Biology subjects

Colas, S.

Publications and source records attributed to Colas, S..

5 recordsLinked to original sources

bioRxiv2023

New sensitive tools to characterize meta-metabolome response to short- and long-term cobalt exposure in dynamic river biofilm communities

Untargeted metabolomics is a non-a priori analysis of biomolecules that characterizes the metabolome variations induced by short- and long-term exposures to stressors. Even if the metabolite annotation remains lacunar due to database gaps, the global metabolomic fingerprint allows for trend analyses of dose-response curves for hundreds of cellular metabolites. The combination of untargeted metabolomic features and benchmark-dose (BMD) calculations then makes it possible to determine concentration range inducing defense responses (CRIDeR) and concentration range inducing damage responses (CRIDaR). To develop this approach in a context of time-dependent microbial community changes, mature river biofilms were exposed for 1 month to four cobalt (Co) concentrations (background concentration, 1 x 10-7, 5 x 10-7 and 1 x 10- 6 M) in an open system of artificial streams. The meta-metabolomic response of biofilms was compared against a multitude of biological parameters (including bioaccumulation, biomass, chlorophyll a content, composition and structure of prokaryotic and eukaryotic communities) monitored at set exposure times (from 1 hour to 28 days). Cobalt exposure induced extremely rapid responses of the meta-metabolome, with time range inducing defense responses (TRIDeR) of around ten seconds, and time range inducing damage responses (TRIDaR) of several hours. Even in biofilms whose structure had been altered by Co bioaccumulation (reduced biomass, chlorophyll a contents and changes in the composition and diversity of prokaryotic and eukaryotic communities), CRIDeRs with similar initiation thresholds (1.41 {+/-} 0.77 x 10-10 M Co2+ added in the exposure medium) were set up at the meta-metabolome level at every time point. In contrast, the CRIDaR initiation thresholds increased by 10 times in long-term Co exposed biofilms. The present study demonstrates that defense and damage responses of biofilm meta-metabolome exposed to Co are rapidly and sustainably impacted, even within tolerant and resistant microbial communities. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/567369v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@e7a87eorg.highwire.dtl.DTLVardef@e712b7org.highwire.dtl.DTLVardef@7de128org.highwire.dtl.DTLVardef@493053_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIProkaryotic community structures were impacted after 1 h of exposure to Co C_LIO_LIBiofilm meta-metabolome was impacted after 36 s of exposure to Co C_LIO_LIBiofilm meta-metabolome response was faster than changes in biofilm communities C_LIO_LIShort- and long-term exposed biofilms have similar CRIDeR initiation thresholds C_LIO_LILong-term exposed biofilms have higher CRIDaR initiation thresholds C_LI

molecular biology↗

bioRxiv2023

How do biomarkers dance? Specific moves of defense and damage biomarkers for biological interpretation of dose-response model trends.

Omics and multi-omics studies are currently increasingly used in ecotoxicology to highlight the induction of known or new biomarkers when an organism is exposed to one (or more) contaminant(s). Although it is virtually impossible to identify all biomarkers from all possible organisms, biomarkers can be grouped into two categories, defense or damage biomarkers and they have a limited number of response trends. Our working hypothesis is that defense and damage biomarkers show different dose-response patterns. A meta-analysis of 156 articles and 2,595 observations of dose-response curves of well-known defense and damage biomarkers was carried out in order to characterize the response trends of these biological parameters in a large panel of living organisms (18 phyla) exposed to a wide variety of inorganic or organic contaminants. Defense biomarkers describe biphasic responses (bell-shaped and U-shaped) to a greater extent than damage biomarkers. In contrast, damage biomarkers varied mainly monotonically (decreasing or increasing). Neither the nature of the contaminant nor the type of organisms, whatever the kingdom (Plantae, Animalia, Chromista or Bacteria), influence these specific responses. This result suggests that cellular defense and damage mechanisms are not specific to stressors and are conserved throughout life. The meta-analysis results confirm the usefulness of trend analysis in dose-response models as a biological interpretation of biomarkers in large dataset and their application in determining the concentration ranges inducing defense responses (CRIDeR) and the concentration ranges inducing damage responses (CRIDaR) regardless of the contaminant tested or the organism studied. HighlightsO_LIWe interpreted 2,595 biomarker dose-response curves generated by chemical exposure. C_LIO_LIDefense biomarkers mainly describe biphasic (bell- or U-shaped) trends. C_LIO_LIDamage biomarkers mainly describe monotonic (decreasing or increasing) trends. C_LIO_LICellular defense and damage responses appear to have been conserved during evolution. C_LIO_LIResponse trend analysis is a promising tool for environmental risk assessment. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=77 SRC="FIGDIR/small/551999v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@14b19c4org.highwire.dtl.DTLVardef@188ae31org.highwire.dtl.DTLVardef@643ed6org.highwire.dtl.DTLVardef@15953cd_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

Multi-omics analyses from a single sample: Prior metabolite extraction does not alter the 16S rRNA-based characterization of prokaryotic community in a diversity of sample types

Massive sequencing of the 16S rRNA gene has become a standard first step to describe and compare microbial communities from various samples. Parallel analysis of high numbers of samples makes it relevant to the statistical testing of the influence of natural or experimental factors and variables. However, these descriptions fail to document changes in community or ecosystem functioning. Non-targeted metabolomics are a suitable tool to bridge this gap, yet extractions protocols are different. In this study, prokaryotic community compositions are documented by 16S rRNA sequencing after direct DNA extraction, or after metabolites extraction followed by DNA extraction. Results obtained using the V3-V4 region on non-axenic cultures of cyanobacteria, lake water column, biofilm, gut of wild and lab-reared fish, indicate that prior extraction of metabolites does not influence the obtained image of prokaryotic communities. This validates sequential extraction of metabolites followed by DNA as a way to combine 16S rRNA sequencing with metabolome characterization from a single sample. This approach has the potential to complement community structure characterization with a proxy of their functioning, without the uncertainties associated with the use of separate samples.

microbiology↗

bioRxiv2023

Meta-metabolomic Responses of River Biofilms to Cobalt Exposure and Use of Dose-response Model Trends as an Indicator of Effects

Metabolites are low molecular-weight molecules produced during cellular metabolism. The global expression of the meta-metabolome (metabolomics at the community level) could thus potentially be used to characterize the exposure of an organism or a community to a specific stressor. Here, the meta-metabolomic fingerprints of mature biofilms were examined after 1, 3 and 7 days of exposure to five concentrations of cobalt (0, 1 x 10-7, 1 x 10-6, 5 x 10-6 and 1 x 10-5 M) in aquatic microcosms. The global changes in meta-metabolomic fingerprints were in good agreement with those of the other biological parameters studied (cobalt bioaccumulation, biomass, chlorophyll content). To better understand the dose-responses of the biofilm meta-metabolome, the untargeted LC-HRMS metabolomic data were further processed using the DRomics tool to build dose-response model curves and to calculate benchmark doses (BMD). These BMDs were aggregated into an empirical cumulative density function. A trend analysis of the metabolite dose-response curves suggests the presence of a concentration range inducing defense mechanisms (CRIDeM) between 4.7 x 10-7 and 2.7 x 10-6 M, and of a concentration range inducing damage mechanisms (CRIDaM) from 2.7 x 10-6 M to the highest Co concentration. The present study demonstrates that the molecular defense and damage mechanisms can be related to contaminant concentrations and represent a promising approach for environmental risk assessment of metals. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/545533v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@179fd06org.highwire.dtl.DTLVardef@1d2cd10org.highwire.dtl.DTLVardef@9508a3org.highwire.dtl.DTLVardef@6a1818_HPS_FORMAT_FIGEXP M_FIG C_FIG SYNOPSISThis study focuses on the interpretation of the metabolite dose-response trends in river biofilms exposed to cobalt to identify concentration range inducing cellular mechanisms and improve the environmental risk assessment of metals.

microbiology↗

bioRxiv2019

Toxicity, transfer and depuration of anatoxin-a (cyanobacterial neurotoxin) in medaka fish exposed by single-dose gavage

The proliferations of cyanobacteria are increasingly prevalent in warm and nutrient-enriched waters and occur in many rivers and water bodies due especially to eutrophication. The aim of this work is to study in female medaka fish the toxicity, the transfer and the depuration of the anatoxin-a, a neurotoxin produced by benthic cyanobacterial biofilms. This work will provide answers regarding acute toxicity induced by single gavage by anatoxin-a and to the risks of exposure by ingestion of contaminated fish flesh, considering that data on these aspects remain particularly limited. The oral LD50 of a single dose of ({+/-})-anatoxin-a was determined at 11.50 {micro}g.g-1. First of all, lethal dose (100% from 20 {micro}g.g-1) provokes rapid respiratory paralysis (in 1-2 min) of the fish inducing the death by asphyxia. Noticeably, no death nor apparent neurotoxicologic effect occurred during the experimentation period for the 45 fish exposed to a single sub-acute dose of ({+/-})-anatoxin-a corresponding to the no observable adverse effect level (NOAEL = 6.67 {micro}g.g-1). Subsequently, the toxico-kinetics of the ({+/-})-anatoxin-a was observed in the guts, the livers and the muscles of female medaka fish for 10 days. In parallel, a protocol for extraction of anatoxin-a has been optimized beforehand by testing 3 different solvents on several matrices, the extraction with 75% methanol + 0.1% formic acid appearing to be the most efficient. Anatoxin-a was quantified by high-resolution qTOF mass spectrometry coupled upstream to a UHPLC chromatographic chain. The toxin could not be detected in the liver after 12 h, and in the gut and muscle after 3 days. The mean clearance rates of ({+/-})-anatoxin-a calculated after 12 h are above 58%, 100% and 90% for the guts, the livers and the muscles, respectively. Non-targeted metabolomics investigations performed on the fish liver indicates that the single sub-acute exposure by gavage induces noticeable metabolome dysregulations, including important phospholipid decreases, with an organism recovery period of above 12-24h. Overall, the medaka fish do not appear to accumulate ({+/-})-anatoxin-a and to largely recover after 24h following a single sub-acute oral liquid exposure at the NOAEL.

pharmacology and toxicology↗