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Jorrin B, Haskett TL, Knights HE, Martyn A, Underwood TJ, Dolliver J, Ledermann R, Poole PS. Stable, fluorescent markers for tracking synthetic communities and assembly dynamics. MICROBIOME 2024; 12:81. [PMID: 38715147 PMCID: PMC11075435 DOI: 10.1186/s40168-024-01792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/09/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechanisms underlying the coalescence of microbial communities. Deciphering microbiome assembly has been technically challenging due to their vast microbial diversity but establishing a synthetic community (SynCom) serves as a key strategy in unravelling this process. Achieving absolute quantification is crucial for establishing causality in assembly dynamics. However, existing approaches are primarily designed to differentiate a specific group of microorganisms within a particular SynCom. RESULTS To address this issue, we have developed the differential fluorescent marking (DFM) strategy, employing three distinguishable fluorescent proteins in single and double combinations. Building on the mini-Tn7 transposon, DFM capitalises on enhanced stability and broad applicability across diverse Proteobacteria species. The various DFM constructions are built using the pTn7-SCOUT plasmid family, enabling modular assembly, and facilitating the interchangeability of expression and antibiotic cassettes in a single reaction. DFM has no detrimental effects on fitness or community assembly dynamics, and through the application of flow cytometry, we successfully differentiated, quantified, and tracked a diverse six-member SynCom under various complex conditions like root rhizosphere showing a different colonisation assembly dynamic between pea and barley roots. CONCLUSIONS DFM represents a powerful resource that eliminates dependence on sequencing and/or culturing, thereby opening new avenues for studying microbiome assembly. Video Abstract.
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Affiliation(s)
- Beatriz Jorrin
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Timothy L Haskett
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Hayley E Knights
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Anna Martyn
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Thomas J Underwood
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Jessica Dolliver
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Raphael Ledermann
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Philip S Poole
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
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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] [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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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] [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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Harris LJ, Berry ED, Blessington T, Erickson M, Jay-Russell M, Jiang X, Killinger K, Michel FC, Millner P, Schneider K, Sharma M, Suslow TV, Wang L, Worobo RW. A framework for developing research protocols for evaluation of microbial hazards and controls during production that pertain to the application of untreated soil amendments of animal origin on land used to grow produce that may be consumed raw. J Food Prot 2013; 76:1062-84. [PMID: 23726206 DOI: 10.4315/0362-028x.jfp-13-007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Application of manure or soil amendments of animal origin (untreated soil amendments; UTSAs) to agricultural land has been a long-standing practice to maintain or improve soil quality through addition of organic matter, nitrogen, and phosphorus. Much smaller quantities of these types of UTSAs are applied to land used for food crops than to land used for animal grain and forage. UTSAs can harbor zoonotic enteric pathogens that may survive for extended periods after application. Additional studies are needed to enhance our understanding of preharvest microbial food safety hazards and control measures pertaining to the application of UTSAs especially for land used to grow produce that may be consumed raw. This document is intended to provide an approach to study design and a framework for defining the scope and type of data required. This document also provides a tool for evaluating the strength of existing data and thus can aid the produce industry and regulatory authorities in identifying additional research needs. Ultimately, this framework provides a means by which researchers can increase consistency among and between studies and facilitates direct comparison of hazards and efficacy of controls applied to different regions, conditions, and practices.
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Affiliation(s)
- Linda J Harris
- Western Center for Food Safety, University of California, One Shields Avenue, Davis, California 95616, USA.
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Sánchez-Cañizares C, Palacios J. Construction of a marker system for the evaluation of competitiveness for legume nodulation in Rhizobium strains. J Microbiol Methods 2013; 92:246-9. [PMID: 23305927 DOI: 10.1016/j.mimet.2012.12.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 12/21/2012] [Accepted: 12/21/2012] [Indexed: 11/21/2022]
Abstract
A marker system has been set up for the analysis of competitiveness of Rhizobium leguminosarum strains for legume nodulation. The strains generated incorporate gusA and celB marker genes at identical positions and allow efficient scoring of single and double infections. Based on this system, we have found that strain UPM791 outcompetes 3841 for nodulation in pea. This technique will be useful to determine the effect of different traits on competitiveness.
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Affiliation(s)
- Carmen Sánchez-Cañizares
- Centro de Biotecnología y Genómica de Plantas (C.B.G.P.), and Departamento de Biotecnología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Carretera M40-km 37.7, 28223 Pozuelo de Alarcón, Madrid, Spain
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Harris LJ, Bender J, Bihn EA, Blessington T, Danyluk MD, Delaquis P, Goodridge L, Ibekwe AM, Ilic S, Kniel K, Lejeune JT, Schaffner DW, Stoeckel D, Suslow TV. A framework for developing research protocols for evaluation of microbial hazards and controls during production that pertain to the quality of agricultural water contacting fresh produce that may be consumed raw. J Food Prot 2012; 75:2251-73. [PMID: 23212026 DOI: 10.4315/0362-028x.jfp-12-252] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Agricultural water may contact fresh produce during irrigation and/or when crop protection sprays (e.g., cooling to prevent sunburn, frost protection, and agrochemical mixtures) are applied. This document provides a framework for designing research studies that would add to our understanding of preharvest microbial food safety hazards and control measures pertaining to agricultural water. Researchers will be able to use this document to design studies, to anticipate the scope and detail of data required, and to evaluate previously published work. This document should also be useful for evaluating the strength of existing data and thus should aid in identifying future research needs. Use of this document by the research community may lead to greater consistency or comparability than currently exists among research studies, which may ultimately facilitate direct comparison of hazards and efficacy of controls among different commodities, conditions, and practices.
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Affiliation(s)
- Linda J Harris
- Western Center for Food Safety, University of California, Davis, CA 95616, USA.
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Monitoring a genetically modified Pseudomonas sp. released on pine leaves reveals concerted successional patterns of the bacterial phyllospheric community. Antonie van Leeuwenhoek 2008; 94:415-22. [PMID: 18574707 DOI: 10.1007/s10482-008-9259-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Accepted: 06/03/2008] [Indexed: 10/21/2022]
Abstract
The fate of a biocontrol agent released on pine phyllosphere in a greenhouse-confined trial was followed over 102 days. The microorganism used, a Pseudomonas sp., isolated from Pinus nigra, carries the cry9a toxin gene from Bacillus thuringiensis. In order to detect the GMM, specific primers were used, and a previously defined protocol for DNA isolation from bacteria colonizing pine needles was applied. The method, based on vortexing in a suspension of glass beads followed by microcolumn extractions, allowed sensitive PCR monitoring of the target transgenes. The presence of the released organism was recorded throughout the trial and compared with its entomocidal performance towards larvae of the pine processionary caterpillar Thaumetopoea pityocampa. At the same time the dynamics of the released Pseudomonas within the whole epiphytic bacterial community, was followed by amplifying 16S rDNA pools and comparing ARDRA profiles at seven sampling points. The resulting dendrogram allowed to follow the time-dependent progressive blending of the Pseudomonas profile into those of the resident biota. PCR-dominance of the released bacterium in the community was extended until 21 days from release while its activity against insect larvae lasted for over 3 months. The prokaryotic epiphytic population, irrespective of any particular impact from the released strain, showed no resilience but a general successional trend, which, remarkably, appeared synchronous on all trees tested, including non-inoculated controls. This observation suggests interesting patterns of concerted environmental shifts by phyllospheric microorganisms.
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Methods and detection limits in tracking a genetically modifiedPseudomonas sp. released in the pine phyllosphere. ANN MICROBIOL 2008. [DOI: 10.1007/bf03179462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Corich V, Giacomini A, Vendramin E, Vian P, Carlot M, Concheri G, Polone E, Casella S, Nuti MP, Squartini A. Long term evaluation of field-released genetically modified rhizobia. ENVIRONMENTAL BIOSAFETY RESEARCH 2007; 6:167-81. [PMID: 18001684 DOI: 10.1051/ebr:2007006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
This is the report of the first open field release of genetically modified microorganisms (GMMs) in Italy. It covers ten years of monitoring, and follows in-field GMM dynamics from strain release to disappearance below detection limits, as well as assessment of impact on resident microorganisms. The bacteria released belong to the nitrogen fixing legume endosymbiont Rhizobium leguminosarum bv. viciae, and were engineered with non-agronomically-proficient traits, in order to assess their behavior and fate without GMM-specific positive feedback from the plant. A DNA cassette containing mercury resistance and ss-galactosidase genes was introduced in either plasmid-borne or chromosomally integrated versions, in order to test the resulting strain stability. A synthetic promoter was used to drive the lacZ gene, conferring high catabolic activity to the GMM. Two different wild-type Rhizobium backgrounds were tested, comparing a non-indigenous vs. an indigenous, highly competitive strain. The latter had much greater persistence, since it was able to survive and establish at technically detectable levels for over four years after release. Selection factors, such as reiterated presence of the plant host, or lactose substrate supply, enhanced long-term survival to different extents. The lactose treatment showed that even a single trophic supplementation can surpass the benefits of symbiotic interaction for a period of several years. Concerning impact, the GMMs did not alter substantially the other soil community general microbiota. However, there were some significant differences in microbiota as a consequence of the Rhizobium inoculation. This effect was observed with either the WT or GMM, and was more evident in the release of the indigenous Rhizobium. Moreover, as the indigenous GMM had its parental, dominant wild-type in the same soil, it was possible to evaluate to what extent the GMM version could result in parent displacement ("self-impact"), and how much the two rhizobia would additively contribute to nodulation.
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Affiliation(s)
- Viviana Corich
- Dipartimento di Biotecnologie Agrarie, Università di Padova, Viale dell'Università 16, 35020 Legnaro, Padova, Italy
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Persistence, population dynamics and competitiveness for nodulation of marker gene-tagged Rhizobium galegae strains in field lysimeters in the boreal climatic zone. FEMS Microbiol Ecol 2003; 46:91-104. [DOI: 10.1016/s0168-6496(03)00210-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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