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Meena M, Nagda A, Mehta T, Yadav G, Sonigra P. Mechanistic basis of the symbiotic signaling pathway between the host and the pathogen. PLANT-MICROBE INTERACTION - RECENT ADVANCES IN MOLECULAR AND BIOCHEMICAL APPROACHES 2023:375-387. [DOI: 10.1016/b978-0-323-91875-6.00001-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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Patra D, Mandal S. Non-rhizobia are the alternative sustainable solution for growth and development of the nonlegume plants. Biotechnol Genet Eng Rev 2022:1-30. [PMID: 36471635 DOI: 10.1080/02648725.2022.2152623] [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: 08/20/2022] [Accepted: 11/13/2022] [Indexed: 12/12/2022]
Abstract
The major research focus for biological nitrogen fixation (BNF) has mostly been on typical rhizobia with legumes. But the newly identified non-rhizobial bacteria, both individually or in combination could also be an alternative for nitrogen supplementation in both legumes and nonlegume plants. Although about 90% of BNF is derived from a legume - rhizobia symbiosis, the non-legumes specially the cereals lack canonical nitrogen fixation system through root-nodule organogenesis. The non-rhizobia may colonize in the rhizosphere or present in endophytic/associative nature. The non-rhizobia are well known for facilitating plant growth through their potential to alleviate various stresses (salt, drought, and pathogens), acquisition of minerals (P, K, etc.), or by producing phytohormones. Bacterial symbiosis in non-legumes represents by the Gram-positive Frankia having a major contribution in overall fortification of usable nitrogenous material in soil where they are associated with their hosts. This review discusses the recent updates on the diversity and association of the non-rhizobial species and their impact on the growth and productivity of their host plants with particular emphasis on major economically important cereal plants. The future application possibilities of non-rhizobia for soil fertility and plant growth enhancement for sustainable agriculture have been discussed.
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Affiliation(s)
- Dipanwita Patra
- Department of Microbiology, University of Calcutta, Kolkata, India
| | - Sukhendu Mandal
- Department of Microbiology, University of Calcutta, Kolkata, India
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Jiang X, Pees T, Reinhold-Hurek B. Deep-learning-based removal of autofluorescence and fluorescence quantification in plant-colonizing bacteria in vivo. THE NEW PHYTOLOGIST 2022; 235:2481-2495. [PMID: 35752974 DOI: 10.1111/nph.18344] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Fluorescence microscopy is common in bacteria-plant interaction studies. However, strong autofluorescence from plant tissues impedes in vivo studies on endophytes tagged with fluorescent proteins. To solve this problem, we developed a deep-learning-based approach to eliminate plant autofluorescence from fluorescence microscopy images, tested for the model endophyte Azoarcus olearius BH72 colonizing Oryza sativa roots. Micrographs from three channels (tdTomato for gene expression, green fluorescent protein (GFP) and AutoFluorescence (AF)) were processed by a neural network based approach, generating images that simulate the background autofluorescence in the tdTomato channel. After subtracting the model-generated signals from each pixel in the genuine channel, the autofluorescence in the tdTomato channel was greatly reduced or even removed. The deep-learning-based approach can be applied for fluorescence detection and quantification, exemplified by a weakly expressed, a cell-density modulated and a nitrogen-fixation gene in A. olearius. A transcriptional nifH::tdTomato fusion demonstrated stronger induction of nif genes inside roots than outside, suggesting extension of the rhizosphere effect for diazotrophs into the endorhizosphere. The pre-trained convolutional neural network model is easily applied to process other images of the same plant tissues with the same settings. This study showed the high potential of deep-learning-based approaches in image processing. With proper training data and strategies, autofluorescence in other tissues or materials can be removed for broad applications.
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Affiliation(s)
- Xun Jiang
- Department of Microbe-Plant Interactions, CBIB Center for Biomolecular Interactions, Faculty of Biology and Chemistry, University of Bremen, PO Box 33 04 40, D-28334, Bremen, Germany
| | - Tobias Pees
- Department of Microbe-Plant Interactions, CBIB Center for Biomolecular Interactions, Faculty of Biology and Chemistry, University of Bremen, PO Box 33 04 40, D-28334, Bremen, Germany
| | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, CBIB Center for Biomolecular Interactions, Faculty of Biology and Chemistry, University of Bremen, PO Box 33 04 40, D-28334, Bremen, Germany
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Hernández-Álvarez C, García-Oliva F, Cruz-Ortega R, Romero MF, Barajas HR, Piñero D, Alcaraz LD. Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 805:150136. [PMID: 34818799 DOI: 10.1016/j.scitotenv.2021.150136] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 05/10/2023]
Abstract
Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N = 48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The β-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. By 16S and shotgun metagenomics, we identified dry-associated taxa such as Cellvibrio, Ensifer adhaerens, and Streptomyces flavovariabilis. With shotgun metagenomic sequencing of rhizospheres (N = 6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.
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Affiliation(s)
- Cristóbal Hernández-Álvarez
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico; Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Mexico
| | - Rocío Cruz-Ortega
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Miguel F Romero
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Hugo R Barajas
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico
| | - Luis D Alcaraz
- Laboratorio de Genómica Ambiental, Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico.
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Mukherjee A. What do we know from the transcriptomic studies investigating the interactions between plants and plant growth-promoting bacteria? FRONTIERS IN PLANT SCIENCE 2022; 13:997308. [PMID: 36186072 PMCID: PMC9521398 DOI: 10.3389/fpls.2022.997308] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/02/2022] [Indexed: 05/21/2023]
Abstract
Major crops such as corn, wheat, and rice can benefit from interactions with various plant growth-promoting bacteria (PGPB). Naturally, several studies have investigated the primary mechanisms by which these PGPB promote plant growth. These mechanisms involve biological nitrogen fixation, phytohormone synthesis, protection against biotic and abiotic stresses, etc. Decades of genetic and biochemical studies in the legume-rhizobia symbiosis and arbuscular mycorrhizal symbiosis have identified a few key plant and microbial signals regulating these symbioses. Furthermore, genetic studies in legumes have identified the host genetic pathways controlling these symbioses. But, the same depth of information does not exist for the interactions between host plants and PGPB. For instance, our knowledge of the host genes and the pathways involved in these interactions is very poor. However, some transcriptomic studies have investigated the regulation of gene expression in host plants during these interactions in recent years. In this review, we discuss some of the major findings from these studies and discuss what lies ahead. Identifying the genetic pathway(s) regulating these plant-PGPB interactions will be important as we explore ways to improve crop production sustainably.
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Santoyo G. How plants recruit their microbiome? New insights into beneficial interactions. J Adv Res 2021; 40:45-58. [PMID: 36100333 PMCID: PMC9481936 DOI: 10.1016/j.jare.2021.11.020] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
Plant-microbiome interaction occurs at the rhizosphere, endosphere, and phyllosphere. Root exudates can favor the recruitment of a beneficial microbiome in the rhizosphere. Plant topology and phytochemistry influence the recruitment of the phyllosphere microbiome. Diverse plant strategies selectively recruit beneficial microbiomes. Multiple plant mechanisms displace potential pathogens from the rhizosphere. The beneficial microbiome helps plants to recruit other beneficial microbiota.
Background Research on beneficial mechanisms by plant-associated microbiomes, such as plant growth stimulation and protection from plant pathogens, has gained considerable attention over the past decades; however, the mechanisms used by plants to recruit their microbiome is largely unknown. Aim of Review Here, we review the latest studies that have begun to reveal plant strategies in selectively recruiting beneficial microbiomes, and how they manage to exclude potential pathogens. Key Scientific concepts of Review: We examine how plants attract beneficial microbiota from the main areas of interaction, such as the rhizosphere, endosphere, and phyllosphere, and demonstrate that such process occurs by producing root exudates, and recognizing molecules produced by the beneficial microbiota or distinguishing pathogens using specific receptors, or by triggering signals that support plant-microbiome homeostasis. Second, we analyzed the main environmental or biotic factors that modulate the structure and successional dynamics of microbial communities. Finally, we review how the associated microbiome is capable of engaging with other synergistic microbes, hence providing an additional element of selection. Collectively, this study reveals the importance of understanding the complex network of plant interactions, which will improve the understanding of bioinoculant application in agriculture, based on a microbiome that interacts efficiently with plant organs under different environmental conditions.
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Affiliation(s)
- Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, 58030 Morelia, Mexico.
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Pankievicz VCS, do Amaral FP, Ané JM, Stacey G. Diazotrophic Bacteria and Their Mechanisms to Interact and Benefit Cereals. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:491-498. [PMID: 33543986 DOI: 10.1094/mpmi-11-20-0316-fi] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plant-growth-promoting bacteria (PGPB) stimulate plant growth through diverse mechanisms. In addition to biological nitrogen fixation, diazotrophic PGPB can improve nutrient uptake efficiency from the soil, produce and release phytohormones to the host, and confer resistance against pathogens. The genetic determinants that drive the success of biological nitrogen fixation in nonlegume plants are understudied. These determinants include recognition and signaling pathways, bacterial colonization, and genotype specificity between host and bacteria. This review presents recent discoveries of how nitrogen-fixing PGPB interact with cereals and promote plant growth. We suggest adopting an experimental model system, such as the Setaria-diazotrophic bacteria association, as a reliable way to better understand the associated mechanisms and, ultimately, increase the use of PGPB inoculants for sustainable agriculture.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
| | - Fernanda Plucani do Amaral
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, U.S.A
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, U.S.A
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Valette M, Rey M, Doré J, Gerin F, Wisniewski-Dyé F. Identification of a small set of genes commonly regulated in rice roots in response to beneficial rhizobacteria. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2537-2551. [PMID: 33424163 PMCID: PMC7772126 DOI: 10.1007/s12298-020-00911-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
Rhizosphere bacteria, whether phytopathogenic or phytobeneficial, are thought to be perceived by the plant as a threat. Plant Growth-Promoting Rhizobacteria (PGPR), such as many strains of the Azospirillum genus known as the main phytostimulator of cereals, cooperate with host plants and favorably affect their growth and health. An earlier study of rice root transcriptome, undertaken with two rice cultivars and two Azospirillum strains, revealed a strain-dependent response during the rice-Azospirillum association and showed that only a few genes, including some implicated in plant defense, were commonly regulated in all tested conditions. Here, a set of genes was selected from previous studies and their expression was monitored by qRT-PCR in rice roots inoculated with ten PGPR strains isolated from various plants and belonging to various genera (Azospirillum, Herbaspirillum, Paraburkholderia). A common expression pattern was highlighted for four genes that are proposed to be markers of the rice-PGPR interaction: two genes involved in diterpenoid phytoalexin biosynthesis (OsDXS3 and OsDTC2) and one coding for an uncharacterized protein (Os02g0582900) were significantly induced by PGPR whereas one defense-related gene encoding a pathogenesis-related protein (PR1b, Os01g0382000) was significantly repressed. Interestingly, exposure to a rice bacterial pathogen also triggered the expression of OsDXS3 while the expression of Os02g0582900 and PR1b was down-regulated, suggesting that these genes might play a key role in rice-bacteria interactions. Integration of these results with previous data led us to propose that the jasmonic acid signaling pathway might be triggered in rice roots upon inoculation with PGPR.
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Affiliation(s)
- Marine Valette
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Marjolaine Rey
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Jeanne Doré
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Florence Gerin
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
| | - Florence Wisniewski-Dyé
- Ecologie Microbienne, CNRS UMR-5557, INRAe UMR-1418, VetAgroSup, Université de Lyon, Université Lyon1, 16 rue Dubois, 69622 Villeurbanne, France
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Sun K, Zhang W, Yuan J, Song SL, Wu H, Tang MJ, Xu FJ, Xie XG, Dai CC. Nitrogen fertilizer-regulated plant-fungi interaction is related to root invertase-induced hexose generation. FEMS Microbiol Ecol 2020; 96:5869223. [PMID: 32643762 DOI: 10.1093/femsec/fiaa139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/08/2020] [Indexed: 11/13/2022] Open
Abstract
The mechanisms underlying nitrogen (N)-regulated plant-fungi interactions are not well understood. N application modulates plant carbohydrate (C) sinks and is involved in the overall plant-fungal association. We hypothesized that N regulates plant-fungi interactions by influencing the carbohydrate metabolism. The mutualistic fungus Phomopsis liquidambaris was found to prioritize host hexose resources through in vitro culture assays and in planta inoculation. Rice-Ph. liquidambaris systems were exposed to N gradients ranging from N-deficient to N-abundant conditions to study whether and how the sugar composition was involved in the dynamics of N-mediated fungal colonization. We found that root soluble acid invertases were activated, resulting in increased hexose fluxes in inoculated roots. These fluxes positively influenced fungal colonization, especially under N-deficient conditions. Further experiments manipulating the carbohydrate composition and root invertase activity through sugar feeding, chemical treatments and the use of different soil types revealed that the external disturbance of root invertase could reduce endophytic colonization and eliminate endophyte-induced host benefits under N-deficient conditions. Collectively, these results suggest that the activation of root invertase is related to N deficiency-enhanced endophytic colonization via increased hexose generation. Certain combinations of farmland ecosystems with suitable N inputs could be implemented to maximize the benefits of plant-fungi associations.
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Affiliation(s)
- Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Jie Yuan
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Shi-Li Song
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Hao 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, China
| | - Meng-Jun Tang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Fang-Ji Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Xing-Guang Xie
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Jiangsu Province, China
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Zuccaro A, Langen G. Breeding for resistance: can we increase crop resistance to pathogens without compromising the ability to accommodate beneficial microbes? THE NEW PHYTOLOGIST 2020; 227:279-282. [PMID: 32445486 DOI: 10.1111/nph.16610] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 04/09/2020] [Indexed: 05/26/2023]
Affiliation(s)
- Alga Zuccaro
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
| | - Gregor Langen
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
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Bünger W, Jiang X, Müller J, Hurek T, Reinhold-Hurek B. Novel cultivated endophytic Verrucomicrobia reveal deep-rooting traits of bacteria to associate with plants. Sci Rep 2020; 10:8692. [PMID: 32457320 PMCID: PMC7251102 DOI: 10.1038/s41598-020-65277-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/30/2020] [Indexed: 02/01/2023] Open
Abstract
Despite the relevance of complex root microbial communities for plant health, growth and productivity, the molecular basis of these plant-microbe interactions is not well understood. Verrucomicrobia are cosmopolitans in the rhizosphere, nevertheless their adaptations and functions are enigmatic since the proportion of cultured members is low. Here we report four cultivated Verrucomicrobia isolated from rice, putatively representing four novel species, and a novel subdivision. The aerobic strains were isolated from roots or rhizomes of Oryza sativa and O. longistaminata. Two of them are the first cultivated endophytes of Verrucomicrobia, as validated by confocal laser scanning microscopy inside rice roots after re-infection under sterile conditions. This extended known verrucomicrobial niche spaces. Two strains were promoting root growth of rice. Discovery of root compartment-specific Verrucomicrobia permitted an across-phylum comparison of the genomic conformance to life in soil, rhizoplane or inside roots. Genome-wide protein domain comparison with niche-specific reference bacteria from distant phyla revealed signature protein domains which differentiated lifestyles in these microhabitats. Our study enabled us to shed light into the dark microbial matter of root Verrucomicrobia, to define genetic drivers for niche adaptation of bacteria to plant roots, and provides cultured strains for revealing causal relationships in plant-microbe interactions by reductionist approaches.
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Affiliation(s)
- Wiebke Bünger
- Department of Microbe-Plant Interactions, University of Bremen, Bremen, Germany
| | - Xun Jiang
- Department of Microbe-Plant Interactions, University of Bremen, Bremen, Germany
| | - Jana Müller
- Department of Microbe-Plant Interactions, University of Bremen, Bremen, Germany.,Department of Botany, University of Bremen, Bremen, Germany
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, University of Bremen, Bremen, Germany
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Chen X, Marszałkowska M, Reinhold-Hurek B. Jasmonic Acid, Not Salicyclic Acid Restricts Endophytic Root Colonization of Rice. FRONTIERS IN PLANT SCIENCE 2020; 10:1758. [PMID: 32063914 PMCID: PMC7000620 DOI: 10.3389/fpls.2019.01758] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/16/2019] [Indexed: 05/20/2023]
Abstract
Research on the interaction between the non-nodule-forming bacterial endophytes and their host plants is still in its infancy. Especially the understanding of plant control mechanisms which govern endophytic colonization is very limited. The current study sets out to determine which hormonal signaling pathway controls endophytic colonization in rice, and whether the mechanisms deviate for a pathogen. The endophyte Azoarcus olearius BH72-rice model was used to investigate root responses to endophytes in comparison to the recently established pathosystem of rice blight Xanthomonas oryzae pv. oryzae PXO99 (Xoo) in flooded roots. In the rice root transcriptome, 523 or 664 genes were found to be differentially expressed in response to Azoarcus or Xoo colonization, respectively; however, the response was drastically different, with only 6% of the differentially expressed genes (DEGs) overlapping. Overall, Xoo infection induced a much stronger defense reaction than Azoarcus colonization, with the latter leading to down-regulation of many defense related DEGs. Endophyte-induced DEGs encoded several enzymes involved in phytoalexin biosynthesis, ROS (reactive oxygen species) production, or pathogenesis-related (PR) proteins. Among putative plant markers related to signal transduction pathways modulated exclusively during Azoarcus colonization, none overlapped with previously published DEGs identified for another rice endophyte, Azospirillum sp. B510. This suggests a large variation in responses of individual genotypic combinations. Interestingly, the DEGs related to jasmonate (JA) signaling pathway were found to be consistently activated by both beneficial endophytes. In contrast, the salicylate (SA) pathway was activated only in roots infected by the pathogen. To determine the impact of SA and JA production on root colonization by the endophyte and the pathogen, rice mutants with altered hormonal responses were employed: mutant cpm2 deficient in jasmonate synthesis, and RNA interference (RNAi) knockdown lines of NPR1 decreased in salicylic acid-mediated defense responses (NPR1-kd). Only in cpm2, endophytic colonization of Azoarcus was significantly increased, while Xoo colonization was not affected. Surprisingly, NPR1-kd lines showed slightly decreased colonization by Xoo, contrary to published results for leaves. These outcomes suggest that JA but not SA signaling is involved in controlling the Azoarcus endophyte density in roots and can restrict internal root colonization, thereby shaping the beneficial root microbiome.
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Affiliation(s)
| | | | - Barbara Reinhold-Hurek
- Department of Microbe-Plant Interactions, Faculty of Biology and Chemistry, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, Bremen, Germany
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13
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Xie S, Yu H, Wang Q, Cheng Y, Ding T. Two rapid and sensitive methods based on TaqMan qPCR and droplet digital PCR assay for quantitative detection of Bacillus subtilis in rhizosphere. J Appl Microbiol 2019; 128:518-527. [PMID: 31602754 DOI: 10.1111/jam.14481] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/22/2019] [Accepted: 10/04/2019] [Indexed: 01/03/2023]
Abstract
AIMS Bacillus subtilis, a typical plant growth-promoting rhizobacteria, can benefit plant through promoting growth and reducing disease. The colonization intensity of B. subtilis in rhizosphere is a key factor for improving their effectiveness of field application. In this study, we developed a rapid and sensitive method for detecting B. subtilis in rhizosphere via TaqMan qPCR and droplet digital PCR (ddPCR) methods. METHODS AND RESULTS The primers/probe set targeting gyrB gene could successfully distinguish B. subtilis from its close-related species. Both the TaqMan qPCR and ddPCR methods exhibited a good linear relationship in the sensitivity assay, suggesting the developed method was specific, effective and reliable. Finally, the two methods were used to detect the colonization dynamic of B. subtilis within Arabidopsis rhizosphere. Both of them showed a consistent trend compared with the traditional cultivation-based and microscopy-based methods. CONCLUSIONS The TaqMan qPCR and droplet digital PCR (ddPCR) methods we developed could be used to rapidly detect B. subtilis in rhizosphere. SIGNIFICANCE AND IMPACT OF THE STUDY The TaqMan qPCR and ddPCR methods developed in this study can be applied to rapid quantitative detection of B. subtilis populations, and will be helpful to evaluate their effectiveness of field application.
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Affiliation(s)
- Shanshan Xie
- The National Key Engineering Lab of Crop Stress Resistance Breeding, College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Hengguo Yu
- The National Key Engineering Lab of Crop Stress Resistance Breeding, College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Qi Wang
- College of Plant protection, Anhui Agricultural University, Hefei, China
| | - Yifeng Cheng
- The National Key Engineering Lab of Crop Stress Resistance Breeding, College of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Ting Ding
- College of Plant protection, Anhui Agricultural University, Hefei, China
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Wu Q, Peng X, Yang M, Zhang W, Dazzo FB, Uphoff N, Jing Y, Shen S. Rhizobia promote the growth of rice shoots by targeting cell signaling, division and expansion. PLANT MOLECULAR BIOLOGY 2018; 97:507-523. [PMID: 30083951 DOI: 10.1007/s11103-018-0756-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 06/29/2018] [Indexed: 05/11/2023]
Abstract
The growth-promotion of rice seedling following inoculation with Sinorhizobium meliloti 1021 was a cumulative outcome of elevated expression of genes that function in accelerating cell division and enhancing cell expansion. Various endophytic rhizobacteria promote the growth of cereal crops. To achieve a better understanding of the cellular and molecular bases of beneficial cereal-rhizobia interactions, we performed computer-assisted microscopy and transcriptomic analyses of rice seedling shoots (Oryza sativa) during early stages of endophytic colonization by the plant growth-promoting Sinorhizobium meliloti 1021. Phenotypic analyses revealed that plants inoculated with live rhizobia had increased shoot height and dry weight compared to control plants inoculated with heat-killed cells of the same microbe. At 6 days after inoculation (DAI) with live cells, the fourth-leaf sheaths showed significant cytological differences including their enlargement of parenchyma cells and reduction in shape complexity. Transcriptomic analysis of shoots identified 2,414 differentially-expressed genes (DEGs) at 1, 2, 5 and 8 DAI: 195, 1390, 1025 and 533, respectively. Among these, 46 DEGs encoding cell-cycle functions were up-regulated at least 3 days before the rhizobia ascended from the roots to the shoots, suggesting that rhizobia are engaged in long-distance signaling events during early stages of this plant-microbe interaction. DEGs involved in phytohormone production, photosynthetic efficiency, carbohydrate metabolism, cell division and wall expansion were significantly elevated at 5 and 8 DAI, consistent with the observed phenotypic changes in rice cell morphology and shoot growth-promotion. Correlation analysis identified 104 height-related DEGs and 120 dry-weight-related DEGs that represent known quantitative-trait loci for seedling vigor and increased plant height. These findings provide multiple evidences of plant-microbe interplay that give insight into the growth-promotion processes associated with this rhizobia-rice beneficial association.
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Affiliation(s)
- Qingqing Wu
- Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Xianjun Peng
- Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Mingfeng Yang
- Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- College of Biotechnology, Beijing University of Agriculture, Beijing, 102206, China
| | - Wenpeng Zhang
- Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Frank B Dazzo
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Norman Uphoff
- SRI International Network and Resources Center (SRI-Rice), Cornell University, Ithaca, NY, 14853, USA
| | - Yuxiang Jing
- Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
| | - Shihua Shen
- Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.
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Konishi N, Okubo T, Yamaya T, Hayakawa T, Minamisawa K. Nitrate Supply-Dependent Shifts in Communities of Root-Associated Bacteria in Arabidopsis. Microbes Environ 2017; 32:314-323. [PMID: 29187692 PMCID: PMC5745015 DOI: 10.1264/jsme2.me17031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Root-associated bacterial communities are necessary for healthy plant growth. Nitrate is a signal molecule as well as a major nitrogen source for plant growth. In this study, nitrate-dependent alterations in root-associated bacterial communities and the relationship between nitrate signaling and root-associated bacteria in Arabidopsis were examined. The bacterial community was analyzed by a ribosomal RNA intergenic spacer analysis (RISA) and 16S rRNA amplicon sequencing. The Arabidopsis root-associated bacterial community shifted depending on the nitrate amount and timing of nitrate application. The relative abundance of operational taxonomic units of 25.8% was significantly changed by the amount of nitrate supplied. Moreover, at the family level, the relative abundance of several major root-associated bacteria including Burkholderiaceae, Paenibacillaceae, Bradyrhizobiaceae, and Rhizobiaceae markedly fluctuated with the application of nitrate. These results suggest that the application of nitrate strongly affects root-associated bacterial ecosystems in Arabidopsis. Bulk soil bacterial communities were also affected by the application of nitrate; however, these changes were markedly different from those in root-associated bacteria. These results also suggest that nitrate-dependent alterations in root-associated bacterial communities are mainly affected by plant-derived factors in Arabidopsis. T-DNA insertion plant lines of the genes for two transcription factors involved in nitrate signaling in Arabidopsis roots, NLP7 and TCP20, showed similar nitrate-dependent shifts in root-associated bacterial communities from the wild-type, whereas minor differences were observed in root-associated bacteria. Thus, these results indicate that NLP7 and TCP20 are not major regulators of nitrate-dependent bacterial communities in Arabidopsis roots.
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Affiliation(s)
- Noriyuki Konishi
- Graduate School of Agricultural Science, Tohoku University.,Division for Interdisciplinary Advanced Research and Education, Tohoku University
| | - Takashi Okubo
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization
| | - Tomoyuki Yamaya
- Division for Interdisciplinary Advanced Research and Education, Tohoku University
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Kandel SL, Joubert PM, Doty SL. Bacterial Endophyte Colonization and Distribution within Plants. Microorganisms 2017; 5:E77. [PMID: 29186821 PMCID: PMC5748586 DOI: 10.3390/microorganisms5040077] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/21/2017] [Accepted: 11/23/2017] [Indexed: 11/16/2022] Open
Abstract
The plant endosphere contains a diverse group of microbial communities. There is general consensus that these microbial communities make significant contributions to plant health. Both recently adopted genomic approaches and classical microbiology techniques continue to develop the science of plant-microbe interactions. Endophytes are microbial symbionts residing within the plant for the majority of their life cycle without any detrimental impact to the host plant. The use of these natural symbionts offers an opportunity to maximize crop productivity while reducing the environmental impacts of agriculture. Endophytes promote plant growth through nitrogen fixation, phytohormone production, nutrient acquisition, and by conferring tolerance to abiotic and biotic stresses. Colonization by endophytes is crucial for providing these benefits to the host plant. Endophytic colonization refers to the entry, growth and multiplication of endophyte populations within the host plant. Lately, plant microbiome research has gained considerable attention but the mechanism allowing plants to recruit endophytes is largely unknown. This review summarizes currently available knowledge about endophytic colonization by bacteria in various plant species, and specifically discusses the colonization of maize plants by Populus endophytes.
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Affiliation(s)
| | | | - Sharon L. Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA; (S.L.K.); (P.M.J.)
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17
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Lehnert H, Serfling A, Enders M, Friedt W, Ordon F. Genetics of mycorrhizal symbiosis in winter wheat (Triticum aestivum). THE NEW PHYTOLOGIST 2017; 215:779-791. [PMID: 28517039 DOI: 10.1111/nph.14595] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/30/2017] [Indexed: 05/23/2023]
Abstract
Bread wheat (Triticum aestivum) is a major staple food and therefore of prime importance for feeding the Earth's growing population. Mycorrhiza is known to improve plant growth, but although extensive knowledge concerning the interaction between mycorrhizal fungi and plants is available, genotypic differences concerning the ability of wheat to form mycorrhizal symbiosis and quantitative trait loci (QTLs) involved in mycorrhization are largely unknown. Therefore, a diverse set of 94 bread wheat genotypes was evaluated with regard to root colonization by arbuscular mycorrhizal fungi. In order to identify genomic regions involved in mycorrhization, these genotypes were analyzed using the wheat 90k iSelect chip, resulting in 17 823 polymorphic mapped markers, which were used in a genome-wide association study. Significant genotypic differences (P < 0.0001) were detected in the ability to form symbiosis and 30 significant markers associated with root colonization, representing six QTL regions, were detected on chromosomes 3A, 4A and 7A, and candidate genes located in these QTL regions were proposed. The results reported here provide key insights into the genetics of root colonization by mycorrhizal fungi in wheat.
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Affiliation(s)
- Heike Lehnert
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Albrecht Serfling
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Matthias Enders
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
| | - Wolfgang Friedt
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Gießen, Germany
| | - Frank Ordon
- Julius Kühn-Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484, Quedlinburg, Germany
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18
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Guha S, Sarkar M, Ganguly P, Uddin MR, Mandal S, DasGupta M. Segregation of nod-containing and nod-deficient bradyrhizobia as endosymbionts of Arachis hypogaea and as endophytes of Oryza sativa in intercropped fields of Bengal Basin, India. Environ Microbiol 2016; 18:2575-90. [PMID: 27102878 DOI: 10.1111/1462-2920.13348] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 04/17/2016] [Indexed: 11/30/2022]
Abstract
Bradyrhizobial invasion in dalbergoid legumes like Arachis hypogaea and endophytic bacterial invasions in non-legumes like Oryza sativa occur through epidermal cracks. Here, we show that there is no overlap between the bradyrhizobial consortia that endosymbiotically and endophytically colonise these plants. To minimise contrast due to phylogeographic isolation, strains were collected from Arachis/Oryza intercropped fields and a total of 17 bradyrhizobia from Arachis (WBAH) and 13 from Oryza (WBOS) were investigated. 16SrRNA and concatenated dnaK-glnII-recA phylogeny clustered the nodABC-positive WBAH and nodABC-deficient WBOS strains in two distinct clades. The in-field segregation is reproducible under controlled conditions which limits the factors that influence their competitive exclusion. While WBAH renodulated Arachis successfully, WBOS nodulated in an inefficient manner. Thus, Arachis, like other Aeschynomene legumes support nod-independent symbiosis that was ineffectual in natural fields. In Oryza, WBOS recolonised endophytically and promoted its growth. WBAH however caused severe chlorosis that was completely overcome when coinfected with WBOS. This explains the exclusive recovery of WBOS in Oryza in natural fields and suggests Nod-factors to have a role in counterselection of WBAH. Finally, canonical soxY1 and thiosulphate oxidation could only be detected in WBOS indicating loss of metabolic traits in WBAH with adaptation of symbiotic lifestyle.
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Affiliation(s)
- Sohini Guha
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Monolina Sarkar
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Pritha Ganguly
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
| | - Md Raihan Uddin
- Department of Microbiology, University of Calcutta, Kolkata, 700019, India
| | - Sukhendu Mandal
- Department of Microbiology, University of Calcutta, Kolkata, 700019, India
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata, 700019, India
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