bioRxiv Science⌕ Search

Biology subjects

Billoir, E.

Publications and source records attributed to Billoir, E..

2 recordsLinked to original sources

Effects of water nutrient concentrations on stream macroinvertebrate community stoichiometry: a large-scale study

Basal resources generally mirror environmental nutrient concentrations in the elemental composition of their tissue, meaning that nutrient alterations can directly reach consumer level. An increased nutrient content (e.g. phosphorus) in primary and detrital resources under nutrient enriched conditions should favour taxa with a high demand for this nutrient. With the nutrient demand of a taxon being correlated to the elemental composition of its body tissue (e.g. phosphorus content), such above described species shifts likely alter the overall community stoichiometry. However, studies addressing stoichiometry at community level are rare and most often restricted to lacustrine planktonic systems, single streams or limited experimental setups. Relying on a stoichiometric database for >200 taxa and >1300 standardized sampling events of macroinvertebrate assemblages from the French national monitoring programme, we investigated the effect of water phosphorus and nitrogen load on stream macroinvertebrate community stoichiometry. Community stoichiometry was significantly affected by water phosphorus concentration and the effect was strongest at low levels of nitrogen. While we could not confirm our hypothesis of increasing community %P (and decreasing C:P, N:P) with increasing water phosphorus concentrations for the overall community, it clearly followed this pattern for both Insecta and Malacostraca. General differences in the elemental composition among major taxonomic groups and a shift among these groups over the nutrient gradient probably explain the response of community stoichiometry. Our results show that assumptions from Ecological Stoichiometry Theory also hold at the community level, at least for two dominant taxa, and on a large spatial scale, with likely consequences for nutrient cycling and ecosystem function.

ecology↗

DRomics, a workflow to model and make sense of dose-response (multi-)omics data in (eco)toxicology

Omics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, describing the dose-response relationships on such high-throughput data is no easy task. In a first part, we review the software available for this purpose, and their main features. We set out arguments on some statistical and modeling choices we have made while developing the R package DRomics and its positioning compared to others tools. The DRomics main analysis workflow is made available through a web interface, namely a shiny app named DRomics-shiny. Next, we present the new functionalities recently implemented. DRomics has been augmented especially to be able to handle varied omics data considering the nature of the measured signal (e.g. counts of reads in RNAseq) and the way data were collected (e.g. batch effect, situation with no experimental replicates). Another important upgrade is the development of tools to ease the biological interpretation of results. Various functions are proposed to visualize, summarize and compare the responses, for different biological groups (defined from biological annotation), optionally at different experimental levels (e.g. measurements at several omics level or in different experimental conditions). A new shiny app named DRomicsInterpreter-shiny is dedicated to the biological interpretation of results. The institutional web page https://lbbe.univ-lyon1.fr/fr/dromics gathers links to all resources related to DRomics, including the two shiny applications.

bioinformatics↗