Eduard Szöcs

taxize: taxonomic search and retrieval in R

All species are hierarchically related to one another, and we use taxonomic names to label the nodes in this hierarchy. Taxonomic data is becoming increasingly available on the web, but scientists need a way to access it in a programmatic fashion that’s easy and reproducible. We have developed taxize, an open-source software package (freely available from http://cran.r-project.org/web/packages/taxize/index.html) for the R language. taxize provides simple, programmatic access to taxonomic data for 13 data sources around the web. We discuss the need for a taxonomic toolbelt in R, and outline a suite of use cases for which taxize is ideally suited (including a full workflow as an appendix). The taxize package facilitates open and reproducible science by allowing taxonomic data collection to be done in the open-source R platform.

Effects of pesticide toxicity, salinity and other environmental variables on selected ecosystem functions in streams and the relevance for ecosystem services

Effects of anthropogenic and environmental stressors on freshwater communities can propagate to ecosystem functions and may in turn impede ecosystem services. We investigated potential shifts in ecosystem functions that provide energy for freshwater ecosystems due to pesticides and salinity in 24 sites in streams of southeast Australia. First, effects on allochthonous organic matter (AOM) breakdown using three different substrates (leaves, cotton strips, wood sticks) in coarse and fine bags were investigated. Second, we examined effects on stream metabolism that delivers information on the ecosystem functions of gross primary production and ecosystem respiration. We found up to a fourfold reduction in AOM breakdown due to exposure to pesticides and salinity, where both stressors contributed approximately equally to the reduction. The effect was additive as, no interaction or correlation between the two stressors was found. Leaf breakdown responded strongly and exclusively to exposure to pesticides and salinity, whereas cotton strip breakdown was less sensitive and responded also to other stressors such as nutrients. No functional redundancy for the effects of pesticides and salinity on leaf breakdown was observed. For wood stick breakdown, no relationship to environmental gradients was found, however, the sample size was lower. We did not detect effects of pesticides or salinity on gross primary production or ecosystem respiration. A reduction in AOM breakdown by pesticides and salinity may impair the ecosystem services of food provision and possibly water purification. Hence, future studies should examine the spatial extent of these effects.

Pesticide mixtures in streams of several European countries and the USA

Given the multitude of pesticides used in agriculture, adjacent streams are typically exposed to pesticide mixtures. Previous studies analysed the ecological risks of a few pesticide mixtures or were limited to an individual region or crop, whereas a large scale analysis of pesticide mixtures is missing. We analysed routine monitoring data from Germany, France, the Netherlands and the USA comprising a total of 4532 sites and 56,084 sampling occasions with the aim to identify the most frequently detected pesticides, their metabolites and mixtures. The most frequently detected compounds were dominated by herbicides and their metabolites. Mixtures mostly comprised of two up to five compounds, whereas mixtures in the USA and France had clearly less compounds than those of Germany and the Netherlands. The number of detected pesticides and thereby the size of mixtures is positively correlated to the number of measured pesticides (r=0.57). In contrast, a low relationship was found to the ratio of agricultural areas within the catchment (r=0.17), and no relationship was found to the size of the catchment (r=0.06). Overall, our study provides priority mixtures for different countries that may be used for future ecotoxicological studies to improve risk assessment for stream ecosystems.

Ecotoxicology is not normal

Ecotoxicologists often encounter count and proportion data that are rarely normally distributed. To meet the assumptions of the linear model, such data are usually transformed or non-parametric methods are used if the transformed data still violate the assumptions. Generalized linear models (GLMs) allow to directly model such data, without the need for transformation. Here, we compare the performance of two parametric methods, i.e., (1) the linear model (assuming normality of transformed data), (2) GLMs (assuming a Poisson, negative binomial, or binomially distributed response), and (3) non-parametric methods. We simulated typical data mimicking low replicated ecotoxicological experiments of two common data types (counts and proportions from counts). We compared the performance of the different methods in terms of statistical power and Type I error for detecting a general treatment effect and determining the lowest observed effect concentration (LOEC). In addition, we outlined differences on a real-world mesocosm data set. For count data, we found that the quasi-Poisson model yielded the highest power. The negative binomial GLM resulted in increased Type I errors, which could be fixed using the parametric bootstrap. For proportions, binomial GLMs performed better than the linear model, except to determine LOEC at extremely low sample sizes. The compared non-parametric methods had generally lower power. We recommend that counts in one-factorial experiments should be analyzed using quasi-Poisson models and proportions from counts by binomial GLMs. These methods should become standard in ecotoxicology.

Analysing chemical-induced changes in macroinvertebrate communities in aquatic mesocosm experiments: a comparison of methods.

Mesocosm experiments that study the ecological impact of chemicals are often analysed using the multivariate method ‘Principal Response Curves’ (PRCs). Recently, the extension of generalised linear models (GLMs) to multivariate data was introduced as a tool to analyse community data in ecology. Moreover, data aggregation techniques that can be analysed with univariate statistics have been proposed. The aim of this study was to compare their performance. We compiled macroinvertebrate abundance datasets of mesocosm experiments designed for studying the effect of various organic chemicals, mainly pesticides, and re-analysed them. GLMs for multivariate data and selected aggregated endpoints were compared to PRCs regarding their performance and potential to identify affected taxa. In addition, we analysed the inter-replicate variability encountered in the studies. Mesocosm experiments characterised by a higher taxa richness of the community and/or lower taxonomic resolution showed a greater inter-replicate variability, whereas variability decreased the more zero counts were encountered in the samples. GLMs for multivariate data performed equally well as PRCs regarding the community response. However, compared to first axis PRCs, GLMs provided a better indication of individual taxa responding to treatments, as separate models are fitted to each taxon. Data aggregation methods performed considerably poorer compared to PRCs. Multivariate community data, which are generated during mesocosm experiments, should be analysed using multivariate methods to reveal treatment-related community-level responses. GLMs for multivariate data are an alternative to the widely used PRCs.

Is there an interaction of the effects of salinity and pesticides on the community structure of macroinvertebrates

Salinization of freshwater ecosystems is a global problem affecting many regions worldwide and can co-occur with pesticides in agricultural regions. Given that both stressors are potent to affect macroinvertebrate communities, their effects could interact. We investigated the effects of salinity and pesticides at 24 sites in an agricultural region of southern Victoria, South-East Australia. We used distance-based redundancy analysis to determine the influence of pesticides, salinity and other environmental variables on the composition of macroinvertebrate communities. Salinity and pesticide toxicity had a statistically significant effect on communities as had the substrate composition and the percentage of pool and riffle sections in the sampled stream reaches. We did not find evidence for interactive effects between salinity and pesticides, i.e. the effect of one of these variables did not depend on the level of the other. Nevertheless, our results show that salinization and exposure to pesticides can be major factors for the structure of macroinvertebrate communities in agricultural regions. Pesticide toxicity acted on a lower taxonomic level compared to salinity, potentially indicating evolutionary adaptation to salinity stress.

Effects of anthropogenic salinization on biological traits and community composition of stream macroinvertebrates.

Salinization of rivers resulting from industrial discharge or road-deicing can adversely affect macroinvertebrates. Trait-based approaches are a promising tool in ecological monitoring and may perform better than taxonomy-based approaches. However only little is known how and which biological traits are affected by salinization. We investigated the effects of anthropogenic salinization on macroinvertebrate communities and biological traits in the Werra River, Germany and compared the taxonomic and trait response. We found a change in macroinvertebrate community and trait composition. Communities at saline sites were characterized by the three exotic species Gammarus tigrinus, Apocorophium lacustre and Potamopyrgus antipodarum. The frequencies of trait modalities long life cycle duration, respiration by gill, ovoviviparity, shredder and multivoltinism were statistically significantly increased at saline sites. The trait-based ordination resulted in a higher explained variance than the taxonomy-based ordination, indicating a better performance of the trait-based approach, resulting in a better discrimination between saline and non-saline sites. Our results are in general agreement with other studies from Europe, indicating a trait convergence for saline streams, being dominated by the traits ovoviviparity and multivoltinism. Three further traits (respiration by gill, life cycle duration and shredders) responded strongly to salinization, but this may primarily be attributed to the dominance of a single invasive species, G. tigrinus, at the saline sites in the Werra River.

Large Scale Risks from Agricultural Pesticides in Small Streams

Small streams are important refuges for biodiversity. In agricultural areas, they may be at risk from pesticide pollution. However, most related studies have been limited to a few streams on the regional level, hampering extrapolation to larger scales. We quantified risks as exceedances of regulatory acceptable concentrations (RACs) and used German monitoring data to quantify the drivers thereof and to assess current risks in small streams on a large scale. The data set was comprised of 1 766 104 measurements of 478 pesticides (including metabolites) related to 24 743 samples from 2301 sampling sites. We investigated the influence of agricultural land use, catchment size, as well as precipitation and seasonal dynamics on pesticide risk taking also concentrations below the limit of quantification into account. The exceedances of risk thresholds dropped 3.7-fold at sites with no agriculture. Precipitation increased detection probability by 43%, and concentrations were the highest from April to June. Overall, this indicates that agricultural land use is a major contributor of pesticides in streams. RACs were exceeded in 26% of streams, with the highest exceedances found for neonicotinoid insecticides. We conclude that pesticides from agricultural land use are a major threat to small streams and their biodiversity. To reflect peak concentrations, current pesticide monitoring needs refinement.

No association between the use of Bti for mosquito control and the dynamics of non-target aquatic invertebrates in French coastal and continental wetlands

The environmental safety of Bacillus thuringiensis subsp. israelensis (Bti) is still controversial, mainly because most of the previous field studies on its undesired effects were spatially limited and did not address the relationship between community similarity and application time and frequency. No general statement can therefore be drawn on the usage conditions of Bti that insure protection of non-target organisms. The present study was conducted in eight sites distributed over the main geographical sectors where mosquito control is implemented in mainland France and Corsica. Changes in non-target aquatic invertebrates were followed at elapsed time after repeated applications of two Bti formulations (VectoBac® WDG or 12AS) up to four consecutive years. We examined the influence of both larvicide treatments and environmental variables on community dynamics and dissimilarity between treated and control areas. As it can be argued that chironomids are the most vulnerable group of non-target invertebrates, we scrutinised potential Bti-related effects on the dynamics of their community. The use of VectoBac® WDG and 12AS in coastal and continental wetlands had no immediate or long-term detectable effect on the taxonomic structure and taxa abundance of non-target aquatic invertebrate communities, including chironomids. This applied to the main habitats where mosquito larvae occur, regardless of their geographic location. Flooding, whose frequency and duration depend on local meteorological and hydrological conditions, was identified as the main environmental driver of invertebrate community dynamics. Our findings add support to the environmental safety of currently available Bti formulations when following recommended application rates and best mosquito control practices.

Structural and functional effects of a short-term pyrethroid pulse exposure on invertebrates in outdoor stream mesocosms

Agricultural land-use frequently results in short pulse exposures of insecticides such as pyrethroids in river systems, adversely affecting local invertebrate communities. In order to assess insecticide-induced effects, stream mesocosms are used within higher tier aquatic risk assessment. Regulatory acceptable concentrations (RACs) derived from those studies are often higher compared with tier 1 RACs. Hence, the present mesocosm study evaluates this aspect using a pulse exposure scenario typical for streams and the pyrethroid insecticide etofenprox. A 6-h pulse exposure with measured concentrations of 0.04, 0.3 and 5.3μgL-1 etofenprox was used. We considered abundance, drift and emergence of invertebrates as structural endpoints and the in situ-measured feeding rates of the isopod Asellus aquaticus as functional endpoint. Most prominent effects were visible at 5.3μgL-1 etofenprox which caused adverse effects of up to 100% at the individual and population level, as well as community structure alterations. Transient effects were observed for invertebrate drift (effect duration ≤24h) and for the invertebrate community (9 days after exposure) at 0.3μgL-1 etofenprox. Furthermore, 0.04μgL-1 etofenprox affected the abundance of the mayfly Cloeon simile (decrease by 66%) and the feeding rate of A. aquaticus (decrease by 44%). Thus, implications for the functional endpoint leaf litter breakdown in heterotrophic ecosystems may be expected. A hypothetical RAC derived from the present mesocosm study (0.004μgL-1) is in line with the official tier 1 RAC (0.0044μgL-1) and thus shows that the present mesocosm study did not result in a higher RAC.