Periodic Reporting for period 1 - MicroERA (Ecological Sensitivity Distribution (ESD): integrating molecular-based structural and functional microbial community responses in a new tool for environmental risk assessment of chemicals)
Okres sprawozdawczy: 2016-10-01 do 2018-09-30
When aiming to integrating data on different levels in an ESD comparable effect thresholds are needed. The microERA project led to the development of a turnkey tool called DRomics (Dose-Response for omics, available as an R package and an online interface http://lbbe-shiny.univ-lyon1.fr/DRomics-shiny/). This tool manages molecular responses obtained in a dose-response framework and allows in fine integrating molecular responses (e.g. genes, metabolites) in ERA. The results highlighted that omics responses were more sensitive than classical endpoints and consequently, genes and metabolites involved in a function showed higher sensitivity than the direct measurement of the functions (e.g. energy metabolism pathway vs. photosynthesis). In conclusion, the use of cumulative sensitivity distributions of omics data could reinforce risk assessment procedures and enable the integration of functions and community studies in ERA.
Second, in a proof-of principle study, the functionality of the tool was demonstrated for an existing dataset, describing the response of the chlorophyte Scenedesmus vacuolatus to the biocide triclosan (6 concentrations including control). Responses were observed at the molecular level (untargeted transcriptomics (microarrays) and metabolomics) and apical/classical endpoints (growth, photosynthesis). This step allowed to first reach our goals on a model organism with a lower biological complexity compared to communities and to identify potential limitations to be solved for consecutive experiments on periphytic communities. Using DRomics, we observed that apical endpoints were less sensitive than most of molecular endpoints and that the well-known sigmoid response was more the exception than the rule at the molecular level. An ESD was built on both transcriptomics and metabolomics responses and clearly highlighted importance of the consideration of omics responses in ERA and reinforced our initial assumptions.
Third, an experiment was performed to investigate the responses of stream periphytic communities to the herbicide diuron on different functional levels. Responses at the molecular level (transcriptomics=sequencing of RNA, metabolomics) were investigated after 1 hour of exposure. Moreover, the same experiment was performed in parallel on communities pre-exposed for one month to diuron in order to investigate potential tolerance acquisition mechanisms on functional responses. A strong effort was also put in the optimization of a protocol to extract RNA in a sufficient quality and quantity for the downstream analysis. Quality control of the extraction and the sequencing of RNA were satisfying. The annotation of the sequencing is still in treatment. An ESD build on community functional responses in the light of metabolic pathways annotation (e.g. KEGG pathways) is under development considering tolerance mechanisms.