Biology subjects

Chiroleu, F.

Publications and source records attributed to Chiroleu, F..

4 recordsLinked to original sources

bioRxiv2026

Distribution of antibiotic resistance genes across contrasted tropical agroecosystems in Reunion Island

This study presents the first exploratory assessment of antibiotic resistance genes (ARGs) and antibiotic residues in agricultural environments on Reunion Island, a French tropical territory in the south-western Indian Ocean. Sixteen samples from diverse matrices (manure, soil, water, and vegetables) across different agroecosystems were analyzed using high-throughput qPCR targeting 332 ARGs and chemical methods targeting 58 antibiotic compounds and trace elements. ARGs were widely detected across all matrices, with highest abundance observed in amended soils and manure. Surprisingly, ARG profiles, in terms of both abundance and average number, were comparable between unamended soils and natural soils. Antibiotic residues were found in only five manure and soil samples, with no clear correlation between the presence of these residues, trace elements and ARG abundance. Organic amendments significantly increased ARG levels in soils and non-metric multidimensional scaling revealed that ARG profiles clustered primarily by matrix type rather than by location. High-risk ARGs were widely prevalent, with 86% detected and 23% ubiquitous across all samples, and their occurrence in water and raw vegetables suggests potential human exposure through the food chain. This study highlights the influence of agricultural practices on environmental antimicrobial resistance in tropical island contexts and supports the need for expanded One Health surveillance integrating the environmental, animal and human compartments. SynopsisThis study shows that agricultural practices can shape the environmental spread of antibiotic resistance in tropical island ecosystems, highlighting potential risks for ecosystems, food safety, and human health. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/702181v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1d07b87org.highwire.dtl.DTLVardef@5e1150org.highwire.dtl.DTLVardef@1c2afe4org.highwire.dtl.DTLVardef@a9be55_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Herbarium Specimen Sequencing Allows Precise Datation of Xanthomonas citri pv. citri Diversification History

Over the past decade, the field of ancient genomics has triggered considerable progress in the study of various pathogens, including those affecting crops. In this context, herbarium collections have been an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography may shed light into the emergence and evolutionary history of plant pathogens. In this study, we reconstructed 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected citrus herbarium specimens using a shotgun-based deep sequencing strategy. Following authentication of the historical genomes based on ancient DNA damage patterns, we compared them to a large set of modern genomes to reconstruct their phylogenetic relationships, pathogeny-associated genes content and estimate several evolutionary parameters, using Bayesian tip-dating calibration and phylogeography inferences. Our results reveal that Xci originated in Southern Asia ~11,500 years ago and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world. This updated scenario links Xci specialization to Neolithic climatic change and the development of agriculture, and its diversification to the human-driven expansion of citriculture through the early East-West trade and later colonization. The analysis of data obtained from such historical specimens is challenging and must undergo adapted treatment before being compared to modern samples. Nevertheless, we confirm here that herbarium collections are a precious tool to improve the knowledge of the evolutionary history of plant pathogens.

evolutionary biology↗

bioRxiv2020

Joint species distributions reveal the combined effects of host plants, abiotic factors and species competition as drivers of community structure in fruit flies

AO_SCPLOWBSTRACTC_SCPLOWThe relative importance of ecological factors and species interactions for phytophagous insect species distributions has long been a controversial issue. Using field abundances of eight sympatric Tephritid fruit flies on 21 host plants, we inferred flies realized niches using joint species distribution modelling and network inference, on the community as a whole and separately on three groups of host plants. These inferences were then confronted to flies fundamental niches estimated through laboratory-measured fitnesses on host plants. Species abundances were mainly determined by host plants followed by climatic factors, with a minor role for competition between species sharing host plants. The relative importance of these factors mildly changed when we focused on particular host plant groups. Despite overlapping fundamental niches, specialists and generalists had almost distinct realized niches, with possible competitive exclusion of generalists by specialists on Cucurbitaceae, and different assembly rules: specialists were mainly influenced by their adaptation to host plants while generalist abundances varied regardless of their fundamental host use.

ecology↗

bioRxiv2020

Phylostems: a new graphical tool to investigate temporal signal of heterochronous sequences at various evolutionary scales

O_LIMolecular tip-dating of phylogenetic trees is a growing discipline that uses DNA sequences sampled at different points in time to co-estimate the timing of evolutionary events with rates of molecular evolution. Such inferences should only be performed when there is sufficient temporal signal within the analysed dataset. Hence, it is important for researchers to be able to test their dataset for the amount and consistency of temporal signal prior to any tip-dating inference. For this purpose, the most popular method considered to-date has been the "root-to-tip regression" which consist in fitting a linear regression of the number of substitutions accumulated from the root to the tips of a phylogenetic tree as a function of sampling times. The main limitation of the regression method, in its current implementation, relies in the fact that the temporal signal can only be tested at the whole-tree evolutionary scale. C_LIO_LITo fill this methodological gap, we introduce phylostems, a new graphical and user-friendly tool developed to investigate temporal signal at every evolutionary scale of a phylogenetic tree. C_LIO_LIPhylostems allows detecting without a priori whether any subset of a tree would contain sufficient temporal signal for tip-based inference to be performed. We provide a "how to" guide by running phylostems on empirical datasets and supply guidance for results interpretation. Phylostems is freely available at https://pvbmt-apps.cirad.fr/apps/phylostems. C_LIO_LIConsidering the impressive increase in availability and use of heterochronous datasets, we hope the new functionality provided by phylostems will help biologists to perform thorough tip-dating inferences. C_LI

evolutionary biology↗