to their unique characteristics, the family Brassicaceae can be seen as a fruitful source of novel beneficial endophytes with applications to crops, as well as to generate new models of study that allow us to better understand the interactions of these amazing fungi with plants.
Collapse
Affiliation(s)
- Jorge Poveda
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Sandra Díaz-González
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
| | - María Díaz-Urbano
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia (MBG), Spanish National Research Council (CSIC), Pontevedra, Spain
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia (MBG), Spanish National Research Council (CSIC), Pontevedra, Spain
| | - Soledad Sacristán
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| |
Collapse
|
16
|
Plaszkó T, Szűcs Z, Vasas G, Gonda S. Interactions of fungi with non-isothiocyanate products of the plant glucosinolate pathway: A review on product formation, antifungal activity, mode of action and biotransformation. PHYTOCHEMISTRY 2022; 200:113245. [PMID: 35623473 DOI: 10.1016/j.phytochem.2022.113245] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 05/02/2022] [Accepted: 05/12/2022] [Indexed: 05/05/2023]
Abstract
The glucosinolate pathway, which is present in the order Brassicales, is one of the most researched defensive natural product biosynthesis pathways. Its core molecules, the glucosinolates are broken down upon pathogen challenge or tissue damage to yield an array of natural products that may help plants defend against the stressor. Though the most widely known glucosinolate decomposition products are the antimicrobial isothiocyanates, there is a wide range of other volatile and non-volatile natural products that arise from this biosynthetic pathway. This review summarizes our current knowledge on the interaction of these much less examined, non-isothiocyanate products with fungi. It deals with compounds including (1) glucosinolates and their biosynthesis precursors; (2) glucosinolate-derived nitriles (e.g. derivatives of 1H-indole-3-acetonitrile), thiocyanates, epithionitriles and oxazolidine-2-thiones; (3) putative isothiocyanate downstream products such as raphanusamic acid, 1H-indole-3-methanol (= indole-3-carbinol) and its oligomers, 1H-indol-3-ylmethanamine and ascorbigen; (4) 1H-indole-3-acetonitrile downstream products such as 1H-indole-3-carbaldehyde (indole-3-carboxaldehyde), 1H-indole-3-carboxylic acid and their derivatives; and (5) indole phytoalexins including brassinin, cyclobrassinin and brassilexin. Herein, a literature review on the following aspects is provided: their direct antifungal activity and the proposed mechanisms of antifungal action, increased biosynthesis after fungal challenge, as well as data on their biotransformation/detoxification by fungi, including but not limited to fungal myrosinase activity.
Collapse
Affiliation(s)
- Tamás Plaszkó
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary; Doctoral School of Pharmaceutical Sciences, University of Debrecen, 4032, Debrecen, Hungary.
| | - Zsolt Szűcs
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary; Healthcare Industry Institute, University of Debrecen, 4032, Debrecen, Hungary.
| | - Gábor Vasas
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
| | - Sándor Gonda
- Department of Botany, Division of Pharmacognosy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
| |
Collapse
|
17
|
Yu J, Tu X, Huang AC. Functions and biosynthesis of plant signaling metabolites mediating plant-microbe interactions. Nat Prod Rep 2022; 39:1393-1422. [PMID: 35766105 DOI: 10.1039/d2np00010e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: 2015-2022Plants and microbes have coevolved since their appearance, and their interactions, to some extent, define plant health. A reasonable fraction of small molecules plants produced are involved in mediating plant-microbe interactions, yet their functions and biosynthesis remain fragmented. The identification of these compounds and their biosynthetic genes will open up avenues for plant fitness improvement by manipulating metabolite-mediated plant-microbe interactions. Herein, we integrate the current knowledge on their chemical structures, bioactivities, and biosynthesis with the view of providing a high-level overview on their biosynthetic origins and evolutionary trajectory, and pinpointing the yet unknown and key enzymatic steps in diverse biosynthetic pathways. We further discuss the theoretical basis and prospects for directing plant signaling metabolite biosynthesis for microbe-aided plant health improvement in the future.
Collapse
Affiliation(s)
- Jingwei Yu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Xingzhao Tu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| | - Ancheng C Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
| |
Collapse
|
18
|
Redkar A, Sabale M, Zuccaro A, Di Pietro A. Determinants of endophytic and pathogenic lifestyle in root colonizing fungi. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102226. [PMID: 35526366 DOI: 10.1016/j.pbi.2022.102226] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Plant-fungal interactions in the soil crucially impact crop productivity and can range from highly beneficial to detrimental. Accumulating evidence suggests that some root-colonizing fungi shift between endophytic and pathogenic behaviour depending on the host species and that combinations of effector proteins collectively shape the fungal lifestyle on a given plant. In this review we discuss recent advances in our understanding of how fungal infection strategies on roots can lead to contrasting outcomes for the host. We highlight functional similarities and differences in compatibility determinants that control the colonization of specific-cell layers within plant roots, ultimately shaping the continuum between endophytic and pathogenic lifestyle.
Collapse
Affiliation(s)
- Amey Redkar
- Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain; Department of Botany, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.
| | - Mugdha Sabale
- Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Alga Zuccaro
- University of Cologne, Institute for Plant Sciences, D-50674, Cologne, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), D-50674, Cologne, Germany
| | - Antonio Di Pietro
- Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain.
| |
Collapse
|
19
|
Sun K, Lu F, Huang PW, Tang MJ, Xu FJ, Zhang W, Zhou JY, Zhao P, Jia Y, Dai CC. Root endophyte differentially regulates plant response to NO 3- and NH 4+ nutrition by modulating N fluxes at the plant-fungal interface. PLANT, CELL & ENVIRONMENT 2022; 45:1813-1828. [PMID: 35274310 DOI: 10.1111/pce.14304] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
In the soil, plant roots associated with fungi often encounter uneven distribution of nitrate (NO3- )/ammonium (NH4+ ) patches, but the mechanism underlying N form-influenced plant-fungal interactions remains limited. We inoculated Arabidopsis with a root endophyte Phomopsis liquidambaris, and evaluated the effects of P. liquidambaris on plant performance under NO3- or NH4+ nutrition. Under NO3- nutrition, P. liquidambaris inoculation promoted seedling growth, whereas under NH4+ nutrition, P. liquidambaris suppressed seedling growth. Under high NH4+ conditions, fungus-colonized roots displayed increased NH4+ accumulation and NH4+ efflux, similar to the effect of ammonium stress caused by elevated NH4+ levels. Notably, this fungus excluded NH4+ during interactions with host roots, thereby leading to increased NH4+ levels at the plant-fungal interface under high NH4+ conditions. A nitrite reductase-deficient strain that excludes NO3- but absorbs NH4+ , decreased NH4+ levels in Arabidopsis shoots and rescued plant growth and nitrogen metabolism under high NH4+ levels. Transcriptomic analysis highlighted that P. liquidambaris had altered transcriptional responses associated with plant response to inorganic N forms. Our results demonstrate that fungus-regulated NO3- /NH4+ dynamics at the plant-fungal interface alters plant response to NO3- /NH4+ nutrition. This study highlights the essential functions of root endophytes in plant adaptation to soil nitrogen nutrients.
Collapse
Affiliation(s)
- Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Fan Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Peng-Wei Huang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Meng-Jun Tang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Fang-Ji Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Jia-Yu Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, China
| | - Ping Zhao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Yong Jia
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| |
Collapse
|
20
|
Adnan M, Islam W, Gang L, Chen HYH. Advanced research tools for fungal diversity and its impact on forest ecosystem. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45044-45062. [PMID: 35460003 DOI: 10.1007/s11356-022-20317-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Fungi are dominant ecological participants in the forest ecosystems, which play a major role in recycling organic matter and channeling nutrients across trophic levels. Fungal populations are shaped by plant communities and environmental parameters, and in turn, fungal communities also impact the forest ecosystem through intrinsic participation of different fungal guilds. Mycorrhizal fungi result in conservation and stability of forest ecosystem, while pathogenic fungi can bring change in forest ecosystem, by replacing the dominant plant species with new or exotic plant species. Saprotrophic fungi, being ecological regulators in the forest ecosystem, convert dead tree logs into reusable constituents and complete the ecological cycles of nitrogen and carbon. However, fungal communities have not been studied in-depth with respect to functional, spatiotemporal, or environmental parameters. Previously, fungal diversity and its role in shaping the forest ecosystem were studied by traditional and laborious cultural methods, which were unable to achieve real-time results and draw a conclusive picture of fungal communities. This review highlights the latest advances in biological methods such as next-generation sequencing and meta'omics for observing fungal diversity in the forest ecosystem, the role of different fungal groups in shaping forest ecosystem, forest productivity, and nutrient cycling at global scales.
Collapse
Affiliation(s)
- Muhammad Adnan
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liu Gang
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Han Y H Chen
- Faculty of Forestry and the Forest Environment, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
| |
Collapse
|
21
|
Hill R, Buggs RJA, Vu DT, Gaya E. Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures. Mol Biol Evol 2022; 39:6575681. [PMID: 35484861 PMCID: PMC9051438 DOI: 10.1093/molbev/msac085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The fungal genus Fusarium (Ascomycota) includes well-known plant pathogens that are implicated in diseases worldwide, and many of which have been genome sequenced. The genus also encompasses other diverse lifestyles, including species found ubiquitously as asymptomatic-plant inhabitants (endophytes). Here, we produced structurally annotated genome assemblies for five endophytic Fusarium strains, including the first whole-genome data for Fusarium chuoi. Phylogenomic reconstruction of Fusarium and closely related genera revealed multiple and frequent lifestyle transitions, the major exception being a monophyletic clade of mutualist insect symbionts. Differential codon usage bias and increased codon optimisation separated Fusarium sensu stricto from allied genera. We performed computational prediction of candidate secreted effector proteins (CSEPs) and carbohydrate-active enzymes (CAZymes)—both likely to be involved in the host–fungal interaction—and sought evidence that their frequencies could predict lifestyle. However, phylogenetic distance described gene variance better than lifestyle did. There was no significant difference in CSEP, CAZyme, or gene repertoires between phytopathogenic and endophytic strains, although we did find some evidence that gene copy number variation may be contributing to pathogenicity. Large numbers of accessory CSEPs (i.e., present in more than one taxon but not all) and a comparatively low number of strain-specific CSEPs suggested there is a limited specialisation among plant associated Fusarium species. We also found half of the core genes to be under positive selection and identified specific CSEPs and CAZymes predicted to be positively selected on certain lineages. Our results depict fusarioid fungi as prolific generalists and highlight the difficulty in predicting pathogenic potential in the group.
Collapse
Affiliation(s)
- Rowena Hill
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond, United Kingdom.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Richard J A Buggs
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond, United Kingdom.,School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Dang Toan Vu
- Research Planning and International Cooperation Department, Plant Resources Center, Hanoi, Vietnam
| | - Ester Gaya
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond, United Kingdom
| |
Collapse
|
22
|
Kundu A, Mishra S, Kundu P, Jogawat A, Vadassery J. Piriformospora indica recruits host-derived putrescine for growth promotion in plants. PLANT PHYSIOLOGY 2022; 188:2289-2307. [PMID: 34791442 PMCID: PMC8968253 DOI: 10.1093/plphys/kiab536] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 06/01/2023]
Abstract
Growth promotion induced by the endosymbiont Piriformospora indica has been observed in various plants; however, except growth phytohormones, specific functional metabolites involved in P. indica-mediated growth promotion are unknown. Here, we used a gas chromatography-mass spectrometry-based untargeted metabolite analysis to identify tomato (Solanum lycopersicum) metabolites whose levels were altered during P. indica-mediated growth promotion. Metabolomic multivariate analysis revealed several primary metabolites with altered levels, with putrescine (Put) induced most significantly in roots during the interaction. Further, our results indicated that P. indica modulates the arginine decarboxylase (ADC)-mediated Put biosynthesis pathway via induction of SlADC1 in tomato. Piriformospora indica did not promote growth in Sladc1-(virus-induced gene silencing of SlADC1) lines of tomato and showed less colonization. Furthermore, using LC-MS/MS we showed that Put promoted growth by elevation of auxin (indole-3-acetic acid) and gibberellin (GA4 and GA7) levels in tomato. In Arabidopsis (Arabidopsis thaliana) adc knockout mutants, P. indica colonization also decreased and showed no plant growth promotion, and this response was rescued upon exogenous application of Put. Put is also important for hyphal growth of P. indica, indicating that it is co-adapted by both host and microbe. Taken together, we conclude that Put is an essential metabolite and its biosynthesis in plants is crucial for P. indica-mediated plant growth promotion and fungal growth.
Collapse
Affiliation(s)
- Anish Kundu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shruti Mishra
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Pritha Kundu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Abhimanyu Jogawat
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | | |
Collapse
|
23
|
Chen XJ, Yin YQ, Zhu XM, Xia X, Han JJ. High Ambient Temperature Regulated the Plant Systemic Response to the Beneficial Endophytic Fungus Serendipita indica. FRONTIERS IN PLANT SCIENCE 2022; 13:844572. [PMID: 35371134 PMCID: PMC8966885 DOI: 10.3389/fpls.2022.844572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Most plants in nature establish symbiotic associations with endophytic fungi in soil. Beneficial endophytic fungi induce a systemic response in the aboveground parts of the host plant, thus promoting the growth and fitness of host plants. Meanwhile, temperature elevation from climate change widely affects global plant biodiversity as well as crop quality and yield. Over the past decades, great progresses have been made in the response of plants to high ambient temperature and to symbiosis with endophytic fungi. However, little is known about their synergistic effect on host plants. The endophytic fungus Serendipita indica colonizes the roots of a wide range of plants, including Arabidopsis. Based on the Arabidopsis-S. indica symbiosis experimental system, we analyzed the synergistic effect of high ambient temperature and endophytic fungal symbiosis on host plants. By transcriptome analysis, we found that DNA replication-related genes were significantly upregulated during the systemic response of Arabidopsis aboveground parts to S. indica colonization. Plant hormones, such as jasmonic acid (JA) and ethylene (ET), play important roles in plant growth and systemic responses. We found that high ambient temperature repressed the JA and ET signaling pathways of Arabidopsis aboveground parts during the systemic response to S. indica colonization in roots. Meanwhile, PIF4 is the central hub transcription factor controlling plant thermosensory growth under high ambient temperature in Arabidopsis. PIF4 is also involving JA and/or ET signaling pathway. We found that PIF4 target genes overlapped with many differentially expressed genes (DEGs) during the systemic response, and further showed that the growth promotion efficiency of S. indica on the pif4 mutant was higher than that on the wild-type plants. In short, our data showed that high ambient temperature strengthened the growth promotion effect of S. indica fungi on the aboveground parts of the host plant Arabidopsis, and the growth promotion effect of the systemic response under high ambient temperature was regulated by PIF4.
Collapse
Affiliation(s)
- Xiao-Jie Chen
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yue-Qing Yin
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Xin-Meng Zhu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Xue Xia
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Jia-Jia Han
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| |
Collapse
|
24
|
Mahdi LK, Miyauchi S, Uhlmann C, Garrido-Oter R, Langen G, Wawra S, Niu Y, Guan R, Robertson-Albertyn S, Bulgarelli D, Parker JE, Zuccaro A. The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. THE ISME JOURNAL 2022; 16:876-889. [PMID: 34686763 PMCID: PMC8857181 DOI: 10.1038/s41396-021-01138-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 12/05/2022]
Abstract
Plant root-associated bacteria can confer protection against pathogen infection. By contrast, the beneficial effects of root endophytic fungi and their synergistic interactions with bacteria remain poorly defined. We demonstrate that the combined action of a fungal root endophyte from a widespread taxon with core bacterial microbiota members provides synergistic protection against an aggressive soil-borne pathogen in Arabidopsis thaliana and barley. We additionally reveal early inter-kingdom growth promotion benefits which are host and microbiota composition dependent. Using RNA-sequencing, we show that these beneficial activities are not associated with extensive host transcriptional reprogramming but rather with the modulation of expression of microbial effectors and carbohydrate-active enzymes.
Collapse
Affiliation(s)
- Lisa K. Mahdi
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany
| | - Shingo Miyauchi
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Charles Uhlmann
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Ruben Garrido-Oter
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Gregor Langen
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany
| | - Stephan Wawra
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Yulong Niu
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Rui Guan
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany
| | - Senga Robertson-Albertyn
- grid.8241.f0000 0004 0397 2876University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Davide Bulgarelli
- grid.8241.f0000 0004 0397 2876University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Jane E. Parker
- grid.419498.90000 0001 0660 6765Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| | - Alga Zuccaro
- grid.6190.e0000 0000 8580 3777University of Cologne, Institute for Plant Sciences, Cologne, Germany ,grid.503026.2Cluster of Excellence on Plant Sciences (CEPLAS), Cologne, Germany
| |
Collapse
|
25
|
Franco MEE, Wisecaver JH, Arnold AE, Ju YM, Slot JC, Ahrendt S, Moore LP, Eastman KE, Scott K, Konkel Z, Mondo SJ, Kuo A, Hayes RD, Haridas S, Andreopoulos B, Riley R, LaButti K, Pangilinan J, Lipzen A, Amirebrahimi M, Yan J, Adam C, Keymanesh K, Ng V, Louie K, Northen T, Drula E, Henrissat B, Hsieh HM, Youens-Clark K, Lutzoni F, Miadlikowska J, Eastwood DC, Hamelin RC, Grigoriev IV, U'Ren JM. Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes. THE NEW PHYTOLOGIST 2022; 233:1317-1330. [PMID: 34797921 DOI: 10.1111/nph.17873] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Although secondary metabolites are typically associated with competitive or pathogenic interactions, the high bioactivity of endophytic fungi in the Xylariales, coupled with their abundance and broad host ranges spanning all lineages of land plants and lichens, suggests that enhanced secondary metabolism might facilitate symbioses with phylogenetically diverse hosts. Here, we examined secondary metabolite gene clusters (SMGCs) across 96 Xylariales genomes in two clades (Xylariaceae s.l. and Hypoxylaceae), including 88 newly sequenced genomes of endophytes and closely related saprotrophs and pathogens. We paired genomic data with extensive metadata on endophyte hosts and substrates, enabling us to examine genomic factors related to the breadth of symbiotic interactions and ecological roles. All genomes contain hyperabundant SMGCs; however, Xylariaceae have increased numbers of gene duplications, horizontal gene transfers (HGTs) and SMGCs. Enhanced metabolic diversity of endophytes is associated with a greater diversity of hosts and increased capacity for lignocellulose decomposition. Our results suggest that, as host and substrate generalists, Xylariaceae endophytes experience greater selection to diversify SMGCs compared with more ecologically specialised Hypoxylaceae species. Overall, our results provide new evidence that SMGCs may facilitate symbiosis with phylogenetically diverse hosts, highlighting the importance of microbial symbioses to drive fungal metabolic diversity.
Collapse
Affiliation(s)
- Mario E E Franco
- BIO5 Institute and Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | - Jennifer H Wisecaver
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - A Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, 85721, USA
| | - Yu-Ming Ju
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Steven Ahrendt
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Lillian P Moore
- BIO5 Institute and Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | - Katharine E Eastman
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Kelsey Scott
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Stephen J Mondo
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alan Kuo
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Richard D Hayes
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sajeet Haridas
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Bill Andreopoulos
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robert Riley
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Kurt LaButti
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jasmyn Pangilinan
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Anna Lipzen
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mojgan Amirebrahimi
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Juying Yan
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Catherine Adam
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Keykhosrow Keymanesh
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vivian Ng
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Katherine Louie
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent Northen
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Elodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, 13288, France
- INRAE, Marseille, 13288, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, DK-2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Huei-Mei Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Ken Youens-Clark
- BIO5 Institute and Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| | | | | | | | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Igor V Grigoriev
- Department of Energy, The Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Jana M U'Ren
- BIO5 Institute and Department of Biosystems Engineering, The University of Arizona, Tucson, AZ, 85721, USA
| |
Collapse
|
26
|
Ntana F, Johnson SR, Hamberger B, Jensen B, Jørgensen HJL, Collinge DB. Regulation of Tomato Specialised Metabolism after Establishment of Symbiosis with the Endophytic Fungus Serendipita indica. Microorganisms 2022; 10:microorganisms10010194. [PMID: 35056642 PMCID: PMC8778627 DOI: 10.3390/microorganisms10010194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/09/2022] [Accepted: 01/09/2022] [Indexed: 12/17/2022] Open
Abstract
Specialised metabolites produced during plant-fungal associations often define how symbiosis between the plant and the fungus proceeds. They also play a role in the establishment of additional interactions between the symbionts and other organisms present in the niche. However, specialised metabolism and its products are sometimes overlooked when studying plant-microbe interactions. This limits our understanding of the specific symbiotic associations and potentially future perspectives of their application in agriculture. In this study, we used the interaction between the root endophyte Serendipita indica and tomato (Solanum lycopersicum) plants to explore how specialised metabolism of the host plant is regulated upon a mutualistic symbiotic association. To do so, tomato seedlings were inoculated with S. indica chlamydospores and subjected to RNAseq analysis. Gene expression of the main tomato specialised metabolism pathways was compared between roots and leaves of endophyte-colonised plants and tissues of endophyte-free plants. S. indica colonisation resulted in a strong transcriptional response in the leaves of colonised plants. Furthermore, the presence of the fungus in plant roots appears to induce expression of genes involved in the biosynthesis of lignin-derived compounds, polyacetylenes, and specific terpenes in both roots and leaves, whereas pathways producing glycoalkaloids and flavonoids were expressed in lower or basal levels.
Collapse
Affiliation(s)
- Fani Ntana
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Copenhagen, Denmark; (F.N.); (B.J.); (H.J.L.J.)
| | - Sean R. Johnson
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA;
| | - Björn Hamberger
- Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd, East Lansing, MI 48824, USA;
| | - Birgit Jensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Copenhagen, Denmark; (F.N.); (B.J.); (H.J.L.J.)
| | - Hans J. L. Jørgensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Copenhagen, Denmark; (F.N.); (B.J.); (H.J.L.J.)
| | - David B. Collinge
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, 1871 Copenhagen, Denmark; (F.N.); (B.J.); (H.J.L.J.)
- Correspondence: ; Tel.: +45-35333356
| |
Collapse
|
27
|
Rane NR, Tapase S, Kanojia A, Watharkar A, Salama ES, Jang M, Kumar Yadav K, Amin MA, Cabral-Pinto MMS, Jadhav JP, Jeon BH. Molecular insights into plant-microbe interactions for sustainable remediation of contaminated environment. BIORESOURCE TECHNOLOGY 2022; 344:126246. [PMID: 34743992 DOI: 10.1016/j.biortech.2021.126246] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
The widespread distribution of organic and inorganic pollutants in water resources have increased due to rapid industrialization. Rhizospheric zone-associated bacteria along with endophytic bacteria show a significant role in remediation of various pollutants. Metaomics technologies are gaining an advantage over traditional methods because of their capability to obtain detailed information on exclusive microbial communities in rhizosphere of the plant including the unculturable microorganisms. Transcriptomics, proteomics, and metabolomics are functional methodologies that help to reveal the mechanisms of plant-microbe interactions and their synergistic roles in remediation of pollutants. Intensive analysis of metaomics data can be useful to understand the interrelationships of various metabolic activities between plants and microbes. This review comprehensively discusses recent advances in omics applications made hitherto to understand the mechanisms of plant-microbe interactions during phytoremediation. It extends the delivery of the insightful information on plant-microbiomes communications with an emphasis on their genetic, biochemical, physical, metabolic, and environmental interactions.
Collapse
Affiliation(s)
- Niraj R Rane
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Savita Tapase
- Department of Biotechnology, Shivaji University, Kolhapur 416004, India
| | - Aakansha Kanojia
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Anuprita Watharkar
- Amity Institute of Biotechnology, Amity University, Bhatan, Panvel, Mumbai, India
| | - El-Sayed Salama
- Occupational and Environmental Health Department, School of Public Health, Lanzhou University, Lanzhou 730000, Gansu Province, People's Republic of China
| | - Min Jang
- Department of Environmental Engineering, Kwangwoon University, Seoul 01897, Republic of Korea
| | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Ratibad, Bhopal, 462044, India
| | - Mohammed A Amin
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Marina M S Cabral-Pinto
- Geobiotec Research Centre, Department of Geoscience, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Jyoti P Jadhav
- Department of Biochemistry, Shivaji University, Kolhapur 416004, India
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea.
| |
Collapse
|
28
|
Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, Hüttel B, Barry KW, Haridas S, Chen C, Bauer D, Andreopoulos W, Pangilinan J, LaButti K, Riley R, Lipzen A, Clum A, Drula E, Henrissat B, Kohler A, Grigoriev IV, Martin FM, Hacquard S. Genetic determinants of endophytism in the Arabidopsis root mycobiome. Nat Commun 2021; 12:7227. [PMID: 34893598 PMCID: PMC8664821 DOI: 10.1038/s41467-021-27479-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 11/11/2021] [Indexed: 02/03/2023] Open
Abstract
The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes of 41 fungal isolates representative of the A. thaliana root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate that root mycobiota members evolved from ancestors with diverse lifestyles and retain large repertoires of plant cell wall-degrading enzymes (PCWDEs) and effector-like small secreted proteins. We identify a set of 84 gene families associated with endophytism, including genes encoding PCWDEs acting on xylan (family GH10) and cellulose (family AA9). Transcripts encoding these enzymes are also part of a conserved transcriptional program activated by phylogenetically-distant mycobiota members upon host contact. Recolonization experiments with individual fungi indicate that strains with detrimental effects in mono-association with the host colonize roots more aggressively than those with beneficial activities, and dominate in natural root samples. Furthermore, we show that the pectin-degrading enzyme family PL1_7 links aggressiveness of endophytic colonization to plant health.
Collapse
Affiliation(s)
- Fantin Mesny
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Shingo Miyauchi
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
| | - Thorsten Thiergart
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Brigitte Pickel
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Lea Atanasova
- Research division of Biochemical Technology, Institute of Chemical, Environmental and Biological Engineering, Vienna University of Technology, Vienna, Austria
- Institute of Food Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Magnus Karlsson
- Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Bruno Hüttel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Kerrie W Barry
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sajeet Haridas
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cindy Chen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Diane Bauer
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - William Andreopoulos
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kurt LaButti
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robert Riley
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alicia Clum
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Elodie Drula
- INRAE, USC1408 Architecture et Fonction des Macromolécules Biologiques, 13009, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Univ., 13009, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Annegret Kohler
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France
| | - Igor V Grigoriev
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, 54280, Champenoux, France.
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design (BAIC-TBMD), Institute of Microbiology, Beijing Forestry University, Tsinghua East Road Haidian District, Beijing, China.
| | - Stéphane Hacquard
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences (CEPLAS), Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
| |
Collapse
|
29
|
Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots. Proc Natl Acad Sci U S A 2021; 118:2111521118. [PMID: 34853170 PMCID: PMC8670527 DOI: 10.1073/pnas.2111521118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2021] [Indexed: 12/11/2022] Open
Abstract
Understanding how host–microbe homeostasis is controlled and maintained in plant roots is key to enhance plant productivity. However, the factors that contribute to the maintenance of this equilibrium between plant roots and their multikingdom microbial communities remain largely unknown. Here, we observed a link between fungal load in roots and plant health, and we showed that modulation of fungal abundance is tightly controlled by a two-layer regulatory circuit involving the host innate immune system on one hand and bacterial root commensals on another hand. Our results shed a light into how host–microbe and microbe–microbe interactions act in concert to prevent dysbiosis in Arabidopsis thaliana roots, thereby promoting plant health and maintaining growth-promoting activities of multikingdom microbial commensals. In nature, roots of healthy plants are colonized by multikingdom microbial communities that include bacteria, fungi, and oomycetes. A key question is how plants control the assembly of these diverse microbes in roots to maintain host–microbe homeostasis and health. Using microbiota reconstitution experiments with a set of immunocompromised Arabidopsis thaliana mutants and a multikingdom synthetic microbial community (SynCom) representative of the natural A. thaliana root microbiota, we observed that microbiota-mediated plant growth promotion was abolished in most of the tested immunocompromised mutants. Notably, more than 40% of between-genotype variation in these microbiota-induced growth differences was explained by fungal but not bacterial or oomycete load in roots. Extensive fungal overgrowth in roots and altered plant growth was evident at both vegetative and reproductive stages for a mutant impaired in the production of tryptophan-derived, specialized metabolites (cyp79b2/b3). Microbiota manipulation experiments with single- and multikingdom microbial SynComs further demonstrated that 1) the presence of fungi in the multikingdom SynCom was the direct cause of the dysbiotic phenotype in the cyp79b2/b3 mutant and 2) bacterial commensals and host tryptophan metabolism are both necessary to control fungal load, thereby promoting A. thaliana growth and survival. Our results indicate that protective activities of bacterial root commensals are as critical as the host tryptophan metabolic pathway in preventing fungal dysbiosis in the A. thaliana root endosphere.
Collapse
|
30
|
Ray P, Guo Y, Chi MH, Krom N, Boschiero C, Watson B, Huhman D, Zhao P, Singan VR, Lindquist EA, Yan J, Adam C, Craven KD. Serendipita Fungi Modulate the Switchgrass Root Transcriptome to Circumvent Host Defenses and Establish a Symbiotic Relationship. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1128-1142. [PMID: 34260261 DOI: 10.1094/mpmi-04-21-0084-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The fungal family Serendipitaceae encompasses root-associated lineages with endophytic, ericoid, orchid, and ectomycorrhizal lifestyles. Switchgrass is an important bioenergy crop for cellulosic ethanol production owing to high biomass production on marginal soils otherwise unfit for food crop cultivation. The aim of this study was to investigate the host plant responses to Serendipita spp. colonization by characterizing the switchgrass root transcriptome during different stages of symbiosis in vitro. For this, we included a native switchgrass strain, Serendipita bescii, and a related strain, S. vermifera, isolated from Australian orchids. Serendipita colonization progresses from thin hyphae that grow between root cells to, finally, the production of large, bulbous hyphae that fill root cells during the later stages of colonization. We report that switchgrass seems to perceive both fungi prior to physical contact, leading to the activation of chemical and structural defense responses and putative host disease resistance genes. Subsequently, the host defense system appears to be quenched and carbohydrate metabolism adjusted, potentially to accommodate the fungal symbiont. In addition, prior to contact, switchgrass exhibited significant increases in root hair density and root surface area. Furthermore, genes involved in phytohormone metabolism such as gibberellin, jasmonic acid, and salicylic acid were activated during different stages of colonization. Both fungal strains induced plant gene expression in a similar manner, indicating a conserved plant response to members of this fungal order. Understanding plant responsiveness to Serendipita spp. will inform our efforts to integrate them into forages and row crops for optimal plant-microbe functioning, thus facilitating low-input, sustainable agricultural practices.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Prasun Ray
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Yingqing Guo
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | | | - Bonnie Watson
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - David Huhman
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Patrick Zhao
- Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A
| | - Vasanth R Singan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Erika A Lindquist
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Juying Yan
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | - Catherine Adam
- United States Department of Energy Joint Genome Institute, Walnut Creek, CA, U.S.A
| | | |
Collapse
|
31
|
Pochonia chlamydosporia Isolate PC-170-Induced Expression of Marker Genes for Defense Pathways in Tomatoes Challenged by Different Pathogens. Microorganisms 2021; 9:microorganisms9091882. [PMID: 34576777 PMCID: PMC8470021 DOI: 10.3390/microorganisms9091882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/25/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022] Open
Abstract
Pochonia chlamydosporia is a fungal parasite of nematode eggs. Studies have shown that some strains of Pochonia chlamydosporia can promote plant growth and induce plants’ systemic resistance to root-knot nematodes by colonizing in their roots. This study aimed to verify the effect of the PC-170 strain on tomato growth and systemic resistance. Split-root experiments were conducted to observe the systemic resistance induced by PC-170. To explore the defense pathway that was excited due to the colonization by PC-170, we tested the expression of marker genes for defense pathways, and used mutant lines to verify the role of plant defense pathways. Our results showed that PC-170 can colonize roots, and promotes growth. We found a role for jasmonic acid (JA) in modulating tomato colonization by PC-170. PC-170 can activate tomato defense responses to reduce susceptibility to infection by the root-knot nematode Meloidogyne incognita, and induced resistance to some pathogens in tomatoes. The marker genes of the defense pathway were significantly induced after PC-170 colonization. However, salicylic acid (SA)- and jasmonic acid (JA)-dependent defenses in roots were variable with the invasion of different pathogens. Defense pathways play different roles at different points in time. SA- and JA-dependent defense pathways were shown to cross-communicate. Different phytohormones have been involved in tomato plants’ responses against different pathogens. Our study confirmed that adaptive JA signaling is necessary to regulate PC-170 colonization and induce systemic resistance in tomatoes.
Collapse
|
32
|
Rufián JS, Elmore JM, Bejarano ER, Beuzon CR, Coaker GL. ER Bodies Are Induced by Pseudomonas syringae and Negatively Regulate Immunity. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:1001-1009. [PMID: 34110257 PMCID: PMC8635791 DOI: 10.1094/mpmi-11-20-0330-sc] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
ER bodies are endoplasmic reticulum-derived organelles present in plants belonging to the Brassicales order. In Arabidopsis thaliana, ER bodies are ubiquitous in cotyledons and roots and are present only in certain cell types in rosette leaves. However, both wounding and jasmonic acid treatment induce the formation of ER bodies in leaves. Formation of this structure is dependent on the transcription factor NAI1. The main components of the ER bodies are β-glucosidases (BGLUs), enzymes that hydrolyze specialized compounds. In Arabidopsis, PYK10 (BGLU23) and BGLU18 are the most abundant ER body proteins. In this work, we found that ER bodies are downregulated as a consequence of the immune responses induced by bacterial flagellin perception. Arabidopsis mutants defective in ER body formation show enhanced responses upon flagellin perception and enhanced resistance to bacterial infections. Furthermore, the bacterial toxin coronatine induces the formation of de novo ER bodies in leaves and its virulence function is partially dependent on this structure. Finally, we show that performance of the polyphagous beet armyworm herbivore Spodoptera exigua increases in plants lacking ER bodies. Altogether, we provide new evidence for the role of the ER bodies in plant immune responses.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- José S. Rufián
- Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Dept. Biología Celular, Genética y Fisiología, Campus de Teatinos, Málaga E-29071, Spain
- Department of Plant Pathology, University of California Davis, Davis, CA 95616, U.S.A
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences; Chinese Academy of Sciences, Shanghai 201602, China
| | - James M. Elmore
- Department of Plant Pathology, University of California Davis, Davis, CA 95616, U.S.A
| | - Eduardo R. Bejarano
- Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Dept. Biología Celular, Genética y Fisiología, Campus de Teatinos, Málaga E-29071, Spain
| | - Carmen R. Beuzon
- Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Dept. Biología Celular, Genética y Fisiología, Campus de Teatinos, Málaga E-29071, Spain
| | - Gitta L. Coaker
- Department of Plant Pathology, University of California Davis, Davis, CA 95616, U.S.A
| |
Collapse
|
33
|
Šečić E, Zanini S, Wibberg D, Jelonek L, Busche T, Kalinowski J, Nasfi S, Thielmann J, Imani J, Steinbrenner J, Kogel KH. A novel plant-fungal association reveals fundamental sRNA and gene expression reprogramming at the onset of symbiosis. BMC Biol 2021; 19:171. [PMID: 34429124 PMCID: PMC8385953 DOI: 10.1186/s12915-021-01104-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/16/2021] [Indexed: 01/15/2023] Open
Affiliation(s)
- Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Silvia Zanini
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Lukas Jelonek
- Institute of Bioinformatics and Systems Biology, Justus Liebig University, 35392, Giessen, Germany
| | - Tobias Busche
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Sabrine Nasfi
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jennifer Thielmann
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jafargholi Imani
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jens Steinbrenner
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany.
| |
Collapse
|
34
|
Oktalira FT, May TW, Dearnaley JDW, Linde CC. Seven new Serendipita species associated with Australian terrestrial orchids. Mycologia 2021; 113:968-987. [PMID: 34338610 DOI: 10.1080/00275514.2021.1919848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Serendipita is one of the main fungal genera that form mutualistic associations with species of orchids (Orchidaceae). Here, seven new Serendipita species associated with various Australian orchid genera are described. These Serendipita species were originally characterized by multilocus DNA sequence species delimitation analyses (three mtDNA and four nuclear genes) and confirmed as distinct with addition of further isolates and reanalysis of nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and nuc 28S rDNA (28S). Culture morphology and microscopic features are presented for each species, three of which are binucleate and four multinucleate. For the ITS region, the seven species have within-species sequence divergence between 1.07% and 4.31%, and all but one of the species pairs is separated by interspecific divergence of at least 4.35%. The newly described Serendipita species, S. australiana, S. communis, S. occidentalis, S. rarihospitum, S. secunda, S. talbotii, and S. warcupii, are shown to be separate species from S. vermifera on the basis of comparison against a sequence from the type. Isolates originally identified by Warcup as Sebacina "vermifera" from Caladenia orchids are revised and shown to belong to three of the species newly described here. Some non-Caladenia isolates identified by Warcup as S. "vermifera" are also shown to be non-conspecific with the type of S. vermifera. On the basis of ITS sequences, 346 isolates from 26 other studies, previously identified under provisional designations, are accommodated under the novel species. The species of Serendipta described here associate with the Australian orchid genera Caladenia, Cyanicula, Elythranthera, Ericksonella, Eriochilus, Glossodia, and Pheladenia. Most of the novel Serendipita species occur widely across Australia, often with widely distributed hosts, but one species, Serendipita rarihospitum, associates with narrowly distributed orchid species.
Collapse
Affiliation(s)
- Fitria T Oktalira
- Ecology and Evolution, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| | - Tom W May
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, VIC 3004, Australia
| | - John D W Dearnaley
- Centre for Crop Health, The University of Southern Queensland, Toowoomba, Queensland 4350, Australia
| | - Celeste C Linde
- Ecology and Evolution, Research School of Biology, College of Science, The Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
35
|
Zhang W, Luo X, Zhang AY, Ma CY, Sun K, Zhang TT, Dai CC. Jasmonate signaling restricts root soluble sugar accumulation and drives root-fungus symbiosis loss at flowering by antagonizing gibberellin biosynthesis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 309:110940. [PMID: 34134852 DOI: 10.1016/j.plantsci.2021.110940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/14/2021] [Accepted: 05/15/2021] [Indexed: 06/12/2023]
Abstract
Jasmonate restricts accumulation of constitutive and fungus-induced root soluble sugars at flowering stage, and thus reduces root beneficial fungal colonization, but little is known about how these are achieved. To determine whether jasmonate-mediated depletion of soluble sugars is the result of direct phytohormonal cross-talk or indirect induced defensive secondary metabolism, we first profiled soluble sugar and tryptophan (Trp)-derived defensive secondary metabolites in the roots of wild-type and jasmonate signaling-impaired Arabidopsis thaliana at flowering upon a beneficial fungus Phomopsis liquidambaris inoculation. Next, jasmonate and gibberellin signaling were manipulated to determine the relationship between jasmonate and gibberellin, and to quantify the effects of these phytohormones on fungal colonization degree, soluble sugar accumulation, Trp-derived secondary metabolites production, and sugar source-sink transport and metabolism. Gibberellin complementation increased Ph. liquidambaris colonization and rescued jasmonate-dependent root soluble sugar depletion and phloem sugar transport and root invertase activity without influencing jasmonate-induced Trp-derived secondary metabolites production at flowering. Furthermore, jasmonate signaling antagonized gibberellin biosynthesis in Ph. liquidambaris-inoculated roots. Our results suggest a phytohormonal antagonism model that jasmonate signaling restricts root soluble sugar accumulation through antagonizing gibberellin biosynthesis rather than through promoting Trp-derived secondary metabolites production and thus drives beneficial fungal colonization decline at flowering.
Collapse
Affiliation(s)
- Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xue Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ai-Yue Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chen-Yu Ma
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ting-Ting Zhang
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China.
| |
Collapse
|
36
|
Clocchiatti A, Hannula SE, van den Berg M, Hundscheid MPJ, de Boer W. Evaluation of Phenolic Root Exudates as Stimulants of Saptrophic Fungi in the Rhizosphere. Front Microbiol 2021; 12:644046. [PMID: 33936001 PMCID: PMC8079663 DOI: 10.3389/fmicb.2021.644046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/08/2021] [Indexed: 01/04/2023] Open
Abstract
The rhizosphere microbial community of crop plants in intensively managed arable soils is strongly dominated by bacteria, especially in the initial stages of plant development. In order to establish more diverse and balanced rhizosphere microbiomes, as seen for wild plants, crop variety selection could be based on their ability to promote growth of saprotrophic fungi in the rhizosphere. We hypothesized that this can be achieved by increasing the exudation of phenolic acids, as generally higher fungal abundance is observed in environments with phenolic-rich inputs, such as exudates of older plants and litter leachates. To test this, a rhizosphere simulation microcosm was designed to establish gradual diffusion of root exudate metabolites from sterile sand into arable soil. With this system, we tested the fungus-stimulating effect of eight phenolic acids alone or in combination with primary root metabolites. Ergosterol-based fungal biomass measurements revealed that most phenolic acids did not increase fungal abundance in the arable soil layer. These results were supported by comparison of fungal biomass in the rhizosphere of wild type Arabidopsis thaliana plants and mutants with altered phenolic acid metabolism. Salicylic acid was the only phenolic acid that stimulated a higher fungal biomass in the arable soil layer of microcosms, but only when combined with a background of primary root metabolites. However, such effect on rhizosphere fungi was not confirmed for a salicylic acid-impaired A. thaliana mutant. For three phenolic acid treatments (chlorogenic acid, salicylic acid, vanillic acid) fungal and bacterial community compositions were analyzed using amplicon sequencing. Despite having little effect on fungal biomass, phenolic acids combined with primary metabolites promoted a higher relative abundance of soil-borne fungi with the ability to invade plant roots (Fusarium, Trichoderma and Fusicolla spp.) in the simulated rhizosphere. Bacterial community composition was also affected by these phenolic acids. Although this study indicates that phenolic acids do not increase fungal biomass in the rhizosphere, we highlight a potential role of phenolic acids as attractants for root-colonizing fungi.
Collapse
Affiliation(s)
- Anna Clocchiatti
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Soil Biology Group, Wageningen University, Wageningen, Netherlands
| | - S Emilia Hannula
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | | | - Wietse de Boer
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands.,Soil Biology Group, Wageningen University, Wageningen, Netherlands
| |
Collapse
|
37
|
Frerigmann H, Piotrowski M, Lemke R, Bednarek P, Schulze-Lefert P. A Network of Phosphate Starvation and Immune-Related Signaling and Metabolic Pathways Controls the Interaction between Arabidopsis thaliana and the Beneficial Fungus Colletotrichum tofieldiae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:560-570. [PMID: 33226310 DOI: 10.1094/mpmi-08-20-0233-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The beneficial root-colonizing fungus Colletotrichum tofieldiae mediates plant growth promotion (PGP) upon phosphate (Pi) starvation in Arabidopsis thaliana. This activity is dependent on the Trp metabolism of the host, including indole glucosinolate (IG) hydrolysis. Here, we show that C. tofieldiae resolves several Pi starvation-induced molecular processes in the host, one of which is the downregulation of auxin signaling in germ-free plants, which is restored in the presence of the fungus. Using CRISPR/Cas9 genome editing, we generated an Arabidopsis triple mutant lacking three homologous nitrilases (NIT1 to NIT3) that are thought to link IG-hydrolysis products with auxin biosynthesis. Retained C. tofieldiae-induced PGP in nit1/2/3 mutant plants demonstrated that this metabolic connection is dispensable for the beneficial activity of the fungus. This suggests that either there is an alternative metabolic link between IG-hydrolysis products and auxin biosynthesis, or C. tofieldiae restores auxin signaling independently of IG metabolism. We show that C. tofieldiae, similar to pathogenic microorganisms, triggers Arabidopsis immune pathways that rely on IG metabolism as well as salicylic acid and ethylene signaling. Analysis of IG-deficient myb mutants revealed that these metabolites are, indeed, important for control of in planta C. tofieldiae growth: however, enhanced C. tofieldiae biomass does not necessarily negatively correlate with PGP. We show that Pi deficiency enables more efficient colonization of Arabidopsis by C. tofieldiae, possibly due to the MYC2-mediated repression of ethylene signaling and changes in the constitutive IG composition in roots.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Henning Frerigmann
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions and Cluster of Excellence on Plant Sciences (CEPLAS), D-50829 Cologne, Germany
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Markus Piotrowski
- Lehrstuhl für Molekulargenetik und Physiologie der Pflanzen, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - René Lemke
- Lehrstuhl für Molekulargenetik und Physiologie der Pflanzen, Ruhr-Universität Bochum, D-44801 Bochum, Germany
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Paul Schulze-Lefert
- Max Planck Institute for Plant Breeding Research, Department of Plant Microbe Interactions and Cluster of Excellence on Plant Sciences (CEPLAS), D-50829 Cologne, Germany
| |
Collapse
|
38
|
Jacoby RP, Koprivova A, Kopriva S. Pinpointing secondary metabolites that shape the composition and function of the plant microbiome. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:57-69. [PMID: 32995888 PMCID: PMC7816845 DOI: 10.1093/jxb/eraa424] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/10/2020] [Indexed: 05/02/2023]
Abstract
One of the major questions in contemporary plant science involves determining the functional mechanisms that plants use to shape their microbiome. Plants produce a plethora of chemically diverse secondary metabolites, many of which exert bioactive effects on microorganisms. Several recent publications have unequivocally shown that plant secondary metabolites affect microbiome composition and function. These studies have pinpointed that the microbiome can be influenced by a diverse set of molecules, including: coumarins, glucosinolates, benzoxazinoids, camalexin, and triterpenes. In this review, we summarize the role of secondary metabolites in shaping the plant microbiome, highlighting recent literature. A body of knowledge is now emerging that links specific plant metabolites with distinct microbial responses, mediated via defined biochemical mechanisms. There is significant potential to boost agricultural sustainability via the targeted enhancement of beneficial microbial traits, and here we argue that the newly discovered links between root chemistry and microbiome composition could provide a new set of tools for rationally manipulating the plant microbiome.
Collapse
Affiliation(s)
- Richard P Jacoby
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Anna Koprivova
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
| |
Collapse
|
39
|
Fungal Endophytes from Orchidaceae: Diversity and Applications. Fungal Biol 2021. [DOI: 10.1007/978-3-030-68260-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
40
|
Fröschel C, Komorek J, Attard A, Marsell A, Lopez-Arboleda WA, Le Berre J, Wolf E, Geldner N, Waller F, Korte A, Dröge-Laser W. Plant roots employ cell-layer-specific programs to respond to pathogenic and beneficial microbes. Cell Host Microbe 2020; 29:299-310.e7. [PMID: 33378688 DOI: 10.1016/j.chom.2020.11.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 10/02/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022]
Abstract
Plant roots are built of concentric cell layers that are thought to respond to microbial infections by employing specific, genetically defined programs. Yet, the functional impact of this radial organization remains elusive, particularly due to the lack of genome-wide techniques for monitoring expression at a cell-layer resolution. Here, cell-type-specific expression of tagged ribosomes enabled the isolation of ribosome-bound mRNA to obtain cell-layer translatomes (TRAP-seq, translating ribosome affinity purification and RNA sequencing). After inoculation with the vascular pathogen Verticillium longisporum, pathogenic oomycete Phytophthora parasitica, or mutualistic endophyte Serendipita indica, root cell-layer responses reflected the fundamentally different colonization strategies of these microbes. Notably, V. longisporum specifically suppressed the endodermal barrier, which restricts fungal progression, allowing microbial access to the root central cylinder. Moreover, localized biosynthesis of antimicrobial compounds and ethylene differed in response to pathogens and mutualists. These examples highlight the power of this resource to gain insights into root-microbe interactions and to develop strategies in crop improvement.
Collapse
Affiliation(s)
- Christian Fröschel
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Julius-von-Sachs Platz 2, 97082 Würzburg, Germany
| | - Jaqueline Komorek
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Julius-von-Sachs Platz 2, 97082 Würzburg, Germany
| | - Agnès Attard
- INRAE, CNRS, ISA, Université Côte d'Azur, 400 Route des Chappes, 06903 Sophia Antipolis, France
| | - Alexander Marsell
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Julius-von-Sachs Platz 2, 97082 Würzburg, Germany
| | - William A Lopez-Arboleda
- Center for Computational and Theoretical Biology, CCTB, Julius-Maximilians-Universität Würzburg, Klara-Oppenheimer-Weg 32, 97074 Würzburg, Germany
| | - Joëlle Le Berre
- INRAE, CNRS, ISA, Université Côte d'Azur, 400 Route des Chappes, 06903 Sophia Antipolis, France
| | - Elmar Wolf
- Department of Biochemistry and Molecular Biology, Biocenter, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Niko Geldner
- Department of Plant Molecular Biology, Université de Lausanne, Biophore Building, Unil-Sorge, 1015 Lausanne, Switzerland
| | - Frank Waller
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Julius-von-Sachs Platz 2, 97082 Würzburg, Germany
| | - Arthur Korte
- Center for Computational and Theoretical Biology, CCTB, Julius-Maximilians-Universität Würzburg, Klara-Oppenheimer-Weg 32, 97074 Würzburg, Germany
| | - Wolfgang Dröge-Laser
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Julius-Maximilians-Universität Würzburg, Julius-von-Sachs Platz 2, 97082 Würzburg, Germany.
| |
Collapse
|
41
|
Kumar N, Galli M, Dempsey D, Imani J, Moebus A, Kogel KH. NPR1 is required for root colonization and the establishment of a mutualistic symbiosis between the beneficial bacterium Rhizobium radiobacter and barley. Environ Microbiol 2020; 23:2102-2115. [PMID: 33314556 DOI: 10.1111/1462-2920.15356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/07/2020] [Accepted: 12/10/2020] [Indexed: 12/22/2022]
Abstract
Non-expressor of pathogenesis-related genes 1 (NPR1) is a key regulator of plant innate immunity and systemic disease resistance. The model for NPR1 function is based on experimental evidence obtained largely from dicots; however, this model does not fit all aspects of Poaceae family, which includes major crops such as wheat, rice and barley. In addition, there is little scientific data on NPR1's role in mutualistic symbioses. We assessed barley (Hordeum vulgare) HvNPR1 requirement during the establishment of mutualistic symbiosis between barley and beneficial Alphaproteobacterium Rhizobium radiobacter F4 (RrF4). Upon RrF4 root-inoculation, barley NPR1-knockdown (KD-hvnpr1) plants lost the typical spatiotemporal colonization pattern and supported less bacterial multiplication. Following RrF4 colonization, expression of salicylic acid marker genes were strongly enhanced in wild-type roots; whereas in comparison, KD-hvnpr1 roots exhibited little to no induction. Both basal and RrF4-induced root-initiated systemic resistance against virulent Blumeria graminis were impaired in leaves of KD-hvnpr1. Besides these immune-related differences, KD-hvnpr1 plants displayed higher root and shoot biomass than WT. However, RrF4-mediated growth promotion was largely compromised in KD-hvnpr1. Our results demonstrate a critical role for HvNPR1 in establishing a mutualistic symbiosis between a beneficial bacterium and a cereal crop.
Collapse
Affiliation(s)
- Neelendra Kumar
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, 35392, Germany
| | - Matteo Galli
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, 35392, Germany
| | - D'Maris Dempsey
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, 35392, Germany
| | - Jafargholi Imani
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, 35392, Germany
| | - Anna Moebus
- Biomedical Research Centre Seltersberg, Justus Liebig University, Giessen, 35392, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, 35392, Germany
| |
Collapse
|
42
|
Nostadt R, Hilbert M, Nizam S, Rovenich H, Wawra S, Martin J, Küpper H, Mijovilovich A, Ursinus A, Langen G, Hartmann MD, Lupas AN, Zuccaro A. A secreted fungal histidine- and alanine-rich protein regulates metal ion homeostasis and oxidative stress. THE NEW PHYTOLOGIST 2020; 227:1174-1188. [PMID: 32285459 DOI: 10.1111/nph.16606] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/01/2020] [Indexed: 05/22/2023]
Abstract
Like pathogens, beneficial endophytic fungi secrete effector proteins to promote plant colonization, for example, through perturbation of host immunity. The genome of the root endophyte Serendipita indica encodes a novel family of highly similar, small alanine- and histidine-rich proteins, whose functions remain unknown. Members of this protein family carry an N-terminal signal peptide and a conserved C-terminal DELD motif. Here we report on the functional characterization of the plant-responsive DELD family protein Dld1 using a combination of structural, biochemical, biophysical and cytological analyses. The crystal structure of Dld1 shows an unusual, monomeric histidine zipper consisting of two antiparallel coiled-coil helices. Similar to other histidine-rich proteins, Dld1 displays varying affinity to different transition metal ions and undergoes metal ion- and pH-dependent unfolding. Transient expression of mCherry-tagged Dld1 in barley leaf and root tissue suggests that Dld1 localizes to the plant cell wall and accumulates at cell wall appositions during fungal penetration. Moreover, recombinant Dld1 enhances barley root colonization by S. indica, and inhibits H2 O2 -mediated radical polymerization of 3,3'-diaminobenzidine. Our data suggest that Dld1 has the potential to enhance micronutrient accessibility for the fungus and to interfere with oxidative stress and reactive oxygen species homeostasis to facilitate host colonization.
Collapse
Affiliation(s)
- Robin Nostadt
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Magdalena Hilbert
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Shadab Nizam
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, Botanical Institute, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Hanna Rovenich
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, Botanical Institute, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Stephan Wawra
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, Botanical Institute, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Jörg Martin
- Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076, Tübingen, Germany
| | - Hendrik Küpper
- Department of Plant Biophysics & Biochemistry, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, University of South Bohemia, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Ana Mijovilovich
- Department of Plant Biophysics & Biochemistry, Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, Branišovská 31/1160, 37005, České Budějovice, Czech Republic
| | - Astrid Ursinus
- Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076, Tübingen, Germany
| | - Gregor Langen
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, Botanical Institute, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| | - Marcus D Hartmann
- Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076, Tübingen, Germany
| | - Andrei N Lupas
- Max Planck Institute for Developmental Biology, Spemannstr. 35, 72076, Tübingen, Germany
| | - Alga Zuccaro
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Cologne Biocenter, Botanical Institute, University of Cologne, Zülpicher Str. 47b, 50674, Cologne, Germany
| |
Collapse
|
43
|
Zuccaro A, Langen G. Breeding for resistance: can we increase crop resistance to pathogens without compromising the ability to accommodate beneficial microbes? THE NEW PHYTOLOGIST 2020; 227:279-282. [PMID: 32445486 DOI: 10.1111/nph.16610] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/09/2020] [Indexed: 05/26/2023]
Affiliation(s)
- Alga Zuccaro
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Gregor Langen
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| |
Collapse
|
44
|
Guo Y, Jud W, Ghirardo A, Antritter F, Benz JP, Schnitzler JP, Rosenkranz M. Sniffing fungi - phenotyping of volatile chemical diversity in Trichoderma species. THE NEW PHYTOLOGIST 2020; 227:244-259. [PMID: 32155672 DOI: 10.1111/nph.16530] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 02/26/2020] [Indexed: 05/23/2023]
Abstract
Volatile organic compounds (VOCs) play vital roles in the interaction of fungi with plants and other organisms. A systematic study of the global fungal VOC profiles is still lacking, though it is a prerequisite for elucidating the mechanisms of VOC-mediated interactions. Here we present a versatile system enabling a high-throughput screening of fungal VOCs under controlled temperature. In a proof-of-principle experiment, we characterized the volatile metabolic fingerprints of four Trichoderma spp. over a 48 h growth period. The developed platform allows automated and fast detection of VOCs from up to 14 simultaneously growing fungal cultures in real time. The comprehensive analysis of fungal odors is achieved by employing proton transfer reaction-time of flight-MS and GC-MS. The data-mining strategy based on multivariate data analysis and machine learning allows the volatile metabolic fingerprints to be uncovered. Our data revealed dynamic, development-dependent and extremely species-specific VOC profiles from the biocontrol genus Trichoderma. The two mass spectrometric approaches were highly complementary to each other, together revealing a novel, dynamic view to the fungal VOC release. This analytical system could be used for VOC-based chemotyping of diverse small organisms, or more generally, for any in vivo and in vitro real-time headspace analysis.
Collapse
Affiliation(s)
- Yuan Guo
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764, Neuherberg, Germany
| | - Werner Jud
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764, Neuherberg, Germany
| | - Andrea Ghirardo
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764, Neuherberg, Germany
| | - Felix Antritter
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764, Neuherberg, Germany
| | - J Philipp Benz
- Holzforschung München, TUM School of Life Sciences Weihenstephan, Technical University of Munich, D-85354, Freising, Germany
| | - Jörg-Peter Schnitzler
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764, Neuherberg, Germany
| | - Maaria Rosenkranz
- Research Unit Environmental Simulation, Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, D-85764, Neuherberg, Germany
| |
Collapse
|
45
|
Pérez-Alonso MM, Guerrero-Galán C, Scholz SS, Kiba T, Sakakibara H, Ludwig-Müller J, Krapp A, Oelmüller R, Vicente-Carbajosa J, Pollmann S. Harnessing symbiotic plant-fungus interactions to unleash hidden forces from extreme plant ecosystems. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3865-3877. [PMID: 31976537 PMCID: PMC7316966 DOI: 10.1093/jxb/eraa040] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/21/2020] [Indexed: 05/15/2023]
Abstract
Global climate change is arguably one of the biggest threats of modern times and has already led to a wide range of impacts on the environment, economy, and society. Owing to past emissions and climate system inertia, global climate change is predicted to continue for decades even if anthropogenic greenhouse gas emissions were to stop immediately. In many regions, such as central Europe and the Mediterranean region, the temperature is likely to rise by 2-5 °C and annual precipitation is predicted to decrease. Expected heat and drought periods followed by floods, and unpredictable growing seasons, are predicted to have detrimental effects on agricultural production systems, causing immense economic losses and food supply problems. To mitigate the risks of climate change, agricultural innovations counteracting these effects need to be embraced and accelerated. To achieve maximum improvement, the required agricultural innovations should not focus only on crops but rather pursue a holistic approach including the entire ecosystem. Over millions of years, plants have evolved in close association with other organisms, particularly soil microbes that have shaped their evolution and contemporary ecology. Many studies have already highlighted beneficial interactions among plants and the communities of microorganisms with which they coexist. Questions arising from these discoveries are whether it will be possible to decipher a common molecular pattern and the underlying biochemical framework of interspecies communication, and whether such knowledge can be used to improve agricultural performance under environmental stress conditions. In this review, we summarize the current knowledge of plant interactions with fungal endosymbionts found in extreme ecosystems. Special attention will be paid to the interaction of plants with the symbiotic root-colonizing endophytic fungus Serendipita indica, which has been developed as a model system for beneficial plant-fungus interactions.
Collapse
Affiliation(s)
- Marta-Marina Pérez-Alonso
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), Campus de Montegancedo, Pozuelo de Alarcón (Madrid), Spain
| | - Carmen Guerrero-Galán
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), Campus de Montegancedo, Pozuelo de Alarcón (Madrid), Spain
| | - Sandra S Scholz
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Takatoshi Kiba
- RIKEN Center for Sustainable Resource Science, Suehiro, Tsurumi, Yokohama, Japan
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Suehiro, Tsurumi, Yokohama, Japan
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | | | - Anne Krapp
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Ralf Oelmüller
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University Jena, Jena, Germany
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), Campus de Montegancedo, Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Stephan Pollmann
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA), Campus de Montegancedo, Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| |
Collapse
|
46
|
Bouffaud ML, Herrmann S, Tarkka MT, Bönn M, Feldhahn L, Buscot F. Oak displays common local but specific distant gene regulation responses to different mycorrhizal fungi. BMC Genomics 2020; 21:399. [PMID: 32532205 PMCID: PMC7291512 DOI: 10.1186/s12864-020-06806-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 06/05/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Associations of tree roots with diverse symbiotic mycorrhizal fungi have distinct effects on whole plant functioning. An untested explanation might be that such effect variability is associated with distinct impacts of different fungi on gene expression in local and distant plant organs. Using a large scale transcriptome sequencing approach, we compared the impact of three ectomycorrhizal (EMF) and one orchid mycorrhizal fungi (OMF) on gene regulation in colonized roots (local), non-colonized roots (short distance) and leaves (long distance) of the Quercus robur clone DF159 with reference to the recently published oak genome. Since different mycorrhizal fungi form symbiosis in a different time span and variable extents of apposition structure development, we sampled inoculated but non-mycorrhizal plants, for which however markedly symbiotic effects have been reported. Local root colonization by the fungi was assessed by fungal transcript analysis. RESULTS The EMF induced marked and species specific effects on plant development in the analysed association stage, but the OMF did not. At local level, a common set of plant differentially expressed genes (DEG) was identified with similar patterns of responses to the three EMF, but not to the OMF. Most of these core DEG were down-regulated and correspond to already described but also new functions related to establishment of EMF symbiosis. Analysis of the fungal transcripts of two EMF in highly colonized roots also revealed onset of a symbiosis establishment. In contrast, in the OMF, the DEG were mainly related to plant defence. Already at short distances, high specificities in transcriptomic responses to the four fungi were detected, which were further enhanced at long distance in leaves, where almost no common DEG were found between the treatments. Notably, no correlation between phylogeny of the EMF and gene expression patterns was observed. CONCLUSIONS Use of clonal oaks allowed us to identify a core transcriptional program in roots colonized by three different EMF, supporting the existence of a common EMF symbiotic pathway. Conversely, the specific responses in non-colonized organs were more closely related to the specific impacts of the different of EMF on plant performance.
Collapse
Affiliation(s)
- Marie-Lara Bouffaud
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany
| | - Sylvie Herrmann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany.
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany.
| | - Mika T Tarkka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany
| | - Markus Bönn
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany
| | - Lasse Feldhahn
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, D-06120, Halle/Saale, Germany
| |
Collapse
|
47
|
Wanke A, Rovenich H, Schwanke F, Velte S, Becker S, Hehemann JH, Wawra S, Zuccaro A. Plant species-specific recognition of long and short β-1,3-linked glucans is mediated by different receptor systems. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:1142-1156. [PMID: 31925978 DOI: 10.1111/tpj.14688] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 12/26/2019] [Accepted: 01/06/2020] [Indexed: 05/21/2023]
Abstract
Plants survey their environment for the presence of potentially harmful or beneficial microbes. During colonization, cell surface receptors perceive microbe-derived or modified-self ligands and initiate appropriate responses. The recognition of fungal chitin oligomers and the subsequent activation of plant immunity are well described. In contrast, the mechanisms underlying β-glucan recognition and signaling activation remain largely unexplored. Here, we systematically tested immune responses towards different β-glucan structures and show that responses vary between plant species. While leaves of the monocots Hordeum vulgare and Brachypodium distachyon can recognize longer (laminarin) and shorter (laminarihexaose) β-1,3-glucans with responses of varying intensity, duration and timing, leaves of the dicot Nicotiana benthamiana activate immunity in response to long β-1,3-glucans, whereas Arabidopsis thaliana and Capsella rubella perceive short β-1,3-glucans. Hydrolysis of the β-1,6 side-branches of laminarin demonstrated that not the glycosidic decoration but rather the degree of polymerization plays a pivotal role in the recognition of long-chain β-glucans. Moreover, in contrast to the recognition of short β-1,3-glucans in A. thaliana, perception of long β-1,3-glucans in N. benthamiana and rice is independent of CERK1, indicating that β-glucan recognition may be mediated by multiple β-glucan receptor systems.
Collapse
Affiliation(s)
- Alan Wanke
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Hanna Rovenich
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
- University of Cologne, Cluster of Excellence on Plant Sciences (CEPLAS), 50679, Cologne, Germany
| | - Florian Schwanke
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
| | - Stefanie Velte
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
| | - Stefan Becker
- Center for Marine Environmental Sciences, University of Bremen, MARUM, 28359, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Jan-Hendrik Hehemann
- Center for Marine Environmental Sciences, University of Bremen, MARUM, 28359, Bremen, Germany
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Stephan Wawra
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
- University of Cologne, Cluster of Excellence on Plant Sciences (CEPLAS), 50679, Cologne, Germany
| | - Alga Zuccaro
- University of Cologne, Institute for Plant Sciences, 50679, Cologne, Germany
- University of Cologne, Cluster of Excellence on Plant Sciences (CEPLAS), 50679, Cologne, Germany
| |
Collapse
|
48
|
Jogawat A, Meena MK, Kundu A, Varma M, Vadassery J. Calcium channel CNGC19 mediates basal defense signaling to regulate colonization by Piriformospora indica in Arabidopsis roots. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2752-2768. [PMID: 31957790 PMCID: PMC7210775 DOI: 10.1093/jxb/eraa028] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/16/2020] [Indexed: 05/20/2023]
Abstract
The activation of calcium signaling is a crucial event for perceiving environmental stress. Colonization by Piriformospora indica, a growth-promoting root endosymbiont, activates cytosolic Ca2+ in Arabidopsis roots. In this study, we examined the role and functional relevance of calcium channels responsible for Ca2+ fluxes. Expression profiling revealed that CYCLIC NUCLEOTIDE GATED CHANNEL 19 (CNGC19) is an early-activated gene, induced by unidentified components in P. indica cell-wall extract. Functional analysis showed that loss-of-function of CNGC19 resulted in growth inhibition by P.indica, due to increased colonization and loss of controlled fungal growth. The cngc19 mutant showed reduced elevation of cytosolic Ca2+ in response to P. indica cell-wall extract in comparison to the wild-type. Microbe-associated molecular pattern-triggered immunity was compromised in the cngc19 lines, as evidenced by unaltered callose deposition, reduced cis-(+)-12-oxo-phytodienoic acid, jasmonate, and jasmonoyl isoleucine levels, and down-regulation of jasmonate and other defense-related genes, which contributed to a shift towards a pathogenic response. Loss-of-function of CNGC19 resulted in an inability to modulate indole glucosinolate content during P. indica colonization. CNGC19-mediated basal immunity was dependent on the AtPep receptor, PEPR. CNGC19 was also crucial for P. indica-mediated suppression of AtPep-induced immunity. Our results thus demonstrate that Arabidopsis CNGC19 is an important Ca2+ channel that maintains a robust innate immunity and is crucial for growth-promotion signaling upon colonization by P. indica.
Collapse
Affiliation(s)
- Abhimanyu Jogawat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Mukesh Kumar Meena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Anish Kundu
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Mahendra Varma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Jyothilakshmi Vadassery
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
- Correspondence:
| |
Collapse
|
49
|
Inaji A, Okazawa A, Taguchi T, Nakamoto M, Katsuyama N, Yoshikawa R, Ohnishi T, Waller F, Ohta D. Rhizotaxis Modulation in Arabidopsis Is Induced by Diffusible Compounds Produced during the Cocultivation of Arabidopsis and the Endophytic Fungus Serendipita indica. PLANT & CELL PHYSIOLOGY 2020; 61:838-850. [PMID: 32016405 DOI: 10.1093/pcp/pcaa008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/25/2020] [Indexed: 06/10/2023]
Abstract
Rhizotaxis is established under changing environmental conditions via periodic priming of lateral root (LR) initiation at the root tips and adaptive LR formation along the primary root (PR). In contrast to the adaptable LR formation in response to nutrient availability, there is little information on root development during interactions with beneficial microbes. The Arabidopsis root system is characteristically modified upon colonization by the root endophytic fungus Serendipita indica, accompanied by a marked stimulation of LR formation and the inhibition of PR growth. This root system modification has been attributed to endophyte-derived indole-3-acetic acid (IAA). However, it has yet to be clearly explained how fungal IAA affects the intrinsic LR formation process. In this study, we show that diffusible compounds (chemical signals) other than IAA are present in the coculture medium of Arabidopsis and S. indica and induce auxin-responsive DR5::GUS expression in specific sections within the pericycle layer. The DR5::GUS expression was independent of polar auxin transport and the major IAA biosynthetic pathways, implicating unidentified mechanisms responsible for the auxin response and LR formation. Detailed metabolite analysis revealed the presence of multiple compounds that induce local auxin responses and LR formation. We found that benzoic acid (BA) cooperatively acted with exogenous IAA to generate a local auxin response in the pericycle layer, suggesting that BA is one of the chemical signals involved in adaptable LR formation. Identification and characterization of the chemical signals will contribute to a greater understanding of the molecular mechanisms underlying adaptable root development and to unconventional technologies for sustainable agriculture.
Collapse
Affiliation(s)
- Aoi Inaji
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531 Japan
| | - Atsushi Okazawa
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531 Japan
| | - Taiki Taguchi
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531 Japan
| | - Masatoshi Nakamoto
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu Shiga, 525-8577 Japan
| | - Nao Katsuyama
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531 Japan
| | - Ryoka Yoshikawa
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531 Japan
| | - Toshiyuki Ohnishi
- Graduate School of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529 Japan
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529 Japan
| | - Frank Waller
- Julius-von-Sachs-Institute, Pharmaceutical Biology, Julius-Maximilians-University Würzburg, Julius-von-Sachs-Platz 2, Würzburg D-97082, Germany
| | - Daisaku Ohta
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531 Japan
- Bioeconomy Research Institute, Research Center for the 21st Century, Osaka Prefecture University, 1-1 Gakuen-cho, Sakai, 599-8531 Japan
| |
Collapse
|
50
|
Barco B, Clay NK. Hierarchical and Dynamic Regulation of Defense-Responsive Specialized Metabolism by WRKY and MYB Transcription Factors. FRONTIERS IN PLANT SCIENCE 2020; 10:1775. [PMID: 32082343 PMCID: PMC7005594 DOI: 10.3389/fpls.2019.01775] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/19/2019] [Indexed: 05/07/2023]
Abstract
The plant kingdom produces hundreds of thousands of specialized bioactive metabolites, some with pharmaceutical and biotechnological importance. Their biosynthesis and function have been studied for decades, but comparatively less is known about how transcription factors with overlapping functions and contrasting regulatory activities coordinately control the dynamics and output of plant specialized metabolism. Here, we performed temporal studies on pathogen-infected intact host plants with perturbed transcription factors. We identified WRKY33 as the condition-dependent master regulator and MYB51 as the dual functional regulator in a hierarchical gene network likely responsible for the gene expression dynamics and metabolic fluxes in the camalexin and 4-hydroxy-indole-3-carbonylnitrile (4OH-ICN) pathways. This network may have also facilitated the regulatory capture of the newly evolved 4OH-ICN pathway in Arabidopsis thaliana by the more-conserved transcription factor MYB51. It has long been held that the plasticity of plant specialized metabolism and the canalization of development should be differently regulated; our findings imply a common hierarchical regulatory architecture orchestrated by transcription factors for specialized metabolism and development, making it an attractive target for metabolic engineering.
Collapse
Affiliation(s)
| | - Nicole K. Clay
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, United States
| |
Collapse
|