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Pal G, Saxena S, Kumar K, Verma A, Kumar D, Shukla P, Pandey A, White J, Verma SK. Seed endophytic bacterium Lysinibacillus sp. (ZM1) from maize (Zea mays L.) shapes its root architecture through modulation of auxin biosynthesis and nitrogen metabolism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108731. [PMID: 38761545 DOI: 10.1016/j.plaphy.2024.108731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 05/20/2024]
Abstract
Seed endophytic bacteria have been shown to promote the growth and development of numerous plants. However, the underlying mechanism still needs to be better understood. The present study aims to investigate the role of a seed endophytic bacterium Lysinibacillus sp. (ZM1) in promoting plant growth and shaping the root architecture of maize seedlings. The study explores how bacteria-mediated auxin biosynthesis and nitrogen metabolism affect plant growth promotion and shape the root architecture of maize seedlings. The results demonstrate that ZM1 inoculation significantly enhances root length, root biomass, and the number of seminal roots in maize seedlings. Additionally, the treated seedlings exhibit increased shoot biomass and higher levels of photosynthetic pigments. Confocal laser scanning microscopy (CLSM) analysis revealed extensive colonization of ZM1 on root hairs, as well as in the cortical and stellar regions of the root. Furthermore, LC-MS analysis demonstrated elevated auxin content in the roots of the ZM1 treated maize seedlings compared to the uninoculated control. Inoculation with ZM1 significantly increased the levels of endogenous ammonium content, GS, and GOGAT enzyme activities in the roots of treated maize seedlings compared to the control, indicating enhanced nitrogen metabolism. Furthermore, inoculation of bacteria under nitrogen-deficient conditions enhanced plant growth, as evidenced by increased root shoot length, fresh and dry weights, average number of seminal roots, and content of photosynthetic pigments. Transcript analysis indicated upregulation of auxin biosynthetic genes, along with genes involved in nitrogen metabolism at different time points in roots of ZM1-treated maize seedlings. Collectively, our findings highlight the positive impact of Lysinibacillus sp. ZM1 inoculation on maize seeds by improving root architecture through modulation of auxin biosynthesis and affecting various nitrogen metabolism related parameters. These findings provide valuable insights into the potential utilization of seed endophytic bacteria as biofertilizers to enhance plant growth and yield in nutrient deficient soils.
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Affiliation(s)
- Gaurav Pal
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 276957612, USA.
| | - Samiksha Saxena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kanchan Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Anand Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Deepak Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Pooja Shukla
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India
| | - Ashutosh Pandey
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - James White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, USA
| | - Satish K Verma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, Uttar Pradesh, 221005, India.
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Jorrin B, Haskett TL, Knights HE, Martyn A, Underwood TJ, Dolliver J, Ledermann R, Poole PS. Stable, fluorescent markers for tracking synthetic communities and assembly dynamics. MICROBIOME 2024; 12:81. [PMID: 38715147 PMCID: PMC11075435 DOI: 10.1186/s40168-024-01792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/09/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechanisms underlying the coalescence of microbial communities. Deciphering microbiome assembly has been technically challenging due to their vast microbial diversity but establishing a synthetic community (SynCom) serves as a key strategy in unravelling this process. Achieving absolute quantification is crucial for establishing causality in assembly dynamics. However, existing approaches are primarily designed to differentiate a specific group of microorganisms within a particular SynCom. RESULTS To address this issue, we have developed the differential fluorescent marking (DFM) strategy, employing three distinguishable fluorescent proteins in single and double combinations. Building on the mini-Tn7 transposon, DFM capitalises on enhanced stability and broad applicability across diverse Proteobacteria species. The various DFM constructions are built using the pTn7-SCOUT plasmid family, enabling modular assembly, and facilitating the interchangeability of expression and antibiotic cassettes in a single reaction. DFM has no detrimental effects on fitness or community assembly dynamics, and through the application of flow cytometry, we successfully differentiated, quantified, and tracked a diverse six-member SynCom under various complex conditions like root rhizosphere showing a different colonisation assembly dynamic between pea and barley roots. CONCLUSIONS DFM represents a powerful resource that eliminates dependence on sequencing and/or culturing, thereby opening new avenues for studying microbiome assembly. Video Abstract.
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Affiliation(s)
- Beatriz Jorrin
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Timothy L Haskett
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Hayley E Knights
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Anna Martyn
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Thomas J Underwood
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Jessica Dolliver
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Raphael Ledermann
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Philip S Poole
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
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Jakuszeit T, Croze OA. Role of tumbling in bacterial scattering at convex obstacles. Phys Rev E 2024; 109:044405. [PMID: 38755868 DOI: 10.1103/physreve.109.044405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/15/2024] [Indexed: 05/18/2024]
Abstract
Active propulsion, as performed by bacteria and Janus particles, in combination with hydrodynamic interaction results in the accumulation of bacteria at a flat wall. However, in microfluidic devices with cylindrical pillars of sufficiently small radius, self-propelled particles can slide along and scatter off the surface of a pillar, without becoming trapped over long times. This nonequilibrium scattering process has been predicted to result in large diffusivities, even at high obstacle density, unlike particles that undergo classical specular reflection. Here, we test this prediction by experimentally studying the nonequilibrium scattering of pusherlike swimmers in microfluidic obstacle lattices. To explore the role of tumbles in the scattering process, we microscopically tracked wild-type (run and tumble) and smooth-swimming (run only) mutants of the bacterium Escherichia coli scattering off microfluidic pillars. We quantified key scattering parameters and related them to previously proposed models that included a prediction for the diffusivity, discussing their relevance. Finally, we discuss potential interpretations of the role of tumbles in the scattering process and connect our work to the broader study of swimmers in porous media.
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Affiliation(s)
- Theresa Jakuszeit
- Institut Curie and Institut Pierre Gilles de Gennes, PSL Research University, CNRS UMR 144, 75005 Paris, France
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ottavio A Croze
- School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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4
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Marik D, Sharma P, Chauhan NS, Jangir N, Shekhawat RS, Verma D, Mukherjee M, Abiala M, Roy C, Yadav P, Sadhukhan A. Peribacillus frigoritolerans T7-IITJ, a potential biofertilizer, induces plant growth-promoting genes of Arabidopsis thaliana. J Appl Microbiol 2024; 135:lxae066. [PMID: 38486365 DOI: 10.1093/jambio/lxae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/28/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
AIMS This study aimed to isolate plant growth and drought tolerance-promoting bacteria from the nutrient-poor rhizosphere soil of Thar desert plants and unravel their molecular mechanisms of plant growth promotion. METHODS AND RESULTS Among our rhizobacterial isolates, Enterobacter cloacae C1P-IITJ, Kalamiella piersonii J4-IITJ, and Peribacillus frigoritolerans T7-IITJ, significantly enhanced root and shoot growth (4-5-fold) in Arabidopsis thaliana under PEG-induced drought stress. Whole genome sequencing and biochemical analyses of the non-pathogenic bacterium T7-IITJ revealed its plant growth-promoting traits, viz., solubilization of phosphate (40-73 µg/ml), iron (24 ± 0.58 mm halo on chrome azurol S media), and nitrate (1.58 ± 0.01 µg/ml nitrite), along with production of exopolysaccharides (125 ± 20 µg/ml) and auxin-like compounds (42.6 ± 0.05 µg/ml). Transcriptome analysis of A. thaliana inoculated with T7-IITJ and exposure to drought revealed the induction of 445 plant genes (log2fold-change > 1, FDR < 0.05) for photosynthesis, auxin and jasmonate signalling, nutrient uptake, redox homeostasis, and secondary metabolite biosynthesis pathways related to beneficial bacteria-plant interaction, but repression of 503 genes (log2fold-change < -1) including many stress-responsive genes. T7-IITJ enhanced proline 2.5-fold, chlorophyll 2.5-2.8-fold, iron 2-fold, phosphate 1.6-fold, and nitrogen 4-fold, and reduced reactive oxygen species 2-4.7-fold in plant tissues under drought. T7-IITJ also improved the germination and seedling growth of Tephrosia purpurea, Triticum aestivum, and Setaria italica under drought and inhibited the growth of two plant pathogenic fungi, Fusarium oxysporum, and Rhizoctonia solani. CONCLUSIONS P. frigoritolerans T7-IITJ is a potent biofertilizer that regulates plant genes to promote growth and drought tolerance.
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Affiliation(s)
- Debankona Marik
- Department of Bioscience and Bioengineering, IIT Jodhpur, Jodhpur 342030, India
| | - Pinki Sharma
- Department of Biochemistry, Maharshi Dayanand University, Rohtak 124001, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak 124001, India
| | - Neelam Jangir
- Department of Bioscience and Bioengineering, IIT Jodhpur, Jodhpur 342030, India
| | | | - Devanshu Verma
- Department of Bioscience and Bioengineering, IIT Jodhpur, Jodhpur 342030, India
| | - Manasi Mukherjee
- Jodhpur City Knowledge and Innovation Foundation, IIT Jodhpur, Jodhpur 342030, India
| | - Moses Abiala
- Department of Biological Sciences, College of Basic and Applied Sciences, Mountain Top University, Prayer City 110106, Nigeria
| | - Chandan Roy
- Department of Genetics and Plant Breeding, Agriculture University Jodhpur, Jodhpur 342304, India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, IIT Jodhpur, Jodhpur 342030, India
| | - Ayan Sadhukhan
- Department of Bioscience and Bioengineering, IIT Jodhpur, Jodhpur 342030, India
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5
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Filan C, Green M, Diering A, Cicerone MT, Cheung LS, Kostka JE, Robles FE. Label-free functional analysis of root-associated microbes with dynamic quantitative oblique back-illumination microscopy. Sci Rep 2024; 14:5812. [PMID: 38461279 PMCID: PMC10925023 DOI: 10.1038/s41598-024-56443-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/06/2024] [Indexed: 03/11/2024] Open
Abstract
The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the functional dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over 5 days, we observed increased dynamics in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize microbial dynamics within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial dynamics and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.
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Affiliation(s)
- Caroline Filan
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30318, USA
| | - Madison Green
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30318, USA
| | - Abigail Diering
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Marcus T Cicerone
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Lily S Cheung
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30318, USA
| | - Francisco E Robles
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30318, USA.
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6
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Semenova MG, Petina AN, Fedorova EE. Autophagy and Symbiosis: Membranes, ER, and Speculations. Int J Mol Sci 2024; 25:2918. [PMID: 38474164 DOI: 10.3390/ijms25052918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
The interaction of plants and soil bacteria rhizobia leads to the formation of root nodule symbiosis. The intracellular form of rhizobia, the symbiosomes, are able to perform the nitrogen fixation by converting atmospheric dinitrogen into ammonia, which is available for plants. The symbiosis involves the resource sharing between two partners, but this exchange does not include equivalence, which can lead to resource scarcity and stress responses of one of the partners. In this review, we analyze the possible involvement of the autophagy pathway in the process of the maintenance of the nitrogen-fixing bacteria intracellular colony and the changes in the endomembrane system of the host cell. According to in silico expression analysis, ATG genes of all groups were expressed in the root nodule, and the expression was developmental zone dependent. The analysis of expression of genes involved in the response to carbon or nitrogen deficiency has shown a suboptimal access to sugars and nitrogen in the nodule tissue. The upregulation of several ER stress genes was also detected. Hence, the root nodule cells are under heavy bacterial infection, carbon deprivation, and insufficient nitrogen supply, making nodule cells prone to autophagy. We speculate that the membrane formation around the intracellular rhizobia may be quite similar to the phagophore formation, and the induction of autophagy and ER stress are essential to the success of this process.
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Affiliation(s)
- Maria G Semenova
- Timiryazev Institute of Plant Physiology, Russian Academy of Science, 127276 Moscow, Russia
| | - Alekandra N Petina
- Timiryazev Institute of Plant Physiology, Russian Academy of Science, 127276 Moscow, Russia
| | - Elena E Fedorova
- Timiryazev Institute of Plant Physiology, Russian Academy of Science, 127276 Moscow, Russia
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7
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Zhou J, Stringlis IA, Wen J, Liu Y, Xu S, Wang R. Interplay between Amaryllidaceae alkaloids, the bacteriome and phytopathogens in Lycoris radiata. THE NEW PHYTOLOGIST 2024; 241:2258-2274. [PMID: 38105545 DOI: 10.1111/nph.19479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 11/28/2023] [Indexed: 12/19/2023]
Abstract
Alkaloids are a large group of plant secondary metabolites with various structures and activities. It is important to understand their functions in the interplay between plants and the beneficial and pathogenic microbiota. Amaryllidaceae alkaloids (AAs) are unique secondary metabolites in Amaryllidaceae plants. Here, we studied the interplay between AAs and the bacteriome in Lycoris radiata, a traditional Chinese medicinal plant containing high amounts of AAs. The relationship between AAs and bacterial composition in different tissues of L. radiata was studied. In vitro experiments revealed that AAs have varying levels of antimicrobial activity against endophytic bacteria and pathogenic fungi, indicating the importance of AA synthesis in maintaining a balance between plants and beneficial/pathogenic microbiota. Using bacterial synthetic communities with different compositions, we observed a positive feedback loop between bacteria insensitive to AAs and their ability to increase accumulation of AAs in L. radiata, especially in leaves. This may allow insensitive bacteria to outcompete sensitive ones for plant resources. Moreover, the accumulation of AAs enhanced by insensitive bacteria could benefit plants when challenged with fungal pathogens. This study highlights the functions of alkaloids in plant-microbe interactions, opening new avenues for designing plant microbiomes that could contribute to sustainable agriculture.
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Affiliation(s)
- Jiayu Zhou
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, 210014, Nanjing, China
| | - Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, P.O. Box 800.56, 3508 TB, Utrecht, the Netherlands
- Laboratory of Plant Pathology, Agricultural University of Athens, 75 Iera Odos St., 11855, Athens, Greece
| | - Jian Wen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, 210014, Nanjing, China
| | - Yifang Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, 210014, Nanjing, China
| | - Sheng Xu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, 210014, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, 210014, Nanjing, China
| | - Ren Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, 210014, Nanjing, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, 210014, Nanjing, China
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8
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Carvia-Hermoso C, Cuéllar V, Bernabéu-Roda LM, van Dillewijn P, Soto MJ. Sinorhizobium meliloti GR4 Produces Chromosomal- and pSymA-Encoded Type IVc Pili That Influence the Interaction with Alfalfa Plants. PLANTS (BASEL, SWITZERLAND) 2024; 13:628. [PMID: 38475474 DOI: 10.3390/plants13050628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/09/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024]
Abstract
Type IVc Pili (T4cP), also known as Tad or Flp pili, are long thin microbial filaments that are made up of small-sized pilins. These appendages serve different functions in bacteria, including attachment, biofilm formation, surface sensing, motility, and host colonization. Despite their relevant role in diverse microbial lifestyles, knowledge about T4cP in bacteria that establish symbiosis with legumes, collectively referred to as rhizobia, is still limited. Sinorhizobium meliloti contains two clusters of T4cP-related genes: flp-1 and flp-2, which are located on the chromosome and the pSymA megaplasmid, respectively. Bundle-forming pili associated with flp-1 are involved in the competitive nodulation of alfalfa plants, but the role of flp-2 remains elusive. In this work, we have performed a comprehensive bioinformatic analysis of T4cP genes in the highly competitive S. meliloti GR4 strain and investigated the role of its flp clusters in pilus biogenesis, motility, and in the interaction with alfalfa. Single and double flp-cluster mutants were constructed on the wild-type genetic background as well as in a flagellaless derivative strain. Our data demonstrate that both chromosomal and pSymA flp clusters are functional in pili biogenesis and contribute to surface translocation and nodule formation efficiency in GR4. In this strain, the presence of flp-1 in the absence of flp-2 reduces the competitiveness for nodule occupation.
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Affiliation(s)
- Cristina Carvia-Hermoso
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Virginia Cuéllar
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Lydia M Bernabéu-Roda
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - Pieter van Dillewijn
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
| | - María J Soto
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, CSIC, 18008 Granada, Spain
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9
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Meyerowitz JT, Larsson EM, Murray RM. Development of Cell-Free Transcription-Translation Systems in Three Soil Pseudomonads. ACS Synth Biol 2024; 13:530-537. [PMID: 38319019 DOI: 10.1021/acssynbio.3c00468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
In vitro transcription-translation (TX-TL) can enable faster engineering of biological systems. This speed-up can be significant, especially in difficult-to-transform chassis. This work shows the successful development of TX-TL systems using three soil-derived wild-type Pseudomonads known to promote plant growth: Pseudomonas synxantha, Pseudomonas chlororaphis, and Pseudomonas aureofaciens. All three species demonstrated multiple sonication, runoff, and salt conditions producing detectable protein synthesis. One of these new TX-TL systems, P. synxantha, demonstrated a maximum protein yield of 2.5 μM at 125 proteins per DNA template, a maximum protein synthesis rate of 20 nM/min, and a range of DNA concentrations with a linear correspondence with the resulting protein synthesis. A set of different constitutive promoters driving mNeonGreen expression were tested in TX-TL and integrated into the genome, showing similar normalized strengths for in vivo and in vitro fluorescence. This correspondence between the TX-TL-derived promoter strength and the in vivo promoter strength indicates that these lysate-based cell-free systems can be used to characterize and engineer biological parts without genomic integration, enabling a faster design-build-test cycle.
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Affiliation(s)
- Joseph T Meyerowitz
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
| | - Elin M Larsson
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
| | - Richard M Murray
- Division of Biology and Biological Engineering, California Institute of Technology 1200 E. California Blvd, MC 138-78, Pasadena, California 91125, United States
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10
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Labarthe MM, Maroniche GA, Lamattina L, Creus CM. Nitric oxide synthase expression in Pseudomonas koreensis MME3 improves plant growth promotion traits. Appl Microbiol Biotechnol 2024; 108:212. [PMID: 38358431 PMCID: PMC10869383 DOI: 10.1007/s00253-024-13029-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 01/03/2024] [Accepted: 01/25/2024] [Indexed: 02/16/2024]
Abstract
The development of novel biotechnologies that promote a better use of N to optimize crop yield is a central goal for sustainable agriculture. Phytostimulation, biofertilization, and bioprotection through the use of bio-inputs are promising technologies for this purpose. In this study, the plant growth-promoting rhizobacteria Pseudomonas koreensis MME3 was genetically modified to express a nitric oxide synthase of Synechococcus SyNOS, an atypical enzyme with a globin domain that converts nitric oxide to nitrate. A cassette for constitutive expression of synos was introduced as a single insertion into the genome of P. koreensis MME3 using a miniTn7 system. The resulting recombinant strain MME3:SyNOS showed improved growth, motility, and biofilm formation. The impact of MME3:SyNOS inoculation on Brachypodium distachyon growth and N uptake and use efficiencies under different N availability situations was analyzed, in comparison to the control strain MME3:c. After 35 days of inoculation, plants treated with MME3:SyNOS had a higher root dry weight, both under semi-hydroponic and greenhouse conditions. At harvest, both MME3:SyNOS and MME3:c increased N uptake and use efficiency of plants grown under low N soil. Our results indicate that synos expression is a valid strategy to boost the phytostimulatory capacity of plant-associated bacteria and improve the adaptability of plants to N deficiency. KEY POINTS: • synos expression improves P. koreensis MME3 traits important for rhizospheric colonization • B. distachyon inoculated with MME3:SyNOS shows improved root growth • MME3 inoculation improves plant N uptake and use efficiencies in N-deficient soil.
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Affiliation(s)
- María M Labarthe
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Guillermo A Maroniche
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Lorenzo Lamattina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- IIB, Universidad Nacional de Mar del Plata, Mar del Plata, Buenos Aires, Argentina
| | - Cecilia M Creus
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Balcarce, Buenos Aires, Argentina.
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Ghitti E, Rolli E, Vergani L, Borin S. Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400. FRONTIERS IN PLANT SCIENCE 2024; 15:1325048. [PMID: 38371405 PMCID: PMC10869545 DOI: 10.3389/fpls.2024.1325048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 01/15/2024] [Indexed: 02/20/2024]
Abstract
Introduction Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress. Methods By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400. Results Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern. Discussions This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.
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Affiliation(s)
| | - Eleonora Rolli
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
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Liu Y, Xu Z, Chen L, Xun W, Shu X, Chen Y, Sun X, Wang Z, Ren Y, Shen Q, Zhang R. Root colonization by beneficial rhizobacteria. FEMS Microbiol Rev 2024; 48:fuad066. [PMID: 38093453 PMCID: PMC10786197 DOI: 10.1093/femsre/fuad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 01/13/2024] Open
Abstract
Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.
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Affiliation(s)
- Yunpeng Liu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Lin Chen
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, 1 Shuizha West Road, Beijing 102300, P.R. China
| | - Weibing Xun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xia Shu
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, P.R. China
| | - Yu Chen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Xinli Sun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Zhengqi Wang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Yi Ren
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
| | - Ruifu Zhang
- State Key Laboratory of Efficient Utilization of Arid and Semi-Arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, 6 Tongwei Road, Nanjing 210095, P.R. China
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Aoki N, Shimasaki T, Yazaki W, Sato T, Nakayasu M, Ando A, Kishino S, Ogawa J, Masuda S, Shibata A, Shirasu K, Yazaki K, Sugiyama A. An isoflavone catabolism gene cluster underlying interkingdom interactions in the soybean rhizosphere. ISME COMMUNICATIONS 2024; 4:ycae052. [PMID: 38707841 PMCID: PMC11069340 DOI: 10.1093/ismeco/ycae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/19/2024] [Accepted: 04/03/2024] [Indexed: 05/07/2024]
Abstract
Plant roots secrete various metabolites, including plant specialized metabolites, into the rhizosphere, and shape the rhizosphere microbiome, which is crucial for the plant health and growth. Isoflavones are major plant specialized metabolites found in legume plants, and are involved in interactions with soil microorganisms as initiation signals in rhizobial symbiosis and as modulators of the legume root microbiota. However, it remains largely unknown the molecular basis underlying the isoflavone-mediated interkingdom interactions in the legume rhizosphere. Here, we isolated Variovorax sp. strain V35, a member of the Comamonadaceae that harbors isoflavone-degrading activity, from soybean roots and discovered a gene cluster responsible for isoflavone degradation named ifc. The characterization of ifc mutants and heterologously expressed Ifc enzymes revealed that isoflavones undergo oxidative catabolism, which is different from the reductive metabolic pathways observed in gut microbiota. We further demonstrated that the ifc genes are frequently found in bacterial strains isolated from legume plants, including mutualistic rhizobia, and contribute to the detoxification of the antibacterial activity of isoflavones. Taken together, our findings reveal an isoflavone catabolism gene cluster in the soybean root microbiota, providing molecular insights into isoflavone-mediated legume-microbiota interactions.
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Affiliation(s)
- Noritaka Aoki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomohisa Shimasaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Wataru Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomoaki Sato
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masaru Nakayasu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Akinori Ando
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shigenobu Kishino
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Sachiko Masuda
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Arisa Shibata
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
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Yan Z, Wang Z, Si G, Chen G, Feng T, Liu C, Chen J. Bacteria-loaded biochar for the immobilization of cadmium in an alkaline-polluted soil. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:1941-1953. [PMID: 38044401 DOI: 10.1007/s11356-023-31299-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
The combination of biochar and bacteria is a promising strategy for the remediation of Cd-polluted soils. However, the synergistic mechanisms of biochar and bacteria for Cd immobilization remain unclear. In this study, the experiments were conducted to evaluate the effects of the combination of biochar and Pseudomonas sp. AN-B15, on Cd immobilization, soil enzyme activity, and soil microbiome. The results showed that biochar could directly reduce the motility of Cd through adsorption and formation of CdCO3 precipitates, thereby protecting bacteria from Cd toxicity in the solution. In addition, bacterial growth further induces the formation of CdCO3 and CdS and enhances Cd adsorption by bacterial cells, resulting in a higher Cd removal rate. Thus, bacterial inoculation significantly enhances Cd removal in the presence of biochar in the solution. Moreover, soil incubation experiments showed that bacteria-loaded biochar significantly reduced soil exchangeable Cd in comparison with other treatments by impacting soil microbiome. In particular, bacteria-loaded biochar increased the relative abundance of Bacillus, Lysobacter, and Pontibacter, causing an increase in pH, urease, and arylsulfatase, thereby passivating soil exchangeable Cd and improving soil environmental quality in the natural alkaline Cd-contaminated soil. Overall, this study provides a systematic understanding of the synergistic mechanisms of biochar and bacteria for Cd immobilization in soil and new insights into the selection of functional strain for the efficient remediation of the contaminated environments by bacterial biochar composite.
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Affiliation(s)
- Zhengjian Yan
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Zitong Wang
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Guangzheng Si
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Guohui Chen
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Tingting Feng
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Chang'e Liu
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
- Yunnan International Cooperative Center of Plateau Lake Ecological Restoration and Watershed Management & Yunnan Think Tank of Ecological Civilization, Kunming, 650091, Yunnan, China
| | - Jinquan Chen
- Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.
- Yunnan International Cooperative Center of Plateau Lake Ecological Restoration and Watershed Management & Yunnan Think Tank of Ecological Civilization, Kunming, 650091, Yunnan, China.
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Chan CS, Dykes GE, Hoover RL, Limmer MA, Seyfferth AL. Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions. Appl Environ Microbiol 2023; 89:e0057023. [PMID: 38009924 PMCID: PMC10734482 DOI: 10.1128/aem.00570-23] [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: 04/06/2023] [Accepted: 09/18/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE In waterlogged soils, iron plaque forms a reactive barrier between the root and soil, collecting phosphate and metals such as arsenic and cadmium. It is well established that iron-reducing bacteria solubilize iron, releasing these associated elements. In contrast, microbial roles in plaque formation have not been clear. Here, we show that there is a substantial population of iron oxidizers in plaque, and furthermore, that these organisms (Sideroxydans and Gallionella) are distinguished by genes for plant colonization and nutrient fixation. Our results suggest that iron-oxidizing and iron-reducing bacteria form and remodel iron plaque, making it a dynamic system that represents both a temporary sink for elements (P, As, Cd, C, etc.) as well as a source. In contrast to abiotic iron oxidation, microbial iron oxidation results in coupled Fe-C-N cycling, as well as microbe-microbe and microbe-plant ecological interactions that need to be considered in soil biogeochemistry, ecosystem dynamics, and crop management.
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Affiliation(s)
- Clara S. Chan
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- School of Marine Science and Policy, University of Delaware, Newark, Delaware, USA
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
| | - Gretchen E. Dykes
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
| | - Rene L. Hoover
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- Microbiology Graduate Program, University of Delaware, Newark, Delaware, USA
- Delaware Biotechnology Institute, Newark, Delaware, USA
| | - Matt A. Limmer
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
| | - Angelia L. Seyfferth
- Department of Earth Sciences, University of Delaware, Newark, Delaware, USA
- Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA
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Vannier N, Mesny F, Getzke F, Chesneau G, Dethier L, Ordon J, Thiergart T, Hacquard S. Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota. Nat Commun 2023; 14:8274. [PMID: 38092730 PMCID: PMC10719396 DOI: 10.1038/s41467-023-43688-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
The identification of processes activated by specific microbes during microbiota colonization of plant roots has been hampered by technical constraints in metatranscriptomics. These include lack of reference genomes, high representation of host or microbial rRNA sequences in datasets, or difficulty to experimentally validate gene functions. Here, we recolonized germ-free Arabidopsis thaliana with a synthetic, yet representative root microbiota comprising 106 genome-sequenced bacterial and fungal isolates. We used multi-kingdom rRNA depletion, deep RNA-sequencing and read mapping against reference microbial genomes to analyse the in planta metatranscriptome of abundant colonizers. We identified over 3,000 microbial genes that were differentially regulated at the soil-root interface. Translation and energy production processes were consistently activated in planta, and their induction correlated with bacterial strains' abundance in roots. Finally, we used targeted mutagenesis to show that several genes consistently induced by multiple bacteria are required for root colonization in one of the abundant bacterial strains (a genetically tractable Rhodanobacter). Our results indicate that microbiota members activate strain-specific processes but also common gene sets to colonize plant roots.
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Affiliation(s)
- Nathan Vannier
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Fantin Mesny
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Institute for Plant Sciences, University of Cologne, 50923, Cologne, Germany
| | - Felix Getzke
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Guillaume Chesneau
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Laura Dethier
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Jana Ordon
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Thorsten Thiergart
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Stéphane Hacquard
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
- Cluster of Excellence on Plant Sciences, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
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Zartdinova R, Nikitin A. Calcium in the Life Cycle of Legume Root Nodules. Indian J Microbiol 2023; 63:410-420. [PMID: 38031601 PMCID: PMC10682328 DOI: 10.1007/s12088-023-01107-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 10/07/2023] [Indexed: 12/01/2023] Open
Abstract
The present review highlights both the fundamental questions of calcium localization, compartmentation, and its participation in symbiosome signaling cascades during nodule formation and functioning. Apparently, the main link of such signaling is the calmodulin…calcium- and calmodulin-dependent protein kinases…CYCLOPS…NIN…target genes cascade. The minimum threshold level of calcium as a signaling agent in the presence of intracellular reserves determines the possibility of oligotrophy and ultraoligotrophy in relation to this element. During the functioning of root nodules, the Ca2+-ATPases activity maintains homeostasis of low calcium concentrations in the cytosol of nodule parenchyma cells. Disturbation of this homeostasis can trigger the root nodule senescence. The same reasons determine the increase in the effectiveness of symbiosis with the help of seed priming with sources of calcium. Examples of calcium response polymorphism in components of nitrogen fixing simbiosis important in practical terms are shown.
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Affiliation(s)
- Rozaliya Zartdinova
- Nitrogen Exchange Laboratory, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Nikitin
- Nitrogen Exchange Laboratory, Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
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Yakubu I, Kong HG. The Relationship between the Sugar Preference of Bacterial Pathogens and Virulence on Plants. THE PLANT PATHOLOGY JOURNAL 2023; 39:529-537. [PMID: 38081313 PMCID: PMC10721386 DOI: 10.5423/ppj.rw.06.2023.0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 12/17/2023]
Abstract
Plant pathogenic bacteria colonize plant surfaces and inner tissues to acquire essential nutrients. Nonstructural sugars hold paramount significance among these nutrients, as they serve as pivotal carbon sources for bacterial sustenance. They obtain sugar from their host by diverting nonstructural carbohydrates en route to the sink or enzymatic breakdown of structural carbohydrates within plant tissues. Despite the prevalence of research in this domain, the area of sugar selectivity and preferences exhibited by plant pathogenic bacteria remains inadequately explored. Within this expository framework, our present review endeavors to elucidate the intricate variations characterizing the distribution of simple sugars within diverse plant tissues, thus influencing the virulence dynamics of plant pathogenic bacteria. Subsequently, we illustrate the apparent significance of comprehending the bacterial preference for specific sugars and sugar alcohols, postulating this insight as a promising avenue to deepen our comprehension of bacterial pathogenicity. This enriched understanding, in turn, stands to catalyze the development of more efficacious strategies for the mitigation of plant diseases instigated by bacterial pathogens.
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Affiliation(s)
- Ismaila Yakubu
- Department of Plant Medicine, College of Agriculture, Life and Environment Science, Chungbuk National University, Cheongju 28644, Korea
- Department of Crop Protection, Faculty of Agriculture/Institute for Agricultural Research, Ahmadu Bello University, Zaria 810211, Nigeria
| | - Hyun Gi Kong
- Department of Plant Medicine, College of Agriculture, Life and Environment Science, Chungbuk National University, Cheongju 28644, Korea
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Filan C, Green M, Diering A, Cicerone MT, Cheung LS, Kostka JE, Robles FE. Label-Free Functional Analysis of Root-Associated Microbes with Dynamic Quantitative Oblique Back-illumination Microscopy. RESEARCH SQUARE 2023:rs.3.rs-3517586. [PMID: 37961396 PMCID: PMC10635382 DOI: 10.21203/rs.3.rs-3517586/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The increasing global demand for food, coupled with concerns about the environmental impact of synthetic fertilizers, underscores the urgency of developing sustainable agricultural practices. Nitrogen-fixing bacteria, known as diazotrophs, offer a potential solution by converting atmospheric nitrogen into bioavailable forms, reducing the reliance on synthetic fertilizers. However, a deeper understanding of their interactions with plants and other microbes is needed. In this study, we introduce a recently developed label-free 3D quantitative phase imaging technology called dynamic quantitative oblique back-illumination microscopy (DqOBM) to assess the dynamic activity of diazotrophs in vitro and in situ. Our experiments involved three different diazotrophs (Sinorhizobium meliloti, Azotobacter vinelandii, and Rahnella aquatilis) cultured on media with amendments of carbon and nitrogen sources. Over five days, we observed increased dynamic activity in nutrient-amended media. These results suggest that the observed bacterial dynamics correlate with their metabolic activity. Furthermore, we applied qOBM to visualize bacterial activity within the root cap and elongation zone of Arabidopsis thaliana primary roots. This allowed us to identify distinct areas of microbial infiltration in plant roots without the need for fluorescent markers. Our findings demonstrate that DqOBM can effectively characterize microbial activity and provide insights into plant-microbe interactions in situ, offering a valuable tool for advancing our understanding of sustainable agriculture.
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Affiliation(s)
- Caroline Filan
- Georgia Institute of Technology, George W. Woodruff School of Mechanical Engineering, Atlanta, GA, 30318, USA
| | - Madison Green
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30318, USA
| | - Abigail Diering
- Georgia Institute of Technology, School of Chemistry and Biochemistry, Atlanta, GA, 30332, USA
| | - Marcus T. Cicerone
- Georgia Institute of Technology, School of Chemistry and Biochemistry, Atlanta, GA, 30332, USA
| | - Lily S. Cheung
- Georgia Institute of Technology, School of Chemical and Biomolecular Engineering, Atlanta, GA, 30332, USA
| | - Joel E. Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30318, USA
| | - Francisco E. Robles
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, GA, 30318, USA
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Duan Y, Han M, Grimm M, Schierstaedt J, Imani J, Cardinale M, Le Jean M, Nesme J, Sørensen SJ, Schikora A. Hordeum vulgare differentiates its response to beneficial bacteria. BMC PLANT BIOLOGY 2023; 23:460. [PMID: 37789272 PMCID: PMC10548682 DOI: 10.1186/s12870-023-04484-5] [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: 06/23/2023] [Accepted: 09/22/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND In nature, beneficial bacteria triggering induced systemic resistance (ISR) may protect plants from potential diseases, reducing yield losses caused by diverse pathogens. However, little is known about how the host plant initially responds to different beneficial bacteria. To reveal the impact of different bacteria on barley (Hordeum vulgare), bacterial colonization patterns, gene expression, and composition of seed endophytes were explored. RESULTS This study used the soil-borne Ensifer meliloti, as well as Pantoea sp. and Pseudomonas sp. isolated from barley seeds, individually. The results demonstrated that those bacteria persisted in the rhizosphere but with different colonization patterns. Although root-leaf translocation was not observed, all three bacteria induced systemic resistance (ISR) against foliar fungal pathogens. Transcriptome analysis revealed that ion- and stress-related genes were regulated in plants that first encountered bacteria. Iron homeostasis and heat stress responses were involved in the response to E. meliloti and Pantoea sp., even if the iron content was not altered. Heat shock protein-encoding genes responded to inoculation with Pantoea sp. and Pseudomonas sp. Furthermore, bacterial inoculation affected the composition of seed endophytes. Investigation of the following generation indicated that the enhanced resistance was not heritable. CONCLUSIONS Here, using barley as a model, we highlighted different responses to three different beneficial bacteria as well as the influence of soil-borne Ensifer meliloti on the seed microbiome. In total, these results can help to understand the interaction between ISR-triggering bacteria and a crop plant, which is essential for the application of biological agents in sustainable agriculture.
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Affiliation(s)
- Yongming Duan
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
| | - Min Han
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
| | - Maja Grimm
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
| | - Jasper Schierstaedt
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ) - Department Plant-Microbe Systems, Theodor-Echtermeyer Weg 1, 14979, Großbeeren, Germany
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Jafargholi Imani
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Massimiliano Cardinale
- Department of Biological and Environmental Sciences and Technologies, University of Salento, SP6 Lecce- Monteroni, Lecce, 73100, Italy
- Institute of Applied Microbiology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Marie Le Jean
- Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), UMR 7360 CNRS, Université de Lorraine, 8 rue du Général Delestraint, Metz, 57070, France
| | - Joseph Nesme
- Department of Biology, Section of Microbiology, Copenhagen University, Universitetsparken 15, Copenhagen, 2100, Denmark
| | - Søren J Sørensen
- Department of Biology, Section of Microbiology, Copenhagen University, Universitetsparken 15, Copenhagen, 2100, Denmark
| | - Adam Schikora
- Julius Kühn Institute (JKI), Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11/12, 38104, Braunschweig, Germany.
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21
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Venturi V, Bez C. Novel T4ASS effector with quorum quenching activity. THE ISME JOURNAL 2023; 17:1523-1525. [PMID: 37620539 PMCID: PMC10504337 DOI: 10.1038/s41396-023-01497-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023]
Affiliation(s)
- Vittorio Venturi
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy.
| | - Cristina Bez
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149, Trieste, Italy
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22
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Dong Q, Yan Q, Zhang B, Zhang LQ, Wu X. Regulation of 2,4-diacetylphloroglucinol biosynthesis and biocontrol capacity by the BolA family protein IbaG in Pseudomonas fluorescens 2P24. Microbiol Spectr 2023; 11:e0098523. [PMID: 37724877 PMCID: PMC10580914 DOI: 10.1128/spectrum.00985-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/23/2023] [Indexed: 09/21/2023] Open
Abstract
The monothiol glutaredoxin GrxD plays an essential role in the biosynthesis of the antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG) and the biocontrol capacity of the soil bacterium Pseudomonas fluorescens 2P24. However, the detailed mechanism underlying GrxD-mediated activation of the production of 2,4-DAPG remains unclear. Here, we found that GrxD directly interacted with IbaG, a BolA protein family member. The mutation of ibaG significantly decreased 2,4-DAPG production. Furthermore, expressing ibaG restored the production of 2,4-DAPG in the grxD ibaG double mutant to wild-type levels in the presence of dithiothreitol, suggesting that IbaG was required for GrxD-mediated regulation of 2,4-DAPG production. Transcriptome sequencing analyses revealed that IbaG plays a global role in gene regulation by affecting the expression of numerous genes throughout the genome. We also demonstrated that IbaG is an important regulator of several cellular processes, including swarming motility, biofilm formation, siderophore production, and acid resistance. Altogether, our data suggest that IbaG has an essential role in 2,4-DAPG production, motility, and biofilm formation. We also propose a regulatory mechanism linking GrxD to 2,4-DAPG production via IbaG. IMPORTANCE The production of 2,4-diacetylphloroglucinol (2,4-DAPG) is positively influenced by the monothiol glutaredoxin GrxD in Pseudomonas fluorescens 2P24. However, the regulatory mechanism underlying GrxD-mediated regulation of 2,4-DAPG biosynthesis is mostly uncharacterized. Here, we show the function of the BolA-like protein IbaG in 2,4-DAPG biosynthesis. We also demonstrate that GrxD directly interacts with IbaG and influences the redox state of IbaG. Altogether, this work provides new insights into the role of the highly conserved IbaG protein in regulating 2,4-DAPG synthesis, biofilm formation, and other biocontrol traits of P. fluorescens.
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Affiliation(s)
- Qiuling Dong
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety/College of Agriculture, Guangxi University, Nanning, China
| | - Qing Yan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, USA
| | - Bo Zhang
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety/College of Agriculture, Guangxi University, Nanning, China
| | - Li-qun Zhang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaogang Wu
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety/College of Agriculture, Guangxi University, Nanning, China
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23
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O'Banion BS, Jones P, Demetros AA, Kelley BR, Knoor LH, Wagner AS, Chen JG, Muchero W, Reynolds TB, Jacobson D, Lebeis SL. Plant myo-inositol transport influences bacterial colonization phenotypes. Curr Biol 2023; 33:3111-3124.e5. [PMID: 37419115 DOI: 10.1016/j.cub.2023.06.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 05/14/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023]
Abstract
Plant microbiomes are assembled and modified through a complex milieu of biotic and abiotic factors. Despite dynamic and fluctuating contributing variables, specific host metabolites are consistently identified as important mediators of microbial interactions. We combine information from a large-scale metatranscriptomic dataset from natural poplar trees and experimental genetic manipulation assays in seedlings of the model plant Arabidopsis thaliana to converge on a conserved role for transport of the plant metabolite myo-inositol in mediating host-microbe interactions. While microbial catabolism of this compound has been linked to increased host colonization, we identify bacterial phenotypes that occur in both catabolism-dependent and -independent manners, suggesting that myo-inositol may additionally serve as a eukaryotic-derived signaling molecule to modulate microbial activities. Our data suggest host control of this compound and resulting microbial behavior are important mechanisms at play surrounding the host metabolite myo-inositol.
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Affiliation(s)
- Bridget S O'Banion
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Piet Jones
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN 37996, USA
| | - Alexander A Demetros
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Brittni R Kelley
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Leah H Knoor
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Andrew S Wagner
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Sarah L Lebeis
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA; DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 38824, USA.
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24
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Martins SJ, Pasche J, Silva HAO, Selten G, Savastano N, Abreu LM, Bais HP, Garrett KA, Kraisitudomsook N, Pieterse CMJ, Cernava T. The Use of Synthetic Microbial Communities to Improve Plant Health. PHYTOPATHOLOGY 2023; 113:1369-1379. [PMID: 36858028 DOI: 10.1094/phyto-01-23-0016-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.
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Affiliation(s)
- Samuel J Martins
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | - Josephine Pasche
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | - Hiago Antonio O Silva
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Gijs Selten
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Noah Savastano
- Department of Plant and Soil Sciences, 311 AP Biopharma, University of Delaware, Newark, DE 19713, U.S.A
| | - Lucas Magalhães Abreu
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Harsh P Bais
- Department of Plant and Soil Sciences, 311 AP Biopharma, University of Delaware, Newark, DE 19713, U.S.A
| | - Karen A Garrett
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | | | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8020, Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, U.K
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25
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Ali A, Dindhoria K, Kumar R. Acinetobacter oleivorans IRS14 alleviates cold stress in wheat by regulating physiological and biochemical factors. J Appl Microbiol 2023; 134:lxad176. [PMID: 37550224 DOI: 10.1093/jambio/lxad176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/27/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
AIMS Climate change is responsible for extreme cold winters, causing a significant loss in crop yield and productivity due to chilling stress. This study aims to investigate the potential of psychrotrophic plant growth-promoting rhizobacteria (PGPR) strain to promote wheat growth under cold stress and explore the adaptive responses of wheat. METHODS AND RESULTS Wheat seeds and seedlings were inoculated with the psychrotrophic strain IRS14 and the plants were cultivated for five weeks at 6°C ± 2°C. The genetic, biochemical, physiological, and molecular analysis of the bacterium and plant was done to evaluate the effect of the PGPR strain in alleviating chilling stress. IRS14 possesses antioxidant activity and produced multiple phytohormones, which enhanced seed germination (∼50%) and plant growth (∼50%) during chilling stress. CONCLUSIONS Here, we reported that the application of IRS14 helps to regulate the biochemical and metabolic pathways in wheat plants. It alleviates chilling stress and increases plant growth rate and biomass. Strain IRS14 in wheat effectively increased chlorophyll content, antioxidants, carotenoid, proline, and endogenous phytohormones compared with untreated wheat.
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Affiliation(s)
- Ashif Ali
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Kiran Dindhoria
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rakshak Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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26
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Sandhu AK, Brown MR, Subramanian S, Brözel VS. Bradyrhizobium diazoefficiens USDA 110 displays plasticity in the attachment phenotype when grown in different soybean root exudate compounds. Front Microbiol 2023; 14:1190396. [PMID: 37275139 PMCID: PMC10233038 DOI: 10.3389/fmicb.2023.1190396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/11/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Bradyrhizobium diazoefficiens, a symbiotic nitrogen fixer for soybean, forms nodules after developing a symbiotic association with the root. For this association, bacteria need to move toward and attach to the root. These steps are mediated by the surface and phenotypic cell properties of bacteria and secreted root exudate compounds. Immense work has been carried out on nodule formation and nitrogen fixation, but little is known about the phenotype of these microorganisms under the influence of different root exudate chemical compounds (RECCs) or how this phenotype impacts the root attachment ability. Methods To address this knowledge gap, we studied the impact of 12 different RECCs, one commonly used carbon source, and soil-extracted solubilized organic matter (SESOM) on attachment and attachment-related properties of B. diazoefficiens USDA110. We measured motility-related properties (swimming, swarming, chemotaxis, and flagellar expression), attachment-related properties (surface hydrophobicity, biofilm formation, and attachment to cellulose and soybean roots), and surface polysaccharide properties (colony morphology, exopolysaccharide quantification, lectin binding profile, and lipopolysaccharide profiling). Results and discussion We found that USDA 110 displays a high degree of surface phenotypic plasticity when grown on the various individual RECCs. Some of the RECCs played specific roles in modulating the motility and root attachment processes. Serine increased cell surface hydrophobicity and root and cellulose attachment, with no EPS formed. Gluconate and lactate increased EPS production and biofilm formation, while decreasing hydrophobicity and root attachment, and raffinose and gentisate promoted motility and chemotaxis. The results also indicated that the biofilm formation trait on hydrophilic surfaces (polystyrene) cannot be related to the attachment ability of Bradyrhizobium to the soybean root. Among the tested phenotypic properties, bacterial cell surface hydrophobicity was the one with a significant impact on root attachment ability. We conclude that USDA 110 displays surface plasticity properties and attachment phenotype determined by individual RECCs from the soybean. Conclusions made based on its behavior in standard carbon sources, such as arabinose or mannitol, do not hold for its behavior in soil.
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Affiliation(s)
- Armaan Kaur Sandhu
- Departments of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - McKenzie Rae Brown
- Departments of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Senthil Subramanian
- Departments of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Volker S. Brözel
- Departments of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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27
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Kaiser CF, Perilli A, Grossmann G, Meroz Y. Studying root-environment interactions in structured microdevices. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad122. [PMID: 37042515 PMCID: PMC10353529 DOI: 10.1093/jxb/erad122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Indexed: 06/19/2023]
Abstract
In negotiating with the environment, plant roots integrate sensory information over space and time, as the basis of decision making in roots under non-uniform conditions. The complexity and dynamic properties of soil across spatial and temporal scales pose a significant technical challenge for research on mechanisms that drive metabolism, growth and development in roots, as well as on inter-organismal networks in the rhizosphere. Synthetic environments, combining microscopic access and manipulation capabilities with soil-like heterogeneity, are needed to elucidate the intriguing tug-of-war that characterises subsurface ecosystems. Microdevices have provided opportunities for innovative approaches to observe, analyse and manipulate plant roots and advanced our understanding of their development, physiology and interactions with the environment. Initially conceived as perfusion platforms for root cultivation under hydroponic conditions, microdevice design has, in recent years, increasingly shifted to better reflect the complex growth conditions in soil. Heterogeneous micro-environments have been created through co-cultivation with microbes, laminar flow-based local stimulation and physical obstacles and constraints. As such, structured microdevices provide an experimental entry point to the complex network behaviour of soil communities.
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Affiliation(s)
- Christian-Frederic Kaiser
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Alessia Perilli
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Guido Grossmann
- Institute of Cell and Interaction Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
- CEPLAS - Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Yasmine Meroz
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
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28
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Xu Z, Liu Y, Zhang N, Xun W, Feng H, Miao Y, Shao J, Shen Q, Zhang R. Chemical communication in plant-microbe beneficial interactions: a toolbox for precise management of beneficial microbes. Curr Opin Microbiol 2023; 72:102269. [PMID: 36682279 DOI: 10.1016/j.mib.2023.102269] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/22/2023]
Abstract
Harnessing the power of beneficial microbes in the rhizosphere to improve crop performance is a key goal of sustainable agriculture. However, the precise management of rhizosphere microbes for crop growth and health remains challenging because we lack a comprehensive understanding of the plant-rhizomicrobiome relationship. In this review, we discuss the latest research progress on root colonisation by representative beneficial microbes (e.g. Bacillus spp. and Pseudomonas spp.). We also highlight the bidirectional chemical communication between microbes and plant roots for precise functional control of beneficial microbes in the rhizosphere, as well as advances in understanding how beneficial microbes overcome the immune system of plants. Finally, we propose future research objectives that will help us better understand the complex network of plant-microbe interactions.
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Affiliation(s)
- Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Nan Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Weibing Xun
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Haichao Feng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China; Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
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29
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Wang Y, Duan S, Xu J, Long Y, Zhang S, Li S, Wu L, Zhang Y. Comparison of the colonization ability of Burkholderia strain B23 in the citrus rhizoplane and rhizosphere and assessment of the underlying mechanisms using full-length 16S rDNA amplicon and metatranscriptomic analyses. Microb Biotechnol 2023. [PMID: 36946260 PMCID: PMC10364312 DOI: 10.1111/1751-7915.14248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/23/2023] Open
Abstract
The characterization of bacterial strains with efficient root colonization ability and the mechanisms responsible for their efficient colonization is critical for the identification and application of beneficial bacteria. In this study, we found that Burkholderia strain B23 exhibited a strong niche differentiation between the rhizosphere and rhizoplane (a niche with more abundant easy-to-use nutrients but stronger selective pressures compared with the tightly adjacent rhizosphere) when inoculated into the field-grown citrus trees. Full-length 16S rDNA amplicon analysis demonstrated that the relative abundance of B23 in the rhizoplane microbiome at 3, 5, and 9 days post-inoculation (dpi) was always higher than that at 1 dpi, whereas its relative abundance in the rhizosphere microbiome was decreased continuously, as demonstrated by a 3.18-fold decrease at 9 dpi compared to 1 dpi. Time-series comparative expression profiling of B23 between the rhizoplane and rhizosphere was performed at representative time points (1, 3, and 9 dpi) through metatranscriptomic analysis, and the results demonstrated that multiple genes involved in the uptake and utilization of easy-to-use carbohydrates and amino acids and those involved in metabolism, energy production, replication, and translation were upregulated in the rhizoplane compared with the rhizosphere at 1 dpi and 3 dpi. Several genes involved in resistance to plant- and microbial competitor-derived stresses exhibited higher expression activities in the rhizoplane compared with the rhizosphere. Furthermore, gene loci responsible for the biosynthesis of the key antifungal and antibacterial metabolites occidiofungin and ornibactin were induced, and their expression levels remained relatively stable from 3 dpi to 9 dpi in the rhizoplane but not in the rhizosphere. Collectively, our findings provide novel lights into the mechanisms underlying the root colonization of the inoculated bacterial strains and serve as a basis for the identification of strains with efficient colonization ability, thus contributing to the development of beneficial bacteria applications.
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Affiliation(s)
- Yu Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Shuo Duan
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Jin Xu
- Citrus Research and Education Center, Department of Plant Pathology, IFAS, University of Florida, Lake Alfred, Florida, 33850, USA
| | - Yunfei Long
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Siyu Zhang
- Citrus Huanglongbing Joint Laboratory, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Shixin Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Lijuan Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yunzeng Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
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30
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Brito-Santana P, Duque-Pedraza JJ, Bernabéu-Roda LM, Carvia-Hermoso C, Cuéllar V, Fuentes-Romero F, Acosta-Jurado S, Vinardell JM, Soto MJ. Sinorhizobium meliloti DnaJ Is Required for Surface Motility, Stress Tolerance, and for Efficient Nodulation and Symbiotic Nitrogen Fixation. Int J Mol Sci 2023; 24:ijms24065848. [PMID: 36982921 PMCID: PMC10055731 DOI: 10.3390/ijms24065848] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Bacterial surface motility is a complex microbial trait that contributes to host colonization. However, the knowledge about regulatory mechanisms that control surface translocation in rhizobia and their role in the establishment of symbiosis with legumes is still limited. Recently, 2-tridecanone (2-TDC) was identified as an infochemical in bacteria that hampers microbial colonization of plants. In the alfalfa symbiont Sinorhizobium meliloti, 2-TDC promotes a mode of surface motility that is mostly independent of flagella. To understand the mechanism of action of 2-TDC in S. meliloti and unveil genes putatively involved in plant colonization, Tn5 transposants derived from a flagellaless strain that were impaired in 2-TDC-induced surface spreading were isolated and genetically characterized. In one of the mutants, the gene coding for the chaperone DnaJ was inactivated. Characterization of this transposant and newly obtained flagella-minus and flagella-plus dnaJ deletion mutants revealed that DnaJ is essential for surface translocation, while it plays a minor role in swimming motility. DnaJ loss-of-function reduces salt and oxidative stress tolerance in S. meliloti and hinders the establishment of efficient symbiosis by affecting nodule formation efficiency, cellular infection, and nitrogen fixation. Intriguingly, the lack of DnaJ causes more severe defects in a flagellaless background. This work highlights the role of DnaJ in the free-living and symbiotic lifestyles of S. meliloti.
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Affiliation(s)
- Paula Brito-Santana
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
| | - Julián J Duque-Pedraza
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
| | - Lydia M Bernabéu-Roda
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
| | - Cristina Carvia-Hermoso
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
| | - Virginia Cuéllar
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
| | - Francisco Fuentes-Romero
- Facultad de Biología, Departamento de Microbiología, Universidad de Sevilla, 41012 Sevilla, Spain
| | - Sebastián Acosta-Jurado
- Centro Andaluz de Biología del Desarrollo, CSIC, Junta de Andalucía, Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, 41013 Seville, Spain
| | - José-María Vinardell
- Facultad de Biología, Departamento de Microbiología, Universidad de Sevilla, 41012 Sevilla, Spain
| | - María J Soto
- Estación Experimental del Zaidín, CSIC, Department of Biotechnology and Environmental Protection, 18008 Granada, Spain
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31
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Rhizobial migration toward roots mediated by FadL-ExoFQP modulation of extracellular long-chain AHLs. THE ISME JOURNAL 2023; 17:417-431. [PMID: 36627434 PMCID: PMC9938287 DOI: 10.1038/s41396-023-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023]
Abstract
Migration from rhizosphere to rhizoplane is a key selecting process in root microbiome assembly, but not fully understood. Rhizobiales members are overrepresented in the core root microbiome of terrestrial plants, and here we report a genome-wide transposon-sequencing of rhizoplane fitness genes of beneficial Sinorhizobium fredii on wild soybean, cultivated soybean, rice, and maize. There were few genes involved in broad-host-range rhizoplane colonization. The fadL mutant lacking a fatty acid transporter exhibited high colonization rates, while mutations in exoFQP (encoding membrane proteins directing exopolysaccharide polymerization and secretion), but not those in exo genes essential for exopolysaccharide biosynthesis, led to severely impaired colonization rates. This variation was not explainable by their rhizosphere and rhizoplane survivability, and associated biofilm and exopolysaccharide production, but consistent with their migration ability toward rhizoplane, and associated surface motility and the mixture of quorum-sensing AHLs (N-acylated-L-homoserine lactones). Genetics and physiology evidences suggested that FadL mediated long-chain AHL uptake while ExoF mediated the secretion of short-chain AHLs which negatively affected long-chain AHL biosynthesis. The fadL and exoF mutants had elevated and depleted extracellular long-chain AHLs, respectively. A synthetic mixture of long-chain AHLs mimicking that of the fadL mutant can improve rhizobial surface motility. When this AHL mixture was spotted into rhizosphere, the migration toward roots and rhizoplane colonization of S. fredii were enhanced in a diffusible way. This work adds novel parts managing extracellular AHLs, which modulate bacterial migration toward rhizoplane. The FadL-ExoFQP system is conserved in Alphaproteobacteria and may shape the "home life" of diverse keystone rhizobacteria.
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32
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Benucci GMN, Beschoren da Costa P, Wang X, Bonito G. Stochastic and deterministic processes shape bioenergy crop microbiomes along a vertical soil niche. Environ Microbiol 2023; 25:352-366. [PMID: 36354216 PMCID: PMC10099798 DOI: 10.1111/1462-2920.16269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022]
Abstract
Sustainable biofuel cropping systems aim to address climate change while meeting energy needs. Understanding how soil and plant-associated microbes respond to these different cropping systems is key to promoting agriculture sustainability and evaluating changes in ecosystem functions. Here, we leverage a long-term biofuel cropping system field experiment to dissect soil and root microbiome changes across a soil-depth gradient in poplar, restored prairie and switchgrass to understand their effects on the microbial communities. High throughput amplicon sequencing of the fungal internal transcribed spacer (ITS) and prokaryotic 16S DNA regions showed a common trend of root and soil microbial community richness decreasing and evenness increasing with depth. Ecological niche (root vs. soil) had the strongest effect on community structure, followed by depth, then crop. Stochastic processes dominated the structuring of fungal communities in deeper soil layers while operational taxonomic units (OTUs) in surface soil layers were more likely to co-occur and to be enriched by plant hosts. Prokaryotic communities were dispersal limited at deeper depths. Microbial networks showed a higher density, connectedness, average degree and module size in deeper soils. We observed a decrease in fungal-fungal links and an increase of bacteria-bacteria links with increasing depth in all crops, particularly in the root microbiome.
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Affiliation(s)
- Gian Maria Niccolò Benucci
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, USA
| | - Pedro Beschoren da Costa
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Xinxin Wang
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Gregory Bonito
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, USA
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA
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33
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Haskett TL, Geddes BA, Paramasivan P, Green P, Chitnavis S, Mendes MD, Jorrín B, Knights HE, Bastholm TR, Ramsay JP, Oldroyd GED, Poole PS. Rhizopine biosensors for plant-dependent control of bacterial gene expression. Environ Microbiol 2023; 25:383-396. [PMID: 36428208 PMCID: PMC10107442 DOI: 10.1111/1462-2920.16288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Engineering signalling between plants and microbes could be exploited to establish host-specificity between plant-growth-promoting bacteria and target crops in the environment. We previously engineered rhizopine-signalling circuitry facilitating exclusive signalling between rhizopine-producing (RhiP) plants and model bacterial strains. Here, we conduct an in-depth analysis of rhizopine-inducible expression in bacteria. We characterize two rhizopine-inducible promoters and explore the bacterial host-range of rhizopine biosensor plasmids. By tuning the expression of rhizopine uptake genes, we also construct a new biosensor plasmid pSIR05 that has minimal impact on host cell growth in vitro and exhibits markedly improved stability of expression in situ on RhiP barley roots compared to the previously described biosensor plasmid pSIR02. We demonstrate that a sub-population of Azorhizobium caulinodans cells carrying pSIR05 can sense rhizopine and activate gene expression when colonizing RhiP barley roots. However, these bacteria were mildly defective for colonization of RhiP barley roots compared to the wild-type parent strain. This work provides advancement towards establishing more robust plant-dependent control of bacterial gene expression and highlights the key challenges remaining to achieve this goal.
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Affiliation(s)
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | | | - Patrick Green
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Samir Chitnavis
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Marta D Mendes
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Beatriz Jorrín
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Tahlia R Bastholm
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, Western Australia, Australia
| | - Joshua P Ramsay
- Curtin Medical School and Curtin Health Innovation Research Institute, Curtin University, Perth, Western Australia, Australia
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
- Crop Science Centre, University of Cambridge, Cambridge, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, UK
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34
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Xiong C, Lu Y. Microbiomes in agroecosystem: Diversity, function and assembly mechanisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:833-849. [PMID: 36184075 DOI: 10.1111/1758-2229.13126] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.
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Affiliation(s)
- Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
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35
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Kumari M, Qureshi KA, Jaremko M, White J, Singh SK, Sharma VK, Singh KK, Santoyo G, Puopolo G, Kumar A. Deciphering the role of endophytic microbiome in postharvest diseases management of fruits: Opportunity areas in commercial up-scale production. FRONTIERS IN PLANT SCIENCE 2022; 13:1026575. [PMID: 36466226 PMCID: PMC9716317 DOI: 10.3389/fpls.2022.1026575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
As endophytes are widely distributed in the plant's internal compartments and despite having enormous potential as a biocontrol agent against postharvest diseases of fruits, the fruit-endophyte-pathogen interactions have not been studied detail. Therefore, this review aims to briefly discuss the colonization patterns of endophytes and pathogens in the host tissue, the diversity and distribution patterns of endophytes in the carposphere of fruits, and host-endophyte-pathogen interactions and the molecular mechanism of the endophytic microbiome in postharvest disease management in fruits. Postharvest loss management is one of the major concerns of the current century. It is considered a critical challenge to food security for the rising global population. However, to manage the postharvest loss, still, a large population relies on chemical fungicides, which affect food quality and are hazardous to health and the surrounding environment. However, the scientific community has searched for alternatives for the last two decades. In this context, endophytic microorganisms have emerged as an economical, sustainable, and viable option to manage postharvest pathogens with integral colonization properties and eliciting a defense response against pathogens. This review extensively summarizes recent developments in endophytic interactions with harvested fruits and pathogens-the multiple biocontrol traits of endophytes and colonization and diversity patterns of endophytes. In addition, the upscale commercial production of endophytes for postharvest disease treatment is discussed.
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Affiliation(s)
- Madhuree Kumari
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Kamal A. Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (R.S.R.C.), Division of Biological and Environmental Sciences and Engineering (B.E.S.E.), King Abdullah University of Science and Technology (K.A.U.S.T.), Thuwal, Saudi Arabia
| | - James White
- Department of Plant Biology, Rutgers University, The State University of New Jersey, New Brunswick, NJ, United States
| | - Sandeep Kumar Singh
- Division of Microbiology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Vijay Kumar Sharma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Gerardo Puopolo
- Center Agriculture Food Environment, University of Trento, Trentino, TN, Italy
| | - Ajay Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
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36
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Tian L, Hu S, Wang X, Guo Y, Huang L, Wang L, Li W. Antagonism of Rhizosphere Streptomyces yangpuensis CM253 against the Pathogenic Fungi Causing Corm Rot in Saffron ( Crocus sativus L.). Pathogens 2022; 11:pathogens11101195. [PMID: 36297252 PMCID: PMC9607649 DOI: 10.3390/pathogens11101195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 01/24/2023] Open
Abstract
Plant diseases lead to a significant decline in the output and quality of Chinese herbal medicines. Actinomycetes play a vital role in the rhizosphere ecosystem. This is especially true for Streptomyces, which have become a valuable biological control resource because of their advantages in producing various secondary metabolites with novel structures and remarkable biological activities. The purpose of this study was to isolate an effective antagonistic actinomycete against the pathogen of corm rot in saffron. An antagonistic actinomycete, CM253, was screened from the rhizosphere soil samples of Crocus sativus, by plate co-culture with four pathogenic fungi (Fusarium oxysporum, Fusarium solani, Penicillium citreosulfuratum, and Penicillium citrinum). CM253 inhibited the growth and development of F. oxysporum hyphae by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Furthermore, by analyzing the degrading enzyme, the growth-promoting performance, and the whole genome of strain CM253, it was identified as Streptomyces yangpuensis, which produces NH3, protease, glucanase, cellulase, IAA, and ACC deaminase. In addition, 24 secondary metabolite synthesis gene clusters were predicted in antiSMASH. We identified genes encoding 2,3-butanediol; methionine; isoprene (metH, mmuM, ispEFH, gcpE, idi, and ilvABCDEH); biofilm formation; and colonization (upp, rfbBC, efp, aftA, pssA, pilD, fliA, and dhaM). Above all, S. yangpuensis CM253 showed the potential for future development as a biocontrol agent.
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37
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Dundas CM, Dinneny JR. Genetic Circuit Design in Rhizobacteria. BIODESIGN RESEARCH 2022; 2022:9858049. [PMID: 37850138 PMCID: PMC10521742 DOI: 10.34133/2022/9858049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/31/2022] [Indexed: 10/19/2023] Open
Abstract
Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.
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Affiliation(s)
| | - José R. Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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38
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Motility Suppression and Trapping Bacteria by ZnO Nanostructures. CRYSTALS 2022. [DOI: 10.3390/cryst12081027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Regulating the swimming motility of bacteria near surfaces is essential to suppress or avoid bacterial contamination and infection in catheters and medical devices with wall surfaces. However, the motility of bacteria near walls strongly depends on the combination of the local physicochemical properties of the surfaces. To unravel how nanostructures and their local chemical microenvironment dynamically affect the bacterial motility near surfaces, here, we directly visualize the bacterial swimming and systematically analyze the motility of Escherichia coli swimming on ZnO nanoparticle films and nanowire arrays with further ultraviolet irradiation. The results show that the ZnO nanowire arrays reduce the swimming motility, thus significantly enhancing the trapping ability for motile bacteria. Additionally, thanks to the wide bandgap nature of a ZnO semiconductor, the ultraviolet irradiation rapidly reduces the bacteria locomotion due to the hydroxyl and singlet oxygen produced by the photodynamic effects of ZnO nanowire arrays in an aqueous solution. The findings quantitatively reveal how the combination of geometrical nanostructured surfaces and local tuning of the steric microenvironment are able to regulate the motility of swimming bacteria and suggest the efficient inhibition of bacterial translocation and infection by nanostructured coatings.
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39
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Differential Genetic Strategies of Burkholderia vietnamiensis and Paraburkholderia kururiensis for Root Colonization of Oryza sativa subsp.
japonica
and O. sativa subsp.
indica
, as Revealed by Transposon Mutagenesis Sequencing. Appl Environ Microbiol 2022; 88:e0064222. [DOI: 10.1128/aem.00642-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Burkholderiaceae
are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species of
Paraburkholderia
have repeatedly been described to stimulate plant growth.
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40
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Kuhl-Nagel T, Rodriguez PA, Gantner I, Chowdhury SP, Schwehn P, Rosenkranz M, Weber B, Schnitzler JP, Kublik S, Schloter M, Rothballer M, Falter-Braun P. Novel Pseudomonas sp. SCA7 Promotes Plant Growth in Two Plant Families and Induces Systemic Resistance in Arabidopsis thaliana. Front Microbiol 2022; 13:923515. [PMID: 35875540 PMCID: PMC9297469 DOI: 10.3389/fmicb.2022.923515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas sp. SCA7, characterized in this study, was isolated from roots of the bread wheat Triticum aestivum. Sequencing and annotation of the complete SCA7 genome revealed that it represents a potential new Pseudomonas sp. with a remarkable repertoire of plant beneficial functions. In vitro and in planta experiments with the reference dicot plant A. thaliana and the original monocot host T. aestivum were conducted to identify the functional properties of SCA7. The isolate was able to colonize roots, modify root architecture, and promote growth in A. thaliana. Moreover, the isolate increased plant fresh weight in T. aestivum under unchallenged conditions. Gene expression analysis of SCA7-inoculated A. thaliana indicated a role of SCA7 in nutrient uptake and priming of plants. Moreover, confrontational assays of SCA7 with fungal and bacterial plant pathogens revealed growth restriction of the pathogens by SCA7 in direct as well as indirect contact. The latter indicated involvement of microbial volatile organic compounds (mVOCs) in this interaction. Gas chromatography-mass spectrometry (GC-MS) analyses revealed 1-undecene as the major mVOC, and octanal and 1,4-undecadiene as minor abundant compounds in the emission pattern of SCA7. Additionally, SCA7 enhanced resistance of A. thaliana against infection with the plant pathogen Pseudomonas syringae pv. tomato DC3000. In line with these results, SA- and JA/ET-related gene expression in A. thaliana during infection with Pst DC3000 was upregulated upon treatment with SCA7, indicating the ability of SCA7 to induce systemic resistance. The thorough characterization of the novel Pseudomonas sp. SCA7 showed a remarkable genomic and functional potential of plant beneficial traits, rendering it a promising candidate for application as a biocontrol or a biostimulation agent.
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Affiliation(s)
- Theresa Kuhl-Nagel
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Patricia Antonia Rodriguez
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Isabella Gantner
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Soumitra Paul Chowdhury
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Patrick Schwehn
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Maaria Rosenkranz
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Baris Weber
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jörg-Peter Schnitzler
- Institute of Biochemical Plant Pathology, Research Unit Environmental Simulation, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Susanne Kublik
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis (COMI), Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Michael Rothballer
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Pascal Falter-Braun
- Institute for Network Biology, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Microbe-Host Interactions, Faculty of Biology, Ludwig-Maximilians-University of Munich, Munich, Germany
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41
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Li Z, Zheng Y, Li Y, Cheng X, Huang S, Yang X, Qin Y. Genotype-Specific Recruitment of Rhizosphere Bacteria From Sandy Loam Soil for Growth Promotion of Cucumis sativus var. hardwickii. Front Microbiol 2022; 13:910644. [PMID: 35832804 PMCID: PMC9271904 DOI: 10.3389/fmicb.2022.910644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022] Open
Abstract
The composition and structure of the rhizosphere microbiome is affected by many factors, including soil type, genotype, and cultivation time of the plant. However, the interaction mechanisms among these factors are largely unclear. We use culture-independent 16S rRNA amplicon sequencing to investigate the rhizosphere bacterial composition and the structure of cultivated cucumber Xintaimici (XT) and wild-type cucumber Cucumis sativus var. hardwickii (HD) in four kinds of soils. We found that soil type, cultivation time, and genotype affected the composition and structure of cucumber rhizosphere bacterial communities. Notably, HD showed better physiological features in sandy soil and sandy loam soil than it did in black soil and farm soil at 50 days post-sowing, which was due to its stronger recruitment ability to Nitrospira, Nocardioides, Bacillus, and Gaiella in sandy soil, and more Tumebacillus, Nitrospira, and Paenibacillus in sandy loam soil. Meanwhile, we also found that HD showed a better recruiting capacity for these bacterial genera than XT in both sandy soil and sandy loam soil. Functional predictions indicated that these bacteria might have had stronger root colonization ability and then promoted the growth of cucumbers by enhancing nitrogen metabolism and active metabolite secretion. In this study, our findings provided a better insight into the relationship between cucumber phenotype, genotype, and the rhizosphere bacterial community, which will offer valuable theoretical references for rhizosphere microbiota studies and its future application in agriculture.
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Affiliation(s)
- Zeyang Li
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingying Zheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yansu Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xu Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Sanwen Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- *Correspondence: Sanwen Huang,
| | - Xueyong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Xueyong Yang,
| | - Yuxuan Qin
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Yuxuan Qin,
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42
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Control of nitrogen fixation and ammonia excretion in Azorhizobium caulinodans. PLoS Genet 2022; 18:e1010276. [PMID: 35727841 PMCID: PMC9249168 DOI: 10.1371/journal.pgen.1010276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/01/2022] [Accepted: 05/26/2022] [Indexed: 11/19/2022] Open
Abstract
Due to the costly energy demands of nitrogen (N) fixation, diazotrophic bacteria have evolved complex regulatory networks that permit expression of the catalyst nitrogenase only under conditions of N starvation, whereas the same condition stimulates upregulation of high-affinity ammonia (NH3) assimilation by glutamine synthetase (GS), preventing excess release of excess NH3 for plants. Diazotrophic bacteria can be engineered to excrete NH3 by interference with GS, however control is required to minimise growth penalties and prevent unintended provision of NH3 to non-target plants. Here, we tested two strategies to control GS regulation and NH3 excretion in our model cereal symbiont Azorhizobium caulinodans AcLP, a derivative of ORS571. We first attempted to recapitulate previous work where mutation of both PII homologues glnB and glnK stimulated GS shutdown but found that one of these genes was essential for growth. Secondly, we expressed unidirectional adenylyl transferases (uATs) in a ΔglnE mutant of AcLP which permitted strong GS shutdown and excretion of NH3 derived from N2 fixation and completely alleviated negative feedback regulation on nitrogenase expression. We placed a uAT allele under control of the NifA-dependent promoter PnifH, permitting GS shutdown and NH3 excretion specifically under microaerobic conditions, the same cue that initiates N2 fixation, then deleted nifA and transferred a rhizopine nifAL94Q/D95Q-rpoN controller plasmid into this strain, permitting coupled rhizopine-dependent activation of N2 fixation and NH3 excretion. This highly sophisticated and multi-layered control circuitry brings us a step closer to the development of a "synthetic symbioses” where N2 fixation and NH3 excretion could be specifically activated in diazotrophic bacteria colonising transgenic rhizopine producing cereals, targeting delivery of fixed N to the crop while preventing interaction with non-target plants. Inoculation of cereal crops with associative diazotrophic bacteria that convert atmospheric nitrogen (N2) into ammonia (NH3) could be used to sustainably improve delivery of nitrogen to crops. However, due to the costly energy demands of N2 fixation, bacteria restrict excess production of NH3 and release to the plants. Diazotrophs can be engineered for excess NH3 production and release, however genetic control is required to minimise growth penalties and prevent unintended provision of NH3 to non-target weed species. Here, we engineer coupled control of N2 fixation and NH3 release in response to the signalling molecule rhizopine supplemented in vitro. This control circuitry represents a prototype for the future development of a “synthetic symbiosis” where bacterial N2 fixation and NH3 excretion could be specifically activated following colonisation of transgenic rhizopine producing cereals in the field, minimising bacterial energy requirements and preventing provision of NH3 to non-target plants.
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Abstract
Inoculation of cereals with diazotrophic (N2-fixing) bacteria offers a sustainable alternative to the application of nitrogen fertilizers in agriculture. While natural diazotrophs have evolved multilayered regulatory mechanisms that couple N2 fixation with assimilation of the product NH3 and prevent release to plants, genetic modifications can permit excess production and excretion of NH3. However, a lack of stringent host-specificity for root colonization by the bacteria would allow growth promotion of target and nontarget plants species alike. Here, we exploit synthetic transkingdom signaling to establish plant host-specific control of the N2-fixation catalyst nitrogenase in Azorhizobium caulinodans occupying barley roots. This work demonstrates how partner-specific interactions can be established to avoid potential growth promotion of nontarget plants. Engineering N2-fixing symbioses between cereals and diazotrophic bacteria represents a promising strategy to sustainably deliver biologically fixed nitrogen (N) in agriculture. We previously developed novel transkingdom signaling between plants and bacteria, through plant production of the bacterial signal rhizopine, allowing control of bacterial gene expression in association with the plant. Here, we have developed both a homozygous rhizopine producing (RhiP) barley line and a hybrid rhizopine uptake system that conveys upon our model bacterium Azorhizobium caulinodans ORS571 (Ac) 103-fold improved sensitivity for rhizopine perception. Using this improved genetic circuitry, we established tight rhizopine-dependent transcriptional control of the nitrogenase master regulator nifA and the N metabolism σ-factor rpoN, which drove nitrogenase expression and activity in vitro and in situ by bacteria colonizing RhiP barley roots. Although in situ nitrogenase activity was suboptimally effective relative to the wild-type strain, activation was specific to RhiP barley and was not observed on the roots of wild-type plants. This work represents a key milestone toward the development of a synthetic plant-controlled symbiosis in which the bacteria fix N2 only when in contact with the desired host plant and are prevented from interaction with nontarget plant species.
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Soil Origin and Plant Genotype Modulate Switchgrass Aboveground Productivity and Root Microbiome Assembly. mBio 2022; 13:e0007922. [PMID: 35384699 PMCID: PMC9040762 DOI: 10.1128/mbio.00079-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Switchgrass (Panicum virgatum) is a model perennial grass for bioenergy production that can be productive in agricultural lands that are not suitable for food production. There is growing interest in whether its associated microbiome may be adaptive in low- or no-input cultivation systems. However, the relative impact of plant genotype and soil factors on plant microbiome and biomass are a challenge to decouple. To address this, a common garden greenhouse experiment was carried out using six common switchgrass genotypes, which were each grown in four different marginal soils collected from long-term bioenergy research sites in Michigan and Wisconsin. We characterized the fungal and bacterial root communities with high-throughput amplicon sequencing of the ITS and 16S rDNA markers, and collected phenological plant traits during plant growth, as well as soil chemical traits. At harvest, we measured the total plant aerial dry biomass. Significant differences in richness and Shannon diversity across soils but not between plant genotypes were found. Generalized linear models showed an interaction between soil and genotype for fungal richness but not for bacterial richness. Community structure was also strongly shaped by soil origin and soil origin × plant genotype interactions. Overall, plant genotype effects were significant but low. Random Forest models indicate that important factors impacting switchgrass biomass included NO3−, Ca2+, PO43−, and microbial biodiversity. We identified 54 fungal and 52 bacterial predictors of plant aerial biomass, which included several operational taxonomic units belonging to Glomeraceae and Rhizobiaceae, fungal and bacterial lineages that are involved in provisioning nutrients to plants.
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Shi W, Xing Y, Zhu Y, Gao N, Ying Y. Diverse responses of pqqC- and phoD-harbouring bacterial communities to variation in soil properties of Moso bamboo forests. Microb Biotechnol 2022; 15:2097-2111. [PMID: 35298867 PMCID: PMC9249317 DOI: 10.1111/1751-7915.14029] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/30/2022] Open
Abstract
Phosphate‐mobilizing bacteria (PMB) play a critical role in the regulation of phosphorus availability in the soil. The microbial genes pqqC and phoD encode pyrroloquinoline quinone synthase and bacterial alkaline phosphatase, respectively, which regulate inorganic and organic phosphorus mobilization, and are therefore used as PMB markers. We examined the effects of soil properties in three Moso bamboo forest sites on the PMB communities that were profiled using high‐throughput sequencing. We observed differentiated responses of pqqC‐ and phoD‐harbouring PMB communities to various soil conditions. There was significant variation among the sites in the diversity and structure of the phoD‐harbouring community, which correlated with variation in phosphorus levels and non‐capillary porosity; soil organic carbon and soil water content also affected the structure of the phoD‐harbouring community. However, no significant difference in the diversity of pqqC‐harbouring community was observed among different sites, while the structure of the pqqC‐harbouring bacteria community was affected by soil organic carbon and soil total nitrogen, but not soil phosphorus levels. Overall, changes in soil conditions affected the phoD‐harbouring community more than the pqqC‐harbouring community. These findings provide a new insight to explore the effects of soil conditions on microbial communities that solubilize inorganic phosphate and mineralize organic phosphate.
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Affiliation(s)
- Wenhui Shi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yijing Xing
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ying Zhu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Ning Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yeqing Ying
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
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Rico-Jiménez M, Roca A, Krell T, Matilla MA. A bacterial chemoreceptor that mediates chemotaxis to two different plant hormones. Environ Microbiol 2022; 24:3580-3597. [PMID: 35088505 PMCID: PMC9543091 DOI: 10.1111/1462-2920.15920] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Indole-3-acetic acid (IAA) is the main naturally occurring auxin and is produced by organisms of all kingdoms of life. In addition to the regulation of plant growth and development, IAA plays an important role in the interaction between plants and growth-promoting and phytopathogenic bacteria by regulating bacterial gene expression and physiology. We show here that a IAA metabolizing plant-associated Pseudomonas putida isolate exhibits chemotaxis to IAA that is independent of auxin metabolism. We found that IAA chemotaxis is based on the activity of the PcpI chemoreceptor and heterologous expression of pcpI conferred IAA taxis to different environmental and human pathogenic isolates of the Pseudomonas genus. Using ligand screening, microcalorimetry and quantitative chemotaxis assays, we found that PcpI failed to bind IAA directly, but recognized and mediated chemoattractions to various aromatic compounds, including the phytohormone salicylic acid. The expression of pcpI and its role in the interactions with plants was also investigated. PcpI extends the range of central signal molecules recognized by chemoreceptors. To our knowledge, this is the first report on a bacterial receptor that responds to two different phytohormones. Our study reinforces the multifunctional role of IAA and salicylic acid as intra- and inter-kingdom signal molecules. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Miriam Rico-Jiménez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Amalia Roca
- Department of Microbiology, Facultad de Farmacia, Campus Universitario de Cartuja, Universidad de Granada, 18071, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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Nazari M, Bickel S, Benard P, Mason-Jones K, Carminati A, Dippold MA. Biogels in Soils: Plant Mucilage as a Biofilm Matrix That Shapes the Rhizosphere Microbial Habitat. FRONTIERS IN PLANT SCIENCE 2022; 12:798992. [PMID: 35095970 PMCID: PMC8792611 DOI: 10.3389/fpls.2021.798992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Mucilage is a gelatinous high-molecular-weight substance produced by almost all plants, serving numerous functions for plant and soil. To date, research has mainly focused on hydraulic and physical functions of mucilage in the rhizosphere. Studies on the relevance of mucilage as a microbial habitat are scarce. Extracellular polymeric substances (EPS) are similarly gelatinous high-molecular-weight substances produced by microorganisms. EPS support the establishment of microbial assemblages in soils, mainly through providing a moist environment, a protective barrier, and serving as carbon and nutrient sources. We propose that mucilage shares physical and chemical properties with EPS, functioning similarly as a biofilm matrix covering a large extent of the rhizosphere. Our analyses found no evidence of consistent differences in viscosity and surface tension between EPS and mucilage, these being important physical properties. With regard to chemical composition, polysaccharide, protein, neutral monosaccharide, and uronic acid composition also showed no consistent differences between these biogels. Our analyses and literature review suggest that all major functions known for EPS and required for biofilm formation are also provided by mucilage, offering a protected habitat optimized for nutrient mobilization. Mucilage enables high rhizo-microbial abundance and activity by functioning as carbon and nutrient source. We suggest that the role of mucilage as a biofilm matrix has been underestimated, and should be considered in conceptual models of the rhizosphere.
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Affiliation(s)
- Meisam Nazari
- Division of Biogeochemistry of Agroecosystems, Georg-August University of Göttingen, Göttingen, Germany
| | - Samuel Bickel
- Physics of Soils and Terrestrial Ecosystems, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Pascal Benard
- Physics of Soils and Terrestrial Ecosystems, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
| | - Kyle Mason-Jones
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Andrea Carminati
- Physics of Soils and Terrestrial Ecosystems, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, Zurich, Switzerland
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Mendoza-Suárez M, Andersen SU, Poole PS, Sánchez-Cañizares C. Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses. FRONTIERS IN PLANT SCIENCE 2021; 12:690567. [PMID: 34489993 PMCID: PMC8416774 DOI: 10.3389/fpls.2021.690567] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Biological nitrogen fixation by Rhizobium-legume symbioses represents an environmentally friendly and inexpensive alternative to the use of chemical nitrogen fertilizers in legume crops. Rhizobial inoculants, applied frequently as biofertilizers, play an important role in sustainable agriculture. However, inoculants often fail to compete for nodule occupancy against native rhizobia with inferior nitrogen-fixing abilities, resulting in low yields. Strains with excellent performance under controlled conditions are typically selected as inoculants, but the rates of nodule occupancy compared to native strains are rarely investigated. Lack of persistence in the field after agricultural cycles, usually due to the transfer of symbiotic genes from the inoculant strain to naturalized populations, also limits the suitability of commercial inoculants. When rhizobial inoculants are based on native strains with a high nitrogen fixation ability, they often have superior performance in the field due to their genetic adaptations to the local environment. Therefore, knowledge from laboratory studies assessing competition and understanding how diverse strains of rhizobia behave, together with assays done under field conditions, may allow us to exploit the effectiveness of native populations selected as elite strains and to breed specific host cultivar-rhizobial strain combinations. Here, we review current knowledge at the molecular level on competition for nodulation and the advances in molecular tools for assessing competitiveness. We then describe ongoing approaches for inoculant development based on native strains and emphasize future perspectives and applications using a multidisciplinary approach to ensure optimal performance of both symbiotic partners.
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Affiliation(s)
| | - Stig U. Andersen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Li E, Zhang H, Jiang H, Pieterse CMJ, Jousset A, Bakker PAHM, de Jonge R. Experimental-Evolution-Driven Identification of Arabidopsis Rhizosphere Competence Genes in Pseudomonas protegens. mBio 2021; 12:e0092721. [PMID: 34101491 PMCID: PMC8262913 DOI: 10.1128/mbio.00927-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 04/30/2021] [Indexed: 11/20/2022] Open
Abstract
Beneficial plant root-associated microorganisms carry out a range of functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming several challenges, including competition with neighboring microorganisms and host immunity. Forward and reverse genetics have led to the identification of mechanisms that are used by beneficial microorganisms to overcome these challenges, such as the production of iron-chelating compounds, the formation of strong biofilms, or the concealment of characteristic microbial molecular patterns that trigger the host immune system. However, how such mechanisms arose from an evolutionary perspective is much less understood. To study bacterial adaptation in the rhizosphere, we employed experimental evolution to track the physiological and genetic dynamics of root-dwelling Pseudomonas protegens in the Arabidopsis thaliana rhizosphere under axenic conditions. This simplified binary one plant/one bacterium system allows for the amplification of key adaptive mechanisms for bacterial rhizosphere colonization. We identified 35 mutations, including single-nucleotide polymorphisms, insertions, and deletions, distributed over 28 genes. We found that mutations in genes encoding global regulators and in genes for siderophore production, cell surface decoration, attachment, and motility accumulated in parallel, underlining the finding that bacterial adaptation to the rhizosphere follows multiple strategies. Notably, we observed that motility increased in parallel across multiple independent evolutionary lines. All together, these results underscore the strength of experimental evolution in identifying key genes, pathways, and processes for bacterial rhizosphere colonization and a methodology for the development of elite beneficial microorganisms with enhanced root-colonizing capacities that can support sustainable agriculture in the future. IMPORTANCE Beneficial root-associated microorganisms carry out many functions that are essential for plant performance. Establishment of a bacterium on plant roots, however, requires overcoming many challenges. Previously, diverse mechanisms that are used by beneficial microorganisms to overcome these challenges were identified. However, how such mechanisms have developed from an evolutionary perspective is much less understood. Here, we employed experimental evolution to track the evolutionary dynamics of a root-dwelling pseudomonad on the root of Arabidopsis. We found that mutations in global regulators, as well as in genes for siderophore production, cell surface decoration, attachment, and motility, accumulate in parallel, emphasizing these strategies for bacterial adaptation to the rhizosphere. We identified 35 mutations distributed over 28 genes. All together, our results demonstrate the power of experimental evolution in identifying key pathways for rhizosphere colonization and a methodology for the development of elite beneficial microorganisms that can support sustainable agriculture.
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Affiliation(s)
- Erqin Li
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Hao Zhang
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Henan Jiang
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Alexandre Jousset
- Ecology and Biodiversity, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Peter A. H. M. Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, The Netherlands
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