The NSERC Canadian Lake Pulse Network: A national assessment of lake health providing science for water management in a changing climate

Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing

The burgeoning field of aquaculture has become a pivotal contributor to global food security and economic growth, presently surpassing capture fisheries in aquatic animal production as evidenced by recent statistics. However, the dense fish populations inherent in aquaculture systems exacerbate abiotic stressors and promote pathogenic spread, posing a risk to sustainability and yield. This study delves into the transformative potential of metagenomics, a method that directly retrieves genetic material from environmental samples, in elucidating microbial dynamics within aquaculture ecosystems. Our findings affirm that metagenomics, bolstered by tools in big data analytics, bioinformatics, and machine learning, can significantly enhance the precision of microbial assessment and pathogen detection. Furthermore, we explore quantum computing's emergent role, which promises unparalleled efficiency in data processing and model construction, poised to address the limitations of conventional computational techniques. Distinct from metabarcoding, metagenomics offers an expansive, unbiased profile of microbial biodiversity, revolutionizing our capacity to monitor, predict, and manage aquaculture systems with high accuracy and adaptability. Despite the challenges of computational demands and variability in data standardization, this study advocates for continued technological integration, thereby fostering resilient and sustainable aquaculture practices in a climate of escalating global food requirements.

Surface sediment elemental compositions of 167 Canadian lakes show widespread exceedance of quality guidelines for metals

Sediments form a key part of lake ecosystems and play important roles in biological and chemical processes. Yet in the most lake-rich country in the world, Canada, there was no standardized portrait of lake sediment elemental compositions and knowledge was lacking about how frequently field data exceeded sediment quality guidelines. To address these gaps and generate a more comprehensive understanding of large-scale spatial patterns in surface sediment geochemistry, we undertook an analysis of 167 lakes sampled by the NSERC Canadian Lake Pulse Network. We analyzed sediment elemental compositions and identified three geographic regions with distinct sediment geochemistry by applying a cascade multivariate regression tree analysis (cMRT). Of these regions, sediments in eastern Canada had relatively high concentrations of metals, while central Canada and southwestern Ontario lakes had relatively high concentrations of detrital elements. Urbanization was correlated with elevated sediment metal concentrations whereas agricultural and pastoral activities were correlated with elevated concentrations of detrital elements. Comparisons between sites with low and high levels of anthropogenic land use indicated limited differences in sediment elemental compositions. However, 70 % of all sites exceeded the guidelines for at least one of the six potentially toxic elements with published sediment quality guidelines that we examined. Since these guidelines were designed to be conservative, we recommend the development of regional sediment quality guidelines for implementation across Canada.

National scale assessment of the occurrence and risk of trace organic contaminants in Canadian Lake sediments

In Canada studies on the presence of trace organic contaminants (TrOCs) such as pharmaceuticals, personal care products, pesticides and flame retardants in lakes have primarily focused on the water column at localized scales. To address this gap, the occurrence of 44 TrOCs, representative of various types of human activities, was investigated in surface sediments (0-2 cm) from 193 lakes across Canada. A total of 28 targeted TrOCs were detected, with 99.5 % of the samples containing at least one detection, and one lake exhibiting up to 12 detections. The most frequently detected contaminants (> 20 % of samples) were the insect-repellent diethyltoluamide (DEET), the UV filter oxybenzone, the flame retardants tris(2-butoxyethyl) phosphate (TBEP), tris(2-chloroethyl) phosphate (TCEP), and triphenyl phosphate (TPP), the stimulant caffeine, and cotinine, a metabolite of the stimulant nicotine. Median reported concentrations of the targeted TrOCs ranged from 0.017 pg g-1 to 359 ng g-1, with a maximum value of 23,700 ng g-1 observed for DEET in one lake. The geographic distribution of analyte concentrations varied by compound class: pharmaceuticals and consumer product additives were predominantly found in the more urbanized regions of Ontario and Quebec, whereas personal care products such as DEET and oxybenzone were more frequently detected in the western provinces of Canada. An environmental risk assessment based on an additive model conducted on three aquatic organisms (algae, cladocerans, and fish) revealed that 4 % and 6 % of the lakes posed a potentially high risk for cladocerans and algae, respectively. A geographical analysis indicated that lakes in the south of the eastern provinces of Canada presented the highest risks for all three species. These findings represent the first large-scale results detailing the extent of contamination caused by TrOCs on Canadian lake sediments. They establish reference levels that can guide future monitoring efforts and inform policy discussions aimed at protecting lake ecosystems.

High-frequency diatom dynamics seen in an ice- and snow-covered temperate lake using an imaging-in-flow cytometer

The study of winter in temperate, ice-covered lakes has largely been neglected, creating a major gap in our understanding of annual phytoplankton cycles. We assessed patterns in biovolumes of Asterionella, cf. Synedra, Urosolenia, and total phytoplankton at three depths during the winter of 2014/2015 as estimated using images from an Imaging FlowCytobot (IFCB) moored in Lac (Lake) Montjoie, Quebec (Canada). Even though the use of the IFCB under-ice presented challenges, these were outstripped by its advantages. The IFCB provided unprecedented high temporal and spatial resolution phytoplankton count and biovolume data that allowed patterns of abundance to be observed in detail. Interestingly, the IFCB captured an abundance of Urosolenia, which may be dissolved in standard Lugol's-preserved grab samples. We found Asterionella grew until mid-December and then slowly decreased towards the spring, whereas cf. Synedra diatoms decreased from early December and then rebounded towards late December as light increased before falling again towards the spring. Urosolenia peaked in late December as cf. Synedra diatoms rebounded and then began to decline towards the spring. Total phytoplankton declined towards late December, increased in the beginning of January and then declined towards the spring. The studied diatoms maintained considerable under-ice seed populations and grew when light was sufficient.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10750-025-05802-8.

Water Quality and Land Use Shape Bacterial Communities Across 621 Canadian Lakes

Human activities such as agriculture and urban development are linked to water quality degradation. Canada represents a large and heterogeneous landscape of freshwater lakes, where variations in climate, geography and geology interact with land cover alteration to influence water quality differently across regions. In this study, we investigated the influence of water quality and land use on bacterial communities across 12 ecozones. At the pan-Canadian scale, total phosphorus (TP) was the most significant water quality variable influencing community structure, and the most pronounced shift was observed at 110 μg/L of TP, corresponding to the transition from eutrophic to hypereutrophic conditions. At the regional scale, water quality significantly explained bacterial community structure in all ecozones. In terms of land use effect, at the pan-Canadian scale, agriculture and, to a lesser extent, urbanisation were significant land use variables influencing community structure. Regionally, in ecozones characterised by extensive agriculture, this land cover variable was consistently significant in explaining community structure. Likewise, in extensively urbanised ecozones, urbanisation was consistently significant in explaining community structure. Overall, these results demonstrate that bacterial richness and community structure are influenced by water quality and shaped by agriculture and urban development in different ways.

A database of nutritional strategies of nanoplankton genera present in North American lake surface waters

A database of nutritional strategies of nanoplankton genera present in North American lake surface waters is presented. This work represents an integrated and updated database of nutritional strategies for nanoplankton genera commonly found in surface waters of North American lakes. We tabulate the nutritional strategies (autotroph, phago-mixotroph and phago-heterotroph) for nanoplankton genera identified during several pan-continental lake surveys: the EPA-NLA surveys conducted in 2012 and 2017 across the continental USA and the NSERC Canadian Lake Pulse survey campaign conducted from 2017 to 2019. We expect that this work will serve others in the plankton community interested in assessing nanoplankton feeding strategies.

A landscape limnology approach to assessing controls on soluble reactive phosphorus in sediment porewater and internal loading risk

Sediment nutrients can be mobilized to overlying water via internal loading, which can be important to aquatic productivity. Using data from 143 Canadian lakes, we show high (~2400-fold) variation of soluble reactive phosphorus (SRP) concentrations in surficial sediment porewater, with results suggesting internal phosphorus loading (IPL) is also likely to vary widely. Consistent with past work at smaller scales, we show that lake depth, pH, trophic status, and bulk sediment Al:P and Fe:P influence porewater SRP, and IPL. Median porewater SRP concentration in lakes with high Al:P (molar ratios >10) were 4.8-fold smaller than in lakes with lower Al:P. In lakes where bulk sedimentary Fe:P molar ratios were >10 porewater SRP was 3.9-fold lower than in lakes with lower Fe:P. High pH (>7.8), along with hyper-eutrophic lakes were associated with higher porewater SRP. Finally, shallow lakes (<4 m depth) had median porewater SRP concentration 6-fold higher than deep lakes (>9 m depth). Important regional differences emerged, linked to regional variation in pH, soils, lake depth and trophic status, and paralleling areas of poor water quality. For example, median porewater SRP in lakes from the Boreal Plains and Prairies ecozones (dominated by Chernozems/Mollisols) was 64-fold and 44-fold higher than in the Boreal Shield (dominated by Podzols/Spodosols) (respectively), although we note that IPL risk is likely important across many ecozones. Using national data, we found in-lake measurements (particularly pH, and salinity) showed strong capacity in predicting porewater SRP (explaining 60-72 % of the variance in the data). Importantly, watershed predictors showed good predictive power, explaining ~50 % of variance in porewater SRP using variables including soil types, and % agriculture. Porewater SRP can be predicted with reasonable accuracy using easily measured variables, as can estimates of internal phosphorus loading, suggesting that landscape limnology holds strong potential in helping to inform lake management by informing understanding of in-lake nutrient sources.

Influence of anthropogenic activities on the trace organic contamination of lakes

Anthropogenic activities and urbanization can lead to the discharge of organic compounds into surface waters. It is important to investigate these relationships further to mitigate contamination better and prioritize protection efforts. This study aimed to verify the effect of specific anthropogenic factors on lake water contamination caused by trace organic contaminants (TrOCs) such as pharmaceuticals, pesticides and consumer product additives. Data on the detection and concentration levels of 54 TrOCs, major anthropogenic land use, and human activities from a large-scale study on Canadian lakes were used to reach this goal. The association of population and livestock densities, the presence of wastewater treatment plants (WWTPs) and hospitals as well as the agricultural and urban land use in the lakes' watersheds on lake water contamination was investigated by applying negative binomial and ordinal logistic regression models. These models were also controlled for lake/watershed area ratio, lake depth, water, residence time, watershed slope, precipitation, and sampling date. The statistical analysis confirmed that agricultural land use, urban land use, and WWTPs plants in lake watersheds are significantly associated with the number of TrOCs detected (incidence rate ratio > 1, p < 0.001) and the summed concentration of targeted TrOCs (odds ratio > 1, p < 0.001). Agricultural land use (odds ratio = 1.58, p < 0.001) and urban land use (odds ratio = 1.19, p < 0.02) were also significantly associated with the summed concentration of the targeted pesticides. This latter outcome thus suggests that urban centers are also important contributors to the concentration levels of pesticides in lakes. Overall, these results demonstrate that even in complex ecosystems such as lakes, it is possible to use a limited number of factors to explain anthropogenic contamination. This can help policymakers make informed decisions on contamination mitigation and provide insights into watershed management.

Diatom species responses along gradients of dissolved inorganic carbon, total phosphorus, and lake depth from lakes across Canada

Diatoms are key components of freshwater ecosystems and are regularly used for paleolimnological reconstructions, in which defining species optima and tolerances is fundamental for interpreting assemblage shifts in a sediment record. Here, we examined responses of diatoms across three major environmental gradients-dissolved inorganic carbon (range: 0.1-230.5 mg · L-1), total phosphorus (range: 3-326 μg · L-1), and maximum lake depth (range: 0.9-55.0 m)-taken from 158 lakes from across Canada. The lakes were sampled as part of the LakePulse Network, which conducted a standardized sampling of lakes spanning 12 Canadian ecozones. Hierarchical logistic regression was used to model the species responses of 37 common taxa, and species optima and tolerances were calculated with weighted average modeling. The most common response detected was the symmetrical unimodal model, suggesting we likely captured the full environmental ranges for many species, although skewed unimodal responses were also common. Indicator species analyses identified taxa with high predictive values and fidelities to particular ecozones, with high-nutrient-adapted taxa such as Stephanodiscus spp. and Cyclotella meneghiniana characteristic of the agriculturally productive Prairie region. The Prairies stood out in the dataset as the region with the most unique flora from the local contribution to beta diversity analysis. Overall, the autecological data provided by our study will allow for improved interpretations of paleolimnological records and other biomonitoring efforts, addressing management concerns and contributing to a better understanding of our changing environment.

Trace organic contaminants in lake waters: Occurrence and environmental risk assessment at the national scale in Canada

Numerous contaminants are produced and used daily, a significant fraction ultimately finding their way into natural waters. However, data on their distribution in lakes is lacking. To address this gap, the presence of 54 trace organic contaminants (TrOCs), representative of various human activities, was investigated in the surface water of 290 lakes across Canada. These lakes ranged from remote to highly impacted by human activities. In 88% of the sampled lakes, contaminants were detected, with up to 28 detections in a single lake. The compounds most frequently encountered were atrazine, cotinine, and deethylatrazine, each of which was present in more than a third of the lakes. The range of detected concentrations was from 0.23 ng/L to about 2200 ng/L for individual compounds, while the maximum cumulative concentration exceeded 8100 ng/L in a single lake. A risk assessment based on effect concentrations for three aquatic species (Pimephales promelas, Daphnia magna, and Tetrahymena pyriformis) was conducted, revealing that 6% of lakes exhibited a high potential risk for at least one species. In 59% of lakes, some contaminants with potential sub-lethal effects were detected, with the detection of up to 17 TrOCs with potential impacts. The results of this work provide the first reference point for monitoring the evolution of contamination in Canadian lakes by TrOCs. They demonstrate that a high proportion of the sampled lakes bear an environmentally relevant anthropogenic chemical footprint.

Variability of sedimentary phosphorus composition across Canadian lakes

Phosphorus (P) in lake sediments is stored within diverse forms, often associated with metals, minerals, and organic matter. Sediment P can be remobilized to the water column, but the environmental conditions influencing the P retention-release balance depend upon the sediment chemistry and forms of P present. Sequential fractionation approaches can be used to help understand forms of P present in the sediments, and their vulnerability to release. We assessed P composition in surficial sediments (as an assemblage of six P-fractions) and its relationship with watershed, and lake-specific explanatory variables from 236 lakes across Canada. Sediment P composition varied widely across the 12 sampled Canadian ecozones. The dominant P-fractions were the residual-P and the labile organic P, while the loosely bound P corresponded to the smallest proportion of sediment TP. Notable contrasts in sediment P composition were apparent across select regions - with the most significant differences between sediment P in lakes from the mid-West Canada region (Prairies and Boreal Plains ecozones) and both Eastern coastal (Atlantic Maritime and Atlantic Highlands) and Western coastal (Pacific Maritime) ecozones. The ecozone attributes most critical to sediment P speciation across Canadian lakes were related to soil types in the watershed (e.g., podzols, chernozems, and Luvisols) and the chemical composition of lake water and sediments, such as dissolved Ca in lake water, bulk sedimentary Ca, Al, and Fe, dissolved SO4 in lake water, lake pH, and salinity. Understanding predictors of the forms of P stored in surficial sediments helps advance our knowledge of in-lake P retention and remobilization processes across the millions of unstudied lakes and can help our understanding of controls on internal P loading.

A genome catalogue of lake bacterial diversity and its drivers at continental scale

Lakes are heterogeneous ecosystems inhabited by a rich microbiome whose genomic diversity is poorly defined. We present a continental-scale study of metagenomes representing 6.5 million km2 of the most lake-rich landscape on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 mostly novel bacterial genomospecies. Lake trophic state was a leading driver of taxonomic and functional diversity among MAG assemblages, reflecting the responses of communities profiled by 16S rRNA amplicons and gene-centric metagenomics. Coupling the MAG catalogue with watershed geomatics revealed terrestrial influences of soils and land use on assemblages. Agriculture and human population density were drivers of turnover, indicating detectable anthropogenic imprints on lake bacteria at the continental scale. The sensitivity of bacterial assemblages to human impact reinforces lakes as sentinels of environmental change. Overall, the LakePulse MAG catalogue greatly expands the freshwater genomic landscape, advancing an integrative view of diversity across Earth's microbiomes.

Climate change amplifies the risk of potentially toxigenic cyanobacteria

Cyanobacterial blooms pose a significant threat to water security, with anthropogenic forcing being implicated as a key driver behind the recent upsurge and global expansion of cyanobacteria in modern times. The potential effects of land-use alterations and climate change can lead to complicated, less-predictable scenarios in cyanobacterial management, especially when forecasting cyanobacterial toxin risks. There is a growing need for further investigations into the specific stressors that stimulate cyanobacterial toxins, as well as resolving the uncertainty surrounding the historical or contemporary nature of cyanobacterial-associated risks. To address this gap, we employed a paleolimnological approach to reconstruct cyanobacterial abundance and microcystin-producing potential in temperate lakes situated along a human impact gradient. We identified breakpoints (i.e., points of abrupt change) in these time series and examined the impact of landscape and climatic properties on their occurrence. Our findings indicate that lakes subject to greater human influence exhibited an earlier onset of cyanobacterial biomass by 40 years compared to less-impacted lakes, with land-use change emerging as the dominant predictor. Moreover, microcystin-producing potential increased in both high- and low-impact lakes around the 1980s, with climate warming being the primary driver. Our findings chronicle the importance of climate change in increasing the risk of toxigenic cyanobacteria in freshwater resources.

Microcystin concentrations and congener composition in relation to environmental variables across 440 north-temperate and boreal lakes

Understanding the environmental conditions and taxa that promote the occurrence of cyanobacterial toxins is imperative for effective management of lake ecosystems. Herein, we modeled total microcystin presence and concentrations with a broad suite of environmental predictors and cyanobacteria community data collected across 440 Canadian lakes using standardized methods. We also conducted a focused analysis targeting 14 microcystin congeners across 190 lakes, to examine how abiotic and biotic factors influence their relative proportions. Microcystins were detected in 30 % of lakes, with the highest total concentrations occurring in the most eutrophic lakes located in ecozones of central Canada. The two most commonly detected congeners were MC-LR (61 % of lakes) and MC-LA (37 % of lakes), while 11 others were detected more sporadically across waterbodies. Congener diversity peaked in central Canada where cyanobacteria biomass was highest. Using a zero-altered hurdle model, the probability of detecting microcystin was best explained by increasing Microcystis biomass, Daphnia and cyclopoid biomass, soluble reactive phosphorus, pH and wind. Microcystin concentrations increased with the biomass of Microcystis and other less dominant cyanobacteria taxa, as well as total phosphorus, cyclopoid copepod biomass, dissolved inorganic carbon and water temperature. Collectively, these models accounted for 34 % and 70 % of the variability, respectively. Based on a multiple factor analysis of microcystin congeners, cyanobacteria community data, environmental and zooplankton data, we found that the relative abundance of most congeners varied according to trophic state and were related to a combination of cyanobacteria genera biomasses and environmental variables.

Geospatial analysis reveals a hotspot of fecal bacteria in Canadian prairie lakes linked to agricultural non-point sources

Lakes are sentinels of environmental changes within their watersheds including those induced by a changing climate and anthropogenic activities. In particular, contamination originating from point or non-point sources (NPS) within watersheds might be reflected in changes in the bacterial composition of lake water. We assessed the abundance of potentially pathogenic bacteria (PPB) sampled in 413 lakes within 8 southern Canadian ecozones that represent a wide diversity of lakes and watershed land use. The study objectives were (1) to explore the diversity of PPB; (2) to build a fecal multi-indicator from a cluster of co-occurring PPB; and (3) to predict the fecal multi-indicator over thousands of lakes. We identified bacterial taxa based on 16S rRNA amplicon sequencing and clustered 33 PPB matching taxa in the Canadian ePATHogen database using a Sørensen dissimilarity index on binary data across the sampled lakes. One cluster contained Erysipelothrix, Desulfovibrio, Bacteroides, Vibrio and Acholeplasma and was related to the NPS fraction of agriculture and pasture within the watershed as its main driver and thus it was determined as the fecal multi-indicator. We subsequently developed a fecal multi-indicator predictive model across 200 212 southern Canadian lakes which explained 55.1% of the deviance. Mapping the predictions showed higher fecal multi-indicator abundances in the Prairies and Boreal Plains compared to the other ecozones. These results represent the first attempt to map a potential fecal multi-indicator at the continental scale, which may be further improved in the future. Lastly, the study demonstrates the capacity of a multi-disciplinary approach leveraging both datasets derived from remote sensing and DNA sequencing to provide mapping information for public health governmental policies.

A resistome survey across hundreds of freshwater bacterial communities reveals the impacts of veterinary and human antibiotics use

Our decreasing ability to fight bacterial infections is a major health concern. It is arising due to the evolution of antimicrobial resistance (AMR) in response to the mis- and overuse of antibiotics in both human and veterinary medicine. Lakes integrate watershed processes and thus may act as receptors and reservoirs of antibiotic resistance genes (ARGs) introduced into the watershed by human activities. The resistome – the diversity of ARGs – under varying anthropogenic watershed pressures has been previously studied either focused on few select genes or few lakes. Here, we link the resistome of ~350 lakes sampled across Canada to human watershed activity, trophic status, as well as point sources of ARG pollution including wastewater treatment plants and hospitals in the watershed. A high percentage of the resistance genes detected was either unimpacted by human activity or highly prevalent in pristine lakes, highlighting the role of AMR in microbial ecology in aquatic systems, as well as a pool of genes available for potential horizontal gene transfer to pathogenic species. Nonetheless, watershed agricultural and pasture area significantly impacted the resistome. Moreover, the number of hospitals and the population density in a watershed, the volume of wastewater entering the lake, as well as the fraction of manure applied in the watershed as fertilizer significantly impacted ARG diversity. Together, these findings indicate that lake resistomes are regularly stocked with resistance genes evolved in the context of both veterinary and human antibiotics use and represent reservoirs of ARGs that require further monitoring.

Pervasive changes in algal indicators since pre-industrial times: A paleolimnological study of changes in primary production and diatom assemblages from ~200 Canadian lakes

Anthropogenic stressors affect lakes around the world, ranging in scale from catchment-specific pollutants to the global impacts of climate change. Canada has a large number and diversity of lakes, yet it is not well understood how, where, and when human impacts have affected these lakes at a national scale. The NSERC Canadian Lake Pulse Network sought to create the first nationwide database of Canadian lake health, undertaking a multi-year survey of 664 lakes spanning 12 ecozones across Canada. A key objective of the network is to determine where, by how much, and why have Canadian lakes changed during the Anthropocene. To address this objective, we compared sedimentary chlorophyll a and diatoms from modern and pre-industrial sediment intervals of ~200 lakes. The lakes spanned a range of sizes, ecozones, and degrees of within-catchment land use change. We inferred the quantity of chlorophyll a, its isomers and main diagenetic products using visible reflectance spectroscopy. We found widespread increases in primary production since pre-industrial times. Primary production increased, on average, across all ecozones, human impact classes, and stratification classes. Likewise, an increase in planktonic diatom taxa over time was detected in the majority of sampled lakes, likely due to recent climate warming. However, regional factors (ecozones) explained the most variation in modern diatom species assemblages as well as their temporal turnover. Furthermore, lakes with high human impact (i.e., higher weighted proportions of human land use in the catchment) exhibited greater taxonomic turnover than lakes with a low human impact class. The greatest diatom turnover was found in the agriculture-rich Prairies and the lowest in the sparsely populated Boreal Shield and Taiga Cordillera ecozones. Overall, our study highlights that drivers operating at different geographic scales (i.e., climatic and land-use changes) have led to significant alterations in algal indicators since pre-industrial times across the country.

Evaluation of Atmospheric Correction Algorithms over Lakes for High-Resolution Multispectral Imagery: Implications of Adjacency Effect

Atmospheric correction of satellite optical imagery over inland waters is a key remaining challenge in aquatic remote sensing. This is due to numerous confounding factors such as the complexity of water optical properties, the surface glint, the heterogeneous nature of atmospheric aerosols, and the proximity of bright land surfaces. This combination of factors makes it difficult to retrieve accurate information about the system observed. Moreover, the impact of radiance coming from adjacent land (adjacency effects) in complex geometries further adds to this challenge, especially for small lakes. In this study, ten atmospheric correction algorithms were evaluated for high-resolution multispectral imagery of Landsat-8 Operational Land Imager and Sentinel-2 MultiSpectral Instrument using in situ optical measurements from ~300 lakes across Canada. The results of the validation show that the performance of the algorithms varies by spectral band and evaluation metrics. The dark spectrum fitting algorithm had the best performance in terms of similarity angle (spectral shape), while the neural network-based models showed the lowest errors and bias per band. However, none of the tested atmospheric correction algorithms meet a 30% retrieval accuracy target across all the visible bands, likely due to uncorrected adjacency effects. To quantify this process, three-dimensional radiative transfer simulations were performed and compared to satellite observations. These simulations show that up to 60% of the top of atmosphere reflectance in the near-infrared bands over the lake was from the adjacent lands covered with green vegetation. The significance of these adjacency effects on atmospheric correction has been analyzed qualitatively, and potential efforts to improve the atmospheric correction algorithms are discussed.

Protist Diversity and Metabolic Strategy in Freshwater Lakes Are Shaped by Trophic State and Watershed Land Use on a Continental Scale

Protists play key roles in aquatic food webs as primary producers, predators, nutrient recyclers, and symbionts. However, a comprehensive view of protist diversity in freshwaters has been challenged by the immense environmental heterogeneity among lakes worldwide. We assessed protist diversity in the surface waters of 366 freshwater lakes across a north temperate to subarctic range covering nearly 8.4 million km² of Canada. Sampled lakes represented broad gradients in size, trophic state, and watershed land use. Hypereutrophic lakes contained the least diverse and most distinct protist communities relative to nutrient-poor lakes. Greater taxonomic variation among eutrophic lakes was mainly a product of heterotroph and mixotroph diversity, whereas phototroph assemblages were more similar under high-nutrient conditions. Overall, local physicochemical factors, particularly ion and nutrient concentrations, elicited the strongest responses in community structure, far outweighing the effects of geographic gradients. Despite their contrasting distribution patterns, obligate phototroph and heterotroph turnover was predicted by an overlapping set of environmental factors, while the metabolic plasticity of mixotrophs may have made them less predictable. Notably, protist diversity was associated with variation in watershed soil pH and agricultural crop coverage, pointing to human impact on the land-water interface that has not been previously identified in studies on smaller scales. Our study exposes the importance of both within-lake and external watershed characteristics in explaining protist diversity and biogeography, critical information for further developing an understanding of how freshwater lakes and their watersheds are impacted by anthropogenic stressors.

IMPORTANCE Freshwater lakes are experiencing rapid changes under accelerated anthropogenic stress and a warming climate. Microorganisms underpin aquatic food webs, yet little is known about how freshwater microbial communities are responding to human impact. Here, we assessed the diversity of protists and their myriad ecological roles in lakes varying in size across watersheds experiencing a range of land use pressures by leveraging data from a continental-scale survey of Canadian lakes. We found evidence of human impact on protist assemblages through an association with lake trophic state and extending to agricultural activity and soil characteristics in the surrounding watershed. Furthermore, trophic state appeared to explain the distributions of phototrophic and heterotrophic protists in contrasting ways. Our findings highlight the vulnerability of lake ecosystems to increased land use and the importance of assessing terrestrial interfaces to elucidate freshwater ecosystem dynamics.

Assessing the current water clarity status of ~100,000 lakes across southern Canada: A remote sensing approach

Canada has more lakes than any other country, making comprehensive monitoring a huge challenge. As more and more satellite data become readily available, and as faster data processing systems make massive satellite data operations possible, new opportunities exist to use remote sensing to develop comprehensive assessments of water quality at very large spatial scales. In this study, we use a published empirical algorithm to estimate Secchi depth from Landsat 8 reflectance data in order to estimate water clarity in lakes across southern Canada. Combined with ancillary information on lake morphological, hydrological, and watershed geological and landuse characteristics, we were able to assess broad spatial patterns in water clarity for the first time. Ecological zones, underlying geological substrate, and lake depth had particularly strong influences on clarity across the whole country. Lakes in western mountain ecozones had significantly clearer waters than those in the prairies and plains, while lakes in sedimentary rock formations tended to have lower clarity than lakes in intrusive rock. Deep lakes were significantly clearer than shallow lakes over most of the country. Water clarity was also significantly influenced by human impact (urbanization, agriculture, and industry) in the watershed, with most lakes in high impact areas having low clarity or very low clarity. Finally, we used in situ measured data to help interpret the underlying optical water column constituents influencing clarity across Canada, and found that chlorophyll-a, total suspended solids, and color dissolved organic matter all had strong but varying underlying effects on water clarity across different ecozones. This research provides an important step towards further research on the relationship between water column optical properties and the health and vulnerability status of lakes across the country.

Comparing microscopy and DNA metabarcoding techniques for identifying cyanobacteria assemblages across hundreds of lakes

Accurately identifying the species present in an ecosystem is vital to lake managers and successful bioassessment programs. This is particularly important when monitoring cyanobacteria, as numerous taxa produce toxins and can have major negative impacts on aquatic ecosystems. Increasingly, DNA-based techniques such as metabarcoding are being used for measuring aquatic biodiversity, as they could accelerate processing time, decrease costs and reduce some of the biases associated with traditional light microscopy. Despite the continuing use of traditional microscopy and the growing use of DNA metabarcoding to identify cyanobacteria assemblages, methodological comparisons between the two approaches have rarely been reported from a wide suite of lake types. Here, we compare planktonic cyanobacteria assemblages generated by inverted light microscopy and DNA metabarcoding from a 379-lake dataset spanning a longitudinal and trophic gradient. We found moderate levels of congruence between methods at the broadest taxonomic levels (i.e., Order, RV=0.40, p < 0.0001). This comparison revealed distinct cyanobacteria communities from lakes of different trophic states, with Microcystis, Aphanizomenon and Dolichospermum dominating with both methods in eutrophic and hypereutrophic sites. This finding supports the use of either method when monitoring eutrophication in lake surface waters. The biggest difference between the two methods was the detection of picocyanobacteria, which are typically underestimated by light microscopy. This reveals that the communities generated by each method currently are complementary as opposed to identical and promotes a combined-method strategy when monitoring a range of trophic systems. For example, microscopy can provide measures of cyanobacteria biomass, which are critical data in managing lakes. Going forward, we believe that molecular genetic methods will be increasingly adopted as reference databases are routinely updated with more representative sequences and will improve as cyanobacteria taxonomy is resolved with the increase in available genetic information.

Lake ecosystem health assessment using a novel hybrid decision-making framework in the Nam Co, Qinghai-Tibet Plateau

Lake health assessment (LHA), a powerful tool for lake ecological protection, provides the foundation for sustainable water environment management. However, existing methods have not yet considered the effects of fuzziness and randomness on LHA. In addition, most of the current studies on LHA focus on the plain areas, lack of quantitative studies in mountain areas, such as the Qinghai-Tibet Plateau. The Pythagorean fuzzy cloud (PFC) integration algorithm drawing on the advantages of Pythagorean fuzzy sets (PFS) and cloud model was proposed. A novel hybrid decision-making framework combining PFC integration algorithm and TOPSIS model was developed to determine the lake health levels with fuzziness and randomness. An indicator system incorporating ecosystem integrity (physical habitat, water quantity and quality, aquatic life) and non-ecological performance (social services) was established. To comprehensively investigate the lake health level in the Qinghai-Tibet Plateau, the Nam Co was selected as study area. Our results confirm that the developed framework in this study can overcome the shortcomings of existing methods and provide a more effective approach for LHA with fuzziness and randomness. In Nam Co, the non-ecological performance was significantly better than the ecosystem integrity. Health levels exhibited a remarkable spatial variation influenced by tourism and grazing, with decreasing health status from the northwestern to southeastern Nam Co. Approximately 85% of the sampling sites were at excellent or healthy levels, 15% were subhealthy, and no sampling sites were unhealthy and sick. Our results highlight that tourism has affected health levels at Nam Co, and effective measures are needed to minimize the impact in ecological fragile areas.

The occurrence of potentially pathogenic fungi and protists in Canadian lakes predicted using geomatics, in situ and satellite-derived variables: Towards a tele-epidemiological approach

Eukaryotic pathogens including fungi and enteroparasites infect humans, animals and plants. As integrators of landscape catchment, lakes can reflect and record biological and geochemical events or anthropogenic changes and provide useful knowledge to formulate public health, food security and water policies to manage and prevent diseases. In this context, potentially pathogenic fungi and parasites were sampled using 18S rRNA gene amplicon sequencing in 382 lakes displaying a broad range of sizes and human impact on the watershed in 10 ecozones across Canada. Based on pathogen classifications from the ePATHogen database published by the Public Health Agency of Canada, we identified 23 health-relevant genera for human and animal hosts, including Cryptococcus and Cryptosporidium. Our study investigated the potential of remote sensing and geomatics to predict microbial contamination in a tele-epidemiological approach. We used boosted regression tree modeling to evaluate the probability of occurrence of the most common genera found in our dataset based on 10 satellite-derivable, geomatics and field survey variables which could be potential sources or transport mechanisms through the watershed or survival factors in the water. We found that southern ecozones that possess the highest agricultural and pasture activities tend to contain lakes with the largest number of potential pathogens including several fungi associated with plant diseases. Bio-optical factors, such as colored dissolved organic matter, were highly related to the occurrence of the genera, potentially by protecting against damage from ultraviolet light. Our results demonstrate the capability of tele-epidemiology to provide useful information to develop government policies for recreational and drinking water regulations as well as for food security.

Multiple Images Improve Lake CDOM Estimation: Building Better Landsat 8 Empirical Algorithms across Southern Canada

Coloured dissolved organic matter (CDOM) is an important water property for lake management. Remote sensing using empirical algorithms has been used to estimate CDOM, with previous studies relying on coordinated field campaigns that coincided with satellite overpass. However, this requirement reduces the maximum possible sample size for model calibration. New satellites and advances in cloud computing platforms offer opportunities to revisit assumptions about methods used for empirical algorithm calibration. Here, we explore the opportunities and limits of using median values of Landsat 8 satellite images across southern Canada to estimate CDOM. We compare models created using an expansive view of satellite image availability with those emphasizing a tight timing between the date of field sampling and the date of satellite overpass. Models trained on median band values from across multiple summer seasons performed better (adjusted R2 = 0.70, N = 233) than models for which imagery was constrained to a 30-day time window (adjusted R2 = 0.45). Model fit improved rapidly when incorporating more images, producing a model at a national scale that performed comparably to others found in more limited spatial extents. This research indicated that dense satellite imagery holds new promise for understanding relationships between in situ CDOM and satellite reflectance data across large areas.

Arctic Freshwater Environment Altered by the Accumulation of Commonly Determined and Potentially New POPs

Chemical composition of Arctic freshwater ecosystems depends on several factors. They include characteristics of the surrounding landscape, its lithology, geomorphology, vegetation, and hydrological features, as well as accumulation of anthropogenic pollution. In the Arctic, the problem of environmental contamination is widespread. That is why research on lakes and river catchments in terms of their chemical composition has enjoyed increasing interest among scientists worldwide. The freshwater reservoirs of the Arctic are fragile and particularly vulnerable to the uptake of pollutants that become trapped in the water and sediments for an extended period. This review summarises selected studies of freshwater bodies in the Arctic to highlight the problem of the accumulation of pollutants in these reservoirs. Moreover, it emphasises the possible negative impact of chemical pollutants on both animal and human health.

Landsat 8 Lake Water Clarity Empirical Algorithms: Large-Scale Calibration and Validation Using Government and Citizen Science Data from across Canada

Water clarity has been extensively assessed in Landsat-based remote sensing studies of inland waters, regularly relying on locally calibrated empirical algorithms, and close temporal matching between field data and satellite overpass. As more satellite data and faster data processing systems become readily accessible, new opportunities are emerging to revisit traditional assumptions concerning empirical calibration methodologies. Using Landsat 8 images with large water clarity datasets from southern Canada, we assess: (1) whether clear regional differences in water clarity algorithm coefficients exist and (2) whether model fit can be improved by expanding temporal matching windows. We found that a single global algorithm effectively represents the empirical relationship between in situ Secchi disk depth (SDD) and the Landsat 8 Blue/Red band ratio across diverse lake types in Canada. We also found that the model fit improved significantly when applying a median filter on data from ever-wider time windows between the date of in situ SDD sample and the date of satellite overpass. The median filter effectively removed the outliers that were likely caused by atmospheric artifacts in the available imagery. Our findings open new discussions on the ability of large datasets and temporal averaging methods to better elucidate the true relationships between in situ water clarity and satellite reflectance data.

Stability issues of microcystins, anabaenopeptins, anatoxins, and cylindrospermopsin during short-term and long-term storage of surface water and drinking water samples

Reproducible analytical procedures and rigorous quality control are imperative for an accurate monitoring of cyanobacterial toxins in environmental water samples. In this study, the short-term and long-term storage stability of diverse cyanotoxins (anatoxins, cylindrospermopsin, anabaenopeptins, and 12 microcystins) was evaluated in water samples, under different scenarios. Transport controls were performed at three monitoring sites in spiked ultrapure water and lake water to investigate short-term stability issues. Medium-term storage stability was evaluated for up to 14-28 days in ultrapure water, chlorine-treated drinking water (amended with reductant), and surface water (filtered and unfiltered) stored at different temperatures (20 °C, 4 °C, and -20 °C). Substantial decreases of cylindrospermopsin and anabaenopeptins were observed in tap water (20 °C) and unfiltered surface water (20 °C or 4 °C). Regardless of matrix type, cyanotoxin recoveries generally remained within an 80-120% range when the water samples were kept frozen. After a prolonged storage duration of 365 days at -20 °C, most cyanotoxins experienced decreases in the range of 10-20%. The notable exception was for the tryptophan-containing MC-LW and MC-WR, with more substantial variations (30% to 50% decrease) and conversion to N-formylkynurenine analogs. Reanalysis of field-collected surface waters after long-term storage at -20 °C also indicated significantly decreasing trends of cyanotoxins (between 6% and 23% decrease). In view of the above, short sample hold times should be favored as recommended in EPA methods.

Microbiology in the Field: Construction and Validation of a Portable Incubator for Real-Time Quantification of Coliforms and Other Bacteria

Performing microbiological assays on environmental samples in field settings poses logistical challenges with respect to the availability of suitable equipment or the ability to get samples to the laboratory in a timely fashion. For example, the viability of some bacteria can decrease greatly between sampling and arrival to the laboratory for processing. We developed and constructed rugged, reliable, and cost-effective portable incubators that were used by 10 independent field teams to perform microbiological assays on surface water samples from lakes across Canada. Rigorous testing and validation of our incubators ensured that incubation conditions were consistent within and across all 10 field teams and 2 sampling years. Samples from all sites were processed in duplicate and bacterial counts were highly repeatable within and across sampling teams. Bacterial counts were also found to be statistically equivalent to counts obtained with standard laboratory techniques using a conventional incubator. Using this method, thermotolerant coliforms (TTCs) and Escherichia coli were quantified from 432 lakes, allowing comparison to both historical datasets that relied on TTCs and those following current guidelines that use E. coli counts. We found higher loads at the shoreline than the middle of lakes and different patterns between ecozones. E. coli was not frequently detected, but many lakes exceeded Canadian guideline values for activities such as swimming and some even exceeded the guideline value for secondary recreational activities such as boating. To the best of our knowledge, this is the largest bacteriological water quality assessment of freshwater lakes to date in terms of both spatial scale and the number of lakes sampled. Our incubator design can be easily adapted for a wide variety of researcher goals and represents a robust platform for field studies and other applications, including those in remote or low-resources settings.

Sediment Metagenomes as Time Capsules of Lake Microbiomes

The reconstruction of ecological time series from lake sediment archives can retrace the environmental impact of human activities. Molecular genetic approaches in paleolimnology have provided unprecedented access to DNA time series, which record evidence of the microbial ecologies that underlaid historical lake ecosystems. Such studies often rely on single-gene surveys, and consequently, the full diversity of preserved microorganisms remains unexplored. In this study, we probed the diversity archived in contemporary and preindustrial sediments by comparative shotgun metagenomic analysis of surface water and sediment samples from three eastern Canadian lakes. In a strategy that was aimed at disentangling historical DNA from the indigenous sediment background, microbial preservation signals were captured by mapping sequence similarities between sediment metagenome reads and reference surface water metagenome assemblies. We detected preserved Cyanobacteria, diverse bacterioplankton, microeukaryotes, and viruses in sediment metagenomes. Among the preserved microorganisms were important groups never before reported in paleolimnological reconstructions, including bacteriophages (Caudovirales) and ubiquitous freshwater Betaproteobacteria (Polynucleobacter and Limnohabitans). In contrast, ultramicroscopic Actinobacteria ("Candidatus Nanopelagicales") and Alphaproteobacteria (Pelagibacterales) were apparently not well preserved in sediment metagenomes even though they were numerically dominant in surface water metagenomes. Overall, our study explored a novel application of whole-metagenome shotgun sequencing for discovering the DNA remains of a broad diversity of microorganisms preserved in lake sediments. The recovery of diverse microbial time series supports the taxonomic expansion of microbiome reconstructions and the development of novel microbial paleoindicators.IMPORTANCE Lakes are critical freshwater resources under mounting pressure from climate change and other anthropogenic stressors. The reconstruction of ecological time series from sediment archives with paleolimnological techniques has been shown to be an effective means of understanding how humans are modifying lake ecosystems over extended timescales. In this study, we combined shotgun DNA sequencing with a novel comparative analysis of surface water and sediment metagenomes to expose the diversity of microorganisms preserved in lake sediments. The detection of DNA from a broad diversity of preserved microbes serves to more fully reconstruct historical microbiomes and describe preimpact lake conditions.

A large-scale assessment of lakes reveals a pervasive signal of land use on bacterial communities

Lakes play a pivotal role in ecological and biogeochemical processes and have been described as "sentinels" of environmental change. Assessing "lake health" across large geographic scales is critical to predict the stability of their ecosystem services and their vulnerability to anthropogenic disturbances. The LakePulse research network is tasked with the assessment of lake health across gradients of land use on a continental scale. Bacterial communities are an integral and rapidly responding component of lake ecosystems, yet large-scale responses to anthropogenic activity remain elusive. Here, we assess the ecological impact of land use on bacterial communities from over 200 lakes covering more than 660,000 km² across Eastern Canada. In addition to community variation between ecozones, land use across Eastern Canada also appeared to alter diversity, community composition, and network structure. Specifically, increasing anthropogenic impact within the watershed lowered diversity. Likewise, community composition was significantly correlated with agriculture and urban development within a watershed. Interaction networks showed decreasing complexity and fewer keystone taxa in impacted lakes. Moreover, we identified potential indicator taxa of high or low lake water quality. Together, these findings point to detectable bacterial community changes of largely unknown consequences induced by human activity within lake watersheds.