Yannick Huot

Overview of Fluorescence Protocols: Theory, Basic Concepts, and Practice

At the request of the editors, this chapter is based on the book section written by Babin (2008), however, much of the manuscript has been revised and updated to address different readerships. While Babin (2008) is aimed at a more general audience interested in understanding the basis of the measurement and the current instruments available, this chapter is aimed at those who will use the fluorescence tool and are interested in understanding more of its underlying theory, as well as the assumptions associated with it. In short, while the first chapter was aimed more at a beginning user, this one is aimed more at an intermediate user. Nevertheless, some sections have seen little changes.

On the non-closure of particle backscattering coefficient in oligotrophic oceans

Many studies have consistently found that the particle backscattering coefficient (bbp) in oligotrophic oceans estimated from remote-sensing reflectance (Rrs) using semi-analytical algorithms is higher than that from in situ measurements. This overestimation can be as high as ~300% for some oligotrophic ocean regions. Various sources potentially responsible for this discrepancy are examined. Further, after applying an empirical algorithm to correct the impact from Raman scattering, it is found that bbp from analytical inversion of Rrs is in good agreement with that from in situ measurements, and that a closure is achieved.

The potential of high-frequency profiling to assess vertical and seasonal patterns of phytoplankton dynamics in lakes: An extension of the Plankton Ecology Group (PEG) model

Abstract 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 the 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 models 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.

Diurnal variations of the optical properties of phytoplankton in a laboratory experiment and their implication for using inherent optical properties to measure biomass

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.

Microbial life under ice: metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered lakes

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.

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered Lakes: Sub-ice Verrucomicrobia genomes in Quebec lakes

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 Wiley & Sons Ltd.

Cultivation of an algae-bacteria consortium in wastewater from an industrial park: Effect of environmental stress and nutrient deficiency on lipid production

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 parks 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.

Bio-optical Modeling of Sun-Induced Chlorophyll- a Fluorescence

Abstract 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.