Stable isotope analysis provides a powerful tool to identify the energy sources which fuel consumers, to understand trophic interactions and to infer consumer trophic position (TP), an important concept that describes the ecological role of consumers in food webs. However, current methods for estimating TP using stable isotopes are limited and do not fulfil the complete potential of the isotopic approach. For instance, researchers typically use point estimates for key parameters including trophic discrimination factors and isotopic baselines, and do not explicitly include variance associated with these parameters when calculating TP. We present “tRophicPosition,” an r package incorporating a Bayesian model for the calculation of consumer TP at the population level using stable isotopes, with one or two baselines. It combines Markov Chain Monte Carlo simulations through JAGS and statistical and graphical analyses using R. We model consumer and baseline observations using relevant statistical distributions, allowing them to be treated as random variables. The calculation of TP—a random parameter—for one baseline follows standard equations linking 15N enrichment per trophic level and the trophic position of the baseline (e.g. a primary producer or primary consumer). In the case of two baselines, a simple mixing model incorporating δ13C allows for the differentiation between two distinct sources of nitrogen, thus including heterogeneity derived from alternatives sources of δ15N. Methods currently implemented in “tRophicPosition” include loading, plotting and summarizing stable isotope data either from multiple sites and/or communities or a local assemblage; loading trophic discrimination factors from an internal database or generating them; defining and initializing a Bayesian model of TP; sampling posterior parameters; analysing, comparing and plotting posterior estimates of TP and other parameters; and calculating a parametric (non‐Bayesian) TP estimate. Additionally, full documentation including examples, multiple vignettes and code are available for download.

We investigated the suitability of an active biomonitoring approach, using the ecologically relevant species Gammarus fossarum, to assess trends of bioavailable contamination in continental waters. Gammarids were translocated into cages at 27 sites, in the Rhône-Alpes region (France) during early autumn 2009. Study sites were chosen to represent different physico-chemical characteristics and various anthropic pressures. Biotic factors such as sex, weight and food availability were controlled in order to provide robust and comparable results. After one week of exposure, concentrations of 11 metals/metalloids (Cd, Pb, Hg, Ni, Zn, Cr, Co, Cu, As, Se and Ag) and 38 hydrophobic organic substances including polycyclic aromatic hydrocarbons (PAHs), polychlorobiphenyles (PCBs), pentabromodiphenylethers (PBDEs) and organochlorine pesticides, were measured in gammarids. All metals except Ag, and 33 organic substances among 38 were quantified in G. fossarum, showing that this species is relevant for chemical biomonitoring. The control of biotic factors allowed a robust and direct inter-site comparison of the bioavailable contamination levels. Overall, our results show the interest and robustness of the proposed methodological approach for assessing trends of bioavailable contamination, notably for metals and hydrophobic organic contaminants, in continental waters. Furthermore, we built threshold values of bioavailable contamination in gammarids, above which measured concentrations are expected to reveal a bioavailable contamination at the sampling site. Two ways to define such values were investigated, a statistical approach and a model fit. Threshold values were determined for almost all the substances investigated in this study and similar values were generally derived from the two approaches. Then, levels of contaminants measured in G. fossarum at the 27 study sites were compared to the threshold values obtained using the model fit. These threshold values could serve as a basis for further implementation of quality grids to rank sites according to the extent of the bioavailable contamination, with regard to the applied methodology.

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AbstractToday, no effective tools are proposed in ecotoxicology to diagnose and predict the accumulation and effects of chemical substances on living organisms, accounting for exposure situations that are known to be complex (routes of exposure, metabolization processes, cocktail effects, etc.). Among elaborated tools, toxicokinetic/toxicodynamic (TKTD) models are now strongly recommended to describe the exposure time-dependency on individual life-history traits from experimental data collected through standard toxicity tests. In particular, the TK part is used to relate the exposure medium concentration to the internal concentration within organisms, considering various processes such as accumulation, depuration, metabolization and excretion (ADME). Regarding plant protection products in marketing authorization applications, regulation No 283/2013 (EU) defines the data requirements for active substances with a bioaccumulation test on fish following OECD guideline 305, which consists in an accumulation phase followed by a depuration phase. The concentration of the substance within fishes is followed over time during both phases thus allowing to describe the exposure time-dependency on individual (fit of TK model) and bioaccumulation factors. On a regulation point of view, these factors are decisive criteria for further estimating the concentration of active substances present in food items of vertebrates and more particularly of piscivorous birds and mammals. This paper presents a new ready-to-use tool providing on-line the estimation of the bioaccumulation factors associated with their uncertainty to facilitate the daily work of regulators, but also of any user, by benefiting of a freely available and user-friendly interface avoiding to invest into underlying methods. This tool, MOSAICBioacc, is available from the following adress: https://mosaic.univ-lyon1.fr/bioacc, and can be used as a turn-key decision making tool in the framework of environmental risk assessment.

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