Biology subjects

Morris, C. E.

Publications and source records attributed to Morris, C. E..

9 recordsLinked to original sources

bioRxiv2025

Ecological ubiquity and phylogeny drive nestedness in phages-bacteria networks and shape the bacterial defensome

Identifying the ecological and evolutionary factors that shape phage-bacterial interactions is key to understanding their dynamics in microbial communities. Yet, such interactions remain poorly characterised in plant agroecosystems. Here, we investigate the ecological determinants of the interaction between a highly diverse set of 23 phages isolated from diseased apricot trees and 44 bacterial strains from the Pseudomonas syringae species complex collected either from diseased apricot trees, healthy plants or non-agricultural environment. Based on their ecological origin, we expected phages to preferentially infect bacterial strains from the same ecological context, forming modular host-range patterns. Contrary to these expectations, we discovered a significantly nested structure, suggesting generalised infection dynamics rather than local adaptation, primarily driven by the broad ecological dynamics of this pathosystem. Analysis of the bacterial genomes showed that both the profiles of anti-phage defence systems and the distribution profiles of prophages are strongly shaped by bacterial phylogeny. Furthermore, while the number of defence systems showed limited correlation with the breadth of bacterial sensitivity to phages, prophage abundance exhibited a strong, non-linear link with phage virulence. Together, these findings provide an ecological and evolutionary perspective on phage-bacterium infection networks and new insights into a better understanding of the role of phages in agricultural ecosystems. Author SummaryViruses that infect bacteria, known as phages, are part of microbial communities and influence the abundance, diversity, and traits of their hosts. In an agriculture-related context, they are commonly considered as potential biocontrol agents, but studying the bases of fundamental phage-bacterial interactions may help us better understand the plant microbiome and its applications. Many factors influence these interactions, and identifying which ones matter most remains a challenge. In our study, we investigated how phages from diseased plants interact with bacteria collected from diseased and healthy plants, as well as from surrounding environments. We expected phages to mainly infect bacteria from similar environments, but instead observed that they often infected bacteria regardless of their source. This suggests that phage activity in this system has few barriers, reflecting the wide ecological distribution of their bacterial hosts. We further investigated how bacteria defend against phages by identifying both defence systems and prophages within their genomes and using this information to explore their contribution to bacterial resistance or sensitivity to phages. Together, our findings offer new insights into how phage-bacterium relationships evolve and function in plant ecosystems.

ecology↗

bioRxiv2024

Some like it hot: efficiency of the Type 3 Secretion System and activation of plant defenses have multiple thermosensitive behaviors in the Pseudomonas syringae complex

The Pseudomonas syringae complex is an important group of ubiquitous bacteria containing plant pathogenic strains of which many cause damage and economic losses to a wide range of crops. Efforts to elucidate the determinants of host range have focused on the repertoires of effectors in the Type 3 Secretion System (T3SS). However, recently, we showed that the inability of a P. syringae pv. actinidiae strain to trigger an hypersensitive response (HR) in A. thaliana is due to an inefficient T3SS and not to the absence of a recognized effector. In this context, we compared the efficiency of the T3SS of several P. syringae strains belonging to different phylogroups. Through statistical analysis, we assessed the temporal dynamics of the induction of ion leakage, an HR indicator, in A. thaliana. We revealed that PtoDC3000 avrB and PmaM6 avrB consistently triggered a strong HR while other strains induced it at significantly different intensities depending on temperature. Among thermosensitive strains, both low and warm temperature-dependencies for T3SS efficiency were observed, irrespective of the in-vitro growth optimum of the strains. Surprisingly, differences were also observed among quasi-clonal strains. These results reveal a strong, strain-specific regulatory role of temperature in effector injection and reinforce the importance of environmental factors in the outcome of plant-bacteria interactions. Moreover, this work highlights the need to study bacterial virulence for a broader set of strains beyond model strains, such as PtoDC3000, that are not representative of the whole P. syringae complex.

microbiology↗

bioRxiv2024

Novel phages of Pseudomonas syringae unveil numerous potential auxiliary metabolic genes

Relatively few phages that infect plant pathogens have been isolated and investigated. The Pseudomonas syringae species complex is present in various environments, including plants. It can cause major crop diseases, such as bacterial canker on apricot trees. This study presents a collection of 25 unique phages genomes that infect P. syringae. These phages were isolated from apricot orchards with bacterial canker symptoms after enrichment with 21 strains of P. syringae. This collection comprises mostly virulent phages, with only three being temperate. They belong to 14 genera, 11 of which are newly discovered, and 18 new species, revealing great genetic diversity within this collection. Novel DNA packaging systems have been identified bioinformatically in one of the new phage species, but experimental confirmation is required to define the precise mechanism. Additionally, many phage genomes contain numerous potential auxiliary metabolic genes with diversified putative functions. At least three phages encode genes involved in bacterial tellurite resistance, a toxic metalloid. This suggests that viruses could play a role in bacterial stress tolerance. This research emphasises the significance of continuing the search for new phages in the agricultural ecosystem to unravel novel ecological diversity and new gene functions. This work contributes to the foundation for future fundamental and applied research on phages infecting phytopathogenic bacteria.

microbiology↗

bioRxiv2023

From lichens to crops: Pathogenic potential of Pseudomonas syringae from Peltigera lichens is similar to world-wide epidemic strains

The presence of bacteria belonging to the Pseudomonas syringae complex (P. syringae) in the natural vegetation of several Icelandic habitat types has been recently reported, raising questions about the risk to Icelandic crops, particularly given the expected increase in agricultural activity due to climate warming. This study takes advantage of Icelands unique characteristics and the discovery of P. syringae in Peltigera lichens to gain a better understanding of the potential risk posed by this newly discovered ecological niche. The main objective is to evaluate the pathogenic potential and fitness in crops of P. syringae strains isolated from Peltigera lichen sampled in Iceland, focusing on strains that belong to phylogroups 1 and 2, which commonly contain epidemic strains. The results indicate that P. syringae isolated from Icelandic Peltigera lichen have a comparable fitness to epidemic strains in eight out of ten tested plant species. Furthermore, pathogenicity assessment on three plant species highlighted that certain strains also caused similar symptoms and disease severity compared to epidemic strains. These findings provide valuable insights into the potential risks posed by P. syringae from Icelandic natural habitats and illustrate how strains from these habitats have a wide pathogenic potential to crops without having encountered these crops in the last several thousand years of their presence in Iceland.

microbiology↗

bioRxiv2022

Comparative seasonal abundance and diversity of populations of the Pseudomonas syringae and Soft Rot Pectobacteriaceae species complexes throughout the Durance River catchment from its French Alps sources to its delta

Rivers, creeks, streams are integrators of biological, chemical and physical processes occurring in a catchment linking land cover from the headwaters to the outlet. The dynamics of human and animal pathogens in catchments have been widely studied in a large variety of contexts allowing the optimization of disease risk reduction. In parallel, there is an emerging awareness that crop pathogens might also be disseminated via surface waters especially when they are used for irrigation. However, there are no studies on the extent to which potential plant pathogens are present - nor about their dynamics - along the full course of a catchment. Here we have compared the seasonal dynamics of populations of the Pseudomonas syringae (Psy) and the Soft Rot Pectobacteriaceae (SRP) species complexes along a 270 km stretch of the Durance River from the upstream alpine reaches to the downstream agricultural production areas at the confluence with the Rhone River at Avignon. Among 168 samples collected at 21 sites in fall, winter, spring and summer of 2016 and 2017, Psy strains were detected at all sampling sites and in 156 of the samples at population densities up to 105 bacteria L-1. In contrast, SRP strains were detected in 98 of the samples, mostly from the southern part of the river, at population densities that did not exceed 3 x 104 bacteria L-1. Among the biological and chemical parameters that were characterized at each sampling site, temperature was the only factor that explained a significant amount of the variability in population size for both species complexes. Psy densities decreased with increasing temperature whereas SRP densities increased with increasing temperature. River-borne populations of SRP were composed mainly of Pectobacterium versatile and P. aquaticum that have little known epidemiological importance. Only a few strains of Pectobacterium and Dickeya species reputed for their epidemiological impact were observed. In contrast, Psy populations at all sites were dominated by a genetic lineage of phylogroup 2 known from other studies for its broad host range and its geographic and habitat ubiquity. Our observations suggest that surveillance of river water for SRP could be leveraged to signal diagnostic and management reactions to avoid disease outbreaks. In contrast, the constant presence of Psy throughout the catchment in absence of regular and widespread disease outbreaks due to this group of bacteria suggests that surveillance should focus on future changes in land use, river water conditions and agronomic practices that could destabilize the mechanisms currently holding Psy outbreaks in check.

ecology↗

bioRxiv2021

The quasi-universality of nestedness in the structure of quantitative plant-parasite interactions

AO_SCPLOWBSTRACTC_SCPLOWUnderstanding the relationships between host range and pathogenicity for parasites, and between the efficiency and scope of immunity for hosts are essential to implement efficient disease control strategies. In the case of plant parasites, most studies have focused on describing qualitative interactions and a variety of genetic and evolutionary models has been proposed in this context. Although plant quantitative resistance benefits from advantages in terms of durability, we presently lack models that account for quantitative interactions between plants and their parasites and the evolution of these interactions. Nestedness and modularity are important features to unravel the overall structure of host-parasite interaction matrices. Here, we analysed these two features on 32 matrices of quantitative pathogenicity trait data gathered from 15 plant-parasite pathosystems consisting of either annual or perennial plants along with fungi or oomycetes, bacteria, nematodes, insects and viruses. The performance of several nestedness and modularity algorithms was evaluated through a simulation approach, which helped interpretation of the results. We observed significant modularity in only six of the 32 matrices, with two or three modules detected. For three of these matrices, modules could be related to resistance quantitative trait loci present in the host. In contrast, we found high and significant nestedness in 30 of the 32 matrices. Nestedness was linked to other properties of plant-parasite interactions. First, pathogenicity trait values were explained in majority by a parasite strain effect and a plant accession effect, with no or minor parasite-plant interaction term. Second, correlations between the efficiency and scope of the resistance of plant genotypes, and between the host range breadth and pathogenicity level of parasite strains were overall positive. This latter result questions the efficiency of strategies based on the deployment of several genetically-differentiated cultivars of a given crop species in the case of quantitative plant immunity.

pathology↗

bioRxiv2020

The Pump-Leak/Donnan ion homeostasis strategies of skeletal muscle fibers and neurons

Skeletal muscle fibers (SMFs) and neurons are low and high duty-cycle excitable cells constituting exceptionally large and extraordinarily small fractions of vertebrate bodies. The immense ClC-1-based chloride-permeability (PCl) of SMFs has thwarted understanding of their Pump-Leak/Donnan (P-L/D) ion homeostasis. After formally defining P-L/D set-points and feedbacks, we therefore devise a simple yet demonstrably realistic model for SMFs. Hyper-stimulated, it approximates rodent fibers ouabain-sensitive ATP-consumption. Size-matched neuron-model/SMF-model comparisons reveal steady-states occupying two ends of an energetics/resilience P-L/D continuum. Excitable neurons costly vulnerable process is Pump-Leak dominated. Electrically-reluctant SMFs robust low-cost process is Donnan dominated: collaboratively, Donnan effectors and [big PCl] stabilize Vrest, while SMFs exquisitely small PNa minimizes ATP-consumption, thus maximizing resilience. "Classic" excitable cell homeostasis ([small PCl][big INaleak]), de rigueur for electrically-agile neurons, is untenable for vertebrates (including humans) major tissue. Vertebrate bodies evolved thanks to syncytially-efficient SMFs using a Donnan dominated ([big PCl][small INaleak]) ion homeostatic strategy.

neuroscience↗

bioRxiv2020

Donnan dominated ion homeostasis and the longevity of ischemic Na+-loaded dystrophic skeletal muscle

The inherited muscle-wasting disease, Duchenne muscular dystrophy (DMD), renders skeletal muscle fibers (SMFs) Na+-overloaded, ischemic, membrane-damaged, cation-leaky, depolarized, and prone to myogenic firing. DMD fibers nevertheless survive up to 3 decades before succumbing to Ca2+-necrosis. The Ca2+-necrosis is explicable, the longevity is not. Modeling here shows that SMFs ion homeostasis strategy, a low-cost resilient Pump-Leak/Donnan feedback process we term "Donnan dominated", underpins that longevity. Together, SMFs huge chloride-permeability and tiny sodium-permeability minimize excitability and pump costs, facilitating the outsized SMF pump-reserve that lets DMD fibers withstand deep ischemia and leaky channels. We illustrate how, as these impairments intensify, patients chronic Na+-overload (now non-invasively evident via Na23-MRI) would change. In simulations, prolonged excitation ([->]physiological Na+-overloading) and/or intense ischemia ([->]too little Na+-pumping) and accumulated bleb-damage ([->]too much Na+-leaking) eventually trigger Ca2+-overloading conditions. Our analysis implies an urgent need to identify SMFs pivotal small PNa, thereby opening new therapeutic remediation routes.

neuroscience↗

bioRxiv2020

Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste

Three phages targeting Pseudomonas syringae GAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to the Autographivirinae subfamily of the family Podoviridae. The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera within Autographivirinae, suggesting that the newly isolated phages could represent a new genus.

microbiology↗