Article
Biology
Enora Dupas, Karine Durand, Adrien Rieux, Martial Briand, Olivier Pruvost, Amandine Cunty, Nicolas Denance, Cecile Donnadieu, Bruno Legendre, Celine Lopez-Roques, Sophie Cesbron, Virginie Ravigne, Marie-Agnes Jacques
Summary: Genomic investigation reveals an American origin and two waves of invasion for the plant pathogen Xylella fastidiosa in France. Since its discovery in Italian olive groves in 2013, a wide diversity of Xylella fastidiosa strains from different subspecies of American origin have been reported in Europe. Strains from the multiplex subspecies (ST6 and ST7) were first identified in France in 2015, and the molecular evolution rate of this subspecies was estimated. A new VNTR-13 scheme was developed to trace the spread of the bacterium in France and suggests an initial introduction and spread in Provence-Alpes-Cote d'Azur (PACA), followed by two waves of introduction in Corsica from the PACA bridgehead populations.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Michael L. L. O'Leary, Lindsey P. P. Burbank
Summary: X. fastidiosa is a significant bacterial plant pathogen that causes high-consequence diseases in agricultural crops worldwide. Variability exists between X. fastidiosa strains regarding virulence on specific host plants and other traits. This study compares conserved type I restriction-modification systems in 129 X. fastidiosa genome assemblies, identifying unique target recognition structures among 50 hsdS alleles that are generally conserved within monophyletic strain clusters.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Editorial Material
Ecology
Lynn Govaert, Florian Altermatt, Luc De Meester, Mathew A. Leibold, Mark A. McPeek, Jelena H. Pantel, Mark C. Urban
Summary: Recent studies show that ecological and evolutionary processes can often interact; however, our understanding of evolution in multi-species communities is still lacking; focusing on interactions between evolutionary biology and community ecology processes can explore eco-evolutionary dynamics in multi-species communities.
FUNCTIONAL ECOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Shdema Filler-Hayut, Kiril Kniazev, Cathy Melamed-Bessudo, Avraham A. Levy
Summary: The study shows that targeted DSBs can be repaired via HR using a homologous chromosome as the template in various chromatin contexts. Gene conversion events were the most frequent outcome of HR, with variable lengths of conversion tracts. This finding suggests the potential use of targeted gene-conversion for precise breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Ecology
Sebastien Lion, Akira Sasaki, Mike Boots
Summary: Understanding the interaction between ecological processes and evolutionary dynamics of quantitative traits in natural systems is a challenge. Two main theoretical frameworks, adaptive dynamics and quantitative genetics, have strengths and limitations and are used by different research communities. To make progress, a novel theoretical framework called 'oligomorphic dynamics' is proposed to bridge the gap between these approaches and strengthen the link to empirical data. Oligomorphic dynamics considers environmental feedback and can analyze eco-evolutionary dynamics, including multimodal trait distributions and non-normal or skewed distributions encountered in nature, facilitating a tighter integration between theory and data.
Article
Ecology
Gianni Gilioli, Anna Simonetto, Michele Colturato, Noelia Bazarra, Jose R. Fernandez, Maria Grazia Naso, Boscia Donato, Domenico Bosco, Crescenza Dongiovanni, Andrea Maiorano, Olaf Mosbach-Schulz, Juan A. Navas Cortes, Maria Saponari
Summary: In this study, an Eco-epidemiological Model (XEM) was proposed to describe the infection dynamics of X. fastidiosa outbreaks. The model considers various factors such as host plant growth, pathogen acquisition and transmission by vectors, vector population dynamics, and vector dispersal. Simulation results showed that vector abundance is the key factor determining the spread rate of the pathogen, and vector control efficacy and time to detection and intervention are crucial for effective eradication strategies. XEM proved to be a suitable tool for decision making in emergency plans related to new outbreaks.
ECOLOGICAL MODELLING
(2023)
Article
Biotechnology & Applied Microbiology
Tiffany N. Batarseh, Abraham Morales-Cruz, Brian Ingel, M. Caroline Roper, Brandon S. Gaut
Summary: This study analyzed the genome sequences of Xylella fastidiosa and found evidence of specialization to specific plant hosts. It also identified genes that may play a role in the arms-race dynamics of the pathogen. These findings are significant for understanding the adaptability of Xylella fastidiosa to different host plants.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Environmental Studies
Francesco Bozzo, Michel Frem, Vincenzo Fucilli, Gianluigi Cardone, Paolo Francesco Garofoli, Stefania Geronimo, Alessandro Petrontino
Summary: This research explores the invasion drivers of Philaenus spumarius in the spread of Xylella fastidiosa in Southern Italy and identifies spatial variation and territorial differentiation in the invaded area. The findings have important implications for effective management and monitoring of the spread of Xf and can also be applied to other countries affected by Xf invasion.
Review
Biochemical Research Methods
Amy M. Campbell, Chris Hauton, Craig Baker-Austin, Ronny van Aerle, Jaime Martinez-Urtaza
Summary: This review proposes a framework that combines genomic evolutionary analysis with climate time-series data to understand past and future evolutionary pathogen responses to climate change. Recommendations are presented to increase the feasibility of interdisciplinary applications, including the importance of robust spatiotemporal metadata accompanying genome submission to databases. These workflows will inform accessible public health tools and early-warning systems to aid decision-making and mitigate future human health threats.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Review
Food Science & Technology
Anton E. Shikov, Iuliia A. Savina, Anton A. Nizhnikov, Kirill S. Antonets
Summary: Bacterial organisms have undergone homologous recombination and horizontal gene transfer multiple times, resulting in enhanced adaptation to new environments, specialization, the emergence of new species, and changes in virulence. Analysis of genomic studies of bacterial species in the past 30 years reveals that these genetic exchanges are associated with ecological diversification, pathogenesis, and symbiosis.
Article
Biology
Karan Pattni, Christopher E. Overton, Kieran J. Sharkey
Summary: A biologically motivated individual-based framework for evolution in network-structured populations is developed to accommodate eco-evolutionary dynamics. The framework is used to construct a network birth and death model, providing new insight into the spread of adaptive mutations in ecological dynamics.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Mathematics, Interdisciplinary Applications
Lixuan Cao, Bin Wu
Summary: This work focuses on a dynamic strategy updating model with payoff-dependent environmental feedback, identifying conditions for stable internal equilibria. Results indicate that sensitivity of environmental degradation rates to defector's payoffs promotes cooperation, while sensitivity of enhancement rates to cooperator's payoffs inhibits cooperation. The relative speed of environmental and strategy dynamics has a qualitative influence on the overall system dynamics.
CHAOS SOLITONS & FRACTALS
(2021)
Article
Plant Sciences
Aina Baro, Laura Montesinos, Esther Badosa, Emilio Montesinos
Summary: The aggressiveness of Spanish isolates of Xylella fastidiosa in almond plants of different cultivars was studied by examining population dynamics, colonization, spread, and dose-effect relationships. Results showed differences in population levels and spread intensity between strains and cultivars. The study highlights the importance of understanding pathogen dynamics and aggressiveness for the epidemiology of X. fastidiosa in almond crops.
Article
Mathematics, Interdisciplinary Applications
Chao Wang, Tian-jiao Feng, Yan Gao, Yi Tao, Cong Li
Summary: Based on Tilman et al.'s (2020) concept of eco-evolutionary game dynamics, this study investigates the dynamical stability and ecologically evolutionarily stable strategy (eco-ESS) of a simple eco-evolutionary game dynamics with density dependence. The main findings demonstrate that the condition of eco-ESS in our model is more restrictive compared to the condition of ESS in classic evolutionary game dynamics.
CHAOS SOLITONS & FRACTALS
(2023)
Article
Oncology
Alexandra Lahtinen, Kari Lavikka, Anni Virtanen, Yilin Li, Sanaz Jamalzadeh, Aikaterini Skorda, Anna Rossberg Lauridsen, Kaiyang Zhang, Giovanni Marchi, Veli-Matti Isoviita, Valeria Ariotta, Oskari Lehtonen, Taru A. Muranen, Kaisa Huhtinen, Olli Carpen, Sakari Hietanen, Wojciech Senkowski, Tuula Kallunki, Antti Hakkinen, Johanna Hynninen, Jaana Oikkonen, Sampsa Hautaniemi
Summary: Ovarian HGSC is often diagnosed at an advanced stage, with genetically diverse clones existing prior to treatment. This study analyzed whole-genome sequencing data from 510 samples of 148 HGSC patients, revealing three evolutionary states with distinct genomic features, pathways, and phenotypes, which showed significant association with treatment response. Pathway analysis suggested two potential evolutionary trajectories, and experiments with tumor organoids supported targeted therapy for tumors with enriched PI3K/AKT pathway. Heterogeneity analysis indicated more unique clones in samples from the site of origin compared to metastatic tumors or ascites. These findings highlight the importance of integrative tumor evolution analysis for identifying patient subtypes.
Article
Plant Sciences
Prabha Liyanapathiranage, Jeffrey B. Jones, Neha Potnis
Summary: This study reveals the significant role of the tssM gene of the T6SS-i3* in the initial asymptomatic colonization of Xanthomonas perforans. The presence of functional TssM contributes to higher aggressiveness and in planta growth of the pathogen, as well as increased epiphytic fitness and dissemination potential. Higher osmotolerance is one mechanism by which TssM enhances epiphytic fitness.
Article
Plant Sciences
Michael L. O'Leary, Luis F. Arias-Giraldo, Lindsey P. Burbank, Leonardo De la Fuente, Blanca B. Landa
Article
Plant Sciences
Marcus Merfa, Eber Naranjo, Deepak Shantharaj, Leonardo De la Fuente
Summary: This study optimized the growth of 'Candidatus Liberibacter asiaticus' (CLas) by amending grapefruit juice with various compounds and culturing under different conditions. The growth of CLas was inversely proportional to the initial inoculum concentration and regulated by cell density-dependent mechanisms. Although sustained exponential growth was not observed, strategies to reduce cell density allowed the bacterium to reach maximum growth within a short time. Additionally, an ex vivo system was established for culturing CLas.
Article
Plant Sciences
Nay C. Dia, Lucas Moriniere, Bart Cottyn, Eduardo Bernal, Jonathan M. Jacobs, Ralf Koebnik, Ebrahim Osdaghi, Neha Potnis, Joel F. Pothier
Summary: The passage provides information about the taxonomy, host range, epidemiology, and control measures of Xanthomonas hortorum.
MOLECULAR PLANT PATHOLOGY
(2022)
Article
Plant Sciences
Qing Ge, Xinyu Zhu, Paul A. Cobine, Leonardo de la Fuente
Summary: This study reveals the functional role of the cutC gene in copper homeostasis in the xylem-limited plant pathogenic bacterium X. fastidiosa. Deletion of the cutC gene increased sensitivity to copper shock, while introducing copper exaggerated disease severity in infected plants. Understanding the mechanisms of copper homeostasis in bacterial pathogens is crucial for further research.
Article
Plant Sciences
Sadegh Zarei, S. Mohsen Taghavi, Touraj Rahimi, Hamzeh Mafakheri, Neha Potnis, Ralf Koebnik, Marion Fischer-Le Saux, Joel F. Pothier, Ana Palacio Bielsa, Jaime Cubero, Perrine Portier, Marie-Agnes Jacques, Ebrahim Osdaghi
Summary: A recent study evaluated the taxonomic status of Xanthomonas arboricola, a group of fruit tree pathogens. The study used DNA similarity indexes and core genome-based phylogeny to determine the members of the species. The results revealed that two pathovars should be elevated to the rank of a new species. Additionally, other mislabeled strains belong to previously described species or represent novel species awaiting formal description.
Review
Plant Sciences
Leonardo De La Fuente, Marcus Merfa, Paul A. Cobine, Jeffrey J. Coleman
Summary: Aggressive pathogens have evolved to colonize the xylem of plants, and once established, they modulate the xylem environment to enhance their growth and virulence. The adaptation to xylem lifestyle leads to genome reduction, but the basis of this adaptation is still not completely understood.
ANNUAL REVIEW OF PHYTOPATHOLOGY
(2022)
Article
Plant Sciences
Eric A. Newberry, Gerald V. Minsavage, Auston Holland, Jeffrey B. Jones, Neha Potnis
Summary: Xanthomonas perforans and X. euvesicatoria are the causal agents of bacterial spot disease of tomato and pepper, respectively. Recent studies have revealed variability within these bacterial species in causing disease in pepper, even without avirulence gene activity. Through genome-wide association analyses, two novel gene candidates associated with pepper-pathogenic X. perforans and X. euvesicatoria were identified. Functional analysis showed that one candidate had a minor effect on symptom development and growth, suggesting that pathogenicity to pepper may have evolved independently within the bacterial species.
Article
Plant Sciences
Deepak Shantharaj, Eber Naranjo, Marcus V. Merfa, Paul A. Cobine, Swadeshmukul Santra, Leonardo de la Fuente
Summary: This study evaluates the efficacy of a novel ZnO-based nanoparticle formulation, Zinkicide TMN110 (ZnK), against the xylem-limited pathogen Xylella fastidiosa. The results show that ZnK has strong antibacterial activity against X. fastidiosa, significantly reducing the population of the pathogen and reducing disease severity under controlled conditions.
Article
Biotechnology & Applied Microbiology
T. Jeffrey Cole, Jennifer K. Parker, Aaron L. Feller, Claus O. Wilke, Bryan W. Davies
Summary: Class II microcins are small bacteriocins produced by Gram-negative bacteria in the Enterobacteriaceae, playing a role in interbacterial competition. Despite limited direct evidence, they show a diverse array of molecular functionalities and target specificities, suggesting untapped potential for discovering peptide antibiotics.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Plant Sciences
Maria Pilar Velasco-Amo, Luis F. Arias-Giraldo, Miguel Roman-ecija, Leonardo De La Fuente, Ester Marco-Noales, Eduardo Moralejo, Juan A. Navas-Cortes, Blanca B. Landa
Summary: Xylella fastidiosa is a pathogenic bacterium causing epidemics and economic losses in olive and almonds in Europe. Complete genomes of X. fastidiosa strains were assembled using Oxford Nanopore Technologies and Illumina sequencing, revealing differences in plasmid content among strains. The genome resources will aid in studying the role of plasmids in the epidemiology, ecology, and evolution of this plant pathogen.
Article
Plant Sciences
M. Roman-ecija, J. A. Navas-Cortes, M. P. Velasco-Amo, L. F. Arias-Giraldo, L. M. Gomez, L. De La Fuente, B. B. Landa
Summary: This passage discusses the differences in phenotype and genome between two subspecies of Xylella fastidiosa from Spain, one of which possesses two plasmids. Experimental results show that both Spanish strains have weaker biofilm formation, cell aggregation, and virulence on tobacco compared to the US reference strains. Genome analysis also reveals unique coding sequences and potential deleterious mutations in each strain. The presence of plasmids should be taken into account in studying the pathogenicity and adaptation mechanisms of X. fastidiosa.
Article
Microbiology
Marcus A. Merfa, Xinyu Zhu, Deepak Shantharaj, Laura Gomez, Eber Naranjo, Neha Potnis, Paul Cobine, Leonardo De La Fuente
Summary: By mutating genes and analyzing their functions, this study investigated the role of 38 genes involved in TFP biosynthesis and regulation in Xylella fastidiosa. The results showed that 10 genes were essential for both bacterial motility and natural competence. Additionally, novel functions of key genes were discovered. Overall, this study provides insights into the complex regulation of TFP in X. fastidiosa and serves as a blueprint for understanding TFP in other bacteria living under flow conditions.
Article
Ecology
Rishi Bhandari, Alvaro Sanz-Saez, Courtney P. Leisner, Neha Potnis
Summary: Though much research has been carried out on the response of plants to biotic and abiotic stresses, little is known about the resilience of associated microbiomes and their contribution to stress tolerance or response. This study evaluated the impact of elevated tropospheric ozone (O-3) and Xanthomonas perforans infection on resistant and susceptible pepper cultivars, and found that while the infection resulted in distinct microbial community structure and functions on the susceptible cultivar, concurrent O-3 stress did not further alter the community structure and function. However, O-3 stress did exacerbate the disease severity on the resistant cultivar. The altered microbial co-occurrence network under simultaneous O-3 stress and pathogen challenge may explain the increased disease severity.
ISME COMMUNICATIONS
(2023)
Article
Microbiology
Margaret D. Weinroth, Kevin M. Thomas, Enrique Doster, Amit Vikram, John W. Schmidt, Terrance M. Arthur, Tommy L. Wheeler, Jennifer K. Parker, Ayanna S. Hanes, Najla Alekoza, Cory Wolfe, Jessica L. Metcalf, Paul S. Morley, Keith E. Belk
Summary: This study characterizes and compares the resistomes and microbiomes of beef, dairy, and organic dairy market cows. Results show that production systems and harvest facilities can impact the associated microbiomes and resistomes.
