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Hao JR, Li Y, Ge Y. Harnessing the plant microbiome for environmental sustainability: From ecological foundations to novel applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175766. [PMID: 39187075 DOI: 10.1016/j.scitotenv.2024.175766] [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: 06/29/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 08/28/2024]
Abstract
In plant environments, there exist heterogeneous microbial communities, referred to as the plant microbiota, which are recruited by plants and play crucial roles in promoting plant growth, aiding in resistance against pathogens and environmental stresses, thereby maintaining plant health. These microorganisms, along with their genomes, collectively form the plant microbiome. Research on the plant microbiome can help unravel the intricate interactions between plants and microbes, providing a theoretical foundation to reduce pesticide use, enhance agricultural productivity, and promote environmental sustainability. Despite significant progress in the field of research, unresolved challenges persist due to ongoing technological limitations and the complexities inherent in studying microorganisms at small scales. Recently, synthetic community (SynCom) has emerged as a novel technique for microbiome research, showing promising prospects for applications in the plant microbiome field. This article systematically introduces the origin and distribution of plant microbiota, the processes of their recruitment and colonization, and the mechanisms underlying their beneficial functions for plants, from the aspects of composition, assembly, and function. Furthermore, we discuss the principles, applications, challenges, and prospects of SynCom for promoting plant health.
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Affiliation(s)
- Jing-Ru Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yan Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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2
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Zadegan SB, Kim W, Abbas HMK, Kim S, Krishnan HB, Hewezi T. Differential symbiotic compatibilities between rhizobium strains and cultivated and wild soybeans revealed by anatomical and transcriptome analyses. FRONTIERS IN PLANT SCIENCE 2024; 15:1435632. [PMID: 39290740 PMCID: PMC11405202 DOI: 10.3389/fpls.2024.1435632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 08/09/2024] [Indexed: 09/19/2024]
Abstract
Various species of rhizobium establish compatible symbiotic relationships with soybean (Glycine max) leading to the formation of nitrogen-fixing nodules in roots. The formation of functional nodules is mediated through complex developmental and transcriptional reprogramming that involves the activity of thousands of plant genes. However, host transcriptome that differentiate between functional or non-functional nodules remain largely unexplored. In this study, we investigated differential compatibilities between rhizobium strains (Bradyrhizobium diazoefficiens USDA110 Bradyrhizobium sp. strain LVM105) and cultivated and wild soybeans. The nodulation assays revealed that both USDA110 and LVM105 strains effectively nodulate G. soja but only USDA110 can form symbiotic relationships with Williams 82. LVM105 formed pseudonodules on Williams 82 that consist of a central nodule-like mass that are devoid of any rhizobia. RNA-seq data revealed that USDA110 and LVM105 induce distinct transcriptome programing in functional mature nodules formed on G. soja roots, where genes involved in nucleosome assembly, DNA replication, regulation of cell cycle, and defense responses play key roles. Transcriptome comparison also suggested that activation of genes associated with cell wall biogenesis and organization and defense responses together with downregulation of genes involved in the biosynthesis of isoprenoids and antioxidant stress are associated with the formation of non-functional nodules on Williams 82 roots. Moreover, our analysis implies that increased activity of genes involved in oxygen binding, amino acid transport, and nitrate transport differentiates between fully-developed nodules in cultivated versus wild soybeans.
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Affiliation(s)
- Sobhan Bahrami Zadegan
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, United States
| | - Wonseok Kim
- Plant Science Division, University of Missouri, Columbia, MO, United States
| | | | - Sunhyung Kim
- Plant Science Division, University of Missouri, Columbia, MO, United States
| | - Hari B Krishnan
- Plant Science Division, University of Missouri, Columbia, MO, United States
- Plant Genetics Research, The United States Department of Agriculture (USDA) Agricultural Research Service, Columbia, MO, United States
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
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3
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Spooren J, van Bentum S, Thomashow LS, Pieterse CMJ, Weller DM, Berendsen RL. Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:1-30. [PMID: 38857541 DOI: 10.1146/annurev-phyto-021622-100127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Plants have coevolved together with the microbes that surround them and this assemblage of host and microbes functions as a discrete ecological unit called a holobiont. This review outlines plant-driven assembly of disease-suppressive microbiomes. Plants are colonized by microbes from seed, soil, and air but selectively shape the microbiome with root exudates, creating microenvironment hot spots where microbes thrive. Using plant immunity for gatekeeping and surveillance, host-plant genetic properties govern microbiome assembly and can confer adaptive advantages to the holobiont. These advantages manifest in disease-suppressive soils, where buildup of specific microbes inhibits the causal agent of disease, that typically develop after an initial disease outbreak. Based on disease-suppressive soils such as take-all decline, we developed a conceptual model of how plants in response to pathogen attack cry for help and recruit plant-protective microbes that confer increased resistance. Thereby, plants create a soilborne legacy that protects subsequent generations and forms disease-suppressive soils.
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Affiliation(s)
- Jelle Spooren
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Sietske van Bentum
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Linda S Thomashow
- Wheat Health, Genetics and Quality Research Unit, US Department of Agriculture, Agricultural Research Service, Pullman, Washington, USA;
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - David M Weller
- Wheat Health, Genetics and Quality Research Unit, US Department of Agriculture, Agricultural Research Service, Pullman, Washington, USA;
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
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Fiorilli V, Martínez-Medina A, Pozo MJ, Lanfranco L. Plant Immunity Modulation in Arbuscular Mycorrhizal Symbiosis and Its Impact on Pathogens and Pests. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:127-156. [PMID: 39251211 DOI: 10.1146/annurev-phyto-121423-042014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Arbuscular mycorrhizal (AM) symbiosis is the oldest and most widespread mutualistic association on Earth and involves plants and soil fungi belonging to Glomeromycotina. A complex molecular, cellular, and genetic developmental program enables partner recognition, fungal accommodation in plant tissues, and activation of symbiotic functions such as transfer of phosphorus in exchange for carbohydrates and lipids. AM fungi, as ancient obligate biotrophs, have evolved strategies to circumvent plant defense responses to guarantee an intimate and long-lasting mutualism. They are among those root-associated microorganisms able to boost plants' ability to cope with biotic stresses leading to mycorrhiza-induced resistance (MIR), which can be effective across diverse hosts and against different attackers. Here, we examine the molecular mechanisms underlying the modulation of plant immunity during colonization by AM fungi and at the onset and display of MIR against belowground and aboveground pests and pathogens. Understanding the MIR efficiency spectrum and its regulation is of great importance to optimizing the biotechnological application of these beneficial microbes for sustainable crop protection.
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Affiliation(s)
- V Fiorilli
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy;
| | - A Martínez-Medina
- Department of Plant-Microbe Interactions, Institute of Natural Resources and Agrobiology of Salamanca, CSIC, Salamanca, Spain
| | - Maria J Pozo
- Department of Soil and Plant Microbiology, Estación Experimental del Zaidín, CSIC, Granada, Spain;
| | - L Lanfranco
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy;
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5
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Qian Y, Jin Y, Han X, Malik K, Li C, Yu B. Effects of Grazing and Leaf Spot Disease on the Structure and Diversity of Phyllosphere Microbiome Communities in Leymus chinensis. PLANTS (BASEL, SWITZERLAND) 2024; 13:2128. [PMID: 39124246 PMCID: PMC11313783 DOI: 10.3390/plants13152128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
Leymus chinensis is a high-quality forage with wide distribution. Disease is an important factor affecting the yield and quality of L. chinensis. To investigate the effect of grazing on the phyllosphere microbiome community and leaf spot disease in L. chinensis, high-throughput sequencing technology was used to study the differences in the composition and structure of the phyllosphere fungal and bacterial communities of healthy and diseased leaves under different grazing intensities. The results showed that grazing significantly reduced leaf spot disease incidence and severity. There were significant differences in the phyllosphere microbiome composition between healthy and diseased leaves, and interestingly, diseased leaves showed more complex microbial activity. Grazing altered the relative abundance of micro-organisms and affected microbial dispersal and colonization either directly through behavior or indirectly by altering plant community structure. In this study, we found that the phyllosphere microbiome responded strongly to pathogen infection, and that plants recruited beneficial microbes to protect themselves after disease development. Grazing could regulate microbial community composition and structure, either directly or indirectly, and plays a crucial role in maintaining the health of L. chinensis.
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Affiliation(s)
- Yani Qian
- Grassland Research Center of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China; (Y.Q.); (X.H.)
| | - Yuanyuan Jin
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (Y.J.); (K.M.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- Gansu Tech Innovation Center of Western China Grassland Industry, Lanzhou University, Lanzhou 730020, China
| | - Xinyao Han
- Grassland Research Center of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China; (Y.Q.); (X.H.)
| | - Kamran Malik
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (Y.J.); (K.M.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- Gansu Tech Innovation Center of Western China Grassland Industry, Lanzhou University, Lanzhou 730020, China
| | - Chunjie Li
- Grassland Research Center of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China; (Y.Q.); (X.H.)
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (Y.J.); (K.M.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- Gansu Tech Innovation Center of Western China Grassland Industry, Lanzhou University, Lanzhou 730020, China
| | - Binhua Yu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (Y.J.); (K.M.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
- Engineering Research Center of Grassland Industry, Ministry of Education, Lanzhou University, Lanzhou 730020, China
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- Gansu Tech Innovation Center of Western China Grassland Industry, Lanzhou University, Lanzhou 730020, China
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Passera A, Escudero-Martinez C. Editorial: Genome and metagenome interactions in the plant holobiont for plant health and productivity. FRONTIERS IN PLANT SCIENCE 2024; 15:1463795. [PMID: 39119491 PMCID: PMC11306166 DOI: 10.3389/fpls.2024.1463795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 08/10/2024]
Affiliation(s)
- Alessandro Passera
- Department of Agricultural and Environmental Sciences, University of Milan, Milan, Italy
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Markova O, Garipova S, Chistoedova A, Matyunina V, Lubyanova A, Lastochkina O, Garipov A, Shpirnaya I, Pusenkova L. Predicting Field Effectiveness of Endophytic Bacillus subtilis Inoculants for Common Bean Using Morphometric and Biochemical Markers. PLANTS (BASEL, SWITZERLAND) 2024; 13:1769. [PMID: 38999609 PMCID: PMC11244252 DOI: 10.3390/plants13131769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/15/2024] [Accepted: 06/22/2024] [Indexed: 07/14/2024]
Abstract
According to four field experiments, after the inoculation of Phaseolus vulgaris L. cultivar Ufimskaya with the commercial strain Bacillus subtilis 26D and the promising strain B. subtilis 10-4, it was found that inoculation with B. subtilis 10-4 improved seed productivity (SP) by 31-41% per plant, but only in dry years. In contrast, all 4 years of inoculation with B. subtilis 26D were ineffective or neutral. It was intended to determine the growing and biochemical characteristics of inoculated 7-day-old plants, which correlate with the field SP of bacterial preparations. The SP of inoculated plants (average of 4 years) correlated with root length (0.83), MDA content (-0.98), and catalase (CAT) activity in roots (-0.96) of week-old seedlings. High correlation coefficients between the H2O2 content in the roots and SP (0.89 and 0.77), as well as between the H2O2 content in shoots and SP (0.98 and 0.56), were observed only in two dry years, when the influence of bacteria was detected. These physiological indicators were identified as potential markers for predicting the effectiveness of the endophytic symbiosis between bean plants and B. subtilis strains. The findings may be used to develop effective microbial-based, eco-friendly technologies for bean production.
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Affiliation(s)
- Oksana Markova
- Institute of Nature and Human, Ufa University of Science and Technology, Zaki Validy Str. 32, 450076 Ufa, Russia
| | - Svetlana Garipova
- Institute of Nature and Human, Ufa University of Science and Technology, Zaki Validy Str. 32, 450076 Ufa, Russia
| | - Aelita Chistoedova
- Institute of Nature and Human, Ufa University of Science and Technology, Zaki Validy Str. 32, 450076 Ufa, Russia
| | - Viktoriia Matyunina
- Institute of Nature and Human, Ufa University of Science and Technology, Zaki Validy Str. 32, 450076 Ufa, Russia
| | - Alsu Lubyanova
- Institute of Biochemistry and Genetics-Subdivision of the Ufa Federal Research Center of the Russian Academy of Sciences, Pr. Oktyabrya 71, 450054 Ufa, Russia
| | - Oksana Lastochkina
- Institute of Biochemistry and Genetics-Subdivision of the Ufa Federal Research Center of the Russian Academy of Sciences, Pr. Oktyabrya 71, 450054 Ufa, Russia
| | - Arsenii Garipov
- Institute of Nature and Human, Ufa University of Science and Technology, Zaki Validy Str. 32, 450076 Ufa, Russia
| | - Irina Shpirnaya
- Institute of Nature and Human, Ufa University of Science and Technology, Zaki Validy Str. 32, 450076 Ufa, Russia
| | - Lyudmila Pusenkova
- Bashkir Research Institute of Agriculture-Subdivision of the Ufa Federal Research Center of the Russian Academy of Sciences, R. Zorge Str. 19, 450059 Ufa, Russia
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8
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Yin C, Larson M, Lahr N, Paulitz T. Wheat Rhizosphere-Derived Bacteria Protect Soybean from Soilborne Diseases. PLANT DISEASE 2024; 108:1565-1576. [PMID: 38105448 DOI: 10.1094/pdis-08-23-1713-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Soybean (Glycine max [L.] Merr.) is an important oilseed crop with a high economic value. However, three damaging soybean diseases, soybean cyst nematode (SCN; Heterodera glycines Ichinohe), Sclerotinia stem rot caused by the fungus Sclerotinia sclerotiorum (Lid.) de Bary, and soybean root rot caused by Fusarium spp., are major constraints to soybean production in the Great Plains. Current disease management options, including resistant or tolerant varieties, fungicides, nematicides, and agricultural practices (crop rotation and tillage), have limited efficacy for these pathogens or have adverse effects on the ecosystem. Microbes with antagonistic activity are a promising option to control soybean diseases with the advantage of being environmentally friendly and sustainable. In this study, 61 bacterial strains isolated from wheat rhizospheres were used to examine their antagonistic abilities against three soybean pathogens. Six bacterial strains significantly inhibited the growth of Fusarium graminearum in the dual-culture assay. These bacterial strains were identified as Chryseobacterium ginsengisoli, C. indologenes, Pseudomonas poae, two Pseudomonas spp., and Delftia acidovorans by 16S rRNA gene sequencing. Moreover, C. ginsengisoli, C. indologenes, and P. poae significantly increased the mortality of SCN second-stage juveniles (J2), and two Pseudomonas spp. inhibited the growth of S. sclerotiorum in vitro. Further growth chamber tests found that C. ginsengisoli and C. indologenes reduced soybean Fusarium root rot disease. C. ginsengisoli and P. poae dramatically decreased SCN egg number on SCN-susceptible soybean 'Williams 82'. Two Pseudomonas spp. protected soybean plants from leaf damage and collapse after being infected by S. sclerotiorum. These bacteria exhibit versatile antagonistic potential. This work lays the foundation for further research on the field control of soybean pathogens.
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Affiliation(s)
- Chuntao Yin
- North Central Agricultural Research Laboratory, USDA-ARS, Brookings, SD
| | - Matt Larson
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD
| | - Nathan Lahr
- North Central Agricultural Research Laboratory, USDA-ARS, Brookings, SD
| | - Timothy Paulitz
- Wheat Health, Genetics, and Quality Research Unit, USDA-ARS, Pullman, WA
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Nakano RT, Shimasaki T. Long-Term Consequences of PTI Activation and Its Manipulation by Root-Associated Microbiota. PLANT & CELL PHYSIOLOGY 2024; 65:681-693. [PMID: 38549511 DOI: 10.1093/pcp/pcae033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/28/2024] [Accepted: 03/27/2024] [Indexed: 05/31/2024]
Abstract
In nature, plants are constantly colonized by a massive diversity of microbes engaged in mutualistic, pathogenic or commensal relationships with the host. Molecular patterns present in these microbes activate pattern-triggered immunity (PTI), which detects microbes in the apoplast or at the tissue surface. Whether and how PTI distinguishes among soil-borne pathogens, opportunistic pathogens, and commensal microbes within the soil microbiota remains unclear. PTI is a multimodal series of molecular events initiated by pattern perception, such as Ca2+ influx, reactive oxygen burst, and extensive transcriptional and metabolic reprogramming. These short-term responses may manifest within minutes to hours, while the long-term consequences of chronic PTI activation persist for days to weeks. Chronic activation of PTI is detrimental to plant growth, so plants need to coordinate growth and defense depending on the surrounding biotic and abiotic environments. Recent studies have demonstrated that root-associated commensal microbes can activate or suppress immune responses to variable extents, clearly pointing to the role of PTI in root-microbiota interactions. However, the molecular mechanisms by which root commensals interfere with root immunity and root immunity modulates microbial behavior remain largely elusive. Here, with a focus on the difference between short-term and long-term PTI responses, we summarize what is known about microbial interference with host PTI, especially in the context of root microbiota. We emphasize some missing pieces that remain to be characterized to promote the ultimate understanding of the role of plant immunity in root-microbiota interactions.
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10
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Zhuang Y, Wang H, Tan F, Wu B, Liu L, Qin H, Yang Z, He M. Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108619. [PMID: 38604013 DOI: 10.1016/j.plaphy.2024.108619] [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: 12/06/2023] [Revised: 03/21/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.
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Affiliation(s)
- Yong Zhuang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
| | - Hao Wang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Furong Tan
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Linpei Liu
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Han Qin
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - ZhiJuan Yang
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China
| | - Mingxiong He
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, 610041, Chengdu, China.
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11
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Batool M, Carvalhais LC, Fu B, Schenk PM. Customized plant microbiome engineering for food security. TRENDS IN PLANT SCIENCE 2024; 29:482-494. [PMID: 37977879 DOI: 10.1016/j.tplants.2023.10.012] [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: 05/10/2022] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
Plant microbiomes play a vital role in promoting plant growth and resilience to cope with environmental stresses. Plant microbiome engineering holds significant promise to increase crop yields, but there is uncertainty about how this can best be achieved. We propose a step-by-step approach involving customized direct and indirect methods to condition soils and to match plants and microbiomes. Although three approaches, namely the development of (i) 'plant- and microbe-friendly' soils, (ii) 'microbe-friendly' plants, and (iii) 'plant-friendly' microbiomes, have been successfully tested in isolation, we propose that the combination of all three may lead to a step-change towards higher and more stable crop yields. This review aims to provide knowledge, future directions, and practical guidance to achieve this goal via customized plant microbiome engineering.
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Affiliation(s)
- Maria Batool
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Lilia C Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Brendan Fu
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peer M Schenk
- Plant-Microbe Interactions Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, 4072, Australia; Sustainable Solutions Hub, Global Sustainable Solutions Pty Ltd, Brisbane, QLD 4105, Australia.
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12
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Rehneke L, Schäfer P. Symbiont effector-guided mapping of proteins in plant networks to improve crop climate stress resilience: Symbiont effectors inform highly interconnected plant protein networks and provide an untapped resource for crop climate resilience strategies. Bioessays 2024; 46:e2300172. [PMID: 38388783 DOI: 10.1002/bies.202300172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/21/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
There is an urgent need for novel protection strategies to sustainably secure crop production under changing climates. Studying microbial effectors, defined as microbe-derived proteins that alter signalling inside plant cells, has advanced our understanding of plant immunity and microbial plant colonisation strategies. Our understanding of effectors in the establishment and beneficial outcome of plant symbioses is less well known. Combining functional and comparative interaction assays uncovered specific symbiont effector targets in highly interconnected plant signalling networks and revealed the potential of effectors in beneficially modulating plant traits. The diverse functionality of symbiont effectors differs from the paradigmatic immuno-suppressive function of pathogen effectors. These effectors provide solutions for improving crop resilience against climate stress by their evolution-driven specification in host protein targeting and modulation. Symbiont effectors represent stringent tools not only to identify genetic targets for crop breeding, but to serve as applicable agents in crop management strategies under changing environments.
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Affiliation(s)
- Laura Rehneke
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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13
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Xing W, Gai X, Xue L, Li S, Zhang X, Ju F, Chen G. Enriched rhizospheric functional microbiome may enhance adaptability of Artemisia lavandulaefolia and Betula luminifera in antimony mining areas. Front Microbiol 2024; 15:1348054. [PMID: 38577689 PMCID: PMC10993014 DOI: 10.3389/fmicb.2024.1348054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/27/2024] [Indexed: 04/06/2024] Open
Abstract
Dominant native plants are crucial for vegetation reconstruction and ecological restoration of mining areas, though their adaptation mechanisms in stressful environments are unclear. This study focuses on the interactions between dominant indigenous species in antimony (Sb) mining area, Artemisia lavandulaefolia and Betula luminifera, and the microbes in their rhizosphere. The rhizosphere microbial diversity and potential functions of both plants were analyzed through the utilization of 16S, ITS sequencing, and metabarcoding analysis. The results revealed that soil environmental factors, rather than plant species, had a more significant impact on the composition of the rhizosphere microbial community. Soil pH and moisture significantly affected microbial biomarkers and keystone species. Actinobacteria, Proteobacteria and Acidobacteriota, exhibited high resistance to Sb and As, and played a crucial role in the cycling of carbon, nitrogen (N), phosphorus (P), and sulfur (S). The genes participating in N, P, and S cycling exhibited metabolic coupling with those genes associated with Sb and As resistance, which might have enhanced the rhizosphere microbes' capacity to endure environmental stressors. The enrichment of these rhizosphere functional microbes is the combined result of dispersal limitations and deterministic assembly processes. Notably, the genes related to quorum sensing, the type III secretion system, and chemotaxis systems were significantly enriched in the rhizosphere of plants, especially in B. luminifera, in the mining area. The phylogenetic tree derived from the evolutionary relationships among rhizosphere microbial and chloroplast whole-genome resequencing results, infers both species especially B. luminifera, may have undergone co-evolution with rhizosphere microorganisms in mining areas. These findings offer valuable insights into the dominant native rhizosphere microorganisms that facilitate plant adaptation to environmental stress in mining areas, thereby shedding light on potential strategies for ecological restoration in such environments.
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Affiliation(s)
- Wenli Xing
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xu Gai
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Liang Xue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Shaocui Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Xiaoping Zhang
- China National Bamboo Research Center, Key Laboratory of State Forestry and Grassland Administration on Bamboo Forest Ecology and Resource Utilization, Hangzhou, Zhejiang, China
| | - Feng Ju
- Key Laboratory of Coastal Environment and Resources of Zhejiang Province, School of Engineering, Westlake University, Hangzhou, China
| | - Guangcai Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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14
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Van Gerrewey T, Chung HS. MAPK Cascades in Plant Microbiota Structure and Functioning. J Microbiol 2024; 62:231-248. [PMID: 38587594 DOI: 10.1007/s12275-024-00114-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 04/09/2024]
Abstract
Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, influencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent findings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.
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Affiliation(s)
- Thijs Van Gerrewey
- Plant Biotechnology Research Center, Department of Environmental Technology, Food Technology and Molecular Biotechnology, Ghent University Global Campus, Incheon, 21985, Republic of Korea
| | - Hoo Sun Chung
- Plant Biotechnology Research Center, Department of Environmental Technology, Food Technology and Molecular Biotechnology, Ghent University Global Campus, Incheon, 21985, Republic of Korea.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
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15
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Liu Y, Xu Z, Chen L, Xun W, Shu X, Chen Y, Sun X, Wang Z, Ren Y, Shen Q, Zhang R. Root colonization by beneficial rhizobacteria. FEMS Microbiol Rev 2024; 48:fuad066. [PMID: 38093453 PMCID: PMC10786197 DOI: 10.1093/femsre/fuad066] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024] Open
Abstract
Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.
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Affiliation(s)
- Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Zhihui 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, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Lin Chen
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, 1 Shuizha West Road, Beijing 102300, P.R. China
| | - Weibing Xun
- 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, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xia Shu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, P.R. China
| | - Yu Chen
- 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, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xinli Sun
- 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, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Zhengqi Wang
- 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, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Yi Ren
- 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, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Qirong Shen
- 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, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Ruifu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- 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, 6 Tongwei Road, Nanjing 210095, P.R. China
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16
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Luo X, Sun K, Li HR, Zhang XY, Pan YT, Luo DL, Wu YB, Jiang HJ, Wu XH, Ma CY, Dai CC, Zhang W. Depletion of protective microbiota promotes the incidence of fruit disease. THE ISME JOURNAL 2024; 18:wrae071. [PMID: 38691444 DOI: 10.1093/ismejo/wrae071] [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: 12/05/2023] [Revised: 03/11/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Plant-associated microbiomes play important roles in plant health and productivity. However, despite fruits being directly linked to plant productivity, little is known about the microbiomes of fruits and their potential association with fruit health. Here, by integrating 16S rRNA gene, ITS high-throughput sequencing data, and microbiological culturable approaches, we reported that roots and fruits (pods) of peanut, a typical plant that bears fruits underground, recruit different bacterial and fungal communities independently of cropping conditions and that the incidence of pod disease under monocropping conditions is attributed to the depletion of Bacillus genus and enrichment of Aspergillus genus in geocarposphere. On this basis, we constructed a synthetic community (SynCom) consisting of three Bacillus strains from geocarposphere soil under rotation conditions with high culturable abundance. Comparative transcriptome, microbiome profiling, and plant phytohormone signaling analysis reveal that the SynCom exhibited more effective Aspergillus growth inhibition and pod disease control than individual strain, which was underpinned by a combination of molecular mechanisms related to fungal cell proliferation interference, mycotoxins biosynthesis impairment, and jasmonic acid-mediated plant immunity activation. Overall, our results reveal the filter effect of plant organs on the microbiome and that depletion of key protective microbial community promotes the fruit disease incidence.
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Affiliation(s)
- 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, Jiangsu Province, 210023, 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, Jiangsu Province, 210023, China
| | - Hao-Ran Li
- 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, 210023, China
| | - Xiang-Yu 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, 210023, 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, 210023, China
| | - De-Lin 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, Jiangsu Province, 210023, China
| | - Yi-Bo Wu
- 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, 210023, 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, 210023, China
| | - Xiao-Han Wu
- 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, 210023, 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, 210023, 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, 210023, 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, 210023, China
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17
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Richards L, Cremin K, Coates M, Vigor F, Schäfer P, Soyer OS. Ammonia leakage can underpin nitrogen-sharing among soil microorganisms. THE ISME JOURNAL 2024; 18:wrae171. [PMID: 39236233 PMCID: PMC11440039 DOI: 10.1093/ismejo/wrae171] [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: 04/15/2024] [Revised: 07/16/2024] [Accepted: 09/04/2024] [Indexed: 09/07/2024]
Abstract
Soil microbial communities host a large number of microbial species that support important ecological functions such as biogeochemical cycling and plant nutrition. The extent and stability of these functions are affected by inter-species interactions among soil microorganisms, yet the different mechanisms underpinning microbial interactions in the soil are not fully understood. Here, we study the extent of nutrient-based interactions among two model, plant-supporting soil microorganisms, the fungi Serendipita indica, and the bacteria Bacillus subtilis. We found that S. indica is unable to grow with nitrate - a common nitrogen source in the soil - but this inability could be rescued, and growth restored in the presence of B. subtilis. We demonstrate that this effect is due to B. subtilis utilising nitrate and releasing ammonia, which can be used by S. indica. We refer to this type of mechanism as ammonia mediated nitrogen sharing (N-sharing). Using a mathematical model, we demonstrated that the pH dependent equilibrium between ammonia (NH3) and ammonium (NH+4) results in an inherent cellular leakiness, and that reduced amonnium uptake or assimilation rates could result in higher levels of leaked ammonia. In line with this model, a mutant B. subtilis - devoid of ammonia uptake - showed higher S. indica growth support in nitrate media. These findings highlight that ammonia based N-sharing can be a previously under-appreciated mechanism underpinning interaction among soil microorganisms and could be influenced by microbial or abiotic alteration of pH in microenvironments.
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Affiliation(s)
- Luke Richards
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Kelsey Cremin
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Mary Coates
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Finley Vigor
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Patrick Schäfer
- Institute of Phytophathology, Justus-Liebig Universität, Heinrich-Buff-Ring 26-32 35392 Giessen, Germany
| | - Orkun S Soyer
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
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18
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Raja Gopalan NS, Yegna Priya S, Mohapatra S. The rhizobacterial strain, Pseudomonas putida AKMP7, causes conditional pathogenesis in Arabidopsis thaliana via negative regulation of salicylic acid signaling, under water stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108262. [PMID: 38091931 DOI: 10.1016/j.plaphy.2023.108262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 02/15/2024]
Abstract
We have previously reported a phenomenon of "conditional pathogenesis", in which, a drought-tolerant rhizobacterium, Pseudomonas putida AKMP7, promotes plant growth under well-watered conditions, while, deteriorating plant health under water-stressed conditions, in Arabidopsis thaliana seedlings. To understand the molecular mechanisms behind this phenomenon, we studied the modulation of salicylic acid (SA) biosynthesis as well as SA-responsive gene expression, involved in systemic acquired resistance (SAR), in A. thaliana, by AKMP7, under well-watered and water-stressed conditions. We found that, the plant SA levels were upregulated by AKMP7, both under, well-watered as well as water-stressed conditions. However, the SA signaling gene, Non-expressor of Pathogenesis Related gene 1 (NPR1) and Pathogenesis Related gene 1 (PR1) were upregulated under well-watered conditions and suppressed under water-stress, in AKMP7 inoculated seedlings. To understand the reason for this, we studied the expression of NPR4, a negative regulator of NPR1, and, NPR3, a negative regulator of PR1. We observed that, AKMP7 suppresses NPR1 and, consequently, PR1 genes, by upregulating NPR4 under water stress. To understand the potential role of NPR4 in conditional-pathogenesis, we performed physiological studies with NPR4 knockout mutants of A. thaliana and found that the NPR4 mutants did not exhibit any signs of the characteristic growth retardation caused by AKMP7 inoculation, under water stress. Preliminary studies with the model pathogen, Pseudomonas syringae, indicate that AKMP7 may lead to enhanced disease suppression under well-watered conditions, but not under water-stress. Taken together, our data suggest that, AKMP7 causes conditional pathogenesis by an overall compromise in plant immune response under water-stress.
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Affiliation(s)
- N S Raja Gopalan
- Department of Biological Sciences, Birla Institute of Technology and Science (Pilani), Hyderabad Campus, Hyderabad, India
| | - S Yegna Priya
- Department of Biological Sciences, Birla Institute of Technology and Science (Pilani), Hyderabad Campus, Hyderabad, India
| | - Sridev Mohapatra
- Department of Biological Sciences, Birla Institute of Technology and Science (Pilani), Hyderabad Campus, Hyderabad, India.
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19
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Svietlova N, Reichelt M, Zhyr L, Majumder A, Scholz SS, Grabe V, Krapp A, Oelmüller R, Mithöfer A. The Beneficial Fungus Mortierella hyalina Modulates Amino Acid Homeostasis in Arabidopsis under Nitrogen Starvation. Int J Mol Sci 2023; 24:16128. [PMID: 38003319 PMCID: PMC10671455 DOI: 10.3390/ijms242216128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/30/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Non-mycorrhizal but beneficial fungi often mitigate (a)biotic stress-related traits in host plants. The underlying molecular mechanisms are mostly still unknown, as in the interaction between the endophytic growth-promoting soil fungus Mortierella hyalina and Arabidopsis thaliana. Here, abiotic stress in the form of nitrogen (N) deficiency was used to investigate the effects of the fungus on colonized plants. In particular, the hypothesis was investigated that fungal infection could influence N deficiency via an interaction with the high-affinity nitrate transporter NRT2.4, which is induced by N deficiency. For this purpose, Arabidopsis wild-type nrt2.4 knock-out and NRT2.4 reporter lines were grown on media with different nitrate concentrations with or without M. hyalina colonization. We used chemical analysis methods to determine the amino acids and phytohormones. Experimental evidence suggests that the fungus does not modulate NRT2.4 expression under N starvation. Instead, M. hyalina alleviates N starvation in other ways: The fungus supplies nitrogen (15N) to the N-starved plant. The presence of the fungus restores the plants' amino acid homeostasis, which was out of balance due to N deficiency, and causes a strong accumulation of branched-chain amino acids. We conclude that the plant does not need to invest in defense and resources for growth are maintained, which in turn benefits the fungus, suggesting that this interaction should be considered a mutualistic symbiosis.
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Affiliation(s)
- Nataliia Svietlova
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; (N.S.); (L.Z.); (A.M.)
| | - Michael Reichelt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
| | - Liza Zhyr
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; (N.S.); (L.Z.); (A.M.)
| | - Anindya Majumder
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; (N.S.); (L.Z.); (A.M.)
| | - Sandra S. Scholz
- Department of Plant Physiology, Matthias-Schleiden-Institute, Friedrich-Schiller-University, 07743 Jena, Germany; (S.S.S.); (R.O.)
| | - Veit Grabe
- Microscopic Imaging Service Group, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
| | - Anne Krapp
- Institut Jean-Pierre Bourgin (IJPB), AgroParisTech, INRAE, Université Paris-Saclay, 78000 Versailles, France;
| | - Ralf Oelmüller
- Department of Plant Physiology, Matthias-Schleiden-Institute, Friedrich-Schiller-University, 07743 Jena, Germany; (S.S.S.); (R.O.)
| | - Axel Mithöfer
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; (N.S.); (L.Z.); (A.M.)
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20
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Oldstone-Jackson C, Huang F, Bergelson J. Microbe-associated molecular pattern recognition receptors have little effect on endophytic Arabidopsis thaliana microbiome assembly in the field. FRONTIERS IN PLANT SCIENCE 2023; 14:1276472. [PMID: 38023837 PMCID: PMC10663345 DOI: 10.3389/fpls.2023.1276472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023]
Abstract
Plant microbiome structure affects plant health and productivity. A limited subset of environmental microbes successfully establishes within plant tissues, but the forces underlying this selectivity remain poorly characterized. Transmembrane pattern recognition receptors (PRRs), used by plants to detect microbe-associated molecular patterns (MAMPs), are strong candidates for achieving this selectivity because PRRs can potentially interact with many members of the microbiome. Indeed, MAMPs found in many microbial taxa, including beneficials and commensals, can instigate a robust immune response that affects microbial growth. Surprisingly, we found that MAMP-detecting PRRs have little effect on endophytic bacterial and fungal microbiome structure in the field. We compared the microbiomes of four PRR knockout lines of Arabidopsis thaliana to wild-type plants in multiple tissue types over several developmental stages and detected only subtle shifts in fungal, but not bacterial, β-diversity in one of the four PRR mutants. In one developmental stage, lore mutants had slightly altered fungal β-diversity, indicating that LORE may be involved in plant-fungal interactions in addition to its known role in detecting certain bacterial lipids. No other effects of PRRs on α-diversity, microbiome variability, within-individual homogeneity, or microbial load were found. The general lack of effect suggests that individual MAMP-detecting PRRs are not critical in shaping the endophytic plant microbiome. Rather, we suggest that MAMP-detecting PRRs must either act in concert and/or are individually maintained through pleiotropic effects or interactions with coevolved mutualists or pathogens. Although unexpected, these results offer insights into the role of MAMP-detecting PRRs in plant-microbe interactions and help direct future efforts to uncover host genetic elements that control plant microbiome assembly.
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Affiliation(s)
| | - Feng Huang
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Joy Bergelson
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Center for Genomics and Systems Biology, Department of Biology, College of Arts and Science, New York University, New York, NY, United States
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21
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Shirakawa M, Matsushita N, Fukuda K. Visualization of root extracellular traps in an ectomycorrhizal woody plant (Pinus densiflora) and their interactions with root-associated bacteria. PLANTA 2023; 258:112. [PMID: 37935872 PMCID: PMC10630192 DOI: 10.1007/s00425-023-04274-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023]
Abstract
MAIN CONCLUSION Extracellular traps in the primary root of Pinus densiflora contribute to root-associated bacterial colonization. Trapped rhizobacteria induce the production of reactive oxygen species in root-associated, cap-derived cells. Ectomycorrhizal (ECM) woody plants, such as members of Pinaceae and Fagaceae, can acquire resistance to biotic and abiotic stresses through the formation of mycorrhiza with ECM fungi. However, germinated tree seedlings do not have mycorrhizae and it takes several weeks for ectomycorrhizae to form on their root tips. Therefore, to confer protection during the early growth stage, bare primary roots require defense mechanisms other than mycorrhization. Here, we attempted to visualize root extracellular traps (RETs), an innate root defense mechanism, in the primary root of Pinus densiflora and investigate the interactions with root-associated bacteria isolated from ECM and fine non-mycorrhizal roots. Histological and histochemical imaging and colony-forming unit assays demonstrated that RETs in P. densiflora, mainly consisting of root-associated, cap-derived cells (AC-DCs) and large amounts of root mucilage, promote bacterial colonization in the rhizosphere, despite also having bactericidal activity via extracellular DNA. Four rhizobacterial strains retarded the mycelial growth of a pathogenic strain belonging to the Fusarium oxysporum species complex in dual culture assay. They also induced the production of reactive oxygen species (ROS) from host tree AC-DCs without being excluded from the rhizosphere of P. densiflora. Applying three Paraburkholderia strains, especially PM O-EM8 and PF T-NM22, showed significant differences in the ROS levels from the control group. These results reveal the indirect contributions of rhizobacteria to host root defense and suggest that root-associated bacteria could be a component of RETs as a first line of defense against root pathogens in the early growth stage of ECM woody plants.
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Affiliation(s)
- Makoto Shirakawa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan.
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kenji Fukuda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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22
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Carrell AA, Clark M, Jawdy S, Muchero W, Alexandre G, Labbé JL, Rush TA. Interactions with microbial consortia have variable effects in organic carbon and production of exometabolites among genotypes of Populus trichocarpa. PLANT DIRECT 2023; 7:e544. [PMID: 38028650 PMCID: PMC10660807 DOI: 10.1002/pld3.544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
Poplar is a short-rotation woody crop frequently studied for its significance as a sustainable bioenergy source. The successful establishment of a poplar plantation partially depends on its rhizosphere-a dynamic zone governed by complex interactions between plant roots and a plethora of commensal, mutualistic, symbiotic, or pathogenic microbes that shape plant fitness. In an exploratory endeavor, we investigated the effects of a consortium consisting of ectomycorrhizal fungi and a beneficial Pseudomonas sp. strain GM41 on plant growth (including height, stem girth, leaf, and root growth) and as well as growth rate over time, across four Populus trichocarpa genotypes. Additionally, we compared the level of total organic carbon and plant exometabolite profiles across different poplar genotypes in the presence of the microbial consortium. These data revealed no significant difference in plant growth parameters between the treatments and the control across four different poplar genotypes at 7 weeks post-inoculation. However, total organic carbon and exometabolite profiles were significantly different between the genotypes and the treatments. These findings suggest that this microbial consortium has the potential to trigger early signaling responses in poplar, influencing its metabolism in ways crucial for later developmental processes and stress tolerance.
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Affiliation(s)
- Alyssa A. Carrell
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Miranda Clark
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | - Sara Jawdy
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
| | | | - Gladys Alexandre
- Department of Biochemistry and Cellular and Molecular BiologyUniversity of Tennessee‐KnoxvilleKnoxvilleTennesseeUSA
| | - Jesse L. Labbé
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
- Present address:
Technology HoldingSalt Lake CityUtahUSA
| | - Tomás A. Rush
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennesseeUSA
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23
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Molinari S, Leonetti P. Resistance to Plant Parasites in Tomato Is Induced by Soil Enrichment with Specific Bacterial and Fungal Rhizosphere Microbiome. Int J Mol Sci 2023; 24:15416. [PMID: 37895095 PMCID: PMC10607013 DOI: 10.3390/ijms242015416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/10/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Commercial formulations of beneficial microbes have been used to enrich the rhizosphere microbiome of tomato plants grown in pots located in a glasshouse. These plants have been subjected to attacks by soil-borne parasites, such as root-knot nematodes (RKNs), and herbivores, such as the miner insect Tuta absoluta. The development of both parasites and the symptoms of their parasitism were restricted in these plants with respect to plants left untreated. A mixture, named in the text as Myco, containing plant growth-promoting rhizobacteria (PGPR), opportunistic biocontrol fungi (BCF), and arbuscular mycorrhizal fungi (AMF) was more effective in limiting pest damage than a formulation containing the sole AMF (Ozor). Therefore, Myco-treated plants inoculated with RKNs were taken as a model for further studies. The PGPR contained in Myco were not able to reduce nematode infection; rather, they worsened symptoms in plants compared with those observed in untreated plants. Therefore, it was argued that both BCF and AMF were the microorganisms that colonized roots and stimulated the plant immune system against RKNs. Beneficial fungi colonized the roots by lowering the activities of the defense supporting enzymes endochitinases and β-1,3-glucanase. However, as early as three days after nematode inoculation, these enzyme activities and the expression of the encoding pathogenesis-related genes (PR-2, PR-3) were found to be enhanced in roots with respect to non-inoculated plants, thus indicating that plants had been primed against RKNs. The addition of paclobutrazol, which reduces salicylic acid (SA) levels in cells, and diphenyliodonium chloride, which inhibits superoxide generation, completely abolished the repressive effect of Myco on nematode infection. Inhibitors of copper enzymes and the alternative cyanide-resistant respiration did not significantly alter resistance induction by Myco. When Myco-treated plants were subjected to moderate water stress and inoculated with nematodes, they retained numbers of developed individuals in the roots similar to those present in regularly watered plants, in contrast to what occurred in roots of untreated stressed plants that hosted very few individuals because of poor nutrient availability.
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Affiliation(s)
- Sergio Molinari
- Institute for Sustainable Plant Protection, IPSP-Bari Unit, Department of Biology, Agricultural and Food Sciences, DISBA, National Council of Research, CNR, 70126 Bari, Italy;
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24
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Guo L, Zhang X, Zhao J, Zhang A, Pang Q. Enhancement of sulfur metabolism and antioxidant machinery confers Bacillus sp. Jrh14-10-induced alkaline stress tolerance in plant. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108063. [PMID: 37827044 DOI: 10.1016/j.plaphy.2023.108063] [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: 04/08/2023] [Revised: 07/11/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023]
Abstract
Alkaline stress is a major environmental challenge that restricts plant growth and agricultural productivity worldwide. Plant growth-promoting rhizobacteria (PGPR) can be used to effectively enhance plant abiotic stress in an environment-friendly manner. However, PGPR that can enhance alkalinity tolerance are not well-studied and the mechanisms by which they exert beneficial effects remain elusive. In this study, we isolated Jrh14-10 from the rhizosphere soil of halophyte Halerpestes cymbalaria (Pursh) Green and found that it can produce indole-3-acetic acid (IAA) and siderophore. By 16S rRNA gene sequencing, it was classified as Bacillus licheniformis. Inoculation Arabidopsis seedlings with Jrh14-10 significantly increased the total fresh weight (by 148.1%), primary root elongation (by 1121.7%), and lateral root number (by 108.8%) under alkaline stress. RNA-Seq analysis showed that 3389 genes were up-regulated by inoculation under alkaline stress and they were associated with sulfur metabolism, photosynthetic system, and oxidative stress response. Significantly, the levels of Cys and GSH were increased by 144.3% and 48.7%, respectively, in the inoculation group compared to the control under alkaline stress. Furthermore, Jrh14-10 markedly enhanced the activities of antioxidant enzymes, resulting in lower levels of O2•-, H2O2, and MDA as well as higher levels of Fv/Fm in alkaline-treated seedlings. In summary, Jrh14-10 can improve alkaline stress resistance in seedlings which was accompanied by an increase in sulfur metabolism-mediated GSH synthesis and antioxidant enzyme activities. These results provide a mechanistic understanding of the interactions between a beneficial bacterial strain and plants under alkaline stress.
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Affiliation(s)
- Lifeng Guo
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Xuchen Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, College of Life Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China
| | - Aiqin Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, People's Republic of China
| | - Qiuying Pang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, People's Republic of China.
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25
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Li J, Yang C, Jousset A, Yang K, Wang X, Xu Z, Yang T, Mei X, Zhong Z, Xu Y, Shen Q, Friman VP, Wei Z. Engineering multifunctional rhizosphere probiotics using consortia of Bacillus amyloliquefaciens transposon insertion mutants. eLife 2023; 12:e90726. [PMID: 37706503 PMCID: PMC10519709 DOI: 10.7554/elife.90726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Abstract
While bacterial diversity is beneficial for the functioning of rhizosphere microbiomes, multi-species bioinoculants often fail to promote plant growth. One potential reason for this is that competition between different species of inoculated consortia members creates conflicts for their survival and functioning. To circumvent this, we used transposon insertion mutagenesis to increase the functional diversity within Bacillus amyloliquefaciens bacterial species and tested if we could improve plant growth promotion by assembling consortia of highly clonal but phenotypically dissimilar mutants. While most insertion mutations were harmful, some significantly improved B. amyloliquefaciens plant growth promotion traits relative to the wild-type strain. Eight phenotypically distinct mutants were selected to test if their functioning could be improved by applying them as multifunctional consortia. We found that B. amyloliquefaciens consortium richness correlated positively with plant root colonization and protection from Ralstonia solanacearum phytopathogenic bacterium. Crucially, 8-mutant consortium consisting of phenotypically dissimilar mutants performed better than randomly assembled 8-mutant consortia, suggesting that improvements were likely driven by consortia multifunctionality instead of consortia richness. Together, our results suggest that increasing intra-species phenotypic diversity could be an effective way to improve probiotic consortium functioning and plant growth promotion in agricultural systems.
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Affiliation(s)
- Jingxuan Li
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Chunlan Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Alexandre Jousset
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Keming Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xiaofang Wang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zhihui Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Tianjie Yang
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Xinlan Mei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Zengtao Zhong
- College of Life Science, Nanjing Agricultural UniversityNanjingChina
| | - Yangchun Xu
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Qirong Shen
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
| | - Ville-Petri Friman
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
- Department of Microbiology, University of HelsinkiHelsinkiFinland
| | - Zhong Wei
- Key Lab of Organic-based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural UniversityNanjingChina
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26
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Wongdee J, Piromyou P, Songwattana P, Greetatorn T, Boonkerd N, Teaumroong N, Giraud E, Gully D, Nouwen N, Kiatponglarp W, Tanthanuch W, Tittabutr P. Exploring the cellular surface polysaccharide and root nodule symbiosis characteristics of the rpoN mutants of Bradyrhizobium sp. DOA9 using synchrotron-based Fourier transform infrared microspectroscopy in conjunction with X-ray absorption spectroscopy. Microbiol Spectr 2023; 11:e0194723. [PMID: 37681944 PMCID: PMC10581086 DOI: 10.1128/spectrum.01947-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/09/2023] [Indexed: 09/09/2023] Open
Abstract
The functional significance of rpoN genes that encode two sigma factors in the Bradyrhizobium sp. strain DOA9 has been reported to affect colony formation, root nodulation characteristics, and symbiotic interactions with Aeschynomene americana. rpoN mutant strains are defective in cellular surface polysaccharide (CSP) production compared with the wild-type (WT) strain, and they accordingly exhibit smaller colonies and diminished symbiotic effectiveness. To gain deeper insights into the changes in CSP composition and the nodules of rpoN mutants, we employed synchrotron-based Fourier transform infrared (SR-FTIR) microspectroscopy and X-ray absorption spectroscopy. FTIR analysis of the CSP revealed the absence of specific components in the rpoN mutants, including lipids, carboxylic groups, polysaccharide-pyranose rings, and β-galactopyranosyl residues. Nodules formed by DOA9WT exhibited a uniform distribution of lipids, proteins, and carbohydrates; mutant strains, particularly DOA9∆rpoNp:ΩrpoNc, exhibited decreased distribution uniformity and a lower concentration of C=O groups. Furthermore, Fe K-edge X-ray absorption near-edge structure and extended X-ray absorption fine structure analyses revealed deficiencies in the nitrogenase enzyme in the nodules of DOA9∆rpoNc and DOA9∆rpoNp:ΩrpoNc mutants; nodules from DOA9WT and DOA9∆rpoNp exhibited both leghemoglobin and the nitrogenase enzyme. IMPORTANCE This work provides valuable insights into how two rpoN genes affect the composition of cellular surface polysaccharides (CSPs) in Bradyrhizobium sp., which subsequently dictates root nodule chemical characteristics and nitrogenase production. We used advanced synchrotron methods, including synchrotron-based Fourier transform infrared (SR-FTIR) microspectroscopy and X-ray absorption spectroscopy (XAS), for the first time in this field to analyze CSP components and reveal the biochemical changes occurring within nodules. These cutting-edge techniques confer significant advantages by providing detailed molecular information, enabling the identification of specific functional groups, chemical bonds, and biomolecule changes. This research not only contributes to our understanding of plant-microbe interactions but also establishes a foundation for future investigations and potential applications in this field. The combined use of the synchrotron-based FTIR and XAS techniques represents a significant advancement in facilitating a comprehensive exploration of bacterial CSPs and their implications in plant-microbe interactions.
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Affiliation(s)
- Jenjira Wongdee
- Institute of Research and Development, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Pongdet Piromyou
- Institute of Research and Development, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Pongpan Songwattana
- Institute of Research and Development, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Teerana Greetatorn
- Institute of Research and Development, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Nantakorn Boonkerd
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
| | - Eric Giraud
- IRD, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Plant Health Institute of Montpellier, UMR-PHIM, Montpellier, France
| | - Djamel Gully
- IRD, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Plant Health Institute of Montpellier, UMR-PHIM, Montpellier, France
| | - Nico Nouwen
- IRD, IRD/CIRAD/INRAE/Université de Montpellier/SupAgro, Plant Health Institute of Montpellier, UMR-PHIM, Montpellier, France
| | - Worawikunya Kiatponglarp
- Thai wah public company limited @CU innovation hub, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Waraporn Tanthanuch
- Synchrotron Light Research Institute (Public Organization), Muang, Nakhon Ratchasima, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Muang, Nakhon Ratchasima, Thailand
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27
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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.
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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
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28
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ALAKUŞ TB. Classification of Microbes with Recurrent Neural Networks. FIRAT ÜNIVERSITESI MÜHENDISLIK BILIMLERI DERGISI 2023. [DOI: 10.35234/fumbd.1302903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Mikroplar insan vücudunun hem içinde hem de dışında yaşayan ve hemen hemen her yerde bulunan tek hücreli küçük canlılardır. Zararlı olabileceği gibi zararı olmayan mikroplarda bulunmaktadır. Bu yüzden mikroplar ekolojik dengenin sağlanmasında büyük bir rol üstlenmektedir. Ancak, bu mikropları birbirinden ayırt edebilmek çoğu zaman meşakkatli bir iş olmaktadır. Mikropların çeşitli özelliklerini anlayan ve taksonomi nüanslarını yorumlayabilen bir uzman bilgisinin gerekmesi ve laboratuvar ihtiyacının olması bu süreci hem maliyetli hem de zaman alıcı yapmaktadır. Bundan dolayı, bilgisayar destekli sistemlerin bu alanda önemi artmış ve günümüzde yapay zeka teknolojileri mikropların sınıflandırılmasında kullanılmaya başlanmıştır. Makine öğrenmesi ve derin öğrenme teknolojilerinin bu alana uygulanmasıyla yüksek seviyede doğruluk skorları elde edilmekte ve biyoçeşitlilikle ilgili değerlendirmeler otomatik bir şekilde yapılabilmektedir. Bu çalışmada da derin öğrenme modellerinden biri olan tekrarlayıcı sinir ağları yapıları kullanılarak, mikropların sınıflandırılması yapılmıştır. Çalışma dört aşamadan meydana gelmiştir. Birinci aşamada, veriler elde edilmiştir. İkinci aşamada bu veriler normalleştirme işlemine tabi tutulmuş ve önişlemden geçirilmiştir. Üçüncü aşamada UKSB ve TSA modelleri tasarlanmış ve sınıflandırılmıştır. Son aşamada ise sınıflandırıcıların performansları doğruluk, kesinlik, duyarlılık, F1-skor ve AUC skoru ile belirlenmiştir. Çalışmanın sonunda TSA sınıflandırıcısı ile %92.53, UKSB sınıflandırıcısıyla ise %99.85 doğruluk skoru elde edilmiştir.
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29
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Proietti S, Falconieri GS, Bertini L, Pascale A, Bizzarri E, Morales-Sanfrutos J, Sabidó E, Ruocco M, Monti MM, Russo A, Dziurka K, Ceci M, Loreto F, Caruso C. Beauveria bassiana rewires molecular mechanisms related to growth and defense in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4225-4243. [PMID: 37094092 PMCID: PMC10400115 DOI: 10.1093/jxb/erad148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/21/2023] [Indexed: 05/03/2023]
Abstract
Plant roots can exploit beneficial associations with soil-inhabiting microbes, promoting growth and expanding the immune capacity of the host plant. In this work, we aimed to provide new information on changes occurring in tomato interacting with the beneficial fungus Beauveria bassiana. The tomato leaf proteome revealed perturbed molecular pathways during the establishment of the plant-fungus relationship. In the early stages of colonization (5-7 d), proteins related to defense responses to the fungus were down-regulated and proteins related to calcium transport were up-regulated. At later time points (12-19 d after colonization), up-regulation of molecular pathways linked to protein/amino acid turnover and to biosynthesis of energy compounds suggests beneficial interaction enhancing plant growth and development. At the later stage, the profile of leaf hormones and related compounds was also investigated, highlighting up-regulation of those related to plant growth and defense. Finally, B. bassiana colonization was found to improve plant resistance to Botrytis cinerea, impacting plant oxidative damage. Overall, our findings further expand current knowledge on the possible mechanisms underlying the beneficial role of B. bassiana in tomato plants.
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Affiliation(s)
- Silvia Proietti
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Gaia Salvatore Falconieri
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Laura Bertini
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Alberto Pascale
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Elisabetta Bizzarri
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Julia Morales-Sanfrutos
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, Carrer Dr Aiguader 88, 08003 Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica, Barcelona Institute of Science and Technology (BIST), Carrer Dr. Aiguader 88, 08003 Barcelona, Spain
- Proteomics Unit, Universitat Pompeu Fabra, Carrer Dr Aiguader 88, 08003 Barcelona, Spain
| | - Michelina Ruocco
- Institute for Sustainable Plant Protection (IPSP-CNR), Piazzale Enrico Fermi, 1, 80055 Portici (NA), Italy
| | - Maurilia M Monti
- Institute for Sustainable Plant Protection (IPSP-CNR), Piazzale Enrico Fermi, 1, 80055 Portici (NA), Italy
| | - Assunta Russo
- Institute for Sustainable Plant Protection (IPSP-CNR), Piazzale Enrico Fermi, 1, 80055 Portici (NA), Italy
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy
| | - Kinga Dziurka
- Department of Biotechnology, The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Marcello Ceci
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
| | - Francesco Loreto
- Department of Biology, Via Cinthia, University of Naples Federico II, 80126, Naples, Italy
| | - Carla Caruso
- Department of Ecological and Biological Sciences, University of Tuscia, largo dell’Università snc, 01100 Viterbo, Italy
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30
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Martins SJ, Pasche J, Silva HAO, Selten G, Savastano N, Abreu LM, Bais HP, Garrett KA, Kraisitudomsook N, Pieterse CMJ, Cernava T. The Use of Synthetic Microbial Communities to Improve Plant Health. PHYTOPATHOLOGY 2023; 113:1369-1379. [PMID: 36858028 DOI: 10.1094/phyto-01-23-0016-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.
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Affiliation(s)
- Samuel J Martins
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | - Josephine Pasche
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | - Hiago Antonio O Silva
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Gijs Selten
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Noah Savastano
- Department of Plant and Soil Sciences, 311 AP Biopharma, University of Delaware, Newark, DE 19713, U.S.A
| | - Lucas Magalhães Abreu
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Harsh P Bais
- Department of Plant and Soil Sciences, 311 AP Biopharma, University of Delaware, Newark, DE 19713, U.S.A
| | - Karen A Garrett
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | | | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8020, Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, U.K
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Tsai HH, Wang J, Geldner N, Zhou F. Spatiotemporal control of root immune responses during microbial colonization. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102369. [PMID: 37141807 DOI: 10.1016/j.pbi.2023.102369] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/23/2023] [Accepted: 03/29/2023] [Indexed: 05/06/2023]
Abstract
The entire evolutionary trajectory of plants towards large and complex multi-cellular organisms has been accompanied by incessant interactions with omnipresent unicellular microbes. This led to the evolution of highly complex microbial communities, whose members display the entire spectrum of pathogenic to mutualistic behaviors. Plant roots are dynamic, fractally growing organs and even small Arabidopsis roots harbor millions of individual microbes of diverse taxa. It is evident that microbes at different positions on a root surface could experience fundamentally different environments, which, moreover, rapidly change over time. Differences in spatial scales between microbes and roots compares to humans and the cities they inhabit. Such considerations make it evident that mechanisms of root-microbe interactions can only be understood if analyzed at relevant spatial and temporal scales. This review attempts to provide an overview of the rapid recent progress that has been made in mapping and manipulating plant damage and immune responses at cellular resolution, as well as in visualizing bacterial communities and their transcriptional activities. We further discuss the impact that such approaches will have for a more predictive understanding of root-microbe interactions.
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Affiliation(s)
- Huei-Hsuan Tsai
- Department of Plant Molecular Biology, Biophore, UNIL-Sorge, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jiachang Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Niko Geldner
- Department of Plant Molecular Biology, Biophore, UNIL-Sorge, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Feng Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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Verbon EH, Liberman LM, Zhou J, Yin J, Pieterse CMJ, Benfey PN, Stringlis IA, de Jonge R. Cell-type-specific transcriptomics reveals that root hairs and endodermal barriers play important roles in beneficial plant-rhizobacterium interactions. MOLECULAR PLANT 2023; 16:1160-1177. [PMID: 37282370 PMCID: PMC10527033 DOI: 10.1016/j.molp.2023.06.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 03/30/2023] [Accepted: 06/01/2023] [Indexed: 06/08/2023]
Abstract
Growth- and health-promoting bacteria can boost crop productivity in a sustainable way. Pseudomonas simiae WCS417 is such a bacterium that efficiently colonizes roots, modifies the architecture of the root system to increase its size, and induces systemic resistance to make plants more resistant to pests and pathogens. Our previous work suggested that WCS417-induced phenotypes are controlled by root cell-type-specific mechanisms. However, it remains unclear how WCS417 affects these mechanisms. In this study, we transcriptionally profiled five Arabidopsis thaliana root cell types following WCS417 colonization. We found that the cortex and endodermis have the most differentially expressed genes, even though they are not in direct contact with this epiphytic bacterium. Many of these genes are associated with reduced cell wall biogenesis, and mutant analysis suggests that this downregulation facilitates WCS417-driven root architectural changes. Furthermore, we observed elevated expression of suberin biosynthesis genes and increased deposition of suberin in the endodermis of WCS417-colonized roots. Using an endodermal barrier mutant, we showed the importance of endodermal barrier integrity for optimal plant-beneficial bacterium association. Comparison of the transcriptome profiles in the two epidermal cell types that are in direct contact with WCS417-trichoblasts that form root hairs and atrichoblasts that do not-implies a difference in potential for defense gene activation. While both cell types respond to WCS417, trichoblasts displayed both higher basal and WCS417-dependent activation of defense-related genes compared with atrichoblasts. This suggests that root hairs may activate root immunity, a hypothesis that is supported by differential immune responses in root hair mutants. Taken together, these results highlight the strength of cell-type-specific transcriptional profiling to uncover "masked" biological mechanisms underlying beneficial plant-microbe associations.
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Affiliation(s)
- Eline H Verbon
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands
| | - Louisa M Liberman
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | - Jiayu Zhou
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands
| | - Jie Yin
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands
| | - Philip N Benfey
- Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA
| | - Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands; Laboratory of Plant Pathology, Agricultural University of Athens, 75 Iera Odos str., 11855 Athens, Greece.
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB Utrecht, the Netherlands.
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King E, Wallner A, Guigard L, Rimbault I, Parrinello H, Klonowska A, Moulin L, Czernic P. Paraburkholderia phytofirmans PsJN colonization of rice endosphere triggers an atypical transcriptomic response compared to rice native Burkholderia s.l. endophytes. Sci Rep 2023; 13:10696. [PMID: 37400579 DOI: 10.1038/s41598-023-37314-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023] Open
Abstract
The plant microbiome has recently emerged as a reservoir for the development of sustainable alternatives to chemical fertilizers and pesticides. However, the response of plants to beneficial microbes emerges as a critical issue to understand the molecular basis of plant-microbiota interactions. In this study, we combined root colonization, phenotypic and transcriptomic analyses to unravel the commonalities and specificities of the response of rice to closely related Burkholderia s.l. endophytes. In general, these results indicate that a rice-non-native Burkholderia s.l. strain, Paraburkholderia phytofirmans PsJN, is able to colonize the root endosphere while eliciting a markedly different response compared to rice-native Burkholderia s.l. strains. This demonstrates the variability of plant response to microbes from different hosts of origin. The most striking finding of the investigation was that a much more conserved response to the three endophytes used in this study is elicited in leaves compared to roots. In addition, transcriptional regulation of genes related to secondary metabolism, immunity, and phytohormones appear to be markers of strain-specific responses. Future studies need to investigate whether these findings can be extrapolated to other plant models and beneficial microbes to further advance the potential of microbiome-based solutions for crop production.
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Affiliation(s)
- Eoghan King
- Plant Health Institute of Montpellier, IRD, CIRAD, University of Montpellier, l'Institut Agro, Montpellier, France.
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain.
| | - Adrian Wallner
- Plant Health Institute of Montpellier, IRD, CIRAD, University of Montpellier, l'Institut Agro, Montpellier, France
- SFR Condorcet - FR CNRS 3417, University of Reims Champagne-Ardenne, Induced Resistance and Plant Bioprotection (RIBP) - EA 4707, Cedex 2, BP1039, 51687, Reims, France
| | - Ludivine Guigard
- Plant Health Institute of Montpellier, IRD, CIRAD, University of Montpellier, l'Institut Agro, Montpellier, France
| | - Isabelle Rimbault
- Plant Health Institute of Montpellier, IRD, CIRAD, University of Montpellier, l'Institut Agro, Montpellier, France
| | - Hugues Parrinello
- Montpellier GenomiX (MGX), c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Agnieszka Klonowska
- Plant Health Institute of Montpellier, IRD, CIRAD, University of Montpellier, l'Institut Agro, Montpellier, France
| | - Lionel Moulin
- Plant Health Institute of Montpellier, IRD, CIRAD, University of Montpellier, l'Institut Agro, Montpellier, France
| | - Pierre Czernic
- Plant Health Institute of Montpellier, IRD, CIRAD, University of Montpellier, l'Institut Agro, Montpellier, France.
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Wicaksono WA, Semler B, Pöltl M, Berg C, Berg G, Cernava T. The microbiome of Riccia liverworts is an important reservoir for microbial diversity in temporary agricultural crusts. ENVIRONMENTAL MICROBIOME 2023; 18:46. [PMID: 37264474 DOI: 10.1186/s40793-023-00501-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/10/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND The microbiota of liverworts provides an interesting model for plant symbioses; however, their microbiome assembly is not yet understood. Here, we assessed specific factors that shape microbial communities associated with Riccia temporary agricultural crusts in harvested fields by investigating bacterial, fungal and archaeal communities in thalli and adhering soil from different field sites in Styria and Burgenland, Austria combining qPCR analyses, amplicon sequencing and advanced microscopy. RESULTS Riccia spec. div. was colonized by a very high abundance of bacteria (1010 16S rRNA gene copies per g of thallus) as well as archaea and fungi (108 ITS copies per g of thallus). Each Riccia thallus contain approx. 1000 prokaryotic and fungal ASVs. The field type was the main driver for the enrichment of fungal taxa, likely due to an imprint on soil microbiomes by the cultivated crop plants. This was shown by a higher fungal richness and different fungal community compositions comparing liverwort samples collected from pumpkin fields, with those from corn fields. In contrast, bacterial communities linked to liverworts are highly specialized and the soil attached to them is not a significant source of these bacteria. Specifically, enriched Cyanobacteria, Bacteroidetes and Methylobacteria suggest a symbiotic interaction. Intriguingly, compared to the surrounding soil, the thallus samples were shown to enrich several well-known bacterial and fungal phytopathogens indicating an undescribed role of liverworts as potential reservoirs of crop pathogens. CONCLUSIONS Our results provide evidence that a stable bacterial community but varying fungal communities are colonizing liverwort thalli. Post-harvest, temporary agricultural biocrusts are important reservoirs for microbial biodiversity but they have to be considered as potential reservoirs for pathogens as well.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Bettina Semler
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Martina Pöltl
- Institute of Biology, University of Graz, Graz, 8010, Austria
| | - Christian Berg
- Institute of Biology, University of Graz, Graz, 8010, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.
- Graz University of Technology, Graz, Austria.
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35
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Nio SA, Mantilen Ludong DP. Beneficial Root-Associated Microbiome during Drought and Flooding Stress in Plants. Pak J Biol Sci 2023; 26:287-299. [PMID: 37859559 DOI: 10.3923/pjbs.2023.287.299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Crop productivity is seriously threatened by the rise in the frequency and severity of drought and flood events around the world. Reduced drought and flooding stress in vulnerable species and ecosystems depends on our ability to comprehend how drought and flooding affect plant physiology and plant-associated microbes. Involvement of both abscisic acid ABA-dependent and ABA-independent pathways has been noted during drought. Hypoxic conditions impede hydraulic conductance, nutrient uptake and plant growth and development, as well as root aerobic respiration. The root microbiome, which works with the roots during drought and flood, is made up of plant growth-promoting rhizosphere, endophytes and mycorrhizas. A large number of phytohormones, primarily auxins, cytokinin and ethylene, as well as enzymes like 1-Aminocyclopropane-1-Carboxylate deaminase (ACC deaminase) and metabolites like exopolysaccharides are produced by rhizospheric microbes. These phytohormones, enzymes and metabolites have role in the induction of systemic drought tolerance in plants. Under hypoxia, anaerobic microbes with the potential to harm the plant due to their pathogenic behavior or soil denitrification ability are more likely to be present in the rhizosphere and roots. This review concentrates on the primary mechanisms of plant-microbe interactions under drought and flood stress as well as the importance of flood and drought-tolerant microbes in maintaining and increasing crop plant productivity under stress.
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Anderson AJ, Hortin JM, Jacobson AR, Britt DW, McLean JE. Changes in Metal-Chelating Metabolites Induced by Drought and a Root Microbiome in Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:1209. [PMID: 36986899 PMCID: PMC10055107 DOI: 10.3390/plants12061209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
The essential metals Cu, Zn, and Fe are involved in many activities required for normal and stress responses in plants and their microbiomes. This paper focuses on how drought and microbial root colonization influence shoot and rhizosphere metabolites with metal-chelation properties. Wheat seedlings, with and without a pseudomonad microbiome, were grown with normal watering or under water-deficit conditions. At harvest, metal-chelating metabolites (amino acids, low molecular weight organic acids (LMWOAs), phenolic acids, and the wheat siderophore) were assessed in shoots and rhizosphere solutions. Shoots accumulated amino acids with drought, but metabolites changed little due to microbial colonization, whereas the active microbiome generally reduced the metabolites in the rhizosphere solutions, a possible factor in the biocontrol of pathogen growth. Geochemical modeling with the rhizosphere metabolites predicted Fe formed Fe-Ca-gluconates, Zn was mainly present as ions, and Cu was chelated with the siderophore 2'-deoxymugineic acid, LMWOAs, and amino acids. Thus, changes in shoot and rhizosphere metabolites caused by drought and microbial root colonization have potential impacts on plant vigor and metal bioavailability.
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Affiliation(s)
- Anne J. Anderson
- Department of Biological Engineering, Utah State University, Logan, UT 84322, USA
| | - Joshua M. Hortin
- Utah Water Research Laboratory, Department of Civil and Environmental Engineering, Utah State University, Logan, UT 84322, USA
| | - Astrid R. Jacobson
- Department of Plants, Soils, and Climate, Utah State University, Logan, UT 84322, USA
| | - David W. Britt
- Department of Biological Engineering, Utah State University, Logan, UT 84322, USA
| | - Joan E. McLean
- Utah Water Research Laboratory, Department of Civil and Environmental Engineering, Utah State University, Logan, UT 84322, USA
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37
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Astragalus-cultivated soil was a suitable bed soil for nurturing Angelica sinensis seedlings from the rhizosphere microbiome perspective. Sci Rep 2023; 13:3388. [PMID: 36854968 PMCID: PMC9974959 DOI: 10.1038/s41598-023-30549-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
Angelica sinensis (Oliv.) Diels is an important Chinese medicinal plant. A. sinensis seedlings are grown on an undisturbed alpine meadow soil to ensure the high-quality seedlings, but these soils are disappearing year after year. Thus, selecting a suitable bed soil for A. sinensis seedlings could ensure their long-term sustainability. Using HiSeq sequencing of 16S and 18S marker genes, we investigated the rhizosphere bacterial and fungal microbiotas of the seedlings grown in wheat, astragalus, potato, and angelica-cultivated soils at a geo-authentic habitat. Co-occurrence network analysis, canonical correspondence analysis, Mantel test, and Envfit test were used to examine the relationship between the microbiotas and the surrounding factors. Astragalus-cultivated soils exhibited the following properties: the highest plant weight, the highest neighborhood connectivity in the bacterial network, the highest ratio of positive/negative relationship in both bacterial and fungal networks, the highest relative abundance of the arbuscular mycorrhizal fungi and the ectomycorrhizal fungi, the lowest relative abundance of Rhizoctonia solani, the suitable soil pH, and the close relationship between the rhizosphere microbiotas and the ecological factors. Moreover, each growth stage has its own major drivers in all crop-cultivated soils. Climate temperature and soil pH at 56 days after planting, precipitation at 98 days, and plant weight as well as microbial biomass C and N at 129 days were the major drivers of the bacterial and fungal microbiotas. Overall, the astragalus-cultivated soil was a suitable bed soil for nurturing A. sinensis seedlings to replace the undisturbed alpine meadow soils.
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Üstüner S, Schäfer P, Eichmann R. Development specifies, diversifies and empowers root immunity. EMBO Rep 2022; 23:e55631. [PMID: 36330761 PMCID: PMC9724680 DOI: 10.15252/embr.202255631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/10/2022] [Accepted: 10/13/2022] [Indexed: 08/04/2023] Open
Abstract
Roots are a highly organised plant tissue consisting of different cell types with distinct developmental functions defined by cell identity networks. Roots are the target of some of the most devastating diseases and possess a highly effective immune system. The recognition of microbe- or plant-derived molecules released in response to microbial attack is highly important in the activation of complex immunity gene networks. Development and immunity are intertwined, and immunity activation can result in growth inhibition. In turn, by connecting immunity and cell identity regulators, cell types are able to launch a cell type-specific immunity based on the developmental function of each cell type. By this strategy, fundamental developmental processes of each cell type contribute their most basic functions to drive cost-effective but highly diverse and, thus, efficient immune responses. This review highlights the interdependence of root development and immunity and how the developmental age of root cells contributes to positive and negative outcomes of development-immunity cross-talk.
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Affiliation(s)
- Sim Üstüner
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
| | - Ruth Eichmann
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and NutritionJustus Liebig UniversityGiessenGermany
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Zhou Y, Pang Z, Yuan Z, Fallah N, Jia H, Ming R. Sex-based metabolic and microbiota differences in roots and rhizosphere soils of dioecious papaya ( Carica papaya L.). FRONTIERS IN PLANT SCIENCE 2022; 13:991114. [PMID: 36311075 PMCID: PMC9612958 DOI: 10.3389/fpls.2022.991114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Dioecious plant species have a high genetic variation that is important for coping with or adapting to environmental stress through natural selection. Intensive studies have reported dimorphism morphism in morphology, physiology, as well as biotic and abiotic stress responses in dioecious plants. Here, we demonstrated the dimorphism of metabolic profile and the preference of some microorganisms in the roots and rhizosphere soils of male and female papaya. The metabolic composition of roots were significantly different between the males and females. Some sex hormones occurred in the differential metabolites in roots and rhizosphere soils. For example, testosterone was up-regulated in male papaya roots and rhizosphere soils, whereas norgestrel was up-regulated in the female papaya roots, indicating a possible balance in papaya roots to control the sexual differentiation. Plant hormones such as BRs, JAs, SA and GAs were also detected among the differential metabolites in the roots and rhizosphere soils of dioecious papaya. In addition, some metabolites that have medicinal values, such as ecliptasaponin A, crocin, berberine and sapindoside A were also expressed differentially between the two sexes. Numerous differential metabolites from the papaya roots were secreted in the soil, resulting in the differences in microbial community structure in the roots and rhizosphere soils. Some nitrogen-fixing bacteria such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Brevundimonas and Microvirga were enriched in the male papaya roots or rhizosphere soils. While Candidatus Solibacter and Tumebacillus, which utilize organic matters, were enriched in the roots or rhizosphere soils of the female papaya. Some differences in the fungi abundance were also observed in both male and female papaya roots. These findings uncovered the effect of sex types on the metabolic and microbiota differences in roots and rhizosphere soils in papaya and will lead to investigations of underlining genomic and molecular mechanisms.
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Affiliation(s)
- Yongmei Zhou
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ziqin Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhaonian Yuan
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Nyumah Fallah
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haifeng Jia
- FAFU and UIUC Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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40
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Plant-Endophyte Interaction during Biotic Stress Management. PLANTS 2022; 11:plants11172203. [PMID: 36079585 PMCID: PMC9459794 DOI: 10.3390/plants11172203] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 01/19/2023]
Abstract
Plants interact with diverse microbial communities and share complex relationships with each other. The intimate association between microbes and their host mutually benefit each other and provide stability against various biotic and abiotic stresses to plants. Endophytes are heterogeneous groups of microbes that live inside the host tissue without showing any apparent sign of infection. However, their functional attributes such as nutrient acquisition, phytohormone modulation, synthesis of bioactive compounds, and antioxidant enzymes of endophytes are similar to the other rhizospheric microorganisms. Nevertheless, their higher colonization efficacy and stability against abiotic stress make them superior to other microorganisms. In recent studies, the potential role of endophytes in bioprospecting has been broadly reported. However, the molecular aspect of host–endophyte interactions is still unclear. In this study, we have briefly discussed the endophyte biology, colonization efficacy and diversity pattern of endophytes. In addition, it also summarizes the molecular aspect of plant–endophyte interaction in biotic stress management.
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41
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Riaz M, Akhtar N, Msimbira LA, Antar M, Ashraf S, Khan SN, Smith DL. Neocosmospora rubicola, a stem rot disease in potato: Characterization, distribution and management. Front Microbiol 2022; 13:953097. [PMID: 36033873 PMCID: PMC9403868 DOI: 10.3389/fmicb.2022.953097] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
Potato (Solanum tuberosum L.) is one of the most important crops in maintaining global food security. Plant stand and yield are affected by production technology, climate, soil type, and biotic factors such as insects and diseases. Numerous fungal diseases including Neocosmospora rubicola, causing stem rot, are known to have negative effects on potato growth and yield quality. The pathogen is known to stunt growth and cause leaf yellowing with grayish-black stems. The infectivity of N. rubicola across a number of crops indicates the need to search for appropriate management approaches. Synthetic pesticides application is a major method to mitigate almost all potato diseases at this time. However, these pesticides significantly contribute to environmental damage and continuous use leads to pesticide resistance by pathogens. Consumers interest in organic products have influenced agronomists to shift toward the use of biologicals in controlling most pathogens, including N. rubicola. This review is an initial effort to carefully examine current and alternative approaches to control N. rubicola that are both environmentally safe and ecologically sound. Therefore, this review aims to draw attention to the N. rubicola distribution and symptomatology, and sustainable management strategies for potato stem rot disease. Applications of plant growth promoting bacteria (PGPB) as bioformulations with synthetic fertilizers have the potential to increase the tuber yield in both healthy and N. rubicola infested soils. Phosphorus and nitrogen applications along with the PGPB can improve plants uptake efficiency and reduce infestation of pathogen leading to increased yield. Therefore, to control N. rubicola infestation, with maximum tuber yield benefits, a pre-application of the biofertilizer is shown as a better option, based on the most recent studies. With the current limited information on the disease, precise screening of the available resistant potato cultivars, developing molecular markers for resistance genes against N. rubicola will assist to reduce spread and virulence of the pathogen.
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Affiliation(s)
- Muhammad Riaz
- Department of Plant Pathology, University of the Punjab, Lahore, Pakistan
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Naureen Akhtar
- Department of Plant Pathology, University of the Punjab, Lahore, Pakistan
- Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
| | | | - Mohammed Antar
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Shoaib Ashraf
- Department of Animal Science, McGill University, Montreal, QC, Canada
| | - Salik Nawaz Khan
- Department of Plant Pathology, University of the Punjab, Lahore, Pakistan
| | - Donald L. Smith
- Department of Plant Science, McGill University, Montreal, QC, Canada
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42
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Dutilloy E, Oni FE, Esmaeel Q, Clément C, Barka EA. Plant Beneficial Bacteria as Bioprotectants against Wheat and Barley Diseases. J Fungi (Basel) 2022; 8:jof8060632. [PMID: 35736115 PMCID: PMC9225584 DOI: 10.3390/jof8060632] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 02/07/2023] Open
Abstract
Wheat and barley are the main cereal crops cultivated worldwide and serve as staple food for a third of the world's population. However, due to enormous biotic stresses, the annual production has significantly reduced by 30-70%. Recently, the accelerated use of beneficial bacteria in the control of wheat and barley pathogens has gained prominence. In this review, we synthesized information about beneficial bacteria with demonstrated protection capacity against major barley and wheat pathogens including Fusarium graminearum, Zymoseptoria tritici and Pyrenophora teres. By summarizing the general insights into molecular factors involved in plant-pathogen interactions, we show to an extent, the means by which beneficial bacteria are implicated in plant defense against wheat and barley diseases. On wheat, many Bacillus strains predominantly reduced the disease incidence of F. graminearum and Z. tritici. In contrast, on barley, the efficacy of a few Pseudomonas, Bacillus and Paraburkholderia spp. has been established against P. teres. Although several modes of action were described for these strains, we have highlighted the role of Bacillus and Pseudomonas secondary metabolites in mediating direct antagonism and induced resistance against these pathogens. Furthermore, we advance a need to ascertain the mode of action of beneficial bacteria/molecules to enhance a solution-based crop protection strategy. Moreover, an apparent disjoint exists between numerous experiments that have demonstrated disease-suppressive effects and the translation of these successes to commercial products and applications. Clearly, the field of cereal disease protection leaves a lot to be explored and uncovered.
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Maize (Zea mays L.) genotypes induce the changes of rhizosphere microbial communities. Arch Microbiol 2022; 204:321. [PMID: 35567648 DOI: 10.1007/s00203-022-02934-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 11/02/2022]
Abstract
Plant-microbe interactions affect ecosystem function, and plant species influence relevant microorganisms. However, the different genotypes of maize that shape the structure and function of the rhizosphere microbial community remain poorly investigated. During this study, the structures of the rhizosphere microbial community among three genotypes of maize were analyzed at the seedling and maturity stages using high-throughput sequencing and bioinformatics analysis. The results demonstrated that Tiannuozao 60 (N) showed higher bacterial and fungal diversity in both periods, while Junlong1217 (QZ) and Fujitai519 (ZL) had lower diversity. The bacterial community structure among the three varieties was significantly different; however, fewer differences were found in the fungal community. The bacterial community composition of N and QZ was similar yet different from ZL at the seedling stage. The bacterial networks of the three cultivars were more complex than the fungal networks, and the networks of the mature stages were more complex than those of the seedling stages, while the opposite was true for the fungi. FAPROTAX functional and FUNGuild functional predictions revealed that different varieties of maize were different in functional abundance at the genus level, and these differences were related to breeding characteristics. This study suggested that different maize genotypes regulated the rhizosphere bacterial and fungal communities, which would help guide practices.
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Li H, Shi H, Xu P, Yu D. Metabolomics and microbiome reveal potential root microbiota affecting the alkaloidal metabolome in Aconitum vilmorinianum Kom. BMC Microbiol 2022; 22:70. [PMID: 35264111 PMCID: PMC8905797 DOI: 10.1186/s12866-022-02486-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/03/2022] [Indexed: 12/23/2022] Open
Abstract
Background The plant microbiome is vital for plant health, fitness, and productivity. Interestingly, plant metabolites and the plant microbiome can influence each other. The combination of metabolomics and microbiome may reveal the critical links between the plant and its microbiome. It is of great significance to agricultural production and human health, especially for Chinese medicine research. Aconitum vilmorinianum Kom. is a herb with alkaloid activities, and its roots are the raw material for some Chinese medicines. Former studies have investigated alkaloidal metabolites and antibacterial activities of endophytes in A. vilmorinianum roots. However, there are limited reports on the root microbiota that can influence the alkaloidal metabolome of A. vilmorinianum. Results This research used ultra performance liquid chromatography-tandem mass spectrometry technology and high-throughput sequencing to examine the alkaloidal metabolome, bacterial microbiota, and fungal microbiota in A. vilmorinianum roots at two different sites in China. The results revealed that the samples from the two sites were rich in distinct alkaloidal metabolites and recruited significantly different root microbiota. Based on bioinformatics analysis, we found the potential bacterial and fungal microbiota impacting the alkaloidal metabolome in A. vilmorinianum. Conclusion Our findings reveal the composition of the alkaloidal metabolome, bacterial root microbiota, and fungal root microbiota in A. vilmorinianum roots at two different sites. Potential root microbiota that can influence the alkaloidal metabolome of A. vilmorinianum are indicated. This study provides a strategy for the cultivation and research of A. vilmorinianum and other Chinese herbs. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02486-1.
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Affiliation(s)
- Hongrui Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongdi Shi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Diqiu Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China.
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Gilbert S, Poulev A, Chrisler W, Acosta K, Orr G, Lebeis S, Lam E. Auxin-Producing Bacteria from Duckweeds Have Different Colonization Patterns and Effects on Plant Morphology. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060721. [PMID: 35336603 PMCID: PMC8950272 DOI: 10.3390/plants11060721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/30/2022] [Accepted: 02/20/2022] [Indexed: 05/30/2023]
Abstract
The role of auxin in plant-microbe interaction has primarily been studied using indole-3-acetic acid (IAA)-producing pathogenic or plant-growth-promoting bacteria. However, the IAA biosynthesis pathway in bacteria involves indole-related compounds (IRCs) and intermediates with less known functions. Here, we seek to understand changes in plant response to multiple plant-associated bacteria taxa and strains that differ in their ability to produce IRCs. We had previously studied 47 bacterial strains isolated from several duckweed species and determined that 79% of these strains produced IRCs in culture, such as IAA, indole lactic acid (ILA), and indole. Using Arabidopsis thaliana as our model plant with excellent genetic tools, we performed binary association assays on a subset of these strains to evaluate morphological responses in the plant host and the mode of bacterial colonization. Of the 21 tested strains, only four high-quantity IAA-producing Microbacterium strains caused an auxin root phenotype. Compared to the commonly used colorimetric Salkowski assay, auxin concentration determined by LC-MS was a superior indicator of a bacteria's ability to cause an auxin root phenotype. Studies with the auxin response mutant axr1-3 provided further genetic support for the role of auxin signaling in mediating the root morphology response to IAA-producing bacteria strains. Interestingly, our microscopy results also revealed new evidence for the role of the conserved AXR1 gene in endophytic colonization of IAA-producing Azospirillum baldaniorum Sp245 via the guard cells.
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Affiliation(s)
- Sarah Gilbert
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
| | - Alexander Poulev
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
| | - William Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA; (W.C.); (G.O.)
| | - Kenneth Acosta
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA; (W.C.); (G.O.)
| | - Sarah Lebeis
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Eric Lam
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, USA; (S.G.); (A.P.); (K.A.)
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Madriz-Ordeñana K, Pazarlar S, Jørgensen HJL, Nielsen TK, Zhang Y, Nielsen KL, Hansen LH, Thordal-Christensen H. The Bacillus cereus Strain EC9 Primes the Plant Immune System for Superior Biocontrol of Fusarium oxysporum. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050687. [PMID: 35270157 PMCID: PMC8912794 DOI: 10.3390/plants11050687] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 05/08/2023]
Abstract
Antibiosis is a key feature widely exploited to develop biofungicides based on the ability of biological control agents (BCAs) to produce fungitoxic compounds. A less recognised attribute of plant-associated beneficial microorganisms is their ability to stimulate the plant immune system, which may provide long-term, systemic self-protection against different types of pathogens. By using conventional antifungal in vitro screening coupled with in planta assays, we found antifungal and non-antifungal Bacillus strains that protected the ornamental plant Kalanchoe against the soil-borne pathogen Fusarium oxysporum in experimental and commercial production settings. Further examination of one antifungal and one non-antifungal strain indicated that high protection efficacy in planta did not correlate with antifungal activity in vitro. Whole-genome sequencing showed that the non-antifungal strain EC9 lacked the biosynthetic gene clusters associated with typical antimicrobial compounds. Instead, this bacterium triggers the expression of marker genes for the jasmonic and salicylic acid defence pathways, but only after pathogen challenge, indicating that this strain may protect Kalanchoe plants by priming immunity. We suggest that the stimulation of the plant immune system is a promising mode of action of BCAs for the development of novel biological crop protection products.
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Affiliation(s)
- Kenneth Madriz-Ordeñana
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Plant and Soil Science, University of Copenhagen, 1871 Frederiksberg, Denmark; (S.P.); (H.J.L.J.); (Y.Z.); (H.T.-C.)
- Correspondence:
| | - Sercan Pazarlar
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Plant and Soil Science, University of Copenhagen, 1871 Frederiksberg, Denmark; (S.P.); (H.J.L.J.); (Y.Z.); (H.T.-C.)
| | - Hans Jørgen Lyngs Jørgensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Plant and Soil Science, University of Copenhagen, 1871 Frederiksberg, Denmark; (S.P.); (H.J.L.J.); (Y.Z.); (H.T.-C.)
| | - Tue Kjærgaard Nielsen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Microbial Ecology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark; (T.K.N.); (L.H.H.)
| | - Yingqi Zhang
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Plant and Soil Science, University of Copenhagen, 1871 Frederiksberg, Denmark; (S.P.); (H.J.L.J.); (Y.Z.); (H.T.-C.)
| | | | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Microbial Ecology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark; (T.K.N.); (L.H.H.)
| | - Hans Thordal-Christensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Section for Plant and Soil Science, University of Copenhagen, 1871 Frederiksberg, Denmark; (S.P.); (H.J.L.J.); (Y.Z.); (H.T.-C.)
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Bagautdinova ZZ, Omelyanchuk N, Tyapkin AV, Kovrizhnykh VV, Lavrekha VV, Zemlyanskaya EV. Salicylic Acid in Root Growth and Development. Int J Mol Sci 2022; 23:ijms23042228. [PMID: 35216343 PMCID: PMC8875895 DOI: 10.3390/ijms23042228] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
In plants, salicylic acid (SA) is a hormone that mediates a plant’s defense against pathogens. SA also takes an active role in a plant’s response to various abiotic stresses, including chilling, drought, salinity, and heavy metals. In addition, in recent years, numerous studies have confirmed the important role of SA in plant morphogenesis. In this review, we summarize data on changes in root morphology following SA treatments under both normal and stress conditions. Finally, we provide evidence for the role of SA in maintaining the balance between stress responses and morphogenesis in plant development, and also for the presence of SA crosstalk with other plant hormones during this process.
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Affiliation(s)
- Zulfira Z. Bagautdinova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
| | - Nadya Omelyanchuk
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
| | - Aleksandr V. Tyapkin
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Vasilina V. Kovrizhnykh
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
| | - Viktoriya V. Lavrekha
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (Z.Z.B.); (N.O.); (A.V.T.); (V.V.K.); (V.V.L.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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Zhang M, Kong X. How plants discern friends from foes. TRENDS IN PLANT SCIENCE 2022; 27:107-109. [PMID: 34785124 DOI: 10.1016/j.tplants.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Microbial-associated molecular pattern (MAMP)-triggered immunity (MTI) is a well-known plant innate immune response to pathogens. Plant commensal microbes have evolved a variety of strategies to interfere with or bypass MTI to establish symbiosis. Recent progress reported by Teixeira et al., Colaianni et al., Zhang et al., Fröschel et al., and Zhou et al. has been made in elucidating how commensal microbes regulate MTI.
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Affiliation(s)
- Mengyue Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, 266237, Shandong, China
| | - Xiangpei Kong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, College of Life Sciences, Shandong University, Qingdao, 266237, Shandong, China.
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Oni FE, Esmaeel Q, Onyeka JT, Adeleke R, Jacquard C, Clement C, Gross H, Ait Barka E, Höfte M. Pseudomonas Lipopeptide-Mediated Biocontrol: Chemotaxonomy and Biological Activity. Molecules 2022; 27:372. [PMID: 35056688 PMCID: PMC8777863 DOI: 10.3390/molecules27020372] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Pseudomonas lipopeptides (Ps-LPs) play crucial roles in bacterial physiology, host-microbe interactions and plant disease control. Beneficial LP producers have mainly been isolated from the rhizosphere, phyllosphere and from bulk soils. Despite their wide geographic distribution and host range, emerging evidence suggests that LP-producing pseudomonads and their corresponding molecules display tight specificity and follow a phylogenetic distribution. About a decade ago, biocontrol LPs were mainly reported from the P. fluorescens group, but this has drastically advanced due to increased LP diversity research. On the one hand, the presence of a close-knit relationship between Pseudomonas taxonomy and the molecule produced may provide a startup toolbox for the delineation of unknown LPs into existing (or novel) LP groups. Furthermore, a taxonomy-molecule match may facilitate decisions regarding antimicrobial activity profiling and subsequent agricultural relevance of such LPs. In this review, we highlight and discuss the production of beneficial Ps-LPs by strains situated within unique taxonomic groups and the lineage-specificity and coevolution of this relationship. We also chronicle the antimicrobial activity demonstrated by these biomolecules in limited plant systems compared with multiple in vitro assays. Our review further stresses the need to systematically elucidate the roles of diverse Ps-LP groups in direct plant-pathogen interactions and in the enhancement of plant innate immunity.
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Affiliation(s)
- Feyisara Eyiwumi Oni
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
- Department of Biological Sciences, Faculty of Science, Anchor University, Ayobo P.M.B 00001, Lagos State, Nigeria
- Unit for Environmental Sciences and Management, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2520, South Africa;
| | - Qassim Esmaeel
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Joseph Tobias Onyeka
- Plant Pathology Unit, National Root Crops Research Institute (NRCRI), Umudike 440001, Abia State, Nigeria;
| | - Rasheed Adeleke
- Unit for Environmental Sciences and Management, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2520, South Africa;
| | - Cedric Jacquard
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Christophe Clement
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tubingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany;
| | - Essaid Ait Barka
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium;
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50
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Bakker PAHM, Berendsen RL. The soil-borne ultimatum, microbial biotechnology and sustainable agriculture. Microb Biotechnol 2022; 15:84-87. [PMID: 34628714 PMCID: PMC8719802 DOI: 10.1111/1751-7915.13947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 11/28/2022] Open
Affiliation(s)
- Peter A H M Bakker
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
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