1
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Wu W, Zhuang Y, Chen D, Ruan Y, Li F, Jackson K, Liu CW, East A, Wen J, Tatsis E, Poole PS, Xu P, Murray JD. Methylated chalcones are required for rhizobial nod gene induction in the Medicago truncatula rhizosphere. New Phytol 2024. [PMID: 38571285 DOI: 10.1111/nph.19701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
Legume nodulation requires the detection of flavonoids in the rhizosphere by rhizobia to activate their production of Nod factor countersignals. Here we investigated the flavonoids involved in nodulation of Medicago truncatula. We biochemically characterized five flavonoid-O-methyltransferases (OMTs) and a lux-based nod gene reporter was used to investigate the response of Sinorhizobium medicae NodD1 to various flavonoids. We found that chalcone-OMT 1 (ChOMT1) and ChOMT3, but not OMT2, 4, and 5, were able to produce 4,4'-dihydroxy-2'-methoxychalcone (DHMC). The bioreporter responded most strongly to DHMC, while isoflavones important for nodulation of soybean (Glycine max) showed no activity. Mutant analysis revealed that loss of ChOMT1 strongly reduced DHMC levels. Furthermore, chomt1 and omt2 showed strongly reduced bioreporter luminescence in their rhizospheres. In addition, loss of both ChOMT1 and ChOMT3 reduced nodulation, and this phenotype was strengthened by the further loss of OMT2. We conclude that: the loss of ChOMT1 greatly reduces root DHMC levels; ChOMT1 or OMT2 are important for nod gene activation in the rhizosphere; and ChOMT1/3 and OMT2 promote nodulation. Our findings suggest a degree of exclusivity in the flavonoids used for nodulation in M. truncatula compared to soybean, supporting a role for flavonoids in rhizobial host range.
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Affiliation(s)
- Wenjuan Wu
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science, Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuxin Zhuang
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science, Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dasong Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, China
| | - Yiting Ruan
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science, Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai, 200032, China
| | - Fuyu Li
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science, Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai, 200032, China
| | - Kirsty Jackson
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Cheng-Wu Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Alison East
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Evangelos Tatsis
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science, Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai, 200032, China
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ping Xu
- Shanghai Collaborative Innovation Center of Plant Germplasm Resources Development, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Jeremy D Murray
- National Key Laboratory of Plant Molecular Genetics, CAS-JIC Centre of Excellence for Plant and Microbial Science, Center for Excellence in Molecular Plant Sciences (CEMPS), Chinese Academy of Sciences, Shanghai, 200032, China
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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2
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Aroney STN, Pini F, Kessler C, Poole PS, Sánchez-Cañizares C. The motility and chemosensory systems of Rhizobium leguminosarum, their role in symbiosis, and link to PTS Ntr regulation. Environ Microbiol 2024; 26:e16570. [PMID: 38216524 DOI: 10.1111/1462-2920.16570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Motility and chemotaxis are crucial processes for soil bacteria and plant-microbe interactions. This applies to the symbiotic bacterium Rhizobium leguminosarum, where motility is driven by flagella rotation controlled by two chemotaxis systems, Che1 and Che2. The Che1 cluster is particularly important in free-living motility prior to the establishment of the symbiosis, with a che1 mutant delayed in nodulation and reduced in nodulation competitiveness. The Che2 system alters bacteroid development and nodule maturation. In this work, we also identified 27 putative chemoreceptors encoded in the R. leguminosarum bv. viciae 3841 genome and characterized its motility in different growth conditions. We describe a metabolism-based taxis system in rhizobia that acts at high concentrations of dicarboxylates to halt motility independent of chemotaxis. Finally, we show how PTSNtr influences cell motility, with PTSNtr mutants exhibiting reduced swimming in different media. Motility is restored by the active forms of the PTSNtr output regulatory proteins, unphosphorylated ManX and phosphorylated PtsN. Overall, this work shows how rhizobia typify soil bacteria by having a high number of chemoreceptors and highlights the importance of the motility and chemotaxis mechanisms in a free-living cell in the rhizosphere, and at different stages of the symbiosis.
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Affiliation(s)
| | | | - Celia Kessler
- Department of Biology, University of Oxford, Oxford, UK
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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4
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Tkacz A, Ledermann R, Martyn A, Schornack S, Oldroyd GED, Poole PS. Nodulation and nitrogen fixation in Medicago truncatula strongly alters the abundance of its root microbiota and subtly affects its structure. Environ Microbiol 2022; 24:5524-5533. [PMID: 36054464 PMCID: PMC9804836 DOI: 10.1111/1462-2920.16164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/07/2022] [Indexed: 01/09/2023]
Abstract
The plant common symbiosis signalling (SYM) pathway has shared function between interactions with rhizobia and arbuscular mycorrhizal fungi, the two most important symbiotic interactions between plants and microorganisms that are crucial in plant and agricultural yields. Here, we determine the role of the plant SYM pathway in the structure and abundance of the microbiota in the model legume Medicago truncatula and whether this is controlled by the nitrogen or phosphorus status of the plant. We show that SYM mutants (dmi3) differ substantially from the wild type (WT) in the absolute abundance of the root microbiota, especially under nitrogen limitation. Changes in the structure of the microbiota were less pronounced and depended on both plant genotype and nutrient status. Thus, the SYM pathway has a major impact on microbial abundance in M. truncatula and also subtly alters the composition of the microbiota.
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Affiliation(s)
| | | | - Anna Martyn
- Department of BiologyUniversity of OxfordOxfordUK
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5
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Pardo-Diaz J, Poole PS, Beguerisse-Díaz M, Deane CM, Reinert G. Generating weighted and thresholded gene coexpression networks using signed distance correlation. Netw Sci (Camb Univ Press) 2022; 10:131-145. [PMID: 36217370 PMCID: PMC7613200 DOI: 10.1017/nws.2022.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Even within well-studied organisms, many genes lack useful functional annotations. One way to generate such functional information is to infer biological relationships between genes or proteins, using a network of gene coexpression data that includes functional annotations. Signed distance correlation has proved useful for the construction of unweighted gene coexpression networks. However, transforming correlation values into unweighted networks may lead to a loss of important biological information related to the intensity of the correlation. Here we introduce a principled method to construct weighted gene coexpression networks using signed distance correlation. These networks contain weighted edges only between those pairs of genes whose correlation value is higher than a given threshold. We analyse data from different organisms and find that networks generated with our method based on signed distance correlation are more stable and capture more biological information compared to networks obtained from Pearson correlation. Moreover, we show that signed distance correlation networks capture more biological information than unweighted networks based on the same metric. While we use biological data sets to illustrate the method, the approach is general and can be used to construct networks in other domains. Code and data are available on https://github.com/javier-pardodiaz/sdcorGCN.
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Affiliation(s)
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | | | | | - Gesine Reinert
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
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6
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Pardo-Diaz J, Beguerisse-Díaz M, Poole PS, Deane CM, Reinert G. Extracting Information from Gene Coexpression Networks of Rhizobium leguminosarum. J Comput Biol 2022; 29:752-768. [PMID: 35588362 DOI: 10.1089/cmb.2021.0600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nitrogen uptake in legumes is facilitated by bacteria such as Rhizobium leguminosarum. For this bacterium, gene expression data are available, but functional gene annotation is less well developed than for other model organisms. More annotations could lead to a better understanding of the pathways for growth, plant colonization, and nitrogen fixation in R. leguminosarum. In this study, we present a pipeline that combines novel scores from gene coexpression network analysis in a principled way to identify the genes that are associated with certain growth conditions or highly coexpressed with a predefined set of genes of interest. This association may lead to putative functional annotation or to a prioritized list of genes for further study.
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Affiliation(s)
- Javier Pardo-Diaz
- Department of Statistics, University of Oxford, Oxford, United Kingdom.,Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Gesine Reinert
- Department of Statistics, University of Oxford, Oxford, United Kingdom
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7
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Abstract
This article comments on: Tian L, Liu L, Xu S, Deng R, Wu P, Jiang H, Wu G, Chen Y. 2022. A d-pinitol transporter, LjPLT11, regulates plant growth and nodule development in Lotus japonicus. Journal of Experimental Botany 73, 351–365.
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Affiliation(s)
- Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Raphael Ledermann
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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8
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Crang N, Borah K, James EK, Jorrín B, Green P, Tkacz A, East AK, Poole PS. Role and Regulation of Poly-3-Hydroxybutyrate in Nitrogen Fixation in Azorhizobium caulinodans. Mol Plant Microbe Interact 2021; 34:1390-1398. [PMID: 34875178 DOI: 10.1094/mpmi-06-21-0138-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
An Azorhizobium caulinodans phaC mutant (OPS0865) unable to make poly-3-hydroxybutyrate (PHB), grows poorly on many carbon sources and cannot fix nitrogen in laboratory culture. However, when inoculated onto its host plant, Sesbania rostrata, the phaC mutant consistently fixed nitrogen. Upon reisolation from S. rostrata root nodules, a suppressor strain (OPS0921) was isolated that has significantly improved growth on a variety of carbon sources and also fixes nitrogen in laboratory culture. The suppressor retains the original mutation and is unable to synthesize PHB. Genome sequencing revealed a suppressor transition mutation, G to A (position 357,354), 13 bases upstream of the ATG start codon of phaR in its putative ribosome binding site (RBS). PhaR is the global regulator of PHB synthesis but also has other roles in regulation within the cell. In comparison with the wild type, translation from the phaR native RBS is increased approximately sixfold in the phaC mutant background, suggesting that the level of PhaR is controlled by PHB. Translation from the phaR mutated RBS (RBS*) of the suppressor mutant strain (OPS0921) is locked at a low basal rate and unaffected by the phaC mutation, suggesting that RBS* renders the level of PhaR insensitive to regulation by PHB. In the original phaC mutant (OPS0865), the lack of nitrogen fixation and poor growth on many carbon sources is likely to be due to increased levels of PhaR causing dysregulation of its complex regulon, because PHB formation, per se, is not required for effective nitrogen fixation in A. caulinodans.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Nick Crang
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Khushboo Borah
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K
| | - Beatriz Jorrín
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Patrick Green
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Alison K East
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
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9
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Spitzer SO, Tkacz A, Savignac HM, Cooper M, Giallourou N, Mann EO, Bannerman DM, Swann JR, Anthony DC, Poole PS, Burnet PW. Postnatal prebiotic supplementation in rats affects adult anxious behaviour, hippocampus, electrophysiology, metabolomics, and gut microbiota. iScience 2021; 24:103113. [PMID: 34611610 PMCID: PMC8476651 DOI: 10.1016/j.isci.2021.103113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/16/2021] [Accepted: 09/08/2021] [Indexed: 12/13/2022] Open
Abstract
We have shown previously that prebiotic (Bimuno galacto-oligosacharides, B-GOS®) administration to neonatal rats increased hippocampal NMDAR proteins. The present study has investigated the effects of postnatal B-GOS® supplementation on hippocampus-dependent behavior in young, adolescent, and adult rats and applied electrophysiological, metabolomic and metagenomic analyses to explore potential underlying mechanisms. The administration of B-GOS® to suckling, but not post-weaned, rats reduced anxious behavior until adulthood. Neonatal prebiotic intake also reduced the fast decay component of hippocampal NMDAR currents, altered age-specific trajectories of the brain, intestinal, and liver metabolomes, and reduced abundance of fecal Enterococcus and Dorea bacteria. Our data are the first to show that prebiotic administration to rats during a specific postnatal period has long-term effects on behavior and hippocampal physiology. The study also suggests that early-life prebiotic intake may affect host brain function through the reduction of stress-related gut bacteria rather than increasing the proliferation of beneficial microbes.
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Affiliation(s)
- Sonia O. Spitzer
- Department of Psychiatry, University of Oxford, Warneford Lane, Oxford, OX3 7JX, UK
| | - Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Helene M. Savignac
- Quadram Institute, Rosalind Franklin Road, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Matthew Cooper
- Department of Physiology, Anatomy and Genomics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
- Oxford Ion Channel Initiative, University of Oxford, Oxford OX1 3PT, UK
| | - Natasa Giallourou
- Department of Metabolism, Digestion and Reproduction, Imperial College, South Kensington Campus, London SW7 2AZ, UK
| | - Edward O. Mann
- Department of Physiology, Anatomy and Genomics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
- Oxford Ion Channel Initiative, University of Oxford, Oxford OX1 3PT, UK
| | - David M. Bannerman
- Oxford Ion Channel Initiative, University of Oxford, Oxford OX1 3PT, UK
- Department of Experimental Psychology, University of Oxford, Anna Watts Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
| | - Jonathan R. Swann
- Department of Metabolism, Digestion and Reproduction, Imperial College, South Kensington Campus, London SW7 2AZ, UK
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Daniel C. Anthony
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Philip W.J. Burnet
- Department of Psychiatry, University of Oxford, Warneford Lane, Oxford, OX3 7JX, UK
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10
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Webb IUC, Xu J, Sánchez-Cañizares C, Karunakaran R, Ramachandran VK, Rutten PJ, East AK, Huang WE, Watmough NJ, Poole PS. Regulation and Characterization of Mutants of fixABCX in Rhizobium leguminosarum. Mol Plant Microbe Interact 2021; 34:1167-1180. [PMID: 34110256 DOI: 10.1094/mpmi-02-21-0037-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Symbiosis between Rhizobium leguminosarum and Pisum sativum requires tight control of redox balance in order to maintain respiration under the microaerobic conditions required for nitrogenase while still producing the eight electrons and sixteen molecules of ATP needed for nitrogen fixation. FixABCX, a cluster of electron transfer flavoproteins essential for nitrogen fixation, is encoded on the Sym plasmid (pRL10), immediately upstream of nifA, which encodes the general transcriptional regulator of nitrogen fixation. There is a symbiotically regulated NifA-dependent promoter upstream of fixA (PnifA1), as well as an additional basal constitutive promoter driving background expression of nifA (PnifA2). These were confirmed by 5'-end mapping of transcription start sites using differential RNA-seq. Complementation of polar fixAB and fixX mutants (Fix- strains) confirmed expression of nifA from PnifA1 in symbiosis. Electron microscopy combined with single-cell Raman microspectroscopy characterization of fixAB mutants revealed previously unknown heterogeneity in bacteroid morphology within a single nodule. Two morphotypes of mutant fixAB bacteroids were observed. One was larger than wild-type bacteroids and contained high levels of polyhydroxy-3-butyrate, a complex energy/reductant storage product. A second bacteroid phenotype was morphologically and compositionally different and resembled wild-type infection thread cells. From these two characteristic fixAB mutant bacteroid morphotypes, inferences can be drawn on the metabolism of wild-type nitrogen-fixing bacteroids.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Isabel U C Webb
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Jiabao Xu
- Department of Engineering, University of Oxford, Parks Road, Oxford OX1 3PJ, U.K
| | | | - Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Vinoy K Ramachandran
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Paul J Rutten
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Alison K East
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Wei E Huang
- Department of Engineering, University of Oxford, Parks Road, Oxford OX1 3PJ, U.K
| | - Nicholas J Watmough
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, U.K
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
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11
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Jorrin B, Maluk M, Atoliya N, Kumar SC, Chalasani D, Tkacz A, Singh P, Basu A, Pullabhotla SVSRN, Kumar M, Mohanty SR, East AK, Ramachandran VK, James EK, Podile AR, Saxena AK, Rao DLN, Poole PS. Genomic Diversity of Pigeon Pea ( Cajanus cajan L. Millsp.) Endosymbionts in India and Selection of Potential Strains for Use as Agricultural Inoculants. Front Plant Sci 2021; 12:680981. [PMID: 34557206 PMCID: PMC8453007 DOI: 10.3389/fpls.2021.680981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/06/2021] [Indexed: 05/27/2023]
Abstract
Pigeon pea (Cajanus cajan L. Millsp. ) is a legume crop resilient to climate change due to its tolerance to drought. It is grown by millions of resource-poor farmers in semiarid and tropical subregions of Asia and Africa and is a major contributor to their nutritional food security. Pigeon pea is the sixth most important legume in the world, with India contributing more than 70% of the total production and harbouring a wide variety of cultivars. Nevertheless, the low yield of pigeon pea grown under dry land conditions and its yield instability need to be improved. This may be done by enhancing crop nodulation and, hence, biological nitrogen fixation (BNF) by supplying effective symbiotic rhizobia through the application of "elite" inoculants. Therefore, the main aim in this study was the isolation and genomic analysis of effective rhizobial strains potentially adapted to drought conditions. Accordingly, pigeon pea endosymbionts were isolated from different soil types in Southern, Central, and Northern India. After functional characterisation of the isolated strains in terms of their ability to nodulate and promote the growth of pigeon pea, 19 were selected for full genome sequencing, along with eight commercial inoculant strains obtained from the ICRISAT culture collection. The phylogenomic analysis [Average nucleotide identity MUMmer (ANIm)] revealed that the pigeon pea endosymbionts were members of the genera Bradyrhizobium and Ensifer. Based on nodC phylogeny and nod cluster synteny, Bradyrhizobium yuanmingense was revealed as the most common endosymbiont, harbouring nod genes similar to those of Bradyrhizobium cajani and Bradyrhizobium zhanjiangense. This symbiont type (e.g., strain BRP05 from Madhya Pradesh) also outperformed all other strains tested on pigeon pea, with the notable exception of an Ensifer alkalisoli strain from North India (NBAIM29). The results provide the basis for the development of pigeon pea inoculants to increase the yield of this legume through the use of effective nitrogen-fixing rhizobia, tailored for the different agroclimatic regions of India.
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Affiliation(s)
- Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marta Maluk
- The James Hutton Institute, Dundee, United Kingdom
| | | | - Shiv Charan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Danteswari Chalasani
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Prachi Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Sarma VSRN Pullabhotla
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | | | - Alison K. East
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | | | | - Appa Rao Podile
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - DLN Rao
- ICAR-Indian Institute of Soil Science, Bhopal, India
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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12
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Knights HE, Jorrin B, Haskett TL, Poole PS. Deciphering bacterial mechanisms of root colonization. Environ Microbiol Rep 2021; 13:428-444. [PMID: 33538402 PMCID: PMC8651005 DOI: 10.1111/1758-2229.12934] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 05/07/2023]
Abstract
Bacterial colonization of the rhizosphere is critical for the establishment of plant-bacteria interactions that represent a key determinant of plant health and productivity. Plants influence bacterial colonization primarily through modulating the composition of their root exudates and mounting an innate immune response. The outcome is a horizontal filtering of bacteria from the surrounding soil, resulting in a gradient of reduced bacterial diversity coupled with a higher degree of bacterial specialization towards the root. Bacteria-bacteria interactions (BBIs) are also prevalent in the rhizosphere, influencing bacterial persistence and root colonization through metabolic exchanges, secretion of antimicrobial compounds and other processes. Traditionally, bacterial colonization has been examined under sterile laboratory conditions that mitigate the influence of BBIs. Using simplified synthetic bacterial communities combined with microfluidic imaging platforms and transposon mutagenesis screening approaches, we are now able to begin unravelling the molecular mechanisms at play during the early stages of root colonization. This review explores the current state of knowledge regarding bacterial root colonization and identifies key tools for future exploration.
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Affiliation(s)
| | - Beatriz Jorrin
- Department of Plant SciencesUniversity of OxfordOxfordOX1 3RBUK
| | | | - Philip S. Poole
- Department of Plant SciencesUniversity of OxfordOxfordOX1 3RBUK
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14
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Schulte CCM, Borah K, Wheatley RM, Terpolilli JJ, Saalbach G, Crang N, de Groot DH, Ratcliffe RG, Kruger NJ, Papachristodoulou A, Poole PS. Metabolic control of nitrogen fixation in rhizobium-legume symbioses. Sci Adv 2021; 7:7/31/eabh2433. [PMID: 34330708 PMCID: PMC8324050 DOI: 10.1126/sciadv.abh2433] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/14/2021] [Indexed: 05/16/2023]
Abstract
Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which catabolize plant-derived dicarboxylates to reduce atmospheric N2 into ammonia. Despite the agricultural importance of this symbiosis, the mechanisms that govern carbon and nitrogen allocation in bacteroids and promote ammonia secretion to the plant are largely unknown. Using a metabolic model derived from genome-scale datasets, we show that carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules. Catabolism of dicarboxylates induces not only a higher oxygen demand but also a higher NADH/NAD+ ratio than sugars. Modeling and 13C metabolic flux analysis indicate that oxygen limitation restricts the decarboxylating arm of the tricarboxylic acid cycle, which limits ammonia assimilation into glutamate. By tightly controlling oxygen supply and providing dicarboxylates as the energy and electron source donors for N2 fixation, legumes promote ammonia secretion by bacteroids. This is a defining feature of rhizobium-legume symbioses.
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Affiliation(s)
- Carolin C M Schulte
- Department of Plant Sciences, University of Oxford, Oxford, UK
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Khushboo Borah
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | | | | | - Nick Crang
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Daan H de Groot
- Systems Biology Lab, AIMMS, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | | | | | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, UK.
- John Innes Centre, Norwich Research Park, Norwich, UK
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15
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Haskett TL, Knights HE, Jorrin B, Mendes MD, Poole PS. A Simple in situ Assay to Assess Plant-Associative Bacterial Nitrogenase Activity. Front Microbiol 2021; 12:690439. [PMID: 34248916 PMCID: PMC8261070 DOI: 10.3389/fmicb.2021.690439] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/25/2021] [Indexed: 11/23/2022] Open
Abstract
Assessment of plant-associative bacterial nitrogen (N) fixation is crucial for selection and development of elite diazotrophic inoculants that could be used to supply cereal crops with nitrogen in a sustainable manner. Although diazotrophic bacteria possess diverse oxygen tolerance mechanisms, most require a sub 21% oxygen environment to achieve optimal stability and function of the N-fixing catalyst nitrogenase. Consequently, assessment of N fixation is routinely carried out on “free-living” bacteria grown in the absence of a host plant and such experiments may not accurately divulge activity in the rhizosphere where the availability and forms of nutrients such as carbon and N, which are key regulators of N fixation, may vary widely. Here, we present a modified in situ acetylene reduction assay (ARA), utilizing the model cereal barley as a host to comparatively assess nitrogenase activity in diazotrophic bacteria. The assay is rapid, highly reproducible, applicable to a broad range of diazotrophs, and can be performed with simple equipment commonly found in most laboratories that investigate plant-microbe interactions. Thus, the assay could serve as a first point of order for high-throughput identification of elite plant-associative diazotrophs.
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Affiliation(s)
- Timothy L Haskett
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Hayley E Knights
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marta D Mendes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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16
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Westhoek A, Clark LJ, Culbert M, Dalchau N, Griffiths M, Jorrin B, Karunakaran R, Ledermann R, Tkacz A, Webb I, James EK, Poole PS, Turnbull LA. Conditional sanctioning in a legume- Rhizobium mutualism. Proc Natl Acad Sci U S A 2021; 118:e2025760118. [PMID: 33941672 PMCID: PMC8126861 DOI: 10.1073/pnas.2025760118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Legumes are high in protein and form a valuable part of human diets due to their interaction with symbiotic nitrogen-fixing bacteria known as rhizobia. Plants house rhizobia in specialized root nodules and provide the rhizobia with carbon in return for nitrogen. However, plants usually house multiple rhizobial strains that vary in their fixation ability, so the plant faces an investment dilemma. Plants are known to sanction strains that do not fix nitrogen, but nonfixers are rare in field settings, while intermediate fixers are common. Here, we modeled how plants should respond to an intermediate fixer that was otherwise isogenic and tested model predictions using pea plants. Intermediate fixers were only tolerated when a better strain was not available. In agreement with model predictions, nodules containing the intermediate-fixing strain were large and healthy when the only alternative was a nonfixer, but nodules of the intermediate-fixing strain were small and white when the plant was coinoculated with a more effective strain. The reduction in nodule size was preceded by a lower carbon supply to the nodule even before differences in nodule size could be observed. Sanctioned nodules had reduced rates of nitrogen fixation, and in later developmental stages, sanctioned nodules contained fewer viable bacteria than nonsanctioned nodules. This indicates that legumes can make conditional decisions, most likely by comparing a local nodule-dependent cue of nitrogen output with a global cue, giving them remarkable control over their symbiotic partners.
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Affiliation(s)
- Annet Westhoek
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
- Systems Biology Doctoral Training Centre, Doctoral Training Centre, University of Oxford, OX1 3NP Oxford, United Kingdom
| | - Laura J Clark
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Michael Culbert
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Neil Dalchau
- Biological Computation, Microsoft Research Cambridge, CB1 2FB Cambridge, United Kingdom
| | - Megan Griffiths
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, NR4 7UH Norwich, United Kingdom
| | - Raphael Ledermann
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Isabel Webb
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Euan K James
- Ecological Sciences, The James Hutton Institute, DD2 5DA Invergowrie, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom;
| | - Lindsay A Turnbull
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom;
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17
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Haskett TL, Tkacz A, Poole PS. Engineering rhizobacteria for sustainable agriculture. ISME J 2021; 15:949-964. [PMID: 33230265 PMCID: PMC8114929 DOI: 10.1038/s41396-020-00835-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 10/29/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023]
Abstract
Exploitation of plant growth promoting (PGP) rhizobacteria (PGPR) as crop inoculants could propel sustainable intensification of agriculture to feed our rapidly growing population. However, field performance of PGPR is typically inconsistent due to suboptimal rhizosphere colonisation and persistence in foreign soils, promiscuous host-specificity, and in some cases, the existence of undesirable genetic regulation that has evolved to repress PGP traits. While the genetics underlying these problems remain largely unresolved, molecular mechanisms of PGP have been elucidated in rigorous detail. Engineering and subsequent transfer of PGP traits into selected efficacious rhizobacterial isolates or entire bacterial rhizosphere communities now offers a powerful strategy to generate improved PGPR that are tailored for agricultural use. Through harnessing of synthetic plant-to-bacteria signalling, attempts are currently underway to establish exclusive coupling of plant-bacteria interactions in the field, which will be crucial to optimise efficacy and establish biocontainment of engineered PGPR. This review explores the many ecological and biotechnical facets of this research.
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Affiliation(s)
- Timothy L. Haskett
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Andrzej Tkacz
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
| | - Philip S. Poole
- grid.4991.50000 0004 1936 8948Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
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18
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Pardo-Diaz J, Bozhilova LV, Beguerisse-Díaz M, Poole PS, Deane CM, Reinert G. Robust gene coexpression networks using signed distance correlation. Bioinformatics 2021; 37:btab041. [PMID: 33523234 PMCID: PMC8557847 DOI: 10.1093/bioinformatics/btab041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 11/30/2020] [Accepted: 01/21/2021] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION Even within well studied organisms, many genes lack useful functional annotations. One way to generate such functional information is to infer biological relationships between genes/proteins, using a network of gene coexpression data that includes functional annotations. However, the lack of trustworthy functional annotations can impede the validation of such networks. Hence, there is a need for a principled method to construct gene coexpression networks that capture biological information and are structurally stable even in the absence of functional information. RESULTS We introduce the concept of signed distance correlation as a measure of dependency between two variables, and apply it to generate gene coexpression networks. Distance correlation offers a more intuitive approach to network construction than commonly used methods such as Pearson correlation and mutual information. We propose a framework to generate self-consistent networks using signed distance correlation purely from gene expression data, with no additional information. We analyse data from three different organisms to illustrate how networks generated with our method are more stable and capture more biological information compared to networks obtained from Pearson correlation or mutual information. SUPPLEMENTARY INFORMATION Supplementary Information and code are available at Bioinformatics and https://github.com/javier-pardodiaz/sdcorGCN online.
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Affiliation(s)
- Javier Pardo-Diaz
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | | | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
| | | | - Gesine Reinert
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
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19
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Aroney STN, Poole PS, Sánchez-Cañizares C. Rhizobial Chemotaxis and Motility Systems at Work in the Soil. Front Plant Sci 2021; 12:725338. [PMID: 34512702 PMCID: PMC8429497 DOI: 10.3389/fpls.2021.725338] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/06/2021] [Indexed: 05/17/2023]
Abstract
Bacteria navigate their way often as individual cells through their chemical and biological environment in aqueous medium or across solid surfaces. They swim when starved or in response to physical and chemical stimuli. Flagella-driven chemotaxis in bacteria has emerged as a paradigm for both signal transduction and cellular decision-making. By altering motility, bacteria swim toward nutrient-rich environments, movement modulated by their chemotaxis systems with the addition of pili for surface movement. The numbers and types of chemoreceptors reflect the bacterial niche and lifestyle, with those adapted to complex environments having diverse metabolic capabilities, encoding far more chemoreceptors in their genomes. The Alpha-proteobacteria typify the latter case, with soil bacteria such as rhizobia, endosymbionts of legume plants, where motility and chemotaxis are essential for competitive symbiosis initiation, among other processes. This review describes the current knowledge of motility and chemotaxis in six model soil bacteria: Sinorhizobium meliloti, Agrobacterium fabacearum, Rhizobium leguminosarum, Azorhizobium caulinodans, Azospirillum brasilense, and Bradyrhizobium diazoefficiens. Although motility and chemotaxis systems have a conserved core, rhizobia possess several modifications that optimize their movements in soil and root surface environments. The soil provides a unique challenge for microbial mobility, since water pathways through particles are not always continuous, especially in drier conditions. The effectiveness of symbiont inoculants in a field context relies on their mobility and dispersal through the soil, often assisted by water percolation or macroorganism movement or networks. Thus, this review summarizes the factors that make it essential to consider and test rhizobial motility and chemotaxis for any potential inoculant.
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20
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Rubia MI, Ramachandran VK, Arrese-Igor C, Larrainzar E, Poole PS. A novel biosensor to monitor proline in pea root exudates and nodules under osmotic stress and recovery. Plant Soil 2020; 452:413-422. [PMID: 32713966 PMCID: PMC7371648 DOI: 10.1007/s11104-020-04577-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS Plant and bacteria are able to synthesise proline, which acts as a compound to counteract the negative effects of osmotic stresses. Most methodologies rely on the extraction of compounds using destructive methods. This work describes a new proline biosensor that allows the monitoring of proline levels in a non-invasive manner in root exudates and nodules of legume plants. METHODS The proline biosensor was constructed by cloning the promoter region of pRL120553, a gene with high levels of induction in the presence of proline, in front of the lux cassette in Rhizobium leguminosarum bv. viciae. RESULTS Free-living assays show that the proline biosensor is sensitive and specific for proline. Proline was detected in both root exudates and nodules of pea plants. The luminescence detected in bacteroids did not show variations during osmotic stress treatments, but significantly increased during recovery. CONCLUSIONS This biosensor is a useful tool for the in vivo monitoring of proline levels in root exudates and bacteroids of symbiotic root nodules, and it contributes to our understanding of the metabolic exchange occurring in nodules under abiotic stress conditions.
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Affiliation(s)
- María I. Rubia
- Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Pública de Navarra, Campus Arrosadia, Pamplona, 31006 Spain
| | | | - Cesar Arrese-Igor
- Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Pública de Navarra, Campus Arrosadia, Pamplona, 31006 Spain
| | - Estíbaliz Larrainzar
- Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Pública de Navarra, Campus Arrosadia, Pamplona, 31006 Spain
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
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21
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Mendoza-Suárez MA, Geddes BA, Sánchez-Cañizares C, Ramírez-González RH, Kirchhelle C, Jorrin B, Poole PS. Optimizing Rhizobium-legume symbioses by simultaneous measurement of rhizobial competitiveness and N 2 fixation in nodules. Proc Natl Acad Sci U S A 2020; 117:9822-9831. [PMID: 32317381 PMCID: PMC7211974 DOI: 10.1073/pnas.1921225117] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Legumes tend to be nodulated by competitive rhizobia that do not maximize nitrogen (N2) fixation, resulting in suboptimal yields. Rhizobial nodulation competitiveness and effectiveness at N2 fixation are independent traits, making their measurement extremely time-consuming with low experimental throughput. To transform the experimental assessment of rhizobial competitiveness and effectiveness, we have used synthetic biology to develop reporter plasmids that allow simultaneous high-throughput measurement of N2 fixation in individual nodules using green fluorescent protein (GFP) and barcode strain identification (Plasmid ID) through next generation sequencing (NGS). In a proof-of-concept experiment using this technology in an agricultural soil, we simultaneously monitored 84 different Rhizobium leguminosarum strains, identifying a supercompetitive and highly effective rhizobial symbiont for peas. We also observed a remarkable frequency of nodule coinfection by rhizobia, with mixed occupancy identified in ∼20% of nodules, containing up to six different strains. Critically, this process can be adapted to multiple Rhizobium-legume symbioses, soil types, and environmental conditions to permit easy identification of optimal rhizobial inoculants for field testing to maximize agricultural yield.
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Affiliation(s)
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | | | | | - Charlotte Kirchhelle
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom;
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22
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Tkacz A, Pini F, Turner TR, Bestion E, Simmonds J, Howell P, Greenland A, Cheema J, Emms DM, Uauy C, Poole PS. Agricultural Selection of Wheat Has Been Shaped by Plant-Microbe Interactions. Front Microbiol 2020; 11:132. [PMID: 32117153 PMCID: PMC7015950 DOI: 10.3389/fmicb.2020.00132] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/21/2020] [Indexed: 12/26/2022] Open
Abstract
The influence of wheat (modern wheat, both bread and pasta, their wild ancestors and synthetic hybrids) on the microbiota of their roots and surrounding soil is characterized. We isolated lines of bread wheat by hybridizing diploid (Aegilops tauschii) with tetraploid Triticum durum and crossed it with a modern cultivar of Triticum aestivum. The newly created, synthetic hybrid wheat, which recapitulate the breeding history of wheat through artificial selection, is found to support a microbiome enriched in beneficial Glomeromycetes fungi, but also in, potentially detrimental, Nematoda. We hypothesize that during wheat domestication this plant-microbe interaction diminished, suggesting an evolutionary tradeoff; sacrificing advantageous nutrient acquisition through fungal interactions to minimize interaction with pathogenic fungi. Increased plant selection for Glomeromycetes and Nematoda is correlated with the D genome derived from A. tauschii. Despite differences in their soil microbiota communities, overall wheat plants consistently show a low ratio of eukaryotes to prokaryotes. We propose that this is a mechanism for protection against soil-borne fungal disease and appears to be deeply rooted in the wheat genome. We suggest that the influence of plants on the composition of their associated microbiota is an integral factor, hitherto overlooked, but intrinsic to selection during wheat domestication.
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Affiliation(s)
- Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Francesco Pini
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Thomas R Turner
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Eloïne Bestion
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - James Simmonds
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Phil Howell
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Andy Greenland
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Jitender Cheema
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - David M Emms
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- National Institute of Agricultural Botany, Cambridge, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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23
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Tkacz A, Bestion E, Bo Z, Hortala M, Poole PS. Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison. mBio 2020; 11:e02785-19. [PMID: 32019791 PMCID: PMC7002342 DOI: 10.1128/mbio.02785-19] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/11/2019] [Indexed: 11/20/2022] Open
Abstract
Plant roots influence the soil microbiota via physical interaction, secretion, and plant immunity. However, it is unclear whether the root fraction or soil is more important in determining the structure of the prokaryotic or eukaryotic community and whether this varies between plant species. Furthermore, the leaf (phyllosphere) and root microbiotas have a large overlap; however, it is unclear whether this results from colonization of the phyllosphere by the root microbiota. Soil, rhizosphere, rhizoplane, and root endosphere prokaryote-, eukaryote-, and fungus-specific microbiotas of four plant species were analyzed with high-throughput sequencing. The strengths of factors controlling microbiota structure were determined using permutational multivariate analysis of variance (PERMANOVA) statistics. The origin of the phyllosphere microbiota was investigated using a soil swap experiment. Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root itself more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. A reciprocal soil swap experiment shows that the phyllosphere is colonized from the soil in which the plant is grown.IMPORTANCE Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root fraction more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined, indicating conserved adaptation of microbial communities to plants. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. We observed a remarkable similarity in the structure of a plant's phyllosphere and root microbiotas and show by reciprocal soil swap experiments that both fractions are colonized from the soil in which the plant is grown. Thus, the phyllosphere is continuously colonized by the soil microbiota.
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Affiliation(s)
- Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Eloïne Bestion
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Zhiyan Bo
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marion Hortala
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Ryu MH, Zhang J, Toth T, Khokhani D, Geddes BA, Mus F, Garcia-Costas A, Peters JW, Poole PS, Ané JM, Voigt CA. Control of nitrogen fixation in bacteria that associate with cereals. Nat Microbiol 2019; 5:314-330. [DOI: 10.1038/s41564-019-0631-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022]
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Abstract
Rhizobia are α- and β-proteobacteria that form a symbiotic partnership with legumes, fixing atmospheric dinitrogen to ammonia and providing it to the plant. Oxygen regulation is key in this symbiosis. Fixation is performed by an oxygen-intolerant nitrogenase enzyme but requires respiration to meet its high energy demands. To satisfy these opposing constraints the symbiotic partners cooperate intimately, employing a variety of mechanisms to regulate and respond to oxygen concentration. During symbiosis rhizobia undergo significant changes in gene expression to differentiate into nitrogen-fixing bacteroids. Legumes host these bacteroids in specialized root organs called nodules. These generate a near-anoxic environment using an oxygen diffusion barrier, oxygen-binding leghemoglobin and control of mitochondria localization. Rhizobia sense oxygen using multiple interconnected systems which enable a finely-tuned response to the wide range of oxygen concentrations they experience when transitioning from soil to nodules. The oxygen-sensing FixL-FixJ and hybrid FixL-FxkR two-component systems activate at relatively high oxygen concentration and regulate fixK transcription. FixK activates the fixNOQP and fixGHIS operons producing a high-affinity terminal oxidase required for bacterial respiration in the microaerobic nodule. Additionally or alternatively, some rhizobia regulate expression of these operons by FnrN, an FNR-like oxygen-sensing protein. The final stage of symbiotic establishment is activated by the NifA protein, regulated by oxygen at both the transcriptional and protein level. A cross-species comparison of these systems highlights differences in their roles and interconnections but reveals common regulatory patterns and themes. Future work is needed to establish the complete regulon of these systems and identify other regulatory signals.
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Affiliation(s)
- Paul J Rutten
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Geddes BA, Paramasivan P, Joffrin A, Thompson AL, Christensen K, Jorrin B, Brett P, Conway SJ, Oldroyd GED, Poole PS. Engineering transkingdom signalling in plants to control gene expression in rhizosphere bacteria. Nat Commun 2019; 10:3430. [PMID: 31366919 PMCID: PMC6668481 DOI: 10.1038/s41467-019-10882-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 06/07/2019] [Indexed: 01/10/2023] Open
Abstract
The root microbiota is critical for agricultural yield, with growth-promoting bacteria able to solubilise phosphate, produce plant growth hormones, antagonise pathogens and fix N2. Plants control the microorganisms in their immediate environment and this is at least in part through direct selection, the immune system, and interactions with other microorganisms. Considering the importance of the root microbiota for crop yields it is attractive to artificially regulate this environment to optimise agricultural productivity. Towards this aim we express a synthetic pathway for the production of the rhizopine scyllo-inosamine in plants. We demonstrate the production of this bacterial derived signal in both Medicago truncatula and barley and show its perception by rhizosphere bacteria, containing bioluminescent and fluorescent biosensors. This study lays the groundwork for synthetic signalling networks between plants and bacteria, allowing the targeted regulation of bacterial gene expression in the rhizosphere for delivery of useful functions to plants. The root microbiota is critical for promoting crop yield. Here, the authors create a synthetic pathway for the production of the rhizopine scyllo-inosamine in Medicago truncatula and barley, and show its perception by rhizosphere bacteria for targeted regulation of bacterial gene expression.
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Affiliation(s)
- Barney A Geddes
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Ponraj Paramasivan
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Amelie Joffrin
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Amber L Thompson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Kirsten Christensen
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Paul Brett
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Stuart J Conway
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Giles E D Oldroyd
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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Geddes BA, Mendoza-Suárez MA, Poole PS. A Bacterial Expression Vector Archive (BEVA) for Flexible Modular Assembly of Golden Gate-Compatible Vectors. Front Microbiol 2019; 9:3345. [PMID: 30692983 PMCID: PMC6339899 DOI: 10.3389/fmicb.2018.03345] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/27/2018] [Indexed: 11/13/2022] Open
Abstract
We present a Bacterial Expression Vector Archive (BEVA) for the modular assembly of bacterial vectors compatible with both traditional and Golden Gate cloning, utilizing the Type IIS restriction enzyme Esp3I, and have demonstrated its use for Golden Gate cloning in Escherichia coli. Ideal for synthetic biology and other applications, this modular system allows a rapid, low-cost assembly of new vectors tailored to specific tasks. Using the principles outlined here, new modules (e.g., origin of replication for plasmids in other bacteria) can easily be designed for specific applications. It is hoped that this vector construction system will be expanded by the scientific community over time by creation of novel modules through an open source approach. To demonstrate the potential of the system, three example vectors were constructed and tested. The Golden Gate level 1 vector pOGG024 (pBBR1-based broad-host range and medium copy number) was used for gene expression in laboratory-cultured Rhizobium leguminosarum. The Golden Gate level 1 vector pOGG026 (RK2-based broad-host range, lower copy number and stable in the absence of antibiotic selection) was used to demonstrate bacterial gene expression in nitrogen-fixing nodules on pea plant roots formed by R. leguminosarum. Finally, the level 2 cloning vector pOGG216 (RK2-based broad-host range, medium copy number) was used to construct a dual reporter plasmid expressing green and red fluorescent proteins.
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Affiliation(s)
| | | | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Abstract
The attachment of bacteria to roots constitutes the first physical step in many plant-microbe interactions. These interactions exert both positive and negative influences on agricultural systems depending on whether a growth-promoting, symbiotic or pathogenic relationship transpires. A common biphasic mechanism of root attachment exists across agriculturally important microbial species, including Rhizobium, Agrobacterium, Pseudomonas, Azospirillum and Salmonella. Attachment studies have revealed how plant-microbe interactions develop, and how to manipulate these relationships for agricultural benefit. Here, we review our current understanding of the molecular mechanisms governing plant-microbe root attachment and draw together a common biphasic model.
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Affiliation(s)
- Rachel M Wheatley
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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Estrada-de Los Santos P, Palmer M, Chávez-Ramírez B, Beukes C, Steenkamp ET, Briscoe L, Khan N, Maluk M, Lafos M, Humm E, Arrabit M, Crook M, Gross E, Simon MF, Dos Reis Junior FB, Whitman WB, Shapiro N, Poole PS, Hirsch AM, Venter SN, James EK. Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera ( Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae. Genes (Basel) 2018; 9:genes9080389. [PMID: 30071618 PMCID: PMC6116057 DOI: 10.3390/genes9080389] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/19/2018] [Accepted: 07/24/2018] [Indexed: 11/21/2022] Open
Abstract
Burkholderia sensu lato is a large and complex group, containing pathogenic, phytopathogenic, symbiotic and non-symbiotic strains from a very wide range of environmental (soil, water, plants, fungi) and clinical (animal, human) habitats. Its taxonomy has been evaluated several times through the analysis of 16S rRNA sequences, concantenated 4–7 housekeeping gene sequences, and lately by genome sequences. Currently, the division of this group into Burkholderia, Caballeronia, Paraburkholderia, and Robbsia is strongly supported by genome analysis. These new genera broadly correspond to the various habitats/lifestyles of Burkholderia s.l., e.g., all the plant beneficial and environmental (PBE) strains are included in Paraburkholderia (which also includes all the N2-fixing legume symbionts) and Caballeronia, while most of the human and animal pathogens are retained in Burkholderia sensu stricto. However, none of these genera can accommodate two important groups of species. One of these includes the closely related Paraburkholderia rhizoxinica and Paraburkholderia endofungorum, which are both symbionts of the fungal phytopathogen Rhizopus microsporus. The second group comprises the Mimosa-nodulating bacterium Paraburkholderia symbiotica, the phytopathogen Paraburkholderia caryophylli, and the soil bacteria Burkholderia dabaoshanensis and Paraburkholderia soli. In order to clarify their positions within Burkholderia sensu lato, a phylogenomic approach based on a maximum likelihood analysis of conserved genes from more than 100 Burkholderia sensu lato species was carried out. Additionally, the average nucleotide identity (ANI) and amino acid identity (AAI) were calculated. The data strongly supported the existence of two distinct and unique clades, which in fact sustain the description of two novel genera Mycetohabitans gen. nov. and Trinickia gen. nov. The newly proposed combinations are Mycetohabitans endofungorum comb. nov., Mycetohabitansrhizoxinica comb. nov., Trinickia caryophylli comb. nov., Trinickiadabaoshanensis comb. nov., Trinickia soli comb. nov., and Trinickiasymbiotica comb. nov. Given that the division between the genera that comprise Burkholderia s.l. in terms of their lifestyles is often complex, differential characteristics of the genomes of these new combinations were investigated. In addition, two important lifestyle-determining traits—diazotrophy and/or symbiotic nodulation, and pathogenesis—were analyzed in depth i.e., the phylogenetic positions of nitrogen fixation and nodulation genes in Trinickia via-à-vis other Burkholderiaceae were determined, and the possibility of pathogenesis in Mycetohabitans and Trinickia was tested by performing infection experiments on plants and the nematode Caenorhabditis elegans. It is concluded that (1) T. symbiotica nif and nod genes fit within the wider Mimosa-nodulating Burkholderiaceae but appear in separate clades and that T. caryophyllinif genes are basal to the free-living Burkholderia s.l. strains, while with regard to pathogenesis (2) none of the Mycetohabitans and Trinickia strains tested are likely to be pathogenic, except for the known phytopathogen T. caryophylli.
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Affiliation(s)
| | - Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
| | - Belén Chávez-Ramírez
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, 11340 Cd. de Mexico, Mexico.
| | - Chrizelle Beukes
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
| | - Leah Briscoe
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Noor Khan
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Marta Maluk
- The James Hutton Institute, Dundee DD2 5DA, UK.
| | | | - Ethan Humm
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Monique Arrabit
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Matthew Crook
- 450G Tracy Hall Science Building, Weber State University, Ogden, 84403 UT, USA.
| | - Eduardo Gross
- Center for Electron Microscopy, Department of Agricultural and Environmental Sciences, Santa Cruz State University, 45662-900 Ilheus, BA, Brazil.
| | - Marcelo F Simon
- Embrapa CENARGEN, 70770-917 Brasilia, Distrito Federal, Brazil.
| | | | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
| | - Nicole Shapiro
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Ann M Hirsch
- Department of Molecular, Cell, and Developmental Biology and Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA.
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0083, South Africa.
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Tkacz A, Hortala M, Poole PS. Absolute quantitation of microbiota abundance in environmental samples. Microbiome 2018; 6:110. [PMID: 29921326 PMCID: PMC6009823 DOI: 10.1186/s40168-018-0491-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/30/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND Microbial communities (microbiota) influence human and animal disease and immunity, geochemical nutrient cycling and plant productivity. Specific groups, including bacteria, archaea, eukaryotes or fungi, are amplified by PCR to assess the relative abundance of sub-groups (e.g. genera). However, neither the absolute abundance of sub-groups is revealed, nor can different amplicon families (i.e. OTUs derived from a specific pair of PCR primers such as bacterial 16S, eukaryotic 18S or fungi ITS) be compared. This prevents determination of the absolute abundance of a particular group and domain-level shifts in microbiota abundance can remain undetected. RESULTS We have developed absolute quantitation of amplicon families using synthetic chimeric DNA spikes. Synthetic spikes were added directly to environmental samples, co-isolated and PCR-amplified, allowing calculation of the absolute abundance of amplicon families (e.g. prokaryotic 16S, eukaryotic 18S and fungal ITS per unit mass of sample). CONCLUSIONS Spikes can be adapted to any amplicon-specific group including rhizobia from soils, Firmicutes and Bifidobacteria from human gut or Enterobacteriaceae from food samples. Crucially, using highly complex soil samples, we show that the absolute abundance of specific groups can remain steady or increase, even when their relative abundance decreases. Thus, without absolute quantitation, the underlying pathology, physiology and ecology of microbial groups may be masked by their relative abundance.
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Affiliation(s)
- Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Marion Hortala
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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Sánchez-Cañizares C, Jorrín B, Poole PS, Tkacz A. Understanding the holobiont: the interdependence of plants and their microbiome. Curr Opin Microbiol 2017; 38:188-196. [PMID: 28732267 DOI: 10.1016/j.mib.2017.07.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 01/06/2023]
Abstract
The holobiont is composed by the plant and its microbiome. In a similar way to ecological systems of higher organisms, the holobiont shows interdependent and complex dynamics [1,2]. While plants originate from seeds, the microbiome has a multitude of sources. The assemblage of these communities depends on the interaction between the emerging seedling and its surrounding environment, with soil being the main source. These microbial communities are controlled by the plant through different strategies, such as the specific profile of root exudates and its immune system. Despite this control, the microbiome is still able to adapt and thrive. The molecular knowledge behind these interactions and microbial '-omic' technologies are developing to the point of enabling holobiont engineering. For a long time microorganisms were in the background of plant biology but new multidisciplinary approaches have led to an appreciation of the importance of the holobiont, where plants and microbes are interdependent.
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Affiliation(s)
- Carmen Sánchez-Cañizares
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, United Kingdom
| | - Beatriz Jorrín
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, United Kingdom
| | - Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford, United Kingdom.
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Hood G, Ramachandran V, East AK, Downie JA, Poole PS. Manganese transport is essential for N 2 -fixation by Rhizobium leguminosarum in bacteroids from galegoid but not phaseoloid nodules. Environ Microbiol 2017; 19:2715-2726. [PMID: 28447383 PMCID: PMC5575495 DOI: 10.1111/1462-2920.13773] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 04/19/2017] [Indexed: 12/14/2022]
Abstract
Rhizobium leguminosarum has two high-affinity Mn2+ transport systems encoded by sitABCD and mntH. In symbiosis, sitABCD and mntH were expressed throughout nodules and also strongly induced in Mn2+ -limited cultures of free-living cells. Growth of a sitA mntH double mutant was severely reduced under Mn2+ limitation and sitA and mntH single mutants were more sensitive to oxidative stress. The double sitA mntH mutant of R. leguminosarum was unable to fix nitrogen (Fix- ) with legumes belonging to the galegoid clade (Pisum sativum, Vicia faba and Vicia hirsuta). The presence of infection thread-like structures and sparsely-packed plant cells in nodules suggest that bacteroid development was blocked, either at a late stage of infection thread progression or during bacteroid-release. In contrast, a double sitA mntH mutant was Fix+ on common bean (Phaseoli vulgaris), a member of the phaseoloid clade of legumes, indicating a host-specific symbiotic requirement for Mn2+ transport.
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Affiliation(s)
- Graham Hood
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Vinoy Ramachandran
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Alison K. East
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - J. Allan Downie
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Philip S. Poole
- Department of Molecular MicrobiologyJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
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Pini F, East AK, Appia-Ayme C, Tomek J, Karunakaran R, Mendoza-Suárez M, Edwards A, Terpolilli JJ, Roworth J, Downie JA, Poole PS. Bacterial Biosensors for in Vivo Spatiotemporal Mapping of Root Secretion. Plant Physiol 2017; 174:1289-1306. [PMID: 28495892 PMCID: PMC5490882 DOI: 10.1104/pp.16.01302] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/06/2017] [Indexed: 05/20/2023]
Abstract
Plants engineer the rhizosphere to their advantage by secreting various nutrients and secondary metabolites. Coupling transcriptomic and metabolomic analyses of the pea (Pisum sativum) rhizosphere, a suite of bioreporters has been developed in Rhizobium leguminosarum bv viciae strain 3841, and these detect metabolites secreted by roots in space and time. Fourteen bacterial lux fusion bioreporters, specific for sugars, polyols, amino acids, organic acids, or flavonoids, have been validated in vitro and in vivo. Using different bacterial mutants (nodC and nifH), the process of colonization and symbiosis has been analyzed, revealing compounds important in the different steps of the rhizobium-legume association. Dicarboxylates and sucrose are the main carbon sources within the nodules; in ineffective (nifH) nodules, particularly low levels of sucrose were observed, suggesting that plant sanctions affect carbon supply to nodules. In contrast, high myo-inositol levels were observed prior to nodule formation and also in nifH senescent nodules. Amino acid biosensors showed different patterns: a γ-aminobutyrate biosensor was active only inside nodules, whereas the phenylalanine bioreporter showed a high signal also in the rhizosphere. The bioreporters were further validated in vetch (Vicia hirsuta), producing similar results. In addition, vetch exhibited a local increase of nod gene-inducing flavonoids at sites where nodules developed subsequently. These bioreporters will be particularly helpful in understanding the dynamics of root exudation and the role of different molecules secreted into the rhizosphere.
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Affiliation(s)
- Francesco Pini
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Alison K East
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Corinne Appia-Ayme
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Jakub Tomek
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford OX1 3PT, United Kingdom
| | | | - Marcela Mendoza-Suárez
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Anne Edwards
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Jason J Terpolilli
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Joshua Roworth
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - J Allan Downie
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
- Department of Molecular Microbiology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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Westhoek A, Field E, Rehling F, Mulley G, Webb I, Poole PS, Turnbull LA. Policing the legume-Rhizobium symbiosis: a critical test of partner choice. Sci Rep 2017; 7:1419. [PMID: 28469244 PMCID: PMC5431162 DOI: 10.1038/s41598-017-01634-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/03/2017] [Indexed: 11/29/2022] Open
Abstract
In legume-Rhizobium symbioses, specialised soil bacteria fix atmospheric nitrogen in return for carbon. However, ineffective strains can arise, making discrimination essential. Discrimination can occur via partner choice, where legumes prevent ineffective strains from entering, or via sanctioning, where plants provide fewer resources. Several studies have inferred that legumes exercise partner choice, but the rhizobia compared were not otherwise isogenic. To test when and how plants discriminate ineffective strains we developed sets of fixing and non-fixing strains that differed only in the expression of nifH - essential for nitrogen fixation - and could be visualised using marker genes. We show that the plant is unable to select against the non-fixing strain at the point of entry, but that non-fixing nodules are sanctioned. We also used the technique to characterise mixed nodules (containing both a fixing and a non-fixing strain), whose frequency could be predicted using a simple diffusion model. We discuss that sanctioning is likely to evolve in preference to partner choice in any symbiosis where partner quality cannot be adequately assessed until goods or services are actively exchanged.
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Affiliation(s)
- Annet Westhoek
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
- Systems Biology Doctoral Training Centre, University of Oxford, Oxford, OX1 3RQ, UK
| | - Elsa Field
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Finn Rehling
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
- Department of Ecology, Philipps-University Marburg, Marburg, D-35043, Germany
| | - Geraldine Mulley
- School of Biological Sciences, University of Reading, Reading, RG6 6AJ, UK
| | - Isabel Webb
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK.
| | - Lindsay A Turnbull
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK.
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Cheng G, Karunakaran R, East AK, Munoz-Azcarate O, Poole PS. Glutathione affects the transport activity of Rhizobium leguminosarum 3841 and is essential for efficient nodulation. FEMS Microbiol Lett 2017; 364:3045905. [PMID: 28333211 PMCID: PMC5407991 DOI: 10.1093/femsle/fnx045] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/22/2017] [Indexed: 01/02/2023] Open
Abstract
As glutathione (GSH) plays an essential role in growth and symbiotic capacity of rhizobia, a glutathione synthetase (gshB) mutant of Rhizobium leguminosarum biovar viciae 3841 (Rlv3841) was characterised. It fails to efficiently utilise various compounds as a sole carbon source, including glucose, succinate, glutamine and histidine, and shows 60%-69% reduction in uptake rates of glucose, succinate and the non-metabolisable substrate α-amino isobutyric acid. The defect in glucose uptake can be overcome by addition of exogenous GSH, indicating GSH, but not its bacterial synthesis, is required for efficient transport. GSH is not involved in the regulation of the activity of Rlv3841's transporters via the global regulator of transport, PtsNTR. Although lack of GSH reduces transcription of the branched amino acid transporter, this was not the case for all uptake transport systems, for example, the amino acid permease. This suggests GSH alters activity and/or assembly of transport systems by an unknown mechanism. In interaction with plants, the gshB mutant is not only severely impaired in rhizosphere colonisation, but also shows a 50% reduction in dry weight of plants and nitrogen-fixation ability. This reveals that changes in GSH metabolism affect the bacterial-plant interactions required for symbiosis.
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Affiliation(s)
- Guojun Cheng
- College of Life Science, South-Central University for Nationalities, Wuhan 430074, China
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Alison K. East
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Oxford, South Parks Road Oxford, OX1 3RB, UK
| | - Olaya Munoz-Azcarate
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Philip S. Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
- Department of Plant Sciences, University of Oxford, South Parks Road Oxford, OX1 3RB, UK
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Terpolilli JJ, Masakapalli SK, Karunakaran R, Webb IUC, Green R, Watmough NJ, Kruger NJ, Ratcliffe RG, Poole PS. Lipogenesis and Redox Balance in Nitrogen-Fixing Pea Bacteroids. J Bacteriol 2016; 198:2864-75. [PMID: 27501983 PMCID: PMC5038014 DOI: 10.1128/jb.00451-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/26/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Within legume root nodules, rhizobia differentiate into bacteroids that oxidize host-derived dicarboxylic acids, which is assumed to occur via the tricarboxylic acid (TCA) cycle to generate NAD(P)H for reduction of N2 Metabolic flux analysis of laboratory-grown Rhizobium leguminosarum showed that the flux from [(13)C]succinate was consistent with respiration of an obligate aerobe growing on a TCA cycle intermediate as the sole carbon source. However, the instability of fragile pea bacteroids prevented their steady-state labeling under N2-fixing conditions. Therefore, comparative metabolomic profiling was used to compare free-living R. leguminosarum with pea bacteroids. While the TCA cycle was shown to be essential for maximal rates of N2 fixation, levels of pyruvate (5.5-fold reduced), acetyl coenzyme A (acetyl-CoA; 50-fold reduced), free coenzyme A (33-fold reduced), and citrate (4.5-fold reduced) were much lower in bacteroids. Instead of completely oxidizing acetyl-CoA, pea bacteroids channel it into both lipid and the lipid-like polymer poly-β-hydroxybutyrate (PHB), the latter via a type III PHB synthase that is active only in bacteroids. Lipogenesis may be a fundamental requirement of the redox poise of electron donation to N2 in all legume nodules. Direct reduction by NAD(P)H of the likely electron donors for nitrogenase, such as ferredoxin, is inconsistent with their redox potentials. Instead, bacteroids must balance the production of NAD(P)H from oxidation of acetyl-CoA in the TCA cycle with its storage in PHB and lipids. IMPORTANCE Biological nitrogen fixation by symbiotic bacteria (rhizobia) in legume root nodules is an energy-expensive process. Within legume root nodules, rhizobia differentiate into bacteroids that oxidize host-derived dicarboxylic acids, which is assumed to occur via the TCA cycle to generate NAD(P)H for reduction of N2 However, direct reduction of the likely electron donors for nitrogenase, such as ferredoxin, is inconsistent with their redox potentials. Instead, bacteroids must balance oxidation of plant-derived dicarboxylates in the TCA cycle with lipid synthesis. Pea bacteroids channel acetyl-CoA into both lipid and the lipid-like polymer poly-β-hydroxybutyrate, the latter via a type II PHB synthase. Lipogenesis is likely to be a fundamental requirement of the redox poise of electron donation to N2 in all legume nodules.
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Affiliation(s)
- Jason J Terpolilli
- Centre for Rhizobium Studies, Murdoch University, Perth, Australia Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | | | - Isabel U C Webb
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Rob Green
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Nicholas J Watmough
- Centre for Molecular Structure and Biochemistry, University of East Anglia, Norwich, United Kingdom
| | - Nicholas J Kruger
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - R George Ratcliffe
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip S Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané JM, Peters JW. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl Environ Microbiol 2016. [PMID: 27084023 DOI: 10.1128/aem.01055-01016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
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Affiliation(s)
- Florence Mus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Matthew B Crook
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amaya Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Evangelia D Kouri
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | | | - Min-Hyung Ryu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané JM, Peters JW. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl Environ Microbiol 2016; 82:3698-3710. [PMID: 27084023 PMCID: PMC4907175 DOI: 10.1128/aem.01055-16] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
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Affiliation(s)
- Florence Mus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Matthew B Crook
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amaya Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Evangelia D Kouri
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | | | - Min-Hyung Ryu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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Cheng G, Karunakaran R, East AK, Poole PS. Multiplicity of Sulfate and Molybdate Transporters and Their Role in Nitrogen Fixation in Rhizobium leguminosarum bv. viciae Rlv3841. Mol Plant Microbe Interact 2016; 29:143-52. [PMID: 26812045 DOI: 10.1094/mpmi-09-15-0215-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Rhizobium leguminosarum Rlv3841 contains at least three sulfate transporters, i.e., SulABCD, SulP1 and SulP2, and a single molybdate transporter, ModABC. SulABCD is a high-affinity transporter whose mutation prevented growth on a limiting sulfate concentration, while SulP1 and SulP2 appear to be low-affinity sulfate transporters. ModABC is the sole high-affinity molybdate transport system and is essential for growth with NO3(-) as a nitrogen source on limiting levels of molybdate (<0.25 μM). However, at 2.5 μM molybdate, a quadruple mutant with all four transporters inactivated, had the longest lag phase on NO3(-), suggesting these systems all make some contribution to molybdate transport. Growth of Rlv3841 on limiting levels of sulfate increased sulB, sulP1, modB, and sulP2 expression 313.3-, 114.7-, 6.2-, and 4.0-fold, respectively, while molybdate starvation increased only modB expression (three- to 7.5-fold). When grown in high-sulfate but not low-sulfate medium, pea plants inoculated with LMB695 (modB) reduced acetylene at only 14% of the wild-type rate, and this was not further reduced in the quadruple mutant. Overall, while modB is crucial to nitrogen fixation at limiting molybdate levels in the presence of sulfate, there is an unidentified molybdate transporter also capable of sulfate transport.
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Affiliation(s)
- Guojun Cheng
- 1 College of Life Science, South-Central University for Nationalities, Wuhan 430074, China
- 2 Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
| | - Ramakrishnan Karunakaran
- 2 Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
| | - Alison K East
- 2 Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
- 3 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
| | - Philip S Poole
- 2 Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
- 3 Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, U.K
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Tkacz A, Cheema J, Chandra G, Grant A, Poole PS. Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition. ISME J 2015; 9:2349-59. [PMID: 25909975 PMCID: PMC4611498 DOI: 10.1038/ismej.2015.41] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 02/05/2015] [Accepted: 02/16/2015] [Indexed: 12/15/2022]
Abstract
We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant-microbe interactions/rhizosphere microbiota/selection.
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Affiliation(s)
- Andrzej Tkacz
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Plant Sciences, Oxford University, Oxford, UK
| | - Jitender Cheema
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Alastair Grant
- Earth and Life Systems Alliance, The School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Philip S Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Plant Sciences, Oxford University, Oxford, UK
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Garcia-Fraile P, Seaman JC, Karunakaran R, Edwards A, Poole PS, Downie JA. Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere. Plant Soil 2015; 390:251-264. [PMID: 26166901 PMCID: PMC4495286 DOI: 10.1007/s11104-015-2389-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/14/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS To form nitrogen-fixing nodules on pea roots, Rhizobium leguminosarum biovar viciae must be competitive in the rhizosphere. Our aim was to identify genes important for rhizosphere fitness. METHODS Signature-tagged mutants were screened using microarrays to identify mutants reduced for growth in pea rhizospheres. Candidate mutants were assessed relative to controls for growth in minimal medium, growth in pea rhizospheres and for infection of peas in mixed inoculants. Mutated genes were identified by DNA sequencing and confirmed by transduction. RESULTS Of 5508 signature-tagged mutants, microarrays implicated 50 as having decreased rhizosphere fitness. Growth tests identified six mutants with rhizosphere-specific phenotypes. The mutation in one of the genes (araE) was in an arabinose catabolism operon and blocked growth on arabinose. The mutation in another gene (pcaM), encoding a predicted solute binding protein for protocatechuate and hydroxybenzoate uptake, decreased growth on protocatechuate. Both mutants were decreased for nodule infection competitiveness with mixed inoculants, but nodulated peas normally when inoculated alone. Other mutants with similar phenotypes had mutations predicted to affect secondary metabolism. CONCLUSIONS Catabolism of arabinose and protocatechuate in the pea rhizosphere is important for competitiveness of R.l. viciae. Other genes predicted to be involved in secondary metabolism are also important.
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Affiliation(s)
- Paula Garcia-Fraile
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: Institute of Microbiology, Academy of Sciences of Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic
| | - Jonathan C. Seaman
- School of Biological Sciences, University of Reading, Reading, RG6 6AJ UK
| | - Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Anne Edwards
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Philip S. Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
- Present Address: Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB UK
| | - J. Allan Downie
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
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Tett AJ, Karunakaran R, Poole PS. Characterisation of SalRAB a salicylic acid inducible positively regulated efflux system of Rhizobium leguminosarum bv viciae 3841. PLoS One 2014; 9:e103647. [PMID: 25133394 PMCID: PMC4136779 DOI: 10.1371/journal.pone.0103647] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 06/05/2014] [Indexed: 12/31/2022] Open
Abstract
Salicylic acid is an important signalling molecule in plant-microbe defence and symbiosis. We analysed the transcriptional responses of the nitrogen fixing plant symbiont, Rhizobium leguminosarum bv viciae 3841 to salicylic acid. Two MFS-type multicomponent efflux systems were induced in response to salicylic acid, rmrAB and the hitherto undescribed system salRAB. Based on sequence similarity salA and salB encode a membrane fusion and inner membrane protein respectively. salAB are positively regulated by the LysR regulator SalR. Disruption of salA significantly increased the sensitivity of the mutant to salicylic acid, while disruption of rmrA did not. A salA/rmrA double mutation did not have increased sensitivity relative to the salA mutant. Pea plants nodulated by salA or rmrA strains did not have altered nodule number or nitrogen fixation rates, consistent with weak expression of salA in the rhizosphere and in nodule bacteria. However, BLAST analysis revealed seventeen putative efflux systems in Rlv3841 and several of these were highly differentially expressed during rhizosphere colonisation, host infection and bacteroid differentiation. This suggests they have an integral role in symbiosis with host plants.
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Affiliation(s)
- Adrian J. Tett
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Frederix M, Edwards A, Swiderska A, Stanger A, Karunakaran R, Williams A, Abbruscato P, Sanchez-Contreras M, Poole PS, Downie JA. Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins. Mol Microbiol 2014; 93:464-78. [PMID: 24942546 PMCID: PMC4149787 DOI: 10.1111/mmi.12670] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2014] [Indexed: 11/27/2022]
Abstract
In Rhizobium leguminosarum bv. viciae, quorum-sensing is regulated by CinR, which induces the cinIS operon. CinI synthesizes an AHL, whereas CinS inactivates PraR, a repressor. Mutation of praR enhanced biofilms in vitro. We developed a light (lux)-dependent assay of rhizobial attachment to roots and demonstrated that mutation of praR increased biofilms on pea roots. The praR mutant out-competed wild-type for infection of pea nodules in mixed inoculations. Analysis of gene expression by microarrays and promoter fusions revealed that PraR represses its own transcription and mutation of praR increased expression of several genes including those encoding secreted proteins (the adhesins RapA2, RapB and RapC, two cadherins and the glycanase PlyB), the polysaccharide regulator RosR, and another protein similar to PraR. PraR bound to the promoters of several of these genes indicating direct repression. Mutations in rapA2, rapB, rapC, plyB, the cadherins or rosR did not affect the enhanced root attachment or nodule competitiveness of the praR mutant. However combinations of mutations in rapA, rapB and rapC abolished the enhanced attachment and nodule competitiveness. We conclude that relief of PraR-mediated repression determines a lifestyle switch allowing the expression of genes that are important for biofilm formation on roots and the subsequent initiation of infection of legume roots.
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Affiliation(s)
| | | | | | - Andrew Stanger
- Department of Molecular Microbiology, John Innes CentreNorwich Research Park, Norwich, NR4 7UH, UK
| | - Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes CentreNorwich Research Park, Norwich, NR4 7UH, UK
| | | | | | | | | | - J Allan Downie
- Department of Molecular Microbiology, John Innes CentreNorwich Research Park, Norwich, NR4 7UH, UK
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Turner TR, Ramakrishnan K, Walshaw J, Heavens D, Alston M, Swarbreck D, Osbourn A, Grant A, Poole PS. Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants. ISME J 2013; 7:2248-58. [PMID: 23864127 PMCID: PMC3834852 DOI: 10.1038/ismej.2013.119] [Citation(s) in RCA: 236] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/10/2013] [Accepted: 05/21/2013] [Indexed: 11/09/2022]
Abstract
Plant-microbe interactions in the rhizosphere have important roles in biogeochemical cycling, and maintenance of plant health and productivity, yet remain poorly understood. Using RNA-based metatranscriptomics, the global active microbiomes were analysed in soil and rhizospheres of wheat, oat, pea and an oat mutant (sad1) deficient in production of anti-fungal avenacins. Rhizosphere microbiomes differed from bulk soil and between plant species. Pea (a legume) had a much stronger effect on the rhizosphere than wheat and oat (cereals), resulting in a dramatically different rhizosphere community. The relative abundance of eukaryotes in the oat and pea rhizospheres was more than fivefold higher than in the wheat rhizosphere or bulk soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, whereas the pea rhizosphere was highly enriched for fungi. Metabolic capabilities for rhizosphere colonisation were selected, including cellulose degradation (cereals), H2 oxidation (pea) and methylotrophy (all plants). Avenacins had little effect on the prokaryotic community of oat, but the eukaryotic community was strongly altered in the sad1 mutant, suggesting that avenacins have a broader role than protecting from fungal pathogens. Profiling microbial communities with metatranscriptomics allows comparison of relative abundance, from multiple samples, across all domains of life, without polymerase chain reaction bias. This revealed profound differences in the rhizosphere microbiome, particularly at the kingdom level between plants.
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Affiliation(s)
- Thomas R Turner
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
- Earth Life Systems Alliance, School of Environmental Sciences, University of East Anglia, Norwich, UK
| | | | | | | | | | | | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich, UK
| | - Alastair Grant
- Earth Life Systems Alliance, School of Environmental Sciences, University of East Anglia, Norwich, UK
| | - Philip S Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
- Earth Life Systems Alliance, School of Environmental Sciences, University of East Anglia, Norwich, UK
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Karunakaran R, East AK, Poole PS. Malonate catabolism does not drive N2 fixation in legume nodules. Appl Environ Microbiol 2013; 79:4496-8. [PMID: 23666330 PMCID: PMC3697510 DOI: 10.1128/aem.00919-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 05/03/2013] [Indexed: 11/20/2022] Open
Abstract
Malonyl-coenzyme A (CoA) decarboxylase, malonyl-CoA synthetase, and malonate transporter mutants of Rhizobium leguminosarum bv. viciae and trifolii fixed N2 at wild-type rates on pea and clover, respectively. Thus, malonate does not drive N2 fixation in legume nodules.
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Affiliation(s)
- Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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Abstract
Plant genomes contribute to the structure and function of the plant microbiome, a key determinant of plant health and productivity. High-throughput technologies are revealing interactions between these complex communities and their hosts in unprecedented detail.
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Affiliation(s)
- Thomas R Turner
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Euan K James
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Philip S Poole
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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47
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Abstract
Symbiotic nitrogen fixation by rhizobia in legume root nodules injects approximately 40 million tonnes of nitrogen into agricultural systems each year. In exchange for reduced nitrogen from the bacteria, the plant provides rhizobia with reduced carbon and all the essential nutrients required for bacterial metabolism. Symbiotic nitrogen fixation requires exquisite integration of plant and bacterial metabolism. Central to this integration are transporters of both the plant and the rhizobia, which transfer elements and compounds across various plant membranes and the two bacterial membranes. Here we review current knowledge of legume and rhizobial transport and metabolism as they relate to symbiotic nitrogen fixation. Although all legume-rhizobia symbioses have many metabolic features in common, there are also interesting differences between them, which show that evolution has solved metabolic problems in different ways to achieve effective symbiosis in different systems.
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Affiliation(s)
- Michael Udvardi
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA.
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48
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Abstract
Symbiotic nitrogen fixation by rhizobia in legume root nodules injects approximately 40 million tonnes of nitrogen into agricultural systems each year. In exchange for reduced nitrogen from the bacteria, the plant provides rhizobia with reduced carbon and all the essential nutrients required for bacterial metabolism. Symbiotic nitrogen fixation requires exquisite integration of plant and bacterial metabolism. Central to this integration are transporters of both the plant and the rhizobia, which transfer elements and compounds across various plant membranes and the two bacterial membranes. Here we review current knowledge of legume and rhizobial transport and metabolism as they relate to symbiotic nitrogen fixation. Although all legume-rhizobia symbioses have many metabolic features in common, there are also interesting differences between them, which show that evolution has solved metabolic problems in different ways to achieve effective symbiosis in different systems.
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Affiliation(s)
- Michael Udvardi
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA.
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Bourdès A, Rudder S, East AK, Poole PS. Mining the Sinorhizobium meliloti transportome to develop FRET biosensors for sugars, dicarboxylates and cyclic polyols. PLoS One 2012; 7:e43578. [PMID: 23028462 PMCID: PMC3454389 DOI: 10.1371/journal.pone.0043578] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 07/24/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Förster resonance energy transfer (FRET) biosensors are powerful tools to detect biologically important ligands in real time. Currently FRET bisosensors are available for twenty-two compounds distributed in eight classes of chemicals (two pentoses, two hexoses, two disaccharides, four amino acids, one nucleobase, two nucleotides, six ions and three phytoestrogens). To expand the number of available FRET biosensors we used the induction profile of the Sinorhizobium meliloti transportome to systematically screen for new FRET biosensors. METHODOLOGY/PRINCIPAL FINDINGS Two new vectors were developed for cloning genes for solute-binding proteins (SBPs) between those encoding FRET partner fluorescent proteins. In addition to a vector with the widely used cyan and yellow fluorescent protein FRET partners, we developed a vector using orange (mOrange2) and red fluorescent protein (mKate2) FRET partners. From the sixty-nine SBPs tested, seven gave a detectable FRET signal change on binding substrate, resulting in biosensors for D-quinic acid, myo-inositol, L-rhamnose, L-fucose, β-diglucosides (cellobiose and gentiobiose), D-galactose and C4-dicarboxylates (malate, succinate, oxaloacetate and fumarate). To our knowledge, we describe the first two FRET biosensor constructs based on SBPs from Tripartite ATP-independent periplasmic (TRAP) transport systems. CONCLUSIONS/SIGNIFICANCE FRET based on orange (mOrange2) and red fluorescent protein (mKate2) partners allows the use of longer wavelength light, enabling deeper penetration of samples at lower energy and increased resolution with reduced back-ground auto-fluorescence. The FRET biosensors described in this paper for four new classes of compounds; (i) cyclic polyols, (ii) L-deoxy sugars, (iii) β-linked disaccharides and (iv) C4-dicarboxylates could be developed to study metabolism in vivo.
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Affiliation(s)
- Alexandre Bourdès
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Steven Rudder
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Alison K. East
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Philip S. Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
- * E-mail:
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50
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Abstract
Biological nitrogen fixation is vital to nutrient cycling in the biosphere and is the major route by which atmospheric dinitrogen (N(2)) is reduced to ammonia. The largest single contribution to biological N(2) fixation is carried out by rhizobia, which include a large group of both alpha and beta-proteobacteria, almost exclusively in association with legumes. Rhizobia must compete to infect roots of legumes and initiate a signaling dialog with host plants that leads to nodule formation. The most common form of infection involves the growth of rhizobia down infection threads which are laid down by the host plant. Legumes form either indeterminate or determinate types of nodules, with these groups differing widely in nodule morphology and often in the developmental program by which rhizobia form N(2) fixing bacteroids. In particular, indeterminate legumes from the inverted repeat-lacking clade (IRLC) (e.g., peas, vetch, alfalfa, medics) produce a cocktail of antimicrobial peptides which cause endoreduplication of the bacterial genome and force rhizobia into a nongrowing state. Bacteroids often become dependent on the plant for provision of key cofactors, such as homocitrate needed for nitrogenase activity or for branched chain amino acids. This has led to the suggestion that bacteroids at least from the IRLC can be considered as ammoniaplasts, where they are effectively facultative plant organelles. A low O(2) tension is critical both to induction of genes needed for N(2) fixation and to the subsequent exchange of nutrient between plants and bacteroids. To achieve high rates of N(2) fixation, the legume host and Rhizobium must be closely matched not only for infection, but for optimum development, nutrient exchange, and N(2) fixation. In this review, we consider the multiple steps of selection and bacteroid development and how these alter the overall efficiency of N(2) fixation.
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Affiliation(s)
- Jason J Terpolilli
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, UK
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