Biology subjects

Bruneaux, M.

Publications and source records attributed to Bruneaux, M..

4 recordsLinked to original sources

bioRxiv2021

isotracer: An R package for the analysis of tracer addition experiments

O_LITracer addition experiments, particularly using isotopic tracers, are becoming increasingly important in a variety of studies aiming at characterizing the flows of molecules or nutrients at different levels of biological organization, from the cellular and tissue levels, to the organismal and ecosystem levels. C_LIO_LIWe present an approach based on Hidden Markov Models (HMM) to estimate nutrient flow parameters across a network, and its implementation in the R package isotracer. C_LIO_LIThe isotracer package is capable of handling a variety of tracer study designs, including continuous tracer drips, pulse experiments, and pulse-chase experiments. It can also take into account tracer decay when radioactive isotopes are used. C_LIO_LITo illustrate its use, we present three case studies based on published data and spanning different levels of biological organization: a molecular-level study of protein synthesis and degradation in Arabidopsis thaliana, an organismal-level study of phosphorus incorporation in the eelgrass Zostera marina, and an ecosystem-level study of nitrogen dynamics in Trinidadian montane streams. C_LIO_LIWith these case studies, we illustrate how isotracer can be used to estimate uptake rates, turnover rates, and total flows, as well as their uncertainty. We also show how to perform model selection to compare alternative hypotheses. C_LIO_LIWe conclude by discussing isotracers further applications, limitations, and possible future improvements and expansions. C_LI

ecology↗

bioRxiv2019

Environmentally triggered evolutionary cascade across trophic levels in an experimental phage-bacteria-insect system

Viruses are key actors of ecosystems and have major impacts on global biogeochemical cycles. Prophages deserve particular attention as they are ubiquitous in bacterial genomes and can enter a lytic cycle when triggered by environmental conditions. We explored how temperature affects the interactions between prophages and other biological levels by using an opportunistic pathogen, the bacterium Serratia marcescens, that harbours several prophages and that had undergone an evolution experiment under several temperature regimes. We found that the release of one of the prophages was temperature-sensitive and malleable to evolutionary changes. We further discovered that the virulence of the bacterium in an insect model also evolved and was positively correlated with phage release rates. We determined through analysis of genetic and epigenetic data that changes in the outer cell wall structure possibly explain this phenomenon. We hypothezise that the temperature-dependent phage release rate acted as a selection pressure on S. marcescens and that it resulted in modified bacterial virulence in the insect host. Our study system illustrates how viruses can mediate the influence of abiotic environmental changes to other biological levels and thus be involved in ecosystem feedback loops.

evolutionary biology↗

bioRxiv2019

Roles of adenosine and cytosine methylation changes and genetic mutations in adaptation to different temperatures

Epigenetic modifications can contribute to adaptation, but the relative contributions of genetic and epigenetic variation are unknown. Previous studies on the role of epigenetic changes in adaptation in eukaryotes have nearly exclusively focused on cytosine methylation (m5C), while prokaryotes exhibit a richer system of methyltransferases targetting adenines (m6A) or cytosines (m4C, m5C). DNA methylation in prokaryotes has many roles, but its potential role in adaptation still needs further investigation. We collected phenotypic, genetic, and epigenetic data using single molecule real-time sequencing of clones of the bacterium Serratia marcescens that had undergone experimental evolution in contrasting temperatures to investigate the relationship between environment and genetic, epigenetic, and phenotypic changes. This data provided a detailed description of the methylation landscape of S. marcescens and allowed us to examine the potential contributions of genetic and epigenetic changes to phenotypic adaptation. The genomic distribution of GATC motifs, which are the main target for m6A methylation, and of partially methylated epiloci pointed to a link between m6A methylation and regulation of gene expression in S. marcescens. Evolved strains, while genetically homogeneous, exhibited many polymorphic m6A epiloci. There was no strong support for a genetic control of methylation changes in our experiment, and no clear evidence of parallel environmentally-induced or environmentally-selected methylation changes at specific epiloci was found. Both some genetic and epigenetic variants were associated with some phenotypic traits. Overall, our results suggest that both genetic and adenine methylation changes have potential to contribute to phenotypic adaptation in S. marcescens, but that any environmentally-induced epigenetic change occurring in our experiment would probably have been quite labile.

evolutionary biology↗

bioRxiv2017

Thermal Tolerance is linked with Virulence in a Fish Pathogen

Although increase in temperatures may boost the number of pathogens, a complex process involving the interaction of a susceptible host, a virulent strain, and environmental factors would influence disease virulence in unpredictable ways. Here we explored if the virulence of an environmentally growing opportunistic fish pathogen, Flavobacterium columnare, would be malleable to evolutionary changes via correlated selection on thermal tolerance. Virulence among the strains increased over years, but tolerance to higher temperatures was associated with reduced virulence. Our results suggest that observed increase in frequency of columnaris epidemics over the last decade is most likely associated with increased length of growing season, or other time dependent change in environment, rather than increased regional average temperatures. Our results also indicate that most virulent bacteria had weaker ability to tolerate outside host environments, which suggest trade-off between more obligate pathogen behaviour and ability to grow outside host.

evolutionary biology↗