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Tyagi R, Pradhan S, Bhattacharjee A, Dubey S, Sharma S. Management of abiotic stresses by microbiome-based engineering of the rhizosphere. J Appl Microbiol 2022; 133:254-272. [PMID: 35352450 DOI: 10.1111/jam.15552] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/27/2022] [Accepted: 03/22/2022] [Indexed: 11/30/2022]
Abstract
Abiotic stresses detrimentally affect both plant and soil health, threatening food security in an ever-increasing world population. Sustainable agriculture is necessary to augment crop yield with simultaneous management of stresses. Limitations of conventional bioinoculants has shifted the focus on more effective alternatives. With the realisation of the potential of rhizospheric microbiome engineering in enhancing plant's fitness under stresses, efforts have accelerated in this direction. Though still in its infancy, microbiome-based engineering has gained popularity because of its advantages over microbe-based approach. This review briefly presents major abiotic stresses afflicting arable land, followed by introduction to the conventional approach of microbe-based enhancement of plant attributes and stress mitigation with its inherent limitations. It then focusses on the significance of rhizospheric microbiome, and harnessing its potential by its strategic engineering for stress management. Further, success stories related to two major approaches of microbiome engineering (generation of synthetic microbial community/consortium, and host-mediated artificial selection) pertaining to stress management have been critically presented. Together with bringing forth the challenges associated with wide application of rhizospheric microbiome engineering in agriculture, the review proposes the adoption of combinatorial scheme for the same, bringing together ecological and reductionist approaches for improvised sustainable agricultural practices.
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Affiliation(s)
- Rashi Tyagi
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Salila Pradhan
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Annapurna Bhattacharjee
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Shubham Dubey
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
| | - Shilpi Sharma
- Department of Biochemical Engineering and, Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi
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2
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Duan S, Declerck S, Zhang L, Feng G. Two-component system in Rahnella aquatilis is impacted by the hyphosphere of the arbuscular mycorrhizal fungus Rhizophagus irregularis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:119-129. [PMID: 34951128 DOI: 10.1111/1758-2229.13039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Two-component systems (TCS) are ubiquitous among bacteria, playing key roles in signalling events. However, to what extent the TCS of Rahnella aquatilis (a Phosphate solubilizing bacteria) is influenced by the hyphosphere of the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis is totally unknown. Here, the expression of 16 genes encoding the TCS of R. aquatilis (i.e. involved in carbon-sensing and nutrient-sensing) and of eight genes regulated by the PhoR TCS (i.e. involved in inorganic and organic phosphorus mobilization) were analysed at regular intervals in presence of hyphae of R. irregularis. The study was conducted under in vitro culture conditions with phytate as the unique source of phosphorus. In presence of the AM fungus, the expression of TCS genes involved in carbon-sensing and nutrient-sensing were stimulated. Only, BaeS at 30 and 120 min, and BaeR at 60 min were inhibited. In addition, the PhoR TCS stimulated the expression of genes encoding phosphatase but inhibited the expression of genes involved in gluconic acid production. As the mechanism of coupling environmental changes with cellular physiological changes, TCS plays a pivotal role in regulating specific gene expression in R. aquatilis, recognizing environmental signals. More importantly, TCS genes may regulate bacteria response to hyphal carbon to mobilize phosphorus efficiently in the hyphosphere.
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Affiliation(s)
- Shilong Duan
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 10093, China
| | - Stéphane Declerck
- Université Catholique de Louvain, Earth and Life Institute, Applied Microbiology, Mycology, Croix du Sud 2, bte L7.05.06, Louvain-la-Neuve, B-1348, Belgium
| | - Lin Zhang
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 10093, China
| | - Gu Feng
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 10093, China
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3
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Understanding Phytomicrobiome: A Potential Reservoir for Better Crop Management. SUSTAINABILITY 2020. [DOI: 10.3390/su12135446] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent crop production studies have aimed at an increase in the biotic and abiotic tolerance of plant communities, along with increased nutrient availability and crop yields. This can be achieved in various ways, but one of the emerging approaches is to understand the phytomicrobiome structure and associated chemical communications. The phytomicrobiome was characterized with the advent of high-throughput techniques. Its composition and chemical signaling phenomena have been revealed, leading the way for “rhizosphere engineering”. In addition to the above, phytomicrobiome studies have paved the way to best tackling soil contamination with various anthropogenic activities. Agricultural lands have been found to be unbalanced for crop production. Due to the intense application of agricultural chemicals such as herbicides, fungicides, insecticides, fertilizers, etc., which can only be rejuvenated efficiently through detailed studies on the phytomicrobiome component, the phytomicrobiome has recently emerged as a primary plant trait that affects crop production. The phytomicrobiome also acts as an essential modifying factor in plant root exudation and vice versa, resulting in better plant health and crop yield both in terms of quantity and quality. Not only supporting better plant growth, phytomicrobiome members are involved in the degradation of toxic materials, alleviating the stress conditions that adversely affect plant development. Thus, the present review compiles the progress in understanding phytomicrobiome relationships and their application in achieving the goal of sustainable agriculture.
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4
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Kumar A, Dubey A. Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production. J Adv Res 2020; 24:337-352. [PMID: 32461810 PMCID: PMC7240055 DOI: 10.1016/j.jare.2020.04.014] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/15/2020] [Accepted: 04/25/2020] [Indexed: 12/29/2022] Open
Abstract
Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.
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Affiliation(s)
- Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, M.P., India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, M.P., India
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5
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Vesty EF, Whitbread AL, Needs S, Tanko W, Jones K, Halliday N, Ghaderiardakani F, Liu X, Cámara M, Coates JC. Cross-kingdom signalling regulates spore germination in the moss Physcomitrella patens. Sci Rep 2020; 10:2614. [PMID: 32054953 PMCID: PMC7018845 DOI: 10.1038/s41598-020-59467-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/17/2020] [Indexed: 01/10/2023] Open
Abstract
Plants live in close association with microorganisms that can have beneficial or detrimental effects. The activity of bacteria in association with flowering plants has been extensively analysed. Bacteria use quorum-sensing as a way of monitoring their population density and interacting with their environment. A key group of quorum sensing molecules in Gram-negative bacteria are the N-acylhomoserine lactones (AHLs), which are known to affect the growth and development of both flowering plants, including crops, and marine algae. Thus, AHLs have potentially important roles in agriculture and aquaculture. Nothing is known about the effects of AHLs on the earliest-diverging land plants, thus the evolution of AHL-mediated bacterial-plant/algal interactions is unknown. In this paper, we show that AHLs can affect spore germination in a representative of the earliest plants on land, the Bryophyte moss Physcomitrella patens. Furthermore, we demonstrate that sporophytes of some wild isolates of Physcomitrella patens are associated with AHL-producing bacteria.
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Affiliation(s)
- Eleanor F Vesty
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,University Centre Shrewsbury, Guildhall, Frankwell Quay, Shrewsbury, Shropshire, UK
| | - Amy L Whitbread
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,Karlsruhe Institute of Technology, Karlsruhe, Baden-Württemberg, Germany
| | - Sarah Needs
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,School of Life, Health and Chemical Sciences, Open University, Walton Hall, Kents Hill, Milton Keynes, UK
| | - Wesal Tanko
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Kirsty Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Nigel Halliday
- National Biofilm Innovations Centre, University of Nottingham Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK
| | | | - Xiaoguang Liu
- National Biofilm Innovations Centre, University of Nottingham Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.,Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Miguel Cámara
- National Biofilm Innovations Centre, University of Nottingham Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham, UK.
| | - Juliet C Coates
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
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McGARVEY JA, Tran TD, Hnasko R, Gorski L. Use of Phyllosphere-Associated Lactic Acid Bacteria as Biocontrol Agents To Reduce Salmonella enterica Serovar Poona Growth on Cantaloupe Melons. J Food Prot 2019; 82:2148-2153. [PMID: 31742440 DOI: 10.4315/0362-028x.jfp-19-246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Foodborne illness associated with fresh, ready-to-eat produce continues to be a significant challenge to public health. In this study, we created a phyllosphere-associated lactic acid bacteria (PLAB) library and screened it via a high-throughput in vitro fluorescent assay to identify bacteria capable of inhibiting the growth of the pathogenic bacterium Salmonella enterica. One isolate, 14B4, inhibited the growth of S. enterica by >45-fold in vitro; it was able to grow and persist on the surfaces of cantaloupe melons at both ambient (25°C) and refrigerator (5°C) temperatures. Isolate 14B4 inhibited the growth of S. enterica on the surfaces of cantaloupes by >3 log when incubated at 25°C for 24 h and by >4 log when the cantaloupes were stored at 5°C for 3 days and the temperature was shifted to 25°C for 2 days. Genomic DNA sequence analysis of isolate 14B4 revealed that it was Lactococcus lactis and that it did not contain any known antibiotic biosynthesis gene clusters, antibiotic resistance genes, or genes encoding any known virulence factors. Organic acid analysis revealed that L. lactis produces substantial amounts of lactic acid, which is likely the inhibitory substance that reduced the growth of Salmonella on the cantaloupes.
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Affiliation(s)
- Jeffery A McGARVEY
- Foodborne Toxin Detection and Prevention Research Unit (ORCID: https://orcid.org/0000-0001-6877-924X [J.A.M.])
| | - Thao D Tran
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, 800 Buchanan Street, Albany, California 94710
| | - Robert Hnasko
- Department of Fish, Wildlife, and Conservation Biology, University of California, Davis, California 95616, USA
| | - Lisa Gorski
- Department of Fish, Wildlife, and Conservation Biology, University of California, Davis, California 95616, USA
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Miura T, Sánchez R, Castañeda LE, Godoy K, Barbosa O. Shared and unique features of bacterial communities in native forest and vineyard phyllosphere. Ecol Evol 2019; 9:3295-3305. [PMID: 30962893 PMCID: PMC6434556 DOI: 10.1002/ece3.4949] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 12/31/2018] [Indexed: 01/06/2023] Open
Abstract
Phyllosphere bacteria have received little attention despite their important roles in shaping plant performance traits. In this study, we characterize the bacterial communities on leaves of native trees inhabiting sclerophyllous forests in central Chile, one of the world's biodiversity hotspots. Additionally, we provide profiles of bacterial communities on grape leaves and berries of organic and conventional vineyards. Results of 16S rRNA gene amplicon sequence analysis showed that 45% of OTUs were shared across forest leaves, grape leaves, and grape berries. Conventional management had higher number of OTUs shared with forest leaves than organic management. In addition, grape leaves subjected to conventional management had higher alpha diversity than those with organic management, while no significant effect of agricultural management was observed in grape berries. Indicator analysis showed that Bdellovibrio, Beijerinckia, and Spirosoma were typical for forest leaves, whereas Enhydrobacter, Delftia, Proteiniclasticum, Arsenicicoccus, and Alkaliphilus were typical for the vineyard phyllosphere. Regarding agricultural managements, Beijerinckia, Sedimentibacter, Nesterenkonia, Gluconobacter, Conexibacter, and Anaeromyxobacter were typical for conventional grape leaves, whereas no genus-level indicator was found for organic vineyard leaves. These results provide new insights of the diversity patterns of the phyllosphere microbiome in native and cultivated lands and suggest that both of these microbiomes are connected and integrated systems.
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Affiliation(s)
- Toshiko Miura
- Instituto de Ecología & Biodiversidad (IEB‐Chile)SantiagoChile
- Research Institute of Environment, Agriculture and FisheriesOsakaJapan
| | - Roland Sánchez
- Instituto de Ecología & Biodiversidad (IEB‐Chile)SantiagoChile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Luis E. Castañeda
- Programa de Genética Humana, Instituto de Ciencias Biomédicas, Facultad de MedicinaUniversidad de ChileSantiagoChile
| | - Karina Godoy
- Instituto de Ecología & Biodiversidad (IEB‐Chile)SantiagoChile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de CienciasUniversidad Austral de ChileValdiviaChile
| | - Olga Barbosa
- Instituto de Ecología & Biodiversidad (IEB‐Chile)SantiagoChile
- Instituto de Ciencias Ambientales y Evolutivas, Facultad de CienciasUniversidad Austral de ChileValdiviaChile
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8
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Mohanram S, Kumar P. Rhizosphere microbiome: revisiting the synergy of plant-microbe interactions. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01448-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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9
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González-Mula A, Lang J, Grandclément C, Naquin D, Ahmar M, Soulère L, Queneau Y, Dessaux Y, Faure D. Lifestyle of the biotroph Agrobacterium tumefaciens in the ecological niche constructed on its host plant. THE NEW PHYTOLOGIST 2018; 219:350-362. [PMID: 29701262 DOI: 10.1111/nph.15164] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/13/2018] [Indexed: 05/23/2023]
Abstract
Agrobacterium tumefaciens constructs an ecological niche in its host plant by transferring the T-DNA from its Ti plasmid into the host genome and by diverting the host metabolism. We combined transcriptomics and genetics for understanding the A. tumefaciens lifestyle when it colonizes Arabidopsis thaliana tumors. Transcriptomics highlighted: a transition from a motile to sessile behavior that mobilizes some master regulators (Hfq, CtrA, DivK and PleD); a remodeling of some cell surface components (O-antigen, succinoglucan, curdlan, att genes, putative fasciclin) and functions associated with plant defense (Ef-Tu and flagellin pathogen-associated molecular pattern-response and glycerol-3-phosphate and nitric oxide signaling); and an exploitation of a wide variety of host resources, including opines, amino acids, sugars, organic acids, phosphate, phosphorylated compounds, and iron. In addition, construction of transgenic A. thaliana lines expressing a lactonase enzyme showed that Ti plasmid transfer could escape host-mediated quorum-quenching. Finally, construction of knock-out mutants in A. tumefaciens showed that expression of some At plasmid genes seemed more costly than the selective advantage they would have conferred in tumor colonization. We provide the first overview of A. tumefaciens lifestyle in a plant tumor and reveal novel signaling and trophic interplays for investigating host-pathogen interactions.
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Affiliation(s)
- Almudena González-Mula
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, F-91190, France
| | - Julien Lang
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, F-91190, France
| | - Catherine Grandclément
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, F-91190, France
| | - Delphine Naquin
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, F-91190, France
| | - Mohammed Ahmar
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires (ICBMS), INSA-Lyon, Université Lyon 1, CNRS, CPE Lyon, ICBMS, UMR5246, INSA Lyon, Villeurbanne, F-69621, France
| | - Laurent Soulère
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires (ICBMS), INSA-Lyon, Université Lyon 1, CNRS, CPE Lyon, ICBMS, UMR5246, INSA Lyon, Villeurbanne, F-69621, France
| | - Yves Queneau
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires (ICBMS), INSA-Lyon, Université Lyon 1, CNRS, CPE Lyon, ICBMS, UMR5246, INSA Lyon, Villeurbanne, F-69621, France
| | - Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, F-91190, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Univ. Paris-Sud, University Paris-Saclay, Gif-sur-Yvette, F-91190, France
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Devi KR, Srinivasan S, Ravi AV. Inhibition of quorum sensing-mediated virulence in Serratia marcescens by Bacillus subtilis R-18. Microb Pathog 2018; 120:166-175. [DOI: 10.1016/j.micpath.2018.04.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 04/12/2018] [Accepted: 04/12/2018] [Indexed: 10/17/2022]
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Niche Construction and Exploitation by Agrobacterium: How to Survive and Face Competition in Soil and Plant Habitats. Curr Top Microbiol Immunol 2018; 418:55-86. [PMID: 29556826 DOI: 10.1007/82_2018_83] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Agrobacterium populations live in different habitats (bare soil, rhizosphere, host plants), and hence face different environmental constraints. They have evolved the capacity to exploit diverse resources and to escape plant defense and competition from other microbiota. By modifying the genome of their host, Agrobacterium populations exhibit the remarkable ability to construct and exploit the ecological niche of the plant tumors that they incite. This niche is characterized by the accumulation of specific, low molecular weight compounds termed opines that play a critical role in Agrobacterium 's lifestyle. We present and discuss the functions, advantages, and costs associated with this niche construction and exploitation.
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12
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Salas ME, Lozano MJ, López JL, Draghi WO, Serrania J, Torres Tejerizo GA, Albicoro FJ, Nilsson JF, Pistorio M, Del Papa MF, Parisi G, Becker A, Lagares A. Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization. Environ Microbiol 2017; 19:3423-3438. [PMID: 28618121 DOI: 10.1111/1462-2920.13820] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/19/2017] [Accepted: 05/26/2017] [Indexed: 11/29/2022]
Abstract
Rhizobia are α- and ß-proteobacteria that associate with legumes in symbiosis to fix atmospheric nitrogen. The chemical communication between roots and rhizobia begins in the rhizosphere. Using signature-tagged-Tn5 mutagenesis (STM) we performed a genome-wide screening for Ensifer meliloti genes that participate in colonizing the rhizospheres of alfalfa and other legumes. The analysis of ca. 6,000 mutants indicated that genes relevant for rhizosphere colonization account for nearly 2% of the rhizobial genome and that most (ca. 80%) are chromosomally located, pointing to the relevance and ancestral origin of the bacterial ability to colonize plant roots. The identified genes were related to metabolic functions, transcription, signal transduction, and motility/chemotaxis among other categories; with several ORFs of yet-unknown function. Most remarkably, we identified a subset of genes that impacted more severely the colonization of the roots of alfalfa than of pea. Further analyses using other plant species revealed that such early differential phenotype could be extended to other members of the Trifoliae tribe (Trigonella, Trifolium), but not the Fabeae and Phaseoleae tribes. The results suggest that consolidation of E. meliloti into its current symbiotic state should have occurred in a rhizobacterium that had already been adapted to rhizospheres of the Trifoliae tribe.
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Affiliation(s)
- María Eugenia Salas
- Instituto de Biotecnología y Biología Molecular-CONICET CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mauricio Javier Lozano
- Instituto de Biotecnología y Biología Molecular-CONICET CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - José Luis López
- Instituto de Biotecnología y Biología Molecular-CONICET CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Walter Omar Draghi
- Instituto de Biotecnología y Biología Molecular-CONICET CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Javier Serrania
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps University, Marburg, Germany
| | - Gonzalo Arturo Torres Tejerizo
- Instituto de Biotecnología y Biología Molecular-CONICET CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Francisco Javier Albicoro
- Instituto de Biotecnología y Biología Molecular-CONICET CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Juliet Fernanda Nilsson
- Instituto de Biotecnología y Biología Molecular-CONICET CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Mariano Pistorio
- Instituto de Biotecnología y Biología Molecular-CONICET CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Florencia Del Papa
- Instituto de Biotecnología y Biología Molecular-CONICET CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology and Faculty of Biology, Philipps University, Marburg, Germany
| | - Antonio Lagares
- Instituto de Biotecnología y Biología Molecular-CONICET CCT-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
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Chen K, Otten L. Natural Agrobacterium Transformants: Recent Results and Some Theoretical Considerations. FRONTIERS IN PLANT SCIENCE 2017; 8:1600. [PMID: 28966626 PMCID: PMC5606197 DOI: 10.3389/fpls.2017.01600] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/31/2017] [Indexed: 05/19/2023]
Abstract
Agrobacterium rhizogenes causes hairy root growth on a large number of plant species. It does so by transferring specific DNA fragments (T-DNA) from its root-inducing plasmid (pRi) into plant cells. Expression of T-DNA genes leads to abnormal root growth and production of specific metabolites (opines) which are taken up by the bacterium and used for its growth. Recent work has shown that several Nicotiana, Linaria, and Ipomoea species contain T-DNA genes from A. rhizogenes in their genomes. Plants carrying such T-DNAs (called cellular T-DNA or cT-DNA) can be considered as natural transformants. In the Nicotiana genus, seven different T-DNAs are found originating from different Agrobacterium strains, and in the Tomentosae section no <4 successive insertion events took place. In several cases cT-DNA genes were found to be expressed. In some Nicotiana tabacum cultivars the opine synthesis gene TB-mas2' is expressed in the roots. These cultivars were found to produce opines. Here we review what is known about natural Agrobacterium transformants, develop a theoretical framework to analyze this unusual phenomenon, and provide some outlines for further research.
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Affiliation(s)
- Ke Chen
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai, China
| | - Léon Otten
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique (CNRS)Strasbourg, France
- *Correspondence: Léon Otten
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Chen K, de Borne FD, Julio E, Obszynski J, Pale P, Otten L. Root-specific expression of opine genes and opine accumulation in some cultivars of the naturally occurring genetically modified organism Nicotiana tabacum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:258-69. [PMID: 27125327 DOI: 10.1111/tpj.13196] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/08/2016] [Accepted: 04/14/2016] [Indexed: 05/21/2023]
Abstract
Previous studies have shown that Nicotiana tabacum contains three Agrobacterium-derived T-DNA sequences inherited from its paternal ancestor Nicotiana tomentosiformis. Among these, the TB locus carries an intact mannopine synthase 2' gene (TB-mas2'). This gene is similar to the Agrobacterium rhizogenes A4-mas2' gene that encodes the synthesis of the Amadori compound deoxyfructosyl-glutamine (DFG or santhopine). In this study we show that TB-mas2' is expressed at very low levels in N. tomentosiformis and in most N. tabacum cultivars; however, some cultivars show high TB-mas2' expression levels. The TB-mas2' promoter sequences of low- and high-expressing cultivars are identical. The low/high level of expression segregates as a single Mendelian factor in a cross between a low- and a high-expression cultivar. pTB-mas2'-GUS and pA4-mas2'-GUS reporter genes were stably introduced in N. benthamiana. Both were mainly expressed in the root expansion zone and leaf vasculature. Roots of tobacco cultivars with high TB-mas2' expression contain detectable levels of DFG.
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Affiliation(s)
- Ke Chen
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes, Rue du Général Zimmer 12, Strasbourg, 67084, France
| | | | - Emilie Julio
- Imperial Tobacco Bergerac, La Tour, Bergerac, 24100, France
| | - Julie Obszynski
- Laboratoire de synthèse, réactivité organiques et catalyse, Institut de Chimie, UMR 7177, Université de Strasbourg, 4 Rue Blaise Pascal, Strasbourg, 67070, France
| | - Patrick Pale
- Laboratoire de synthèse, réactivité organiques et catalyse, Institut de Chimie, UMR 7177, Université de Strasbourg, 4 Rue Blaise Pascal, Strasbourg, 67070, France
| | - Léon Otten
- Department of Molecular Mechanisms of Phenotypic Plasticity, Institut de Biologie Moléculaire des Plantes, Rue du Général Zimmer 12, Strasbourg, 67084, France.
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15
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Porter SS, Chang PL, Conow CA, Dunham JP, Friesen ML. Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium. ISME JOURNAL 2016; 11:248-262. [PMID: 27420027 PMCID: PMC5315480 DOI: 10.1038/ismej.2016.88] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 05/23/2016] [Accepted: 05/25/2016] [Indexed: 01/18/2023]
Abstract
The genetic variants that underlie microbial environmental adaptation are key components of models of microbial diversification. Characterizing adaptive variants and the pangenomic context in which they evolve remains a frontier in understanding how microbial diversity is generated. The genomics of rhizobium adaptation to contrasting soil environments is ecologically and agriculturally important because these bacteria are responsible for half of all current biologically fixed nitrogen, yet they live the majority of their lives in soil. Our study uses whole-genome sequencing to describe the pan-genome of a focal clade of wild mesorhizobia that show contrasting levels of nickel adaptation despite high relatedness (99.8% identity at 16S). We observe ecotypic specialization within an otherwise genomically cohesive population, rather than finding distinct specialized bacterial lineages in contrasting soil types. This finding supports recent reports that heterogeneous environments impose selection that maintains differentiation only at a small fraction of the genome. Our work further uses a genome-wide association study to propose candidate genes for nickel adaptation. Several candidates show homology to genetic systems involved in nickel tolerance and one cluster of candidates correlates perfectly with soil origin, which validates our approach of ascribing genomic variation to adaptive divergence.
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Affiliation(s)
- Stephanie S Porter
- School of Biological Sciences, Washington State University, Vancouver, WA, USA
| | - Peter L Chang
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.,Department of Plant Pathology and Nematology, University of California, Davis, CA, USA
| | - Christopher A Conow
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Joseph P Dunham
- Section of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Maren L Friesen
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
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16
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Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané JM, Peters JW. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl Environ Microbiol 2016. [PMID: 27084023 DOI: 10.1128/aem.01055-01016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
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Affiliation(s)
- Florence Mus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Matthew B Crook
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amaya Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Evangelia D Kouri
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | | | - Min-Hyung Ryu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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17
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Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané JM, Peters JW. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl Environ Microbiol 2016; 82:3698-3710. [PMID: 27084023 PMCID: PMC4907175 DOI: 10.1128/aem.01055-16] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
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Affiliation(s)
- Florence Mus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Matthew B Crook
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amaya Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Evangelia D Kouri
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | | | - Min-Hyung Ryu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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Han SR, Lee JH, Kang S, Park H, Oh TJ. Complete genome sequence of opine-utilizing Variovorax sp. strain PAMC28711 isolated from an Antarctic lichen. J Biotechnol 2016; 225:46-7. [PMID: 27034019 DOI: 10.1016/j.jbiotec.2016.03.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 10/22/2022]
Abstract
We report the complete genome sequence of Variovorax sp. strain PAMC28711 isolated from the Antarctic lichen Himantormia sp. Whole genome sequencing revealed opine oxidase- and octopine dehydrogenase-related gene clusters that are involved in octopine utilization. These data will lead to future genetic and biochemical studies on the unusual catabolic traits of opine and octopine utilization in extremely cold environments.
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Affiliation(s)
- So-Ra Han
- Department of BT-Convergent Pharmaceutical Engineering, SunMoon University, #100, Kalsan-ri, Tangjeong-myeon, Asansi, Chungnam 31460, Republic of Korea
| | - Joo-Ho Lee
- Department of BT-Convergent Pharmaceutical Engineering, SunMoon University, #100, Kalsan-ri, Tangjeong-myeon, Asansi, Chungnam 31460, Republic of Korea
| | - Seunghyun Kang
- Korea Polar Research Institute (KOPRI), 213-3, Songdo-dong, Yeonsu-gu, Incheon 21990, Republic of Korea
| | - Hyun Park
- Korea Polar Research Institute (KOPRI), 213-3, Songdo-dong, Yeonsu-gu, Incheon 21990, Republic of Korea; Polar Sciences, University of Science & Technology, Yuseong-gu, Daejeon 34113, Republic of Korea.
| | - Tae-Jin Oh
- Department of BT-Convergent Pharmaceutical Engineering, SunMoon University, #100, Kalsan-ri, Tangjeong-myeon, Asansi, Chungnam 31460, Republic of Korea.
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19
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Dessaux Y, Grandclément C, Faure D. Engineering the Rhizosphere. TRENDS IN PLANT SCIENCE 2016; 21:266-278. [PMID: 26818718 DOI: 10.1016/j.tplants.2016.01.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/14/2015] [Accepted: 01/04/2016] [Indexed: 05/25/2023]
Abstract
All components of the rhizosphere can be engineered to promote plant health and growth, two features that strongly depend upon the interactions of living organisms with their environment. This review describes the progress in plant and microbial molecular genetics and ecology that has led to a wealth of potential applications. Recent efforts especially deal with the plant defense machinery that is instrumental in engineering plant resistance to biotic stresses. Another approach involves microbial population engineering rather than single strain engineering. More generally, the plants (and the associated microbes) are no longer seen as 'individual' but rather as a holobiont, in other words a unit of selection in evolution, a concept that holds great promise for future plant breeding programs.
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Affiliation(s)
- Yves Dessaux
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France.
| | - Catherine Grandclément
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France
| | - Denis Faure
- Institute for Integrative Biology of the Cell (I2BC), Commissariat à l'Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette CEDEX, France
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20
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Whole-Genome Sequence and Annotation of Octopine-Utilizing Pseudomonas kilonensis (Previously P. fluorescens) Strain 1855-344. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00463-15. [PMID: 25977435 PMCID: PMC4432341 DOI: 10.1128/genomea.00463-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Here, we report the whole-genome sequence and annotation of Pseudomonas kilonensis 1855-344 (previously known as P. fluorescens 1855-344). The genome contains an octopine oxidase gene cluster consistent with the ability to utilize octopine. A biosynthetic gene cluster was identified for mangotoxin and aryl-polyene using the antiSMASH server.
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21
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Geddes BA, Ryu MH, Mus F, Garcia Costas A, Peters JW, Voigt CA, Poole P. Use of plant colonizing bacteria as chassis for transfer of N₂-fixation to cereals. Curr Opin Biotechnol 2015; 32:216-222. [PMID: 25626166 DOI: 10.1016/j.copbio.2015.01.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
Abstract
Engineering cereal crops that are self-supported by nitrogen fixation has been a dream since the 1970s when nitrogenase was transferred from Klebsiella pneumoniae to Escherichia coli. A renewed interest in this area has generated several new approaches with the common aim of transferring nitrogen fixation to cereal crops. Advances in synthetic biology have afforded the tools to rationally engineer microorganisms with traits of interest. Nitrogenase biosynthesis has been a recent target for the application of new synthetic engineering tools. Early successes in this area suggest that the transfer of nitrogenase and other supporting traits to microorganisms that already closely associate with cereal crops is a logical approach to deliver nitrogen to cereal crops.
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Affiliation(s)
- Barney A Geddes
- Department of Plant Sciences, Oxford University, Oxford OX1 3RB, United Kingdom
| | - Min-Hyung Ryu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Florence Mus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Amaya Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Philip Poole
- Department of Plant Sciences, Oxford University, Oxford OX1 3RB, United Kingdom.
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22
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Quiza L, St-Arnaud M, Yergeau E. Harnessing phytomicrobiome signaling for rhizosphere microbiome engineering. FRONTIERS IN PLANT SCIENCE 2015; 6:507. [PMID: 26236319 PMCID: PMC4500914 DOI: 10.3389/fpls.2015.00507] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 06/25/2015] [Indexed: 05/18/2023]
Abstract
The goal of microbiome engineering is to manipulate the microbiome toward a certain type of community that will optimize plant functions of interest. For instance, in crop production the goal is to reduce disease susceptibility, increase nutrient availability increase abiotic stress tolerance and increase crop yields. Various approaches can be devised to engineer the plant-microbiome, but one particularly promising approach is to take advantage of naturally evolved plant-microbiome communication channels. This is, however, very challenging as the understanding of the plant-microbiome communication is still mostly rudimentary and plant-microbiome interactions varies between crops species (and even cultivars), between individual members of the microbiome and with environmental conditions. In each individual case, many aspects of the plant-microorganisms relationship should be thoroughly scrutinized. In this article we summarize some of the existing plant-microbiome engineering studies and point out potential avenues for further research.
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Affiliation(s)
- Liliana Quiza
- Energy, Mining and Environment, National Research Council Canada, MontréalQC, Canada
- Institut de Recherche en Biologie Végétale – Jardin Botanique de Montréal and Université de Montréal, MontréalQC, Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale – Jardin Botanique de Montréal and Université de Montréal, MontréalQC, Canada
| | - Etienne Yergeau
- Energy, Mining and Environment, National Research Council Canada, MontréalQC, Canada
- *Correspondence: Etienne Yergeau, National Research Council Canada, 6100 Royalmount Avenue, Montréal, QC H4P 2R2, Canada,
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Geetha SJ, Joshi SJ. Engineering rhizobial bioinoculants: a strategy to improve iron nutrition. ScientificWorldJournal 2013; 2013:315890. [PMID: 24319357 PMCID: PMC3836376 DOI: 10.1155/2013/315890] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/26/2013] [Indexed: 11/18/2022] Open
Abstract
Under field conditions, inoculated rhizobial strains are at a survival disadvantage as compared to indigenous strains. In order to out-compete native rhizobia it is not only important to develop strong nodulation efficiency but also increase their competence in the soil and rhizosphere. Competitive survival of the inoculated strain may be improved by employing strain selection and by genetic engineering of superior nitrogen fixing strains. Iron sufficiency is an important factor determining the survival and nodulation by rhizobia in soil. Siderophores, a class of ferric specific ligands that are involved in receptor specific iron transport into bacteria, constitute an important part of iron acquisition systems in rhizobia and have been shown to play a role in symbiosis as well as in saprophytic survival. Soils predominantly have iron bound to hydroxamate siderophores, a pool that is largely unavailable to catecholate-utilizing rhizobia. Outer membrane receptors for uptake of ferric hydroxamates include FhuA and FegA which are specific for ferrichrome siderophore. Increase in nodule occupancy and enhanced plant growth of the fegA and fhuA expressing engineered bioinoculants rhizobial strain have been reported. Engineering rhizobia for developing effective bioinoculants with improved ability to utilize heterologous siderophores could provide them with better iron acquisition ability and consequently, rhizospheric stability.
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Affiliation(s)
- S. J. Geetha
- Department of Biology, College of Science, Sultan Qaboos University, P.O. Box 36, Muscat 123, Oman
| | - Sanket J. Joshi
- Department of Biology, College of Science, Sultan Qaboos University, P.O. Box 36, Muscat 123, Oman
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Flores-Mireles AL, Eberhard A, Winans SC. Agrobacterium tumefaciens can obtain sulphur from an opine that is synthesized by octopine synthase using S-methylmethionine as a substrate. Mol Microbiol 2012; 84:845-56. [PMID: 22486934 PMCID: PMC3359404 DOI: 10.1111/j.1365-2958.2012.08061.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Agrobacterium tumefaciens incites plant tumours that produce nutrients called opines, which are utilized by the bacteria during host colonization. Various opines provide sources of carbon, nitrogen and phosphorous, but virtually nothing was previously known about how A. tumefaciens acquires sulphur during colonization. Some strains encode an operon required for the catabolism of the opine octopine. This operon contains a gene, msh, that is predicted to direct the conversion of S-methylmethionine (SMM) and homocysteine (HCys) to two equivalents of methionine. Purified Msh carried out this reaction, suggesting that SMM could be an intermediate in opine catabolism. Purified octopine synthase (Ocs, normally expressed in plant tumours) utilized SMM and pyruvate to produce a novel opine, designated sulfonopine, whose catabolism by the bacteria would regenerate SMM. Sulfonopine was produced by tobacco and Arabidopsis when colonized by A. tumefaciens and was utilized as sole source of sulphur by A. tumefaciens. Purified Ocs also used 13 other proteogenic and non-proteogenic amino acids as substrates, including three that contain sulphur. Sulfonopine and 11 other opines were tested for induction of octopine catabolic operon and all were able to do so. This is the first study of the acquisition of sulphur, an essential element, by this pathogen.
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Affiliation(s)
| | - Anatol Eberhard
- Department of Microbiology, Cornell University, Ithaca, New York 14853
| | - Stephen C. Winans
- Department of Microbiology, Cornell University, Ithaca, New York 14853
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Abstract
Although 'cheaters' potentially destabilize the legume-rhizobium mutualism, we lack a comprehensive review of host-symbiont fitness correlations. Studies measuring rhizobium relative or absolute fitness and host benefit are surveyed. Mutant studies are tallied for evidence of pleiotropy; studies of natural strains are analyzed with meta-analysis. Of 80 rhizobium mutations, 19 decrease both partners' fitness, four increase both, two increase host fitness but decrease symbiont fitness and none increase symbiont fitness at the host's expense. The pooled correlation between rhizobium nodulation competitiveness and plant aboveground biomass is 0.65 across five experiments that compete natural strains against a reference, whereas, across 14 experiments that compete rhizobia against soil populations or each other, the pooled correlation is 0.24. Pooled correlations between aboveground biomass and nodule number and nodule biomass are 0.76 and 0.83. Positive correlations between legume and rhizobium fitness imply that most ineffective rhizobia are 'defective' rather than 'defectors'; this extends to natural variants, with only one significant fitness conflict. Most studies involve non-coevolved associations, indicating that fitness alignment is the default state. Rhizobium mutations that increase both host and symbiont fitness suggest that some plants maladaptively restrict symbiosis with novel strains.
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Affiliation(s)
- Maren L Friesen
- Center for Population Biology, University of California, Davis, One Shields Ave., Davis, CA 95616, USA
- Present address: Section of Molecular and Computational Biology, Department of Biology, University of Southern California, 1050 Childs Way, RRI 201-B Los Angeles, CA 90089, USA
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26
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Lassalle F, Campillo T, Vial L, Baude J, Costechareyre D, Chapulliot D, Shams M, Abrouk D, Lavire C, Oger-Desfeux C, Hommais F, Guéguen L, Daubin V, Muller D, Nesme X. Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens. Genome Biol Evol 2011; 3:762-81. [PMID: 21795751 PMCID: PMC3163468 DOI: 10.1093/gbe/evr070] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species.
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Affiliation(s)
- Florent Lassalle
- Université de Lyon, Université Lyon 1, CNRS, INRA, Laboratoire Ecologie Microbienne Lyon, UMR 5557, USC 1193, Villeurbanne, France
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A mutant GlnD nitrogen sensor protein leads to a nitrogen-fixing but ineffective Sinorhizobium meliloti symbiosis with alfalfa. Proc Natl Acad Sci U S A 2008; 105:18958-63. [PMID: 19020095 DOI: 10.1073/pnas.0808048105] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nitrogen-fixing symbiosis between rhizobia and legume plants is a model of coevolved nutritional complementation. The plants reduce atmospheric CO(2) by photosynthesis and provide carbon compounds to symbiotically associated bacteria; the rhizobia use these compounds to reduce (fix) atmospheric N(2) to ammonia, a form of nitrogen the plants can use. A key feature of symbiotic N(2) fixation is that N(2) fixation is uncoupled from bacterial nitrogen stress metabolism so that the rhizobia generate "excess" ammonia and release this ammonia to the plant. In the symbiosis between Sinorhizobium meliloti and alfalfa, mutations in GlnD, the major bacterial nitrogen stress response sensor protein, led to a symbiosis in which nitrogen was fixed (Fix(+)) but was not effective (Eff(-)) in substantially increasing plant growth. Fixed (15)N(2) was transported to the shoots, but most fixed (15)N was not present in the plant after 24 h. Analysis of free-living S. meliloti strains with mutations in genes related to nitrogen stress response regulation (glnD, glnB, ntrC, and ntrA) showed that catabolism of various nitrogen-containing compounds depended on the NtrC and GlnD components of the nitrogen stress response cascade. However, only mutants of GlnD with an amino terminal deletion had the unusual Fix(+)Eff(-) symbiotic phenotype, and the data suggest that these glnD mutants export fixed nitrogen in a form that the plants cannot use. These results indicate that bacterial nitrogen stress regulation is important to symbiotic productivity and suggest that GlnD may act in a novel way to influence symbiotic behavior.
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Somers E, Vanderleyden J, Srinivasan M. Rhizosphere Bacterial Signalling: A Love Parade Beneath Our Feet. Crit Rev Microbiol 2008; 30:205-40. [PMID: 15646398 DOI: 10.1080/10408410490468786] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Plant roots support the growth and activities of a wide variety of microorganisms that may have a profound effect on the growth and/or health of plants. Among these microorganisms, a high diversity of bacteria have been identified and categorized as deleterious, beneficial, or neutral with respect to the plant. The beneficial bacteria, termed plant growth-promoting rhizobacteria (PGPR), are widely studied by microbiologists and agronomists because of their potential in plant production. Azospirillum, a genus of versatile PGPR, is able to enhance the plant growth and yield of a wide range of economically important crops in different soils and climatic regions. Plant beneficial effects of Azospirillum have mainly been attributed to the production of phytohormones, nitrate reduction, and nitrogen fixation, which have been subject of extensive research throughout the years. These elaborate studies made Azospirillum one of the best-characterized genera of PGPR. However, the genetic and molecular determinants involved in the initial interaction between Azospirillum and plant roots are not yet fully understood. This review will mainly highlight the current knowledge on Azospirillum plant root interactions, in the context of preceding and ongoing research on the association between plants and plant growth-promoting rhizobacteria.
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Affiliation(s)
- E Somers
- Centre of Microbial and Plant Genetics, K U Leuven, Heverlee, Belgium.
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Schoffers E, Gurung SR, Kohler PR, Rossbach S. Chemical synthesis of scyllo-inosamine and catabolism studies in Sinorhizobium meliloti. Bioorg Med Chem 2008; 16:7838-42. [DOI: 10.1016/j.bmc.2008.06.040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 06/14/2008] [Accepted: 06/20/2008] [Indexed: 11/26/2022]
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Barriuso J, Ramos Solano B, Fray RG, Cámara M, Hartmann A, Gutiérrez Mañero FJ. Transgenic tomato plants alter quorum sensing in plant growth-promoting rhizobacteria. PLANT BIOTECHNOLOGY JOURNAL 2008; 6:442-452. [PMID: 18384507 DOI: 10.1111/j.1467-7652.2008.00331.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Two Gram-negative, plant growth-promoting rhizobacteria (PGPRs), denominated as M12 and M14, were classified by 16S rDNA sequencing as Burkholderia graminis species. Both strains were shown to produce a variety of N-acyl-homoserine lactone (AHL) quorum sensing (QS) signalling molecules. The involvement of these molecules in plant growth promotion and the induction of protection against salt stress was examined. AHL production was evaluated in vitro by thin-layer chromatography using AHL biosensors, and the identity of the AHLs produced was determined by liquid chromatography-tandem mass spectrometry. The in situ production of AHLs by M12 and M14 in the rhizosphere of Arabidopsis thaliana plants was detected by co-inoculation with green fluorescent protein-based biosensor strains and confocal laser scanning microscopy. To determine whether plant growth promotion and protection against salt stress were mediated by QS, these PGPRs were assayed on wild-type tomato plants, as well as their corresponding transgenics expressing YenI (short-chain AHL producers) and LasI (long-chain AHL producers). In wild-type tomato plants, only M12 promoted plant growth, and this effect disappeared in both transgenic lines. In contrast, M14 did not promote growth in wild-type tomatoes, but did so in the LasI transgenic line. Resistance to salt stress was induced by M14 in wild-type tomato, but this effect disappeared in both transgenic lines. The strain M12, however, did not induce salt resistance in wild-type tomato, but did so in LasI tomato plants. These results reveal that AHL QS signalling molecules mediate the ability of both PGPR strains M12 and M14 to promote plant growth and to induce protection against salt stress.
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Affiliation(s)
- Jorge Barriuso
- Universidad San Pablo CEU, Facultad Farmacia, PO Box 67, Boadilla del Monte, 28668 Madrid, Spain.
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Kiers ET, Hutton MG, Denison RF. Human selection and the relaxation of legume defences against ineffective rhizobia. Proc Biol Sci 2008; 274:3119-26. [PMID: 17939985 DOI: 10.1098/rspb.2007.1187] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Enforcement mechanisms are thought to be important in maintaining mutualistic cooperation between species. A clear example of an enforcement mechanism is how legumes impose sanctions on rhizobial symbionts that fail to provide sufficient fixed N2. However, with domestication and breeding in high-soil-N environments, humans may have altered these natural legume defences and reduced the agricultural benefits of the symbiosis. Using six genotypes of soya beans, representing 60 years of breeding, we show that, as a group, older cultivars were better able to maintain fitness than newer cultivars (seed production) when infected with a mixture of effective and ineffective rhizobial strains. Additionally, we found small differences among cultivars in the ratio of effective:ineffective rhizobia released from their nodules, an indicator of future rhizobial strain fitness. When infected by symbionts varying in quality, legume defences against poor-quality partners have apparently worsened under decades of artificial selection.
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Affiliation(s)
- E Toby Kiers
- Faculteit der Aard-en Levenswetenschappen, De Boelelaan 1085-1087, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands.
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Jafra S, Przysowa J, Czajkowski R, Michta A, Garbeva P, van der Wolf JM. Detection and characterization of bacteria from the potato rhizosphere degrading N-acyl-homoserine lactone. Can J Microbiol 2007; 52:1006-15. [PMID: 17110970 DOI: 10.1139/w06-062] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Quorum sensing plays a role in the regulation of soft rot diseases caused by the plant pathogenic bacterium Pectobacterium carotovorum subsp. carotovorum. The signal molecules involved in quorum sensing in P. carotovorum subsp. carotovorum belong to the group of N-acyl homoserine lactones (AHLs). In our study, we screened bacteria isolated from the potato rhizosphere for the ability to degrade AHLs produced by P. carotovorum subsp. carotovorum. Six isolates able to degrade AHLs were selected for further studies. According to 16S rDNA sequence analysis and fatty acid methyl ester profiling, the isolates belonged to the genera Ochrobactrum, Rhodococcus, Pseudomonas, Bacillus, and Delftia. For the genera Ochrobactrum and Delftia, for the first time AHL-degrading isolates were found. Data presented in this study revealed for the first time that Ochrobactrum sp. strain A44 showed the capacity to inactivate various synthetic AHL molecules; the substituted AHLs were inactivated with a lower efficiency than the unsubstituted AHLs. Compared with the other isolates, A44 was very effective in the degradation of AHLs produced by P. carotovorum subsp. carotovorum. It was verified by polymerase chain reaction, DNA-DNA hybridization, and a lactone ring reconstruction assay that Ochrobactrum sp. strain A44 did not possess AHL lactonase activity. AHL degradation in Ochrobactrum sp. strain A44 occurred intracellularly; it was not found in the culture supernatant. AHL-degrading activity of A44 was thermo sensitive. Experiments in planta revealed that Ochrobactrum sp. strain A44 significantly inhibited the maceration of potato tuber tissue. Since A44 did not produce antibiotics, the attenuation of the decay might be due to the quenching of quorum- sensing-regulated production of pectinolytic enzymes. The strain can potentially serve to control P. carotovorum subsp. carotovorum in potato.
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Affiliation(s)
- S Jafra
- Plant Research International, Wageningen, Netherlands.
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Karamanoli K, Lindow SE. Disruption of N-acyl homoserine lactone-mediated cell signaling and iron acquisition in epiphytic bacteria by leaf surface compounds. Appl Environ Microbiol 2006; 72:7678-86. [PMID: 16997987 PMCID: PMC1694201 DOI: 10.1128/aem.01260-06] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Since N-acyl homoserine lactones (AHLs) are key mediators of cell density-dependent regulation of traits involved in virulence and epiphytic fitness in gram-negative bacteria such as Pseudomonas syringae, a variety of plant species were examined to determine their production of leaf surface compounds that could interact with these signaling systems. Leaf washings of 17 of 52 plant species tested stimulated or inhibited AHL-dependent traits in at least one of the bacterial reporter strains used. The active compounds from most plants could be distinguished from known AHLs due to different patterns of mobility during C8 and C18 reverse-phase thin-layer chromatography (TLC) and normal-phase TLC compared to the patterns for authentic bacterial AHLs. All plant extracts were also tested to determine their abilities to sequester iron and trigger bacterial siderophore synthesis on a medium containing abundant iron. Leaf washings from 16 of the 52 plant species, as well as tannic acid solutions, stimulated pyoverdine synthesis in P. syringae in a high-iron medium. These preparations also inhibited the growth of a P. syringae mutant unable to produce pyoverdine siderophores but not the growth of the wild-type bacterium. The stimulation of siderophore production and the growth inhibition by plant extracts and purified tannins were both reversed by addition of ferric chloride to culture media, indicating that iron was made unavailable by the compounds released onto the leaf surface.
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Scott RA, Weil J, Le PT, Williams P, Fray RG, von Bodman SB, Savka MA. Long- and short-chain plant-produced bacterial N-acyl-homoserine lactones become components of phyllosphere, rhizosphere, and soil. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2006; 19:227-39. [PMID: 16570653 DOI: 10.1094/mpmi-19-0227] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Two N-acyl-homoserine lactone (acyl-HSL) synthase genes, lasI from Pseudomonas aeruginosa and yenI from Yersinia enterocolitica, were introduced into tobacco, individually and in combination. Liquid chromatograph-tandem mass spectrometry and thin-layer chromatography confirmed products of lasI and yenI activity in single and cotransformants. Cotransformants expressing plastid-localized LasI and YenI synthases produced the major acyl-HSLs for each synthase in all tissues tested. Total acyl-HSL signals accumulated in leaf tissue up to 3 pmol/mg of fresh weight, half as much in stem tissue, and approximately 10-fold less in root tissues. Acyl-HSLs were present in aqueous leaf washes from greenhouse-grown transgenic plants. Transgenic lines grown for 14 days under axenic conditions produced detectable levels of acyl-HSLs in root exudates. Ethyl acetate extractions of rhizosphere and nonrhizosphere soil from transgenically grown plants contained active acyl-HSLs, whereas plant-free soil or rhizosphere and nonrhizosphere soil from wild-type plants lacked detectable amounts of acyl-HSLs. This work shows that bioactive acyl-HSLs are exuded from leaves and roots and accumulate in the phytosphere of plants engineered to produce acyl-HSLs. These data further suggest that plants that are bioengineered to synthesize acyl-HSLs can foster beneficial plant-bacteria communications or deter deleterious interactions. Therefore, it is feasible to use bioengineered plants to supplement soils with specific acyl-HSLs to modulate bacterial phenotypes and plant-associated bacterial community structures.
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Affiliation(s)
- Russell A Scott
- Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY 14623, USA
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Sy A, Timmers ACJ, Knief C, Vorholt JA. Methylotrophic metabolism is advantageous for Methylobacterium extorquens during colonization of Medicago truncatula under competitive conditions. Appl Environ Microbiol 2005; 71:7245-52. [PMID: 16269765 PMCID: PMC1287603 DOI: 10.1128/aem.71.11.7245-7252.2005] [Citation(s) in RCA: 141] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Facultative methylotrophic bacteria of the genus Methylobacterium are commonly found in association with plants. Inoculation experiments were performed to study the importance of methylotrophic metabolism for colonization of the model legume Medicago truncatula. Competition experiments with Methylobacterium extorquens wild-type strain AM1 and methylotrophy mutants revealed that the ability to use methanol as a carbon and energy source provides a selective advantage during colonization of M. truncatula. Differences in the fitness of mutants defective in different stages of methylotrophic metabolism were found; whereas approximately 25% of the mutant incapable of oxidizing methanol to formaldehyde (deficient in methanol dehydrogenase) was recovered, 10% or less of the mutants incapable of oxidizing formaldehyde to CO2 (defective in biosynthesis of the cofactor tetrahydromethanopterin) was recovered. Interestingly, impaired fitness of the mutant strains compared with the wild type was found on leaves and roots. Single-inoculation experiments showed, however, that mutants with defects in methylotrophy were capable of plant colonization at the wild-type level, indicating that methanol is not the only carbon source that is accessible to Methylobacterium while it is associated with plants. Fluorescence microscopy with a green fluorescent protein-labeled derivative of M. extorquens AM1 revealed that the majority of the bacterial cells on leaves were on the surface and that the cells were most abundant on the lower, abaxial side. However, bacterial cells were also found in the intercellular spaces inside the leaves, especially in the epidermal cell layer and immediately underneath this layer.
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Affiliation(s)
- Abdoulaye Sy
- Laboratoire des Interactions Plantes Micro-organismes, INRA/CNRS, BP27, 31326 Castanet-Tolosan, France
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Patriarca EJ, Tatè R, Ferraioli S, Iaccarino M. Organogenesis of legume root nodules. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 234:201-62. [PMID: 15066376 DOI: 10.1016/s0074-7696(04)34005-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The N(2)-fixing nodules elicited by rhizobia on legume roots represent a useful model for studying plant development. Nodule formation implies a complex progression of temporally and spatially regulated events of cell differentiation/dedifferentiation involving several root tissues. In this review we describe the morphogenetic events leading to the development of these histologically well-structured organs. These events include (1) root hair deformation, (2) development and growth of infection threads, (3) induction of the nodule primordium, and (4) induction, activity, and persistence of the nodular meristem and/or of foci of meristematic activities. Particular attention is given to specific aspects of the symbiosis, such as the early stages of intracellular invasion and to differentiation of the intracellular form of rhizobia, called symbiosomes. These developmental aspects were correlated with (1) the regulatory signals exchanged, (2) the plant genes expressed in specific cell types, and (3) the staining procedures that allow the recognition of some cell types. When strictly linked with morphogenesis, the nodulation phenotypes of plant and bacterial mutants such as the developmental consequence of the treatment with metabolic inhibitors, metabolic intermediates, or the variation of physical parameters are described. Finally, some aspects of nodule senescence and of regulation of nodulation are discussed.
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Affiliation(s)
- Eduardo J Patriarca
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, Consiglio Nazionale delle Ricerche, 80125 Naples, Italy
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Abstract
The spermosphere represents a short-lived, rapidly changing, and microbiologically dynamic zone of soil surrounding a germinating seed. It is analogous to the rhizosphere, being established largely by the carbon compounds released into the soil once the seed begins to hydrate. These seed exudations drive the microbial activities that take place in the spermosphere, many of which can have long-lasting impacts on plant growth and development as well as on plant health. In this review, I discuss the nature of the spermosphere habitat and the factors that give rise to its character, with emphasis on the types of microbial activities in the spermosphere that have important implications for disease development and biological disease control. This review, which represents the first comprehensive synthesis of the literature on spermosphere biology, is meant to illustrate the unique nature of the spermosphere and how studies of interactions in this habitat may serve as useful experimental models for testing hypotheses about plant-microbe associations and microbial ecology.
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Affiliation(s)
- Eric B Nelson
- Department of Plant Pathology, Cornell University, Ithaca, New York 14853, USA.
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Tzfira T, Frankman LR, Vaidya M, Citovsky V. Site-specific integration of Agrobacterium tumefaciens T-DNA via double-stranded intermediates. PLANT PHYSIOLOGY 2003; 133:1011-23. [PMID: 14551323 PMCID: PMC281598 DOI: 10.1104/pp.103.032128] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2003] [Revised: 08/28/2003] [Accepted: 08/28/2003] [Indexed: 05/18/2023]
Abstract
Agrobacterium tumefaciens-mediated genetic transformation involves transfer of a single-stranded T-DNA molecule (T strand) into the host cell, followed by its integration into the plant genome. The molecular mechanism of T-DNA integration, the culmination point of the entire transformation process, remains largely obscure. Here, we studied the roles of double-stranded breaks (DSBs) and double-stranded T-DNA intermediates in the integration process. We produced transgenic tobacco (Nicotiana tabacum) plants carrying an I-SceI endonuclease recognition site that, upon cleavage with I-SceI, generates DSB. Then, we retransformed these plants with two A. tumefaciens strains: one that allows transient expression of I-SceI to induce DSB and the other that carries a T-DNA with the I-SceI site and an integration selection marker. Integration of this latter T-DNA as full-length and I-SceI-digested molecules into the DSB site was analyzed in the resulting plants. Of 620 transgenic plants, 16 plants integrated T-DNA into DSB at their I-SceI sites; because DSB induces DNA repair, these results suggest that the invading T-DNA molecules target to the DNA repair sites for integration. Furthermore, of these 16 plants, seven plants incorporated T-DNA digested with I-SceI, which cleaves only double-stranded DNA. Thus, T-strand molecules can be converted into double-stranded intermediates before their integration into the DSB sites within the host cell genome.
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Affiliation(s)
- Tzvi Tzfira
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, New York 11794, USA.
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López-Lara IM, Sohlenkamp C, Geiger O. Membrane lipids in plant-associated bacteria: their biosyntheses and possible functions. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2003; 16:567-579. [PMID: 12848422 DOI: 10.1094/mpmi.2003.16.7.567] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Membrane lipids in most bacteria generally consist of the glycerophospholipids phosphatidylglycerol, cardiolipin, and phosphatidylethanolamine (PE). A subset of bacteria also possesses the methylated derivatives of PE, monomethylphosphatidylethanolamine, dimethylphosphatidylethanolamine, and phosphatidylcholine (PC). In Sinorhizobium meliloti, which can form a nitrogen-fixing root nodule symbiosis with Medicago spp., PC can be formed by two entirely different biosynthetic pathways, either the PE methylation pathway or the recently discovered PC synthase pathway. In the latter pathway, one of the building blocks for PC formation, choline, is obtained from the eukaryotic host. Under phosphorus-limiting conditions of growth, S. meliloti replaces its membrane phospholipids by membrane-forming lipids that do not contain phosphorus; namely, the sulfolipid sulfoquinovosyl diacylglycerol, ornithine-derived lipids, and diacylglyceryl-N,N,N-trimethylhomoserine. Although none of these phosphorus-free lipids is essential for growth in culture media rich in phosphorus or for the symbiotic interaction with the legume host, they are expected to have major roles under free-living conditions in environments poor in accessible phosphorus. In contrast, sinorhizobial mutants deficient in PC show severe growth defects and are completely unable to form nodules on their host plants. Even bradyrhizobial mutants with reduced PC biosynthesis can form only root nodules displaying reduced rates of nitrogen fixation. Therefore, in the cases of these microsymbionts, the ability to form sufficient bacterial PC is crucial for a successful interplay with their host plants.
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Affiliation(s)
- Isabel M López-Lara
- Centro de Investigación sobre Fijación de Nitrógeno, Universidad Nacional Autónoma de Mexico, Apdo. Postal 565-A, Cuernavaca, Morelos, CP62210, México
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Duffy B, Schouten A, Raaijmakers JM. Pathogen self-defense: mechanisms to counteract microbial antagonism,. ANNUAL REVIEW OF PHYTOPATHOLOGY 2003; 41:501-538. [PMID: 12730392 DOI: 10.1146/annurev.phyto.41.052002.095606] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Natural and agricultural ecosystems harbor a wide variety of microorganisms that play an integral role in plant health, crop productivity, and preservation of multiple ecosystem functions. Interactions within and among microbial communities are numerous and range from synergistic and mutualistic to antagonistic and parasitic. Antagonistic and parasitic interactions have been exploited in the area of biological control of plant pathogenic microorganisms. To date, biocontrol is typically viewed from the perspective of how antagonists affect pathogens. This review examines the other face of this interaction: how plant pathogens respond to antagonists and how this can affect the efficacy of biocontrol. Just as microbial antagonists utilize a diverse arsenal of mechanisms to dominate interactions with pathogens, pathogens have surprisingly diverse responses to counteract antagonism. These responses include detoxification, repression of biosynthetic genes involved in biocontrol, active efflux of antibiotics, and antibiotic resistance. Understanding pathogen self-defense mechanisms for coping with antagonist assault provides a novel approach to improving the durability of biologically based disease control strategies and has implications for the deployment of transgenes (microorganisms or plants).
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Affiliation(s)
- Brion Duffy
- Swiss Federal Research Center for Fruit Production, Viticulture and Horticulture, FAW, Postfach 185, CH-8820 Wadenswil, Switzerland.
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