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Principal response curves technique for the analysis of multivariate biomonitoring time series
Abstract
Although chemical and biological monitoring is often used to evaluate the quality of surface waters for regulatory purposes and/or to evaluate environmental status and trends, the resulting biological and chemical data sets are large and difficult to evaluate. Multivariate techniques have long been used to analyse complex data sets. This paper discusses the methods currently in use and introduces the principal response curves method, which overcomes the problem of cluttered graphical results representation that is a great drawback of most conventional methods. To illustrate this, two example data sets are analysed using two ordination techniques, principal component analysis and principal response curves. Whereas PCA results in a difficult-to-interpret diagram, principal response curves related methods are able to show changes in community composition in a diagram that is easy to read. The principal response curves method is used to show trends over time with an internal reference (overall mean or reference year) or external reference (e.g. preferred water quality or reference site). Advantages and disadvantages of both methods are discussed and illustrated.
... This may come as a consequence of a higher availability of substrate when compared with the other treatments. The principal response curve redundancy analysis (PRC) [41] was used to identify the ASVs that drove these community differences (i.e. had weights higher or lower than one) or contributed to similarities (i.e. had weights close to one) between treatments (Fig. 1b). Interestingly, many of the ASVs that were contributing towards the differences between the amorphous PET biofilm and no carbon control treatments were not present in the BHET treatment or were present only in very low relative abundances and vice versa ( Fig. 1c; Table S2). ...
... Whilst HMM searches of the JGI genomes used the default E value cut-off of 0.01, we further verified the presence of PETases within our predicted metagenomes by (i) computing a distance matrix [97] from the tree output by PICRUSt2 to find the PETase-containing organism most closely related (by 16S rRNA sequence) to each of the ASVs predicted to contain a PETase; and (ii) obtaining the predicted PETase sequences from these organisms and performing manual NCBI conserved domain searches [56]. Principal response curves [41] were calculated using the vegan package in R [98] and all other analyses were carried out using custom Python (version 3.7.6) scripts (https:// github.com/R-Wright-1/PET-plastisphere). ...
Background
Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere.
Results
We found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation.
Conclusions
Overall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris.
... It tests and displays treatment effects of a time series in comparison to a reference site (e.g. Van den Brink et al., 2009). The technique uses redundancy analysis and introduces interaction between sampling dates as covariables and treatment as explanatory variables (Van den Brink and Ter Braak, 1999). ...
... The technique uses redundancy analysis and introduces interaction between sampling dates as covariables and treatment as explanatory variables (Van den Brink and Ter Braak, 1999). This divides the variance into parts that can be attributed to differences in time, to treatment differences in time, and to differences between replicates ( Van den Brink et al., 2009). As a result, the PRC diagram contrasts each treatment in the vertical axis with the control across time. ...
Determining the resistance and resilience of resources and benthic invertebrates connected to instream refuges and species re-colonization in post-flood periods may help to elucidate mechanisms behind community recovery. This experiment simulated flow pulses in a small temporary stream in an extremely wet year, using upstream control and downstream flooded reaches at three sites in order to assess community resistance and resilience (benthos and drift), and analyse resources (periphyton and benthic organic matter) and invertebrates at pre- and post-flood time periods. The hyporheos was sampled in order to explore species exchanges with benthos. Fewer resources and benthic invertebrates at the beginning of the experiment were found than in previous studies when base flow conditions prevailed. Resource stocks and benthic invertebrates showed high resistance to the flow pulse. Interestingly, there was low resilience of benthic organic matter to natural seasonal flooding. Chlorophyll a did not recover after experimental floods; instead, it was reduced after floods, despite the more benign flow conditions and non-limiting irradiance levels, pointing to top-down control by consumers. Additionally, the experimental flood significantly disturbed only the invertebrate composition in the groundwater-fed stream, which was inhabited by the fewest adapted-to-flood-disturbances macroinvertebrates. Despite the low resilience observed, richness and densities of benthos increased during the study, evidencing progressive colonization. Around 50–60% of macroinvertebrates were present in both benthos and hyporheos. Richness increased after flooding, suggesting that the hyporheic zone could be the main source of colonizers. Three species traits characterized the hyporheos: small size, cocoons and feeders of microorganisms within the fine sediment matrix. The main results indicate that longer-than-normal flood periods in early spring may constrain invertebrate succession before the next summer drought in temporary streams. This study underscores the importance of hyporheic fauna as a significance source of colonizers, highlighting the importance of connectivity to the groundwater.
... We show mathematically that these methods are identical for complete data, but that differences appear with unequal replication. As a corollary we show that, for complete data, a particularly attractive form of ASCA, which displays a main effect together with an interaction, is a special case of principal response curve analysis (PRC) [22][23][24]. The fact that ASCA+ and WE-ASCA, which differ in factor coding, are different versions of ASCA, shows that ASCA is coding dependent, whereas RDA is not. ...
... These methods allow the identification of covarying stressors and the effects of anthropogenic stressors along environmental gradients that might otherwise confound clear contaminant patterns. Principal response curves analyse temporal changes in community composition and are always standardised to some kind of control, whether this is an 'unaffected' ecosystem or a reference point in time (van den Brink et al., 2009). ...
This chapter presents an overview of biomarkers and ecological indicators
used to measure radiation stress in invertebrates. Using examples, we will show
how and in what context the different biomarkers can be used and on which invertebrate
species. We will also describe how the biomarker techniques can be adapted
from other taxa including humans and developed for use in invertebrate species.
Biomarkers generally fall into two categories – biomarkers for exposure and effect.
Invertebrates have not frequently been used to investigate radiation-induced stress
but they offer great potential. Here, we present biomarkers that have been used in
different ecotoxicological contexts and are appropriate for measuring radiation
exposure: comet assay, micronucleus assay, cytochrome p450 and oxidative stress.
The majority of previous studies that have used biomarkers for environmental
stressors have been conducted on either mussel for aquatic systems or earthworms
in terrestrial systems. We also present an overview of how ecological indicators
benefit understanding of the consequences that radiation exposure to individuals
living in contaminated environments, focussing on alterations to reproduction and
behaviour.
... Compared to standardized single-species tests, the main advantage of microcosm studies in environmental risk assessments is that intra-and interspecific interactions within a community can be investigated over the long-term (Brock et al., 2015). With this approach, both direct and indirect effects of the substances of interest at the population and community level can be taken into account (van den Brink et al., 2009). Up to now, microcosms have been used in studies of the effects of different substances on freshwater meiobenthos, especially nematodes (summarized in Höss, 2021). ...
Microplastics in a wide range of shapes and polymer types (MPs; <5 mm) accumulate in freshwater sediments, where they may pose an environmental threat to sediment-dwelling micro- and meiobenthos. To date, the effects of MPs on those organisms have mostly been studied in single-species experiments exposed to high particle concentrations. By contrast, there have been few investigations of the effects resulting from the long-term exposure of natural communities to environmental relevant MPs. This research gap was addressed in the present study. A microcosm experiment was conducted to examine the impact of a mixture of MPs of varying polymer composition, shape, and size (50% polystyrene (PS) beads: 1-μm diameter; 37% polyethylene terephthalate (PET) fragments: 32 × 21 μm in size, and 13% polyamide (PA) fibers 104 × 15 μm in size; % based on the total particle number) provided at two concentrations (low: 4.11 × 10⁵ MPs/kg sediment dw and high: 4.11 × 10⁷ MPs/kg sediment dw) and two exposure durations (4 and 12 weeks) on a micro- and meiobenthic community collected from a freshwater sediment. MPs exposure did not alter the abundance of protozoa (ciliates and flagellates) as well as the abundance and biomass of meiobenthic organisms (nematodes, rotifers, oligochaetes, gastrotrichs, nauplii), whereas the abundance and biomass of harpacticoid copepods was affected. Neither nematode species diversity (species richness, Shannon-Wiener index, and evenness) nor the NemaSPEAR[%]-index (pollution-sensitive index based on freshwater nematodes) changed in response to the MPs. However, changes in the structure of the meiobenthic and nematode community in the presence of environmentally relevant MPs mixtures cannot be excluded, such that microcosms experiments may be of value in detecting subtle, indirect effects of MPs.
... We used Principal Response Curves to visually assess differences in repeatedsampling microhabitat characteristics (i.e., light intensity, subcanopy air temperature, and ground-level air temperature) between spruce restoration site categories and the occupied site across the sampling period. This analysis is an extension of Redundancy Analysis to allow for visualization of differences in continuous variables among categories (e.g., sites) over time (Van den Brink and Ter Braak 1999;Van den Brink et al. 2009). We used the daily time series for this analysis, and standardized the response data (mean ¼ 0, standard deviation ¼ 1) because the variables had different units and scales. ...
The Central Appalachian Spruce Restoration Initiative was formed to promote restoration of red spruce Picea rubens forests in Central Appalachia. One goal of the initiative is to increase availability and enhance quality of habitat for wildlife, including the threatened Cheat Mountain salamander Plethodon nettingi. The purpose of this research was to compare microhabitat characteristics between an occupied Cheat Mountain salamander site and early-stage spruce restoration sites, and between four occupied sites and proximal non-detection sites. We found that soil pH was higher and soil moisture was lower at spruce restoration sites compared to the occupied site, and that light intensity, sub-canopy air temperature, and ground-level air temperature were higher in spruce restoration prescriptions with reduced canopy cover. We found that soil moisture was higher at occupied sites compared to proximal non-detection sites, but soil pH was not significantly different. Our study suggests that Cheat Mountain salamanders are associated with low soil pH and high soil moisture, and thus spruce restoration could enhance habitat quality for this species in the long-term.
... To determine plant successional dynamics in riparian communities following stabilization, we computed Principal Response Curves (PRC, Van den Brink and Braak, 1999), for each riverbank level separately. This analysis expresses the species composition of each stabilization technique as a deviation from a comparison benchmark (natural sites) along a time axis (Van den Brink et al., 2009). Prior to running the PRC, the effect of the stream identity was partialled out with a redundancy analysis (RDA) on Hellinger-transformed species abundance data. ...
Bioengineering techniques have been encouraged over “hard” civil engineering such as riprap for recovering naturalness on stabilized riverbanks, but their effectiveness in reproducing the plant species diversity and vegetation succession present on non-stabilized (natural) riverbanks has rarely been assessed. Here, we compared alpha and beta diversity and successional trajectories of plant communities along the vertical profile of natural (40 sites), bioengineered (51) and riprap (33) riverbanks, in 55 streams of the second- to seventh-order in the province of Quebec (eastern Canada). Richness of total, hydrochorous and native species was higher on natural riverbanks than on those stabilized by riprap techniques along all riverbank elevations (upper, middle and lower parts of the riverbank). Bioengineered sites showed intermediate values. Natural sites contributed most to beta diversity on the upper bank, riprap sites on the middle bank. Temporal changes in species richness were observed only on the upper and middle banks, with an increase on riprap sites and a decrease on bioengineered sites. Beta diversity was mainly stable through time. Plant composition on bioengineered sites converged to that on natural sites for all bioengineering techniques at all bank levels, whereas for ripraps it did so only on the lower bank. For all bioengineering techniques, plant succession was driven by increasing native and hydrochorous species at all bank levels. Bioengineering is an effective alternative to riprap on stabilized riverbanks that leads to plant diversity and succession that most resemble those on natural riverbanks.
... To more clearly visualize temporal shifts in species assemblages, and identify which taxa were most responsive to treatment and thus responsible for compositional changes, we used principal response curves (PRC; Van den Brink et al. 2008). Principal response curves are a type of redundancy analyses contrasting divergence in composition between reference (control) and perturbed (treated) sites in a chronological fashion. ...
Anthropogenic environmental change is causing habitat deterioration at unprecedented rates in freshwater ecosystems. Despite increasing more rapidly than other agents of global change, synthetic chemical pollution -including agrochemicals such as pesticides- has received relatively little attention in freshwater community and ecosystem ecology. Determining the combined effects of multiple agrochemicals on complex biological properties remains a major challenge, requiring a cross-field integration of ecology and ecotoxicology. Using a large-scale array of experimental ponds, we investigated the response of zooplankton community properties (biomass, composition, and diversity metrics) to the individual and joint presence of three globally widespread agrochemicals: the herbicide glyphosate, the neonicotinoid insecticide imidacloprid, and nutrient fertilizers. We tracked temporal variation in zooplankton biomass and community structure (i.e., composition and diversity) along single and combined pesticide gradients (each spanning eight levels), under low (mesotrophic) and high (eutrophic) nutrient-enriched conditions, and quantified (i) response threshold concentrations, (ii) agrochemical interactions, and (iii) community resistance and recovery. We found that the biomass of major zooplankton groups differed in their sensitivity to pesticides: ≥0.3 mg/L glyphosate elicited long-lasting declines in rotifer communities, both pesticides impaired copepods (≥3 µg/L imidacloprid and ≥5.5 mg/L glyphosate), whereas some cladocerans were highly tolerant to pesticide contamination. Strong interactive effects of pesticides were only recorded in ponds treated with the combination of the highest doses. Overall, glyphosate was the most influential driver of aggregate community properties of zooplankton, with biomass and community structure responding rapidly but recovering unequally over time. Total community biomass showed little resistance when first exposed to glyphosate, but rapidly recovered and even increased with glyphosate concentration over time; in contrast, taxon richness decreased in more contaminated ponds but failed to recover. Our results indicate that the biomass of tolerant taxa compensated for the loss of sensitive species after the first exposure, conferring greater community resistance upon a subsequent contamination event; a case of pollution-induced community tolerance in freshwater animals. These findings suggest that zooplankton biomass may be more resilient to agrochemical pollution than community structure; yet all community properties measured in this study were affected at glyphosate concentrations below common water quality guidelines in North America.
... We followed ANOSIM with analysis of indicators of parasitoid family differences (De Caceres and Legendre 2009). Lastly, to initially view any predictable changes in communities over time (converting sampling dates into weeks of sampling) in relation to field position and management, we used PRC (Principle Response Curves), prc"vegan" (van den Brink et al. 2009) using 999 permutations for RDA analysis. PRC is a multivariate approach designed to simplify the display and interpretability of repeated measures of communities over space and time (Auber et al. 2017). ...
In blueberry crops, there are multiple pest species, and some of those can be suppressed by natural enemies including parasitoid wasps and predators. Parasitoid wasps occur within the environment often tracking pest species for food resources to complete their lifecycle. These small wasps are also sensitive to agricultural environments including agrichemicals, habitat availability, and climate. We investigated how the structure of parasitoid communities varied between organic and conventional blueberry systems, and how the communities of these parasitoids varied within field spatial scales (forested border vs edge vs interior). With the lower intensity of agricultural interventions occurring in organic systems and forested borders, we predicted more stable parasitoid numbers that would be insulated from predicted climate variability. In our study, parasitoids were observed in low abundance in each cropping system, with community structure dependent on both management practice and field position. Unmanaged blueberry fields and forested field borders contained more parasitoid families, and in conventional systems, we saw fewer families present in the field interior as compared to field borders. In this first study to characterize Southern parasitoid communities in blueberry production systems, we observed over 50 genera of parasitoids, with a few dominant families (Braconidae and Ichneumonidae) that would contribute to biological control in blueberry systems. Overall, we captured few parasitoids, which indicates a potential vulnerability in biological control, and the need for further research using other sampling techniques to better understand these parasitoid communities.
... Principal Response Curves (PRC) analysis was used to test the effect over time of forest thinning intensity on sporocarp community composition. This multivariate analysis allows to describe the treatment effect on species composition over time (van den Brink et al., 2009). To better understand the fruiting compositional dynamics and patterns we performed PRC analysis on two different sporocarp datasets: i) the sporocarp abundance of each fungal species (i.e., dry biomass quantitative abundance, kg in dry weight ha -1 ), and ii) the presence/absence of sporocarps of each fungal species (i.e., qualitative abundance). ...
The main objective of this thesis was to understand, describe and quantify the coupled effects of forest thinning, tree growth and climate on fungal biomass, productivity and community composition. To this end, huge amount of dataset from different disciplines has been compiled during several years (mid- to long-term) and at different spatial scales across Europe, covering in turn manifold approaches: mycological data, dendrochronological information, climatic data and forest stand parameters. The results showed that: (i) only under more water-limited conditions, both the tree growth and the mushroom productivity are more sensitive to precipitation events, resulting in higher synchrony between both processes; (ii) models may be used to reconstruct mushroom production along historical periods based on dendrochronological information, but also to predict future mushroom yields based on climate-sensitive tree and stand growth predictions; (iii) forest thinning may cause potential short-term shifts in resource allocation of fungi from below- to above-ground structures; and (iv) forest thinning practices with a careful removal of trees does not compromise the sporocarp diversity, but lead to short-term successional changes in fungal assemblages.
http://hdl.handle.net/10803/671578
... The y-axis in the PRC diagram represents the first principal component of the variance explained by differences between treatments in time, and the xaxis shows years of the study. On the right side of the PRC diagram there is an additional axis showing species scores and their affinity for the response shown in the diagram (Van den Brink and Ter Braak, 1999;Van den Brink et al., 2009). ...
The value of leaving tree retention groups (TRGs) in clear-cuts has been verified in the last 30 years on the basis of the responses of various organisms, including carabid beetles. Most such research in Europe has been conducted in the Fennoscandian taiga. However, there is a lack of such studies of TRGs in the lowland temperate pine forests of Central Europe. Therefore I conducted a follow-up of carabid beetles in TRGs over the first three years after clear-cutting. The treatments were TRGs of different sizes, i.e. large (0.07 ha), medium (0.05 ha) and small (0.02 ha), together with the surrounding space in the clear-cuts and the neighboring control, i.e. mature unharvested pine stands. There were 3 sites, each with 6 TRGs (2 TRGs in each of the 3 size). (1) The rarefied species number, abundance and percentage of small zoophages in the assemblages inhabiting the control stands and TRGs were similar. (2) The proportion of forest fauna was higher in the assemblages inhabiting the control stands than in the TRGs, which was associated with colonization of TRGs by non-forest fauna and by the dominance it achieved. (3) Between the first and second year, the rarefied species number increased in the control stands and in the largest TRGs. (4) As the distance from the TRGs increased, the abundance and percentages of individuals representing small zoophages and forest species decreased, while the percentage of hemizoophages, generalists and open-habitat species increased. (5) In successive years there was a decrease in the proportion of forest fauna in the clearing and an increase in the rarefied species number, abundance, and proportion of individuals representing large zoophages and open-habitat species. (6) In the first two years of the study the carabid assemblages living in the control stands and those in the large TRGs were the most similar. (7) At the species level, Carabus violaceus was characteristic of large TRGs, and Amara consularis of small TRGs. Harpalus latus was a species characteristic of the area of the clearing furthest from the TRGs. In contrast with other research, I conclude that even such small TRGs as the ones I studied provide support for forest carabids in the first few years after clear-cutting. However, among the three sizes of TRGs, the largest ones (0.07 ha) offer the best protection for forest fauna. It is important to leave several such TRGs in the clear-cut area to form an archipelago of “habitat islands” facilitating the movement and survival of forest species.
... Principal response curves. To test the hypothesis that bryophyte community composition is altered by long-term warming, we applied principal response curves (PRCs) (van den Brink et al. 2009) to the species composition (with bryophyte cover as an abundance measure) matrix data for the years 1995, 1999, 2001 and 2013. Because of unbalanced data for 2013, we opted not to conduct a formal permutation test. ...
Climate change is expected to affect alpine and Arctic tundra communities. Most previous long-term studies have focused on impacts on vascular plants, this study examined impacts of long-term warming on bryophyte communities. Experimental warming with open-top chambers (OTCs) was applied for 18 years to a mesic meadow and a dry heath alpine plant community. Species abundance was measured in 1995, 1999, 2001 and 2013. Species composition changed significantly from original communities in the heath, but remained similar in mesic meadow. Experimental warming increased beta diversity in the heath. Bryophyte cover and species richness both declined with long-term warming, while Simpson diversity showed no significant responses. Over the 18-year period, bryophyte cover in warmed plots decreased from 43 % to 11 % in heath and from 68 % to 35 % in meadow (75 % and 48 % decline, respectively, in original cover), while richness declined by 39 % and 26 %, respectively. Importantly, the decline in cover and richness first emerged after 7 years. Warming caused significant increase in litter in both plant communities. Deciduous shrub and litter cover had negative impact on bryophyte cover. We show that bryophyte species do not respond similarly to climate change. Total bryophyte cover declined in both heath and mesic meadow under experimental long-term warming (by 1.5–3 °C), driven by general declines in many species. Principal response curve, cover and richness results suggested that bryophytes in alpine heath are more susceptible to warming than in meadow, supporting the suggestion that bryophytes may be less resistant in drier environments than in wetter habitats. Species loss was slower than the decline in bryophyte abundance, and diversity remained similar in both communities. Increased deciduous shrub and litter cover led to decline in bryophyte cover. The non-linear response to warming over time underlines the importance of long-term experiments and monitoring.
... The PRC focuses on effects of treatments factoring out variations between replicate microcosms and differing dates 54 . The first principal component of variance, being explained by the interaction of treatment and time, is displayed on the y-axis, whereas sampling dates are depicted on the x-axis 54 . Additionally, species scores on a second y-axis reflect the affinity of single species to the community-based response curve. ...
Herbivores are constitutive elements of most terrestrial ecosystems. Understanding effects of herbivory on ecosystem dynamics is thus a major, albeit challenging task in community ecology. Effects of mammals on plant communities are typically explored by comparing plant densities or diversity in exclosure experiments. This might overestimate long-term herbivore effects at community levels as early life stage mortality is driven by a multitude of factors. Addressing these challenges, we established a set of 100 pairs of ungulate exclosures and unfenced control plots (25 m 2) in mixed montane forests in the Alps in 1989 covering a forest area of 90 km 2. Investigations ran until 2013. Analogous to the gap-maker-gap-filler approach, dynamically recording the height of the largest trees per tree species in paired plots with and without exclosures might allow for assessing herbivore impacts on those individuals with a high probability of attaining reproductive stages. We thus tested if recording maximum heights of regenerating trees would better reflect effects of ungulate herbivory on long-term dynamics of tree regeneration than recording of stem density, and if species dominance patterns would shift over time. For quantifying the effects of ungulate herbivory simultaneously at community and species level we used principle response curves (PRC). PRCs yielded traceable results both at community and species level. Trajectories of maximum heights yielded significant results contrary to trajectories of total stem density. Response patterns of tree species were not uniform over time: e.g., both Norway spruce and European larch switched in their response to fencing. Fencing explained about 3% of the variance of maximum tree heights after nine years but increased to about 10% after 24 years thus confirming the importance of long-term surveys. Maximum height dynamics of tree species, addressed in our study, can thus reflect local dominance of tree species via asymmetric plant competition. Such effects, both within and among forest patches, can accrue over time shaping forest structure and composition.
... Although PRCs have proven to be a powerful tool to show effects on interacting communities that can often not be elucidated by univariate methods (e.g. van den Brink et al. 2009;Moser et al. 2007;Heegaard & Vandvik 2004;van den Brink et al. 2003;Frampton et al. 2000;Kedwards et al. 1999) and have been judged as eventually helpful (ISO 2014), they are not included as standard tools in guidelines yet. ...
The purpose of this project was to provide scientifically robust and practical information on the variability of the endpoints assessed in earthworm field studies, the statistical significance of the results and the level of the statistically detectable effects of the chemicals tested - with the aim of developing suggestions for improving the test design. Best-practice studies reveal low power to detect differences between control and test chemical treatment plots. An adapted test design should contain an option to perform regression (ECx) approaches, which have been suggested as an alternative to the currently performed threshold (NOEC) approach. A pilot field study was performed according to a newly developed combined NOEC- and ECx-test design with the test
chemical carbendazim. The ECx design leads to more robust conclusions for environmental risk assessment. The calculation of effect thresholds (NOEC/LOEC) should be conducted with the most powerful multiple test procedure for given data prerequisites. If applicable to the data, the closure principle computational approach test (CPCAT) is the preferred option. The evaluation and interpretation of the data at plot (pooled samples of 1 m2 in total used as replicates) and sub-plot level (single samples as replicates of 0.25 m2) should be requested. According to the experiences made during the performance of the pilot study and the results of the statistical analyses, a draft OECD test guideline was developed. As of now, the discussion of the draft test guideline is ongoing.
... Principal Component Analysis was completed on the correlation matrix to choose the environmental variables associated with each of the first few principal axes most strongly. The redundancy analysis (RDA) was chosen because linear responses are expected along a gradient smaller than 3.0 standard given by (Braak, 2009). Due to a large number of environmental variables, the forwarded selections were used to determine the least number of significant variables (P˂0.05) to include in the model. ...
... Differences in terms of ecological guilds, life forms and eco-morphological groups among the three phases of the hydrological cycle were tested using the analysis of the variance (ANOVA) followed by a Tukey's post-hoc test (PAST 3.12; Hammer et al., 2001). Finally, changes in the relative abundances of diatom species only during the rewetting phase were analysed with the Principal Response Curves (PRC, van den Brink et al., 2009) with the function "prc" of the package vegan (Oksanen et al., 2015) in the R statistical software (R Core Team, 2018). Significance was tested by means of a Monte Carlo test with 999 permutations. ...
Over the last decades, the ongoing global climate change, combined with consequent increasing water demand for human needs, is causing recurrent droughts in previously perennial streams. These phenomena have been dramatically increasing their extent, with significant repercussions on the entire food web. Consequences of water scarcity are particularly remarkable in mountain streams, where the frequency of droughts is increasing at a rate that does not allow species to adapt. In the present research, we monitored benthic diatom communities within an intermittent Alpine river (Pellice River; North-Western Italy) during the three key phases of its hydrological cycle: i) stable flow ii) lentification iii) rewetting of the riverbed after a supraseasonal drought lasting five months. We tested the response of diatom communities in terms of compositional, structural and functional metrics (primary production, species composition, ecological guilds, life forms and eco-morphological groups) hypothesising both taxonomic and functional changes during the different steps of this hydrological cycle. Significant changes in benthic chlorophyll a occurred in the three hydrological phases. In particular, the relative proportion of the chlorophyll a of the three main autotrophic groups inhabiting the periphyton (namely diatoms, cyanobacteria and green algae) resulted as a reliable metric for the evaluation of the hydrological disturbance. Diatom chlorophyll a significantly decreased during both lentification and drought. The three phases were significantly characterized by different species and functional groups. During the stable flow the low profile (i.e., species of short stature, adapted to high current velocities and low nutrients concentrations) was the most representative guild and Achnanthidium pyrenaicum was the most abundant species; this phase was also characterized by the presence of stalked taxa. We observed a significant decrease of high profile species (i.e., species of tall stature, adapted to high nutrients concentrations and low current velocities) during the lentification phase, which was characterized by taxa belonging to the genera Navicula, Nitzschia and Ulnaria. During the rewetting, small and medium sized high profile diatoms as well as motile ones (i.e., fast moving species) characterized the assemblages. Our results showed that the complete recovery of diatom communities took at least 70 days after water return. The rapid and widespread extension of droughts in the Alpine area will have severe consequences on the river biota, also favouring the spread of invasive taxa. For this reason, outlining patterns of diatom response to droughts and detecting reliable metrics for the evaluation of this specific impact is very urgent and important.
... We used the prc function in the vegan package(Oksanen et al., 2019) to perform these analyses. The principal response curve method is based on redundancy analysis (RDA) and is commonly used to assess changes in biological communities to stressors, from an eco-toxicological perspective (van den Brink, den Besten, bijde Vaate, & ter Braak, 2009). The The PRC method allows estimating which species gain in abundance at the expense of others in response to the treatment and with "time" as an explicit factor (Van denBrink & Ter Braak, 1999). ...
... Two diagrams were generated: the first PRC diagram corresponds to the year of sampling (pooled samples obtained in all seasons), whereas the second one corresponds to the seasons in both years. The second axis on the right side of the PRC diagram shows species scores and affinities of each species according to the response shown in the diagram (Van den Brink & Ter Braak, 1999;Van den Brink et al., 2009). The PRC curve was plotted for the two treatments: the control stands, forming the horizontal line of the PRC diagram, and the clear-cuts, plotted under the horizontal axis. ...
A 2‐year study of litter dwelling beetles was conducted in different mature pine stands and clear‐cuts in Lithuania using the litter sifting method. We hypothesized that clear‐cutting and subsequent ploughing would increase species diversity and the abundance of beetles, and also would encourage the immediate appearance of early‐successional beetle species replacing late successional species in the clear‐cuts.
We did not confirm a hypothesis regarding increase in the number of species and abundance of beetles in clear‐cuts.
Our hypothesis regarding the immediate appearance of early successional species and disappearance of late‐successional species in clear‐cuts was confirmed.
We also revealed that subsequent soil ploughing in clear‐cuts did not accelerate this process, which was linked to the possibility of late successional species surviving in the undisturbed spaces between the strips of ploughed soil.
The present study shows that late‐successional forest litter‐dwelling coleopteran species of old pine forests have a better chance of survival in a ploughed clear‐cut, at least in northern Europe, than has been reported in other studies.
... den Besten, bijde Vaate, & ter Braak, 2009). The significance of the principal component PRC diagrams was tested by permutation tests (9,999 permutations). ...
Grassland habitats are particularly threatened in Europe, especially in marginal areas where funds and manpower for their conservative management are limited. Knowledge of the vegetation dynamics is crucial for the timeliness and economy of any conservation actions. However, there is a lack of studies on effective and rapid containment of tall rhizomatous geophytes, such as asphodel (Asphodelus macrocarpus Parl. subsp. macrocarpus), which are particularly active in the earliest stages of the natural vegetation succession. We present an interdisciplinary study carried out on an abandoned semi‐natural grassland (European Union habitat code 6210*) colonized by Asphodel within a Natura 2000 site in the central Apennines (Italy). This experimental trial lasted 4 years (2012–2015) and applied three different treatments (mowing with removal of cut material, mowing without removal of cut material and chopping), compared to the control (abandonment). The results highlight that the disturbance produced by biomass removal has positive effects on biodiversity. In particular, mowing (both with or without removal of cut material) provided better results for restoration of the grassland biodiversity, even over the short term. Chopping is not a viable alternative to mowing, especially because of the risk of eutrophication over time, and the consequent settlement and increase in nitrophilous species.
... The effects caused by the pesticide are dangerous on the organism and the community described by interaction between all organism in environment such as competition or predation and indirect effects (Preston, 2002) The comet assay has been used as an important tool for monitoring genotoxicity in aquatic environments (Lemos et al., 2005) there are large amounts of pesticides application globally and given the fact that they are prepared to be harm to all organism, there is a high probability for counteractive environmental effects also on non-target pollutant (Oerke EC et al, 2004) Among the tests for genotoxicity, the micronucleus test has been widely utilized in fish to determine exposure to water pollutants, in environment as well as under experimental laboratory conditions (Minissi et al., 1996). Farmers are using a variety of pesticides indiscriminately and a sharp increase was observed during the last decades (Rahman, 2013). The application of pesticides may lead to contamination of the aquatic environment through several ways including: spray drift, runoff, and leaching . ...
In this study, the molecular biomarker (comet assay) was used as a technique in order to study the effect of the pesticides on some aquatic organism, since the exposure to the pesticides in the environment are very widely. (Cerithium tenellum) was selected as one species of snail in al-Hilla river, collected from al-Hilla river and exposed to three concentration from insect pesticides (0.001 ppm, 0.015ppm, 0.02ppm). After 24 hours, the observation was conduct for the selected concentration and it was found that the first concentration of the pesticide caused slow movement in species but the second and three concentration caused death of the species. During the reading of the (DNA) through technique (comet assay), depending on the comet length and tail moment, the first concentration the ratio damage of (DNA) was (36), while the second concentration (47) and third concentration was (92), these results refer to the first concentration which has a slight effect, while second and third concentration its effect was deadly. From the results, the main conclusion is that the concentrations (0.015 ppm, 0.02 ppm) highly recommend not to use in agriculture or aquatic environment, because of its effect on organism sand aquatic environment specially if the exposure was daily to the pesticides.
... We grouped the zooplankton into pelagic (Daphnia parvula, Ceriodaphnia lacustris, Diaphanasoma bergei, Bosmina longirostris, and Moina sp.) and littoral (Scapholeberis mucronata, Chydorus sphaericus, Pleuroxus denticulatus, Alona setulosa, and Lathonura rectirostris) groups following Thorp and Covich (2010) and Sinclair et al. (2015) for comparing alpha and gamma richness, because zebra mussels negatively influence pelagic zooplankton species, while promoting littoral zooplankton species (Dzialowski 2013. Thus, if there was sufficient turnover from pelagic-dominated to littoral-dominated communities, we may not observe a change in alpha richness, even though species are being ❖ www.esajournals.org ...
The global increase in anthropogenic disturbances has introduced patterns of heterogeneity across many landscapes. Local disturbances are often studied from the perspective of the local habitat patch, where their direct effects on local community composition are more evident. However, local disturbances can have regional implications when connected to other patches within a metacommunity. Invasive species provide a unique opportunity for studying the influence of biologically induced disturbances on metacommunity dynamics, because invasive species are influential in structuring local communities and have a propensity for dispersing across landscapes, producing gradients in disturbance intensity. The invasive zebra mussel, Dreissena polymorpha, is widespread throughout the eastern USA and is having negative impacts on native communities. Using zebra mussels to induce disturbances in mesocosm zooplankton communities, we tested how the relative abundance of disturbed and undisturbed habitat patches within a metacommunity influenced community and metacommunity biodiversity and composition. The zebra mussels negatively affected pelagic zooplankton species richness, while facilitating the population growth of littoral species. Undisturbed communities mitigated disturbance‐induced local and regional pelagic species loss in heterogeneous metacommunities, while the fully disturbed metacommunity experienced significant losses of pelagic zooplankton at local and regional scales. Disturbed communities influenced undisturbed communities in heterogeneous metacommunities by increasing the densities of littoral zooplankton species. Overall, these results highlight the important effects that undisturbed habitat patches can have on mitigating species loss in locally disturbed patches and maintaining regional biodiversity in heterogeneous metacommunities.
... Also the use of the distance between subsequent sampling dates has been applied successfully before (Ernest and Brown, 2001;Thibault and Brown, 2008). There are also some other methods available to assess community shifts over time, such as the use of Principle Response Curves (van den Brink et al., 2009;Florentine et al., 2015;Tebby et al., 2017), but this is less suitable to our situation, as we are using natural communities without a clear control community. Hence, we conclude that using Hellinger distances is an appropriate analysis tool to make community responses comparable across contexts. ...
Extreme climatic events can have profound effects on ecosystems. Climate change is causing an increase in the frequency and intensity of extreme events, which raises the probability that natural ecosystems will be exposed to subsequent or simultaneous extreme events. Exposure to multiple extreme events may involve very different abiotic stressors, which makes it hard to compare their consequences for more than a single or a few species, limiting our knowledge of community level effects. Here, we propose a novel approach to assess how different abiotic stressors influenced soil arthropod communities in a coastal ecosystem, using a species abundance time series of more than 2 years. We first correlated shifts in community composition with the climatic conditions preceding the sampling dates. Temperature was found to be the most important factor influencing community composition in both locations. Based on local meteorological data, we then defined five types of extreme events which occurred during our monitoring period: heat, cold, drought, heavy precipitation, and high sea water levels. To compare the effect of different types of extreme climatic events on community composition, we calculated the multidimensional Hellinger distance between two subsequent sampling dates, which is a measure for the compositional dissimilarity between communities. Extreme events were expected to result in a larger change in community composition between sampling dates and thus a larger Hellinger distance. However, no significant difference in Hellinger distance was found for intervals with or without extreme events in three out of the four location-vegetation combinations. In the saline location with an open vegetation type we found that Hellinger's distance was reduced when extreme events had occurred, which is discussed in the light of the buffering potential of different vegetation types. Our study illustrates the novel use of an established method from the community ecological toolbox to facilitate direct comparison of different types of extreme climatic events on community composition. We highly encourage other ecologists with long-term monitoring datasets to perform similar analyses and test the general applicability of this method.
... On the PRC diagram, the first principal component of the variance explained by treatment differences in time is displayed on the y-axis, while time (sampling data) is shown on the x-axis. The additional axis on the right side of the PRC diagram shows species scores and the affinity of different species for the re- sponse shown in the diagram (Van den Brink and Ter Braak, 1999; Van den Brink et al., 2009). The PRC curve was plotted for 4 variants: the least disturbed stands formed the horizontal axis of the PRC diagram, and the pine plantation and the moderately and severely disturbed stands were plotted above the horizontal axis. ...
... In experiment I, arthropod abundances were analysed between collection dates by constructing principal response curves (PRS) (Brink et al. 2008) to compare population dynamics in each of the three data sets collected throughout the season. Mean number of arthropods per sample plot unit (sample plot units at the same location, i.e. same host plant plot side and middle) per host plant per sampling date was considered. ...
The predation rate of pea aphids, Acyrthosiphon pisum Harris by ladybird-beetles, spiders, and parasitism by hymenopterous parasitoids (braconids) within complex habitats was tested. Altogether 20 pea, 20 alfalfa and 20 red clover plots were established in a sequential block design, whereupon the aphids along with their predators and parasitoids were assessed both in the middle and at the field margins. The performance of aphids and predation/parasitism were also tested in meso-environments (i.e. enclosed field cages) with two different host plant species per environment. The data shows that spider density on pea is generally high, but it is lower on plants in the vicinity of clover and alfalfa. Braconid parasitoids, Aphidius ervi Haliday parasitized pea aphids on all host plants and similar parasitoid pressure was observed on all host plants tested. Meso-environment experiments further explained the low predation of ladybirds when foraging for prey on pea plants. Using five polymorphic microsatellite markers, it was found that whilst there was no clear trend in terms of the pattern of population genetic variation detected, the fact that some pea aphid populations on certain sample plots showed marginally statistically significant differences (divergence) in terms of interpopulation Fst values, may well reflect predator choice in relation to plant host. Overall, aphids appear to be under various selective pressures from both higher and lower trophic levels.
... In the present study, our objective was instead to look specifically at the trajectory of temporal change and to ask questions about plots' divergence from initial conditions, not just from each other. We used a modified Principal Response Curve (PRC) method as described in Van den Brink et al. (2009) where, instead of comparing to a dynamic reference community, we created a static reference that was not allowed to change over time so that the PRC analysis compared all six herbivore treatments to this reference at each time step. The reference community was defined as the cover of each species in 1999 averaged across all herbivore treatments for each block (to create one average value per Compositional turnover (more turnover means less stability) extent of change in community composition from one time step to another absolute value of change in PRC score between consecutive sample periods no differences by herbivore treatment; compositional turnover was greatest during droughts and post-drought periods block). ...
... We tested for a treatment effect using 1000 restricted permutations, taking the nested structure of sampling locations within channels into account (Legendre et al., 2011). To determine the LOEC at the community level we performed a Principal Components Analysis (PCA) on the transformed invertebrate abundances separately for each sampling date (Van den Brink et al., 2009). The sample scores of this PCA were subsequently analyzed by using Linear Mixed Models, LMM (Bates et al., 2015) with stream channel as random intercept. ...
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.
Heavily modified water bodies (HMWB) have been seriously affected by human activities and natural processes promoting their imbalance, and impacting their functioning and biodiversity. This study explores a new approach of monitoring and assessing water quality in Mediterranean reservoirs using phytoplankton communities across a disturbance gradient, according to water framework directive. Phytoplankton and environmental data were sampled in 34 reservoirs over 8 years. Two types of reservoirs were analyzed: Type1 “run-of-river reservoirs” (located in the main rivers, with a low residence time); and Type2 “true reservoirs” (located in tributaries, with high residence time). The transition from deeper and colder reservoirs (reference sites) to shallow and warmer (impaired sites) was clear in Type2, correlated to organic pollution and mineral gradients. Impaired sites from both types showed a higher richness of tolerant taxa. Principal response curve (PRC) provided a concise summary of phytoplankton temporal dynamics and assessed ecosystem health for Mediterranean HMWBs. PRC will provide a powerful tool for environmental quality assessment and be incorporated into monitoring and assessment programs. This approach can help policymakers to manage natural capital to achieve multiple objectives, mainly increasing ecosystem services, and improve readability and interpretation of spatial patterns in temporal changes.
There is increasing interest in further developing the plant protection product environmental risk assessment, particularly within the European Union, to include the assessment of soil microbial community composition, as measured by metabarcoding approaches. However, to date, there has been little discussion as to how this could be implemented in a standardised, reliable, and robust manner suitable for regulatory decision making. Introducing metabarcoding-based assessments of the soil microbiome into the plant protection product risk assessment would represent a significant increase in the degree of complexity of the data that needs to be processed and analysed in comparison to the existing risk assessment on in-soil organisms. The bioinformatics procedures to process DNA sequences into community compositional datasets currently lack standardisation, while little information exists on how this data should be used to generate regulatory endpoints and the ways in which these endpoints should be interpreted. Through a thorough and critical review, we explore these challenges. We conclude that currently, we do not have a sufficient degree of standardisation or understanding of the required bioinformatics and data analysis procedures to consider their use in an environmental risk assessment context. However, we highlight critical knowledge gaps and the further research required to understand whether metabarcoding-based assessments of the soil microbiome can be utilised in a statistically and ecologically relevant manner within a plant protection product risk assessment. Only once these challenges are addressed can we consider if and how we should use metabarcoding as a tool for regulatory decision making to assess and monitor ecotoxicological effects on soil microorganisms within an environmental risk assessment of plant protection products.
Windstorms impact the functioning and structure of forests and cause economic losses. For this reason, various potential methods of regenerating windthrown stands are investigated. Some of these studies use invertebrates, such as carabid beetles (Col., Carabidae). Salvage logging is used to recoup some of the economic ecosystem losses but increases the environmental impact of windthrow. I sampled ground beetles annually over 19 years (2003-2021y) in stands without salvage logging to test the effect of three varying levels of disturbance (severely, moderately and least disturbed stands with canopy cover of 10-30 %, 40-60 % and 70-90 %, respectively) on the regeneration of carabid assemblages and to determine its association with changes in the soil environment and in the recovering stands. Increased disturbance severity increased the abundance (up to 0.4 ind/trap/day) and species richness of ground beetles (up to 16.4) and proportion of beetles associated with early successional habitats (up to 53.5 %). Recovery of carabid assemblages and the environment was slowest in the severely disturbed stands, where at high soil pH nitrification initially increased the pool of nitrogen in the soil (up to 0.3), which was exploited by nitrophilous grasses taking over the space (up to 37,5 %), limiting the occurrence of forest species (decrease from 82.2 % to 51.4 %) and delaying the development of natural regeneration. Carabid recovery and ecosystem regeneration were associated with forest mosses surviving (84.1 % coverage) in patches with a high leaf area index (up to 1.9) and with the presence of Vaccinium vitis-idaea (up to 53.3 % coverage) in the moderately and least disturbed stands. The study indicated advanced successional development of carabid assemblages in less disturbed stands which can regenerate naturally. Natural recovery of carabids and regeneration of the most disturbed stands, rapidly taken over by nitrophilous grasses, was impeded; therefore, such stands should be regenerated traditionally.
Pesticides constitute an integral part of modern agriculture. However, there are still concerns about their effects on non-target organisms. To address this the European Commission has imposed a stringent regulatory scheme for new pesticide compounds. Assessment of the aquatic toxicity of pesticides is based on a range of advanced tests. This does not apply to terrestrial ecosystems, where the toxicity of pesticides on soil microorganisms, is based on an outdated and crude test (N mineralization). This regulatory gap is reinforced by the recent methodological and standardization advances in soil microbial ecology. The inclusion of such standardized tools in a revised risk assessment scheme will enable the accurate estimation of the toxicity of pesticides on soil microorganisms and on associated ecosystem services. In this review we (i) summarize recent work in the assessment of the soil microbial toxicity of pesticides and point to ammonia-oxidizing microorganisms (AOM) and arbuscular mycorrhizal fungi (AMF) as most relevant bioindicator groups (ii) identify limitations in the experimental approaches used and propose mitigation solutions, (iii) identify scientific gaps and (iv) propose a new risk assessment procedure to assess the effects of pesticides on soil microorganisms.
Ecosystem-level effects of stress are the net result of the direct effects of the stressor and indirect effects caused by altered interactions between organisms and between biotic and abiotic components of the environment. Measuring impacts of any single stressor at the ecosystem level means acknowledging, and accounting for, a number of simultaneously acting processes.It is therefore highly unlikely that there are radiation-specific responses at an ecosystem level. In the field, ecosystem-level responses will be the net result of the effects of the various radionuclides, other contaminants, environmental conditions and species interactions. However, this does not mean that we should not attempt to measure ecosystem-level endpoints, but in order to pinpoint the relative contribution of radiation in this multi-factorial situation, robust sampling and statistics and a sound ecological foundation is required.What, then, are ecosystem-relevant endpoints? They include those that describe ecosystem structure and function and sometimes also the services an ecosystem provides to humans. Quantifying ecosystem effects may thus include measuring species composition, abundance, biodiversity, food web complexity and connectivity, habitat complexity (ie. aspects of ecosystem structure) and production, decomposition, pollination, functional or trait
diversity (ie. ecosystem function). Many of these may also be used to estimate impacts on ecosystem services (e.g., provision of food, carbon storage). Many are by necessity proxy measures which we assume reflect the state of the ecosystem, since overall ecosystem condition is very hard to quantify. However, in risk assessment these proxies are sometimes combined into general measures of ‘ecological status’ and in ecosystem science, various metrics are used as integrative measures of the vulnerability or resilience of the ecosystem.In this paper, I give an overview of the ways we can address and measure ecosystem-relevant and ecosystem-level endpoints in science and risk assessment, including community structure and function, ecological traits, ecosystem processes, ecological network metrics, ecological integrity and ecosystem services. I draw on examples from ecosystem science, stress ecology, ecotoxicology and environmental impact and risk assessment and discuss how these can inform assessment of radiation impacts.
Background:
Increasing evidence indicates that psychopathological disorders are associated with the gut microbiota. However, data are largely lacking from long-term longitudinal birth cohorts, especially those comprising low-risk healthy individuals. Therefore, this study aims to describe gut microbiota development in healthy children from birth till age 10 years, as well as to investigate potential associations with internalizing and externalizing behavior.
Results:
Fecal microbial composition of participants in an ongoing longitudinal study (N = 193) was analyzed at 1, 3 and 4 months, and 6 and 10 years of age by 16S ribosomal RNA gene sequencing. Based on these data, three clusters were identified in infancy, two of which were predominated by Bifidobacterium. In childhood, four clusters were observed, two of which increased in prevalence with age. One of the childhood clusters, similar to an enterotype, was highly enriched in genus-level taxon Prevotella_9. Breastfeeding had marked associations with microbiota composition up till age 10, implying an extended role in shaping gut microbial ecology. Microbial clusters were not associated with behavior. However, Prevotella_9 in childhood was positively related to mother-reported externalizing behavior at age 10; this was validated in child reports.
Conclusions:
This study validated previous findings on Bifidobacterium-enriched and -depleted clusters in infancy. Importantly, it also mapped continued development of gut microbiota in middle childhood. Novel associations between gut microbial composition in the first 10 years of life (especially Prevotella_9), and externalizing behavior at age 10 were found. Replications in other cohorts, as well as follow-up assessments, will help determine the significance of these findings.
Fungal communities are especially relevant in Mediterranean regions, a ‘hotspot’ of fungal diversity, and where the value of edible commercial sporocarps may be much higher than the income from timber products. Assessing the effects of forest management practices together with the modulating role of climate on sporocarp community composition and diversity is crucial for understanding their impacts on fungal-related ecosystem services. Yet, previous research on forest management impacts on aboveground fungal diversity and community composition is scant, sometimes contradictory and mainly focused on rather short-term impacts. We quantified the long-term response of the sporocarp community composition and diversity to different forest thinning intensities in Mediterranean Pinus pinaster forest stands, and the interactions with weather conditions in modulating the fungal response. We relied on 28 permanent plots representing a thinning intensity gradient, monitored for sporocarp diversity on a weekly basis during eleven consecutive years. Weather conditions of each plot were obtained through interpolation from different meteorological stations. Overall, the fungal sporocarp community composition showed short-term (
Loss of vegetation and soil erosion are symptoms of widespread rangeland degradation across most of the Icelandic highlands. Areas at different stages of degradation coexist as a mosaic that includes both vegetated heathlands, and exposed gravelly deserts. Revegetation efforts have included fertilizer applications and grazing exclusion to increase plant biomass and reduce bare ground, but their effectiveness is predicted to differ depending on the stage of degradation for a certain area. In this study, we used a four-year field experiment to test the predictions of a state-and-transition model for the Icelandic highlands. We measured the combined effects of grazing exclusion and factorial applications of nitrogen (N), phosphorus (P) and potassium (K) fertilizers, on plant biomass, species richness, amount of exposed bare ground and plant community composition in a dwarf-shrub heathland and a gravelly desert habitat. After four years: 1) grazing exclusion alone had no effect in either habitat; 2) fertilizers increased biomass in both habitats, especially in plots treated with NP or NK; 3) the combination of fertilizers and grazing exclusion produced the greatest amount of aboveground biomass, predominantly of forb and graminoid species. In the dwarf-shrub heath, the increase in biomass in fertilized and fenced plots also corresponded to a loss in species richness, whereas in the gravelly desert, increased biomass reduced the amount of bare ground without reducing species richness. Our results reinforce the importance in understanding the effects of different management interventions across ecological conditions to determine the most effective revegetation approach.
Agricultural pollution with fertilizers and pesticides is a common disturbance to freshwater biodiversity. Bacterioplankton communities are at the base of aquatic food webs, but their responses to these potentially interacting stressors are rarely explored. To test the extent of resistance and resilience in bacterioplankton communities faced with agricultural stressors, we exposed freshwater mesocosms to single and combined gradients of two commonly used pesticides: the herbicide glyphosate (0‐15 mg/L) and the neonicotinoid insecticide imidacloprid (0‐60 μg/L), in high or low nutrient backgrounds. Over the 43‐day experiment, we tracked variation in bacterial density with flow cytometry, carbon substrate use with Biolog EcoPlates, and taxonomic diversity and composition with environmental 16S rRNA gene amplicon sequencing. We show that only glyphosate (at the highest dose, 15 mg/L), but not imidacloprid, nutrients, or their interactions measurably changed community structure, favoring members of the Proteobacteria including the genus Agrobacterium. However, no change in carbon substrate use was detected throughout, suggesting functional redundancy despite taxonomic changes. We further show that communities are resilient at broad, but not fine taxonomic levels: 24 days after glyphosate application the precise amplicon sequence variants do not return, and tend to be replaced by phylogenetically close taxa. We conclude that high doses of glyphosate – but still within commonly acceptable regulatory guidelines – alter freshwater bacterioplankton by favoring a subset of higher taxonomic units (i.e. genus to phylum) that transiently thrive in the presence of glyphosate. Longer‐term impacts of glyphosate at finer taxonomic resolution merit further investigation.
Few studies have been conducted with regard to the effects of insecticides on population dynamics of shrimps and associated groups such as macrophytes, phytoplankton, microorganisms etc. In the present study, effects of a single application of fenoxycarb were tested using indoor freshwater systems dominated by Neocaridina palmata and Ceratophyllum demersum (Dicotyledons: Ceratophyllales). The no observed effect concentration (NOEC) and lowest observed effect concentration (LOEC) for the N. palmata, as scaled by liberated chitobiase, were 6.48 μg/L and 27.76 μg/L, and the dose-related effect lasted for 14 days. Results of principal components analysis (PCA) and that of principal response curves (PRC) method showed that the biomass of C. demersum and concentrations of chlorophyll-a were suppressed, while the concentrations of phycocyanin were promoted. Illumina high-throughput sequencing was adopted to determine the diversity of bacteria and fungi in the media. Result of PCA and PRC showed that the fenoxycarb promoted photosynthetic bacteria (e.g. Cyanobacteria and Rhodobacterales) and suppressed groups involved in nitrogen and sulfur the transformation (e.g. Flavobacterium, hgcI_clade, Cystobasidium, Rhodotorula and Rhizobiales). Promotion in pathogen such as Pseudomonas and Cercozoa and suppression in beneficial taxa such as Novosphingobium and Rhodotorula were also sighted. Result of study suggested a water quality deterioration due to fenoxycarb applications.
Background and aim Global warming is expected to have large impacts on high alpine and Arctic ecosystems in future. Here we report the effects of 18 years of experimental warming on two contrasting high alpine plant communities in subarctic Sweden.Methods Using open-top chambers (OTCs), we analysed the effects of long-term passive experimental warming on two high alpine plant communities, a species- and nutrient-poor heath and a more nutrient- and species-rich mesic meadow. We determined the impact on species composition, species diversity (at the level of rare, frequent and dominant species in each community), and phylogenetic and functional diversity.Key results Long-term warming drove differentiation in the species composition in both heath and meadow vegetation, with the warmed plots having distinctly different species composition in 2013 compared with 1995. In addition, variability in species composition increased in the meadow, while it decreased in the heath. The long-term warming had a significant negative effect on the three orders of phylogenetic Hill diversity in the meadow. There was a similar tendency in the heath, but only the phylogenetic diversity of dominant species was significantly affected. Long-term warming caused a reduction in graminoids in the heath, while deciduous shrubs increased. In the meadow, cushion-forming plants showed an increase in abundance from 2001 to 2013 in the warmed plots. Conclusions Responses in species and phylogenetic diversity to experimental warming varied over both time (medium vs long-term responses) and space (i.e. between the two neighbouring plant communities heath and meadow). The meadow community was more negatively affected in terms of species and phylogenetic diversity than the heath community. A potential driver for the changes in the meadow may be decreased soil moisture caused by the long-term warming.
Alongside fires, windthrows are among the strongest forest disturbances, which is why research on the regeneration of windthrown forests is so important for silviculture. While there have been many studies devoted to the regeneration of windthrown boreal spruce forests, few have dealt with the regeneration of Scots pine forests in the temperate zone.
In Pisz Forest (northern Poland), the State Forests administration left 475.6 ha of pine stands disturbed by windthrow for research on spontaneous ecosystem recovery, leaving all broken trees untouched. For the 11-year study (beginning in 2008, six years after the windthrow, when saplings became more abundant), 10 × 10 m research plots were established in pine stands with different classes of severity of windthrow disturbance: severely disturbed stands (canopy cover up to 30%), moderately disturbed stands (canopy cover of 40–60%) and the least disturbed stands (canopy cover of 70–90%). Each year all saplings on the plots were recorded, with measurements of their height, diameter at breast height, and changes in the percentage cover of forest floor vegetation and its species composition. Selected environmental variables were measured as well. Density of pine saplings in the severely disturbed stands was lower than in the moderately and least disturbed stands, while the density of birch saplings was higher in the moderately disturbed stands than in the least disturbed stands. Moss P. schreberi particularly favored spontaneous regeneration of pine saplings, while the nitrophilous grass D. flexuosa, overgrowing entire surfaces, impeded it. Soil cover by a litter layer alone also significantly hampered the emergence of tree saplings. An elevated content of nitrogen in the soil was conducive to rapid coverage of the area by D. flexuosa, while limiting cover by moss P. schreberi. Moss P. schreberi and shrubs V. vitis-idaea preferred soil with a high respiration
rate, while grass D. flexuosa avoided it. Two directions of spontaneous regeneration of windthrown stands were shown, depending on cover by grass or mosses and on the initial content of nitrogen in the soil, which provided the basis for indicating two different forest management strategies in windthrown pine forests.
• Aquatic ecosystems are biodiversity hot spots across many landscapes; therefore, the degradation of these habitats can lead to decreases in biodiversity across multiple scales. Salinisation is a global issue that threatens freshwater ecosystems by reducing water quality and local biodiversity. The effects of salinity on local processes have been studied extensively; however, the effects of salinisation or similar environmental stressors within a metacommunity (a dispersal network of several distinct communities) have not been explored.
• We tested how the spatial heterogeneity and the environmental contrast between freshwater and saline habitat patches influenced cladoceran biodiversity and species composition at local and regional scales in a metacommunity mesocosm experiment. We defined spatial heterogeneity as the proportion of freshwater to saltwater patches within the metacommunity, ranging from a freshwater‐dominated metacommunity to a saltwater‐dominated metacommunity. Environmental contrast was defined as the environmental distance between habitat patches along the salinity gradient in which low‐contrast metacommunities consisted of freshwater and low‐salinity patches and high‐contrast metacommunities consisted of freshwater and high‐salinity patches.
• We hypothesised that the α‐richness of freshwater patches and metacommunity γ‐richness would decrease as freshwater patches became less abundant along the spatial heterogeneity gradient in both low‐ and high‐contrast metacommunities, because there would be fewer freshwater patches that could serve as source populations for declining populations. We hypothesised that low‐contrast metacommunities would support more species across the spatial heterogeneity gradient than high‐contrast metacommunities, because, via dispersal, low‐salinity patches can support halotolerant freshwater species that can mitigate population declines in neighbouring freshwater patches, whereas` high‐salinity patches will mostly support halophilic species, providing fewer potential colonisers to freshwater patches.
• We found that α‐richness of freshwater mesocosms and metacommunity γ‐richness declined in saline‐dominated metacommunities regardless of the environmental contrast between the freshwater and saline mesocosms. We found that environmental contrast influenced freshwater and saline community composition in low‐contrast metacommunities by increasing the abundances of species that could tolerate low‐salinity environments through dispersal, whereas freshwater and high‐salinity communities showed limited interactions through dispersal.
• Freshwater mesocosms had a disproportionate effect on the local and regional biodiversity in these experimental metacommunities, indicating that habitat identity may be more important than habitat diversity for maintaining biodiversity in some metacommunities. This study further emphasises the importance in maintaining multiple species‐rich habitat patches across landscapes, particularly those experiencing landscape‐wide habitat degradation.
Plant community composition and functional traits respond to chronic drivers such as climate change and nitrogen (N) deposition. In contrast, pulse disturbances from ecosystem management can additionally change resources and conditions. Community responses to combined environmental changes may further depend on land-use legacies. Disentangling the relative importance of these global change drivers is necessary to improve predictions of future plant communities. We performed a multi-factor global change experiment to disentangle drivers of herbaceous plant community trajectories in a temperate deciduous forest. Communities of five species, assembled from a pool of fifteen forest herb species with varying ecological strategies, were grown in 384 mesocosms on soils from ancient forest (forested since at least 1,850) and post-agricultural forest (forested since 1950) collected across Europe. Mesocosms were exposed to two-level full-factorial treatments of warming, light addition (representing changing forest management) and N enrichment. We measured plant height, specific leaf area (SLA), and species cover over the course of three growing seasons. Increasing light availability followed by warming reordered species towards a taller herb community, with limited effects of N enrichment or the forest land-use history. Two-way interactions between treatments and incorporating intraspecific trait variation (ITV) did not yield additional inference on community height change. Contrastingly, community SLA differed when considering ITV along with species reordering, which highlights ITV's importance for understanding leaf morphology responses to nutrient enrichment in dark conditions. Contrary to our expectations, we found limited evidence of land-use legacies affecting community responses to environmental changes, perhaps because dispersal limitation was removed in the experimental design. These findings can improve predictions of community functional trait responses to global changes by acknowledging ITV, and subtle changes in light availability. Adaptive forest management to impending global change could benefit the restoration and conservation of understorey plant communities by reducing the light availability.
Knowledge on predator diet and drivers of prey selection is particularly of interest for an efficient management of predator and prey populations where predators potentially compete with humans for resources. Actual or perceived predation by Eurasian otter ( Lutra lutra ) on fish stocks generates conflicts in many countries. Recently, conflicts are heating up in riverine habitats, where multiple stressors affect stream fish populations. We combined dietary analysis of otter faeces and prey fish availability in three Austrian streams to assess spatial and seasonal differences in diet composition, the extent of (salmonid) fish consumption and the selection for specific salmonid fish sizes relative to their availability. Otters in upper reaches of temperate salmonid streams occupied a narrow trophic niche. Overall, otters fed predominantly on fish with salmonids dominating diet, both in terms of frequency and ingested biomass measures. Within the category of salmonids, otters selected for specific size classes. Concurrently, otters also displayed an opportunistic feeding behaviour, and seasonally and locally non-fish prey and other fish species than salmonids became key resources. Diet composition and salmonid size selection varied significantly within and between streams, which we relate to spatio-temporal variations of prey community composition and stream-specific habitat characteristics affecting prey vulnerability.
Large herbivores can shape young forest stands and determine the successional trajectory of forested ecosystems by selectively browsing palatable species at the sapling stage. Moose (Alces alces) is the dominant vertebrate herbivore in Fennoscandian boreal forests, and high population densities have raised concerns about potential negative effects on ecosystem functioning and properties including biological diversity and timber production. We used 31 herbivore exclosures in Norway to investigate how forests developed after clear‐cutting with or without moose present. We tested how tree demography, abundances of understory plant functional groups, community composition, and plant diversity (including bryophytes) across multiple scales varied with moose exclusion. After seven years, the exclosures were dominated by deciduous trees, including many large rowan (Sorbus aucuparia) individuals, a functionally important keystone species. In contrast, the open plots subject to moose impacts (browsing, trampling, defecation) were dominated by economically important coniferous trees and there was next to no rowan recruitment to taller height classes. The biomass of large herbs and ferns was much greater inside exclosures. This study emphasizes the large immediate effect of moose on early successional boreal forest stands. Landscape‐level alterations caused by reduced deciduous dominance, and a reduction in large flowering herbs is likely to lead to cascading effects on ecosystem functioning. The management of boreal production forests needs to account for the combined effects of silvicultural practices and ungulate herbivory to ensure ecosystem functioning, but this management goal may be jeopardized in our study regions due to drastically reduced abundance of keystone species.
The extent of drought in Mediterranean streams has been intensifying recently, and the mean annual discharge is expected to experience a decreasing trend in coming years, with significant effects on aquatic ecosystems. The aim of this study was to analyse colonisation patterns of diatom communities that differed in terms of taxonomic composition and percentage of endangered taxa exploring the possible development of resistance mechanisms. To this end, we selected three Mediterranean streams comparable in terms of water quality, but different in terms of surrounding land use, and we performed two experimental treatments. The first treatment consisted in artificially drying and cleaning of substrates (cobbles) to analyse the post-drought recolonisation process that is only driven by drift and immigration. In the second treatment cobbles coming from a site experiencing a seasonal drought were transplanted upstream in a perennial stretch to explore the possible development of resistance mechanisms within diatom communities periodically exposed to droughts. We observed that stream identity played an important role in determining diatom assemblage composition. Highly natural stretches had a high abundance of endangered species, which were less resilient to drought than assemblages composed of general and widespread taxa. Moreover, according to our results, resistance mechanisms did not play a significant role in recovery patterns. Improving our knowledge of diatom resilience mechanisms is very important in a global climate change scenario, especially in Mediterranean streams.
Epicutaneous (EC) sensitization to food allergens may occur when the skin has been lightly damaged. The study here tested whether cutaneous exposure to pigeon pea protein(s) may cause allergic sensitization. BALB/c mice were either orally gavaged or epicutaneously sensitized by repeated application of pigeon pea crude protein extract (CPE) on undamaged areas of skin without any adjuvant; afterwards, both groups were orally challenged with the pigeon pea CPE. The experimental results support the hypothesis that in addition to oral exposure, skin exposure to food allergens can promote Th2-dependent sensitization, IgE-mediated anaphylaxis and intestinal changes after oral challenge. Based on this, an avoidance of cutaneous exposures to allergens might prevent development of food anaphylaxis.
Methods
1. Epicutaneous and oral treatment.
2. Analysis of signs and symptoms of anaphylaxis.
3. Type 1 skin test.
4. Measures of specific IgE and IgG1 and of MCPT-1 and TSLP.
5. Histopathology of skin and intestine.
6. Expression of cytokines and TFs.
7. Isolation of skin and intestinal proteins and Western blotting.
8. Mast cell staining.
Results
In the epicutaneously-sensitized mice, elevated levels of specific IgE and IgG1, as well as of MCPT-1, TSLP, TH2 cytokines and TFs, higher anaphylactic scores and histological changes in the skin and intestine were indicative of sensitization ability via both routes in the pigeon pea CPE-treated hosts. Elevated levels of mast cells were observed in both the skin and intestine. Decreased levels of filaggrin in skin may have played a key role in the skin barrier dysfunction, increasing the chances of sensitization.
Conclusions
Little is known regarding the prevention of food allergy development via the EC exposure. The current study identified an IgE-mediated anaphylaxis following oral challenge and induction of TH2-biased adaptive immune responses when mice were exposed to pigeon pea proteins on their healthy intact skin. An additional interesting finding was that EC sensitization also yielded intestinal changes with regard to mast cells. The immune response caused by IL-4 and IL-13 contributes to the impairment in filaggrin, therefore neutralization of IL-4 and IL-13 that may improve skin barrier dysfunction. These findings support the hypothesis that cutaneous exposure to food allergens may be a risk factor for the allergic sensitization and development of food allergy.
Ecotoxicological studies mainly consist of single‐species experiments evaluating the effects of a single stressor. However, under natural conditions aquatic communities are exposed to a mixture of stressors. This study was set up to identify how the toxicity of zinc (Zn) is affected by increased temperature (T) and increased phosphorus supply (P) and how these interactions vary among species, functional groups, community structure and function. Aquatic microcosms were subjected to three Zn concentrations (background: no Zn added; 75 µg Zn/L and 300 µg Zn/L), two temperatures (16‐19 °C and 21‐24 °C) and 2 different P additions (low: 0.02 mg P L−1 week−1 and high: 0.4 mg P L−1 week−1) for five weeks using a full factorial design. During this study consistent interactions between Zn and T were only rarely found at the species level (4%), but were frequently found at the functional group level (36%), for community structure (100%) and for community function (100%, such as Dissolved Organic Carbon concentrations and total chlorophyll). The majority of the Zn × T interactions were observed at 300 µg Zn/L and generally indicated a smaller effect of Zn at higher T. Furthermore, no clear indication was found that high P addition by itself significantly affected the overall effects of Zn on the community at any level of organisation. Interestingly though, 90% of all the Zn × T interactions observed at the species, group and community composition level were found under high P addition. Collectively, our study with the model chemical Zn suggests that temperature and phosphorus loading to freshwater systems should be accounted for in risk assessment, as these factors may modify the effects of chemicals on the structure and functioning of aquatic communities, especially at higher levels of biological organisation. This article is protected by copyright. All rights reserved
Seasonal aquatic insect emergence represents a critical subsidy link between aquatic and terrestrial ecosystems. Early and late instar larvae developing in wetlands near neonicotinoid‐treated cropland are at risk of chronic insecticide exposure. An in situ wetland limnocorral experiment compared emergent insect community responses to imidacloprid, clothianidin, and thiamethoxam. Over 15 weeks, 21 limnocorrals were dosed weekly for 9 weeks to target peak nominal doses of 0.0, 0.05 or 0.5 µg/L, followed by a 6‐week recovery period. Thirty‐nine aquatic insect taxa were recorded but 11 taxa groups made up 97% of the community composition. Principal response curves indicated that during the dosing period, community composition among the treatments resembled the controls. During the 6‐week recovery period, significant deviance was observed in the high imidacloprid treatment with similar trends in the clothianidin treatment, suggesting that community effects from neonicotinoid exposure can be delayed. Non‐biting midges (Diptera: Chironomidae) and damselflies (Odonata: Zygoptera) also emerged 18 to 25 days earlier in the imidacloprid and clothianidin neonicotinoid treatments, relative to controls. These data suggest that phenology and subtle community effects can occur at measured neonicotinoid concentrations of 0.045 µg/L (imidacloprid) and 0.038 µg/L (clothianidin) under chronic repeated exposure conditions. Synchronization and community dynamics are critical to aquatic insects and consumers; thus, neonicotinoids may have broad implications for wetland ecosystem function. This article is protected by copyright. All rights reserved
Although environmental effects are mostly assessed via standard individual species the ecological relevance of multispecies testing is well-recognised and highly recommended. Hence, the effect of copper oxide nanomaterials (CuONM) and CuCl2 were assessed using the validated soil multispecies system (SMS). Besides the individual species (IS) “standard” tests for all, a predation study was done. Toxicity was higher in the SMS than in the IS, and longer exposure showed increased toxicity. The predator (Hypoaspis aculeifer) preyed most on smaller species, but the net biomass consumed was similar across species. Internal Cu in Folsomia candida reached ca. 140 µg Cu/g dry weight, fluctuating over time, especialy for CuCl2. Copper was mostly bound to soil components for both Cu forms (<0.2% of the total Cu in soil solution, <0.007% on the ionic form, but the soil solution content increased with the total added concentration). Hazard Concentrations (HC5) showed higher toxicity and more similarity between Cu forms at longer-term exposure. Risk of NMs is relatively limited at present (IS based instead of SMS) with short exposure times (i.e. longer is required) and too few IS tested. The impact of species interactions is highlighted and is of key importance to include in ecosystem hazard prediction.
Microbial ecology as a scientific field is fundamentally driven by technological advance. The past decade's revolution in DNA sequencing cost and throughput has made it possible for most research groups to map microbial community composition in environments of interest. However, the computational and statistical methodology required to analyse this kind of data is often not part of the biologist training. In this review, we give a historical perspective on the use of sequencing data in microbial ecology and restate the current need for this method; but also highlight the major caveats with standard practices for handling these data, from sample collection and library preparation to statistical analysis. Further, we outline the main new analytical tools that have been developed in the past few years to bypass these caveats, as well as highlight the major requirements of common statistical practices and the extent to which they are applicable to microbial data. Besides delving into the meaning of select alpha- and beta-diversity measures, we give special consideration to techniques for finding the main drivers of community dissimilarity and for interaction network construction. While every project design has specific needs, this review should serve as a starting point for considering what options are available.
Background:
The development of gut microbiota in infancy is important in the maturation of the immune system. Deviations in colonization patterns have been associated with allergic manifestations (e.g. eczema), but exact microbiome dysfunctions underlying allergies remain unclear. We studied the gut microbiota of 138 infants at increased risk of developing allergy, participating in a clinical trial investigating the effectiveness of a partially hydrolyzed protein formula supplemented with non-digestible oligosaccharides (pHF-OS) on the prevention of eczema.
Objective:
The effects of the interventions and breastfeeding on fecal microbiota were investigated. Additionally, we aimed to identify microbial patterns associated with the onset of eczema.
Methods:
Bacterial taxonomic compositions in the first 26 weeks of life were analyzed using 16S rRNA-gene sequencing. Additionally, fecal pH and microbial metabolites were measured.
Results:
Fecal microbial composition, metabolites and pH of infants receiving pHF-OS was closer to breastfed infants than to infants receiving standard cow's milk formula. Infants developing eczema by 18 months showed temporal differences that were marked by decreased relative abundances of Parabacteroides and Enterobacteriaceae at 4 weeks, and decreased relative abundances of lactate-utilizing bacteria producing butyrate at 26 weeks, namely Eubacterium and Anaerostipes spp., supported by increased lactate and decreased butyrate levels.
Conclusions:
We showed that a pHF with specific prebiotics modulated the gut microbiota closer to that of breastfed infants. Additionally, we identified a potential link between the microbial activity and onset of eczema, which may reflect a suboptimal implementation of gut microbiota at specific developmental stages in infants at high-risk for allergy.
A new approach to assess environmental integrity based on PRC analysis was proposed, tested, validated and developed. Environmental health assessment and community studies usually result in complex biological data sets. In order to find ecologically relevant patterns and tendencies from such sets of data it is necessary to reduce all the information to a summarised and simplified form, which might be more easily interpreted by ecologists, politicians, end-users and the population in general. However, several multivariate ordination methods currently used (e.g. redundancy analysis, principal component analysis, or multi-dimensional scaling) produce complex diagrams for the non-ecologist, which do not allow changes in biological communities over time to be easily understood. Here, we propose a recently developed method, principal response curves (PRC) analysis, to overcome these issues. This method has advantages over traditional ordination techniques, or any biotic index, in that it provides a powerful statistical analysis of temporal data series along spatial gradients. The PRC technique can make use of non-disturbed or unpolluted areas as reference sites with which other areas are compared, making it possible to assess changes in species composition between different areas over time. Moreover, individual species responses to stress agents can be inferred from the PRC curves. As well as providing insights into the behaviour of natural ecosystems - in particular, how ecosystem integrity changes over time - this new approach can potentially provide a practical tool for monitoring and implementing environmental policy instruments.
In this paper a novel multivariate method is proposed for the analysis of community response data from designed experiments repeatedly sampled in time. The long-term effects of the insecticide chlorpyrifos on the invertebrate community and the dissolved oxygen (DO)–pH–alkalinity–conductivity syndrome, in outdoor experimental ditches, are used as example data. The new method, which we have named the principal response curve method (PRC), is based on redundancy analysis (RDA), adjusted for overall changes in community response over time, as observed in control test systems. This allows the method to focus on the time-dependent treatment effects. The principal component is plotted against time, yielding a principal response curve of the community for each treatment. The PRC method distills the complexity of time-dependent, community-level effects of pollutants into a graphic form that can be appreciated more readily than the results of other currently available multivariate techniques. The PRC method also enables a quantitative interpretation of effects towards the species level.
Before using macroinvertebrates in water quality assessment in the Chusovaya River (Russia, the Urals, 50°55'N, 60° E), preliminary results of three sampling methods were compared: handnet, circular shovel and a standardized artificial substrate sampler. The artificial substrate consisted of glass marbles (ϕ 20 mm). To compare the efficiency of these sampling methods the total numbers of taxa found at each location per sampling data were considered to be 100%. The highest efficiency was reached with the artificial substrate sampler. 75-100% of the taxa at the different locations were collected with this sampler. Only 5-19% and 10-20% of the taxa at each location per sampling date were collected with the circular shovel in the sand and gravel substrate respectively, being the lowest efficiency. Intermediate results were obtained with the hand net. 23-38% of the taxa were collected with this net. Based on these results and requirements placed upon sampling methods in general, the standardized artificial substrate sampler has been considered to be an optimal sampling device for macroinvertebrates in biological monitoring.
We used aquatic invertebrates to assess environmental impacts of timber harvest on a bottomland hardwood wetland in the Coosawhatchie River floodplain, Jasper County, SC. Two years (1998, 1999) of preharvest baseline data were collected during winter floods in three 1113-ha tracts of wetland forest. The following autumn of 1999 one tract was completely clearcut. In a second tract the majority of the area was also clearcut, but three 0.20.6-ha islands of intact forest were retained (i.e., patch-retention treatment). The third tract remained intact and served as the control. We continued to sample invertebrates in the three tracts for another 2 years (2000, 2001) after harvests. Invertebrate communities in the clearcut tract differed significantly from previous baseline conditions in that habitat and also from the nearby control tract. The patch-retention tract induced a lesser response than the clearcut, suggesting that retention islands helped mitigate impacts. Timber harvest caused a decline in some invertebrate populations (Asellidae, Crangonyctidae, Planorbidae), but an increase in others (Culicidae). Overall invertebrate abundance and family richness was not affected by harvest, only community composition. Invertebrate change probably reflected a conversion of a fauna typical of forested wetland to one typical of herbaceous wetland. FOR. SCI. 51(4):284291.
Range extensions of aquatic Ponto-Caspian macroinvertebrate species in Europe have mainly been facilitated by the interconnection of river basins through man-made canals and intentional introductions. Three inland migration corridors can be distinguished: (i) a northern corridor: Volga → Lake Beloye → Lake Onega → Lake Ladoga → Neva → Baltic Sea, (ii) a central corridor connecting the rivers Dnieper → Vistula → Oder → Elbe → Rhine, and (iii) a southern corridor connecting the Danube and Rhine rivers. Important trade harbours in Europe were connected via these corridors allowing further range extensions of macroinvertebrate species attached to a vessel's hull or in ballast water. The central corridor was the main migration route before 1992, after which the southern corridor became the most important migration route for the range expansions to the west because of the reopening of the Main-Danube Canal, connecting the Rhine and Danube basins. Especially the water level maintenance in the upper part of the canal, with water supply from the Danube basin, facilitated migration of mobile animals (e.g., crustaceans) from the Danube basin towards the Rhine basin; however, contribution of other transport mechanisms (e.g., shipping) is expected in the near future.
This chapter concerns data analysis techniques that assist the interpretation of community composition in terms of species' responses to environmental gradients in the broadest sense. All species occur in a characteristic, limited range of habitats; and within their range, they tend to be most abundant around their particular environmental optimum. The composition of biotic communities thus changes along environmental gradients. Direct gradient analysis is a regression problem—fitting curves or surfaces to the relation between each species' abundance, probability of occurrence, and one or more environmental variables. Ecologists have independently developed a variety of alternative techniques. Many of these techniques are essentially heuristic, and have a less secure theoretical basis. This chapter presents a theory of gradient analysis, in which the heuristic techniques are integrated with regression, calibration, ordination and constrained ordination as distinct, well-defined statistical problems. The various techniques used for each type of problem are classified in families according to their implicit response model and the method used to estimate parameters of the model. Three such families are considered. The treatment shown here unites such apparently disparate data analysis techniques as linear regression, principal components analysis, redundancy analysis, Gaussian ordination, weighted averaging, reciprocal averaging, detrended correspondence analysis, and canonical correspondence analysis in a single theoretical framework.
Experiments in microcosms and mesocosms, which can be carried out in an advanced tier of risk assessment, usually result in large data sets on the dynamics of biological communities of treated and control cosms. Multivariate techniques are an accepted tool to evaluate the community treatment effects resulting from these complex experiments. In this paper two methods of multivariate analysis are discussed on their merits: 1) the canonical ordination technique Principal Response Curves (PRC) and 2) the similarity indices of Bray-Curtis and Stander. For this, the data sets of a microcosm experiment were used to simultaneously study the impact of nutrient loading and insecticide application. Both similarity indices display, in a single graph, the total effect size against time and do not allow a direct interpretation down to the taxon level. In the PRC method, the principal components of the treatment effects are plotted against time. Since the species of the example data sets, react in qualitatively different ways to the treatments, more than one PRC is needed for a proper description of the treatment effects. The first PRC of one of the data sets describes the effects due to the chlorpyrifos addition, the second one the effects as a result of the nutrient loading. The resulting principal response curves jointly summarize the essential features of the response curves of the individual taxa. This paper goes beyond the first PRC to visualize the effects of chemicals at the community level. In both multivariate analysis methods the statistical significance of the effects can be assessed by Monte Carlo permutation testing.
We examined long-term ecological change in two Hudson River tributaries, the Wappinger and Fishkill Creek watersheds in Dutchess
County, New York State. Fish data spanning 65years (1936, 1988, 1992, and 2001) and shorter term macroinvertebrate data (1988,
2001) were used to assess the influence of land use practices. Between 1988 and 2001, macroinvertebrate index Biotic Assessment
Profile (BAP) improved by 113–165% in the Fishkill Creek watershed, and fish Index of Biotic Integrity (IBI) improved by 117–140%.
Fish IBI and fish species richness were significantly different (p < 0.01) between the watersheds, with Wappinger Creek in better condition. Long-term fish IBI scores showed degradation in both watersheds
since the 1930s. Changes in species composition suggest community homogenization on par with overall changes in the fish fauna
of New York. Most notable were increases in tolerant species and declines in intolerant or moderately tolerant species. Whereas
Fishkill Creek IBIs showed decline in 1988 relative to 1936, followed by improvement, Wappinger Creek declined monotonically
in environmental quality. Development has intensified in both watersheds, but Fishkill Creek is improving while Wappinger
Creek watershed is undergoing less mitigated degradation. We find that older, semi-quantitative data can be used to construct
environmental quality indicators, and can be of great use for measuring long-term change.
A method is proposed to partition the variation of species abundance data into independent components: pure spatial, pure environmental, spatial component of environmental influence, and undetermined. The new method uses pre-existing techniques and computer programs of canonical ordination. The intrinsic spatial component of community structure is partialled out of the species-environment relationship in order to see if the environmental control model still holds. The method is illustrated using oribatid mites in a peat blanket, forest vegetation data, and aquatic heterotrophic bacteria. In this latter example, the new method is shown to be complementary to another approach based on partial Mantel tests.
Water demands in arid and semi-arid areas, coupled with increased human populations and concomitant changes in land use, can greatly alter aquatic ecosystems. A good example of this type of system occurs along the eastern slope of the Colorado Rocky Mountains, U.S.A. Long-term macroinvertebrate metric data from the Big Thompson and Cache la Poudre Rivers, Colorado, were collected at one site above, and three sites in and downstream from urban areas. These data were compared both with regional reference and single reference sites in the respective rivers. Using the surrogate variables of potential urban impact (population and housing units), and the environmental gradient represented primarily by chemical factors, it was determined that there was an effect of urban land use that was reflected in the macroinvertebrate assemblages in both rivers. The most robust results were usually seen when regional reference data were used. However, even using only the upstream reference site in either river indicated some negative impacts from the urban areas. The long-term data, particularly in the Cache la Poudre River, showed that water quality has not been getting worse and there is some evidence of a slight improvement in downstream reaches, even with increased urban development.
Environmental management depends on accurate monitoring and assessment of ecological conditions. Bioassessments are generally based on the measurement of selected indicators. However, the accuracy of these indicators is difficult to evaluate because the true biological impairment of a system is almost always unknown. We describe a simulation procedure that allows objective comparisons of estimated indicator values against known impairment. We modeled how densities changed with increasing stress as a function of tolerance values. We applied this procedure to data from five reference sites and compared non-metric multidimensional scaling (NMDS) and observed taxa richness for detecting known impairments. NMDS showed that the trajectories of impairment caused by stress were all evident at 100, 300, or 600 counts. However, the discrimination of stress levels within ordination space greatly improved with increasing count. Estimates of richness based on 100- or 300-count samples often severely underestimated true taxa loss and frequently indicated taxa gain. Estimates of taxa loss based on 600 counts also underestimated true taxa loss, but these estimates were strongly correlated with true taxa loss. This simulation procedure should be applicable to the evaluation of how well a variety of biotic indicators measure biological impairment.
In this paper a novel multivariate method is proposed for the analysis of community response data from designed experiments repeatedly sampled in time. The long-term effects of the insecticide chlorpyrifos on the invertebrate community and the dissolved oxygen (DO)-pH-alkalinity-conductivity syndrome, in outdoor experimental ditches, are used as example data. The new method, which we have named the principal response curve method (PRC), is based on redundancy analysis (RDA), adjusted for overall changes in community response over time, as observed in control test systems. This allows the method to focus on the time-dependent treatment effects. The principal component is plotted against time, yielding a principal response curve of the community for each treatment. The PRC method distills the complexity of time-dependent, community-level effects of pollutants into a graphic form that can be appreciated more readily than the results of other currently available multivariate techniques. The PRC method also enables a quantitative interpretation of effects towards the species level.
1. Lough Neagh, Northern Ireland, has been invaded by three non-indigenous amphipod species this century; the North American Gammarus tigrinus and Cragonyx pseudogracilis, plus the European G. pulex. These species have come into contact with the sole native Lough species, G. duebeni celticus. 2. The Lough and its associated rivers were surveyed in 1993-94 and a selection of sites re-sampled the following year. The distributions, relative abundances and habitat utilization patterns of the four amphipod species were determined. All single and mixed species combinations of the four species were found. Gammarus pulex and G. d. celticus are ubiquitous in their habitat selection; however, the former species is replacing the latter. Gammarus tigrinus occurs in deep, mid-Lough areas and, to a limited extent, colonizes sheltered, vegetated shores. Cragonyx pseudogracilis has a fragmented distribution, but utilizes a variety of habitats. 3. Considering those habitat types utilized by all four species, evidence was found for species interactions from field data. First, although both North American species have much greater reproductive outputs, their mean densities were significantly lower than the mean densities of both G. d. celticus and G. pulex. Secondly, the mean density of total Gammarus was significantly higher where C. pseudogracilis was absent compared to where it was present. Thirdly, re-sampling at selected sites in 1994-95 revealed that G. tigrinus and C. pseudogracilis had disappeared from areas dominated by the other two Gammarus species. 4. Since differential mutual predation has been linked to the replacement of G. d. celticus by G. pulex in Irish rivers, predatory interactions among all other combinations of the four species of Lough Neagh were investigated. Male G. d. celticus and G. pulex preyed significantly more frequently on moulted female G. tigrinus than did male G. tigrinus in reciprocal interactions. Predatory/survival abilities may be influenced by body size (G. d. celticus > G. pulex > G. tigrinus). However, G. tigrinus preyed on female G. d. celticus significantly more frequently than on female G. pulex. 5. All three Gammarus species preyed heavily on the smaller C. pseudogracilis, with G. pulex the most severe predator, followed by G. d. celticus and then G. tigrinus. Such predation occurred regardless of the moult state of victims, and frequencies of predation were particularly high on reproductive females. Thus, high rates of Gammarus predation may explain the limited invasion success of C. pseudogracilis. 6. The dynamic nature of Lough Neagh's amphipod communities appears to arise from a combination of overlapping habitat utilization, differential predation and episodes of local immigration/exclusion. Species diversity, and probably biomass, have increased following the introductions, which are likely to have significant effects on other species and at other trophic levels.
Invasions by alien species in freshwater habitats are discussed for the Dutch Rhine delta, as a model of a large Western European river strongly influenced by anthropogenic activities. The barriers to dispersal were lifted in this area by introductions and escapes from aquariums, aquaculture etc. (65% of the alien species), as well as by canals connecting rivers (25%) and invasions from the seaports caused by seagoing ships (10%). Habitat change and deterioration of water quality has led to changes in and weakening of indigenous flora and fauna. Periods of pollution and chemical spills followed by partial restoration of the water quality have led to increasingly successful invasions suppressing the population development of returned indigenous species. This fits in well with the hypothesis that anthropogenic disturbance paves the way for new invasions, as disturbance leads to unused resources from which invaders can profit.
Harmonization exercises organized by the European Communities in the 1970s on biological water assessment methods for running waters, because the usual methods were difficult or impossible to apply, explicitly stressed the need for development of standardized sampling procedures for monitoring large and deep rivers and canals. To meet this objective, an extensive monitoring campaign was organized in Belgium and The Netherlands to test the efficiency of artificial substrates colonized by macroinvertebrates as an alternative for natural communities sampled with a handnet. Two types of artificial substrates were tested: a Belgian substrate, composed of a plastic netting filled with medium-sized pieces of brick, and a Dutch substrate consisting of a stainless steel box filled with marbles. The collected biocoenoses were compared qualitatively and quantitatively. Water quality was assessed by means of several biotic indexes. The results show that both the Belgian and the Dutch artificial substrate sampler can replace the usual samples obtained by means of a handnet, and provide a correct assessment. A major drawback of the use of artificial substrates in uncontrolled monitoring sites remains the unforeseen losses. For that reason the cost price of the substrates may have to be considered when making a selection.
In cooperation with several other institutes, RIZA started a Biological Monitoring Programme in 1992. The main goals are recording long-term trends and evaluation of the national policy regarding water quality. Selected parameters of biological monitoring include (semi)aquatic vegetation, phyto- and zooplankton, macro-invertebrates, fish, water birds and ecotoxicological parameters. Results are published in annual reports and in a series of more elaborate reports on separate water systems. Parameters like densities of selected species are compared to densities in a reference situation, which is visualized in an AMOEBA-diagram in order to help measure progress and evaluate government measures. The ecological changes achieved so far leave room for moderate optimism. The decrease of heavy metal and PCB concentrations as a result of international policy were followed by the first signs of recovery of riverine fauna. Measures against eutrophication have resulted in decreasing phosphate levels and in a number of (semijstagnant waters the diversity of flora and fauna seems to have increased. However, standards for both micropollutants and nutrients and transparency are not yet met in most waters. In most waters, biodiversity is still lower than it used to be, while a few tolerant species reach enormous densities. To a certain extent, recovery may be inhibited by explosive invasions of foreign species that benefit from reduced competitive ability of native species under present conditions. Biological monitoring will help us understand these processes and the acquired knowledge will help increase the effectiveness of water management.
Dugesia polychroa, D. lugubris and Planaria torva preyed upon snails of differing morphologies and while the Dugesia spp. fed approximately in proportion to snail abundance, PL torva was more selective on Potamopyrgus jenkinsi. The incidence of feeding on four snail taxa by the Dugesia spp. was significantly correlated and differed strikingly from that of PI. torva where feeding was related to its annual life cycle. Large peaks of feeding coincided in the Dugesia spp. for the four snail types; this was attributed to snail vulnerability being increased by environmental disturbance. Comparison of feeding by Dugesia spp. in the presence and absence of PI. torva indicated that severe competition was occurring for food with PI. torva having a food refuge in P. jenkinsi. The distribution of PI. torva in Britain is largely confined to productive habitats in the Glasgow-Edinburgh and East Anglia regions. It is concluded that historical rather than ecological events have played the major part in its distribution to date. The strong association of PL torva with port areas and the canal system suggests that it is a recent introduction via the timber trade with Fennoscania.
The theory of gradient analysis is presented in this chapter, in which the heuristic techniques are integrated with regression, calibration, ordination and constrained ordination as distinct, well-defined statistical problems. The various techniques used for each type of problem are classified into families according to their implicit response model and the method used to estimate parameters of the model. Three such families are considered. First, the family of standard statistical techniques based on the linear response model is dealt with, because they are conceptually the simplest and provide a basis for what follows, even though their ecological application is restricted. Second, a family of somewhat more complex statistical techniques are outlined which are formal extensions of the standard linear techniques and incorporate unimodal (Gaussian-like) response models explicitly. Finally, the family of heuristic techniques is considered based on weighted averaging. These are not more complex than the standard linear techniques, but implicitly fit a simple unimodal response model rather than a linear one. Ordination diagrams and their interpretation on bi plots and joint plots are also given in the chapter. This chapter has discussed which response model to choose from direct and indirect gradient analysis, and then in direct system, which one to choose from regression and constrained ordination.
Population densities of six dominant macroinvertebrate taxa (mayfly nymphs Jappa kutera, Atalophlebia sp., Tasma-nocoenis sp., Baetis sp. and the caddisfly larvae Cheumatopsyche sp. and Ecnomus sp.) were negatively correlated to total endosulfan concentrations in the Namoi River (New South Wales, Australia) in the 1995/96 and 1997/98 cotton growing seasons (November-March). Total endosulfan concentrations measured in solvent-filled polyethylene bags (passive samplers) at the exposed sites correlated with rainfall, suggesting that endosulfan entered the riverine environment in runoff from land. At the start of both surveys, in November 1995 and November 1997, there was no significant difference (p < 0.05) between the reference and exposed sites for both total endosulfan concentrations and mean population densities of the combined study taxa. This indicates distance downstream, which was negatively correlated with exposure, was not an important variable in explaining the significantly higher population densities in other months at the reference sites compared with those at sites subsequently exposed to increased (10–25-fold) total endosulfan concentrations. The multivariate analysis of the 1997/98 data with the principal response curves (PRC) method indicated that endosulfan explained a significant proportion (25%) of the variation in the total macroinvertebrate community. Principal components analysis (PCA) indicated other covariables were involved, including river discharge. River discharge was positively correlated to increased densities of the mayfly taxa at the reference sites in the 1995/96 survey, but these correlations were reduced to near zero, except for Baetis sp., in the 1997/98 survey.
Experimental ditches were teated with Dursban®4E at nominal concentrations of 0, 0.1, 0.9, 6, and 44 μg/L of the active ingredient chlorpyrifos. Continuous oxygen, pH, and temperature measurements were made to determine the ecosystem metabolism. In addition, alkalinity and conductivity were determined weekly. Oxygen concentrations and pH were elevated at the highest treatment level. The “dissolved oxygen-pH-alkalinity-conductivity syndrome” was analyzed with the multivariate ordination technique “redundancy analysis” and indicated a temporary effect of chlorpyrifos. Whole-system gross primary production and oxygen consumption were both lowered in relation to the treatment, with oxygen consumption showing the most prominent decrease. These effects are explained as a decrease in decomposition after the arthropods are killed. The effect of chlorpyrifos on the ecosystem metabolism is slight. The influence of the state of the ecosystem on the response of ecosystem functions to insecticide treatment is also discussed.
Non-point-sources of nitrogen (N) and phosphorus (P) are recognized as major causes of eutrophication of surface waters. Adoption of policies to reduce pollution in the former German Democratic Republic following re-unification of Germany in 1990 provided an opportunity to examine how taking agricultural land out of production affected nutrient loads and aquatic biota in a small rural watershed. Between 1994 and 1996, soluble reactive phosphorus (SRP) and dissolved inorganic nitrogen (DIN) loads in a first-order agricultural stream decreased by >90% while instream concentrations decreased by 89% for DIN and 40% for SRP. This reduction in nutrients coincided with a decrease in precipitation (from 760 to 440mm between 1994 and 1996) and an increase in the area of land set aside from agricultural production (from 0.3% in 1990 to a maximum of 8% in 1994). The biomass of primary producers (episammic algae) showed no clear response to this decrease in nutrient concentrations. However, benthic invertebrate composition shifted from a chironomid–amphipod to an oligochaete–gastropod dominated community in response to the decrease in DIN and changes in episammic algal abundance and sediment organic carbon concentrations. Results from our 4-year study showed reductions in soil nutrient losses combined with less precipitation resulted in less P and N in a rural stream and a change in benthic invertebrate community composition and abundance.
Significant anthropogenic pressure in the Dutch part of the River Rhine is present from the 12th century. River engineering
and water pollution were the main stress factors for flora and fauna. From the middle of the 20th century measures were taken
to reduce water pollution. Recently, from 1987 onwards, these activities were put into a wider context of ecological river
rehabilitation. Effects of improvements on fish and macroinvertebrates in the main distributaries in the Rhine delta are reviewed.
The conclusions are that (a) most of the alterations in the Rhine delta are irreversible due to hard socio-economic boundary
conditions (e.g. safety, navigation); (b) chances for the development of riverine biotopes have therefore to be found in the
forelands and not in the main channels of the Rhine delta; (c) further reduction of pollutants, especially thermal pollution,
is needed to help original species to colonise the Rhine delta again; (d) non-indigenous species clearly leave a mark on recolonisation
possibilities of original species.
The normalized difference vegetation index (NDVI) is widely accepted as a good indicator for providing vegetation properties and associated changes for large scale geographic regions. Using multivariate time series data analysis methods based on principal component transform and wavelet decomposition, a sequence of 11-year monthly Advanced Very High Resolution Radiometer (AVHRR)-derived NDVI data from 1982 to 1992 is examined to study the vegetation and climate variation trends over the United States. We find that one interannual NDVI variation signal over the United States, exhibits a strong relationship with the El Niño/Southern Oscillation (ENSO) Index, which is a measure of the phase and amplitude of the Southern Oscillations (SOs). The corresponding spatial patterns of NDVI anomaly are also extracted for mapping the possible impacts of ENSO activity. The NDVI anomaly patterns approximately agree with the main documented precipitation and temperature anomaly patterns associated with ENSO, but also show additional patterns not related to ENSO. This study shows that ENSO activity effects may have regionally significant effects for vegetation in the United States.
Effects of chronic application of the fungicide Derosal(R) (active ingredient carbendazim) were studied in indoor macrophyte-dominated freshwater microcosms. The concentrations (0, 3.3, 33, 100, 330 and 1000 microg/l) were kept at a constant level for 4 weeks. This paper is the second of a series of two; it describes the effects on zooplankton and primary producers and presents an overall discussion. The zooplankton community was negatively affected by the three highest treatment levels (NOEC(community)=33 microg/l). At higher treatment levels Cladocera taxa were completely eliminated, while Copepod numbers were reduced. Rotatoria taxa decreased (Keratella quadrata and Lecane sp.) or increased in abundance (Testudinella parva) at the highest treatment level only. Due to the reduced grazing pressure, the abundance of some phytoplankton taxa and the chlorophyll-a content of the phytoplankton increased at the three highest treatment levels (NOEC(community)=33 microg/l). This effect was not observed for the periphyton, most probably because the reduced grazing pressure was compensated by the increased abundance of some snail species such as Lymnaea stagnalis and Physella acuta. At the end of the experimental period the biomass of the macrophyte Elodea nuttallii was significantly elevated at the two highest treatment levels. It is hypothesised that carbendazim might have caused, directly or indirectly, the removal of pathogene organisms from the macrophyte.
This paper describes the usefulness of the group of multivariate techniques belonging to ordination for the analysis of ecotoxi cological data sets. It is argued that although ecotoxicologists often gather multivariate data sets, they usually do not evaluate them w ith techniques that can handle multivariate data. Ordination techniques enable the researcher to extract an underlying structure out of a data set (eg. differences in composition of macro-invertebrate community between sites) and, if measured, relate this structure to explanator y variables (eg. concentrations of toxicants at the same sites). Five example data sets are presented to illustrate the underlying theory a nd the possibilities of ordination techniques. Two methods are presented, one based on weighted summation (eg. Principal Component Analysis, PCA) an d one on weighted averaging (eg. Correspondence Analysis, CA). These techniques differ in the shape of the modelled response (lin ear versus unimodal) as the type of data they model (absolute versus relative). Results of these two methods are illustrated using a data set comprising levels of different PCB congeners measured in the blood of Adélie penguins in three periods. After this the constrai ned forms of PCA and CA are discussed, ie. constrained means that they are able to optimally display the differences in species compositi on (here levels of PCB congeners) due to explanatory variables (here period). Further examples illustrate the use of covariables, contin uous and nominal explanatory variables, supplementary explanatory variables and forward selection of explanatory variables. Finally, two examples of Principal Response Curves (PRC) analyses are given. PRC is a technique that is especially developed to analyse time-series i n which a control or reference is present. The PRC results are discussed for a designed experiment and a monitoring data set. The paper ends with a discussion focussing on the comparison between ordination techniques and other multivariate techniques used in the field of e cotoxicology. we try to demonstrate that multivariate techniques can be valuable in the analysis of a variety of ecotoxicological data. In this paper we will restrict ourselves to ordination techniques that operate on the original data set for its analysis and thus allow a direct interpretation in terms of the original variables, in most cases species (Ter Braak 1994 1995). These techniques are more direct than techniques that operate on (dis)similarity indices (eg. similarity analysis, clustering and multidimensional scaling). The techniques used in this paper and those based on (dis)similarity indices will be compared in the discussion section. Ordination techniques are capable of summarising very complex responses because they are not restricted to a single dimension (as for instance (dis)similarity analysis). When combined with Monte Carlo permutation testing not only is a graphical summary of the structure present in the data set obtained, but also the statistical significance of hypothesised differences (Ter Braak and smilauer 2002). This paper will present the analysis of five example data sets to illustrate the value of multivariate methods for the analysis of ecotoxicological data. We go beyond the traditional example in which a sample by species matrix is compared with a sample by environmental/explanatory variables matrix. In our examples, toxicity values, contaminant concentrations and physico-chemical parameters play the part of the species; and time, geographical position, chemical treatment and molecule characteristics play the part of explanatory variables. c
To assess the impact of pesticides on aquatic organisms under realistic worst-case conditions, a macroinvertebrate community of small ditches was sampled at 40 sites of the orchard region Altes Land near Hamburg, Germany. To differentiate between pesticide impact and other variables, the ditches selected for sampling were located at different distanc