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Diatoms are a very diverse group of microalgae that encompass about 100 000 taxa. This makes an excellent bioindicator especially of rivers. The majority of biotic indices based on diatoms are constructed on species pollution-sensitivities. Nevertheless, recent studies showed the interest to use complementary metrics for biomonitoring: life-forms, cell-sizes and ecological guilds. Unfortunately, taxa memberships to such metrics are scattered in numerous floras and papers. Therefore, studies using such metrics often referred to grey literature or home-made checklists. The objective of this paper is to make available to the scientific community an important check-list of taxa frequently observed in European rivers with their memberships to these metrics. After defining these metrics, 1115 taxa were codified using Biofresh and Omnidia codes in an Excel file. Metrics memberships were then explored in a taxonomical framework. It clearly appears that metrics memberships are determined by taxonomy. Life-forms and cell sizes taxa memberships and their study in the framework of evolutionary history of diatoms is a field that is worth studying for a better understanding of diatoms ecology. Such inputs should be beneficial for the future improvement of diatom-based monitoring tools.

For almost two years (2006–2007), phytoplankton structure and distribution were monitored using a combination of methods in the Marne Reservoir (France). We used the bbe FluoroprobeTM spectrofluorometer, which provides vertical profiles for different algal classes and chlorophyll analysis, based on the in vivo autofluorescence characteristics of the phytoplankton. In parallel, we measured chlorophyll a (chl a) concentrations using the classical extraction method coupled with spectrophotometric analyses, and calculated the biovolume of all the taxa identified using inverted light microscopy. A very close correlation (ρ = 0.93, n = 243, p < 0.0001) was found between the total equivalent chl a concentrations given by the bbe FluoroprobeTM and the total chl a concentrations (g·L−1) provided by the spectrophotometric analysis. The closest correlation was obtained for concentrations below 6.9 μg·L−1 whereas little or no correlation was found for those above 21.6 μg·L−1. The relationship was highly significant when total phytoplankton biovolume was compared with data from the probe (ρ = 0.6, n = 243, p < 0.0001), the strongest correlation being found for the group composed of diatoms, dinoflagellates and chrysophyceae (ρ = 0.67, p < 0.0001), while the weakest relationship was for the blue-green cyanobacteria (ρ = 0.33, p < 0.0001), although it was still highly significant. Our analysis, based on a large dataset, indicates that the FluoroprobeTM appears to be a reliable tool suitable for use by fresh water managers to monitor phytoplankton on any relevant time and space scales.

Organic contaminants, and herbicides in particular, represent a risk for aquatic ecosystems. The primary target of herbicides are producers, the base of food webs, but frequently they end up far from the application point affecting non-target species. Its presence can work as sub-lethal stimulus, which sort the genetic and phenotypic differences within a species. Intraspecific variation allows adaptation to changes in the environment but also to new niches due to variations in species’ sensitivity and biochemical response to a certain chemical. A better understanding of these variations can lead to the development of improved strategies for ecosystem protection. This research aimed to compare a sensitive and a tolerant strain of the freshwater diatom Nitzschia palea to atrazine. Strains were exposed to three concentrations within their tolerance range, during 96 h. The activity of the antioxidant enzymes superoxide dismutase, catalase, glutathione-S-transferases and glutathione peroxidases was determined. In addition, chlorophylls a and c, carotenoids, reduced glutathione, proteins and lipid peroxidation were quantified. Both strains displayed different strategies to deal with atrazine toxicity: while the sensitive strain decreased the oxidative stress, increasing the activity of antioxidant enzymes such as superoxide dismutase, the tolerant strain invested in conjugation pathways and carotenoids’ maintenance. [ABSTRACT FROM AUTHOR]

Benthic diatoms are relevant indicators of the ecological status of the littoral zone of lakes. Their use as bio-indicators is based on their morphological identification at species level using microscopy which is time consuming, requires taxonomic expertise, and is consequently expensive. To overcome these limitations, a molecular approach for diatom identification has been tested with success in rivers. DNA metabarcoding enables species identification from a standardized DNA barcode and high-throughput sequencing (HTS), using DNA reference library. The suitability of the morphological and molecular approaches to assess the diatom community structure and the ecological status of the littoral zone of the largest deep lake in France (Lake Bourget) was compared. 66 sites were sampled in August 2015 along the shoreline, all around the lake. The composition of diatom assemblages was similar with both morphological and molecular approaches, and diatom assemblages were structured by the same environmental factors. However, the ecological status of Lake Bourget differed significantly among approaches since floristic inventories to species level also differed significantly. The main source of this difference was the incompleteness of the DNA reference library. Nevertheless, in a near future, when this constraint will be solved, the use of DNA metabarcoding for biomonitoring purposes seems promising. [ABSTRACT FROM AUTHOR]

Ecological status assessment of watercourses is based on the calculation of quality indices using pollution sensitivity of targeted biological groups, including diatoms. The determination and quantification of diatom species is generally based on microscopic morphological identification, which requires expertise and is time-consuming and costly. In Europe, this morphological approach is legally imposed by standards and regulatory decrees by the Water Framework Directive (WFD). Over the past decade, a DNA-based molecular biology approach has newly been developed to identify species based on genetic criteria rather than morphological ones (i.e. DNA metabarcoding). In combination with high throughput sequencing technologies, metabarcoding makes it possible both to identify all species present in an environmental sample and to process several hundred samples in parallel. This article presents the results of two recent studies carried out on the WFD networks of rivers of Mayotte (2013–2018) and metropolitan France (2016–2018). These studies aimed at testing the potential application of metabarcoding for biomonitoring in the context of the WFD. We discuss the various methodological developments and optimisations that have been made to make the taxonomic inventories of diatoms produced by metabarcoding more reliable, particularly in terms of species quantification. We present the results of the application of this DNA approach on more than 500 river sites, comparing them with those obtained using the standardised morphological method. Finally, we discuss the potential of metabarcoding for routine application, its limits of application and propose some recommendations for future implementation in WFD.

Biomonitoring is central to the European Union's Water Framework Directive (WFD) and to the French water and aquatic environmental law, but most diatom indices do not separate different anthropogenic impacts. To address this gap, the effect of water chemistry on diatom ecological guilds and life forms was assessed in order to indicate stream perturbations. Generalised additive models (GAMs) were built on a large-scale data set of 1571 samples from the French monitoring network. The relationships between diatom ecological guild and life form metrics were investigated by Principal components analysis and the results predicted by GAMs. The models characterised eight chemical parameters that modified adaptive strategies (ecological guilds) and growth morphology (life forms). Total phosphorus, conductivity, nitrate and pH are the main influencing factors, followed by temperature, dissolved oxygen and organic matter. The findings confirm three groups of diatoms with different adaptive strategies: 1 – fast moving species, 2 – species growing close to the substrate and 3 – species extending to the surface layers of the biofilm. Thirteen diatom metrics displayed a variety of responses to different ranges of the eight chemical parameters. These metrics could be used to help to identify and quantify which chemical alterations are caused by polluted effluents in rivers.

Post-mining reservoirs are distinguished by characteristic environmental conditions where specific diatom communities can be observed. Reservoirs created as a part of the reclamation plan after human mining activities are marked by unique chemical and physical water parameters. In the course of research on the diatoms from Bogdałów reservoir, we examined the taxonomic and morphological diversity of Nitzschia taxa from the section Lanceolatae occurring in a post-mining lignite reservoir. Our study describes a new species of Nitzschia from a post-mining reservoir, Nitzschianandorii Olszyński, Zakrzewski & Żelazna-Wieczorek, sp. nov. Morphometry and morphology analyses of new species were performed with light and scanning electron microscopy. Chloroplast morphology analysis was conducted with differential interference contrast microscopy and confocal laser scanning microscopy. Molecular data from SSU 18S, rbcL and psbC sequences were obtained from cultures of this taxon. Differential diagnosis of Nitzschianandorii Olszyński, Zakrzewski & Żelazna-Wieczorek, sp. nov. with co-occurring taxa: N.lacuum and N.alpinobacillum was performed using morphological traits and nMDS analysis of the valves' morphometry., Competing Interests: The authors have declared that no competing interests exist., (Rafał M. Olszyński, Piotr K. Zakrzewski, Frédéric Rimet, Julia Sulkowska, Łukasz Peszek, Joanna Żelazna-Wieczorek.)

Phytoplankton is a key biological group used to assess the ecological status of lakes. The classical monitoring approach relies on microscopic identification and counting of phytoplankton species, which is time-consuming and requires high taxonomic expertise. High-throughput sequencing, combined with metabarcoding, has recently demonstrated its potential as an alternative approach for plankton surveys. Several studies have confirmed the relevance of the diatom metabarcoding approach to calculate biotic indices based on species ecology. However, phytoplankton communities have not yet benefited from such validation. Here, by comparing the results obtained with the two methods (molecular and microscopic counting), we evaluated the relevance of metabarcoding approach for phytoplankton monitoring by considering different metrics: alpha diversity, taxonomic composition, community structure and a phytoplankton biotic index used to assess the trophic level of lakes. For this purpose, 55 samples were collected in four large alpine lakes (Aiguebelette, Annecy, Bourget, Geneva) during the year 2021. For each sample, a metabarcoding analysis based on two genetic markers (16S and 23S rRNA) was performed, in addition to the microscopic count. Regarding the trophic level of lakes, significant differences were found between index values obtained with the two approaches. The main hypothesis to explain these differences comes from the incompleteness, particularly at the species level, of the barcode reference library for the two genetic markers. It is therefore necessary to complete reference libraries for using such species-based biotic indices with metabarcoding data. Besides this, species richness and diversity were higher in the molecular inventories than in the microscopic ones. Moreover, despite differences in taxonomic composition of the floristic lists obtained by the two approaches, their community structures were similar. These results support the possibility of using metabarcoding for phytoplankton monitoring but in a different way. We suggest exploring alternative approaches to index development, such as a taxonomy-free approach., Competing Interests: Declaration of competing interest The achievement of this manuscript has not been influenced by competing financial, personal, or professional interests., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Freshwater algae exhibit complex dynamics, particularly in meso-oligotrophic lakes with sudden and dramatic increases in algal biomass following long periods of low background concentration. While the fundamental prerequisites for algal blooms, namely light and nutrient availability, are well-known, their specific causation involves an intricate chain of conditions. Here we examine a recent massive Uroglena bloom in Lake Geneva (Switzerland/France). We show that a certain sequence of meteorological conditions triggered this specific algal bloom event: heavy rainfall promoting excessive organic matter and nutrients loading, followed by wind-induced coastal upwelling, and a prolonged period of warm, calm weather. The combination of satellite remote sensing, in-situ measurements, ad-hoc biogeochemical analyses, and three-dimensional modeling proved invaluable in unraveling the complex dynamics of algal blooms highlighting the substantial role of littoral-pelagic connectivities in large low-nutrient lakes. These findings underscore the advantages of state-of-the-art multidisciplinary approaches for an improved understanding of dynamic systems as a whole., Competing Interests: Competing interestsThe authors declare no competing interests., (© The Author(s) 2024.)

Little is still known about the low dose effects of radiation on the microbial communities in the environment. Mineral springs are ecosystems than can be affected by natural radioactivity. These extreme environments are, therefore, observatories for studying the influence of chronic radioactivity on the natural biota. In these ecosystems we find diatoms, unicellular microalgae, playing an essential role in the food chain. The present study aimed to investigate, using DNA metabarcoding, the effect of natural radioactivity in two environmental compartments (i.e. spring sediments and water) on the genetic richness, diversity and structure of diatom communities in 16 mineral springs in the Massif Central, France. Diatom biofilms were collected during October 2019, and a 312 bp region of the chloroplast gene rbcL (coding for the Ribulose Bisphosphate Carboxylase) used as a barcode for taxonomic assignation. A total of 565 amplicon sequence variants (ASV) were found. The dominant ASV were associated with Navicula sanctamargaritae, Gedaniella sp., Planothidium frequentissimum, Navicula veneta, Diploneis vacillans, Amphora copulata, Pinnularia brebissonii, Halamphora coffeaeformis, Gomphonema saprophilum, and Nitzschia vitrea, but some of the ASVs could not be assigned at the species level. Pearson correlation failed to show a correlation between ASV' richness and radioactivity parameters. Non-parametric MANOVA analysis based on ASVs occurrence or abundances revealed that geographical location was the main factor influencing ASVs distribution. Interestingly, 238 U was the second factor that explained diatom ASV structure. Among the ASVs in the mineral springs monitored, ASV associated with one of the genetic variants of Planothidium frequentissimum was well represented in the springs and with higher levels of 238 U, suggesting its high tolerance to this particular radionuclide. This diatom species may therefore represent a bio-indicator of high natural levels of uranium., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Diatoms are widely used as ecological indicators and show various degrees of endemism. Many studies that support the idea of endemic species integrate several climate zones, a variety of ecosystem types, and often focus on a global scale. Here, we investigated whether endemism could be detected when considering a homogeneous type of ecosystem in a single climate zone. We sampled stone biofilms at 40-50 cm depth in high-altitude lakes in the Alpine climate zone. A total of 149 samples were obtained from the French and Georgian mountains, two areas separated by ∼3000 km. Using Amplicon Sequence Variants derived from DNA metabarcoding, we assessed taxonomic turnover and Zeta-diversity (a measure of endemism). We ran haplotype networks and phylogenetic tests to measure geographical signal in the phylogenies of dominant taxa. The French and Georgian communities shared 51 % of species. Species that were not shared across both regions were mostly rare, and often not characteristic of lakes but of neighboring habitats instead. In contrast, at the sub-species level, 87 % of the genotypes showed restricted distributions. Whereas endemism was the rule at sub-species level, most species were shared across both French and Georgian lakes, suggesting that geographic barriers strongly limited dispersal at the sub-species level but not species level. Dominant species hosted higher levels of sub-specific diversity than rare species. In contrast to global-scale studies, we did not find any significant geographical structuring in the phylogeny of the investigated species. This could indicate ongoing dispersal at a frequency fast enough to prevent allopatric divergence, yet slow enough to prevent sharing most haplotypes between France and Georgia. These results have implications for biomonitoring: depending on the taxonomic level chosen, robust generic tools (species level) or tools dedicated to a region able to discriminate fine pressures differences (sub-species level) may be developed., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Environmental filtering is often found to dominate assembly rules in diatoms. These microalgae are diverse, especially at subspecies level, and tend to exhibit a niche phylogenetic conservatism. Therefore, other rules, such as competition or mass effects, should be detectable when environmental gradients and dispersal barriers are limited. We used metabarcoding to analyse benthic littoral diatom communities in 153 sites in a large lake (Geneva) exhibiting weak geographical barriers and weak environmental gradients outside river estuaries. We assessed assembly rules using variance partitioning, phylogenetic and source tracking analyses. No phylogenetic over-dispersion of communities, indicative of exclusive competition, was detected. Instead, we found these communities to be phylogenetically over-clustered, indicating environmental filtering, which was even stronger near river estuaries where environmental gradients are stronger. Finally, using a Bayesian method (SourceTracker), we found that rivers flowing into the lake bring communities that settle, especially in sites close to estuaries. Rivers with the highest discharges are primarily responsible for immigration, explaining 27% of lake composition. Therefore, despite favourable conditions to observe other rules, our results support that diatom communities are prominently assembled by environmental filtering and immigration processes, in particular from rivers. However, this does not exclude that other assembly rules may be at play at a finer spatial, temporal and/or phylogenetic scale., (© 2022 John Wiley & Sons Ltd.)