Co-occurrence, ecological profiles and geographical distribution based on unique molecular identifiers of the common freshwater diatoms Fragilaria and Ulnaria

Diatom taxonomy has evolved in recent years, with many new species described and new approaches such as molecular genetics showing the existence of cryptic diversity within currently accepted species. This cryptic diversity is not well understood even for common freshwater genera such as Fragilaria and Ulnaria. The purpose of our study was to define taxon-specific ecological profiles and geographical distributions for unique molecular identifiers (amplicon sequence variants, ASVs) linked to curated taxonomy for these genera. Our goal is to contribute to the development of ecological assessment methods, and to the understanding why we often observe so many diatom species co-occurring in a single sample. We filtered a large (770 samples) metabarcoding dataset with linked environmental data covering several countries in Europe for genetic variants (ASVs) assigned to currently accepted species of our target genera. We studied the geographical distribution of the ASVs, and tested for ASV-pair co-occurrence. We modelled ASV-specific preferences for pH, alkalinity, total nitrogen, total phosphorus and conductivity, and analysed their preference for lakes or streams as habitat. Our study confirmed that there seems to be no general geographical barrier for the distribution of freshwater benthic diatom ASVs in Europe, but that dispersal is not rapid enough to hide historical events. The Fragilaria and Ulnaria ASVs in our study showed considerable overlap in geographical distribution, habitat and ecological preferences. We found evidence that only large differences in preferences for the analysed water chemistry variables prevented the co-occurrence of ASVs at the same sites. Instead, Fragilaria and Ulnaria ASVs co-occurred frequently in samples. We found subtle differences in ecological preferences for some ASV pairs, which might in part explain the co-occurrence by the avoidance of direct competition. However, the great overlap in distribution and ecological preferences suggests that other factors not studied here were also responsible for the observed co-occurrences and high richness of ASVs found at many sites. To our knowledge, we are the first to use ASVs in combination with a curated taxonomy to understand co-occurrence, specific ecological profiles and large-scale geographical distribution for unique identifiers not biased by the quality of reference databases, clustering methods, or non-harmonized morphological identification. Thus, our results can now be used in subsequent projects to interpret ASV occurrences, e.g. for development of ecological assessment methods

Co-occurrence, ecological profiles and geographical distribution based on unique molecular identifiers of the common freshwater diatoms Fragilaria and Ulnaria

Diatom taxonomy has evolved in recent years, with many new species described and new approaches such as molecular genetics showing the existence of cryptic diversity within currently accepted species. This cryptic diversity is not well understood even for common freshwater genera such as Fragilaria and Ulnaria. The purpose of our study was to define taxon-specific ecological profiles and geographical distributions for unique molecular identifiers (amplicon sequence variants, ASVs) linked to curated taxonomy for these genera. Our goal is to contribute to the development of ecological assessment methods, and to the understanding why we often observe so many diatom species co-occurring in a single sample. We filtered a large (770 samples) metabarcoding dataset with linked environmental data covering several countries in Europe for genetic variants (ASVs) assigned to currently accepted species of our target genera. We studied the geographical distribution of the ASVs, and tested for ASV-pair co-occurrence. We modelled ASV-specific preferences for pH, alkalinity, total nitrogen, total phosphorus and conductivity, and analysed their preference for lakes or streams as habitat. Our study confirmed that there seems to be no general geographical barrier for the distribution of freshwater benthic diatom ASVs in Europe, but that dispersal is not rapid enough to hide historical events. The Fragilaria and Ulnaria ASVs in our study showed considerable overlap in geographical distribution, habitat and ecological preferences. We found evidence that only large differences in preferences for the analysed water chemistry variables prevented the co-occurrence of ASVs at the same sites. Instead, Fragilaria and Ulnaria ASVs co-occurred frequently in samples. We found subtle differences in ecological preferences for some ASV pairs, which might in part explain the co-occurrence by the avoidance of direct competition. However, the great overlap in distribution and ecological preferences suggests that other factors not studied here were also responsible for the observed co-occurrences and high richness of ASVs found at many sites. To our knowledge, we are the first to use ASVs in combination with a curated taxonomy to understand co-occurrence, specific ecological profiles and large-scale geographical distribution for unique identifiers not biased by the quality of reference databases, clustering methods, or non-harmonized morphological identification. Thus, our results can now be used in subsequent projects to interpret ASV occurrences, e.g. for development of ecological assessment methods

Ecosystem services provided by freshwater and marine diatoms

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

Autumn drought drives functional diversity of benthic diatom assemblages of continental intermittent streams

International audienceClimate 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

Presence, variation, and potential ecological impact of microplastics in the largest shallow lake of Central Europe

The presence of microplastics (MPs) in the global ecosystem has generated a rapidly growing concern worldwide. Although their presence in the marine environment has been well-studied, much less data are available on their abundance in freshwaters. MPs alone and in combination with different chemicals has been shown to cause acute and chronic effects on algae and aquatic invertebrate and vertebrate species at different biological levels. However, the combined ecotoxicological effects of MPs with different chemicals on aquatic organisms are still understudied in many species and the reported data are often controversial. In the present study, we investigated, for the first time, the presence of MPs in Lake Balaton, which is the largest shallow lake of Central Europe and an important summer holiday destination. Moreover, we exposed neonates of the well-established ecotoxicological model organism Daphnia magna to different MPs (polystyrene [3 μm] or polyethylene [≤ 100 μm]) alone and in combination with three progestogen compounds (progesterone, drospirenone, levonorgestrel) at an environmentally relevant concentration (10 ng L−1) for 21 days. The presence of 7 polymer types of MPs in the size range of 50–100 μm was detected in Lake Balaton. Similarly to the global trends, polypropylene and polyethylene MPs were the most common types of polymer. The calculated polymer-independent average particle number was 5.5 particles m−3 (size range: 50 μm – 100 μm) which represents the values detected in other European lakes. Our ecotoxicological experiments confirmed that MPs and progestogens can affect D. magna at the behavioral (body size and reproduction) and biochemical (detoxification-related enzyme activity) levels. The joint effects were negligible. The presence of MPs may lead to reduced fitness in the aquatic biota in freshwaters such as Lake Balaton, however, the potential threat of MPs as vectors for progestogens may be limited

Spatial heterogeneity of littoral benthic diatoms in a large lake: monitoring implications

International audienceBenthic 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

Data supplementing the article "Assessing ecological status with diatoms DNA metabarcoding : scaling-up on a WFD monitoring network (Mayotte island, France)" V. Vasselon, F. Rimet, K. Tapolczai, A. Bouchez submitted to Ecological Indicators journal

These data supplement the article"Assessing ecological status with DNA metabarcoding or microscopy? Comparison using benthic diatoms in tropical rivers" V. Vasselon, F. Rimet, K. Tapolczai, A. Bouchez submitted to Ecological Indicators journal. The directory contains the following files: 80 PGM sequencing libraries (raw data, fastq files).rar - contains the 80 fastq files provided by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments). 80 fastq files information.xlsx - contains the information relative to the 80 samples including: the ID used in Mothur analyses (corresponding to the name of the fastq files), the sample name, the sampling site code, the name of the river, the monitoring network to which rivers belong, the year of sampling and the GPS coordinates of sampling sites. OTU (95 percent of similarity) list of 80 Mayotte samples.xlsx - contains the final OTU list obtained after applying all the bioinformatics treatments (trimming, clustering,...): OTUs created at 95% of similarity, the number of DNA reads per sample was normalized at 5710 reads (the smallest values obtained in one sample). A DNA representative sequence and the taxonomic assignment determined using Mothur (using classify.otu command) are also provided for each OTU

Trait-based ecological classifications for benthic algae: review and perspectives

International audienceA 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

Diatom DNA metabarcoding for biomonitoring: strategies to avoid major taxonomical and bioinformatical biases Llmiting molecular indices capacities

International audienceRecent years provided intense progression in the implementation of molecular techniques in a wide variety of research fields in ecology. Biomonitoring and bioassessment can greatly benefit from DNA metabarcoding and High-Throughput Sequencing (HTS) methods that potentially provide reliable, high quantity and quality standardized data in a cost- and time-efficient way. However, DNA metabarcoding has its drawbacks, introducing biases at all the steps of the process, particularly during bioinformatics treatments used to prepare HTS data for ecological analyses. The high diversity of bioinformatics methods (e.g., OTU clustering, chimera detection, taxonomic assignment) and parameters (e.g., percentage similarity threshold used to define OTUs) make inter-studies comparison difficult, limiting the development of standardized and easy-accessible bioassessment procedures for routine freshwater monitoring. In order to study and overcome these drawbacks, we constructed four de novo indices to assess river ecological status based on the same biological samples of diatoms analyzed with morphological and molecular methods. The biological inventories produced are (i) morphospecies identified by microscopy, (ii) OTUs provided via metabarcoding and hierarchical clustering of sequences using a 95% similarity threshold, (iii) individual sequence units (ISUs) via metabarcoding and only minimal bioinformatical quality filtering, and (iv) exact sequence variants (ESVs) using DADA2 denoising algorithm. The indices based on molecular data operated directly with ecological values estimated for OTUs/ISUs/ESVs. Our study used an approach of bypassing taxonomic assignment, so bias related to unclassified sequences missing from reference libraries could be handled and no information on ecology of sequences is lost. Additionally, we showed that the indices based on ISUs and ESVs were equivalent, outperforming the OTU-based one in terms of predictive power and accuracy by revealing the hidden ecological information of sequences that are otherwise clustered in the same OTU (intra-species/intra-population variability). Furthermore, ISUs, ESVs, and morphospecies indices provided similar estimation of site ecological status, validating that ISUs with limited bioinformatics treatments may be used for DNA freshwater monitoring. Our study is a proof of concept where taxonomy- and clustering-free approach is presented, that we believe is a step forward a standardized and comparable DNA bioassessment, complementary to morphological methods