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Particle size distribution (PSD) is a fundamental property that affects almost every aspect of the marine ecosystem, including ecological trophic interactions and transport of organic matter and trace elements. We measured PSDs using a suite of seven instruments in waters near Ocean Station Papa in the Northeast Pacific Ocean. These instruments and their sizing ranges are: Laser In-Situ Scattering and Transmissometer (LISST)-Volume Scattering Function meter (VSF) and Multispectral Volume Scattering Meter (MVSM), both sizing particles from 0.02 µm to 2000 µm; the LISST-100X, from 3 µm to 180 µm; the ViewSizer, from 0.3 µm to 2 µm; the Coulter Counter, from 2 µm to 40 µm; the Imaging Flow CytoBot (IFCB), from 5 µm to 100 μm; and the underwater vision profiler (UVP), from 100 µm to 2000 µm. Together, they cover an unprecedented size range spanning 5 orders of magnitude from 20 nm to 2 mm. The differences in size definition for the different instruments cause biases in comparing PSDs. The absolute differences in PSDs, after correcting for mean biases, were less than a factor of 3 among all the instruments, and within 50% among LISST-100X, LISST+MVSM, Coulter Counter and IFCB. We also found that particles of sizes 50 µm. The merged PSDs, ranging from 0.02 µm to 2000 µm, showed little variation in the PSD slope in the upper 75 m of the water column even though the total number of particles decreased with depth. While submicrometer particles are numerically dominant, particles of sizes 1 µm to 100 µm account for 70–90% of the solid volume of particles. We expect that the results of this study will lead to improved estimates of mass and carbon flux in the study area. more...

Phytoplankton images were collected using an Imaging Flow Cytobot moored in the mesotrophic lake Lac Montjoie (Quebec, Canada). Cystodinium—an unusual dinoflagellate genus—was found during manual classification of the images into taxonomic groups while building an automated classifier. Cystodinium’s particularity is that while it can take a typical motile dinoflagellate form, it is thought to exist primarily as an immotile photosynthetically competent parasitic cyst in the shape of a crescent moon. Observations presented here are of this immotile lunate cyst. Manually classified images revealed that the majority of the Cystodinium found (86%) were attached to other microalgae or detrital material while the rest were unattached. The established auto-classifier was only able to correctly identify unattached Cystodinium images and thus was used to generate time series as cells per 100 mL for the unattached cell subset. Our observations, coupled with a literature review, lead us to question the parasitic nature of this taxonomic group. more...

Despite decades of research and mitigation efforts, declines in freshwater quality resulting from anthropogenic nutrient input remain a persistent issue worldwide. Canada has the greatest number of freshwater lakes in the world, yet we have a limited understanding of the magnitude and scale at which most lakes have been affected by human activities, namely Land Use/Land Cover (LULC) alterations. In response, the NSERC Canadian Lake Pulse Network has compiled the first nationwide systematic database of lake quality metrics by surveying 664 lakes across 12 ecozones over three years. To assess the influence of catchment development on water quality and its spatial variation, we built models quantifying the association between watershed LULC and water quality. We found that agricultural and urban land use explained the greatest proportion of variation in water quality among LULC categories (R2= 0.20–0.29). Overall, our study highlights that drivers of water quality are similar across regions; however, baseline conditions vary, so freshwater ecosystem management strategies must consider their geographic context to better predict where water quality thresholds will be surpassed. more...

Lakes are highly heterogenous ecosystems inhabited by a rich microbiome whose genomic diversity remains poorly defined compared to other major biomes. Here, we present a continental-scale study of metagenomes collected across one of the most lake-rich landscapes on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 bacterial genomospecies spanning a broad phylogenetic and metabolic diversity. Lake trophic state was a significant determinant of taxonomic and functional turnover of MAG assemblages. We detected a role for resource availability, particularly carbohydrate diversity, in driving biogeographic patterns. Coupling the MAG catalogue with geomatics information on watershed characteristics revealed an influence of soil properties and human land use on MAG assemblages. Agriculture and human population density were particularly influential on MAG functional turnover, signifying a detectable human footprint in lake bacterial communities. Overall, the Canadian lake MAG catalogue greatly expands the freshwater microbial genomic landscape, bringing us closer to an integrative view of bacterial genome diversity across Earth’s biomes. more...

Protists play key roles in aquatic food webs as primary producers, predators, nutrient recyclers, and symbionts. Yet, 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 extent 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 at smaller scales. Our study exposes the importance of both within-lake and external watershed characteristics in explaining protist diversity and biogeography, critical information in further developing an understanding of how freshwater lakes and their watersheds are impacted by anthropogenic stressors.ImportanceFreshwater 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. more...

Profitability of biofuel production from microalgae is difficult to achieve but co-locating production with wastewater treatment plants is a possible avenue help to reduce costs. A microalgae cultu... more...

International audience; The goal of the EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) field campaign is to develop a predictive understanding of the export, fate, and carbon cycle impacts of global ocean net primary production. To accomplish this goal, observations of export flux pathways, plankton community composition, food web processes, and optical, physical, and biogeochemical (BGC) properties are needed over a range of ecosystem states. Here we introduce the first EXPORTS field deployment to Ocean Station Papa in the Northeast Pacific Ocean during summer of 2018, providing context for other papers in this special collection. The experiment was conducted with two ships: a Process Ship, focused on ecological rates, BGC fluxes, temporal changes in food web, and BGC and optical properties, that followed an instrumented Lagrangian float; and a Survey Ship that sampled BGC and optical properties in spatial patterns around the Process Ship. An array of autonomous underwater assets provided measurements over a range of spatial and temporal scales, and partnering programs and remote sensing observations provided additional observational context. The oceanographic setting was typical of late-summer conditions at Ocean Station Papa: a shallow mixed layer, strong vertical and weak horizontal gradients in hydrographic properties, sluggish sub-inertial currents, elevated macronutrient concentrations and low phytoplankton abundances. Although nutrient concentrations were consistent with previous observations, mixed layer chlorophyll was lower than typically observed, resulting in a deeper euphotic zone. Analyses of surface layer temperature and salinity found three distinct surface water types, allowing for diagnosis of whether observed changes were spatial or temporal. The 2018 EXPORTS field deployment is among the most comprehensive biological pump studies ever conducted. A second deployment to the North Atlantic Ocean occurred in spring 2021, which will be followed by focused work on data synthesis and modeling using the entire EXPORTS data set. more...

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. more...

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 km(2) 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. more...

Adoption of microalgae-sourced products depends on the economic feasibility. In the case of fatty acids, it is crucial to obtain high lipid yield, especially in the form of storage lipids (TAGs). However, the production of these lipids often comes into competition with the microalgae biomass, resulting in a decrease in growth. A microalgae culture integration project was conducted in an industrial park in Canada in order to cultivate microalgae from park’s wastewaters and then obtain products from the biomass. Different deficiencies and stresses were tested to evaluate what condition allowed the induction of the highest lipids accumulation without compromising the growth of microalgae. The results showed that the medium controlled to pH 7.0 allowed reaching the largest amount of extracted lipids (28 ± 4.3%). Companies involved in this project could be able to make significant savings by the reduced wastewater treatment costs and by not adding expensive nutrients in culture. more...

Diel variations of inherent optical properties (absorption coefficient, attenuation coefficient and volume scattering function at 124°) of four species of phytoplankton were measured in the laboratory and were simulated using a homogeneous spherical model, a coated spherical model and a homogeneous hexahedral model. The required inputs to run each optical model were acquired from the measurements; the real and imaginary parts of the refractive index were determined from the intracellular carbon and absorption coefficient, and particle size distributions from the Coulter counter. We conducted a sensitivity analysis on the inherent optical properties in response to changes in the slope of Junge distributions that were used to represent non-phytoplankton particles of radii less than 1.12 µm (the minimum size of the Coulter counter), realistic maximum and minimum values of the refractive indices used for the shell and core, shell thickness, cell radius and the number of cells. We found that the shell's refractive index is the most important factor influencing the backscattering ratio. We found that the coated spherical model reproduced the observed optical properties best for all species possessing a shell. The hexahedral and homogenous spherical models give relatively good results for the absorption and attenuation coefficients; but underestimated the volume scattering function at 124°. Correlations between the measured backscattering cross sections and carbon are significant only for E. huxleyi and D. tertiolecta. In situ measurements will be necessary to determine if our models can reproduce the diel variations of backscattering that are observed in the ocean. more...

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. more...

The vertical distribution of chlorophyll in stratified lakes and reservoirs frequently exhibits a maximum peak deep in the water column, referred to as the deep chlorophyll maximum (DCM). DCMs are ecologically important hot spots of primary production and nutrient cycling, and their location can determine vertical habitat gradients for primary consumers. Consequently, the drivers of DCM structure regulate many characteristics of aquatic food webs and biogeochemistry. Previous studies have identified light and thermal stratification as important drivers of summer DCM depth, but their relative importance across a broad range of lakes is not well resolved. We analyzed profiles of chlorophyll fluorescence, temperature, and light during summer stratification from 100 lakes in the Global Lake Ecological Observatory Network (GLEON) and quantified two characteristics of DCM structure: depth and thickness. While DCMs do form in oligotrophic lakes, we found that they can also form in eutrophic to dystrophic lakes. Using a random forest algorithm, we assessed the relative importance of variables associated with light attenuation vs. thermal stratification for predicting DCM structure in lakes that spanned broad gradients of morphometry and transparency. Our analyses revealed that light attenuation was a more important predictor of DCM depth than thermal stratification and that DCMs deepen with increasing lake clarity. DCM thickness was best predicted by lake size with larger lakes having thicker DCMs. Additionally, our analysis demonstrates that the relative importance of light and thermal stratification on DCM structure is not uniform across a diversity of lake types. more...

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 220 lakes covering more than 660 000 km2across Eastern Canada. Alteration of communities was found on every level examined including richness, community composition, community network structure and indicator taxa of high or low lake water quality. Specifically, increasing anthropogenic impact within the watershed lowered richness mediated by changes in salinity. 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. Together, these findings point to vast bacterial community changes of largely unknown consequences induced by human activity within lake watersheds.Significance StatementLakes play central roles in Earth’s ecosystems and are sentinels of climate change and other watershed alterations. Assessing lake health across large geographic scales is therefore critical to predict ecosystem stability and lake vulnerability to anthropogenic disturbances. In this context, the LakePulse research network is tasked with a large-scale assessment of lake health across Canada. Bacterial communities are an integral and rapidly responding component of lake ecosystems, yet their large-scale responses to anthropogenic activity remain unknown. Here, we assessed the anthropogenic impact on bacterial communities of over 200 lakes located across large environmental gradients. We found communities to be impacted on every level investigated, indicating that human activities within watersheds cause vast bacterial community changes of largely unknown consequences. more...

The Arctic ice scape is composed by a mosaic of ridges, hummocks, melt ponds, leads, and snow. Under such heterogeneous surfaces, drifting phytoplankton communities are experiencing a wide range of irradiance conditions and intensities that cannot be sampled representatively using single-location measurements. Combining experimentally derived photosynthetic parameters with transmittance measurements acquired at spatial scales ranging from hundreds of meters (using a remotely operated vehicle, ROV) to thousands of meters (using a surface and underice trawl, SUIT), we assessed the sensitivity of water column primary production estimates to multiscale underice light measurements. Daily primary production calculated from transmittance from both the ROV and the SUIT ranged between 0.004 and 939 mgC.m(-2).day(-1). Upscaling these estimates at larger spatial scales using satellite-derived sea ice concentration reduced the variability by 22% (0.004-731 mgC.m(-2).day(-1)). The relative error in primary production estimates was two times lower when combining remote sensing and in situ data compared to ROV-based estimates alone. These results suggest that spatially extensive in situ measurements must be combined with large-footprint sea ice coverage sampling (e.g., remote sensing, aerial imagery) to accurately estimate primary production in ice-covered waters. Also, the results indicated a decreasing error of primary production estimates with increasing sample size and the spatial scale at which in situ measurements are performed. Conversely, existing estimates of spatially integrated phytoplankton primary production in ice-covered waters derived from single-location light measurements may be associated with large statistical errors. Considering these implications is important for modeling scenarios and interpretation of existing measurements in a changing Arctic ecosystem. more...

The widespread and persistent contamination of freshwater environments by low concentrations of pesticides is a growing concern worldwide. In aquatic environments, herbicide pollution is of greatest concern for phytoplankton, due to their similarities to terrestrial plants. Through the use of Fast Repetition Rate Fluorometry (FRRF) during weeklong experiments on 10 phytoplankton cultures from 4 classes and 4 natural communities, we demonstrate that PSII-inhibiting herbicides, notably atrazine that is extensively used in North America, consistently have effects on freshwater phytoplankton photophysiology at concentrations far below concentrations affecting the most sensitive species in previous studies. The parameters specific to FRRF (Ρ, σ, τ1, τ2, τ3) were those most sensitive to PSII inhibitors, compared to the standard fluorescence parameters derived from other fluorescence protocols such as Pulse Amplitude Modulation (PAM) fluorometry (F0, Fm, Fv/Fm) and extracted chlorophyll a concentrations. Based on these findings, existing national environmental guidelines and standards are insufficient to adequately prevent adverse effects of atrazine and other PSII inhibiting herbicides on algal physiology in aquatic ecosystems. more...

International audience; Comprehensively sampling the ocean in situ remains a challenge, even in the current era of rapid technological development. In less than a decade, the deployment of thousands of autonomous profiling floats increased the number of ocean temperature profiles by an order of magnitude compared to ship-based sampling in the past. But expendable floats cannot sample all the physical and biogeochemical regimes in the global ocean. A promising avenue that could guide in situ sampling is to partition oceans based on selected properties in order to identify "homogeneous" areas. This approach greatly reduces the number of measurements needed to represent the state of the ocean. However, homogeneous areas can be partitioned in many ways: depending on whether a single or several properties are considered; and on whether the definition of boundaries is left to expert knowledge or derived from objective analysis techniques. Here, we use a clustering method to map and partition many surface variables, and we further examine how this partitioning is affected by various ways of averaging or normalizing the input data. We performed this study using 15 different surface fields of physical and biological properties derived from satellite remote sensing observations and from global model outputs at a monthly resolution. The area of study is the Indian Ocean-one of the least-sampled oceans-which is the focus of a global research effort under the auspices of the second International Indian Ocean Expedition (IIOE-2). We show a strong effect of the average absolute values of the data, which can be removed to better examine the phenology of the properties. However, normalization is not mandatory; the technique selected should depend on the scientific questions at hand. Our clusters did generally did not match closely the regions identified by Longhurst in his seminal work on ocean provinces. more...

Studying the biogeochemistry of the Southern Ocean using remote sensing relies on accurate interpretation of ocean colour through bio-optical and biogeochemical relationships between quantities and properties of interest. During the Antarctic Circumnavigation Expedition of the 2016/2017 Austral Summer, we collected a spatially comprehensive dataset of phytoplankton pigment concentrations, particulate absorption and particle size distribution and compared simple bio-optical and particle property relationships as a function of chlorophyll a. Similar to previous studies we find that the chlorophyll-specific phytoplankton absorption coefficient is significantly lower than in other oceans at comparable chlorophyll concentrations. This appears to be driven in part by lower concentrations of accessory pigments per unit chlorophyll a as well as increased pigment packaging due to relatively larger sized phytoplankton at low chlorophyll a than is typically observed in other oceans. We find that the contribution of microphytoplankton (>20 µm size) to chlorophyll a estimates of phytoplankton biomass is significantly higher than expected for the given chlorophyll a concentration, especially in higher latitudes south of the Southern Antarctic Circumpolar Current Front. Phytoplankton pigments are more packaged in larger cells, which resulted in a flattening of phytoplankton spectra as measured in these samples when compared to other ocean regions with similar chlorophyll a concentration. Additionally, we find that at high latitude locations in the Southern Ocean, pheopigment concentrations can exceed mono-vinyl chlorophyll a concentrations. Finally, we observed very different relationships between particle volume and chlorophyll a concentrations in high and low latitude Southern Ocean waters, driven by differences in phytoplankton community composition and acclimation to environmental conditions and varying contribution of non-algal particles to the particulate matter. Our data confirm that, as previously suggested, the relationships between bio-optical properties and chlorophyll a in the Southern Ocean are different to other oceans. In addition, distinct bio-optical properties were evident between high and low latitude regions of the Southern Ocean basin. Here we provide a region-specific set of power law functions describing the phytoplankton absorption spectrum as a function of chlorophyll a. more...

Small spectral differences from the mean remote sensing reflectance (Rrs) of the ocean - anomalies - can provide unique environmental information from ocean color satellite data. First, we describe the average relationship between three input spectral bands and an output band by developing a look-up table (WT) based on the fully normalized Rrs from the MODIS AQUA sensor. By dividing the Rrs measured at the output wavelength by the prediction from the LUT, we obtain several anomalies depending on the combination of input and output bands. None of these anomalies are correlated with chlorophyll concentration on the global scale. Some anomalies are strongly correlated with previously described data products (e.g., CDOM index, backscattering coefficients from semi-analytical inversion models), but others are not correlated with any product currently distributed by NASA. In the latter case, new information about oceanic optical properties is extracted from the ocean color spectra, which allows identification of water masses that was otherwise impossible with standard ocean color products. It was not possible, in some cases, to identify the optical source of this information, which may be spatially and temporally variable. We also show that by removing the main source of variability, the anomalies show interesting potential to identify subtle shifts in sensor response in satellite time series. (C) 2016 Elsevier Inc. All rights reserved. more...

SummaryNorthern lakes are ice-covered for a large part of the year, yet our understanding of microbial diversity and activity during winter lags behind that of the ice-free period. In this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 16S rRNA sequencing, metagenomics and metatranscriptomics. Verrucomicrobia, particularly the V1, V3 and V4 subdivisions, were abundant during ice-covered periods. A diversity of Verrucomicrobia genomes were reconstructed from Quebec lake metagenomes. Several genomes were associated with the ice-covered period and were represented in winter metatranscriptomes, supporting the notion that Verrucomicrobia are metabolically active under ice. Verrucomicrobia transcriptome analysis revealed a range of metabolisms potentially occurring under ice, including carbohydrate degradation, glycolate utilization, scavenging of chlorophyll degradation products, and urea use. Genes for aerobic sulfur and hydrogen oxidation were expressed, suggesting chemolithotrophy may be an adaptation to conditions where labile carbon may be limited. The expression of genes for flagella biosynthesis and chemotaxis was detected, suggesting Verrucomicrobia may be actively sensing and responding to winter nutrient pulses, such as phytoplankton blooms. These results increase our understanding on the diversity and metabolic processes occurring under ice in northern lakes ecosystems. more...

When growth irradiance changes, phytoplank- ton acclimates by changing allocations to cellular compo- nents to re-balance their capacity to absorb photons versus their capacity to use the electrons from the oxidation of water at photosystem II. Published changes in the cellular allocations resulting from photoacclimation across algal groups highlight that algae adopt different strategies. We examined the photoacclimation of the photosynthetic ap- paratus of six marine phytoplankters under near-natural diel irradiance patterns. For most of the phytoplankters, Chl a per structural photosystem II unit decreased with increasing growth irradiance, but a parallel decline in op- tical packaging effect allowed cells to maintain their functional absorption cross section serving active photo- system II units (rPSII). Furthermore, no significant changes were observed in the ratio of Chl a per photosystem I. The diatom Skeletonema marinoi proved an exception to this pattern as Chl a per photosystem II is stable and Chl a per photosystem I slightly decreased with light intensity. A clear decrease in the photosystem content per cell was observed for all species except for Thalassiosira oceanica and S. marinoi. Rubisco content per cell showed little variation with irradiance for most algae, except for a 3-fold increase in S. marinoi .A *700 % increase in the Rubis- co:photosystem ratio across species with increasing growth irradiance indicates this is a key cellular stoichiometric adjustment to balance photon absorption capacity and the carbon reduction capacity. Increasing the Rubisco:photo- system ratio occurs through a decrease in the photosystems per cell for most of the phytoplankters in this study, except in the case of S. marinoi where Rubisco per cell increased. more...

Diurnal variations of phytoplankton size distributions, chlorophyll, carbon and nitrogen content, in vivo fluorescence and associated optical absorption and scattering properties were observed in the laboratory to help understand in situ and spatial observations. We grew triplicate semi-continuous cultures of T. pseudonana, D. tertiolecta, P. tricornutum and E. huxleyi under a sinusoidal light regime. We observed diurnal variations in the particulate absorption (ap), scattering (bp), attenuation (cp), and backscattering coefficients (bbp), which correlate with carbon and Chl concentrations. Relative variations from sunrise of bbp are slightly lower than those of cp, suggesting that bbp diurnal increases observed in nature are partly caused by phytoplankton. Non-concurrent changes of carbon and Chl-specific backscattering and scattering coefficients and optical cross-sections however indicates that using backscattering to infer scattering or biomass must be done with care. more...

Northern lakes are ice-covered for a large part of the year, yet our understanding of microbial diversity and activity during winter lags behind that of the ice-free period. In this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 16S rRNA sequencing, metagenomics and metatranscriptomics. Verrucomicrobia, particularly the V1, V3 and V4 subdivisions, were abundant during ice-covered periods. A diversity of Verrucomicrobia genomes were reconstructed from Quebec lake metagenomes. Several genomes were associated with the ice-covered period and were represented in winter metatranscriptomes, supporting the notion that Verrucomicrobia are metabolically active under ice. Verrucomicrobia transcriptome analysis revealed a range of metabolisms potentially occurring under ice, including carbohydrate degradation, glycolate utilization, scavenging of chlorophyll degradation products, and urea use. Genes for aerobic sulfur and hydrogen oxidation were expressed, suggesting chemolithotrophy may be an adaptation to conditions where labile carbon may be limited. The expression of genes for flagella biosynthesis and chemotaxis was detected, suggesting Verrucomicrobia may be actively sensing and responding to winter nutrient pulses, such as phytoplankton blooms. These results increase our understanding on the diversity and metabolic processes occurring under ice in northern lakes ecosystems.© 2018 Society for Applied Microbiology and John WileySons Ltd. more...

The distribution and quality of water resources vary dramatically across Canada, and human impacts such as land-use and climate changes are exacerbating uncertainties in water supply and security. At the national level, Canada has no enforceable standards for safe drinking water and no comprehensive water-monitoring program to provide detailed, timely reporting on the state of water resources. To provide Canada's first national assessment of lake health, the NSERC Canadian Lake Pulse Network was launched in 2016 as an academic-government research partnership. LakePulse uses traditional approaches for limnological monitoring as well as state-of-the-art methods in the fields of genomics, emerging contaminants, greenhouse gases, invasive pathogens, paleolimnology, spatial modelling, statistical analysis, and remote sensing. A coordinated sampling program of about 680 lakes together with historical archives and a geomatics analysis of over 80,000 lake watersheds are used to examine the extent to which lakes are being altered now and in the future, and how this impacts aquatic ecosystem services of societal importance. Herein we review the network context, objectives and methods. more...

In the aquatic environment, particles can be broadly separated into phytoplankton (PHY), non-algal particle (NAP) and dissolved (or very small particle, VSP) fractions. Typically, absorption spectra are inverted to quantify these fractions, but volume scattering functions (VSFs) can also be used. Both absorption spectra and VSFs were used to estimate particle fractions for an experiment in the Chesapeake Bay. A complete set of water inherent optical properties was measured using a suite of commercial instruments and a prototype Multispectral Volume Scattering Meter (MVSM); the chlorophyll concentration, [Chl] was determined using the HPLC method. The total scattering coefficient measured by an ac-s and the VSF at a few backward angles measured by a HydroScat-6 and an ECO-VSF agreed with the LISST and MVSM data within 5%, thus indicating inter-instrument consistency. The size distribution and scattering parameters for PHY, NAP and VSP were inverted from measured VSFs. For the absorption inversion, the "dissolved" absorption spectra were measured for filtrate passing through a 0.2 μm filter, whereas [Chl] and NAP absorption spectra were inverted from the particulate fraction. Even though the total scattering coefficient showed no correlation with [Chl], estimates of [Chl] from the VSF-inversion agreed well with the HPLC measurements (r = 0.68, mean relative errors = −20%). The scattering associated with NAP and VSP both correlated well with the NAP and "dissolved" absorption coefficients, respectively. While NAP dominated forward, and hence total, scattering, our results also suggest that the scattering by VSP was far from negligible and dominated backscattering. Since the sizes of VSP range from 0.02 to 0.2 μm, covering (a portion of) the operationally defined "dissolved" matter, the typical assumption that colored dissolved organic matter (i.e., CDOM) does not scatter may not hold, particularly in a coastal or estuarine environment. more...

To model phytoplankton primary production from remotely sensed data, a method to estimate photosynthetic parameters describing the photosynthetic rates per unit biomass is required. Variability in these parameters must be related to environmental variables that are measurable remotely. In the Arctic, a limited number of measurements of photosynthetic parameters have been carried out with the concurrent environmental variables needed. Such measurements and their relationship to environmental variables will be required to improve the accuracy of remotely sensed estimates of phytoplankton primary production and our ability to predict future changes. During the MALINA cruise, a large dataset of these parameters was obtained. Together with previously published datasets, we use environmental and trophic variables to provide functional relationships for these parameters. In particular, we describe several specific aspects: the maximum rate of photosynthesis (Pmaxchl) normalized to chlorophyll decreases with depth and is higher for communities composed of large cells; the saturation parameter (Ek) decreases with depth but is independent of the community structure; and the initial slope of the photosynthesis versus irradiance curve (αchl) normalized to chlorophyll is independent of depth but is higher for communities composed of larger cells. The photosynthetic parameters were not influenced by temperature over the range encountered during the cruise (−2 to 8 °C). more...

While empirical and semi-analytical algorithms that retrieve phytoplankton biomass from satellite ocean color have matured over the last few decades, the use of Sun-induced chlorophyll fluorescence data measured by spaceborne sensors remains in its infancy. Sun-induced fluorescence has the potential to provide a synoptic global view of aspects of phytoplankton biology that go beyond biomass by observing the quantum yield of fluorescence. While several algorithms have been developed to retrieve the quantum yield, they are prone to biases from different sources. In this study, we assessed the accuracy of several ocean color algorithms to estimate phytoplankton chlorophyll or absorption when they are used together with Sun-induced fluorescence algorithms. Our analysis led us to develop a new type of algorithm for retrieving variability in the quantum yield of fluorescence. Based on a three dimensional lookup table, this algorithm avoided many of the biases present in older algorithms and provided distributions of the quantum yield that showed significant differences compared to previous methods. This algorithmic approach also has the advantage of being robust with respect to sensor characteristics and to the set of underlying proxies that are used, namely phytoplankton biomass, the absorption by chromophoric dissolved organic matter, and the incident irradiance. As such, it would be suitable for merging data from multiple satellite ocean color sensors. more...

Sun-induced chlorophyll- a fluorescence (SICF) is the emission of red light by chlorophyll- a in the presence of sunlight. In surface waters, chlorophyll- a is present in phytoplankton and SICF is observable in the light leaving the water surface. This allows, in principle, the estimation of phytoplankton absorption from measurements of light leaving water. However, while the concentration of phytoplankton in surface waters is the dominant source of optical variability, phytoplankton physiology and the optical characteristics of water also play a significant role in altering the observed emission. The latter have a particularly strong impact in inland and coastal waters. To examine these interactions and their impact on the observed light field, a four-component bio-optical model was developed to create synthetic datasets of reflectance spectra. These synthetic spectra are used together with field measurements of reflectance to understand the relationships between SICF, phytoplankton abundance, colored dissolved organic matter absorption, and suspended inorganic matter concentration in inland and coastal waters. The retrieval of SICF using hyperspectral data and fluorescence line height algorithms is analyzed by considering the wavebands of past, current, and future ocean color sensors. The use of fluorescence signatures in polarimetric observations and applications to algal bloom detection are also discussed. more...

International audience; Excitation-emission fluorescence matrices of phytoplankton communities were simulated from laboratory-grown algae and cyanobacteria cultures, to define the optical configurations of theoretical fluorometers that either minimize or maximize the representation of these phytoplankton groups in community variable fluorescence measurements. Excitation sources that match the photosystem II (PSII) action spectrum of cyanobacteria do not necessarily lead to equal representation of cyanobacteria in community fluorescence. In communities with an equal share of algae and cyanobacteria, inducible PSII fluorescence in algae can be retrieved from community fluorescence under blue excitation (450-470 nm) with high accuracy (R (2) = 1.00). The highest correlation between community and cyanobacterial variable fluorescence is obtained under orange-red excitation in the 590-650 nm range (R (2) = 0.54). Gaussian band decomposition reveals that in the presence of cyanobacteria, the emission detection slit must be narrow (up to 10 nm) and centred on PSII chlorophyll-a emission (similar to 683 nm) to avoid severe dampening of the signal by weakly variable phycobilisomal fluorescence and non-variable photosystem I fluorescence. When these optimizations of the optical configuration of the fluorometer are followed, both cyanobacterial and algal cultures in nutrient replete exponential growth exhibit values of the maximum quantum yield of charge separation in PSII in the range of 0.65-0.7. more...

The particulate scattering, bp, and backscattering, bbp, coefficients are determined by the concentration and physical properties of suspended particles in the ocean. They provide a simple description of the influence of these particles on the scattering of light within the water column. For the remote observation of ocean color, bbp along with the total absorption coefficient govern the amount and spectral qualities of light leaving the sea surface. However, for the construction and validation of ocean color models measurements of bbp are still lacking, especially at low chlorophyll a concentrations ([Chl]). Here, we examine the relationships between spectral bbp and bp vs. [Chl] along an 8000 km transect crossing the Case 1 waters of the eastern South Pacific Gyre. In these waters, over the entire range of [Chl] encountered (~0.02–2 mg m3), both bbp and bp can be related to [Chl] by power functions (i.e. bp or bbp=α[Chl]β). Regression analyses are carried out to provide the parameters α and β for several wavelengths throughout the visible for both bbp and bp. When applied to the data, these functions retrieve the same fraction of variability in bbp and bp (coefficients of determination between 0.82 and 0.88). The bbp coefficient fall within the bounds of previous measurements at intermediate and high [Chl] recently published. Its dependence on [Chl] below ~0.1 mg m−3 is described for the first time with in situ data. The backscattering ratio (i.e. bbp/bp) with values near 0.01 for all stations appears to be spectrally neutral and not significantly dependent on [Chl]. These results should foster the development of improved forward models of the mean optical properties for oceanic Case 1 waters as well as inverse models based upon them. more...

The use of high-frequency sensors on profiling buoys to investigate physical, chemical, and biological processes in lakes is increasing rapidly. Profiling buoys with automated winches and sensors that collect high-frequency chlorophyll fluorescence (ChlF) profiles in 11 lakes in the Global Lake Ecological Observatory Network (GLEON) allowed the study of the vertical and temporal distribution of ChlF, including the formation of subsurface chlorophyll maxima (SSCM). The effectiveness of 3 methods for sampling phytoplankton distributions in lakes, including (1) manual profiles, (2) single-depth buoys, and (3) profiling buoys were assessed. High-frequency ChlF surface data and profiles were compared to predictions from the Plankton Ecology Group (PEG) model. The depth-integrated ChlF dynamics measured by the profiling buoy data revealed a greater complexity that neither conventional sampling nor the generalized PEG model captured. Conventional sampling techniques would have missed SSCM in 7 of 11 study lakes. Although surface-only ChlF data underestimated average water column ChlF, at times by nearly 2-fold in 4 of the lakes, overall there was a remarkable similarity between surface and mean water column data. Contrary to the PEG model’s proposed negligible role for physical control of phytoplankton during the growing season, thermal structure and light availability were closely associated with ChlF seasonal depth distribution. Thus, an extension of the PEG model is proposed, with a new conceptual framework that explicitly includes physical metrics to better predict SSCM formation in lakes and highlight when profiling buoys are especially informative. more...

Global ocean color algorithms designed to estimate chlorophyll a concentration (chla) are not accurate at high latitudes. Although a regional Arctic OC4L algorithm was designed to be applicable to high northern latitudes, its applicability remains uncertain. To examine these issues, we investigated the light absorption coefficients of phytoplankton, non-algal particles (NAP), and colored dissolved organic matter (CDOM) and remote sensing reflectance, R-rs(lambda), covering most of the western Arctic Ocean. A higher pigment packaging effect was identified relative to that at lower latitudes. The CDOM absorption dominated and accounted for 76% of the total non-water absorption at 443 nm and did not covary with variations in chla. This absorption is significantly higher than those in other marine environments. We also examined the backscattering coefficient of particles obtained from the inversion of R-rs(lambda) and found that it covaried well with variation in NAP absorption. Our evaluation shows that when turbid waters (R-rs(670) > 0.00042 sr(-1)) are excluded, the performance of the OC4L is good and much better than that of the sea-viewing wide field-of-view sensor (SeaWiFS) OC4V4 and the moderate-resolution imaging spectroradiometer (MODIS) OC3M (root mean square error (RMSE) of 0.13, 0.21, and 0.22, respectively). The reason why the OC4L performs well despite strong CDOM absorption is discussed. more...

During its lifetime, a space-borne ocean color sensor provides world-wide information about important biogeochemical properties of the upper ocean every 2 to 4 days in cloudless regions. Merging simultaneous or complementary data from such sensors to obtain better spatial and temporal coverage is a recurring objective, but it can only be reached if the consistency of the sensor-specific products, as delivered by the various Space Agencies, has first been carefully examined. The goal of the present study is to provide a procedure for establishing a coherency of open ocean (Case-1 waters) data products, for which the various data processing methods are sufficiently similar. The development of the procedure includes a detailed comparison of the marine algorithms used (after atmospheric corrections) by space agencies for the production of standard products, such as the chlorophyll concentration, [Chl], and the diffuse attenuation coefficient, Kd. The MODIS-Aqua, SeaWiFS and MERIS [Chl] products agree over a wide range, between ∼0.1 and 3 mg m −3 , whereas increasing divergences occur for oligotrophic waters ([Chl] (from 0.02 to 0.09 mg m −3 ). For the Kd(490) coefficient, different algorithms are in use, with differing results. Based on a semi-analytical reflectance model and hyperspectral approach, the present work proposes a harmonization of the algorithms allowing the products of the various sensors to be comparable, and ultimately, meaningfully merged (the merging procedures themselves are not examined). Additional potential products, obtained by using [Chl] as an intermediate tool, are also examined and proposed. These products include the thickness of the layer heated by the sun, the depth of the euphotic zone, and the Secchi disk depth. The physical limitations in the predictive skill of such downward extrapolations, made from information concerning only the upper layer, are stressed. more...

We discuss important sources of variability in sun-induced chlorophyll fluorescence and examine difficulties in deriving fluorescence data products from satellite imagery, with a focus on the MODerate-resolution Imaging Spectroradiometer (MODIS) sensor. Our results indicate that there are limitations in the present MODIS algorithms that could lead to biases in the interpretation of the fluorescence products across gradients of chlorophyll concentration. To avoid some of these limitations, we suggest replacing the calculation of absorbed radiation by phytoplankton (ARP) over a finite depth with integration over the entire water column, and including a term accounting for cellular reabsorption of fluoresced light. These suggestions are incorporated into two new algorithms, based on established bio-optical models for case 1 waters (most open ocean waters), to retrieve chlorophyll concentration and the quantum yield of fluorescence. We compare our results to the results using MODIS algorithms for two regions: one located off the coast of Central America, including the Costa Rica Dome, and the other in the Arabian Sea. The new algorithms provide a similar field for the quantum yield of fluorescence in the first region, while they provide a different and more uniform field in the second region. We suggest that this discrepancy originates from the use of the water leaving radiance at 412 nm in the MODIS standard algorithm, which is not used in our algorithm and can be problematic under certain environmental conditions (e.g., absorbing aerosols or highly scattering waters). more...

Autonomous underwater vehicles (AUVs) can map water conditions at high spatial (horizontal and vertical) and temporal resolution, including under cloudy conditions when satellite and airborne remote sensing are not feasible. Applications of this technology are numerous, and harnessing the full potential of AUV platforms for oceanographic research will require innovative sampling and data processing techniques, particularly in shallow littoral environments. We deployed a passive radiometer on a small AUV called the Remote Environmental Monitoring UnitS (REMUS; Hydroid) to demonstrate a novel method that uses one optical sensor at depth to characterize variability in underwater clarity and the constituents of coastal seawater (i.e., dissolved organic material, algal biomass, and other particles). This approach uses spectral differences between attenuation coefficients that are computed from ratios of downwelling irradiance measured at one depth assuming a constant shape, but not magnitude, for the solar irradiance spectrum at the surface. A spectral inversion model provides estimates of the absorption coefficients (m−1) of the constituents above the sensor. There is no requirement for sensors at the ocean surface using this approach and, compared to inversion methods for subsurface reflectance, the effects of bottom reflectance in shallow waters are minimal. Maps of biooptical properties at high spatial resolution demonstrate that our approach can be used for characterizing shallow and highly variable coastal waters. This simple and robust technique is also applicable to other in situ sampling platforms (e.g., gliders, moorings, Argo floats). more...