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Solanki MK, Joshi NC, Singh PK, Singh SK, Santoyo G, Basilio de Azevedo LC, Kumar A. From concept to reality: Transforming agriculture through innovative rhizosphere engineering for plant health and productivity. Microbiol Res 2024; 279:127553. [PMID: 38007891 DOI: 10.1016/j.micres.2023.127553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/14/2023] [Accepted: 11/19/2023] [Indexed: 11/28/2023]
Abstract
The plant rhizosphere is regarded as a microbial hotspot due to a wide array of root exudates. These root exudates comprise diverse organic compounds such as phenolic, polysaccharides, flavonoids, fatty acids, and amino acids that showed chemotactic responses towards microbial communities and mediate significant roles in root colonization. The rhizospheric microbiome is a crucial driver of plant growth and productivity, contributing directly or indirectly by facilitating nutrient acquisition, phytohormone modulation, and phosphate solubilization under normal and stressful conditions. Moreover, these microbial candidates protect plants from pathogen invasion by secreting antimicrobial and volatile organic compounds. To enhance plant fitness and yield, rhizospheric microbes are frequently employed as microbial inoculants. However, recent developments have shifted towards targeted rhizosphere engineering or microbial recruitments as a practical approach to constructing desired plant rhizospheres for specific outcomes. The rhizosphere, composed of plants, microbes, and soil, can be modified in several ways to improve inoculant efficiency. Rhizosphere engineering is achieved through three essential mechanisms: a) plant-mediated modifications involving genetic engineering, transgenics, and gene editing of plants; b) microbe-mediated modifications involving genetic alterations of microbes through upstream or downstream methodologies; and c) soil amendments. These mechanisms shape the rhizospheric microbiome, making plants more productive and resilient under different stress conditions. This review paper comprehensively summarizes the various aspects of rhizosphere engineering and their potential applications in maintaining plant health and achieving optimum agricultural productivity.
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Affiliation(s)
- Manoj Kumar Solanki
- Department of Life Sciences and Biological Sciences, IES University, Bhopal, Madhya Pradesh, India; Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Naveen Chandra Joshi
- Amity Institute of Microbial Technology, Amity University, Noida, Uttar Pradesh, 201313, India
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College Campus, Mizoram University (A Central University), Aizawl 796001, India
| | - Sandeep Kumar Singh
- Department of Microbiology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58030, Mexico
| | - Lucas Carvalho Basilio de Azevedo
- Instituto de Ciências Agrárias, Campus Glória-Bloco CCG, Universidade Federal de Uberlândia, RodoviaBR-050, KM 78, S/N, Uberlândia CEP 38410-337, Brazil
| | - Ajay Kumar
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201313, India.
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Lyng M, Jørgensen JPB, Schostag MD, Jarmusch SA, Aguilar DKC, Lozano-Andrade CN, Kovács ÁT. Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas marginalis. THE ISME JOURNAL 2024; 18:wrad001. [PMID: 38365234 PMCID: PMC10811728 DOI: 10.1093/ismejo/wrad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 02/18/2024]
Abstract
Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera, like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin (BB) in an antagonistic interaction with Pseudomonas marginalis. The presence of BB strongly influenced the outcome of the interaction in an iron-dependent manner. The BB producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of BB restricted B. subtilis colony growth. To explore the specificity of the antagonism, we cocultured B. subtilis with a collection of fluorescent Pseudomonas spp. and found that the Bacillus-Pseudomonas interaction is conserved, expanding our understanding of the interplay between two of the most well-studied genera of soil bacteria.
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Affiliation(s)
- Mark Lyng
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Johan P B Jørgensen
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Morten D Schostag
- Bacterial Ecophysiology & Biotechnology, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Scott A Jarmusch
- Natural Product Discovery, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Diana K C Aguilar
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Carlos N Lozano-Andrade
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
- Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
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Nguyen TP, Meng DR, Chang CH, Su PY, Ou CA, Hou PF, Sung HM, Chou CH, Ohme-Takagi M, Huang HJ. Antifungal mechanism of volatile compounds emitted by Actinomycetota Paenarthrobacter ureafaciens from a disease-suppressive soil on Saccharomyces cerevisiae. mSphere 2023; 8:e0032423. [PMID: 37750721 PMCID: PMC10597458 DOI: 10.1128/msphere.00324-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
Increasing evidence suggests that in disease-suppressive soils, microbial volatile compounds (mVCs) released from bacteria may inhibit the growth of plant-pathogenic fungi. However, the antifungal activities and molecular responses of fungi to different mVCs remain largely undescribed. In this study, we first evaluated the responses of pathogenic fungi to treatment with mVCs from Paenarthrobacter ureafaciens. Then, we utilized the well-characterized fungal model organism Saccharomyces cerevisiae to study the potential mechanistic effects of the mVCs. Our data showed that exposure to P. ureafaciens mVCs leads to reduced growth of several pathogenic fungi, and in yeast cells, mVC exposure prompts the accumulation of reactive oxygen species. Further experiments with S. cerevisiae deletion mutants indicated that Slt2/Mpk1 and Hog1 MAPKs play major roles in the yeast response to P. ureafaciens mVCs. Transcriptomic analysis revealed that exposure to mVCs was associated with 1,030 differentially expressed genes (DEGs) in yeast. According to gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses, many of these DEGs are involved in mitochondrial dysfunction, cell integrity, mitophagy, cellular metabolism, and iron uptake. Genes encoding antimicrobial proteins were also significantly altered in the yeast after exposure to mVCs. These findings suggest that oxidative damage and mitochondrial dysfunction are major contributors to the fungal toxicity of mVCs. Furthermore, our data showed that cell wall, antioxidant, and antimicrobial defenses are induced in yeast exposed to mVCs. Thus, our findings expand upon previous research by delineating the transcriptional responses of the fungal model. IMPORTANCE Since the use of bacteria-emitted volatile compounds in phytopathogen control is of considerable interest, it is important to understand the molecular mechanisms by which fungi may adapt to microbial volatile compounds (mVCs). Paenarthrobacter ureafaciens is an isolated bacterium from disease-suppressive soil that belongs to the Actinomycetota phylum. P. ureafaciens mVCs showed a potent antifungal effect on phytopathogens, which may contribute to disease suppression in soil. However, our knowledge about the antifungal mechanism of mVCs is limited. This study has proven that mVCs are toxic to fungi due to oxidative stress and mitochondrial dysfunction. To deal with mVC toxicity, antioxidants and physical defenses are required. Furthermore, iron uptake and CAP proteins are required for antimicrobial defense, which is necessary for fungi to deal with the thread from mVCs. This study provides essential foundational knowledge regarding the molecular responses of fungi to inhibitory mVCs.
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Affiliation(s)
- Tri-Phuong Nguyen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - De-Rui Meng
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Han Chang
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan
| | - Pei-Yu Su
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chieh-An Ou
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Fu Hou
- Kaohsiung District Agricultural Research and Extension Station, Pingtung, Taiwan
| | - Huang-Mo Sung
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chang-Hung Chou
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Masaru Ohme-Takagi
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan
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Plant Protection Mediated Through an Array of Metabolites Produced by Pantoea dispersa Isolated from Pitcher Plant. Appl Biochem Biotechnol 2023; 195:1607-1629. [PMID: 36350486 DOI: 10.1007/s12010-022-04179-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 11/11/2022]
Abstract
In the study, the bacterial isolate NhPB54 purified from the pitcher of Nepenthes plant was observed to have activity against Pythium aphanidermatum by dual culture and well diffusion. Hence, it was subjected to 16S rDNA sequencing and BLAST analysis, where the NhPB54 was found to have 100% identity to Pantoea dispersa. Upon screening for the plant beneficial properties, Pantoea dispersa NhPB54 was found to be positive for phosphate, potassium and zinc solubilization, nitrogen fixation, indole-3-acetic acid, ammonia, 1-aminocyclopropane-1-carboxylate deaminase, biofilm and biosurfactant production. Further to this, Solanum lycopersicum seedlings primed with P. dispersa NhPB54 were studied for the improved plant growth and disease protection. Here, the seedlings pre-treated with the NhPB54 culture supernatant were found to have enhanced plant growth and protection from damping off and fruit rot caused by P. aphanidermatum. From the LC-QTOF-MS/MS and GC MS analysis, P. dispersa NhPB54 was found to produce a blend of chemicals including 1-hydroxyphenazine, surfactin, and other bioactive metabolites with the likely basis of its observed antifungal and plant growth-promoting properties. From the results of the study, plants with unique adaptations can expect to harbor microbial candidates with beneficial applications.
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LeBlanc N. Green Manures Alter Taxonomic and Functional Characteristics of Soil Bacterial Communities. MICROBIAL ECOLOGY 2023; 85:684-697. [PMID: 35112152 DOI: 10.1007/s00248-022-01975-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Incorporation of plant biomass into soil as green manures can reduce soilborne diseases and improve crop and soil health in agricultural ecosystems. Soil microbial communities can mediate beneficial effects of these amendments, but their response to different types of green manures is poorly understood. This study tested the effect of green manures from broccoli, marigold, and sudangrass on taxonomic and functional characteristics of soil bacterial communities. Green manures were amended to field soil and maintained in microcosms artificially infested with the soilborne plant pathogen Verticillium dahliae. Lettuce seedlings were transplanted into green manure amended and fallow soil and maintained under growth chamber conditions for 12 weeks. Bacterial communities in bulk and rhizosphere soils were characterized using nanopore sequencing of 16S rRNA and shotgun metagenome libraries. Under microcosm conditions, all green manures reduced the abundance of the soilborne plant pathogen V. dahliae and altered the taxonomic composition of bacterial communities. Twelve weeks following amendment, green manures had differential effects on lettuce yield as well as the taxonomic diversity and composition of soil bacterial communities. In addition, multiple green manures increased the abundance of bacterial functional traits in rhizosphere soil related to iron and polysaccharide acquisition and decreased the abundance of functional traits related to bacterial protein secretion systems. This study demonstrates green manures alter the taxonomic composition and functional traits in soil bacterial communities suggesting these changes may impact beneficial effects of green manures on plant and soil health.
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Affiliation(s)
- Nicholas LeBlanc
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, 1636 E. Alisal St., Salinas, CA, 93905, USA.
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Iron acquisition strategies in pseudomonads: mechanisms, ecology, and evolution. Biometals 2022:10.1007/s10534-022-00480-8. [PMID: 36508064 PMCID: PMC10393863 DOI: 10.1007/s10534-022-00480-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
AbstractIron is important for bacterial growth and survival, as it is a common co-factor in essential enzymes. Although iron is very abundant in the earth crust, its bioavailability is low in most habitats because ferric iron is largely insoluble under aerobic conditions and at neutral pH. Consequently, bacteria have evolved a plethora of mechanisms to solubilize and acquire iron from environmental and host stocks. In this review, I focus on Pseudomonas spp. and first present the main iron uptake mechanisms of this taxa, which involve the direct uptake of ferrous iron via importers, the production of iron-chelating siderophores, the exploitation of siderophores produced by other microbial species, and the use of iron-chelating compounds produced by plants and animals. In the second part of this review, I elaborate on how these mechanisms affect interactions between bacteria in microbial communities, and between bacteria and their hosts. This is important because Pseudomonas spp. live in diverse communities and certain iron-uptake strategies might have evolved not only to acquire this essential nutrient, but also to gain relative advantages over competitors in the race for iron. Thus, an integrative understanding of the mechanisms of iron acquisition and the eco-evolutionary dynamics they drive at the community level might prove most useful to understand why Pseudomonas spp., in particular, and many other bacterial species, in general, have evolved such diverse iron uptake repertoires.
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Singh VS, Dubey BK, Rai S, Singh SP, Tripathi AK. Engineering D-glucose utilization in Azospirillum brasilense Sp7 promotes rice root colonization. Appl Microbiol Biotechnol 2022; 106:7891-7903. [DOI: 10.1007/s00253-022-12250-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/07/2022] [Accepted: 10/12/2022] [Indexed: 11/08/2022]
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8
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Shalev O, Ashkenazy H, Neumann M, Weigel D. Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms. THE ISME JOURNAL 2022; 16:1235-1244. [PMID: 34897280 PMCID: PMC9038753 DOI: 10.1038/s41396-021-01168-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 11/09/2022]
Abstract
AbstractPlants are protected from pathogens not only by their own immunity but often also by colonizing commensal microbes. In Arabidopsis thaliana, a group of cryptically pathogenic Pseudomonas strains often dominates local populations. This group coexists in nature with commensal Pseudomonas strains that can blunt the deleterious effects of the pathogens in the laboratory. We have investigated the interaction between one of the Pseudomonas pathogens and 99 naturally co-occurring commensals, finding plant protection to be common among non-pathogenic Pseudomonas. While protective ability is enriched in one specific lineage, there is also a substantial variation for this trait among isolates of this lineage. These functional differences do not align with core-genome phylogenies, suggesting repeated gene inactivation or loss as causal. Using genome-wide association, we discovered that different bacterial genes are linked to plant protection in each lineage. We validated a protective role of several lineage-specific genes by gene inactivation, highlighting iron acquisition and biofilm formation as prominent mechanisms of plant protection in this Pseudomonas lineage. Collectively, our work illustrates the importance of functional redundancy in plant protective traits across an important group of commensal bacteria.
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Meena M, Yadav G, Sonigra P, Nagda A, Mehta T, Zehra A, Swapnil P. Role of Microbial Bioagents as Elicitors in Plant Defense Regulation. TRANSCRIPTION FACTORS FOR BIOTIC STRESS TOLERANCE IN PLANTS 2022:103-128. [DOI: 10.1007/978-3-031-12990-2_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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Wang H, Liu R, You MP, Barbetti MJ, Chen Y. Pathogen Biocontrol Using Plant Growth-Promoting Bacteria (PGPR): Role of Bacterial Diversity. Microorganisms 2021; 9:microorganisms9091988. [PMID: 34576883 PMCID: PMC8470069 DOI: 10.3390/microorganisms9091988] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
A vast microbial community inhabits in the rhizosphere, among which, specialized bacteria known as Plant Growth-Promoting Rhizobacteria (PGPR) confer benefits to host plants including growth promotion and disease suppression. PGPR taxa vary in the ways whereby they curtail the negative effects of invading plant pathogens. However, a cumulative or synergistic effect does not always ensue when a bacterial consortium is used. In this review, we reassess the disease-suppressive mechanisms of PGPR and present explanations and illustrations for functional diversity and/or stability among PGPR taxa regarding these mechanisms. We also provide evidence of benefits when PGPR mixtures, rather than individuals, are used for protecting crops from various diseases, and underscore the critical determinant factors for successful use of PGPR mixtures. Then, we evaluate the challenges of and limitations to achieving the desired outcomes from strain/species-rich bacterial assemblages, particularly in relation to their role for plant disease management. In addition, towards locating additive or synergistic outcomes, we highlight why and how the benefits conferred need to be categorized and quantified when different strains/species of PGPR are used in combinations. Finally, we highlight the critical approaches needed for developing PGPR mixtures with improved efficacy and stability as biocontrols for utilization in agricultural fields.
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Affiliation(s)
- Hao Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Research Center of Soil and Water Conservation and Ecological Environment, Chinese Academy of Sciences, Xianyang 712100, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Runjin Liu
- Institute of Mycorrhizal Biotechnology, Qingdao Agricultural University, Qingdao 266109, China;
| | - Ming Pei You
- The UWA Institute of Agriculture, and School of Agriculture and Environment, The University of Western Australia, LB 5005, Perth, WA 6009, Australia; (M.P.Y.); (M.J.B.)
| | - Martin J. Barbetti
- The UWA Institute of Agriculture, and School of Agriculture and Environment, The University of Western Australia, LB 5005, Perth, WA 6009, Australia; (M.P.Y.); (M.J.B.)
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and Environment, The University of Western Australia, LB 5005, Perth, WA 6009, Australia; (M.P.Y.); (M.J.B.)
- Correspondence:
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Bhattacharyya A, Pablo CHD, Mavrodi OV, Weller DM, Thomashow LS, Mavrodi DV. Rhizosphere plant-microbe interactions under water stress. ADVANCES IN APPLIED MICROBIOLOGY 2021; 115:65-113. [PMID: 34140134 DOI: 10.1016/bs.aambs.2021.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Climate change, with its extreme temperature, weather and precipitation patterns, is a major global concern of dryland farmers, who currently meet the challenges of climate change agronomically and with growth of drought-tolerant crops. Plants themselves compensate for water stress by modifying aerial surfaces to control transpiration and altering root hydraulic conductance to increase water uptake. These responses are complemented by metabolic changes involving phytohormone network-mediated activation of stress response pathways, resulting in decreased photosynthetic activity and the accumulation of metabolites to maintain osmotic and redox homeostasis. Phylogenetically diverse microbial communities sustained by plants contribute to host drought tolerance by modulating phytohormone levels in the rhizosphere and producing water-sequestering biofilms. Drylands of the Inland Pacific Northwest, USA, illustrate the interdependence of dryland crops and their associated microbiota. Indigenous Pseudomonas spp. selected there by long-term wheat monoculture suppress root diseases via the production of antibiotics, with soil moisture a critical determinant of the bacterial distribution, dynamics and activity. Those pseudomonads producing phenazine antibiotics on wheat had more abundant rhizosphere biofilms and provided improved tolerance to drought, suggesting a role of the antibiotic in alleviation of drought stress. The transcriptome and metabolome studies suggest the importance of wheat root exudate-derived osmoprotectants for the adaptation of these pseudomonads to the rhizosphere lifestyle and support the idea that the exchange of metabolites between plant roots and microorganisms profoundly affects and shapes the belowground plant microbiome under water stress.
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Affiliation(s)
- Ankita Bhattacharyya
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Clint H D Pablo
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Olga V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - David M Weller
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda S Thomashow
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Dmitri V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States.
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Mavrodi OV, McWilliams JR, Peter JO, Berim A, Hassan KA, Elbourne LDH, LeTourneau MK, Gang DR, Paulsen IT, Weller DM, Thomashow LS, Flynt AS, Mavrodi DV. Root Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas. Front Microbiol 2021; 12:651282. [PMID: 33936009 PMCID: PMC8079746 DOI: 10.3389/fmicb.2021.651282] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model for economically important food, feed, forage, and biomass crops of the grass family. We collected and analyzed root exudates of B. distachyon and demonstrated the presence of multiple carbohydrates, amino acids, organic acids, and phenolic compounds. The subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many of these metabolites provide carbon and energy for the Pseudomonas strains. RNA-seq profiling of bacterial cultures amended with root exudates revealed changes in the expression of genes encoding numerous catabolic and anabolic enzymes, transporters, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost half of the differentially expressed genes mapped to the variable part of the strains’ pangenome, reflecting the importance of the variable gene content in the adaptation of P. fluorescens to the rhizosphere lifestyle. Our results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant hosts.
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Affiliation(s)
- Olga V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Janiece R McWilliams
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Jacob O Peter
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Anna Berim
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Karl A Hassan
- School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Liam D H Elbourne
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Melissa K LeTourneau
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - David R Gang
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Ian T Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - David M Weller
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Linda S Thomashow
- USDA Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, United States
| | - Alex S Flynt
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
| | - Dmitri V Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS, United States
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Zboralski A, Filion M. Genetic factors involved in rhizosphere colonization by phytobeneficial Pseudomonas spp. Comput Struct Biotechnol J 2020; 18:3539-3554. [PMID: 33304453 PMCID: PMC7711191 DOI: 10.1016/j.csbj.2020.11.025] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022] Open
Abstract
Plant growth-promoting rhizobacteria (PGPR) actively colonize the soil portion under the influence of plant roots, called the rhizosphere. Many plant-beneficial Pseudomonas spp. have been characterized as PGPR. They are ubiquitous rod-shaped motile Gram-negative bacteria displaying a high metabolic versatility. Their capacity to protect plants from pathogens and improve plant growth closely depends on their rhizosphere colonization abilities. Various molecular and cellular mechanisms are involved in this complex process, such as chemotaxis, biofilm formation, secondary metabolites biosynthesis, metabolic versatility, and evasion of plant immunity. The burst in Pseudomonas spp. genome sequencing in recent years has been crucial to better understand how they colonize the rhizosphere. In this review, we discuss the recent advances regarding these mechanisms and the underlying bacterial genetic factors required for successful rhizosphere colonization.
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Affiliation(s)
- Antoine Zboralski
- Department of Biology, Université de Moncton, Moncton, NB E1A 3E9, Canada
| | - Martin Filion
- Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada
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14
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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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Zhang J, Mavrodi DV, Yang M, Thomashow LS, Mavrodi OV, Kelton J, Weller DM. Pseudomonas synxantha 2-79 Transformed with Pyrrolnitrin Biosynthesis Genes Has Improved Biocontrol Activity Against Soilborne Pathogens of Wheat and Canola. PHYTOPATHOLOGY 2020; 110:1010-1017. [PMID: 32065038 PMCID: PMC7238759 DOI: 10.1094/phyto-09-19-0367-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A four-gene operon (prnABCD) from Pseudomonas protegens Pf-5 encoding the biosynthesis of the antibiotic pyrronitrin was introduced into P. synxantha (formerly P. fluorescens) 2-79, an aggressive root colonizer of both dryland and irrigated wheat roots that naturally produces the antibiotic phenazine-1-carboxylic acid and suppresses both take-all and Rhizoctonia root rot of wheat. Recombinant strains ZHW15 and ZHW25 produced both antibiotics and maintained population sizes in the rhizosphere of wheat that were comparable to those of strain 2-79. The recombinant strains inhibited in vitro the wheat pathogens Rhizoctonia solani anastomosis group 8 (AG-8) and AG-2-1, Gaeumannomyces graminis var. tritici, Sclerotinia sclerotiorum, Fusarium culmorum, and F. pseudograminearum significantly more than did strain 2-79. Both the wild-type and recombinant strains were equally inhibitory of Pythium ultimum. When applied as a seed treatment, the recombinant strains suppressed take-all, Rhizoctonia root rot of wheat, and Rhizoctonia root and stem rot of canola significantly better than did wild-type strain 2-79.
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Affiliation(s)
- Jibin Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
- Department of Plant Pathology, Washington State University, Pullman 99164-6430, U.S.A
| | - Dmitri V. Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, U.S.A
- Department of Plant Pathology, Washington State University, Pullman 99164-6430, U.S.A
| | - Mingming Yang
- Department of Plant Pathology, Washington State University, Pullman 99164-6430, U.S.A
- Department of Agronomy, Northwest A&F University, Yangling, P. R. China
| | - Linda S. Thomashow
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430, U.S.A
| | - Olga V. Mavrodi
- School of Biological, Environmental, and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, U.S.A
- Department of Plant Pathology, Washington State University, Pullman 99164-6430, U.S.A
| | - Jason Kelton
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430, U.S.A
| | - David M. Weller
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA 99164-6430, U.S.A
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Kramer J, Özkaya Ö, Kümmerli R. Bacterial siderophores in community and host interactions. Nat Rev Microbiol 2020; 18:152-163. [PMID: 31748738 PMCID: PMC7116523 DOI: 10.1038/s41579-019-0284-4] [Citation(s) in RCA: 407] [Impact Index Per Article: 101.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 01/06/2023]
Abstract
Iron is an essential trace element for most organisms. A common way for bacteria to acquire this nutrient is through the secretion of siderophores, which are secondary metabolites that scavenge iron from environmental stocks and deliver it to cells via specific receptors. While there has been tremendous interest in understanding the molecular basis of siderophore synthesis, uptake and regulation, questions about the ecological and evolutionary consequences of siderophore secretion have only recently received increasing attention. In this Review, we outline how eco-evolutionary questions can complement the mechanistic perspective and help to obtain a more integrated view of siderophores. In particular, we explain how secreted diffusible siderophores can affect other community members, leading to cooperative, exploitative and competitive interactions between individuals. These social interactions in turn can spur co-evolutionary arms races between strains and species, lead to ecological dependencies between them and potentially contribute to the formation of stable communities. In brief, this Review shows that siderophores are much more than just iron carriers: they are important mediators of interactions between members of microbial assemblies and the eukaryotic hosts they inhabit.
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Affiliation(s)
- Jos Kramer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Özhan Özkaya
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Rolf Kümmerli
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
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Metabolic and Genomic Traits of Phytobeneficial Phenazine-Producing Pseudomonas spp. Are Linked to Rhizosphere Colonization in Arabidopsis thaliana and Solanum tuberosum. Appl Environ Microbiol 2020; 86:AEM.02443-19. [PMID: 31811040 DOI: 10.1128/aem.02443-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/03/2019] [Indexed: 01/01/2023] Open
Abstract
Bacterial rhizosphere colonization is critical for phytobeneficial rhizobacteria such as phenazine-producing Pseudomonas spp. To better understand this colonization process, potential metabolic and genomic determinants required for rhizosphere colonization were identified using a collection of 60 phenazine-producing Pseudomonas strains isolated from multiple plant species and representative of the worldwide diversity. Arabidopsis thaliana and Solanum tuberosum (potato) were used as host plants. Bacterial rhizosphere colonization was measured by quantitative PCR using a newly designed primer pair and TaqMan probe targeting a conserved region of the phenazine biosynthetic operon. The metabolic abilities of the strains were assessed on 758 substrates using Biolog phenotype microarray technology. These data, along with available genomic sequences for all strains, were analyzed in light of rhizosphere colonization. Strains belonging to the P. chlororaphis subgroup colonized the rhizospheres of both plants more efficiently than strains belonging to the P. fluorescens subgroup. Metabolic results indicated that the ability to use amines and amino acids was associated with an increase in rhizosphere colonization capability in A. thaliana and/or in S. tuberosum The presence of multiple genetic determinants in the genomes of the different strains involved in catabolic pathways and plant-microbe and microbe-microbe interactions correlated with increased or decreased rhizosphere colonization capabilities in both plants. These results suggest that the metabolic and genomic traits found in different phenazine-producing Pseudomonas strains reflect their rhizosphere competence in A. thaliana and S. tuberosum Interestingly, most of these traits are associated with similar rhizosphere colonizing capabilities in both plant species.IMPORTANCE Rhizosphere colonization is crucial for plant growth promotion and biocontrol by antibiotic-producing Pseudomonas spp. This colonization process relies on different bacterial determinants which partly remain to be uncovered. In this study, we combined a metabolic and a genomic approach to decipher new rhizosphere colonization determinants which could improve our understanding of this process in Pseudomonas spp. Using 60 distinct strains of phenazine-producing Pseudomonas spp., we show that rhizosphere colonization abilities correlated with both metabolic and genomic traits when these bacteria were inoculated on two distant plants, Arabidopsis thaliana and Solanum tuberosum Key metabolic and genomic determinants presumably required for efficient colonization of both plant species were identified. Upon further validation, these targets could lead to the development of simple screening tests to rapidly identify efficient rhizosphere colonizers.
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Mohd Taha MD, Mohd Jaini MF, Saidi NB, Abdul Rahim R, Md Shah UK, Mohd Hashim A. Biological control of Erwinia mallotivora, the causal agent of papaya dieback disease by indigenous seed-borne endophytic lactic acid bacteria consortium. PLoS One 2019; 14:e0224431. [PMID: 31841519 PMCID: PMC6913974 DOI: 10.1371/journal.pone.0224431] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 10/15/2019] [Indexed: 11/18/2022] Open
Abstract
Dieback disease caused by Erwinia mallotivora is a major threat to papaya plantation in Malaysia. The current study was conducted to evaluate the potential of endophytic lactic acid bacteria (LAB) isolated from papaya seeds for disease suppression of papaya dieback. Two hundred and thirty isolates were screened against E. mallotivora BT-MARDI, and the inhibitory activity of the isolates against the pathogen was ranging from 11.7–23.7 mm inhibition zones. The synergistic experiments revealed that combination of W. cibaria PPKSD19 and Lactococcus lactis subsp. lactis PPSSD39 increased antibacterial activity against the pathogen. The antibacterial activity was partially due to the production of bacteriocin-like inhibitory substances (BLIS). The nursery experiment confirmed that the application of bacterial consortium W. cibaria PPKSD19 and L. lactis subsp. lactis PPSSD39 significantly reduced disease severity to 19% and increased biocontrol efficacy to 69% of infected papaya plants after 18 days of treatment. This study showed that W. cibaria PPKSD19 and L. lactis subsp. lactis PPSSD39 are potential candidate as biocontrol agents against papaya dieback disease.
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Affiliation(s)
- Mariam Dayana Mohd Taha
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohammad Fahrulazri Mohd Jaini
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Noor Baity Saidi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Umi Kalsom Md Shah
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Amalia Mohd Hashim
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- * E-mail:
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Köhl J, Kolnaar R, Ravensberg WJ. Mode of Action of Microbial Biological Control Agents Against Plant Diseases: Relevance Beyond Efficacy. FRONTIERS IN PLANT SCIENCE 2019; 10:845. [PMID: 31379891 PMCID: PMC6658832 DOI: 10.3389/fpls.2019.00845] [Citation(s) in RCA: 345] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/12/2019] [Indexed: 05/19/2023]
Abstract
Microbial biological control agents (MBCAs) are applied to crops for biological control of plant pathogens where they act via a range of modes of action. Some MBCAs interact with plants by inducing resistance or priming plants without any direct interaction with the targeted pathogen. Other MBCAs act via nutrient competition or other mechanisms modulating the growth conditions for the pathogen. Antagonists acting through hyperparasitism and antibiosis are directly interfering with the pathogen. Such interactions are highly regulated cascades of metabolic events, often combining different modes of action. Compounds involved such as signaling compounds, enzymes and other interfering metabolites are produced in situ at low concentrations during interaction. The potential of microorganisms to produce such a compound in vitro does not necessarily correlate with their in situ antagonism. Understanding the mode of action of MBCAs is essential to achieve optimum disease control. Also understanding the mode of action is important to be able to characterize possible risks for humans or the environment and risks for resistance development against the MBCA. Preferences for certain modes of action for an envisaged application of a MBCA also have impact on the screening methods used to select new microbials. Screening of MBCAs in bioassays on plants or plant tissues has the advantage that MBCAs with multiple modes of action and their combinations potentially can be detected whereas simplified assays on nutrient media strongly bias the selection toward in vitro production of antimicrobial metabolites which may not be responsible for in situ antagonism. Risks assessments for MBCAs are relevant if they contain antimicrobial metabolites at effective concentration in the product. However, in most cases antimicrobial metabolites are produced by antagonists directly on the spot where the targeted organism is harmful. Such ubiquitous metabolites involved in natural, complex, highly regulated interactions between microbial cells and/or plants are not relevant for risk assessments. Currently, risks of microbial metabolites involved in antagonistic modes of action are often assessed similar to assessments of single molecule fungicides. The nature of the mode of action of antagonists requires a rethinking of data requirements for the registration of MBCAs.
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Affiliation(s)
- Jürgen Köhl
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
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Plant growth-promoting Rhizopseudomonas: expanded biotechnological purposes and antimicrobial resistance concern. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1389-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Kenny DJ, Balskus EP. Engineering chemical interactions in microbial communities. Chem Soc Rev 2018; 47:1705-1729. [PMID: 29210396 DOI: 10.1039/c7cs00664k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Microbes living within host-associated microbial communities (microbiotas) rely on chemical communication to interact with surrounding organisms. These interactions serve many purposes, from supplying the multicellular host with nutrients to antagonizing invading pathogens, and breakdown of chemical signaling has potentially negative consequences for both the host and microbiota. Efforts to engineer microbes to take part in chemical interactions represent a promising strategy for modulating chemical signaling within these complex communities. In this review, we discuss prominent examples of chemical interactions found within host-associated microbial communities, with an emphasis on the plant-root microbiota and the intestinal microbiota of animals. We then highlight how an understanding of such interactions has guided efforts to engineer microbes to participate in chemical signaling in these habitats. We discuss engineering efforts in the context of chemical interactions that enable host colonization, promote host health, and exclude pathogens. Finally, we describe prominent challenges facing this field and propose new directions for future engineering efforts.
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Affiliation(s)
- Douglas J Kenny
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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de Bruijn I, Liu Y, Wiegertjes GF, Raaijmakers JM. Exploring fish microbial communities to mitigate emerging diseases in aquaculture. FEMS Microbiol Ecol 2017; 94:4675208. [DOI: 10.1093/femsec/fix161] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 11/28/2017] [Indexed: 12/21/2022] Open
Affiliation(s)
- Irene de Bruijn
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands
| | - Yiying Liu
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands
| | - Geert F Wiegertjes
- Cell Biology and Immunology group, Department of Animal Sciences, Wageningen University & Research, De Elst 1, Wageningen 6708WD, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, Wageningen 6708PB, The Netherlands
- Institute of Biology (IBL), Leiden University, Sylviusweg 72, Leiden 2333 BE, Leiden, The Netherlands
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Siderophore cheating and cheating resistance shape competition for iron in soil and freshwater Pseudomonas communities. Nat Commun 2017; 8:414. [PMID: 28871205 PMCID: PMC5583256 DOI: 10.1038/s41467-017-00509-4] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 06/29/2017] [Indexed: 11/17/2022] Open
Abstract
All social organisms experience dilemmas between cooperators performing group-beneficial actions and cheats selfishly exploiting these actions. Although bacteria have become model organisms to study social dilemmas in laboratory systems, we know little about their relevance in natural communities. Here, we show that social interactions mediated by a single shareable compound necessary for growth (the iron-scavenging pyoverdine) have important consequences for competitive dynamics in soil and pond communities of Pseudomonas bacteria. We find that pyoverdine non- and low-producers co-occur in many natural communities. While non-producers have genes coding for multiple pyoverdine receptors and are able to exploit compatible heterologous pyoverdines from other community members, producers differ in the pyoverdine types they secrete, offering protection against exploitation from non-producers with incompatible receptors. Our findings indicate that there is both selection for cheating and cheating resistance, which could drive antagonistic co-evolution and diversification in natural bacterial communities. Lab strains of Pseudomonas are model systems for the evolution of cooperation over public goods (iron-scavenging siderophores). Here, Butaitė et al. add ecological and evolutionary insight into this system by showing that cheating and resistance to cheating both shape competition for iron in natural Pseudomonas communities.
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Abstract
Microbes in nature often live in unfavorable conditions. To survive, they have to occupy niches close to food sources and efficiently utilize nutrients that are often present in very low concentrations. Moreover, they have to possess an arsenal of attack and defense mechanisms against competing bacteria. In this review, we will discuss strategies used by microbes to compete with each other in the rhizosphere and on fruits, with a focus on mechanisms of inter- and intra-species antagonism. Special attention will be paid to the recently discovered roles of volatile organic compounds. Several microbes with proven capabilities in the art of warfare are being applied in products used for the biological control of plant diseases, including post-harvest control of fruits and vegetables.
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Affiliation(s)
- Ben Lugtenberg
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands
| | - Faina Kamilova
- Koppert Biological Systems, Veilingweg 14, PO Box 155, 2650 AD Berkel en Rodenrijs, Netherlands
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Pyoverdine and histicorrugatin-mediated iron acquisition in Pseudomonas thivervalensis. Biometals 2016; 29:467-85. [DOI: 10.1007/s10534-016-9929-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 03/19/2016] [Indexed: 12/17/2022]
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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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Berendsen RL, van Verk MC, Stringlis IA, Zamioudis C, Tommassen J, Pieterse CMJ, Bakker PAHM. Unearthing the genomes of plant-beneficial Pseudomonas model strains WCS358, WCS374 and WCS417. BMC Genomics 2015. [PMID: 26198432 PMCID: PMC4509608 DOI: 10.1186/s12864-015-1632-z] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Plant growth-promoting rhizobacteria (PGPR) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (ISR). In the past 30 years, the Pseudomonas spp. PGPR strains WCS358, WCS374 and WCS417 of the Willie Commelin Scholten (WCS) collection have been studied in detail in pioneering papers on the molecular basis of PGPR-mediated ISR and mechanisms of biological control of soil-borne pathogens via siderophore-mediated competition for iron. Results The genomes of the model WCS PGPR strains were sequenced and analyzed to unearth genetic cues related to biological questions that surfaced during the past 30 years of functional studies on these plant-beneficial microbes. Whole genome comparisons revealed important novel insights into iron acquisition strategies with consequences for both bacterial ecology and plant protection, specifics of bacterial determinants involved in plant-PGPR recognition, and diversity of protein secretion systems involved in microbe-microbe and microbe-plant communication. Furthermore, multi-locus sequence alignment and whole genome comparison revealed the taxonomic position of the WCS model strains within the Pseudomonas genus. Despite the enormous diversity of Pseudomonas spp. in soils, several plant-associated Pseudomonas spp. strains that have been isolated from different hosts at different geographic regions appear to be nearly isogenic to WCS358, WCS374, or WCS417. Interestingly, all these WCS look-a-likes have been selected because of their plant protective or plant growth-promoting properties. Conclusions The genome sequences of the model WCS strains revealed that they can be considered representatives of universally-present plant-beneficial Pseudomonas spp. With their well-characterized functions in the promotion of plant growth and health, the fully sequenced genomes of the WCS strains provide a genetic framework that allows for detailed analysis of the biological mechanisms of the plant-beneficial traits of these PGPR. Considering the increasing focus on the role of the root microbiome in plant health, functional genomics of the WCS strains will enhance our understanding of the diversity of functions of the root microbiome. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1632-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Marcel C van Verk
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands. .,Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Christos Zamioudis
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Jan Tommassen
- Molecular Microbiology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Peter A H M Bakker
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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Huguenot D, Bois P, Cornu JY, Jezequel K, Lollier M, Lebeau T. Remediation of sediment and water contaminated by copper in small-scaled constructed wetlands: effect of bioaugmentation and phytoextraction. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:721-732. [PMID: 25106519 DOI: 10.1007/s11356-014-3406-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 07/30/2014] [Indexed: 06/03/2023]
Abstract
The use of plants and microorganisms to mitigate sediment contaminated by copper was studied in microcosms that mimic the functioning of a stormwater basin (SWB) connected to vineyard watershed. The impact of phytoremediation and bioaugmentation with siderophore-producing bacteria on the fate of Cu was studied in two contrasted (batch vs. semi-continuous) hydraulic regimes. The fate of copper was characterised following its discharge at the outlet of the microcosms, its pore water concentration in the sediment, the assessment of its bioaccessible fraction in the rhizosphere and the measurement of its content in plant tissues. Physico-chemical (pH, redox potential) and biological parameters (total heterotrophic bacteria) were also monitored. As expected, the results showed a clear impact of the hydraulic regime on the redox potential and thus on the pore water concentration of Cu. Copper in pore water was also dependent on the frequency of Cu-polluted water discharges. Repeated bioaugmentation increased the total heterotrophic microflora as well as the Cu bioaccessibility in the rhizosphere and increased the amount of Cu extracted by Phragmites australis by a factor of ~2. Sugar beet pulp, used as a filter to avoid copper flushing, retained 20% of outcoming Cu and led to an overall retention of Cu higher than 94% when arranged at the outlet of microcosms. Bioaugmentation clearly improved the phytoextraction rate of Cu in a small-scaled SWB designed to mimic the functioning of a full-size SWB connected to vineyard watershed. Highlights: Cu phytoextraction in constructed wetlands much depends on the hydraulic regime and on the frequency of Cu-polluted water discharges. Cu phytoextraction increases with time and plant density. Cu bioaccessibility can be increased by bioaugmentation with siderophore-producing bacteria.
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Affiliation(s)
- D Huguenot
- Equipe Dépollution Biologique des Sols, Université de Haute Alsace, EA 3991 LVBE (Laboratoire Vigne Biotechnologies et Environnement), 33 rue de Herrlisheim, BP 50568 68008, Colmar, France,
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Niranjana SR, Hariprasad P. Understanding the Mechanism Involved in PGPR-Mediated Growth Promotion and Suppression of Biotic and Abiotic Stress in Plants. Fungal Biol 2014. [DOI: 10.1007/978-1-4939-1188-2_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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Ferric-pyoverdine recognition by Fpv outer membrane proteins of Pseudomonas protegens Pf-5. J Bacteriol 2012; 195:765-76. [PMID: 23222724 DOI: 10.1128/jb.01639-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The soil bacterium Pseudomonas protegens Pf-5 (previously called P. fluorescens Pf-5) produces two siderophores, enantio-pyochelin and a compound in the large and diverse pyoverdine family. Using high-resolution mass spectroscopy, we determined the structure of the pyoverdine produced by Pf-5. In addition to producing its own siderophores, Pf-5 also utilizes ferric complexes of some pyoverdines produced by other strains of Pseudomonas spp. as sources of iron. Previously, phylogenetic analysis of the 45 TonB-dependent outer membrane proteins in Pf-5 indicated that six are in a well-supported clade with ferric-pyoverdine receptors (Fpvs) from other Pseudomonas spp. We used a combination of phylogenetics, bioinformatics, mutagenesis, pyoverdine structural determinations, and cross-feeding bioassays to assign specific ferric-pyoverdine substrates to each of the six Fpvs of Pf-5. We identified at least one ferric-pyoverdine that was taken up by each of the six Fpvs of Pf-5. Functional redundancy of the Pf-5 Fpvs was also apparent, with some ferric-pyoverdines taken up by all mutants with a single Fpv deletion but not by a mutant having deletions in two of the Fpv-encoding genes. Finally, we demonstrated that phylogenetically related Fpvs take up ferric complexes of structurally related pyoverdines, thereby establishing structure-function relationships that can be employed in the future to predict the pyoverdine substrates of Fpvs in other Pseudomonas spp.
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Matthijs S, Laus G, Meyer JM, Abbaspour-Tehrani K, Schäfer M, Budzikiewicz H, Cornelis P. Siderophore-mediated iron acquisition in the entomopathogenic bacterium Pseudomonas entomophila L48 and its close relative Pseudomonas putida KT2440. Biometals 2011; 22:951-64. [PMID: 19459056 DOI: 10.1007/s10534-009-9247-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 05/05/2009] [Indexed: 11/26/2022]
Abstract
Pseudomonas entomophila L48 is a recently identified entomopathogenic bacterium which, upon ingestion, kills Drosophila melanogaster, and is closely related to P. putida. The complete genome of this species has been sequenced and therefore a genomic, genetic and structural analysis of the siderophore-mediated iron acquisition was undertaken. P. entomophila produces two siderophores, a structurally new and unique pyoverdine and the secondary siderophore pseudomonine, already described in P. fluorescens species. Structural analysis of the pyoverdine produced by the closely related P. putida KT2440 showed that this strain produces an already characterised pyoverdine, but different from P. entomophila, and no evidence was found for the production of a second siderophore. Growth stimulation assays with heterologous pyoverdines demonstrated that P. entomophila is able to utilize a large variety of structurally distinct pyoverdines produced by other Pseudomonas species. In contrast, P. putida KT2440 is able to utilize only its own pyoverdine and the pyoverdine produced by P. syringae LMG 1247. Our data suggest that although closely related, P. entomophila is a more efficient competitor for iron than P. putida.
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Affiliation(s)
- Sandra Matthijs
- Laboratory of Microbial Interactions, Department of Molecular and Cellular Interactions, Flanders Interuniversity Institute for Biotechnology, Vrije Universiteit Brussel, Building E, Pleinlaan 2, 1050 Brussels, Belgium
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Belgrove A, Steinberg C, Viljoen A. Evaluation of Nonpathogenic Fusarium oxysporum and Pseudomonas fluorescens for Panama Disease Control. PLANT DISEASE 2011; 95:951-959. [PMID: 30732104 DOI: 10.1094/pdis-06-10-0409] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Nonpathogenic Fusarium oxysporum endophytes from healthy banana roots were evaluated for their ability to reduce Fusarium wilt of banana (Panama disease). Isolates were identified morphologically and by using species-specific primers. Pathogenicity was confirmed by inoculating banana plantlets in the greenhouse. Nonpathogenic F. oxysporum isolates were grouped into 14 haplotype groups by polymerase chain reaction restriction fragment length polymorphism analysis of the intergenic spacer region, and representative isolates evaluated for biocontrol of F. oxysporum f. sp. cubense. In the greenhouse, 10 nonpathogenic F. oxysporum isolates were able to significantly reduce Fusarium wilt of banana. The isolate that protected banana plantlets best in the greenhouse, a nonpathogenic F. oxysporum from the root rhizosphere, and Pseudomonas fluorescens WCS 417 were then field tested. When the putative biological control organisms were tested in the field, neither the nonpathogenic F. oxysporum, P. fluorescens, nor combinations thereof reduced Fusarium wilt development significantly. A number of factors could contribute to the lack of field protection, including soil microbial and chemical composition and reduced survival of biocontrol organisms in banana roots. A lack of knowledge regarding the etiology of Fusarium wilt of 'Cavendish' banana in the subtropics and the effect of F. oxysporum f. sp. cubense race and banana cultivar in protection of banana by biocontrol organisms should be further investigated.
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Affiliation(s)
- A Belgrove
- Agricultural Research Council-Grain Crops Institute, Potchefstroom 2520, South Africa, and Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - C Steinberg
- INRA-Université de Bourgogne, Microbiology of Soil and Environment, Dijon, France
| | - A Viljoen
- Department of Plant Pathology, University of Stellenbosch, Matieland 7602, South Africa
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Hartney SL, Mazurier S, Kidarsa TA, Quecine MC, Lemanceau P, Loper JE. TonB-dependent outer-membrane proteins and siderophore utilization in Pseudomonas fluorescens Pf-5. Biometals 2010; 24:193-213. [PMID: 21080032 DOI: 10.1007/s10534-010-9385-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 10/16/2010] [Indexed: 12/30/2022]
Abstract
The soil bacterium Pseudomonas fluorescens Pf-5 produces two siderophores, a pyoverdine and enantio-pyochelin, and its proteome includes 45 TonB-dependent outer-membrane proteins, which commonly function in uptake of siderophores and other substrates from the environment. The 45 proteins share the conserved β-barrel and plug domains of TonB-dependent proteins but only 18 of them have an N-terminal signaling domain characteristic of TonB-dependent transducers (TBDTs), which participate in cell-surface signaling systems. Phylogenetic analyses of the 18 TBDTs and 27 TonB-dependent receptors (TBDRs), which lack the N-terminal signaling domain, suggest a complex evolutionary history including horizontal transfer among different microbial lineages. Putative functions were assigned to certain TBDRs and TBDTs in clades including well-characterized orthologs from other Pseudomonas spp. A mutant of Pf-5 with deletions in pyoverdine and enantio-pyochelin biosynthesis genes was constructed and characterized for iron-limited growth and utilization of a spectrum of siderophores. The mutant could utilize as iron sources a large number of pyoverdines with diverse structures as well as ferric citrate, heme, and the siderophores ferrichrome, ferrioxamine B, enterobactin, and aerobactin. The diversity and complexity of the TBDTs and TBDRs with roles in iron uptake clearly indicate the importance of iron in the fitness and survival of Pf-5 in the environment.
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Affiliation(s)
- Sierra L Hartney
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, USA
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Dulla GFJ, Krasileva KV, Lindow SE. Interference of quorum sensing in Pseudomonas syringae by bacterial epiphytes that limit iron availability. Environ Microbiol 2010; 12:1762-74. [DOI: 10.1111/j.1462-2920.2010.02261.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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Joshi FR, Kholiya SP, Archana G, Desai AJ. Siderophore cross-utilization amongst nodule isolates of the cowpea miscellany group and its effect on plant growth in the presence of antagonistic organisms. Microbiol Res 2008; 163:564-70. [PMID: 16962753 DOI: 10.1016/j.micres.2006.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2006] [Revised: 08/07/2006] [Accepted: 08/09/2006] [Indexed: 10/24/2022]
Abstract
Nodule isolates from the cowpea miscellany group of legumes produced varying concentrations of catecholate and hydroxamate types of siderophores under iron-limiting conditions. The nodule isolates differed with respect to siderophore cross-utilizing abilities; some were proficient at using siderophores of other nodule isolates (homologous siderophores) while others could utilize siderophores produced by other rhizospheric bacteria (heterologous siderophores). Utilization of siderophore of rhizospheric bacterium PsB, a plant pathogen, benefited the nodule isolate G11 in terms of growth under iron-limiting laboratory conditions, while PsB was clearly inhibited in the presence of G11. Plate assays showed that siderophore of G11 could withhold iron from PsB and hence PsB was inhibited in the presence of G11. Isolates G11 and PsB when applied simultaneously to peanut seedlings under sterile soil conditions, provided a clear advantage to the plant in terms of reduction in the inhibitory effect of PsB. The count of the nodule isolate G11 increased in the soil when co-inoculated with PsB, as compared to when inoculated alone. Thus, the increased growth of the plant can be attributed to the iron sequestration and plant growth promoting properties of G11. The isolate G11 could utilize the siderophores produced by many other rhizospheric isolates while the siderophore of G11 was not being utilized by these rhizospheric isolates.
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Affiliation(s)
- Falguni R Joshi
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
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Timely awareness and prevention of emerging chemical and biochemical risks in foods: proposal for a strategy based on experience with recent cases. Food Chem Toxicol 2008; 47:992-1008. [PMID: 18790713 DOI: 10.1016/j.fct.2008.08.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Revised: 08/19/2008] [Accepted: 08/20/2008] [Indexed: 12/21/2022]
Abstract
A number of recent food safety incidents have involved chemical substances, while various activities aim at the early identification of emerging chemical risks. This review considers recent cases of chemical and biochemical risks, as a basis for recommendations for awareness and prevention of similar risks at an early stage. These cases include examples of unapproved genetically modified food crops, intoxications with botanical products containing unintentionally admixed toxic herbs, residues of unapproved antibiotics and contaminants in farmed aquaculture species such as shrimp and salmon; and adverse effects of chemical and biological pesticides of natural origin. Besides case-specific recommendations for mitigation of future incidents of the same nature, general inferences and recommendations are made. It is recommended, for example, to establish databases for contaminants potentially present within products. Pro-active reconnaissance can facilitate the identification of products potentially contaminated with hazardous substances. In international trade, prevention and early identification of hazards are aided by management systems for product quality and safety, rigorous legislation, and inspections of consignments destined for export. Cooperation with the private sector and foreign authorities may be required to achieve these goals. While food and feed safety are viewed from the European perspective, the outcomes also apply to other regions.
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Mercado-Blanco J, Bakker PAHM. Interactions between plants and beneficial Pseudomonas spp.: exploiting bacterial traits for crop protection. Antonie Van Leeuwenhoek 2007; 92:367-89. [PMID: 17588129 DOI: 10.1007/s10482-007-9167-1] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 03/12/2007] [Indexed: 11/29/2022]
Abstract
Specific strains of fluorescent Pseudomonas spp. inhabit the environment surrounding plant roots and some even the root interior. Introducing such bacterial strains to plant roots can lead to increased plant growth, usually due to suppression of plant pathogenic microorganisms. We review the modes of action and traits of these beneficial Pseudomonas bacteria involved in disease suppression. The complex regulation of biological control traits in relation to the functioning in the root environment is discussed. Understanding the complexity of the interactions is instrumental in the exploitation of beneficial Pseudomonas spp. in controlling plant diseases.
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Affiliation(s)
- Jesús Mercado-Blanco
- Departamento de Protección de Cultivos, Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Apartado 4084, 14080 Cordoba, Spain.
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40
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Weller DM. Pseudomonas biocontrol agents of soilborne pathogens: looking back over 30 years. PHYTOPATHOLOGY 2007; 97:250-6. [PMID: 18944383 DOI: 10.1094/phyto-97-2-0250] [Citation(s) in RCA: 235] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
ABSTRACT Pseudomonas spp. are ubiquitous bacteria in agricultural soils and have many traits that make them well suited as biocontrol agents of soilborne pathogens. Tremendous progress has been made in characterizing the process of root colonization by pseudomonads, the biotic and abiotic factors affecting colonization, bacterial traits and genes contributing to rhizosphere competence, and the mechanisms of pathogen suppression. This review looks back over the last 30 years of Pseudomonas biocontrol research and highlights key studies, strains, and findings that have had significant impact on shaping our current understanding of biological control by bacteria and the direction of future research.
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Lemanceau P, Robin A, Mazurier S, Vansuyt G. Implication of Pyoverdines in the Interactions of Fluorescent Pseudomonads with Soil Microflora and Plant in the Rhizosphere. SOIL BIOLOGY 2007. [DOI: 10.1007/978-3-540-71160-5_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Weller DM, Landa BB, Mavrodi OV, Schroeder KL, De La Fuente L, Blouin Bankhead S, Allende Molar R, Bonsall RF, Mavrodi DV, Thomashow LS. Role of 2,4-diacetylphloroglucinol-producing fluorescent Pseudomonas spp. in the defense of plant roots. PLANT BIOLOGY (STUTTGART, GERMANY) 2007; 9:4-20. [PMID: 17058178 DOI: 10.1055/s-2006-924473] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Plants have evolved strategies of stimulating and supporting specific groups of antagonistic microorganisms in the rhizosphere as a defense against diseases caused by soilborne plant pathogens owing to a lack of genetic resistance to some of the most common and widespread soilborne pathogens. Some of the best examples of natural microbial defense of plant roots occur in disease suppressive soils. Soil suppressiveness against many different diseases has been described. Take-all is an important root disease of wheat, and soils become suppressive to take-all when wheat or barley is grown continuously in a field following a disease outbreak; this phenomenon is known as take-all decline (TAD). In Washington State, USA and The Netherlands, TAD results from the enrichment during monoculture of populations of 2,4-diacetylphloroglucinol (2,4-DAPG)-producing Pseudomonas fluorescens to a density of 10 (5) CFU/g of root, the threshold required to suppress the take-all pathogen, Gaeumannomyces graminis var. tritici. 2,4-DAPG-producing P. fluorescens also are enriched by monoculture of other crops such as pea and flax, and evidence is accumulating that 2,4-DAPG producers contribute to the defense of plant roots in many different agroecosystems. At this time, 22 distinct genotypes of 2,4-DAPG producers (designated A - T, PfY and PfZ) have been defined by whole-cell repetitive sequence-based (rep)-PCR analysis, restriction fragment length polymorphism (RFLP) analysis of PHLD, and phylogenetic analysis of PHLD, but the number of genotypes is expected to increase. The genotype of an isolate is predictive of its rhizosphere competence on wheat and pea. Multiple genotypes often occur in a single soil and the crop species grown modulates the outcome of the competition among these genotypes in the rhizosphere. 2,4-DAPG producers are highly effective biocontrol agents against a variety of plant diseases and ideally suited for serving as vectors for expressing other biocontrol traits in the rhizosphere.
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Affiliation(s)
- D M Weller
- USDA-ARS Root Disease and Biological Control Research Unit, Washington State University, P.O. Box 646430, 367 Johnson Hall, Pullman, WA 99164-6430, USA.
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Robin A, Mougel C, Siblot S, Vansuyt G, Mazurier S, Lemanceau P. Effect of ferritin overexpression in tobacco on the structure of bacterial and pseudomonad communities associated with the roots. FEMS Microbiol Ecol 2006; 58:492-502. [PMID: 17117991 DOI: 10.1111/j.1574-6941.2006.00174.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The genetic structures of total bacterial and pseudomonad communities were characterized in rhizosphere soil and rhizoplane+root tissues of tobacco wild type and a ferritin overexpressor transgenic line (P6) by a cultivation-independent method using directly extracted DNA at the end of three consecutive plant cultures. The structure of total bacterial communities was characterized by automated ribosomal intergenic spacer analysis (A-RISA), and that of pseudomonad communities was characterized by PCR-restriction fragment length polymorphism (PCR-RFLP) from DNA amplified with specific primers. The structure of total bacterial communities was significantly modified in the rhizosphere soil by the overaccumulation of iron in the tobacco transgenic P6 line at the first culture, to a lesser extent at the second culture, and not at all at the third culture. No significant difference was recorded between the total communities associated with the roots (rhizoplane+root tissues) of the two plant genotypes in any of the cultures. In contrast, the difference in pseudomonad structure between the two plant genotypes increased with successive culture at the root level, but was not detected at a significant level in the rhizosphere soil. The impact of iron overaccumulation by the tobacco transgenic P6 line on pseudomonads supports previous findings on the importance of iron competition among fluorescent pseudomonads.
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Affiliation(s)
- Agnès Robin
- INRA-Université de Bourgogne, UMR Microbiologie et Géochimie des Sols, Dijon, France
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Rajendran G, Mistry S, Desai AJ, Archana G. Functional expression of Escherichia coli fhuA gene in Rhizobium spp. of Cajanus cajan provides growth advantage in presence of Fe3+: ferrichrome as iron source. Arch Microbiol 2006; 187:257-64. [PMID: 17136381 DOI: 10.1007/s00203-006-0191-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Accepted: 10/20/2006] [Indexed: 11/24/2022]
Abstract
Cajanus cajan rhizobial isolates were found to be unable to utilize iron bound to ferrichrome, desferrioxamine B or rhodotorulic acid, all being hydroxamate type siderophores. A broad host range expression vector containing the Escherichia coli fhuA gene, encoding the outer membrane receptor for Fe-ferrichrome, was constructed. The plasmid construct (pGR1), designed to express fhuA under the lac promoter of E. coli, complemented E. coli MB97 DeltafhuA mutant for ferri-ferrichrome utilization and also allowed Rhizobium spp. ST1 and Rhizobium spp. IC3123 to grow using iron bound to ferrichrome. Sensitivity to the antibiotic albomycin, transported via the FhuA receptor, was found in case of MB97 as well as rhizobial transformants harboring pGR1. The rhizobial transformants expressing fhuA showed growth stimulation when co-inoculated with Ustilago maydis, a fungal species known to produce ferrichrome under iron starved conditions. Growth stimulation was also observed in the presence of externally supplied ferrichrome. The significance of these findings in terms of the potential for improving the survivability of rhizobial bioinoculant strains in natural soils is discussed.
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Affiliation(s)
- Geetha Rajendran
- Department of Microbiology and Biotechnology Centre, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
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Joshi F, Archana G, Desai A. Siderophore cross-utilization amongst rhizospheric bacteria and the role of their differential affinities for Fe3+ on growth stimulation under iron-limited conditions. Curr Microbiol 2006; 53:141-7. [PMID: 16845564 DOI: 10.1007/s00284-005-0400-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Accepted: 04/03/2006] [Indexed: 10/24/2022]
Abstract
The majority of bacteria isolated from rhizospheres of Arachis hypogea (Groundnut) and Vigna radiata (Mung bean) predominantly produced catechol-type siderophores except for a few fluorescent pseudomonads that produced hydroxamates in addition to catecholates. The rhizospheric isolates differed in their ability to cross-utilize siderophores produced by other rhizospheric isolates (heterologous); some were highly proficient at utilizing heterologous siderophores, while others were poor cross-utilizers. Isolate G9, which utilized hydroxamate as well as catecholate siderophores, was found to be an efficient siderophore cross-utilizer, while isolates G2 and G6 were poor-utilizers of catecholate and non-utilizers of hydroxamate siderophores. Growth stimulation of two isolates G9 and G6 was seen when grown in the presence of externally supplied heterologous siderophores, which they cross-utilized. The iron-regulated outer membrane protein (IROMP) profiles differed for the most cross-utilizer and the least cross-utilizer strains, but in both the cases no new outer membrane proteins (OMP) were induced in response to the exogenous siderophores supplied. The growth of the organisms in the presence of heterologous siderophores that they failed to cross-utilize led to growth inhibition in the case of isolate G9. This appears to be due to a lower affinity of the siderophore of G9 as compared to the exogenously supplied G6 siderophore. A simple method was devised to measure relative affinities of respective siderophores for iron based on CAS solution decolorization by the siderophore preparations. The effect on the growth of the differential affinities of the siderophores for iron and the interactions of the organisms through cross-utilization is also discussed.
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Affiliation(s)
- Falguni Joshi
- Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Baroda, India
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Compant S, Duffy B, Nowak J, Clément C, Barka EA. Use of plant growth-promoting bacteria for biocontrol of plant diseases: principles, mechanisms of action, and future prospects. Appl Environ Microbiol 2005; 71:4951-9. [PMID: 16151072 PMCID: PMC1214602 DOI: 10.1128/aem.71.9.4951-4959.2005] [Citation(s) in RCA: 866] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Stéphane Compant
- Laboratoire de Stress, Défenses et Reproduction des Plantes, Unité de Recherche Vignes et Vins de Champagne, UPRES EA 2069, UFR Sciences, Université de Reims Champagne-Ardenne, 51687 Reims Cedex 2, France
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Bhatt G, Denny TP. Ralstonia solanacearum iron scavenging by the siderophore staphyloferrin B is controlled by PhcA, the global virulence regulator. J Bacteriol 2004; 186:7896-904. [PMID: 15547261 PMCID: PMC529077 DOI: 10.1128/jb.186.23.7896-7904.2004] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PhcA is a transcriptional regulator that activates expression of multiple virulence genes in the plant pathogen Ralstonia solanacearum. Relative to their wild-type parents, phcA mutants overproduced iron-scavenging activity detected with chrome azurol S siderophore detection medium. Transposon mutagenesis of strain AW1-PC (phcA1) generated strain GB6, which was siderophore negative but retained weak iron-scavenging activity. The ssd gene inactivated in GB6 encodes a protein similar to group IV amino acid decarboxylases, and its transcription was repressed by iron(III) and PhcA. ssd is the terminal gene in a putative operon that also appears to encode three siderophore synthetase subunits, a integral membrane exporter, and three genes with no obvious role in siderophore production. A homologous operon was found in the genomes of Ralstonia metallidurans and Staphylococcus aureus, both of which produce the polycarboxylate siderophore staphyloferrin B. Comparison of the siderophores present in culture supernatants of R. solanacearum, R. metallidurans, and Bacillus megaterium using chemical tests, a siderophore utilization bioassay, thin-layer chromatography, and mass spectroscopy indicated that R. solanacearum produces staphyloferrin B rather than schizokinen as was reported previously. Inactivation of ssd in a wild-type AW1 background resulted in a mutant almost incapable of scavenging iron but normally virulent on tomato plants. AW1 did not produce siderophore activity when cultured in tomato xylem sap, suggesting that the main location in tomato for R. solanacearum during pathogenesis is iron replete.
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Affiliation(s)
- Garima Bhatt
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
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Bergsma-Vlami M, Prins ME, Raaijmakers JM. Influence of plant species on population dynamics, genotypic diversity and antibiotic production in the rhizosphere by indigenous Pseudomonas spp. FEMS Microbiol Ecol 2004; 52:59-69. [PMID: 16329893 DOI: 10.1016/j.femsec.2004.10.007] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2004] [Revised: 09/02/2004] [Accepted: 10/21/2004] [Indexed: 11/25/2022] Open
Abstract
The population dynamics, genotypic diversity and activity of naturally-occurring 2,4-diacetylphloroglucinol (DAPG)-producing Pseudomonas spp. was investigated for four plant species (wheat, sugar beet, potato, lily) grown in two different soils. All four plant species tested, except lily and in some cases wheat, supported relatively high rhizosphere populations (5 x 10(4) to 1 x 10(6) CFU/g root) of indigenous DAPG-producing Pseudomonas spp. during successive cultivation in both a take-all suppressive and a take-all conducive soil. Although lily supported on average the highest population densities of fluorescent Pseudomonas spp., it was the least supportive of DAPG-producing Pseudomonas spp. of all four plant species. The genotypic diversity of 492 DAPG-producing Pseudomonas isolates, assessed by Denaturing Gradient Gel Electrophoresis (DGGE) analysis of the phlD gene, revealed a total of 7 genotypes. Some of the genotypes were found only in the rhizosphere of a specific plant, whereas the predominant genotypes were found at significantly higher frequencies in the rhizosphere of three plant species (wheat, sugar beet and potato). Statistical analysis of the phlD(+) genotype frequencies showed that the diversity of the phlD(+) isolates from lily was significantly lower than the diversity of phlD(+) isolates found on wheat, sugar beet or potato. Additionally, soil type had a significant effect on both the phlD(+) population density and the phlD(+) genotype frequencies, with the take-all suppressive soil being the most supportive. HPLC analysis further showed that the plant species had a significant effect on DAPG-production by the indigenous phlD(+) population: the wheat and potato rhizospheres supported significantly higher amounts of DAPG produced per cell basis than the rhizospheres of sugar beet and lily. Collectively, the results of this study showed that the host plant species has a significant influence on the dynamics, composition and activity of specific indigenous antagonistic Pseudomonas spp.
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Affiliation(s)
- Maria Bergsma-Vlami
- Laboratory of Phytopathology, Wageningen University, Binnenhaven 5, P.O. Box 8025, 6709, PD Wageningen, The Netherlands
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Shaukat SS, Siddiqui IA. Impact of biocontrol agents Pseudomonas fluorescens CHA0 and its genetically modified derivatives on the diversity of culturable fungi in the rhizosphere of mungbean. J Appl Microbiol 2003; 95:1039-48. [PMID: 14633033 DOI: 10.1046/j.1365-2672.2003.02074.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
AIMS To assess whether Pseudomonas fluorescens strain CHA0 and its genetically modified derivatives, CHA0/pME3424 (antibiotic over-producer) and CHA89 (antibiotic-deficient) could have an impact on the fungal community structure and composition in the rhizosphere of mungbean. METHODS AND RESULTS Under glasshouse conditions, mungbean was grown repeatedly in the same soil, which was inoculated with CHA0, CHA0/pME3424, CHA89 or was left untreated. Treatments were applied to soil at the start of each 36-day mungbean growth cycle, and their effects on the diversity of the rhizosphere populations of culturable fungi were assessed at the end of the first, second and third cycles. The effects of CHA0 and CHA0/pME3424 did differ from the controls while CHA89 did not. Whereas all major fungal species were frequently isolated from both bacterized and nonbacterized rhizospheres, certain fungal species were exclusively promoted or specifically suppressed from Pseudomonas-treated soils. In general, fungal diversity and equitability tended to decrease with time while species richness slightly increased. Whilst a total of 29 fungal species were isolated from the mungbean rhizosphere, only eight species colonized the root tissues. CONCLUSIONS Soil inoculation with Ps. fluorescens CHA0 or CHA0/pME3424 altered fungal community structure in mungbean rhizosphere but strain CHA89 failed to produce such effect. SIGNIFICANCE AND IMPACT OF THE STUDY Pseudomonas fluorescens-mediated alteration in the composition and structure of fungal communities might have acute or lasting effects on ecosystem functioning. Furthermore, the study provides useful data pertinent to characterization of the fate of genetically modified inoculants (e.g. antibiotic-overproducing Pseudomonas strains) released into the environment.
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Affiliation(s)
- S S Shaukat
- Department of Botany, Soil Biology and Ecology Laboratory, University of Karachi, Karachi, Pakistan.
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Roberts DP, Lohrke SM. United States Department of Agriculture-Agricultural Research Service research programs in biological control of plant diseases. PEST MANAGEMENT SCIENCE 2003; 59:654-664. [PMID: 12846315 DOI: 10.1002/ps.613] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A number of USDA-ARS programs directed at overcoming impediments to the use of biocontrol agents on a commercial scale are described. These include improvements in screening techniques, taxonomic studies to identify beneficial strains more precisely, and studies on various aspects of the large-scale production of biocontrol agents. Another broad area of studies covers the ecological aspects of biocontrol agents-their interaction with the pathogen, with the plant and with other aspects of the environmental complex. Examples of these studies are given and their relevance to the further development and expansion of biocontrol agents is discussed.
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Affiliation(s)
- Daniel P Roberts
- Sustainable Agricultural Systems Laboratory, USDA-ARS, Beltsville, MD 20705-2350, USA.
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