Pesticides in Agricultural Soils: Major Findings from Various Monitoring Campaigns in Switzerland.

Synthetic pesticides are widely applied in modern agriculture, where they are used against diseases, pests, and weeds to secure crop yield and quality. However, their intensive application has led to widespread contamination of the environment, including soils. Due to their inherent toxicity, they might pose a risk to soil health by causing harm to non-target organisms and disrupting ecosystem services in both agricultural and other exposed soils. Following the Swiss National Action Plan on the reduction of pesticide risks, Agroscope has conducted several soil monitoring studies that are briefly presented here. All of them resort to different multi-residue trace analytical approaches to simultaneously quantify up to about 150 modern pesticides by either accelerated solvent, or Quick, Easy, Cheap, Efficient, Rugged, Safe (QuEChERS) extraction, followed by separation and detection with liquid chromatography-triple quadrupole mass spectrometry. While partly still in progress, our investigations led to the following major findings this far: Multiple pesticides are commonly present in soils, with individual concentrations in agricultural soils often reaching up to a few tens of µg/kg. Pesticide occurrence and concentrations in agricultural soils primarily depend on land use, land use history and cultivated crops. Pesticides can prevail much longer than predicted by their half-lives, and were found in soils even decades after conversion from conventional to organic farming. Corresponding residual fractions can be in the order of a few percent of the originally applied amounts. We further found negative associations of pesticide residues with the abundance of beneficial soil life, underpinning their potential risk to the fertility of agricultural soils. Traces of pesticides are also detected in soils to which they were never applied, indicating contamination, e.g., via spray drift or atmospheric deposition. These results confirm the general notion of both scientists and legislators that prospective risk assessments (RA; as executed during registration and use authorization) should be confirmed and adjusted by retrospective RA (e.g., by environmental monitoring studies of currently used compounds) to jointly lead to an overall reduced environmental risk of pesticides.

A multi-residue method for trace analysis of pesticides in soils with special emphasis on rigorous quality control.

A multi-residue trace analytical method is presented to accurately quantify 146 currently used pesticides in (agricultural) soils with varying soil properties. Pesticides were extracted using an optimized quick, easy, cheap, effective, rugged, and safe (QuEChERS) approach and chemical analysis was carried out by liquid chromatography coupled to tandem mass spectrometry (triple quadrupole). Quantification was based on matrix-matched internal standards calibration, using 95 isotopically labeled analyte analogues. In contrast to the common approach of method validation using soils freshly spiked with analytes shortly before the extraction, our method is additionally validated via an in-house prepared partly aged soil, which contains all target pesticides and via agricultural field soils with native pesticide residues. The developed method is highly sensitive (median method limit of quantification: 0.2 ng/g), precise (e.g., median intra-day and inter-day method precision both ~ 4% based on field soils), and true ((i) quantified pesticide concentrations of the partly aged soil remained stable during 6 months, were close to the initially spiked nominal concentration of 10 ng/g, and thus can be used to review trueness in the future; (ii) median freshly spiked relative recovery: 103%; and (iii) participation in a ring trial: median z-scores close to one (good to satisfactory result)). Its application to selected Swiss (agricultural) soils revealed the presence of in total 77 different pesticides with sum concentrations up to 500 ng/g. The method is now in use for routine soil monitoring as part of the Swiss Action Plan for Risk Reduction and Sustainable Use of Plant Protection Products.

Analysis of the Phialocephala subalpina Transcriptome during Colonization of Its Host Plant Picea abies.

BACKGROUND: Phialocephala subalpina belongs to the Phialocephala fortinii s.l.-Acepphala applanata species complex (PAC) forming one of the major groups belonging to the dark septate endophytes (DSE). Depending on the strain, PAC was shown to form neutral to pathogenic associations with its host plant Picea abies. To understand PACs lifestyle we investigated the effect of presence/absence of Picea abies on the transcriptome of strain 6_70_1. MATERIALS AND METHODS: PAC strain 6_70_1 was grown in liquid Pachlewski media either induced by its host plant Picea abies or without host plant as a control. Mycelia were harvested in a time course (1, 2, 3, 4, 7, 11, 18 days) with and without induction by the host plant and the fungal transcriptome revealed by Illumina sequencing. Differential gene expression analysis over the time course comparing control and treatment at each time point using the 'edgeR glm approach' and a gene enrichment analysis using GO categories were performed. RESULTS: The three main functional groups within differentially expressed genes were 'metabolism', 'transport' and 'cell rescue, defense and virulence'. Additionally, genes especially involved in iron metabolism could be detected by gene set enrichment analysis. CONCLUSION: In conclusion, we found PAC strain 6_70_1 to be metabolically very active during colonization of its host plant Picea abies. A major shift in functional groups over the time course of this experiment could not be observed but GO categories which were found to be enriched showed different emphasis depending in the day post induction.

Composition of fungal soil communities varies with plant abundance and geographic origin.

Interactions of belowground fungal communities with exotic and native plant species may be important drivers of plant community structure in invaded grasslands. However, field surveys linking plant community structure with belowground fungal communities are missing. We investigated whether a selected number of abundant and relatively rare plants, either native or exotic, from an old-field site associate with different fungal communities. We also assessed whether these plants showed different symbiotic relationships with soil biota through their roots. We characterized the plant community and collected roots to investigate fungal communities using 454 pyrosequencing and assessed arbuscular mycorrhizal colonization and enemy-induced lesions. Differences in fungal communities were considered based on the assessment of α- and ß diversity depending on plant 'abundance' and 'origin'. Plant abundance and origin determined the fungal community. Fungal richness was higher for native abundant as opposed to relatively rare native plant species. However, this was not observed for exotics of contrasting abundance. Regardless of their origin, ß diversity was higher for rare than for abundant species. Abundant exotics in the community, which happen to be grasses, were the least mycorrhizal whereas rare natives were most susceptible to enemy attack. Our results suggest that compared with exotics, the relative abundance of remnant native plant species in our old-field site is still linked to the structure of belowground fungal communities. In contrast, exotic species may act as a disturbing agent contributing towards the homogenization of soil fungal communities, potentially changing feedback interactions.

Mitigation of antagonistic effects on plant growth due to root co-colonization by dark septate endophytes and ectomycorrhiza.

Dark septate endophytes (DSE) are very common root colonizers of woody plant species. Ascomycetes of the Phialocephala fortinii s.l.-Acephala applanata species complex (PAC) are the main representatives of DSE fungi in forest ecosystems. PAC and mycorrhizal fungi share the same habitat, but interactions among PAC, mycorrhizal fungi and plants are poorly understood. We compared the effects of single and dual inoculation of Norway spruce seedlings with PAC and the ectomycorrhizal (ECM) fungus Hebeloma crustuliniforme on host growth, degree of mycorrhization and density of endophytic PAC biomass. Single colonization by H. crustuliniforme or PAC significantly reduced plant biomass. Dual colonization reduced or neutralized plant growth depression caused by single fungal colonization. The degree of mycorrhization was independent on PAC colonization, and mycorrhization significantly reduced endophytic PAC biomass. Plant biomass of dually colonized plants positively correlated with PAC biomass. These results demonstrate the ability of dual inoculation of PAC and H. crustuliniforme to neutralize plant growth depression caused by single fungal inoculation. Our explanations of enhanced plant growth in dually inoculated plants are the inhibition of PAC during root colonization by the ECM mantle and ECM-mediated access to plant growth-promoting nutrients resulting from the mineralization of the potting medium by PAC.

Mycorrhiza reduces adverse effects of dark septate endophytes (DSE) on growth of conifers.

Mycorrhizal roots are frequently colonized by fungi of the Phialocephala fortinii s.l.-Acephala applanata species complex (PAC). These ascomycetes are common and widespread colonizers of tree roots. Some PAC strains reduce growth increments of their hosts but are beneficial in protecting roots against pathogens. Nothing is known about the effects of PAC on mycorrhizal fungi and the PAC-mycorrhiza association on plant growth, even though these two fungal groups occur closely together in natural habitats. We expect reduced colonization rates and reduced negative effects of PAC on host plants if roots are co-colonized by an ectomycorrhizal fungus (ECM). Depending on the temperature regime interactions among the partners in this tripartite ECM-PAC-plant system might also change. To test our hypotheses, effects of four PAC genotypes (two pathogenic and two non-pathogenic on the Norway spruce), mycorrhization by Laccaria bicolor (strain S238N) and two temperature regimes (19°C and 25°C) on the biomass of the Douglas-fir (Pseudotsuga menziesii) and Norway spruce (Picea abies) seedlings were studied. Mycorrhization compensated the adverse effects of PAC on the growth of the Norway spruce at both temperatures. The growth of the Douglas-fir was not influenced either by PAC or mycorrhization at 19°C, but at 25°C mycorrhization had a similar protective effect as in the Norway spruce. The compensatory effects probably rely on the reduction of the PAC-colonization density by mycorrhizae. Temperature and the PAC strain only had a differential effect on the biomass of the Norway spruce but not on the Douglas-fir. Higher temperature reduced mycorrhization of both hosts. We conclude that ectomycorrhizae form physical and/or physiological barriers against PAC leading to reduced PAC-colonization of the roots. Additionally, our results indicate that global warming could cause a general decrease of mycorrhization making primary roots more accessible to other symbionts and pathogens.

Host species and strain combination determine growth reduction of spruce and birch seedlings colonized by root-associated dark septate endophytes.

Interactions of Betula pendula and Picea abies with dark septate endophytes of the Phialocephala fortinii-Acephala applanata species complex (PAC) were studied. PAC are ubiquitous fungal root symbionts of many woody plant species but their ecological role is largely unknown. Sterile birch and spruce seedlings in monoculture and mixed culture were exposed to four PAC strains, added either singularly or paired in all possible combinations at 18°C and 23°C. Plant and fungal biomass was determined after 4 months. The most significant factors were strain and host combination. One of the strains significantly reduced biomass gain of spruce but not of birch. Plant biomass was negatively correlated with total endophytic fungal biomass in half of the strain - plant combinations. Endophytic PAC biomass was four times higher in spruce (≈ 40 mg g(-1) drw) than in birch (≈ 10 mg g(-1) drw). Competition between strains was strain-dependent with some strains significantly reducing colonization density of other strains, and, thus, attenuating adverse effects of 'pathogenic' strains on plant growth in some strain - plant combinations. Biomass gain of spruce but not of birch was significantly reduced at higher temperature. In conclusion, host, fungal genotype, colonization density and presence of a competing PAC strain were the main determining factors for plant growth.

Microsatellite-based quantification method to estimate biomass of endophytic Phialocephala species in strain mixtures.

Fungi of the Phialocephala fortinii sensu lato-Acephala applanata species complex (PAC) are ubiquitous endophytic colonizers of tree roots in which they form genotypically diverse communities. Measurement of the colonization density of each of the fungal colonizers is a prerequisite to study the ecology of these communities. Up to now, there is no method readily available for the quantification of PAC strains co-colonizing the same root. The new DNA quantification method presented here is based on the amplification of microsatellites by competitive polymerase chain reaction (PCR). The method proved to be suitable to detect and quantify at least two strains within one single sample by the addition of a known amount of mycelium of a reference strain before DNA extraction. The method exploits the correlation between the reference/target ratio of light emitted during microsatellite detection (peak ratio) and the reference/target ratio of mycelial weights to determine the biomass of the target strain. Hence, calibration curves were obtained by linear regression of the peak ratios on the weight ratios for different mixtures of reference and target strains. The slopes of the calibration curves and the coefficients of determination were close to 1, indicating that peak ratios are good predictors of weight ratios. Estimates of fungal biomass in mycelial test mixtures of known composition laid within the 95% prediction interval and deviated on average by 16% (maximally 50%) from the true biomass. On average, 3-6% of the root biomass of Norway spruce seedlings consisted of mycelial biomass of either one of two inoculated PAC strains. Biomass estimates obtained by real-time quantitative PCR were correlated with the estimates obtained by the microsatellite-based method, but variation between the two estimates from the same root was high in some samples. The microsatellite-based DNA quantification method described here is currently the best method for strainwise estimation of endophytic biomass of PAC fungi in small root samples.