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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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Keyes S, van Veelen A, McKay Fletcher D, Scotson C, Koebernick N, Petroselli C, Williams K, Ruiz S, Cooper L, Mayon R, Duncan S, Dumont M, Jakobsen I, Oldroyd G, Tkacz A, Poole P, Mosselmans F, Borca C, Huthwelker T, Jones DL, Roose T. Multimodal correlative imaging and modelling of phosphorus uptake from soil by hyphae of mycorrhizal fungi. New Phytol 2022; 234:688-703. [PMID: 35043984 PMCID: PMC9307049 DOI: 10.1111/nph.17980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/01/2021] [Accepted: 01/03/2022] [Indexed: 05/29/2023]
Abstract
Phosphorus (P) is essential for plant growth. Arbuscular mycorrhizal fungi (AMF) aid its uptake by acquiring P from sources distant from roots in return for carbon. Little is known about how AMF colonise soil pore-space, and models of AMF-enhanced P-uptake are poorly validated. We used synchrotron X-ray computed tomography to visualize mycorrhizas in soil and synchrotron X-ray fluorescence/X-ray absorption near edge structure (XRF/XANES) elemental mapping for P, sulphur (S) and aluminium (Al) in combination with modelling. We found that AMF inoculation had a suppressive effect on colonisation by other soil fungi and identified differences in structure and growth rate between hyphae of AMF and nonmycorrhizal fungi. Our results showed that AMF co-locate with areas of high P and low Al, and preferentially associate with organic-type P species over Al-rich inorganic P. We discovered that AMF avoid Al-rich areas as a source of P. Sulphur-rich regions were found to be correlated with higher hyphal density and an increased organic-associated P-pool, whilst oxidized S-species were found close to AMF hyphae. Increased S oxidation close to AMF suggested the observed changes were microbiome-related. Our experimentally-validated model led to an estimate of P-uptake by AMF hyphae that is an order of magnitude lower than rates previously estimated - a result with significant implications for the modelling of plant-soil-AMF interactions.
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Affiliation(s)
- Sam Keyes
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Arjen van Veelen
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
- Material Science and Technology DivisionLos Alamos National LaboratoryLos AlamosNM87545USA
- Stanford Synchrotron Radiation LightsourceSLAC National Accelerator LaboratoryMenlo ParkCA94025USA
| | - Dan McKay Fletcher
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Callum Scotson
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Nico Koebernick
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Chiara Petroselli
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Katherine Williams
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Siul Ruiz
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Laura Cooper
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Robbie Mayon
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Simon Duncan
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Marc Dumont
- School of Biological SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Iver Jakobsen
- Department of Plant and Environmental SciencesUniversity of CopenhagenThorvaldsensvej 40FrederiksbergDK‐1871Denmark
| | - Giles Oldroyd
- Crop Science CentreUniversity of Cambridge93 Lawrence Weaver RoadCambridgeCB3 0LEUK
| | - Andrzej Tkacz
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Philip Poole
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Fred Mosselmans
- Diamond Light SourceDiamond House, Harwell Science & Innovation CampusDidcotOX11 0DEUK
| | - Camelia Borca
- Swiss Light SourcePSIForschungsstrasse 111Villigen5232Switzerland
| | | | - David L. Jones
- School of Natural SciencesBangor UniversityBangorLL57 2DGUK
- SoilsWest, Food Futures InstituteMurdoch University90 South StreetMurdochWA6150Australia
| | - Tiina Roose
- Bioengineering Sciences Research GroupDepartment of Mechanical EngineeringSchool of EngineeringFaculty of Engineering and Physical SciencesUniversity of SouthamptonSouthamptonSO17 1BJUK
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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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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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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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6
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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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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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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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9
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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: 80] [Impact Index Per Article: 20.0] [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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Carrasco J, Tello ML, de Toro M, Tkacz A, Poole P, Pérez-Clavijo M, Preston G. Casing microbiome dynamics during button mushroom cultivation: implications for dry and wet bubble diseases. Microbiology (Reading) 2019; 165:611-624. [PMID: 30994437 DOI: 10.1099/mic.0.000792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The casing material required in mushroom cultivation presents a very rich ecological niche, which is inhabited by a diverse population of bacteria and fungi. In this work three different casing materials, blonde peat, black peat and a 50 : 50 mixture of both, were compared for their capacity to show a natural suppressive response against dry bubble, Lecanicillium fungicola (Preuss) Zare and Gams, and wet bubble, Mycogone perniciosa (Magnus) Delacroix. The highest mushroom production was collected from crops cultivated using the mixed casing and black peat, which were not significantly different in yield. However, artificial infection with mycoparasites resulted in similar yield losses irrespective of the material used, indicating that the casing materials do not confer advantages in disease suppression. The composition of the microbiome of the 50 : 50 casing mixture along the crop cycle and the compost and basidiomes was evaluated through next-generation sequencing (NGS) of the V3-V4 region of the bacterial 16S rRNA gene and the fungal ITS2 region. Once colonized by Agaricus bisporus, the bacterial diversity of the casing microbiome increased and the fungal diversity drastically decreased. From then on, the composition of the casing microbiome remained relatively stable. Analysis of the composition of the bacterial microbiome in basidiomes indicated that it is highly influenced by the casing microbiota. Notably, L. fungicola was consistently detected in uninoculated control samples of compost and casing using NGS, even in asymptomatic crops. This suggests that the naturally established casing microbiota was able to help to suppress disease development when inoculum levels were low, but was not effective in suppressing high pressure from artificially introduced fungal inoculum. Determination of the composition of the casing microbiome paves the way for the development of synthetic casing communities that can be used to investigate the role of specific components of the casing microbiota in mushroom production and disease control.
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Affiliation(s)
- Jaime Carrasco
- 2Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH), Autol, Spain.,1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1, UK
| | - Maria Luisa Tello
- 2Centro Tecnológico de Investigación del Champiñón de La Rioja (CTICH), Autol, Spain
| | - Maria de Toro
- 3Plataforma de Genómica y Bioinformática, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | - Andrzej Tkacz
- 1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1, UK
| | - Philip Poole
- 1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1, UK
| | | | - Gail Preston
- 1Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1, UK
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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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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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Abstract
The growing human population requires increasing amounts of food, but modern agriculture has limited possibilities for increasing yields. New crop varieties may be bred to have increased yields and be more resistant to environmental stress and pests. However, they still require fertilization to supplement essential nutrients that are normally limited in the soil. Soil microorganisms present an opportunity to reduce the requirement for inorganic fertilization in agriculture. Microorganisms, due to their enormous genetic pool, are also a potential source of biochemical reactions that recycle essential nutrients for plant growth. Microbes that associate with plants can be considered to be part of the plant's pan-genome. Therefore, it is essential for us to understand microbial community structure and their 'metagenome' and how it is influenced by different soil types and crop varieties. In the future we may be able to modify and better utilize the soil microbiota potential for promoting plant growth.
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Affiliation(s)
- Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Philip Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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Mordarski M, Tkacz A, Goodfellow M, Pulverer G, Peters G, Schumacher-Perdreau F. Ribosomal ribonucleic acid similarities in the classification ofStaphylococcus. FEMS Microbiol Lett 1981. [DOI: 10.1111/j.1574-6968.1981.tb06955.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Mordarski M, Goodfellow M, Tkacz A, Pulverer G, Schaal KP. Ribosomal ribonucleic acid similarities in the classification of Rhodococcus and related taxa. J Gen Microbiol 1980; 118:313-9. [PMID: 6160195 DOI: 10.1099/00221287-118-2-313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Duplexes were prepared between 14C-labelled rRNA from both Rhodococcus equi C7 and Rhodococcus rhodochrous N54 and DNA from 16 actinomycetes representing the genera Rhodococcus, Mycobacterium, Nocardia, Saccharopolyspora and Streptomyces. The relationships between the organisms were determined by plotting the temperature at which 50% of the duplex was denatured (Tm(e)) against the percentage of rRNA binding (microgram 14C-labelled rRNA duplexed per 100 micrograms filter-bound DNA). All of the strains formed stable duplexes but each organism occupied a definite area on the rRNA similarity map. All of the organisms share a close phylogenetic relationship but representatives of the genera Rhodococcus, Mycobacterium, Nocardia and Streptomyces fell into four recognizable clusters on the similarity map. These data support and extend current trends in the classification of Rhodococcus and allied taxa. The guanine plus cytosine content of the DNA from the test strains was within the range 69.3 to 76.9 mol %.
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Goodfellow M, Mordarski M, Tkacz A, Szyba K, Pulverer G. Polynucleotide Sequence Divergence Among Some Coagulase-negative Staphylococci. ACTA ACUST UNITED AC 1980. [DOI: 10.1016/s0172-5599(80)80094-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Goodfellow M, Mordarski M, Tkacz A, Szyba K, Pulverer G. Polynucleotide sequence divergence among some coagulase-negative staphylococci. Zentralbl Bakteriol A 1980; 246:10-22. [PMID: 7424234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The degree of binding was determined, at both exacting and non-exacting temperatures, between deoxyribonucleic acid (DNA) preparations from coagulase-negative staphylococci and carbon (14C) labelled DNA from nine reference strains, Staphylococcus capitis LK499, S. cohnii GH137, S. epidermidis GH37, S. haemolyticus SM131, S. hominis DM122, S. saprophyticus CCM883, S. simulans SM128, S. warneri AW25 and S. xylosus KL162. The close similarity in nucleotide sequences found between five of the six representatives received as S. capitis, S. hominis and S. warneri indicate that these organisms are separated into too many species. In contrast, little homology was found between the pairs of strains representing S. cohnii and S. haemolyticus, respectively. The divergence indices of the nine reference strains were calculated and the relationship between them expressed in a sorted similarity matrix and dendrogram based upon the average linkage algorithm. The pattern of nucleotide heterogeneity was found by plotting the relative DNA bound at the exacting temperature against the divergence indices. The coagulase-negative staphylococci exhibit extensive genetic diversity due mainly to random mutation.
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Pulverer G, Mordarski M, Tkacz A, Szyba K, Heczko P, Goodfellow M. Relationships among some coagulase-negative staphylococci based upon deoxyribonucleic acid re-association. FEMS Microbiol Lett 1978. [DOI: 10.1111/j.1574-6968.1978.tb01882.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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