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      Impact of Phage Therapy on Pseudomonas syringae pv. syringae and Plant Microbiome Dynamics Through Coevolution and Field Experiments

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          ABSTRACT

          Bacteriophages (phages) are viruses that infect and lyse bacteria and have the potential for controlling bacterial diseases. Isolation of phages targeting the cherry pathogen Pseudomonas syringae pv. syringae ( Pss) led to five distinct phage genotypes. Building on previous in vitro coevolution experiments, the coevolution of the five phages (individually and as a cocktail) with Pss on cherry leaves was conducted in glasshouse and field experiments. Phages effectively reduced Pss numbers on detached leaves, with no evidence of phage resistance emerging in the bacterial population. Field application of phages in a cherry orchard in Southeast England evaluated phage survival, viability and impact on bacterial populations and the microbial community. The bacterial population and phages persisted in the leaf and shoot environment as long as the bacterial host was present. In contrast to in vitro studies, the plant environment constrained the emergence of phage resistant Pss populations. Application of phage cocktail in the orchard did not affect the cherry leaf microbiome. These observations provide essential knowledge for using phage treatments to control bacterial diseases while minimising the impact on the plant microbiome, highlighting phages' potential to safely control bacterial diseases in trees.

          Abstract

          The coevolution of phages with Pseudomonas syringae on cherry leaves reduced bacterial numbers on detached leaves without resistance emerging. Field application of phages in a cherry orchard showed that phages and bacteria persisted as long as the bacterial host was present, with the plant environment limiting the emergence of phage resistant populations.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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              Fitting Linear Mixed-Effects Models Usinglme4

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                Author and article information

                Contributors
                mojgan.rabiey@warwick.ac.uk
                Journal
                Environ Microbiol
                Environ Microbiol
                10.1111/(ISSN)1462-2920
                EMI
                Environmental Microbiology
                John Wiley & Sons, Inc. (Hoboken, USA )
                1462-2912
                1462-2920
                12 March 2025
                March 2025
                : 27
                : 3 ( doiID: 10.1111/emi.v27.3 )
                : e70076
                Affiliations
                [ 1 ] NIAB EMR West Malling UK
                [ 2 ] School of Biosciences and the Birmingham Institute of Forest Research University of Birmingham Edgbaston UK
                [ 3 ] School of Life Sciences University of Warwick, Gibbet Hill Campus Coventry UK
                [ 4 ] School of Life Sciences University of Warwick, Innovation Campus Stratford‐upon‐Avon UK
                Author notes
                [*] [* ] Correspondence:

                Mojgan Rabiey ( mojgan.rabiey@ 123456warwick.ac.uk )

                Author information
                https://orcid.org/0000-0001-6248-685X
                https://orcid.org/0000-0002-7409-9571
                https://orcid.org/0009-0000-7364-1210
                https://orcid.org/0000-0002-4308-8335
                https://orcid.org/0000-0002-2042-4105
                https://orcid.org/0000-0001-8463-9087
                Article
                EMI70076 EMI-2024-1148.R2
                10.1111/1462-2920.70076
                11903928
                40075541
                4bb3a7cd-0a66-444c-8443-252c990e1757
                © 2025 The Author(s). Environmental Microbiology published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 14 February 2025
                : 29 September 2024
                : 20 February 2025
                Page count
                Figures: 7, Tables: 3, Pages: 16, Words: 11800
                Funding
                Funded by: The University of Warwick start‐up fund
                Funded by: Plant Bacterial Diseases programme
                Award ID: BB/T010568/1
                Funded by: JABBS Foundation , doi 10.13039/501100016132;
                Funded by: Applied Microbiology International
                Funded by: East Malling Trust
                Funded by: Worshipful Company of Fruiterers
                Funded by: Biotechnology and Biological Sciences Research Council , doi 10.13039/501100000268;
                Award ID: BB/S019669/1
                Award ID: BB/X019683/1
                Funded by: University of Birmingham , doi 10.13039/501100000855;
                Categories
                Research Article
                Research Article
                Custom metadata
                2.0
                March 2025
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.5.4 mode:remove_FC converted:13.03.2025

                Microbiology & Virology
                bacteriophage,biocontrol,cherry canker,microbiome, pseudomonas syringae
                Microbiology & Virology
                bacteriophage, biocontrol, cherry canker, microbiome, pseudomonas syringae

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