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Roman-Reyna V, Heiden N, Butchacas J, Toth H, Cooperstone JL, Jacobs JM. The timing of bacterial mesophyll infection shapes the leaf chemical landscape. Microbiol Spectr 2024; 12:e0413823. [PMID: 38426767 PMCID: PMC10986523 DOI: 10.1128/spectrum.04138-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/14/2024] [Indexed: 03/02/2024] Open
Abstract
Chemistry in eukaryotic intercellular spaces is shaped by both hosts and symbiotic microorganisms such as bacteria. Pathogenic microorganisms like barley-associated Xanthomonas translucens (Xt) swiftly overtake the inner leaf tissue becoming the dominant microbial community member during disease development. The dynamic metabolic changes due to Xt pathogenesis in the mesophyll spaces remain unknown. Genomic group I of Xt consists of two barley-infecting lineages: pathovar translucens (Xtt) and pathovar undulosa (Xtu). Xtu and Xtt, although genomically distinct, cause similar water-soaked lesions. To define the metabolic signals associated with inner leaf colonization, we used untargeted metabolomics to characterize Xtu and Xtt metabolism signatures associated with mesophyll growth. We found that mesophyll apoplast fluid from infected tissue yielded a distinct metabolic profile and shift from catabolic to anabolic processes over time compared to water-infiltrated control. The pathways with the most differentially expressed metabolites by time were glycolysis, tricarboxylic acid cycle, sucrose metabolism, pentose interconversion, amino acids, galactose, and purine metabolism. Hierarchical clustering and principal component analysis showed that metabolic changes were more affected by the time point rather than the individual colonization of the inner leaves by Xtt compared to Xtu. Overall, in this study, we identified metabolic pathways that explain carbon and nitrogen usage during host-bacterial interactions over time for mesophyll tissue colonization. This foundational research provides initial insights into shared metabolic strategies of inner leaf colonization niche occupation by related but phylogenetically distinct phyllosphere bacteria. IMPORTANCE The phyllosphere is a habitat for microorganisms including pathogenic bacteria. Metabolic shifts in the inner leaf spaces for most plant-microbe interactions are unknown, especially for Xanthomonas species in understudied plants like barley (Hordeum vulgare). Xanthomonas translucens pv. translucens (Xtt) and Xanthomonas translucens pv. undulosa (Xtu) are phylogenomically distinct, but both colonize barley leaves for pathogenesis. In this study, we used untargeted metabolomics to shed light on Xtu and Xtt metabolic signatures. Our findings revealed a dynamic metabolic landscape that changes over time, rather than exhibiting a pattern associated with individual pathovars. These results provide initial insights into the metabolic mechanisms of X. translucens inner leaf pathogenesis.
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Affiliation(s)
- Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Nathaniel Heiden
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Jules Butchacas
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Hannah Toth
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Jessica L. Cooperstone
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio, USA
- Department of Food Science and Technology, The Ohio State University, Columbus, Ohio, USA
| | - Jonathan M. Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
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Gutierrez-Castillo DE, Barrett E, Roberts R. A recently collected Xanthomonas translucens isolate encodes TAL effectors distinct from older, less virulent isolates. Microb Genom 2024; 10:001177. [PMID: 38189214 PMCID: PMC10868612 DOI: 10.1099/mgen.0.001177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
Xanthomonas translucens, the causal agent of bacterial leaf streak disease (BLS) in cereals, is a re-emerging pathogen that is becoming increasingly destructive across the world. While BLS has caused yield losses in the past, there is anecdotal evidence that newer isolates may be more virulent. We observed that two X. translucens isolates collected from two sites in Colorado, USA, are more aggressive on current wheat and barley varieties compared to older isolates, and we hypothesize that genetic changes between recent and older isolates contribute to the differences in isolate aggressiveness. To test this, we phenotyped and genetically characterized two X. translucens isolates collected from Colorado in 2018, which we designated CO236 (from barley) and CO237 (from wheat). Using pathovar-specific phenotyping and PCR primers, we determined that CO236 belongs to pathovar translucens (Xtt) and CO237 belongs to pathovar undulosa (Xtu). We sequenced the full genomes of the isolates using Oxford Nanopore long-read sequencing, and compared their whole genomes against published X. translucens genomes. This analysis confirmed our pathovar designations for Xtt CO236 and Xtu CO237, and showed that, at the whole-genome level, there were no obvious genomic structural changes between Xtt CO236 and Xtu CO237 and other respective published pathovar genomes. Focusing on pathovar undulosa (Xtu CO237), we then compared putative type III effectors among all available Xtu isolate genomes and found that they were highly conserved. However, there were striking differences in the presence and sequence of various transcription activator-like effectors between Xtu CO237 and published undulosa genomes, which correlate with isolate virulence. Here, we explore the potential implications of the differences in these virulence factors, and provide possible explanations for the increased virulence of recently emerged isolates.
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Affiliation(s)
| | - Emma Barrett
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Robyn Roberts
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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Ledman KE, Osdaghi E, Curland RD, Liu Z, Dill-Macky R. Epidemiology, Host Resistance, and Genomics of the Small Grain Cereals Pathogen Xanthomonas translucens: New Advances and Future Prospects. PHYTOPATHOLOGY 2023; 113:2037-2047. [PMID: 36996338 DOI: 10.1094/phyto-11-22-0403-sa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Bacterial leaf streak (BLS) primarily affects barley and wheat and is mainly caused by the pathogens Xanthomonas translucens pv. translucens and X. translucens pv. undulosa, respectively. BLS is distributed globally and poses a risk to food security and the supply of malting barley. X. translucens pv. cerealis can infect both wheat and barley but is rarely isolated from these hosts in natural infections. These pathogens have undergone a confusing taxonomic history, and the biology has been poorly understood, making it difficult to develop effective control measures. Recent advancements in the ability and accessibility to sequence bacterial genomes have shed light on phylogenetic relationships between strains and identified genes that may play a role in virulence, such as those that encode Type III effectors. In addition, sources of resistance to BLS have been identified in barley and wheat lines, and ongoing efforts are being made to map these genes and evaluate germplasm. Although there are still gaps in BLS research, progress has been made in recent years to further understand epidemiology, diagnostics, pathogen virulence, and host resistance.
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Affiliation(s)
- Kristi E Ledman
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Ebrahim Osdaghi
- Department of Plant Protection, University of Tehran, Karaj, Iran
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, U.S.A
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
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4
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Heiden N, Roman-Reyna V, Curland RD, Dill-Macky R, Jacobs JM. Comparative Genomics of Barley-Infecting Xanthomonas translucens Shows Overall Genetic Similarity but Globally Distributed Virulence Factor Diversity. PHYTOPATHOLOGY 2023; 113:2056-2061. [PMID: 35727947 DOI: 10.1094/phyto-04-22-0113-sc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Xanthomonas translucens pv. translucens (Xtt) is a global barley patho-gen and a concern for resistance breeding and regulation. Long-read whole genome sequences allow in-depth understanding of pathogen diversity. We have completed long-read PacBio sequencing of two Minnesotan Xtt strains and an in-depth analysis of available Xtt genomes. We found that average nucleotide identity (ANI)-based approaches organize Xtt strains different from the previous standard multilocus sequencing analysis approach. According to ANI, Xtt forms a separate clade from X. translucens pv. undulosa and consists of three main groups which are represented on multiple continents. Some virulence factors, such as 17 Type III-secreted effectors, are highly conserved and offer potential targets for the elicitation of broad resistance. However, there is a high degree of variation in virulence factors, meaning that germplasm should be screened for resistance with a diverse panel of Xtt.
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Affiliation(s)
- Nathaniel Heiden
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
| | - Rebecca D Curland
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Ruth Dill-Macky
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210
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Complete Genomes of Two Xanthomonas translucens pv. translucens Strains Isolated from Barley in North Dakota. Microbiol Resour Announc 2022; 11:e0001022. [PMID: 35343804 PMCID: PMC9022509 DOI: 10.1128/mra.00010-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Xanthomonas translucens causes the disease bacterial leaf streak in several cereal crops and grasses. Here, we report the complete genome sequences of two isolates of X. translucens pv. translucens that were isolated from barley in an important cereal crop production region.
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Goettelmann F, Roman-Reyna V, Cunnac S, Jacobs JM, Bragard C, Studer B, Koebnik R, Kölliker R. Complete Genome Assemblies of All Xanthomonas translucens Pathotype Strains Reveal Three Genetically Distinct Clades. Front Microbiol 2022; 12:817815. [PMID: 35310401 PMCID: PMC8924669 DOI: 10.3389/fmicb.2021.817815] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
The Xanthomonas translucens species comprises phytopathogenic bacteria that can cause serious damage to cereals and to forage grasses. So far, the genomic resources for X. translucens were limited, which hindered further understanding of the host–pathogen interactions at the molecular level and the development of disease-resistant cultivars. To this end, we complemented the available complete genome sequence of the X. translucens pv. translucens pathotype strain DSM 18974 by sequencing the genomes of all the other 10 X. translucens pathotype strains using PacBio long-read technology and assembled complete genome sequences. Phylogeny based on average nucleotide identity (ANI) revealed three distinct clades within the species, which we propose to classify as clades Xt-I, Xt-II, and Xt-III. In addition to 2,181 core X. translucens genes, a total of 190, 588, and 168 genes were found to be exclusive to each clade, respectively. Moreover, 29 non-transcription activator-like effector (TALE) and 21 TALE type III effector classes were found, and clade- or strain-specific effectors were identified. Further investigation of these genes could help to identify genes that are critically involved in pathogenicity and/or host adaptation, setting the grounds for the development of new resistant cultivars.
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Affiliation(s)
- Florian Goettelmann
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Sébastien Cunnac
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States
| | - Claude Bragard
- Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Ralf Koebnik
- Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Roland Kölliker
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
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7
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Gluck-Thaler E, Cerutti A, Perez-Quintero AL, Butchacas J, Roman-Reyna V, Madhavan VN, Shantharaj D, Merfa MV, Pesce C, Jauneau A, Vancheva T, Lang JM, Allen C, Verdier V, Gagnevin L, Szurek B, Beckham GT, De La Fuente L, Patel HK, Sonti RV, Bragard C, Leach JE, Noël LD, Slot JC, Koebnik R, Jacobs JM. Repeated gain and loss of a single gene modulates the evolution of vascular plant pathogen lifestyles. SCIENCE ADVANCES 2020; 6:6/46/eabc4516. [PMID: 33188025 PMCID: PMC7673761 DOI: 10.1126/sciadv.abc4516] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/30/2020] [Indexed: 05/21/2023]
Abstract
Vascular plant pathogens travel long distances through host veins, leading to life-threatening, systemic infections. In contrast, nonvascular pathogens remain restricted to infection sites, triggering localized symptom development. The contrasting features of vascular and nonvascular diseases suggest distinct etiologies, but the basis for each remains unclear. Here, we show that the hydrolase CbsA acts as a phenotypic switch between vascular and nonvascular plant pathogenesis. cbsA was enriched in genomes of vascular phytopathogenic bacteria in the family Xanthomonadaceae and absent in most nonvascular species. CbsA expression allowed nonvascular Xanthomonas to cause vascular blight, while cbsA mutagenesis resulted in reduction of vascular or enhanced nonvascular symptom development. Phylogenetic hypothesis testing further revealed that cbsA was lost in multiple nonvascular lineages and more recently gained by some vascular subgroups, suggesting that vascular pathogenesis is ancestral. Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits.
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Affiliation(s)
- Emile Gluck-Thaler
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aude Cerutti
- LIPM, Université de Toulouse, INRAE, CNRS, Université Paul Sabatier, Castanet-Tolosan, France
| | | | - Jules Butchacas
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Verónica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, USA
| | | | - Deepak Shantharaj
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Marcus V Merfa
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Céline Pesce
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
- Earth & Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
- HM Clause (Limagrain group), Davis, CA, 95618, USA
| | - Alain Jauneau
- Institut Fédératif de Recherche 3450, Plateforme Imagerie, Pôle de Biotechnologie Végétale, Castanet-Tolosan, France
| | - Taca Vancheva
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
- Earth & Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jillian M Lang
- Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Caitilyn Allen
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Valerie Verdier
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | - Lionel Gagnevin
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | - Boris Szurek
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Leonardo De La Fuente
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | | | - Ramesh V Sonti
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Claude Bragard
- Earth & Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jan E Leach
- Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Laurent D Noël
- LIPM, Université de Toulouse, INRAE, CNRS, Université Paul Sabatier, Castanet-Tolosan, France
| | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Koebnik
- IRD, CIRAD, Université Montpellier, IPME, Montpellier, France.
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA.
- Infectious Disease Institute, The Ohio State University, Columbus, OH 43210, USA
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