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In the present study, we developed a new Swedish phosphorus diatom index (PDISE) to improve the poor fit of existing indices to match the needs of water managers to detect and mitigate eutrophication. We took advantage of a large amount of data (820 Swedish sites) collected in recent years. During our work, we found an unexpected bimodal response of the diatom taxa to phosphorus, with the taxa clustering into either an assemblage with a low, or with a high site-specific averaged optimum comprised of the diatom taxa optima. We could not find a characteristic diatom assemblage for sites with intermediate TP-site-specific averaged optima. To our knowledge, this bimodal community response has not been shown earlier. We found that the PDISE responded better than the currently used TDI and IPS to changes in TP concentrations, and thus should replace the TDI in the Swedish standard method. The modeled sensitivity values (expressed as categories) for TP were different compared to the TDI for most of the taxa included in the index development, indicating that the realized niche for these morphotaxa was different between Sweden and the UK where the TDI was developed originally. The correlation of the PDISE to TP was among the highest reported for other diatom nutrient indices globally, thus we believe that it might be worth to test it for other bioregions with similar geography and climate.

Zoosporic parasites (i.e. fungi and fungi-like aquatic microorganisms) constitute important drivers of natural populations, causing severe host mortality. Economic impacts of parasitic diseases are notable in the microalgae biotech industry, affecting production of food ingredients, biofuels, pharma- and nutraceuticals. While scientific research on this topic is gaining traction by increasing studies elucidating the functional role of zoosporic parasites in natural ecosystems, we are currently lacking integrated and interdisciplinary efforts for effectively detecting and controlling parasites in the microalgae industry. To fill this gap we propose to establish an innovative, dynamic European network connecting scientists, industries and stakeholders to optimize information exchange, equalize access to resources and to develop a joint research agenda. ParAqua aims at compiling and making available all information on the occurrence of zoosporic parasites and their relationship with hosts, elucidate drivers and evaluate impacts of parasitism in natural and man-made aquatic environments. We aim to implement new tools for monitoring and prevention of infections, and to create protocols and a Decision Support Tool for detecting and controlling parasites in the microalgae biotech production. Applied knowledge on zoosporic parasites can feed back from industry to ecology, and we therefore will explore whether the developed tools can be applied for monitoring lakes and reservoirs. Short-Term Scientific Missions and Training Schools will be organised specifically for early stage scientists and managers – with a specific focus on ITC – with the aim to share and integrate both scientific and applied expertise and increase exchange between basic and applied researchers and stakeholders.

Diatoms, a unique group of algae colonising a wide range of aquatic habitats and contributing to human well-being in many ways. We list and summarise these services using the classification of the Millennium Ecosystem Assessment (MEA), i.e. supporting, regulating, provisioning and cultural services. The most relevant supporting services are photosynthesis and primary production, as well as sediment formation. They also play a key role in nutrient cycling and habitat provisioning and serve as food for many organisms. Regulating services as oxygen production, climate control or sediment stabilisation are difficult to discuss without diatoms. Many provisioning services, directly used by humans, can be obtained from diatoms. These are tangible products such as medicines and immunostimulants but direct technologies such as wastewater treatment, micro- and nanotechnologies were also developed using diatoms. Studying of the past, present, and future linked to diatoms as a tool for palaeolimnology, ecological status assessment of waters and climate modelling is essential. Finally, the impressive morphology and ornaments of diatom frustules make them one of the most spectacular microorganisms, inspiring artists or providing a number of educational opportunities. Therefore, protecting aquatic habitats they inhabit is not simply a nature conservation issue but the key for human well-being in the future.

International audience; Permanent ponds are valuable freshwater systems and biodiversity hotspots. They provide diverse ecosystem services (ES), including water quality improvement and supply, food provisioning and biodiversity support. This is despite being under significant pressure from multiple anthropogenic stressors and the impacts of ongoing global change. However, ponds are largely overlooked in management plans and legislation, and ecological research has focused on large freshwater ecosystems, such as rivers or lakes. Protection of ponds is often insufficient or indirectly provided via associated habitats such as wetlands. This phenomenon is likely exacerbated due to lacking a full-scale understanding of the importance of ponds. In this review, we provided a detailed overview of permanent ponds across Europe, including their usages and the biodiversity they support. By discussing the concepts of pondscape and metacommunity theory, we highlighted the importance of connectivity among and between ponds and identified fluxes of emerging insects as another ES of ponds. Those insects are rich in essential nutrients such as polyunsaturated fatty acids (PUFA), which are delivered through them to the terrestrial environment, however the extent and impact of this ES remains largely unexplored. Several potential stressors, especially related to ongoing global change, which influence pond diversity and integrity were discussed. To conclude this review, we provided our insights on future pond management. Adaptive measures, taking into account the pond system per se within the pondscape, were found to be the most promising to mitigate the loss of natural ponds and restore and conserve natural small water bodies as refuges and diversity hotspots in increasingly urbanized landscapes.

Highlights • Amplicon Sequence Variants (ASVs) are a promising unit for diatom nutrient indices. • Diatom indices based on morphology, ASVs and traits were related to TotP concentrations. • Correlations of indices to TotP was best for ASVs, followed by morphology and traits. We developed and compared the performance of freshwater benthic diatom indices calculated from (i) traditional morphological species identification, (ii) Amplicon Sequence Variants (ASVs) obtained via DNA metabarcoding, and (iii) morphological traits to indicate eutrophication in rivers and lakes in Fennoscandia. Based on the results, we provided recommendations for the future routine use of diatom bioassessment tools in environmental monitoring and assessment. Our results show that ASVs are the most promising candidates to be used in environmental assessment. Indices based on ASVs correlated better with TotP concentrations than morphological taxa data, whereas the trait indices correlated least. We could see by studying the taxonomic assignments of the ASVs that traditional morphotaxa were divided up into several ASVs with different ecological profiles, which explained part of the better index performance and also encourages further studies on diatom diversity and ecological preferences. In general, ASV- and morphotaxon-specific optima differed slightly between streams and lakes, but were significantly correlated with each other. This means that it should be possible to develop a common index that is applicable in both streams and lakes, but boundary values with respect to TotP might need to be set separately for them. More knowledge on diatom traits is required to enable their use for environmental assessment.

Karst ecosystems play a unique role as exceptional natural habitats in sustaining biodiversity. This study focuses on diatoms, a diverse group of microeukaryotes in the periphytic community of a karstic river. In a multi-microhabitat study along the Krka River (Croatia), our goal was to obtain a detailed overview of diatom diversity and community structure using morphological and molecular approaches, and to assess the applicability of eDNA metabarcoding as a reliable tool for biomonitoring assessment. The results revealed a relatively low agreement in the diatom community composition between the two approaches, but also provided complementary information, with no differences in beta diversity detected between microhabitats. The SIMPER analysis underlined the importance of the molecular approach in identifying diatom community composition, due to errors in distinguishing between deposited diatom cells that occurred in the morphological analysis. In contrast, the morphological approach indicated a clear diatom community separation along the river with a strong location effect. Despite certain differences, both approaches provided a feasible assessment of the ecological status according to the relationship to environmental pressures, classifying the Krka River as High (morphological approach) or Good (molecular approach) throughout the most of its course. Moreover, diatom diversity based on both approaches provides a reliable dataset applicable in routine monitoring assessment and offers a deeper understanding of the presented ecological status. The incompleteness of a reference database presents one major drawback of the molecular approach, which needs further updating in order to improve routine diatom metabarcoding.

During the past decade genetic approaches have been developed to monitor biodiversity in aquatic ecosystems. These enable access to taxonomic and genetic information from biological communities using DNA from environmental samples (e.g. water, biofilm, soil) and methods based on high-throughput sequencing technologies, such as DNA metabarcoding. Within the context of the Water Framework Directive (WFD), such approaches could be applied to assess Biological Quality Elements (BQE). These are used as indicators of the ecological status of aquatic ecosystems as part of national monitoring programs of the european network of 110,000 surface water monitoring sites with 79.5% rivers and 11% lake sites (Charles et al. 2020). A high-throughput method has the potential to increase our spatio-temporal monitoring capacity and to accelerate the transfer of information to water managers with the aim to increase protection of aquatic ecosystems. Good progress has been made with developing DNA metabarcoding approaches for benthic diatom assemblages. Technological innovation and protocol optimization have allowed robust taxonomic (species) and genetic (OTU, ESV) information to be obtained from which diatom quality indices can be calculated to infer ecological status to rivers and lakes. Diatom DNA metabarcoding has been successfully applied for biomonitoring at the scale of national river monitoring networks in several countries around the world and can now be considered technically ready for routine application (e.g. Apothéloz-Perret-Gentil et al. 2017, Bailet et al. 2019, Mortágua et al. 2019, Vasselon et al. 2019, Kelly et al. 2020, Pérez-Burillo et al. 2020, Pissaridou et al. 2021). However, protocols and methods used by each laboratory still vary between and within countries, limiting their operational transferability and the ability to compare results. Thus, routine use of DNA metabarcoding for diatom biomonitoring requires standardization of all steps of the metabarcoding procedure, from the sampling to the final ecological status assessment in order to define good practices and standards. Following previous initiatives which resulted in a CEN technical report for biofilm sampling and preservation (CEN 2018), a set of experiments was initiated during the DNAqua-Net WG2 diatom workshop (Cyprus, 2019) to focus on DNA extraction and PCR amplification steps in order to evaluate: i) the transferability and reproducibility of a protocol between different laboratories; ii) the variability introduced by different protocols currently applied by the scientific community. 19 participants from 14 countries performed DNA extraction and PCR amplification in parallel, using i) the same fixed protocol and ii) their own protocol. Experiments were performed by each participant on a set of standardized DNA and biofilm samples (river, lake, mock community). In order to specifically test the variability of DNA extraction and PCR amplification steps, all other steps of the metabarcoding process were fixed and the preparation of the Miseq sequencing was performed by only one laboratory. The variability within and between participants will be evaluated on DNA extracts quantity, taxonomic (genus, species) and genetic richness, community structure comparison and diatom quality index scores (IPS). We will also evaluate the variability introduced by different DNA extraction and PCR amplification protocols on diatom quality index scores and the final ecological status assessment. The results from this collaborative work will not serve to define “one protocol to rule them all”, but will provide valuable information to define guidelines and minimum requirements that should be considered when performing diatom metabarcoding for biomonitoring.

The process of travertine formation and carbonate deposition in the rivers is unique, delicate, and depends on the activity of algae and mosses. Although diatoms have been used extensively in hydrobiological studies, the comparative analysis data on diatom communities of the travertine barriers in karstic rivers are still scarce. The study aimed to detect the diatom composition on travertine barriers in the Una River, the large karstic river in Bosnia and Herzegovina. An integrated classical morphological identification approach with metabarcoding was applied on eight samples across the river length profile. Morphological analyses were performed using both light and scanning electron microscopes. Subsequent DNA metabarcoding of the chloroplastic gene 312bp rbcL was done. The DADA2 pipeline was used for the bioinformatic treatment of the demultiplexed MiSeq reads to infer Amplicon Sequence Variants (ASVs). ASVs were taxonomically assigned using the Diat.barcode v7 reference database. A total of 126 species were identified using the morphological approach, while 133 ASVs were taxonomically assigned to 58 unique taxa with the molecular approach. Diatom community structures in terms of molecular and morphological approaches were congruent with 49 shared species. Species from genera Gomphonema, Navicula and Encyonema were less assigned in molecular analysis. The most abundant taxa in the Una River are alkaliphilous, belonging to the genera Gomphonema, Nitzshia and Navicula. Although specific for their extremely good chemical status, the travertine barriers of the Una River are largely inhabited with meso-eutraphentic taxa.

This report presents the outcome of the joint work of PhD students and senior researchers working with DNA-based biodiversity assessment approaches with the goal to facilitate others the access to definitions and explanations about novel DNA-based methods. The work was performed during a PhD course (SLU PNS0169) at the Swedish University of Agricultural Sciences (SLU) in Uppsala, Sweden. The course was co-organized by the EU COST research network DNAqua-Net and the SLU Research Schools Focus on Soils and Water (FoSW) and Ecology - basics and applications. DNAqua-Net (COST Action CA15219, 2016-2020) is a network connecting researchers, water managers, politicians and other stakeholders with the aim to develop new genetic tools for bioassessment of aquatic ecosystems in Europe and beyond. The PhD course offered a comprehensive overview of the paradigm shift from traditional morphology-based species identification to novel identification approaches based on molecular markers. We covered the use of molecular tools in both basic research and applied use with a focus on aquatic ecosystem assessment, from species collection to the use of diversity in environmental legislation. The focus of the course was on DNA (meta)barcoding and aquatic organisms. The knowledge gained was shared with the general public by creating Wikipedia pages and through this collaborative Open Access publication, co-authored by all course participants.

International audience; Climate change is predicted to increase drought occurrence and severity in small continental watercourses. Here, we studied the structure and the functional diversity of benthic diatom assemblages in lowland intermittent and permanent watercourses of the Carpathian Basin. We assumed that the community structure of intermittent and permanent watercourses would be markedly different, and the functional diversity in both would be strongly influenced by autumn drought. We found that intermittent streams were primarily characterized by small-sized generalists and aerophilic taxa, while permanent watercourses were inhabited by large-sized planktic or fast moving groups. The functional richness was significantly lower in intermittent than in permanent streams. This decrease in the functional richness of benthic algal communities may negatively affect the functioning of lotic algal communities. We conclude that diatom assemblages in lowland intermittent watercourses are sensitive indicators of changes in ecosystem properties, and should be considered in appropriate evaluation and management of extreme climatic events on aquatic ecosystems.

International audience; Extensive studies on the taxonomic resolution required for bioassessment purposes have determined that resolution above species level (genus, family) is sufficient for their use as indicators of relevant environmental pressures. The high‐throughput se - quencing (HTS) and meta‐barcoding methods now used for bioassessment tradition - ally employ an arbitrary sequence similarity threshold (SST) around 95% or 97% to cluster sequences into operational taxonomic units, which is considered descriptive of species‐level resolution. In this study, we analyzed the effect of the SST on the resulting diatom‐based ecological quality index, which is based on OTU abundance distribution along a defined environmental gradient, ideally avoiding taxonomic as - signments that could result in high rates of unclassified OTUs and biased final values. A total of 90 biofilm samples were collected in 2014 and 2015 from 51 stream sites on Mayotte Island in parallel with measures of relevant physical and chemical param - eters. HTS sequencing was performed on the biofilms using the rbcL region as the genetic marker and diatom‐specific primers. Hierarchical clustering was used to group sequences into OTUs using 20 experimental SST levels (80%–99%). An OTU‐ based quality index (Idx OTU ) was developed based on a weighted average equation using the abundance profiles of the OTUs. The developed Idx OTU revealed significant correlations between the Idx OTU values and the reference pressure gradient, which reached maximal performance using an SST of 90% (well above species level delimi - tation). We observed an interesting and important trade‐off with the power to dis - criminate between sampling sites and index stability that will greatly inform future applications of the index. Taken together, the results from this study detail a thor - oughly optimized and validated approach to generating robust, reproducible, and complete indexes that will greatly facilitate effective and efficient environmental monitoring

International audience; Land-use imposes an important potential threat on the aquatic ecosystems of riverine habitats. In this study, DNA metabarcoding was used to assess the effect of land-use on diatom assemblages, with a special focus on cropland area as an integrative proxy for several direct-acting pressures. The so-called taxonomy-free approach was tested using exact sequence variants (ESVs) without pre-clustering and without assigning them to traditional taxonomy. Our hypothesis is that the taxonomy-free approach gives better interpretation of the effect of agricultural land use and it provides a more efficient index to indicate agricultural stress than the classical method with taxonomical clustering. Classical ordination techniques (PCA, NMDS) were performed to study the effects of cropland area proportion on diatom assemblages and a modified version of the Zelinka-Marvan equation for the index development. Results showed that (i) although ESVs provided better results when studying land-use effects on diatoms, taxonomic assignment after analysis was necessary to give ecological interpretations and that (ii) a better performing index could be developed by using the taxonomy-free approach. By using ESVs without taxonomic assignment, information on the ecology of sequences belonging to the same species and of unassigned sequences could be kept. New types of clustering methods are welcome in the future of biomonitoring where the delimitation of taxonomic units should be refined based on a higher emphasis on their ecology rather than on morphological or genetical criteria.

International audience; Climatic extreme events such as droughts (unpredictable), dry periods (predictable) or even flush floods, threaten freshwater ecosystems worldwide. The filtering mechanisms of these events and their strength on communities, however, can be different among regions. While time-for-adaptation theory defines whether or not water scarcity can be considered as disturbance, the stress-dominance theory predicts an increase in importance of environmental filtering and a decrease in the role of biotic interactions in communities with increasing environmental stress. Here, we tested whether environmental filtering (leading to trait convergence) or limiting similarity (leading to trait divergence) is the main assembly rule shaping the structure and trait composition of benthic diatom assemblages in Mediterranean (Portuguese) and continental (Hungarian) temporary and perennial streams. We assumed that the trait composition of diatom assemblages in the two stream types would be less different in the Mediterranean than in the continental region (addressed to time-for-adaptation theory). We also hypothesized that trait composition would be shaped by environmental filtering in the Hungarian streams while by biotic interactions in Portuguese streams (addressed to stress-dominance theory). Our results supported our first hypothesis since traits, which associated primarily to temporary streams were found only in the continental region. Our findings, however, only partially proved the stress-dominance hypothesis. In the continental region, where drying up of streams were induced by unpredictable droughts, biotic interactions were the main assembly rules shaping community structure. In contrast, environmental filtering was nearly as important as limiting similarity in structuring trait composition in the Mediterranean region during the predictable dry phase with no superficial flow. These analyses also highlighted that drought events (both predictable and unpredictable ones) have a complex and strong influence on benthic diatom assemblages resulting even in irreversible changes in trait composition and thereby in ecosystem functioning.

International audience; Benthic diatoms inhabiting littoral zones are regarded as promising bioindicators in lakes. Some pre-standard protocols were proposed and suggested to collect a single site per lake to assess its overall quality. In large lakes, such as Lake Geneva, a spatial heterogeneity of diatom assemblages was suspected, because of differing human pressures. Thirty-five sites were sampled along the shoreline in locations showing various population densities and crossed by rivers flowing into the lake. Different assemblages were found; one corresponded to more oligotrophic areas and was mostly situated on the shoreline next to low population densities; it was mostly composed of low-profile diatoms. A second one corresponded to more eutrophic areas and was mostly situated near densely inhabited areas; it was composed of many high-profile diatoms. A third one was in close vicinity to river inlets, with high abundances of motile diatoms. This last assemblage was spatially restricted to the river plume. After testing several diatom indices, one showed better capacities to assess nutrient level (EPI-L). If we avoid areas near river inlets, the ecological quality assessed with diatom indices ranged from moderate to high ecological status depending on the vicinity situated more or less near densely populated areas.

Diatoms are used routinely to assess pollution level in rivers and lakes. Current methods are based on identification by light microscopy, which is laborious. An alternative is to identify species based on short DNA fragments and High-Throughput Sequencing (HTS). However a potential limitation is the incomplete coverage of species in reference barcode libraries. Usually these libraries are compiled by isolating cells, before culturing and sequencing them, which is tedious and often unsuccessful. Here we propose the use of rbcL sequences from environmental samples analysed by HTS. We set several criteria to ensure good sequence quality and correspondence with the target species observed in microscopy: the sequence needed to be abundant in the sample, and with no insertions nor deletions or stop codon, phylogenetic neighbour taxa had to correspond to neighbour taxonomic taxa expected from morphological observations. Four species from tropical rivers are given as examples, including one that is new to science. info:eu-repo/semantics/publishedVersion

International audience; 1. In recent years, remarkable progress has been made in developing environmental DNA metabarcoding. However, its ability to quantify species relative abundance remains uncertain, limiting its application for biomonitoring. In diatoms, although the rbcL gene appears to be a suitable barcode for diatoms, providing relevant qualitative data to describe taxonomic composition, improvement of species quantifica-tion is still required. 2. Here, we hypothesized that rbcL copy number is correlated with diatom cell biovol-ume (as previously described for the 18S gene) and that a correction factor (CF) based on cell biovolume should be applied to improve taxa quantification. We carried out a laboratory experiment using pure cultures of eight diatom species with contrasted cell biovolumes in order to (1) verify the relationship between rbcL copy numbers (estimated by qPCR) and diatom cell biovolumes and (2) define a potential CF. In order to evaluate CF efficiency, five mock communities were created by mixing different amounts of DNA from the eight species, and were sequenced using HTS and targeting the same rbcL barcode. 3. As expected, the correction of DNA reads proportions by the CF improved the congruence between morphological and molecular inventories. Final validation of the CF was obtained on environmental samples (metabarcoding data from 80 ben-thic biofilms) for which the application of CF allowed differences between molecular and morphological water quality indices to be reduced by 47%. 4. Overall, our results highlight the usefulness of applying a CF factor, which is effective in reducing over-estimation of high biovolume species, correcting quantitative biases in diatom metabarcoding studies and improving final water quality assessment. K E Y W O R D S benthic diatom, biovolume correction factor, freshwater ecosystems, gene copy number variation, quantitative metabarcoding

At low trophic state, stable stratified water columns may provide favorable conditions for adapted phytoplankton species to form deep chlorophyll maxima (DCM). Such maxima occur regularly in Lake Stechlin, mainly contributed by the cyanobacterial species Cyanobium sp. and occasionally by Planktothrix rubescens. In the early twenty-first century, a rapid invasion by nostocalean cyanobacteria occurred in the lake and a number of Dolichospermum species together with Aphanizomenon flos-aquae appeared. As revealed by both microscopic and fluorimetric methods, during the summer stratification of 2013, a multispecific DCM was formed by Cyanobium, Planktothrix rubescens, and A. flos-aquae, however with spatial segregation. Planktothrix occurred in the upper hypolimnion, Aphanizomenon and Cyanobium dominated in the metalimnetic layer. Coexistence of these three cyanoprokaryota is possibly the consequence of different environmental factors limiting them (light, availability of N and P). This study represents a rare case when spatial niche segregation of phytoplankton species occurs in close to equilibrium conditions. DCM formed by Aphanizomenon and Cyanobium was detected by the fluoroprobe; Planktothrix with its different pigment compositions remained largely hidden. Our results indicate the necessity of parallel microscopic investigations and the need of careful calibration when fluorimetric methods are used for detecting cyanobacterial populations.

International audience; Diatoms are excellent ecological indicators of water quality because they are broadly distributed, they show high species diversity and they respond rapidly to human pressures. In Europe, the Water Framework Directive (WFD) gives the legal basis for the use of this indicator for water quality assessment and its management. Several quality indices, like the Specific Polluosensitivity Index (SPI), were developed to assess the ecological quality status of rivers based on diatom communities. It is based on morphological identifications and count of diatom species present in natural biofilms using a microscope. This methodology requires high taxonomic skills and several hours of analysis per sample as 400 individuals must be identified to species level. Since several years, a molecular approach based on DNA metabarcoding combined to High-Throughput Sequencing (HTS) is developed to characterize species assemblages in environmental samples which is potentially faster and cheaper. The ability of this approach to provide reliable diatom inventories has been demonstrated and its application to water quality assessment is currently being improved. Despite optimization of the DNA metabarcoding process with diatoms, few studies had yet extended it at the scale of a freshwater monitoring network and evaluated the reliability of its quality assessment compared to the classical morphological approach. In the present study we applied DNA metabarcoding to the river monitoring network of the tropical Island Mayotte. This island is a French departement since 2011 and the WFD has to be applied. This offered the opportunity to scale up the comparison of molecular and morphological approaches and their ability to produce comparable community inventories and water quality assessments. Benthic diatoms were sampled following WFD standards in 45 river sites in 2014 and 2015 (80 samples). All samples were submitted in parallel to the molecular and the morphological approaches. DNA metabarcoding was carried out using Genelute DNA extraction method, rbcL DNA barcode and PGM sequencing, while microscopic counts were carried out for the classical methodology. Diatom community structures in terms of molecular (OTUs) and of morphological (species) were significantly correlated. However, only 13% of the species was shared by both approaches, with qualitative and quantitative variation due to i) the incompleteness of the reference library (82% of morphological species are not represented in the database), ii) limits in taxonomic knowledge and iii) biases in the estimation of relative abundances linked to diatom cell biovolume. However, ecological quality status assessed with the molecular and morphological SPI values were congruent, and little affected by sequencing depth. DNA metabarcoding of diatom communities allowed a reliable estimation of the quality status for most of the rivers at the scale of the full biomonitoring network of Mayotte Island.

Diatom-based ecological quality assessment methods have been implemented and used regularly in the Water Framework Directive. These indices use the species' abundance profiles along a specific environmental gradient, which they aim to assess. However, this approach has several problematic issues including the unstable and fast-changing diatom taxonomy. The use of traits can be a solution if their responses to the environmental pressure are well-defined. Here, we developed taxonomy-based and trait-based diatom assemblage indices to assess the ecological status of riverine sites on a tropical island. The two indices are based on two sub-indices that measure the diatom assemblage response to a nutrient and organic matter/turbidity gradient. Both taxonomy- and trait-based indices correlated significantly with the selected environmental gradients of the test database, which was not used during index development. We showed that traits could be used for quality assessment of the Mayotte rivers and require much less effort than taxonomy-based indices. There were differences between the two types of indices, which are discussed in this paper. As a perspective for further studies, tests of trait-based indices among different eco-regions would be challenging.

Freshwaters worldwide face serious threats, making their protection increasingly important. Freshwater monitoring has historically produced valuable data and continues to develop. Rapid improvements to biomolecular techniques are revolutionizing the way scientists describe biological communities and are bringing about major changes in biomonitoring. Combined with high-throughput sequencing, DNA metabarcoding is fast and cost-effective, generating massive amounts of data. In a world with numerous ecological threats, "big data" constitute a tremendous opportunity to improve the efficiency of biological monitoring. These fundamental changes in biomonitoring will require freshwater ecologists and environmental managers to reconsider how they handle large amounts of data.

International audience; A high number of species often represents a relevant redundancy in terms of ecological adaptation strategies. Collecting species to groups based on their functional adaptations can handle this redundancy and obtain the "real" functional complexity of ecosystems. Functional traits are proxies of adaptation strategies under particular environmental conditions, and a set of functional traits are interpreted as life-strategies. Organisms with life-strategies occupying a similar niche can be collected in ecological groups (functional group/guild). In this study, we review the latest trait-based approaches and existing attempts at functional classifications in phytobenthos studies. Advantages and shortcomings of these classifications are discussed with perspectives of their utility in ecological status assessment.

In winter of 2009/2010, Aphanizomenonflos-aquae bloomed in the ice and snow covered oligo-mesotrophic Lake Stechlin, Germany. The photosynthesis of the natural population was measured at eight temperatures in the range of 2–35°C, at nine different irradiance levels in the range of 0–1,320 μmol m−2 s−1 PAR at each applied temperature. The photoadaptation parameter (Ik) and the maximum photosynthetic rate (Pmax) correlated positively with the temperature between 2 and 30°C, and there was a remarkable drop in both parameters at 35°C. The low Ik at low temperatures enabled the active photosynthesis of overwintering populations at low irradiance levels under ice and snow cover. The optimum of the photosynthesis was above 20°C at irradiances above 150 μmol m−2 s−1. At lower irradiance levels (7.5–30 μmol m−2 s−1), the photosynthesis was the most intensive in the temperature range of 2–5°C. The interaction between light and temperature allowed the proliferation of A. flos-aquae in Lake Stechlin resulting in winter water bloom in this oligo-mesotrophic lake. The applied 2°C is the lowest experimental temperature ever in the photosynthesis/growth studies of A. flos-aquae, and the results of the P–I and P–T measurements provide novel information about the tolerance and physiological plasticity of this species.

International audience; Over the last decades, mass developments by the filamentous conjugating green alga Mougeotia have been followed in three large peri-alpine lakes (Lake Geneva, Lake Garda, Lake Maggiore) and in the sub-tropical Lake Kinneret. The aim of this study is to highlight annual and interannual patterns of Mougeotia biomass in the studied lakes and select key environmental parameters that may favour and maintain its mass development. Our results confirm former studies that planktic Mougeotia favours meso-oligotrophic conditions and becomes dominant when annual mean total phosphorus concentrations in the epilimnion fall below 20 A mu g l(-1). This triggering factor has effect with interactions of other environmental circumstances such as the water column stability. Physiological and morphological features of the taxon make it a successful competitor under stratified conditions. Results also showed that in three out of the four studied lakes, the annual peak was higher when the annual population development started earlier. Focusing on Lake Geneva, depth and strength of the thermocline, as well as wind speed in the beginning of summer that can cause nutrient replenishment and mix the epilimnion are key factors in the blooming of the taxon.