Local and regional-scale effects of hedgerows on grassland- and forest-associated bird populations within agroecosystems

Linear woody features (LWFs), like hedgerows along field edges, provide wildlife habitat and support biodiversity in agroecosystems. Assessments of LWFs usually focus on community-level indices, such as species richness. However, effective conservation actions need to balance the contrasting habitat preferences of different wildlife species, necessitating a focus on population-level effects in working landscapes. We assessed associations between LWFs and abundance for 45 bird species within an intensive agroecosystem in eastern Ontario, Canada. We used distance- and removal-sampling methods across 4 years (2016-2019) to estimate local bird abundance in habitats representing a range of LWF densities. We also predicted abundance across a subset of the study region with and without LWFs to understand their contribution to regional population density. Associations between local bird abundance and LWFs were variable among species, but overall community effects were clearly positive, particularly for forest and shrubland species. At the site level, 20/45 species (44%) had higher densities associated with greater LWF presence on average, compared to 5/45 (11%) with negative associations. At the regional scale, LWFs had predicted benefits on total abundance for 31 species (69%), contributing to an estimated 20% increase on average. Positive effects were most pronounced in areas with greater agricultural land use (primarily field crops), suggesting LWFs may provide crucial habitat in heavily modified landscapes but have little to no additional benefit for the avian community in areas with greater existing heterogeneity and habitat retention. Species that responded negatively tended to be at risk with strong habitat preferences for intact forests or large, open grasslands and, thus, greater sensitivity to potential edge effects. With rapidly declining songbird populations and a global need for food security, conservation strategies that amplify biodiversity and enhance agricultural productivity through ecosystem services such as pest control, pollination, and water regulation are vital. We demonstrate the benefits of habitat heterogeneity in agroecosystems on songbird densities and highlight the need to integrate local and landscape-level assessments in conservation planning. An effective, balanced strategy includes concentrating LWFs in areas of extensive arable crops, with habitat retention patches where possible, while maintaining heterogeneity through mixtures of natural habitats and pastoral farming in less intensive regions.

Three novel multiplex PCR assays for rapid detection of virulence, antimicrobial resistance, and toxin genes in Acinetobacter calcoaceticus-baumannii complex species

The Acinetobacter calcoaceticus-baumannii (ACB) complex is an often-overlooked group of nosocomial pathogens with a significant environmental presence. Rapid molecular screening methods for virulence, antimicrobial resistance, and toxin (VAT) genes are required to investigate the potential pathogenicity of environmental isolates. This study aimed to develop and apply novel ACB complex-specific multiplex PCR (mPCR) primers and protocols for the rapid detection of eight VAT genes. We optimized three single-tube mPCR assays using reference DNA from ACB complex and other Acinetobacter species. These assays were then applied to detect VAT genes in cultured ACB complex isolates recovered from clinical and environmental sources. Widespread detection of VAT genes in environmental isolates confirmed the validity, functionality, and applicability of these novel assays. Overall, the three newly developed ACB complex species-specific mPCR assays are rapid and simple tools that can be adopted in diagnostic and clinical lab settings. The detection of VAT genes in environmental isolates suggests that environmental niches could serve as a reservoir for potentially pathogenic ACB complex and warrants further investigation. The newly developed mPCR assays are specific, sensitive, and efficient, making them well-suited for high-throughput screening in epidemiological studies and evaluating the potential pathogenicity of ACB complex recovered from various sources.

Modeling West Nile Virus transmission in birds and humans: Advantages of using a cellular automata approach

In Canada, the periodic circulation of West Nile Virus (WNV) is difficult to predict and, beyond climatic factors, appears to be related to the migratory movements of infected birds from the southern United States. This hypothesis has not yet been explored in a spatially distributed model. The main objective of this work was to develop a spatially explicit dynamic model for the transmission of WNV in Canada, that allows us to explore non-climate related hypotheses associated with WNV transmission. A Cellular Automata (CA) approach for multiple hosts (birds and humans) is used for a test region in eastern Ontario, Canada. The tool is designed to explore the role of host and vector spatial heterogeneity, host migration, and vector feeding preferences. We developed a spatialized compartmental SEIRDS-SEI model for WNV transmission with a study region divided into 4 k m 2 rectangular cells. We used 2010-2021 bird data from the eBird project and 2010-2019 mosquito data collected by Ontario Public Health to mimic bird and mosquito seasonal variation. We considered heterogeneous bird densities (high and low suitability areas) and homogeneous mosquito and human densities. In high suitability areas for birds, we identified 5 entry points for WNV-infected birds. We compared our simulations with pools of WNV-infected field collected mosquitoes. Simulations and sensitivity analyses were performed using MATLAB software. The results showed good correspondence between simulated and observed epidemics, supporting the validity of our model assumptions and calibration. Sensitivity analysis showed that a 5% increase or decrease in each parameter of our model except for the biting rate of bird by mosquito (c ( B , M ) ) and mosquito natural mortality rate (d M ), had a very limited effect on the total number of cases (newly infected birds and humans), prevalence peak, or date of occurrence. We demonstrate the utility of the CA approach for studying WNV transmission in a heterogeneous landscape with multiple hosts.

A cost-effective RNA extraction and RT-qPCR approach to detect California serogroup viruses from pooled mosquito samples

Mosquito-borne diseases pose ongoing global health concerns, demanding more cost-efficient methods to detect pathogens to support enhanced surveillance efforts. This study introduces an adapted TRIzol-based high-throughput RNA extraction protocol, tailored for the detection of California serogroup viruses in pooled mosquito samples in a rapid and cost-effective manner. This approach provided consistent RNA yields and sensitive viral detection relative to two commercial extraction kits (QIAGEN RNeasy Mini Kit and MACHEREY-NAGEL NucleoSpin RNA Plus Kit). The incorporation of a user-friendly and non-spiking-based RT-qPCR internal control designed for the 18S rRNA gene in mosquitoes minimizes potential false positives/negatives, improving the fidelity of viral detection outcomes. Effective RNA yields, purity, and successful target amplification across 25 mosquito species and varied pool sizes (1-50 mosquitoes per tube) affirm the reliability of our approach. The extraction method is cost-effective, with an incurred cost of $0.58 CAD per sample, in contrast to the $5.25 CAD cost per sample of the two kits, rendering it promising for mosquito-borne disease surveillance initiatives.

Relationships between water quality and mosquito presence and abundance: a systematic review and meta-analysis

Mosquito-borne diseases (MBDs) are emerging in response to climate and land use changes. As mosquito (Diptera: Culicidae) habitat selection is often contingent on water availability for egg and larval development, studies have recognized water quality also influences larval habitats. However, underlying species-, genera-, and mosquito level preferences for water quality conditions are varied. This systematic review and meta-analysis aimed to identify, characterize, appraise, and synthesize available global data on the relationships between water quality and mosquito presence and abundance (MPA); with the goal to further our understanding of the geographic expansion of MBD risks. A systematic review was conducted to identify studies investigating the relationships between water quality properties and MPA. Where appropriate, random-effects meta-analyses were conducted to provide pooled estimates for the association between the most reported water quality properties and MPA. The most reported water quality parameters were pH (87%), nitrogen concentrations (56%), turbidity (56%), electrical conductivity (54%), dissolved oxygen (43%), phosphorus concentrations (30%), and alkalinity (10%). Overall, pH (P = 0.05), turbidity (P < 0.0001), electrical conductivity (P = 0.005), dissolved oxygen (P < 0.0001), nitrogen (P < 0.0001), and phosphorus (P < 0.0001) showed significantly positive pooled correlations with MPA, while alkalinity showed a nonsignificant null pooled correlation (P = 0.85). We observed high heterogeneity in most meta-analyses, and climate zonation was shown to influence the pooled estimates. Linkages between MPA and water quality properties will enhance our capacity to predict MBD risks under changing environmental and land use changes.

Identification of microplastics extracted from field soils amended with municipal biosolids

Microplastic particles in arable soil are expected to impact the environment and potentially human health. The application of municipal biosolids (MBs) to agricultural land presents a further dilemma in that biosolids act as a fertilizer for crop growth, and a disposal pathway for wastewater treatment plants. They are also a direct path for emerging contaminants, such as microplastics to enter the terrestrial environment. Reliable methods are needed to identify and quantify microplastics, found in agricultural soils to determine how microplastics are being cycled in the terrestrial environment. In this study, we developed a method for extracting microplastics from soil, and characterized their composition and identity for particles sized 5 μm to 2 mm. Method development was initially completed using natural soils spiked with microplastics and MBs, followed by the analyses of soil sampled from an agricultural field where MBs were recently applied at a rate of 13 tons dw/ha. The procedures that used the spiked samples showed that microplastics can be reliably extracted from soil in a laboratory setting, and identified and semi-quantified by thermogravimetric analysis combined with Fourier-transform infrared spectroscopy (TGA-FTIR). However, when the same methods were applied to the soil samples collected from the agricultural field, reproducibility became a challenge, as the number and type of microplastics changed even within the same soils (i.e., collected the same day from the same exact location). The variation in reproducibility observed between laboratory and field samples underscores the significant heterogeneity present in the environment. This heterogeneity, in turn, affects the identification and quantity of microplastics detected, a phenomenon observed even when comparing different fields within a single treatment regimen.

Pathogenicity assessment of Arcobacter butzleri isolated from Canadian agricultural surface water

BACKGROUND

Water is considered a source for the transmission of Arcobacter species to both humans and animals. This study was conducted to assess the prevalence, distribution, and pathogenicity of A. butzleri strains, which can potentially pose health risks to humans and animals. Cultures were isolated from surface waters of a mixed-use but predominately agricultural watershed in eastern Ontario, Canada. The detection of antimicrobial resistance (AMR) and virulence-associated genes (VAGs), as well as enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) assays were performed on 913 A. butzleri strains isolated from 11 agricultural sampling sites.

RESULTS

All strains were resistant to one or more antimicrobial agents, with a high rate of resistance to clindamycin (99%) and chloramphenicol (77%), followed by azithromycin (48%) and nalidixic acid (49%). However, isolates showed a significantly (p < 0.05) high rate of susceptibility to tetracycline (1%), gentamycin (2%), ciprofloxacin (4%), and erythromycin (5%). Of the eight VAGs tested, ciaB, mviN, tlyA, and pldA were detected at high frequency (> 85%) compared to irgA (25%), hecB (19%), hecA (15%), and cj1349 (12%) genes. Co-occurrence analysis showed A. butzleri strains resistant to clindamycin, chloramphenicol, nalidixic acid, and azithromycin were positive for ciaB, tlyA, mviN and pldA VAGs. ERIC-PCR fingerprint analysis revealed high genetic similarity among strains isolated from three sites, and the genotypes were significantly associated with AMR and VAGs results, which highlight their potential environmental ubiquity and potential as pathogenic.

CONCLUSIONS

The study results show that agricultural activities likely contribute to the contamination of A. butzleri in surface water. The findings underscore the importance of farm management practices in controlling the potential spread of A. butzleri and its associated health risks to humans and animals through contaminated water.

The role of species ecology in predicting Toxoplasma gondii prevalence in wild and domesticated mammals globally

Macroecological approaches can provide valuable insight into the epidemiology of globally distributed, multi-host pathogens. Toxoplasma gondii is a protozoan that infects any warm-blooded animal, including humans, in almost every habitat worldwide. Toxoplasma gondii infects its hosts through oocysts in the environment, carnivory of tissue cysts within intermediate host prey and vertical transmission. These routes of infection enable specific predictions regarding the ecological and life history traits that should predispose specific taxa to higher exposure and, thus infection rates of T. gondii. Using T. gondii prevalence data compiled from 485 studies representing 533 free-ranging wild mammalian species, we examined how ecological (habitat type, trophic level) and life history (longevity, vagility, gestation duration and torpor) traits influence T. gondii infection globally. We also compared T. gondii prevalence between wild and domesticated species from the same taxonomic families using data compiled from 540 studies of domestic cattle, sheep, and pigs. Across free-ranging wildlife, we found the average T. gondii prevalence was 22%, which is comparable to the global human estimate. Among ecological guilds, terrestrial species had lower T. gondii prevalence than aquatic species, with freshwater aquatic taxa having an increased prevalence compared to marine aquatic species. Dietary niches were also influential, with carnivores having an increased risk compared to other trophic feeding groups that have reduced tissue cyst exposure in their diet. With respect to influential life history traits, we found that more vagile wildlife species had higher T. gondii infection rates, perhaps because of the higher cumulative risk of infection during movement through areas with varying T. gondii environmental loads. Domestic farmed species had a higher T. gondii prevalence compared to free-ranging confamilial wildlife species. Through a macroecological approach, we determined the relative significance of transmission routes of a generalist pathogen, demonstrating an increased infection risk for aquatic and carnivorous species and highlighting the importance of preventing pathogen pollution into aquatic environments. Toxoplasma gondii is increasingly understood to be primarily an anthropogenically-associated pathogen whose dissemination is enhanced by ecosystem degradation and human subsidisation of free-roaming domestic cats. Adopting an ecosystem restoration approach to reduce one of the world's most common parasites would synergistically contribute to other initiatives in conservation, feline and wildlife welfare, climate change, food security and public health.

How many microplastic particles are present in Canadian biosolids?

Application of treated sewage sludge (biosolids) from wastewater treatment plants (WWTPs) to farmlands is an important pathway through which microplastic particles (MPs) enter terrestrial ecosystems. Yet, microplastic concentrations in Canadian biosolids have only been estimated in samples from four WWTPs previously. We aimed to fill this knowledge gap by quantifying microplastics in biosolids from 22 WWTPs located in nine provinces and two commercial fertilizer producers in Canada. All samples had substantial microplastic concentrations ranging from 228 to 1353 particles per gram dry weight (median = 636 particles), which are orders of magnitude greater than MPs reported from earlier investigations of biosolids from other countries. Fibers (median: 86%) were the most common type of MPs observed, followed by fragments (median: 13%). There were no statistically significant differences in the amount of microplastics observed in the biosolids from different geographical regions, WWTP types, and sludge treatment processes. This suggests that diverse combinations of local sewershed characteristics, site-specific treatment approaches, and daily flow at WWTPs may be influencing concentrations of microplastics in biosolids. Our results indicate that microplastic concentrations in biosolids are substantially higher than they are in other environmental matrices, and this has important implications to managing microplastic pollution in terrestrial ecosystems.

Impacts of repeated coastal flooding on soil and groundwater following managed dike realignment

Coastal defense structures (e.g., dikes, seawalls) protect vulnerable communities along marine coastlines and estuaries from the physical and chemical influences of adjacent water bodies. These structures are susceptible to overtopping or breaching by tides and waves, with risks amplified by climate change-induced sea-level rise. Repeated inundation by saline water can contaminate freshwater resources and salinize soil, impacting land-use activities, including agricultural productivity. Managed ecosystem-based dike realignment and salt marsh restoration can provide alternatives to traditional coastal adaptation approaches. We assess the changes to soil salinity at a managed dike realignment project prior to the transformation from a diked terrestrial environment to an estuarine environment. Baseline data are compared to conditions following 8-10 months of intermittent flooding at spring tides. Results show that an increase in salinity occurred over the entire site in the shallow subsurface, with the most significant contamination occurring in low-lying areas. Bulk soil electrical conductivity (salinity proxy) measured from geophysical surveys increased from the previous freshwater condition of ~300 μS/cm to over 6000 μS/cm following <20 flood events, while successive flooding resulted in increased soil moisture as infiltrated floodwater propagated to greater depths. Sediment deposition occurred at high rates, with up to 4 cm of sediment deposited per flood, converting much of the previously cultivated land into tidal mudflats. Deeper sediments and groundwater (i.e., >1.8 m depth) were not impacted over the time scale of this research. This study demonstrates that intermittent shallow flooding can rapidly increase moisture content and soil salinity in surficial sediments and, in turn, adversely impact conditions suitable for agricultural crop production. The realignment zone serves as an engineered analog of coastal flooding, presenting an opportunity to investigate how low-lying coastal environments may experience regular flooding in the future due to sea-level rise and intensifying coastal storms.

Future land-use change predictions using Dyna-Clue to support mosquito-borne disease risk assessment

Mosquitoes are known vectors for viral diseases in Canada, and their distribution is driven by climate and land use. Despite that, future land-use changes have not yet been used as a driver in mosquito distribution models in North America. In this paper, we developed land-use change projections designed to address mosquito-borne disease (MBD) prediction in a 38 761 km2 area of Eastern Ontario. The landscape in the study area is marked by urbanization and intensive agriculture and hosts a diverse mosquito community. The Dyna-CLUE model was used to project land-use for three time horizons (2030, 2050, and 2070) based on historical trends (from 2014 to 2020) for water, forest, agriculture, and urban land uses. Five scenarios were generated to reflect urbanization, agricultural expansion, and natural areas. An ensemble of thirty simulations per scenario was run to account for land-use conversion uncertainty. The simulation closest to the average map generated was selected to represent the scenario. A concordance matrix generated using map pair analysis showed a good agreement between the simulated 2020 maps and 2020 observed map. By 2050, the most significant changes are predicted to occur mainly in the southeastern region's rural and forested areas. By 2070, high deforestation is expected in the central west. These results will be integrated into risk models predicting mosquito distribution to study the possibility of humans' increased exposure risk to MBDs.

Environmental Concentrations of the Type 2 Diabetes Medication Metformin and its Transformation Product Guanylurea in Surface Water and Sediment in Ontario and Quebec, Canada

Metformin, used to treat Type 2 Diabetes, is the active ingredient of one of the most prescribed drugs in the world, with over 120 million yearly prescriptions globally. In wastewater treatment plants (WWTPs), metformin can undergo microbial transformation to form the transformation product guanylurea, which could have toxicological relevance in the environment. Surface water samples from 2018-2020 and sediment samples from 2020 were collected from 6 mixed-use watersheds in Quebec and Ontario, Canada and analyzed to determine the metformin and guanylurea concentrations at each site. Metformin and guanylurea were present above their limits of quantification in 51.0 and 50.7% of all water samples, and in 64% and 21% of all sediment samples, respectively. In surface water, guanylurea was often present at higher concentrations than metformin, while the inverse was true in sediment, with metformin frequently detected at higher concentrations than guanylurea. Additionally, at all sites influenced solely by agriculture, concentrations of metformin and guanylurea were lower than 1 µg/L in surface water, suggesting that agriculture is not a significant source of these compounds in the investigated watersheds. These data suggest that WWTPs and potentially septic system leaks are the most likely sources of the compounds in the environment. Guanylurea was detected at many of these sites above environmental concentrations of concern, where critical processes in fish may be affected. Due to the scarcity of available ecotoxicological data and the prominence of guanylurea across all sample sites, there is a need to perform more toxicological investigations of this transformation product and revisit regulations. This report will help provide toxicologists with environmentally relevant concentration ranges in Canada.

Core and conditionally rare taxa as indicators of agricultural drainage ditch and stream health and function

BACKGROUND

The freshwater microbiome regulates aquatic ecological functionality, nutrient cycling, pathogenicity, and has the capacity to dissipate and regulate pollutants. Agricultural drainage ditches are ubiquitous in regions where field drainage is necessary for crop productivity, and as such, are first-line receptors of agricultural drainage and runoff. How bacterial communities in these systems respond to environmental and anthropogenic stressors are not well understood. In this study, we carried out a three year study in an agriculturally dominated river basin in eastern Ontario, Canada to explore the spatial and temporal dynamics of the core and conditionally rare taxa (CRT) of the instream bacterial communities using a 16S rRNA gene amplicon sequencing approach. Water samples were collected from nine stream and drainage ditch sites that represented the influence of a range of upstream land uses.

RESULTS

The cross-site core and CRT accounted for 5.6% of the total number of amplicon sequence variants (ASVs), yet represented, on average, over 60% of the heterogeneity of the overall bacterial community; hence, well reflected the spatial and temporal microbial dynamics in the water courses. The contribution of core microbiome to the overall community heterogeneity represented the community stability across all sampling sites. CRT was primarily composed of functional taxa involved in nitrogen (N) cycling and was linked to nutrient loading, water levels, and flow, particularly in the smaller agricultural drainage ditches. Both the core and the CRT were sensitive responders to changes in hydrological conditions.

CONCLUSIONS

We demonstrate that core and CRT can be considered as holistic tools to explore the temporal and spatial variations of the aquatic microbial community and can be used as sensitive indicators of the health and function of agriculturally dominated water courses. This approach also reduces computational complexity in relation to analyzing the entire microbial community for such purposes.

Monitoring of Environmental Contaminants in Mixed-Use Watersheds Combining Targeted and Nontargeted Analysis with Passive Sampling

Understanding the environmental fate, transport, and occurrence of pesticides and pharmaceuticals in aquatic environments is of utmost concern to regulators. Traditionally, monitoring of environmental contaminants in surface water has consisted of liquid chromatography-tandem mass spectrometry analyses for a set of targeted compounds in discrete samples. These targeted approaches are limited by the fact that they only provide information on compounds within a target list present at the time and location of sampling. To address these limitations, there has been considerable interest in suspect screening and nontargeted analysis (NTA), which allow for the detection of all ionizable compounds in the sample with the added benefit of data archiving for retrospective mining. Even though NTA can detect a large number of contaminants, discrete samples only provide a snapshot perspective of the chemical disposition of an aquatic environment at the time of sampling, potentially missing episodic events. We evaluated two types of passive chemical samplers for nontargeted analysis in mixed-use watersheds. Nontargeted data were processed using MS-DIAL to screen against our in-house library and public databases of more than 1300 compounds. The data showed that polar organic chemicals integrative samplers (POCIS) were able to capture the largest number of analytes with better reproducibility than organic compound-diffusive gradients in thin film (o-DGT), resulting from the greater amount of binding sorbent. We also showed that NTA combined with passive sampling gives a more representative picture of the contaminants present at a given site and enhances the ability to identify the nature of point and nonpoint pollution sources and ecotoxicological impacts. Environ Toxicol Chem 2022;41:1131-1143. © 2021 Her Majesty the Queen in Right of Canada Environmental Toxicology and Chemistry © 2021 SETAC. Reproduced with the permission of the Minister of Agriculture and Agri-Food Canada.

Effects of land use and weather on the presence and abundance of mosquito-borne disease vectors in a urban and agricultural landscape in Eastern Ontario, Canada

Weather and land use can significantly impact mosquito abundance and presence, and by consequence, mosquito-borne disease (MBD) dynamics. Knowledge of vector ecology and mosquito species response to these drivers will help us better predict risk from MBD. In this study, we evaluated and compared the independent and combined effects of weather and land use on mosquito species occurrence and abundance in Eastern Ontario, Canada. Data on occurrence and abundance (245,591 individuals) of 30 mosquito species were obtained from mosquito capture at 85 field sites in 2017 and 2018. Environmental variables were extracted from weather and land use datasets in a 1-km buffer around trapping sites. The relative importance of weather and land use on mosquito abundance (for common species) or occurrence (for all species) was evaluated using multivariate hierarchical statistical models. Models incorporating both weather and land use performed better than models that include weather only for approximately half of species (59% for occurrence model and 50% for abundance model). Mosquito occurrence was mainly associated with temperature whereas abundance was associated with precipitation and temperature combined. Land use was more often associated with abundance than occurrence. For most species, occurrence and abundance were positively associated with forest cover but for some there was a negative association. Occurrence and abundance of some species (47% for occurrence model and 88% for abundance model) were positively associated with wetlands, but negatively associated with urban (Culiseta melanura and Anopheles walkeri) and agriculture (An. quadrimaculatus, Cs. minnesotae and An. walkeri) environments. This study provides predictive relationships between weather, land use and mosquito occurrence and abundance for a wide range of species including those that are currently uncommon, yet known as arboviruses vectors. Elucidation of these relationships has the potential to contribute to better prediction of MBD risk, and thus more efficiently targeted prevention and control measures.

Human density is associated with the increased prevalence of a generalist zoonotic parasite in mammalian wildlife

Macroecological approaches can provide valuable insight into the epidemiology of globally distributed, multi-host pathogens. Toxoplasma gondii is a zoonotic protozoan that infects any warm-blooded animal, including humans, in almost every ecosystem worldwide. There is substantial geographical variation in T. gondii prevalence in wildlife populations and the mechanisms driving this variation are poorly understood. We implemented Bayesian phylogenetic mixed models to determine the association between species' ecology, phylogeny and climatic and anthropogenic factors on T. gondii prevalence. Toxoplasma gondii prevalence data were compiled for free-ranging wild mammal species from 202 published studies, encompassing 45 079 individuals from 54 taxonomic families and 238 species. We found that T. gondii prevalence was positively associated with human population density and warmer temperatures at the sampling location. Terrestrial species had a lower overall prevalence, but there were no consistent patterns between trophic level and prevalence. The relationship between human density and T. gondii prevalence is probably mediated by higher domestic cat abundance and landscape degradation leading to increased environmental oocyst contamination. Landscape restoration and limiting free-roaming in domestic cats could synergistically increase the resiliency of wildlife populations and reduce wildlife and human infection risks from one of the world's most common parasitic infections.

Mosquito Identification From Bulk Samples Using DNA Metabarcoding: a Protocol to Support Mosquito-Borne Disease Surveillance in Canada

Approximately 80 species of mosquitoes (Diptera: Culicidae) have been documented in Canada. Exotic species such as Aedes albopictus (Skuse) (Diptera: Culicidae) are becoming established. Recently occurring endemic mosquito-borne diseases (MBD) in Canada including West-Nile virus (WNV) and Eastern Equine Encephalitis (EEE) are having significant public health impacts. Here we explore the use of DNA metabarcoding to identify mosquitoes from CDC light-trap collections from two locations in eastern Canada. Two primer pairs (BF2-BR2 and F230) were used to amplify regions of the cytochrome c oxidase subunit I (CO1) gene. High throughput sequencing was conducted using an Illumina MiSeq platform and GenBank-based species identification was applied using a QIIME 1.9 bioinformatics pipeline. From a site in southeastern Ontario, Canada, 26 CDC light trap collections of 72 to >300 individual mosquitoes were used to explore the capacity of DNA metabarcoding to identify and quantify captured mosquitoes. The DNA metabarcoding method identified 33 species overall while 24 species were identified by key. Using replicates from each trap, the dried biomass needed to identify the majority of species was determined to be 76 mg (equivalent to approximately 72 mosquitoes), and at least two replicates from the dried biomass would be needed to reliably detect the majority of species in collections of 144-215 mosquitoes and three replicates would be advised for collections with >215 mosquitoes. This study supports the use of DNA metabarcoding as a mosquito surveillance tool in Canada which can help identify the emergence of new mosquito-borne disease potential threats.

The Effects of Ditch Management in Agroecosystems on Embryonic and Tadpole Survival, Growth, and Development of Northern Leopard Frogs (Lithobates pipiens)

Agricultural drainage ditches help remove excess water from fields and provide habitat for wildlife. Drainage ditch management, which includes various forms of vegetation clearing and sediment dredging, can variably affect the ecological function of these systems. To determine whether ditch conditions following dredging/vegetation clearing management affected the survival, growth, and development of embryos and tadpoles of northern leopard frogs (Lithobates pipiens), we conducted three field studies using in situ cages over 2 years. We measured nutrients, pesticides, and other water quality properties in vegetated/unmanaged (i.e., no clearing or dredging) and newly cleared/dredged (i.e., treeless, then dredged), clay-bottomed drainage ditches in a river basin in Eastern Ontario, Canada. Nutrients, atrazine, and total neonicotinoid concentrations were generally lower at the cleared/dredged sites, whereas glyphosate was at higher concentrations. In contrast, water-quality variables measured in situ, particularly temperature, dissolved oxygen, and turbidity, tended to be higher in the cleared/dredged sites. Total phosphorous and total organic carbon concentrations at all sites were above the recommended limits for amphibian assays. No significant differences were detected in the survival, hatching success, or development of embryos among the ditch management treatments, but premature hatching was observed at one vegetated/unmanaged site where high specific conductivity may have been formative. We found the cleared/dredged sites supported earlier tadpole growth and development, likely as a result of the higher water temperatures. Increased temperature may have offset other growth/development stressors, such as those related to water chemistry. However, the long-term consequences of these differences on amphibian populations requires further study.

Loop-mediated isothermal amplification: Development, validation and application of simple and rapid assays for quantitative detection of species of Arcobacteraceae family- and species-specific Aliarcobacter faecis and Aliarcobacter lanthieri

Aim

The family Arcobacteraceae formerly genus Arcobacter has recently been reclassified into six genera. Among nine species of the genus Aliarcobacter, Aliarcobacter faecis and Aliarcobacter lanthieri have been identified as emerging pathogens potentially cause health risks to humans and animals. This study was designed to develop/optimize, validate and apply Arcobacteraceae family‐ and two species‐specific (A. faecis and A. lanthieri) loop‐mediated isothermal amplification (LAMP) assays to rapidly detect and quantify total number of cells in various environmental niches.

Methods and Results

Three sets of LAMP primers were designed from conserved and variable regions of 16S rRNA (family‐specific) and gyrB (species‐specific) genes. Optimized Arcobacteraceae family‐specific LAMP assay correctly amplified and detected 24 species, whereas species‐specific LAMP assays detected A. faecis and A. lanthieri reference strains as well as 91 pure and mixed culture isolates recovered from aquatic and faecal sources. The specificity of LAMP amplification of A. faecis and A. lanthieri was further confirmed by restriction fragment length polymorphism analysis. Assay sensitivities were tested using variable DNA concentrations extracted from simulated target species cells in an autoclaved agricultural water sample by achieving a minimum detection limit of 10 cells mL⁻¹ (10 fg). Direct DNA‐based quantitative detection, from agricultural surface water, identified A. faecis (17%) and A. lanthieri (1%) at a low frequency compared to family‐level (93%) with the concentration ranging from 2·1 × 10¹ to 2·2 × 10⁵ cells 100 mL⁻¹.

Conclusions

Overall, these three DNA‐based rapid and cost‐effective novel LAMP assays are sensitive and can be completed in less than 40 min. They have potential for on‐site quantitative detection of species of family Arcobacteraceae, A. faecis and A. lanthieri in food, environmental and clinical matrices.

Significance and Impact of the Study

The newly developed LAMP assays are specific, sensitive, accurate with higher reproducibility that have potential to facilitate in a less equipped lab setting and can help in early quantitative detection and rate of prevalence in environmental niches. The assays can be adopted in the diagnostic labs and epidemiological studies.

Real-time quantitative PCR assay development and application for assessment of agricultural surface water and various fecal matter for prevalence of Aliarcobacter faecis and Aliarcobacter lanthieri

BACKGROUND

Aliarcobacter faecis and Aliarcobacter lanthieri are recently identified as emerging human and animal pathogens. In this paper, we demonstrate the development and optimization of two direct DNA-based quantitative real-time PCR assays using species-specific oligonucleotide primer pairs derived from rpoB and gyrA genes for A. faecis and A. lanthieri, respectively. Initially, the specificity of primers and amplicon size of each target reference strain was verified and confirmed by melt curve analysis. Standard curves were developed with a minimum quantification limit of 100 cells mL^- 1 or g^- 1 obtained using known quantities of spiked A. faecis and A. lanthieri reference strains in autoclaved agricultural surface water and dairy cow manure samples.

RESULTS

Each species-specific qPCR assay was validated and applied to determine the rate of prevalence and quantify the total number of cells of each target species in natural surface waters of an agriculturally-dominant and non-agricultural reference watershed. In addition, the prevalence and densities were determined for human and various animal (e.g., dogs, cats, dairy cow, and poultry) fecal samples. Overall, the prevalence of A. faecis for surface water and feces was 21 and 28%, respectively. The maximum A. faecis concentration for water and feces was 2.3 × 10⁷ cells 100 mL^{- 1} and 1.2 × 10⁷ cells g^- 1, respectively. A. lanthieri was detected at a lower frequency (2%) with a maximum concentration in surface water of 4.2 × 10⁵ cells 100 mL^- 1; fecal samples had a prevalence and maximum density of 10% and 2.0 × 10⁶ cells g^- 1, respectively.

CONCLUSIONS

The results indicate that the occurrence of these species in agricultural surface water is potentially due to fecal contamination of water from livestock, human, or wildlife as both species were detected in fecal samples. The new real-time qPCR assays can facilitate rapid and accurate detection in < 3 h to quantify total numbers of A. faecis and A. lanthieri cells present in various complex environmental samples.

Chlorophyll-a, dissolved organic carbon, turbidity and other variables of ecological importance in river basins in southern Ontario and British Columbia, Canada

Optical sensing of chlorophyll-a (chl-a), turbidity, and fluorescent dissolved organic matter (fDOM) is often used to characterize the quality of water. There are many site-specific factors and environmental conditions that can affect optically sensed readings; notwithstanding the comparative implication of different procedures used to measure these properties in the laboratory. In this study, we measured these water quality properties using standard laboratory methods, and in the field using optical sensors (sonde-based) at water quality monitoring sites located in four watersheds in Canada. The overall objective of this work was to explore the relationships among sonde-based and standard laboratory measurements of the aforementioned water properties, and evaluate associations among these eco-hydrological properties and land use, environmental, and ancillary water quality variables such as dissolved organic carbon (DOC) and total suspended solids (TSS). Differences among sonde versus laboratory relationships for chl-a suggest such relationships are impacted by laboratory methods and/or site specific conditions. Data mining analysis indicated that interactive site-specific factors predominately impacting chl-a values across sites were specific conductivity and turbidity (variables with positive global associations with chl-a). The overall linear regression predicting DOC from fDOM was relatively strong (R² = 0.77). However, slope differences in the watershed-specific models suggest laboratory DOC versus fDOM relationships could be impacted by unknown localized water quality properties affecting fDOM readings, and/or the different standard laboratory methods used to estimate DOC. Artificial neural network analyses (ANN) indicated that higher relative chl-a concentrations were associated with low to no tree cover around sample sites and higher daily rainfall in the watersheds examined. Response surfaces derived from ANN indicated that chl-a concentrations were higher where combined agricultural and urban land uses were relatively higher.

Qualifying the effects of single and multiple stressors on the food web structure of Dutch drainage ditches using a literature review and conceptual models

In September 2017, a workshop was held at Wageningen University and Research to determine the current state of knowledge of multiple stressor effects on aquatic ecosystems and to assess how to improve prediction of these effects. We developed a theoretical framework that integrates species-level responses to stressors to predict how these effects propagate through higher levels of biological organisation. Here, we present the application of the framework for drainage ditch ecosystems in the Netherlands. We used food webs to assess single and multiple stressor effects of common stressors on ditch communities. We reviewed the literature for the effects of targeted stressors (nutrients, pesticides, dredging and mowing, salinization, and siltation) on each functional group present in the food web and qualitatively assessed the relative sensitivity of groups. Using this information, we created a stressor-response matrix of positive and negative direct effects of each stressor-functional group combination. Fungicides, salinization, and sedimentation were identified as particularly detrimental to most groups, although destructive management practices, such as dredging with almost complete community removal, would take precedence depending on frequency. Using the stressor-response matrix we built, first, a series of conceptual null models of single stressor effects on food web structure and, second, a series of additive null models to illustrate potential paired-stressor effects. We compared these additive null models with published studies of the same pairs of combined single stressors to explore more complex interactions. Our approach serves as a first-step to considering multiple stressor scenarios in systems that are understudied or data-poor and as a baseline from which more complex models that include indirect effects and quantitative data may be developed. We make specific suggestions for appropriate management strategies that could be taken to support the biodiversity of these systems for individual stressors and their combined impacts.

Towards a general framework for the assessment of interactive effects of multiple stressors on aquatic ecosystems: Results from the Making Aquatic Ecosystems Great Again (MAEGA) workshop

A workshop was held in Wageningen, The Netherlands, in September 2017 to collate data and literature on three aquatic ecosystem types (agricultural drainage ditches, urban floodplains, and urban estuaries), and develop a general framework for the assessment of multiple stressors on the structure and functioning of these systems. An assessment framework considering multiple stressors is crucial for our understanding of ecosystem responses within a multiply stressed environment, and to inform appropriate environmental management strategies. The framework consists of two components: (i) problem identification and (ii) impact assessment. Both assessments together proceed through the following steps: 1) ecosystem selection; 2) identification of stressors and quantification of their intensity; 3) identification of receptors or sensitive groups for each stressor; 4) identification of stressor-response relationships and their potential interactions; 5) construction of an ecological model that includes relevant functional groups and endpoints; 6) prediction of impacts of multiple stressors, 7) confirmation of these predictions with experimental and monitoring data, and 8) potential adjustment of the ecological model. Steps 7 and 8 allow the assessment to be adaptive and can be repeated until a satisfactory match between model predictions and experimental and monitoring data has been obtained. This paper is the preface of the MAEGA (Making Aquatic Ecosystems Great Again) special section that includes three associated papers which are also published in this volume, which present applications of the framework for each of the three aquatic systems.

Estimating cumulative wastewater treatment plant discharge influences on acesulfame and Escherichia coli in a highly impacted watershed with a fully-integrated modelling approach

Wastewater treatment plant (WWTP) discharge is often considered a principal source of surface water contamination. In this study, a three-dimensional fully-integrated groundwater-surface water model was used to simulate the transport characteristics and cumulative loading of an artificial sweetener (acesulfame) and fecal indicator bacteria (Escherichia coli) from WWTPs within a 6800 km² mixed-use, highly impacted watershed in Ontario, Canada. The model, which employed 3.5 × 10⁶ computational nodes and 15 layers, facilitated a comprehensive assessment of groundwater-surface water interactions under high and low flow conditions; processes typically not accounted for in WWTP cumulative effects models. Simulations demonstrate that the model had significant capacity in reproducing the average and transient multi-year groundwater and surface water flow conditions in the watershed. As a proxy human-specific conservative tracer, acesulfame was useful for model validation and to help inform the representation of watershed-scale transport processes. Using a uniform WWTP acesulfame loading rate of 7.14 mg person^-1 day^-1, the general spatial trends and magnitudes of the acesulfame concentration profile along the main river reach within the watershed were reproduced; however, model performance was improved by tuning individual WWTP loading rates. Although instream dilution and groundwater-surface water interactions were strongly dependent on flow conditions, the main reach primarily consisted of groundwater discharge zones. For this reason, hydrodynamic dispersion in the hyporheic zone is shown as the predominant mechanism driving acesulfame into near-stream shallow groundwater, while under high flow conditions, the simulations demonstrate the potential for advective flushing of the shallow groundwater. Regarding the cumulative impact of the WWTPs on E. coli concentrations in the surface flow system, simulated transient E. coli levels downstream of WWTPs in the watershed were significantly lower than observed values, thus highlighting the potential importance of other sources of E. coli in the watershed.

Do reductions in agricultural field drainage during the growing season impact bacterial densities and loads in small tile-fed watersheds?

Predicting bacterial levels in watersheds in response to agricultural beneficial management practices (BMPs) requires understanding the germane processes at both the watershed and field scale. Controlling subsurface tile drainage (CTD) is a highly effective BMP at reducing nutrient losses from fields, and watersheds when employed en masse, but little work has been conducted on CTD effects on bacterial loads and densities in a watershed context. This study compared fecal indicator bacteria (FIB) [E. coli, Enterococcus, Fecal coliform, Total coliform, Clostridium perfringens] densities and unit area loads (UAL) from a pair of flat tile-drained watersheds (∼250-467 ha catchment areas) during the growing season over a 10-year monitoring period, using a before-after-control-impact (BACI) design (i.e., test CTD watershed vs. reference uncontrolled tile drainage (UCTD) watershed during a pre CTD intervention period and a CTD-intervention period where the test CTD watershed had CTD deployed on over 80% of the fields). With no tile drainage management, upstream tile drainage to ditches comprised ∼90% of total ditch discharge. We also examined FIB loads from a subset of tile drained fields to determine field load contributions to the watershed drainage ditches. Statistical evidence of a CTD effect on FIB UAL in the surface water systems was not strong; however, there was statistical evidence of increased FIB densities [pronounced when E. coli >200 most probable number (MPN) 100 mL^-1] in the test CTD watershed during the CTD-intervention period. This was likely a result of reduced dilution/flushing in the test CTD watershed ditch due to CTD significantly decreasing the amount of tile drainage water entering the surface water system. Tile E. coli load contributions to the ditches were low; for example, during the 6-yr CTD-intervention period they amounted to on average only ∼3 and ∼9% of the ditch loads for the test CTD and reference UCTD watersheds, respectively. This suggests in-stream, or off-field FIB reservoirs and bacteria mobilization drivers, dominated ditch E. coli loads in the watersheds during the growing season. Overall, this study suggested that decision making regarding deployment of CTD en masse in tile-fed watersheds should consider drainage practice effects on bacterial densities and loads, as well as CTD's documented capacity to boost crop yields and reduce seasonal nutrient pollution.

Novel virulence, antibiotic resistance and toxin gene-specific PCR-based assays for rapid pathogenicity assessment of Arcobacter faecis and Arcobacter lanthieri

Background

Arcobacter faecis and A. lanthieri are two newly classified species of genus Arcobacter. The prevalence and distribution of virulence, antibiotic resistance and toxin (VAT) genes in these species are required to assess their potential pathogenic health impacts to humans and animals. This study (i) developed species- and gene-specific primer pairs for the detection of six virulence, two antibiotic resistance, and three toxin genes in two target species; (ii) optimized eight single-tube multiplex and three monoplex PCR protocols using the newly developed species- and gene-specific primers; and (iii) conducted specificity and sensitivity evaluations as well as validation of eleven mono- and multiplex PCR assays by testing A. faecis (n= 29) and A. lanthieri (n= 10) strains isolated from various fecal and agricultural water sources to determine the prevalence and distribution of VAT genes and assess the degree of pathogenicity within the two species.

Results

Detection of all ten and eleven target VAT genes, and expression of cytolethal distending toxin (cdtA, cdtB and cdtC) genes in A. faecis and A. lanthieri reference strains with high frequency in field isolates suggest that they are potentially pathogenic strains. These findings indicate that these two species can pose a health risk to humans and animals.

Conclusions

The study results show that the developed mono- and multiplex PCR (mPCR) assays are simple, rapid, reliable and sensitive for the simultaneous assessment of the potential pathogenicity and antibiotic resistance profiling of tet(O) and tet(W) genes in these two newly discovered species. Also, these assays can be useful in diagnostic and analytical laboratories to determine the pathotypes and assessment of the virulence and toxin factors associated to human and animal infections.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1357-7) contains supplementary material, which is available to authorized users.

Aquatic Bacterial Communities Associated With Land Use and Environmental Factors in Agricultural Landscapes Using a Metabarcoding Approach

This study applied a 16S rRNA gene metabarcoding approach to characterize bacterial community compositional and functional attributes for surface water samples collected within, primarily, agriculturally dominated watersheds in Ontario and Québec, Canada. Compositional heterogeneity was best explained by stream order, season, and watercourse discharge. Generally, community diversity was higher at agriculturally dominated lower order streams, compared to larger stream order systems such as small to large rivers. However, during times of lower relative water flow and cumulative 2-day rainfall, modestly higher relative diversity was found in the larger watercourses. Bacterial community assemblages were more sensitive to environmental/land use changes in the smaller watercourses, relative to small-to-large river systems, where the proximity of the sampled water column to bacteria reservoirs in the sediments and adjacent terrestrial environment was greater. Stream discharge was the environmental variable most significantly correlated (all positive) with bacterial functional groups, such as C/N cycling and plant pathogens. Comparison of the community structural similarity via network analyses helped to discriminate sources of bacteria in freshwater derived from, for example, wastewater treatment plant effluent and intensity and type of agricultural land uses (e.g., intensive swine production vs. dairy dominated cash/livestock cropping systems). When using metabarcoding approaches, bacterial community composition and coexisting pattern rather than individual taxonomic lineages, were better indicators of environmental/land use conditions (e.g., upstream land use) and bacterial sources in watershed settings. Overall, monitoring changes and differences in aquatic microbial communities at regional and local watershed scales has promise for enhancing environmental footprinting and for better understanding nutrient cycling and ecological function of aquatic systems impacted by a multitude of stressors and land uses.

Quantitative real-time PCR-based assessment of tile drainage management influences on bacterial pathogens in tile drainage and groundwater

This study compared the impact of controlled tile drainage (CD) and freely draining (FD) systems on the prevalence and quantitative real-time PCR-based enumeration of four major pathogens including Arcobacter butzleri, Campylobacter jejuni, Campylobacter coli, and Helicobacter pylori in tile- and groundwater following a fall liquid swine manure (LSM) application on clay loam field plots. Although the prevalence of all target pathogens were detected in CD and FD systems, the loads of A. butzleri, C. jejuni, and C. coli were significantly lower in CD tile-water (p<0.05), in relation to FD tile-water. However, concentrations of A. butzleri were significantly greater in CD than FD tile-water (p<0.05). In shallow groundwater (1.2m depth), concentrations of A. butzleri, C. coli, and H. pylori showed no significant difference between CD and FD plots, while C. jejuni concentrations were significantly higher in FD plots (p<0.05). No impact of CD on the H. pylori was observed since quantitative detection in tile- and groundwater was scarce. Although speculative, H. pylori occurrence may have been related to the application of municipal biosolids four years prior to the LSM experiment. Overall, CD can be used to help minimize off-field export of pathogens into surface waters following manure applications to land, thereby reducing waterborne pathogen exposure risks to humans.

Enhanced Single-tube Multiplex PCR Assay for Detection and Identification of Six Arcobacter Species

AIM

A single-tube multiplex PCR (mPCR) assay was developed for rapid, sensitive and simultaneous detection and identification of six Arcobacter species including two new species, A. lanthieri and A. faecis, along with A. butzleri, A. cibarius, A. cryaerophilus and A. skirrowii on the basis of differences in the lengths of their PCR products. Previously designed monoplex, mPCR and RFLP assays do not detect or differentiate A. faecis and A. lanthieri from other closely related known Arcobacter spp.

METHODS AND RESULTS

Primer pairs for each target species (except A. skirrowii) and mPCR protocol were newly designed and optimized using variable regions of housekeeping including cpn60, gyrA, gyrB and rpoB genes. The accuracy and specificity of the mPCR assay was assessed using DNA templates from six targets and 11 other Arcobacter spp. as well as 50 other bacterial reference species and strains. Tests on the DNA templates of target Arcobacter spp. were appropriately identified, whereas all 61 other DNA templates from other bacterial species and strains were not amplified. Sensitivity and specificity of the mPCR assay was 10 pg μl^-1 of DNA concentration per target species. The optimized assay was further evaluated, validated and compared with other mPCR assays by testing Arcobacter cultures isolated from various faecal and water sources.

CONCLUSIONS

Study results confirm that the newly developed mPCR assay is rapid, accurate, reliable, simple, and valuable for the simultaneous detection and routine diagnosis of six human- and animal-associated Arcobacter spp.

SIGNIFICANCE AND IMPACT OF THE STUDY

The new mPCR assay is useful not only for pure but also mixed cultures. Moreover, it has the ability to rapidly detect six species which enhances the value of this technology for aetiological and epidemiological studies.

Impact of pre-application treatment on municipal sludge composition, soil dynamics of antibiotic resistance genes, and abundance of antibiotic-resistance genes on vegetables at harvest

In many jurisdictions sludge recovered from the sewage treatment process is a valued fertilizer for crop production. Pre-treatment of sewage sludge prior to land application offers the potential to abate enteric microorganisms that carry genes conferring resistance to antibiotics. Pre-treatment practices that accomplish this should have the desirable effect of reducing the risk of contamination of crops or adjacent water with antibiotic resistance genes carried in these materials. In the present study, we obtained municipal sludge that had been subjected to one of five treatments. There were, anaerobic-digestion or aerobic-digestion, in both instances with and without dewatering; and heat-treatment and pelletization. Each of the five types of biosolids was applied to an agricultural field at commercial rates, following which lettuce, carrots and radishes were planted. Based on qPCR, the estimated antibiotic gene loading rates were comparable with each of the five biosolids. However, the gene abundance in soil following application of the pelletized biosolids was anomalously lower than expected. Following application, the abundance of antibiotic resistance genes decreased in a generally coherent fashion, except sul1 which increased in abundance during the growing season in the soil fertilized with pelletized biosolids. Based on qPCR and high throughput sequencing evidence for transfer of antibiotic resistance genes from the biosolids to the vegetables at harvest was weak. Clostridia were more abundant in soils receiving any of the biosolids except the pelletized. Overall, the behavior of antibiotic resistance genes in soils receiving aerobically or anaerobically-digested biosolids was consistent and coherent with previous studies. However, dynamics of antibiotic resistance genes in soils receiving the heat treated pelletized biosolids were very different, and the underlying mechanisms merit investigation.

Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity

Denitrification transforms nitrogen applied as fertilizer and emits N₂ O, which is a potent greenhouse gas. Very little is known about the identities of abundant and active denitrifiers in agricultural soils. We coupled DNA stable-isotope probing (DNA-SIP) with flow-through reactors (FTRs) to detect active agricultural soil denitrifiers. The FTRs were incubated with nitrate and ¹³ C₆ -glucose under anoxic conditions and sampled at multiple time points. Labelled DNA from active microorganisms was analyzed by 16S rRNA gene fingerprinting, amplicon and shotgun metagenomic sequencing. Taxonomic representation of heavy fractions was consistent across sites and time points, including Betaproteobacteria (71%; Janthinobacterium, Acidovorax, Azoarcus and Dechloromonas), Alphaproteobacteria (8%; Rhizobium), Gammaproteobacteria (4%; Pseudomonas) and Actinobacteria (4%; Streptomycetaceae). Most nitrite-reductase reads from heavy DNA annotated to the copper-containing form (nirK). Assigned taxonomies of active denitrifiers based on reads matching the nirK gene were comparable to those obtained through nitric oxide (norB) and RNA polymerase (rpoB) annotations but not the nitrous oxide reductase gene (nosZ). Analysis of recovered metagenomes from heavy DNA demonstrated extensive nirK sequence family diversity, including novel taxonomic groups that are not captured by existing primers.

Brominated flame retardants and perfluoroalkyl acids in groundwater, tile drainage, soil, and crop grain following a high application of municipal biosolids to a field

Dewatered municipal biosolids (DMB) were applied at a rate of 22Mgdwha^-1 to an agricultural field in fall 2008. Concentrations of polybrominated diphenyl ethers (PBDEs; BDE-47, -99, -100, -153, -154, -183, -197, -207, -209), other brominated flame retardants (BFRs; HBB, PBEB, DBDPE, BTBPE) and perfluoroalkyl acids (PFAAs; PFHxS, PFOS, PFDS, PFOSA, PFHpA, PFOA, PFNA, PFDA, PFUnA, PFDoA, PFTA) were monitored in tile drainage, groundwater (2m, 4m and 6m depth), soil cores (0-0.3m) pre- and post-application, DMB aggregates incorporated into the soil post-application, and in wheat (Triticum spp.) planted post-application. Several compounds were detected in soil and water pre-application and on a reference field plot. PBDEs, other BFRs and PFAAs were detected in tile drainage and 2m groundwater throughout the post-application study period; a few PBDEs were also detected sporadically at lower depths in groundwater. Some of these compounds had not been detected pre-application, while some exceeded reference field plot/pre-application levels (some significantly (p<0.05) in tile drainage); both cases indicating biosolid-based water contamination. In DMB aggregates, several PBDE congeners were found to have dissipated exponentially, with reductions >90% in many of them within 1year post-application. Exponential dissipation of other BFRs and PFAAs in DMB aggregates were not significant. No PBDEs, other BFRs, or PFAAs were detected in wheat grain.

Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity

Denitrification transforms nitrogen applied as fertilizer and emits N₂ O, which is a potent greenhouse gas. Very little is known about the identities of abundant and active denitrifiers in agricultural soils. We coupled DNA stable-isotope probing (DNA-SIP) with flow-through reactors (FTRs) to detect active agricultural soil denitrifiers. The FTRs were incubated with nitrate and ¹³ C₆ -glucose under anoxic conditions and sampled at multiple time points. Labelled DNA from active microorganisms was analyzed by 16S rRNA gene fingerprinting, amplicon and shotgun metagenomic sequencing. Taxonomic representation of heavy fractions was consistent across sites and time points, including Betaproteobacteria (71%; Janthinobacterium, Acidovorax, Azoarcus and Dechloromonas), Alphaproteobacteria (8%; Rhizobium), Gammaproteobacteria (4%; Pseudomonas) and Actinobacteria (4%; Streptomycetaceae). Most nitrite-reductase reads from heavy DNA annotated to the copper-containing form (nirK). Assigned taxonomies of active denitrifiers based on reads matching the nirK gene were comparable to those obtained through nitric oxide (norB) and RNA polymerase (rpoB) annotations but not the nitrous oxide reductase gene (nosZ). Analysis of recovered metagenomes from heavy DNA demonstrated extensive nirK sequence family diversity, including novel taxonomic groups that are not captured by existing primers.

Isolation and Characterization of Acinetobacter baumannii Recovered from Campylobacter Selective Medium

Acinetobacter baumannii, a Gram-negative opportunistic pathogen, is known to cause multidrug resistant infections. This organism has primarily been isolated from clinical environments and its environmental reservoirs remain largely unknown. In the present study, we recovered seven isolates of A. baumannii growing under conditions selective for Campylobacter spp. (microaerophilic at 42°C and in the presence of antibiotics) from dairy cattle manure storage tank or surface water impacted by livestock effluents. Antibiotic susceptibility tests revealed that all of these isolates were less susceptible to at least two different clinically relevant antibiotics, compared to the type strain A. baumannii ATCC17978. Expression of resistance-nodulation-division efflux pumps, an important mechanism of intrinsic resistance in these organisms, was analyzed, and adeB was found to be overexpressed in one and adeJ was overexpressed in three isolates. Comparison of these isolates using genomic DNA Macro-Restriction Fragment Pattern Analysis (MRFPA) revealed relatively low relatedness among themselves or with some of the clinical isolates from previous studies. This study suggests that A. baumannii isolates are capable of growing under selective conditions for Campylobacter spp. and that this organism can be present in manure and water.

Towards a more accurate quantitative assessment of seasonal Cryptosporidium infection risks in surface waters using species and genotype information

Many Cryptosporidium species/genotypes are not considered infectious to humans, and more realistic estimations of seasonal infection risks could be made using human infectious species/genotype information to inform quantitative microbial risk assessments (QMRA). Cryptosporidium oocyst concentration and species/genotype data were collected from three surface water surveillance programs in two river basins [South Nation River, SN (2004-09) and Grand River, GR (2005-13)] in Ontario, Canada to evaluate seasonal infection risks. Main river stems, tributaries, agricultural drainage streams, water treatment plant intakes, and waste water treatment plant effluent impacted sites were sampled. The QMRA employed two sets of exposure data to compute risk: one assuming all observed oocysts were infectious to humans, and the other based on the fraction of oocysts that were C. hominis and/or C. parvum (dominant human infectious forms of the parasite). Viability was not considered and relative infection risk was evaluated using a single hypothetical recreational exposure. Many sample site groupings for both river systems, had significant seasonality in Cryptosporidium occurrence and concentrations (p ≤ 0.05); occurrence and concentrations were generally highest in autumn for SN, and autumn and summer for GR. Mean risk values (probability of infection per exposure) for all sites combined, for each river system, were roughly an order of magnitude lower (avg. of SN and GR 5.3 × 10^-5) when considering just C. parvum and C. hominis oocysts, in relation to mean infection risk (per exposure) assuming all oocysts were infectious to humans (5.5 × 10^-4). Seasonality in mean risk (targeted human infectious oocysts only) was most strongly evident in SN (e.g., 7.9 × 10^-6 in spring and 8.1 × 10^-5 in summer). Such differences are important if QMRA is used to quantify effects of water safety/quality management practices where inputs from a vast array of fecal pollution sources can readily occur. Cryptosporidium seasonality in water appears to match the seasonality of human infections from Cryptosporidium in the study regions. This study highlights the importance of Cryptosporidium species/genotype data to help determine surface water pollution sources and seasonality, as well as to help more accurately quantify human infection risks by the parasite.

Biosolids applied to agricultural land: Influence on structural and functional endpoints of soil fauna on a short- and long-term scale

Biosolids have well-documented crop and soil benefits similar to other sources of organic amendment, but there is environmental concern due to biosolids-associated pollutants. The present study investigated two field sites that had received biosolids at commercial-scale rates in parallel to associated field sections which were managed similarly but without receiving biosolids (controls). The investigated endpoints were abundance and diversity of soil organisms (nematodes, enchytraeids and earthworms) and soil fauna feeding activity as measured by the bait lamina assay. Repeated sampling of one of the field sites following the only biosolids application demonstrated an enrichment effect typical for organic amendments, which was mostly exhausted after 44months. After an initial suppression, the proportion of free-living plant-parasitic nematodes tended to increase in the biosolids-amended soil over time. Yet, none of the endpoints at this site indicated significant negative effects resulting from the biosolids until 44months post application. In contrast to the repeatedly tilled first field site, the second one was left fallow after three biosolids applications, and was sampled 96months post last application. It was only at this field site that potential evidence for a long-term impact of biosolids was detected with regard to two endpoints: earthworm abundance and structure of the nematode assemblage. Agricultural management and correlation with abiotic soil parameters explained the observed difference in earthworm abundance. Yet, the development of a highly structured and mature nematode assemblage at the control but not at the biosolids-amended section of this fallow field could not be explained by such correlations nor by soil metal concentrations. Overall, the present study found only weak evidence for negative long-term impacts of biosolids applied at commercial rates on soil fauna. High-level community parameters such as the nematode structure index (SI) appeared more suitable to detect deleterious effects on soil fauna than simple abundance measurements.

Detection of virulence, antibiotic resistance and toxin (VAT) genes in Campylobacter species using newly developed multiplex PCR assays

Campylobacter species are one of the leading causes of bacterial gastroenteritis in humans worldwide. This twofold study was sought to: i) develop and optimize four single-tube multiplex PCR (mPCR) assays for the detection of six virulence (ciaB, dnaJ, flaA, flaB, pldA and racR), three toxin (cdtA, cdtB and cdtC) and one antibiotic resistance tet(O) genes in thermophilic Campylobacter spp. and ii) apply and evaluate the developed mPCR assays by testing 470 previously identified C. jejuni, C. coli and C. lari isolates from agricultural water. In each mPCR assay, a combination of two or three sets of primer pairs for virulence, antibiotic resistance and toxin (VAT) genes was used and optimized. Assay 1 was developed for the detection of dnaJ, racR and cdtC genes with expected amplification sizes of 720, 584 and 182bp. Assay 2 generated PCR amplicons for tet(O) and cdtA genes of 559 and 370bp. Assay 3 amplified cdtB ciaB, and pldA genes with PCR amplicon sizes of 620, 527 and 385bp. Assay 4 was optimized for flaA and flaB genes that generated PCR amplicons of 855 and 260bp. The primer pairs and optimized PCR protocols did not show interference and/or cross-amplification with each other and generated the expected size of amplification products for each target VAT gene for the C. jejuni ATCC 33291 reference strain. Overall, all ten target VAT genes were detected at a variable frequency in tested isolates of thermophilic Campylobacter spp. where cdtC, flaB, ciaB, cdtB, cdtA and pldA were commonly detected compared to the flaA, racR, dnaJ and tet(O) genes which were detected with less frequency. The developed mPCR assays are simple, rapid, reliable and sensitive tools for simultaneously assessing potential pathogenicity and antibiotic resistance profiling in thermophilic Campylobacter spp. The mPCR assays will be useful in diagnostic and analytical settings for routine screening of VAT characteristics of Campylobacter spp. as well as being applicable in epidemiological studies by providing information that could be related to the risk of human infection.

Persistence of antibiotic resistance and plasmid-associated genes in soil following application of sewage sludge and abundance on vegetables at harvest

Sewage sludge recovered from wastewater treatment plants contains antibiotic residues and is rich in antibiotic resistance genes, selected for and enriched in the digestive tracts of human using antibiotics. The use of sewage sludge as a crop fertilizer constitutes a potential route of human exposure to antibiotic resistance genes through consumption of contaminated crops. Several gene targets associated with antibiotic resistance (catA1, catB3, ereA, ereB, erm(B), str(A), str(B), qnrD, sul1, and mphA), mobile genetic elements (int1, mobA, IncW repA, IncP1 groups -α, -β, -δ, -γ, -ε), and bacterial 16S rRNA (rrnS) were quantified by qPCR from soil and vegetable samples obtained from unamended and sludge-amended plots at an experimental field in London, Ontario. The qPCR data reveals an increase in abundance of gene targets in the soil and vegetables samples, indicating that there is potential for additional crop exposure to antibiotic resistance genes carried within sewage sludge following field application. It is therefore advisable to allow an appropriate delay period before harvesting of vegetables for human consumption.

Development and evaluation of multiplex PCR assays for rapid detection of virulence-associated genes in Arcobacter species

As the pathogenicity of Arcobacter species might be associated with various virulence factors, this study was aimed to develop and optimize three single-tube multiplex PCR (mPCR) assays that can efficiently detect multiple virulence-associated genes (VAGs) in Arcobacter spp. including the Arcobacter butzleri, Arcobacter cryaerophilus and Arcobacter skirrowii, respectively. The recognized target virulence factors used in the study were fibronectin binding protein (cj1349), filamentous hemagglutinin (hecA), hemolysin activation protein (hecB), hemolysin (tlyA), integral membrane protein virulence factor (mviN), invasin (ciaB), outer membrane protein (irgA) and phospholipase (pldA). Identical results were obtained between singleplex PCR and mPCR assays and no cross- and/or non-specific amplification products were obtained when tested against other closely related bacterial species. The sensitivities of these three mPCR assays were ranging from 1ngμL(-1) to 100ngμL(-1) DNA. The developed assays with combinations of duplex or triplex PCR primer pairs of VAGs were further evaluated and validated by applying them to isolates of the A. butzleri, A. cryaerophilus and A. skirrowii recovered from fecal samples of human and animal origins. The findings revealed that the distribution of the ciaB (90%), mviN (70%), tlyA (50%) and pldA (45%) genes among these target species was significantly higher than the hecA (16%), hecB (10%) and each of irgA and cj1349 (6%) genes, respectively. The newly developed mPCR assays can be used as rapid technique and useful markers for the detection, prevalence and profiling of VAGs in the Arcobacter spp. Moreover, these assays can easily be performed with a high throughput to give a presumptive identification of the causal pathogen in epidemiological investigation of human infections.

Identification, characterization and description of Arcobacter faecis sp. nov., isolated from a human waste septic tank

A study on the taxonomic classification of Arcobacter species was performed on the cultures isolated from various fecal sources where an Arcobacter strain AF1078(T) from human waste septic tank near Ottawa, Ontario, Canada was characterized using a polyphasic approach. Genetic investigations including 16S rRNA, atpA, cpn60, gyrA, gyrB and rpoB gene sequences of strain AF1078(T) are unique in comparison with other arcobacters. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain is most closely related to Arcobacter lanthieri and Arcobacter cibarius. Analyses of atpA, cpn60, gyrA, gyrB and rpoB gene sequences suggested that strain AF1078(T) formed a phylogenetic lineage independent of other species in the genus. Whole-genome sequence, DNA-DNA hybridization, fatty acid profile and phenotypic analysis further supported the conclusion that strain AF1078(T) represents a novel Arcobacter species, for which the name Arcobacter faecis sp. nov. is proposed, with type strain AF1078(T) (=LMG 28519(T); CCUG 66484(T)).

Quantitative Campylobacter spp., antibiotic resistance genes, and veterinary antibiotics in surface and ground water following manure application: Influence of tile drainage control

This work investigated chlortetracycline, tylosin, and tetracycline (plus transformation products), and DNA-based quantitative Campylobacter spp. and Campylobacter tetracycline antibiotic resistant genes (tet(O)) in tile drainage, groundwater, and soil before and following a liquid swine manure (LSM) application on clay loam plots under controlled (CD) and free (FD) tile drainage. Chlortetracycline/tetracycline was strongly bound to manure solids while tylosin dominated in the liquid portion of manure. The chlortetracycline transformation product isochlortetracycline was the most persistent analyte in water. Rhodamine WT (RWT) tracer was mixed with manure and monitored in tile and groundwater. RWT and veterinary antibiotic (VA) concentrations were strongly correlated in water which supported the use of RWT as a surrogate tracer. While CD reduced tile discharge and eliminated application-induced VA movement (via tile) to surface water, total VA mass loading to surface water was not affected by CD. At both CD and FD test plots, the biggest 'flush' of VA mass and highest VA concentrations occurred in response to precipitation received 2d after application, which strongly influenced the flow abatement capacity of CD on account of highly elevated water levels in field initiating overflow drainage for CD systems (when water level <0.3m below surface). VA concentrations in tile and groundwater became very low within 10d following application. Both Campylobacter spp. and Campylobacter tet(O) genes were present in groundwater and soil prior to application, and increased thereafter. Unlike the VA compounds, Campylobacter spp. and Campylobacter tet(O) gene loadings in tile drainage were reduced by CD, in relation to FD.

Long-Term Observations of Nitrogen and Phosphorus Export in Paired-Agricultural Watersheds under Controlled and Conventional Tile Drainage

Controlled tile drainage (CTD) regulates water and nutrient export from tile drainage systems. Observations of the effects of CTD imposed en masse at watershed scales are needed to determine the effect on downstream receptors. A paired-watershed approach was used to evaluate the effect of field-to-field CTD at the watershed scale on fluxes and flow-weighted mean concentrations (FWMCs) of N and P during multiple growing seasons. One watershed (467-ha catchment area) was under CTD management (treatment [CTD] watershed); the other (250-ha catchment area) had freely draining or uncontrolled tile drainage (UCTD) (reference [UCTD] watershed). The paired agricultural watersheds are located in eastern Ontario, Canada. Analysis of covariance and paired tests were used to assess daily fluxes and FWMCs during a calibration period when CTD intervention on the treatment watershed was minimal (2005-2006, when only 4-10% of the tile-drained area was under CTD) and a treatment period when the treatment (CTD) watershed had prolific CTD intervention (2007-2011 when 82% of tile drained fields were controlled, occupying >70% of catchment area). Significant linear regression slope changes assessed using ANCOVA ( ≤ 0.1) for daily fluxes from upstream and downstream monitoring sites pooled by calibration and treatment period were -0.06 and -0.20 (stream water) (negative values represent flux declines in CTD watershed), -0.59 and -0.77 (NH-N), -0.14 and -0.15 (NO-N), -1.77 and -2.10 (dissolved reactive P), and -0.28 and 0.45 (total P). Total P results for one site comparison contrasted with other findings likely due to unknown in-stream processes affecting total P loading, not efficacy of CTD. The FWMC results were mixed and inconclusive but suggest physical abatement by CTD is the means by which nutrient fluxes are predominantly reduced at these scales. Overall, our study results indicate that CTD is an effective practice for reducing watershed scale fluxes of stream water, N, and P during the growing season.

The distribution of Salmonella enterica serovars and subtypes in surface water from five agricultural regions across Canada

Serovar prevalence of the zoonotic pathogen, Salmonella enterica, was compared among 1624 surface water samples collected previously from five different Canadian agricultural watersheds over multiple years. Phagetyping, pulsed field gel electrophoresis (PFGE), and antimicrobial resistance subtyping assays were performed on serovars Enteritidis, Typhimurium, and Heidelberg. Serovars and subtypes from surface water were compared with those from animal feces, human sewage, and serovars reported to cause salmonellosis in Canadians. Sixty-five different serovars were identified in surface water; only 32% of these were isolated from multiple watersheds. Eleven of the 13 serovars most commonly reported to cause salmonellosis in Canadians were identified in surface water; isolates of these serovars constituted >40% of the total isolates. Common phagetypes and PFGE subtypes of serovars associated with illness in humans such as S. Enteritidis and S. Typhimurium were also isolated from surface water and animal feces. Antimicrobial resistance was generally low, but was highest among S. Typhimurium. Monitoring of these rivers helps to identify vulnerable areas of a watershed and, despite a relatively low prevalence of S. enterica overall, serovars observed in surface water are an indication of the levels of specific S. enterica serovars present in humans and animals.

Arcobacter lanthieri sp. nov., isolated from pig and dairy cattle manure

A study was undertaken to determine the prevalence and diversity of species of the genus Arcobacter in pig and dairy cattle manure, which led to the identification of strains AF1440T, AF1430 and AF1581. Initially identified as Arcobacter butzleri based on colony morphology and initial PCR-confirmation tests, analyses of 16S rRNA gene sequences of these strains confirmed that they belonged to the genus Arcobacter and were different from all known species of the genus. The isolates formed a distinct group within the genus Arcobacter based on their 16S rRNA, gyrB, rpoB, cpn60, gyrA and atpA gene sequences and fatty acid profiles. Their unique species status was further supported by physiological properties and DNA-DNA hybridization that allowed phenotypic and genotypic differentiation of the strains from other species of the genus Arcobacter. The isolates were found to be oxidase, catalase and esterase positive and urease negative; they grew well at 30 °C under microaerophilic conditions and produced nitrite and acetoin. Based on their common origin and various physiological properties, it is proposed that the isolates are classified as members of a novel species with the name Arcobacter lanthieri sp. nov. The type strain is AF1440T ( = LMG 28516T = CCUG 66485T); strains AF1430 ( = LMG 28515 = CCUG 66486) and AF1581 ( = LMG 28517 = CCUG 66487) are reference strains.

Dissipation of triclosan, triclocarban, carbamazepine and naproxen in agricultural soil following surface or sub-surface application of dewatered municipal biosolids

In many jurisdictions land application of municipal biosolids is a valued source of nutrients for crop production. The practice must be managed to ensure that crops and adjacent water are not subject to contamination by pharmaceuticals or other organic contaminants. The broad spectrum antimicrobial agents triclosan (TCS) and triclocarban (TCC), the anti-epileptic drug carbamazepine (CBZ), and the nonsteroidal anti-inflammatory drug naproxen (NAP) are widely used and are carried in biosolids. In the present study, the effect of biosolids and depth of placement in the soil profile on the rates of TCS, TCC, CBZ, and NAP dissipation were evaluated under semi-field conditions. Aggregates of dewatered municipal biosolids (DMBs) supplemented with (14)C-labeled residues were applied either on the soil surface or in the subsurface of the soil profile, and incubated over several months under ambient outdoor conditions. The dissipation of TCS, TCC and NAP was significantly faster in sub-surface than surface applied biosolid aggregates. In contrast the dissipation rate for CBZ was the same in surface applied and incorporated aggregates. Overall, the present study has determined a significant effect of depth of placement on the dissipation rate of biodegradable molecules.

Combined impacts of future climate and land use changes on discharge, nitrogen and phosphorus loads for a Canadian river basin

Both climate and land use changes can influence water quality and quantity in different ways. Thus, for predicting future water quality and quantity trends, simulations should ideally account for both projected climate and land use changes. In this paper, land use projections and climate change scenarios were integrated with a hydrological model to estimate the relative impact of climate and land use projections on a suite of water quality and quantity endpoints for a Canadian watershed. Climatic time series representing SRES change scenario A2 were generated by downscaling the outputs of the Canadian Regional Climate Model (version 4.1.1) using a combination of quantile-quantile transformation and nearest neighbor search. The SWAT (Soil and Water Assessment Tool) model was used to simulate streamflow, nitrogen and phosphorus loading under different climate and land use scenarios. Results showed that a) climate change will drive up maximum monthly streamflow, nitrate loads, and organic phosphorus loads, while decreasing organic nitrogen and nitrite loads; and b) land use changes were found to drive the same water quality/quantity variables in the same direction as climate change, except for organic nitrogen loads, for which the effects of the two stressors had a reverse impact on loading.

Using AnnAGNPS to Predict the Effects of Tile Drainage Control on Nutrient and Sediment Loads for a River Basin

Controlled tile drainage (CTD) can reduce pollutant loading. The Annualized Agricultural Nonpoint Source model (AnnAGNPS version 5.2) was used to examine changes in growing season discharge, sediment, nitrogen, and phosphorus loads due to CTD for a ∼3900-km agriculturally dominated river basin in Ontario, Canada. Two tile drain depth scenarios were examined in detail to mimic tile drainage control for flat cropland: 600 mm depth (CTD) and 200 mm (CTD) depth below surface. Summed for five growing seasons (CTD), direct runoff, total N, and dissolved N were reduced by 6.6, 3.5, and 13.7%, respectively. However, five seasons of summed total P, dissolved P, and total suspended solid loads increased as a result of CTD by 0.96, 1.6, and 0.23%. The AnnAGNPS results were compared with mass fluxes observed from paired experimental watersheds (250, 470 ha) in the river basin. The "test" experimental watershed was dominated by CTD and the "reference" watershed by free drainage. Notwithstanding environmental/land use differences between the watersheds and basin, comparisons of seasonal observed and predicted discharge reductions were comparable in 100% of respective cases. Nutrient load comparisons were more consistent for dissolved, relative to particulate water quality endpoints. For one season under corn crop production, AnnAGNPS predicted a 55% decrease (CTD) in dissolved N from the basin. AnnAGNPS v. 5.2 treats P transport from a surface pool perspective, which is appropriate for many systems. However, for assessment of tile drainage management practices for relatively flat tile-dominated systems, AnnAGNPS may benefit from consideration of P and particulate transport in the subsurface.

Rainfall-induced runoff from exposed streambed sediments: an important source of water pollution

When surface water levels decline, exposed streambed sediments can be mobilized and washed into the water course when subjected to erosive rainfall. In this study, rainfall simulations were conducted over exposed sediments along stream banks at four distinct locations in an agriculturally dominated river basin with the objective of quantifying the potential for contaminant loading from these often overlooked runoff source areas. At each location, simulations were performed at three different sites. Nitrogen, phosphorus, sediment, fecal indicator bacteria, pathogenic bacteria, and microbial source tracking (MST) markers were examined in both prerainfall sediments and rainfall-induced runoff water. Runoff generation and sediment mobilization occurred quickly (10-150 s) after rainfall initiation. Temporal trends in runoff concentrations were highly variable within and between locations. Total runoff event loads were considered large for many pollutants considered. For instance, the maximum observed total phosphorus runoff load was on the order of 1.5 kg ha. Results also demonstrate that runoff from exposed sediments can be a source of pathogenic bacteria. spp. and spp. were present in runoff from one and three locations, respectively. Ruminant MST markers were also present in runoff from two locations, one of which hosted pasturing cattle with stream access. Overall, this study demonstrated that rainfall-induced runoff from exposed streambed sediments can be an important source of surface water pollution.

A national investigation of the prevalence and diversity of thermophilic Campylobacter species in agricultural watersheds in Canada

The occurrence and diversity of thermophilic Campylobacter species (C. jejuni, coli, and lari) were studied in water samples from four river basins located across Canada. These basins located in Quebec (Bras d'Henri), Alberta (Oldman), Ontario (South Nation), and British Columbia (Sumas) represented some of the most intensive farming areas in Canada for hog, beef cattle, dairy cattle, and poultry, respectively. This study analyzed 769 water samples collected from 23 monitoring sites with agricultural influence, and four reference sites with limited or no agricultural influence. Water samples were collected bi-weekly over two years and analyzed for Campylobacter using a semi-quantitative minimum probable number (MPN) enrichment protocol. Putative isolates were confirmed by genus- and species-specific multiplex polymerase chain reaction (PCR) assays. A total of 377 (49%) water samples were positive for campylobacters with 355 samples having a cell density ranging from 4 to 4000 MPN L(-1). Campylobacters were more common at agricultural than reference sites in each river basin, although this difference was not significant in the Oldman and South Nation (p > 0.05). Campylobacter was significantly more common in the Bras d'Henri and Sumas (63%) compared to the South Nation (45%) and Oldman (33%) River basins (p < 0.05). C. jejuni, C. coli and C. lari were detected in each river basin, and these species occurred in 45% (n = 168), 34% (n = 128) and 19% (n = 73), of all Campylobacter positive samples, respectively. The remaining Campylobacter positive water samples without these three species (n = 67; 18%) were identified as other Campylobacter species. C. jejuni was the predominant species occurring in the Sumas, Oldman and South Nation River basins. However, in the Bras d'Henri River basin with intensive hog production, C. coli was the predominant species. This study found campylobacters to be common in some agricultural systems with intensive livestock farming activities, and different river basins could have strikingly different profiles of either C. jejuni or C. coli as the predominant waterborne thermophilic Campylobacter species.

Comprehensive nitrogen budgets for controlled tile drainage fields in eastern ontario, Canada

Excessive N loading from subsurface tile drainage has been linked to water quality degradation. Controlled tile drainage (CTD) has the potential to reduce N losses via tile drainage and boost crop yields. While CTD can reduce N loss from tile drainage, it may increase losses through other pathways. A multiple-year field-scale accounting of major N inputs and outputs during the cropping season was conducted on freely drained and controlled tile drained agricultural fields under corn ( L.)-soybean [ (L.) Merr.] production systems in eastern Ontario, Canada. Greater predicted gaseous N emissions for corn and soybean and greater observed lateral seepage N losses were observed for corn and soybean fields under CTD relative to free-draining fields. However, observed N losses from tile were significantly lower for CTD fields, in relation to freely drained fields. Changes in residual soil N were essentially equivalent between drainage treatments, while mass balance residual terms were systematically negative (slightly more so for CTD). Increases in plant N uptake associated with CTD were observed, probably resulting in higher grain yields for corn and soybean. This study illustrates the benefits of CTD in decreasing subsurface tile drainage N losses and boosting crop yields, while demonstrating the potential for CTD to increase N losses via other pathways related to gaseous emissions and groundwater seepage.