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Orole OO, Adewumi T, Adefolalu A. Biological assessment and radiological impact in Keana, North Central Nigeria: environmental implication and metabolites production. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:756. [PMID: 39033483 DOI: 10.1007/s10661-024-12919-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024]
Abstract
The objective of the research was to examine microbial characteristics, metabolites produced, and the potential radiological risks present in mining soils located in Keana, North Central Nigeria. Soil samples were collected from various locations within Keana, Nasarawa State. Bacterial isolation was carried out, and molecular techniques were employed to characterize the bacteria found in the collected soil samples. Additionally, the susceptibility of these isolates to antibiotics was determined, and the bacteria screened for their ability to produce metabolites. The isolated bacteria were classified into three groups: Actinobacteria, Firmicutes, and Proteobacteria. The analysis of the spectra revealed that 1595 compounds were produced, including carboxylic acids, nitro compounds, aldehydes, anhydrides, esters, ketones, amides, phenols, alcohols, alkanes, alkenes, alkynes, and arenes. Some of the metabolites produced were oleic acid, 1,3-dioxolane, linoelaidic acid and oleic acid, 1-nonadecene, butylated hydroxytoluene, diisooctyl phthalate, bis(2-ethylhexyl) phthalate among others, and 1,2-benzenedicarboxylic acid (85.32%) as the most produced metabolite. Among the antibiotics tested, levofloxacin and ciprofloxacin exhibited the strongest antibacterial properties against the isolates. Airborne gamma-ray spectrometry analysis identified elevated levels of potassium, thorium, and uranium in the soils, indicating potential environmental hazards. However, no significant correlation was found between the presence of bacteria and radioactive elements. These findings emphasize the importance of comprehensive environmental monitoring in Keana to address potential health risks associated with microbial contamination and radioactive materials. Additionally, the study highlighted the role of microbial diversity in Keana soils in promoting the production of secondary metabolites with potential applications in pharmaceutical and industrial sectors..
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Affiliation(s)
| | - Taiwo Adewumi
- Department of Physics, Federal University of Lafia, Lafia, Nasarawa State, Nigeria, 950101
| | - Adedotun Adefolalu
- Department of Biochemistry, Federal University of Lafia, Lafia, Nasarawa State, Nigeria, 950101
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2
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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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Singh BK, Delgado-Baquerizo M, Egidi E, Guirado E, Leach JE, Liu H, Trivedi P. Climate change impacts on plant pathogens, food security and paths forward. Nat Rev Microbiol 2023; 21:640-656. [PMID: 37131070 PMCID: PMC10153038 DOI: 10.1038/s41579-023-00900-7] [Citation(s) in RCA: 98] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/04/2023]
Abstract
Plant disease outbreaks pose significant risks to global food security and environmental sustainability worldwide, and result in the loss of primary productivity and biodiversity that negatively impact the environmental and socio-economic conditions of affected regions. Climate change further increases outbreak risks by altering pathogen evolution and host-pathogen interactions and facilitating the emergence of new pathogenic strains. Pathogen range can shift, increasing the spread of plant diseases in new areas. In this Review, we examine how plant disease pressures are likely to change under future climate scenarios and how these changes will relate to plant productivity in natural and agricultural ecosystems. We explore current and future impacts of climate change on pathogen biogeography, disease incidence and severity, and their effects on natural ecosystems, agriculture and food production. We propose that amendment of the current conceptual framework and incorporation of eco-evolutionary theories into research could improve our mechanistic understanding and prediction of pathogen spread in future climates, to mitigate the future risk of disease outbreaks. We highlight the need for a science-policy interface that works closely with relevant intergovernmental organizations to provide effective monitoring and management of plant disease under future climate scenarios, to ensure long-term food and nutrient security and sustainability of natural ecosystems.
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Affiliation(s)
- Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia.
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia.
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Emilio Guirado
- Multidisciplinary Institute for Environment Studies 'Ramon Margalef', University of Alicante, Alicante, Spain
| | - Jan E Leach
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Hongwei Liu
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Pankaj Trivedi
- Microbiome Newtork and Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
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Baroukh C, Cottret L, Pires E, Peyraud R, Guidot A, Genin S. Insights into the metabolic specificities of pathogenic strains from the Ralstonia solanacearum species complex. mSystems 2023; 8:e0008323. [PMID: 37341493 PMCID: PMC10470067 DOI: 10.1128/msystems.00083-23] [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: 01/25/2023] [Accepted: 04/14/2023] [Indexed: 06/22/2023] Open
Abstract
All the strains grouped under the species Ralstonia solanacearum represent a species complex responsible for many diseases on agricultural crops throughout the world. The strains have different lifestyles and host range. Here, we investigated whether specific metabolic pathways contribute to strain diversification. To this end, we carried out systematic comparisons on 11 strains representing the diversity of the species complex. We reconstructed the metabolic network of each strain from its genome sequence and looked for the metabolic pathways differentiating the different reconstructed networks and, by extension, the different strains. Finally, we conducted an experimental validation by determining the metabolic profile of each strain with the Biolog technology. Results revealed that the metabolism is conserved between strains, with a core metabolism composed of 82% of the pan-reactome. The three species composing the species complex could be distinguished according to the presence/absence of some metabolic pathways, in particular, one involving salicylic acid degradation. Phenotypic assays revealed that the trophic preferences on organic acids and several amino acids such as glutamine, glutamate, aspartate, and asparagine are conserved between strains. Finally, we generated mutants lacking the quorum-sensing-dependent regulator PhcA in four diverse strains, and we showed that the phcA-dependent trade-off between growth and production of virulence factors is conserved across the R. solanacearum species complex. IMPORTANCE Ralstonia solanacearum is one of the most important threats to plant health worldwide, causing disease on a very large range of agricultural crops such as tomato or potato. Behind the R. solanacearum name are hundreds of strains with different host range and lifestyle, classified into three species. Studying the differences between strains allows to better apprehend the biology of the pathogens and the specificity of some strains. None of the published genomic comparative studies have focused on the metabolism of the strains so far. We developed a new bioinformatic pipeline to build high-quality metabolic networks and used a combination of metabolic modeling and high-throughput phenotypic Biolog microplates to look for the metabolic differences between 11 strains across the three species. Our study revealed that genes encoding enzymes are overall conserved, with few variations between strains. However, more variations were observed when considering substrate usage. These variations probably result from regulation rather than the presence or absence of enzymes in the genome.
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Affiliation(s)
- Caroline Baroukh
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Ludovic Cottret
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Emma Pires
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Rémi Peyraud
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Alice Guidot
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Stéphane Genin
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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Luneau JS, Baudin M, Quiroz Monnens T, Carrère S, Bouchez O, Jardinaud M, Gris C, François J, Ray J, Torralba B, Arlat M, Lewis JD, Lauber E, Deutschbauer AM, Noël LD, Boulanger A. Genome-wide identification of fitness determinants in the Xanthomonas campestris bacterial pathogen during early stages of plant infection. THE NEW PHYTOLOGIST 2022; 236:235-248. [PMID: 35706385 PMCID: PMC9543026 DOI: 10.1111/nph.18313] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/07/2022] [Indexed: 05/31/2023]
Abstract
Plant diseases are an important threat to food production. While major pathogenicity determinants required for disease have been extensively studied, less is known on how pathogens thrive during host colonization, especially at early infection stages. Here, we used randomly barcoded-transposon insertion site sequencing (RB-TnSeq) to perform a genome-wide screen and identify key bacterial fitness determinants of the vascular pathogen Xanthomonas campestris pv campestris (Xcc) during infection of the cauliflower host plant (Brassica oleracea). This high-throughput analysis was conducted in hydathodes, the natural entry site of Xcc, in xylem sap and in synthetic media. Xcc did not face a strong bottleneck during hydathode infection. In total, 181 genes important for fitness were identified in plant-associated environments with functional enrichment in genes involved in metabolism but only few genes previously known to be involved in virulence. The biological relevance of 12 genes was independently confirmed by phenotyping single mutants. Notably, we show that XC_3388, a protein with no known function (DUF1631), plays a key role in the adaptation and virulence of Xcc possibly through c-di-GMP-mediated regulation. This study revealed yet unsuspected social behaviors adopted by Xcc individuals when confined inside hydathodes at early infection stages.
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Affiliation(s)
- Julien S. Luneau
- LIPME, Université de Toulouse, INRAE, CNRSUniversité Paul Sabatier31320Castanet‐TolosanFrance
| | - Maël Baudin
- Plant Gene Expression Center, USDAAlbanyCA94710USA
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCA94720USA
| | - Thomas Quiroz Monnens
- LIPME, Université de Toulouse, INRAE, CNRSUniversité Paul Sabatier31320Castanet‐TolosanFrance
| | - Sébastien Carrère
- LIPME, Université de Toulouse, INRAE, CNRSUniversité Paul Sabatier31320Castanet‐TolosanFrance
| | - Olivier Bouchez
- Genotoul Genome & Transcriptome (GeT‐PlaGe), INRAE31320Castanet‐TolosanFrance
| | | | - Carine Gris
- LIPME, Université de Toulouse, INRAE, CNRSUniversité Paul Sabatier31320Castanet‐TolosanFrance
| | - Jonas François
- LIPME, Université de Toulouse, INRAE, CNRSUniversité Paul Sabatier31320Castanet‐TolosanFrance
| | - Jayashree Ray
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Babil Torralba
- LIPME, Université de Toulouse, INRAE, CNRSUniversité Paul Sabatier31320Castanet‐TolosanFrance
| | - Matthieu Arlat
- LIPME, Université de Toulouse, INRAE, CNRSUniversité Paul Sabatier31320Castanet‐TolosanFrance
| | - Jennifer D. Lewis
- Plant Gene Expression Center, USDAAlbanyCA94710USA
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCA94720USA
| | - Emmanuelle Lauber
- LIPME, Université de Toulouse, INRAE, CNRSUniversité Paul Sabatier31320Castanet‐TolosanFrance
| | - Adam M. Deutschbauer
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCA94720USA
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Laurent D. Noël
- LIPME, Université de Toulouse, INRAE, CNRSUniversité Paul Sabatier31320Castanet‐TolosanFrance
| | - Alice Boulanger
- LIPME, Université de Toulouse, INRAE, CNRSUniversité Paul Sabatier31320Castanet‐TolosanFrance
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6
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Oliveira A, Cunha E, Cruz F, Capela J, Sequeira JC, Sampaio M, Sampaio C, Dias O. Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool. J Integr Bioinform 2022; 19:jib-2022-0014. [PMID: 36054839 PMCID: PMC9521827 DOI: 10.1515/jib-2022-0014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/02/2022] [Indexed: 11/24/2022] Open
Abstract
Genome-scale metabolic models (GEMs) are essential tools for in silico phenotype prediction and strain optimisation. The most straightforward GEMs reconstruction approach uses published models as templates to generate the initial draft, requiring further curation. Such an approach is used by BiGG Integration Tool (BIT), available for merlin users. This tool uses models from BiGG Models database as templates for the draft models. Moreover, BIT allows the selection between different template combinations. The main objective of this study is to assess the draft models generated using this tool and compare them BIT, comparing these to CarveMe models, both of which use the BiGG database, and curated models. For this, three organisms were selected, namely Streptococcus thermophilus, Xylella fastidiosa and Mycobacterium tuberculosis. The models’ variability was assessed using reactions and genes’ metabolic functions. This study concluded that models generated with BIT for each organism were differentiated, despite sharing a significant portion of metabolic functions. Furthermore, the template seems to influence the content of the models, though to a lower extent. When comparing each draft with curated models, BIT had better performances than CarveMe in all metrics. Hence, BIT can be considered a fast and reliable alternative for draft reconstruction for bacteria models.
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Affiliation(s)
- Alexandre Oliveira
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Emanuel Cunha
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Fernando Cruz
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - João Capela
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - João C Sequeira
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Marta Sampaio
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Cláudia Sampaio
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
| | - Oscar Dias
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.,LABBELS -Associate Laboratory, Braga, Guimarães, Portugal
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7
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Landa BB, Saponari M, Feitosa-Junior OR, Giampetruzzi A, Vieira FJD, Mor E, Robatzek S. Xylella fastidiosa's relationships: the bacterium, the host plants, and the plant microbiome. THE NEW PHYTOLOGIST 2022; 234:1598-1605. [PMID: 35279849 DOI: 10.1111/nph.18089] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Xylella fastidiosa is the causal agent of important crop diseases and is transmitted by xylem-sap-feeding insects. The bacterium colonizes xylem vessels and can persist with a commensal or pathogen lifestyle in more than 500 plant species. In the past decade, reports of X. fastidiosa across the globe have dramatically increased its known occurrence. This raises important questions: How does X. fastidiosa interact with the different host plants? How does the bacterium interact with the plant immune system? How does it influence the host's microbiome? We discuss recent strain genetic typing and plant transcriptome and microbiome analyses, which have advanced our understanding of factors that are important for X. fastidiosa plant infection.
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Affiliation(s)
- Blanca B Landa
- Institute for Sustainable Agriculture, CSIC, Alameda del Obispo S/N, Córdoba, 14004, Spain
| | - Maria Saponari
- CNR - Institute for Sustainable Plant Protection (IPSP), Via Amendola 165/A, Bari, 70126, Italy
| | | | - Annalisa Giampetruzzi
- CNR - Institute for Sustainable Plant Protection (IPSP), Via Amendola 165/A, Bari, 70126, Italy
| | - Filipe J D Vieira
- Genetics, LMU Biocentre, Grosshadener Strasse 4, Planegg, 82152, Germany
| | - Eliana Mor
- Genetics, LMU Biocentre, Grosshadener Strasse 4, Planegg, 82152, Germany
| | - Silke Robatzek
- Genetics, LMU Biocentre, Grosshadener Strasse 4, Planegg, 82152, Germany
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Petit G, Bleve G, Gallo A, Mita G, Montanaro G, Nuzzo V, Zambonini D, Pitacco A. Susceptibility to Xylella fastidiosa and functional xylem anatomy in Olea europaea: revisiting a tale of plant-pathogen interaction. AOB PLANTS 2021; 13:plab027. [PMID: 34316336 PMCID: PMC8300559 DOI: 10.1093/aobpla/plab027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/19/2021] [Indexed: 05/09/2023]
Abstract
Xylella fastidiosa is a xylem-limited bacterium causing the Olive Quick Decline Syndrome, which is currently devastating the agricultural landscape of Southern Italy. The bacterium is injected into the xylem vessels of leaf petioles after the penetration of the insect vector's stylet. From here, it is supposed to colonize the xylem vasculature moving against water flow inside conductive vessels. Widespread vessel clogging following the bacterial infection and causing the failure of water transport seemed not to fully supported by the recent empirical xylem anatomical observations in infected olive trees. We tested the hypothesis that the higher susceptibility to the X. fastidiosa's infection in Cellina di Nardò compared with Leccino is associated to the higher vulnerability to air embolism of its larger vessels. Such hypothesis is motivated by the recognized ability of X. fastidiosa in degrading pit membranes and also because air embolism would possibly provide microenvironmental conditions more favourable to its more efficient aerobic metabolism. We revised the relevant literature on bacterium growth and xylem physiology, and carried out empirical field, mid-summer measurements of xylem anatomy and native embolism in olive cultivars with high (Cellina di Nardò) and low susceptibility (Leccino) to the infection by X. fastidiosa. Both cultivars had similar shoot mass traits and vessel length (~80 cm), but the highly susceptible one had larger vessels and a lower number of vessels supplying a given leaf mass. Native air embolism reduced mean xylem hydraulic conductance by ~58 % (Cellina di Nardò) and ~38 % (Leccino). The higher air-embolism vulnerability of the larger vessels in Cellina di Nardò possibly facilitates the X. fastidiosa's infection compared to Leccino. Some important characteristics of the vector-pathogen-plant interactions still require deep investigations acknowledging both the pathogen metabolic pathways and the biophysical principles of xylem hydraulics.
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Affiliation(s)
- Giai Petit
- Department of Land, Environment, Agriculture and Forestry (LEAF/TESAF), University of Padua, Viale dell’Università 16, 35020 Legnaro (PD), Italy
| | - Gianluca Bleve
- Institute of Sciences of Food Production, National research Council (ISPA-CNR), via Provinciale Lecce-Monteroni 73100 Lecce, Italy
| | - Antonia Gallo
- Institute of Sciences of Food Production, National research Council (ISPA-CNR), via Provinciale Lecce-Monteroni 73100 Lecce, Italy
| | - Giovanni Mita
- Institute of Sciences of Food Production, National research Council (ISPA-CNR), via Provinciale Lecce-Monteroni 73100 Lecce, Italy
| | - Giuseppe Montanaro
- Department of European and Mediterranean Culture (DiCEM), University of Basilicata, Via Lanera, 20, 75100 Matera, Italy
| | - Vitale Nuzzo
- Department of European and Mediterranean Culture (DiCEM), University of Basilicata, Via Lanera, 20, 75100 Matera, Italy
| | - Dario Zambonini
- Department of Land, Environment, Agriculture and Forestry (LEAF/TESAF), University of Padua, Viale dell’Università 16, 35020 Legnaro (PD), Italy
| | - Andrea Pitacco
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’Università 16, 35020 Legnaro (PD), Italy
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9
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Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans. Viruses 2021; 13:v13050725. [PMID: 33919362 PMCID: PMC8143317 DOI: 10.3390/v13050725] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/12/2021] [Accepted: 04/17/2021] [Indexed: 12/21/2022] Open
Abstract
Xylella fastidiosa (Xf) is a plant pathogen causing significant losses in agriculture worldwide. Originating from America, this bacterium caused recent epidemics in southern Europe and is thus considered an emerging pathogen. As the European regulations do not authorize antibiotic treatment in plants, alternative treatments are urgently needed to control the spread of the pathogen and eventually to cure infected crops. One such alternative is the use of phage therapy, developed more than 100 years ago to cure human dysentery and nowadays adapted to agriculture. The first step towards phage therapy is the isolation of the appropriate bacteriophages. With this goal, we searched for phages able to infect Xf strains that are endemic in the Mediterranean area. However, as Xf is truly a fastidious organism, we chose the phylogenetically closest and relatively fast-growing organism X. albineans as a surrogate host for the isolation step. Our results showed the isolation from various sources and preliminary characterization of several phages active on different Xf strains, namely, from the fastidiosa (Xff), multiplex (Xfm), and pauca (Xfp) subspecies, as well as on X. albilineans. We sequenced their genomes, described their genomic features, and provided a phylogeny analysis that allowed us to propose new taxonomic elements. Among the 14 genomes sequenced, we could identify two new phage species, belonging to two new genera of the Caudoviricetes order, namely, Usmevirus (Podoviridae family) and Subavirus (Siphoviridae family). Interestingly, no specific phages could be isolated from infected plant samples, whereas one was isolated from vector insects captured in a contaminated area, and several from surface and sewage waters from the Marseille area.
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Morinière L, Lecomte S, Gueguen E, Bertolla F. In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to discriminate between core and contextual essential genes. Microb Genom 2019; 7. [PMID: 33760724 PMCID: PMC8627662 DOI: 10.1099/mgen.0.000546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The essential genome of a bacterium encompasses core genes associated with basic cellular processes and conditionally essential genes dependent upon environmental conditions or the genetic context. Comprehensive knowledge of those gene sets allows for a better understanding of fundamental bacterial biology and offers new perspectives for antimicrobial drug research against detrimental bacteria such as pathogens. We investigated the essential genome of Xanthomonas hortorum pv. vitians, a gammaproteobacterial plant pathogen of lettuce (Lactuca sativa L.) which belongs to the plant-pathogen reservoir genus Xanthomonas and is affiliated to the family Xanthomonadaceae. No practical means of disease control or prevention against this pathogen is currently available, and its molecular biology is virtually unknown. To reach a comprehensive overview of the essential genome of X. hortorum pv. vitians LM16734, we developed a mixed approach combining high-quality full genome sequencing, saturated transposon insertion sequencing (Tn-Seq) in optimal growth conditions, and coupled computational analyses such as comparative genomics, synteny assessment and phylogenomics. Among the 370 essential loci identified by Tn-Seq, a majority was bound to critical cell processes conserved across bacteria. The remaining genes were either related to specific ecological features of Xanthomonas or Xanthomonadaceae species, or acquired through horizontal gene transfer of mobile genetic elements and associated with ancestral parasitic gene behaviour and bacterial defence systems. Our study sheds new light on our usual concepts about gene essentiality and is pioneering in the molecular and genomic study of X. hortorum pv. vitians.
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Affiliation(s)
- Lucas Morinière
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
| | - Solène Lecomte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
| | - Erwan Gueguen
- Univ Lyon, Université Claude Bernard Lyon 1, INSA, CNRS, UMR Microbiologie, Adaptation, Pathogénie, F 69622 Villeurbanne, France
| | - Franck Bertolla
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F 69622 Villeurbanne, France
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