Biology subjects

Pedron, J.

Publications and source records attributed to Pedron, J..

7 recordsLinked to original sources

bioRxiv2026

The influence of nutrient enrichment and fish addition on microbial communities in water and fish guts during mesocosm experiments conducted in a tropical freshwater lagoon (Lagoon Aghien, Cote dIvoire)

Freshwater ecosystems in the intertropical zone have received considerably less scientific attention than those in temperate regions, with the notable exception of a few large and iconic lakes, such as Lake Victoria. Consequently, the diversity, functioning, and pollution sensitivity of microbial communities in these systems remain poorly understood. To investigate the short-term responses of microbial communities to nutrient enrichment and fish addition, we conducted in situ mesocosm experiments at two stations in a freshwater lagoon near Abidjan (Cote dIvoire). Phosphorus enrichment, either alone or in combination with nitrogen, led to a consistent increase in bacterial abundance across mesocosms, suggesting a potential phosphorus limitation of bacterial growth by these nutrients and consequently a potential competition for this resource between bacteria and microphytoplankton. In contrast, picophytoplankton abundances showed no clear or consistent response to nutrient enrichment, suggesting that other ecological processes may play a more important role in regulating these communities. High-throughput Illumina sequencing revealed contrasting patterns in the relative abundance of cyanobacterial and chloroplast-associated reads, depending on both nutrient enrichment and fish addition. These results, consistent with those obtained by cell counting in a previous study, suggest a potential top-down control of cyanobacteria by fish in Lagoon Aghien. In addition, nutrient (phosphorus and nitrogen combined) enrichment and fish addition significantly affected the amplicon sequence variant (ASV) composition of bacterial communities. Overall, these findings provide new insights into the drivers shaping microbial community structure in tropical freshwater ecosystems and are discussed in the context of previously published data on phytoplankton dynamics from the same experimental system.

ecology↗

bioRxiv2025

Comparative essentialome analysis of six Pectobacteriaceae strains using the TNSEEK pipeline identifies conserved and strain-specific fitness determinants

Transposon sequencing (Tn-seq) is a powerful technique for defining the essential genes required for bacterial survival. However, gene essentiality can vary significantly across taxonomic levels, and comparing large Tn-seq datasets from multiple strains presents considerable analytical challenges. To address this, we developed TNSEEK, a fully automated bioinformatics pipeline for the systematic and comparative analysis of transposon sequencing experiments. We applied TNSEEK to analyze six Soft Rot Pectobacteriaceae (SRP) strains, encompassing species from the Dickeya and Pectobacterium genera, grown in a rich medium. This approach identified a core essentialome of 225 genes, primarily involved in fundamental cellular maintenance, conserved across all six strains, a set comparable in size to that of the broader Enterobacteriaceae family. Only a few genus-specific essential genes were found highlighting interesting distinct metabolic capabilities between Dickeya and Pectobacterium genera. In striking contrast, we discovered a large variable essentialome comprising 181 strain-specific genes, many of which of unknown function. A portion of these strain-specific essential genes are components of defense systems and prophage genomic regions. The unexpected essentiality of these modules suggests they form a constitutively active frontline defense. Furthermore, a comparison with the E. coli essentialome demonstrates that discrepancies in gene essentiality can often be attributed to differences in growth conditions, particularly temperature, as well as variations in genetic redundancy. In conclusion, the TNSEEK pipeline is a robust tool for exploring functional genomics across multiple strains. IMPORTANCEDickeya and Pectobacterium are two genera of the Pectobacteriaceae family that contain mainly plant pathogenic bacteria. To analyze the diversity within bacteria of this family, we performed a Tn-seq analysis on six strains representing a range of ecological niches. To this aim we developed a bioinformatics pipeline, termed TNSEEK which allows the comparative analysis of results across diverse experimental conditions and multiple strains. Applied to growth in rich medium of the tested strains, it allowed the identification of an essentialome of 225 genes at the family level, few genus-specific essential genes but a large essentialome comprising 181 strain-specific genes, many of which of unknown function. Thus, TNSEEK proved its ability to analyze a large data set coming from different Tn-seq experiments and it offers an unparalleled flexibility in handling any number of strains and experiments.

genomics↗

bioRxiv2025

Pectobacterium versatile beta-lactamase, a common good of the soft rot Pectobacteriaceae (SRP) species complex

Little is known about the role of antibiotics and associated resistance in microbial ecosystems in the absence of clinical antibiotic pressure. The Soft Rot Pectobacteriaceae (SRP) species complex, which comprises 37 bacterial species that are collectively responsible for the severe rotting of many crops, is an interesting model to analyse the role of {beta}-lactam and {beta}-lactamases in natural ecosystems. In particular, within this complex, most Pectobacterium versatile strains harbour a {beta}-lactamase called BlaPEC-1. The aim of our work was to analyse the role of BlaPEC-1 during infection. To this end, two blaPEC-1-deleted strains were constructed and compared with their wild-type counterparts in vitro and in potato tuber infections. In vitro, the BlaPEC-1 {beta}-lactamase enables P. versatile to resist ampicillin or carbapenem produced by Pectobacterium brasiliense. In mono-infections on potato tubers, blaPEC-1-deleted strains were unaffected in terms of virulence, fitness or association with commensal bacteria. In mixed infections, the BlaPEC-1 {beta}-lactamase proved necessary for the coexistence of P. versatile with the carbapenem-producing strain, and also for the protection of carbapenem-sensitive strains both in vitro and in planta. Interestingly, in planta protection was observed even if the blaPEC-1 gene was repressed and bacteria expressing BlaPEC-1 were in the minority within the symptom. These results indicate that BlaPEC-1 exerts a true {beta}-lactamase function during the infection process and acts as a public good of the SRP species complex. Finally, our results highlight the important role of {beta}-lactamase in maintaining of strains diversity in natural ecosystem. Statements relating to our ethics and integrity policiesThe data shown in this paper are available within the article and supplementary materials. The funding of the ANR, ANR-19-CE35-0016-03, is acknowledged. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication. The authors declare that there are no conflicts of interest. All applicable local, national and international regulations and conventions, as well as normal scientific ethical practices, were followed in the preparation of this work. This manuscript has not been previously or simultaneously published or submitted elsewhere and was critically reviewed and approved by all co-authors before submission. The CRediT of all authors is provided.

microbiology↗

bioRxiv2024

Tailocin-mediated interactions in Soft Rot Pectobacteriaceae

Bacteria carry phage-derived elements within their genomes, some of which can produce phage-like particles (tailocins) used as weapons to kill kin strains in response to environmental conditions. This study investigates the production and activity of tailocins by plant pathogenic bacteria: Pectobacterium, Dickeya, and Musicola genera, which compete for niche, providing an attractive model to study the ecological role of tailocins. Microscopy revealed that most analyzed strains (88%) produced tailocins. Tailocin-mediated killing interactions were assessed across 351 strain pairs, showing that Dickeya spp. had a higher likelihood of killing neighbors (57.1%) than Pectobacterium spp. (21.6%). Additionally, Dickeya spp. strains exhibited broader phylogenetic killing, targeting both Pectobacterium spp. and Musicola sp., while Pectobacterium spp. tailocins were genus-specific. Mutual killing was observed in 33.9% of interactions, predominantly within Dickeya spp. Although tailocins were morphologically indistinguishable between producers, genomic analyses identified conserved clusters having distinct differences between Pectobacterium spp. and Dickeya spp tailocins. This suggests different origins of these particles. Induction experiments demonstrated that tailocin production was boosted by hydrogen peroxide, supporting the role of these particles in bacteria-bacteria competition during infection. Tailocins were detectable in infected potato tissue but not in river water, highlighting the particular ecological relevance of tailocins in plant environments.

microbiology↗

bioRxiv2023

Bacterial pathogens dynamic during multi-species infections

Soft rot Pectobacteriacea (SRP) gathers more than 30 bacterial species that collectively rot a wide range of plants by producing and secreting a large set of plant cell wall degrading enzymes (PCWDEs). Worldwide potato field surveys identified 15 different SRP species on symptomatic plants and tubers. The abundance of each species observed during outbreaks varies over space and time and the mechanisms driving species shift during outbreak are unknown. Furthermore, multi-species infections are frequently observed and the dynamics of these coinfections are not well understood. To understand the dynamics of coinfections, we set up 16 different synthetic communities of 6 SRP strains to mimic coinfections. The bacteria present in each tested community were representative of 2 different species, with 3 strains per species. These communities were inoculated in potato tubers or on synthetic media and their outcome was followed by amplification and Illumina sequencing of the discriminatory housekeeping gene gapA. We also compared disease incidence and bacterial multiplication in potato tubers during mixed-species infection and single-species infection. A species that was unable to induce disease in potato was efficiently maintained and eventually became dominant in some of the communities tested, indicating that cheating can shape dominant species. Modeling indicates that the cost of PCWDEs production and secretion, the rate of potato degradation and the diffusion rate of degraded substrate could favor the cheater species. Interaction outcomes differed between potato tuber and synthetic medium, highlighting the driving effect of environmental conditions, with higher antagonistic interactions observed in potato tubers. Antagonistic interactions were strain specific and not species specific. Toxicity interference was also observed within some communities, allowing the maintenance of strains otherwise sensitive to toxic compounds. Overall, the results indicate that intraspecific competition, cooperation through trophic interaction and toxicity interference contribute to the maintenance of SRP diversity. The implications of these processes for epidemiological surveillance are discussed.

microbiology↗

bioRxiv2021

The epigenetic eraser LSD1 lies at the apex of a reversible erythroid to myeloid cell fate decision

H3K4Me demethylase KDM1a/LSD1 is a therapeutic target for multiple diseases, including the {beta}-globinopathies (sickle cell disease and {beta}-thalassemia) since its inactivation has been shown to lead to robust induction of the fetal globin genes. Here we examined the consequences of conditional inactivation of Lsd1 in adult red blood cells using a new Gata1creERT2 BAC transgene. Loss of Lsd1 activity in mice blocked erythroid differentiation and expanded GMP-like cells, converting hematopoietic differentiation potential from an erythroid to a myeloid fate. The analogous phenotype was also observed in human HSPC, coincident with induction of myeloid transcription factors (e.g. PU.1 and CEBP). Finally, blocking the activity of myeloid transcription factors PU.1 or RUNX1 at the same time as LSD1 reverted myeloid lineage conversion to an erythroid phenotype. The data show that LSD1 promotes erythropoiesis by repressing myeloid cell fate, and that inhibition of myeloid differentiation reverses the lineage switch caused by LSD1 inactivation.

developmental biology↗

bioRxiv2018

Characterization of the early response of Arabidopsis thaliana to Dickeya dadantii infection using expression profiling

To draw a global view of plant responses to interactions with the phytopathogenic enterobacterale Dickeya dadantii, a causal agent of soft rot diseases on many plant species, we analysed the early Arabidopsis responses to D. dadantii infection. We performed a genome-wide analysis of the Arabidopsis thaliana transcriptome during D. dadantii infection and conducted a genetic study of identified responses.\n\nA limited set of genes related to plant defence or interactions with the environment were induced at an early stage of infection, with an over-representation of genes involved in both the metabolism of indole glucosinolates (IGs) and the jasmonate (JA) defence pathway. Bacterial type I and type II secretion systems are required to trigger the induction of IG and JA-related genes while the type III secretion system appears to partially inhibit these defence pathways. Using Arabidopsis mutants impaired in JA biosynthesis or perception, we showed that induction of some IG metabolism genes was COI1-dependent but, surprisingly, JA-independent. Moreover, characterisation of D. dadantii disease progression in Arabidopsis mutants impaired in JA or IG pathways showed that JA triggers an efficient plant defence response that does not involve IGs.\n\nThe induction of the IG pathway by bacterial pathogens has been reported several times in vitro. This study shows for the first time, that this induction does indeed occur in planta, but also that this line of defence is ineffective against D. dadantii infection, in contrast to its role to counteract herbivorous or fungal pathogen attacks.

plant biology↗