A new application of principal response curves for summarizing abrupt and cyclic shifts of communities over space

Application of a new approach method to assess the hazard of complex legacy contaminated groundwater mixtures on fathead minnows in outdoor mesocosms

Assessing the environmental risks of contaminated groundwater presents significant challenges due to its often-complex chemical composition and to dynamic processes affecting exposure of organisms in receiving surface waters. The objective of this study was to characterize the effects of groundwater collected from a legacy contaminated industrial site, in fish under environmentally relevant conditions. A 21-day fish short-term reproduction assay was conducted in outdoor wetland mesocosms by exposing adult fathead minnows (Pimephales promelas) to graded concentrations of groundwater (1 %, 3 %, and 6 %). Offspring were held in mesocosms up to four days post-hatch to apply a new approach method (NAM), the EcoToxChip™, to explore whether traditional apical endpoints could be predicted using an alternative mechanistic approach. None of the groundwater concentrations used in this study were lethal to fish. There was greater cumulative number of eggs produced at the highest concentration of exposure. However, no abnormal histological appearance was observed in the liver and gonads of fish and no significant effect was observed in the relative expression of genes, tubercle counts, and erythrocyte micronuclei counts compared to the negative control. Food availability in the mesocosms was also assessed and the abundance of zooplankton increased in all groundwater-treated mesocosms. Fathead minnow findings are in contrast to those obtained from previous controlled laboratory studies that revealed significant genotoxicity, hepatotoxicity, and reprotoxicity of the same mixtures. Several factors could explain these observations, including the aging of groundwater in mesocosms before fish addition resulting in photo- and biodegradation and binding to sediments of toxic components. Our static exposure scenario likely underestimated realistic exposure scenarios where groundwater inflow to surface water is generally semi-continuous. Nevertheless, focused transcriptome analysis using EcoToxChips also observed greater toxicity during previous laboratory tests compared to mesocosm scenarios, and thus, our results support the use of this NAM in the ecological risk assessment of contaminated groundwater.

Microplastics at Environmentally Relevant Concentrations Had Minimal Impacts on Pelagic Zooplankton Communities in a Large In-Lake Mesocosm Experiment

To assess the potential risks of contemporary levels of plastic pollution in freshwater ecosystems, a large-scale experiment was conducted over 10 weeks in a boreal lake at the IISD-Experimental Lakes Area (Ontario, Canada). Fragments of common polymers (polyethylene, polystyrene, and polyethylene terephthalate), each with distinct colors and buoyancies, were added as a single pulse to seven in-lake mesocosms in equal contributions in a range of environmentally relevant nominal concentrations (6-29,240 particles/L). Two additional mesocosms with no added microplastics were used as controls. Zooplankton ingested low levels of microplastics (mean of 0.06 particles/individual ± SD 0.07) and generally their total abundance and community composition were not negatively impacted. Temporary changes were however observed; total zooplankton abundance and abundance of calanoid copepods were temporarily stimulated by increasing nominal microplastic concentrations, and modest, short-term reductions in egg production of the cyclopoid copepod Tropocyclops extensus and abundance of copepod nauplii occurred. Collectively, these results suggest that microplastics could have complex impacts on zooplankton communities, stimulating some species while negatively impacting others.

From behaviour to complex communities: Resilience to anthropogenic noise in a fish-induced trophic cascade

Sound emissions from human activities represent a pervasive environmental stressor. Individual responses in terms of behaviour, physiology or anatomy are well documented but whether they propagate through nested ecological interactions to alter complex communities needs to be better understood. This is even more relevant for freshwater ecosystems that harbour a disproportionate fraction of biodiversity but receive less attention than marine and terrestrial systems. We conducted a mesocosm investigation to study the effect of chronic exposure to motorboat noise on the dynamics of a freshwater community including phytoplankton, zooplankton, and roach as a planktivorous fish. In addition, we performed a microcosm investigation to test whether roach's feeding behaviour was influenced by the noise condition they experienced in the mesocosms. Indeed, compared to other freshwater fish, the response of roach to motorboat noise apparently does not weaken with repeated exposure, suggesting the absence of habituation. As expected under the trophic cascade hypothesis, predation by roach induced structural changes in the planktonic communities with a decrease in the main grazing zooplankton that slightly benefited green algae. Surprisingly, although the microcosm investigation revealed persistent alterations in the feeding behaviour of the roach exposed to chronic noise, the dynamics of the roach-dominated planktonic communities did not differ between the noisy and noiseless mesocosms. It might be that roach's individual response to noise was not strong enough to cascade or that the biological cues coming from the conspecifics and the many planktonic organisms have diverted each fish's attention from noise. Our work suggests that the top-down structuring influence of roach on planktonic communities might be resilient to noise and highlights how extrapolating impacts from individual responses to complex communities can be tricky.

A Glyphosate-Based Herbicide Cross-Selects for Antibiotic Resistance Genes in Bacterioplankton Communities

Agrochemicals often contaminate freshwater bodies, affecting microbial communities that underlie aquatic food webs. For example, the herbicide glyphosate has the potential to indirectly select for antibiotic-resistant bacteria. Such cross-selection could occur if the same genes (encoding efflux pumps, for example) confer resistance to both glyphosate and antibiotics. To test for cross-resistance in natural aquatic bacterial communities, we added a glyphosate-based herbicide (GBH) to 1,000-liter mesocosms filled with water from a pristine lake. Over 57 days, we tracked changes in bacterial communities with shotgun metagenomic sequencing and annotated metagenome-assembled genomes (MAGs) for the presence of known antibiotic resistance genes (ARGs), plasmids, and resistance mutations in the enzyme targeted by glyphosate (enolpyruvyl-shikimate-3-phosphate synthase; EPSPS). We found that high doses of GBH significantly increased ARG frequency and selected for multidrug efflux pumps in particular. The relative abundance of MAGs after a high dose of GBH was predictable based on the number of ARGs in their genomes (17% of variation explained) and, to a lesser extent, by resistance mutations in EPSPS. Together, these results indicate that GBHs can cross-select for antibiotic resistance in natural freshwater bacteria. IMPORTANCE Glyphosate-based herbicides (GBHs) such as Roundup formulations may have the unintended consequence of selecting for antibiotic resistance genes (ARGs), as demonstrated in previous experiments. However, the effects of GBHs on ARGs remain unknown in natural aquatic communities, which are often contaminated with pesticides from agricultural runoff. Moreover, the resistance provided by ARGs compared to canonical mutations in the glyphosate target enzyme, EPSPS, remains unclear. Here, we performed a freshwater mesocosm experiment showing that a GBH strongly selects for ARGs, particularly multidrug efflux pumps. These selective effects were evident after just a few days, and the ability of bacteria to survive and thrive after GBH stress was predictable by the number of ARGs in their genomes and, to a lesser extent, by mutations in EPSPS. Intensive GBH application may therefore have the unintended consequence of selecting for ARGs in natural freshwater communities.

Resistance, resilience, and functional redundancy of freshwater bacterioplankton communities facing a gradient of agricultural stressors in a mesocosm experiment

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, favouring 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 favouring 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.

Parasitoid Communities in the Variable Agricultural Environments of Blueberry Production in the Southeastern United States

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.

Measuring change in biological communities: multivariate analysis approaches for temporal datasets with low sample size

Effective and robust ways to describe, quantify, analyse, and test for change in the structure of biological communities over time are essential if ecological research is to contribute substantively towards understanding and managing responses to ongoing environmental changes. Structural changes reflect population dynamics, changes in biomass and relative abundances of taxa, and colonisation and extinction events observed in samples collected through time. Most previous studies of temporal changes in the multivariate datasets that characterise biological communities are based on short time series that are not amenable to data-hungry methods such as multivariate generalised linear models. Here, we present a roadmap for the analysis of temporal change in short-time-series, multivariate, ecological datasets. We discuss appropriate methods and important considerations for using them such as sample size, assumptions, and statistical power. We illustrate these methods with four case-studies analysed using the R data analysis environment.

Changes in the analysis of temporal community dynamics data: a 29-year literature review

BACKGROUND

Understanding how biological communities change over time is of increasing importance as Earth moves into the Anthropocene. A wide variety of methods are used for multivariate community analysis and are variously applied to research that aims to characterise temporal dynamics in community composition. Understanding these methods and how they are applied is useful for determining best practice in community ecology.

METHODOLOGY

We reviewed the ecological literature from 1990 to 2018 that used multivariate methods to address questions of temporal community dynamics. For each paper that fulfilled our search criteria, we recorded the types of multivariate analysis used to characterise temporal community dynamics in addition to the research aim, habitat type, location, taxon and the experimental design.

RESULTS

Most studies had relatively few temporal replicates; the median number was seven time points. Nearly 70% of studies applied more than one analysis method; descriptive methods such as bar graphs and ordination were the most commonly applied methods. Surprisingly, the types of analyses used were only related to the number of temporal replicates, but not to research aim or any other aspects of experimental design such as taxon, or habitat or year of study.

CONCLUSIONS

This review reveals that most studies interested in understanding community dynamics use relatively short time series meaning that several, more sophisticated, temporal analyses are not widely applicable. However, newer methods using multivariate dissimilarities are growing in popularity and many can be applied to time series of any length.

Trait structure and redundancy determine sensitivity to disturbance in marine fish communities

Trait diversity is believed to influence ecosystem dynamics through links between organismal traits and ecosystem processes. Theory predicts that key traits and high trait redundancy-large species richness and abundance supporting the same traits-can buffer communities against environmental disturbances. While experiments and data from simple ecological systems lend support, large-scale evidence from diverse, natural systems under major disturbance is lacking. Here, using long-term data from both temperate (English Channel) and tropical (Seychelles Islands) fishes, we show that sensitivity to disturbance depends on communities' initial trait structure and initial trait redundancy. In both ecosystems, we found that increasing dominance by climatically vulnerable traits (e.g., small, fast-growing pelagics/corallivores) rendered fish communities more sensitive to environmental change, while communities with higher trait redundancy were more resistant. To our knowledge, this is the first study demonstrating the influence of trait structure and redundancy on community sensitivity over large temporal and spatial scales in natural systems. Our results exemplify a consistent link between biological structure and community sensitivity that may be transferable across ecosystems and taxa and could help anticipate future disturbance impacts on biodiversity and ecosystem functioning.