The use of diatoms in ecotoxicology and bioassessment: Insights, advances and challenges

Holographic tomography of the diatom Skeletonema pseudocostatum used as a bioindicator of heavy metal-polluted waters

Heavy metal contamination in aquatic environments poses a significant threat to microbial communities, yet the subcellular responses of phytoplankton to metal stress remain poorly understood. In particular, the effects of heavy metal exposure on the structural and physiological properties of diatoms require further investigation. Here, we analyze the impact of cadmium (Cd) and copper (Cu) exposure on the subcellular structures of the diatom Skeletonema pseudocostatum using holographic tomography. This imaging technique enables detailed visualization and quantitative analysis of diatom subcomponents, including frustules, protoplasm, vacuoles, and chloroplasts, under varying metal concentrations. The study aims to understand the changes in the mean refractive index (RI) and concentration (e.g., the ratio among cell dry mass and its biovolume) as indicators of cellular response to metal stress and to infer if such diatom can be used as sentinel species of heavy metal pollution. Findings indicate that diatoms exhibit significant variations in RI and internal cell density when exposed to different metal concentrations. Lower RI values observed at higher metal concentrations, can be considered as a sign of stress due to cytoplasm extrusion and/or vacuolization. The results highlight the potential of using S. pseudocostatum as a bioindicator for monitoring water metal pollution. Moreover, the results show that holographic tomography as useful tool for non-invasive, high-resolution cellular imaging of phytoplankton in environmental studies.

Oxidative Stress Biomarkers in Fish Exposed to Environmental Concentrations of Pharmaceutical Pollutants: A Review

Pharmaceutical residues are a result of human activities and are increasingly recognized as environmental contaminants that pose significant risks to aquatic ecosystems. There are many well-known pathways (agricultural runoff, veterinary use, human excretion, etc.) for the entry of these pharmaceuticals into the aquatic environment, and among them, the inability to remove these biologically active compounds from wastewater treatment plant (WWTP) effluents is becoming increasingly significant in the context of societal evolution. Once introduced, pharmaceuticals persist at low concentrations, exerting sub-lethal effects that disrupt the physiological processes of aquatic organisms. Among these effects, oxidative stress (OS) has gained attention as a key mechanism that is induced by pharmaceutical toxicity, serving as a sentinel indicator of homeostatic disturbance. Thus, studying OS biomarkers in fish is crucial for understanding the extent of pharmaceutical pollution, as these biomarkers provide early warning signals of environmental stress and help assess sub-lethal impacts on aquatic organisms. Their application, correlated with other eco-physiological investigations, can improve ecological risk assessments. In this context, this review explores the role of OS biomarkers by assessing the effects of pharmaceutical contaminants on fish. It highlights the utility and limitations of these biomarkers for environmental monitoring, while also identifying key research gaps-particularly regarding long-term ecological consequences.

Benthic diatoms as indicators of water quality in Sharda (Kali), a transboundary Himalayan River

Bioassessment studies in river systems of India are rather scarce and most of the monitoring programmes still rely on the traditional physical and chemical analysis. We explored the biomonitoring potential of benthic diatoms from the Sharda (Kali) river in the Himalayas, which is due interlinking with the Yamuna River under the National River Linking Programme (NRLP) in India. Seventeen sites along the Sharda were sampled in November 2022 for the analysis of 14 physical and chemical variables and benthic diatoms. Hierarchical agglomerative cluster analysis (HACA) and principal component analysis (PCA) of the physico-chemical data set revealed two major groups of sites; the majorly unpolluted sites at higher elevations of Kumaun Himalayas (KH) and the low or moderately polluted sites of Terai Plains (TP) at lower elevations. Application of Water Quality Index (WQI) assigned a good water quality class (B) to all selected sites. A total of 31 genera including 107 species of diatoms were recorded during the present study. Achnanthes pseudoswazi, Achnanthidium minutissimum, Achnanthidium pusillum, Geissleria decussis, and Reimeria sinuata were the most abundant forms from KH whereas Gomphonema acuminatum, Cymbella excisa, Cocconeis pediculus, Nitzschia linearis, and Navicula angusta were the dominant forms recorded from TP. A decrease in diatom diversity was observed from KH to TP sites due to hydrogeomorphological changes and human interventions. Significant differences (p < 0.05 and p < 0.01) between diatom diversity index scores was observed between KH and TP sites. Diversity indices correlated significantly with important water quality variables. The results of the diatom indices such as Trophic Diatom Index (TDI), Specific Pollution Sensitivity Index (IPS), Generic Diatom Index (IDG), and Louis Leclercq Diatom Index (IDSE) corroborated well with the recorded physicochemical variables and WQI values. IPS diatom index exhibited better resolution than WQI with reference to categorization of sites and subsequent establishment of ecological status. IPS was found to be the most suitable index and could be utilized for a pre-linkage ecological status establishment for the Sharda River. However, weak correlations of diatom indices and water quality variables along with low percentage of taxa included for computation of diatom indices reiterates the importance of establishment of region specific autecological preferences of diatoms and subsequent formulation of a customized diatom index for the Sharda River system.

Using diatom chain length as a bioindicator of heavy-metals contamination in marine environments

The increasing release of toxic heavy metals into marine environments poses significant risks due to their persistence and bioaccumulation. Diatoms are ideal bioindicators because of their sensitivity to environmental changes. Despite traditional methods for detecting these persistent pollutants effectively identify composition and concentration, they are time-consuming, they often require the use of harmful reagents, and do not allow a fast assessment of detrimental impacts on marine organisms. To fill this gap, we have successfully investigated the toxicity of different heavy metals in the marine diatom Skeletonema pseudocostatum thanks to a newly developed high-power terahertz (THz) spectrometer. By combining THz spectroscopy, microscopy and ecotoxicological assays, we found that the formation of long diatom chains is significantly inhibited by the presence of lead, copper, and chromium, which disrupt their metabolism. Although the THz absorption and refractive index spectra were not affected by diatom concentration in undoped samples, THz frequencies were highly sensitive to changes in diatom chain length due to heavy metals exposure. These findings suggest that this approach allows to investigate the biochemical processes involved in chain formation in S. pseudocostatum and related algae. THz spectroscopy could therefore provide deeper insights into the microscopic metabolic activity of diatoms, addressing key biochemical questions surrounding these organisms. Furthermore, we propose this novel approach for environmental pollution monitoring, since it could provide a rapid, harmless and sensitive detection method to assess heavy metal toxicity in marine diatoms, key organisms at the basis of the trophic chain.

Forensic Diatom Analysis: Where Do We Stand and What Are the Latest Diagnostic Advances?

Background: diatoms are unicellular algae that have been used for more than a century for forensic purposes to diagnose drowning, with more or less success depending on the historical era. Although many years have passed, scientific research on diatoms has never ceased, which testifies to their enduring allure in forensics. Of course, diatom research has evolved and expanded over time, changing with the availability of new techniques and technologies. The volume of articles and their production over a period of many years has resulted in old, current, and new knowledge on diatoms being scattered over a large number of books and articles. Objectives: the purpose of this narrative literature review is, therefore, to summarize all this information and bring it together in a single work that can be useful for those who are studying diatoms and their usefulness for forensics for the first time, for those who are looking for proven methods of analysis, and finally for those who are interested in exploring new frontiers of research. Methods: a comprehensive literature search that included all studies dealing with the applications of diatoms in forensic science was performed in the most popular electronic databases. Results: traditional methods have been complemented by molecular and imaging methods and, more recently, by artificial intelligence. In addition, new biological substrates have been found for the analysis of diatoms. Conclusions: all this has led, on the one hand, to the consolidation of a whole body of knowledge on diatoms, on which this forensic analysis is still based, and, on the other hand, has opened up numerous new research directions.

Investigating the interaction of uranium(VI) with diatoms and their bacterial community: A microscopic and spectroscopic study

Diatoms and bacteria play a vital role in investigating the ecological effects of heavy metals in the environment. Despite separate studies on metal interactions with diatoms and bacteria, there is a significant gap in research regarding heavy metal interactions within a diatom-bacterium system, which closely mirrors natural conditions. In this study, we aim to address this gap by examining the interaction of uranium(VI) (U(VI)) with Achnanthidium saprophilum freshwater diatoms and their natural bacterial community, primarily consisting of four successfully isolated bacterial strains (Acidovorax facilis, Agrobacterium fabrum, Brevundimonas mediterranea, and Pseudomonas peli) from the diatom culture. Uranium (U) bio-association experiments were performed both on the xenic A. saprophilum culture and on the four bacterial isolates. Scanning electron microscopy and transmission electron microscopy coupled with spectrum imaging analysis based on energy-dispersive X-ray spectroscopy revealed a clear co-localization of U and phosphorus both on the surface and inside A. saprophilum diatoms and the associated bacterial cells. Time-resolved laser-induced fluorescence spectroscopy with parallel factor analysis identified similar U(VI) binding motifs both on A. saprophilum diatoms and the four bacterial isolates. This is the first work providing valuable microscopic and spectroscopic data on U localization and speciation within a diatom-bacterium system, demonstrating the contribution of the co-occurring bacteria to the overall interaction with U, a factor non-negligible for future modeling and assessment of radiological effects on living microorganisms.

Cellular uptake of multi-walled carbon nanotubes is associated to genotoxic and teratogenic effects towards the freshwater diatom Nitzschia linearis

The increase in industrial production of multi-walled carbon nanotubes (MWCNTs) raises concerns about their potential adverse effects associated to environmental releases, especially in aquatic environments where they are likely to accumulate. This study focuses on the environmental impact of MWCNTs, specifically on a benthic freshwater diatom (Nitzschia linearis), which plays a major role in the primary production of water bodies. The obtained results indicate that exposure to MWCNTs in the presence of natural organic matter (NOM) inhibits diatom's growth in a dose-dependent manner after 72 h of exposure. Interestingly, the photosystem II quantum yield (PSIIQY) in diatoms remains unaffected even after exposure to MWCNTs at 10 mg/L. After 48 h of exposure, MWCNTs are found to bind preferentially to extracellular polymeric substances (EPS) produced by diatoms, which could decrease their toxicity by limiting their interaction with this organism. However, measurement of genotoxicity and teratogenicity in diatoms exposed to MWCNTs revealed that the exposure to MWCNTs increased the occurrence of cells with micronuclei and abnormal frustules. Microscopy analyses including two-photon excitation microscopy (TPEM) revealed the internalization of MWCNTs. Investigations of the diatom's frustule structure using Scanning electron microscopy (SEM) indicated that the presence of pore structures constitutes a pathway allowing MWCNTs uptake. The presence in the diatom's cytoplasm of MWCNTs might possibly induce disturbances of the cellular components, leading to the observed genotoxic and teratogenic effects. In view of previous studies, this work underscores the need for further studies on the interaction between nanomaterials and different diatom species, given the species-specific nature of the interactions.

A rapid and multi-endpoint ecotoxicological test using Mychonastes afer for efficient screening of metals and herbicides

Microalgal growth-based tests are international standards for ecotoxicity assessment; however, their long exposure times, large sample volumes, and reliance on a single growth-endpoint make them inadequate for rapid toxicity screening. Here, we aimed to develop a rapid and simple ecotoxicological test using the fast-growing green alga Mychonastes afer, with multiple endpoints-growth, lipid content, and photosynthesis. We exposed M. afer to two metals-silver and copper-and two herbicides-atrazine and diuron-for 24 h and identified the most sensitive and reliable endpoints for each toxicant: the maximum electron transport rate (ETRmax) for Ag, Cu and atrazine, and the lipid content for diuron. Lipid content was found to be both a sensitive and reliable biomarker, meeting the effluent limit guidelines in both the Republic of Korea and the USA. The sensitivity of M. afer to Ag and atrazine also closely matched the HC5 values derived from the species sensitivity distribution approach, confirming its reliability for setting regulatory concentrations of these contaminants. Our calculated predicted no-effect concentration (PNEC) values were similar to established European Union PNECs for Ag, Cu, atrazine, and diuron, underlining the utility of these biological endpoints for ecological risk assessment and regulatory decision making. This method required lower sample volume (2 mL vs 100 mL) and exposure time (24 h vs 72-120 h) than conventional green algal tests, and eliminated the need for labour-intensive cell counting, expensive equipment, and chlorophyll fluorescence measurement expertise. Overall, this M. afer test can be a valuable tool for the rapid screening of wastewater for metals and herbicides, contributing to environmental protection and management practices.

Experimental testing of two urban stressors on freshwater biofilms

Aquatic ecosystems and their communities are exposed to numerous stressors of various natures (chemical and physical), whose impacts are often poorly documented. In urban areas, the use of biocides such as dodecyldimethylbenzylammonium chloride (DDBAC) and their subsequent release in wastewater result in their transfer to urban aquatic ecosystems. DDBAC is known to be toxic to most aquatic organisms. Artificial light at night (ALAN) is another stressor that is increasing globally, especially in urban areas. ALAN may have a negative impact on photosynthetic cycles of periphytic biofilms, which in turn may result in changes in their metabolic functioning. Moreover, studies suggest that exposure to artificial light could increase the biocidal effect of DDBAC on biofilms. The present study investigates the individual and combined effects of DDBAC and/or ALAN on the functioning and structure of photosynthetic biofilms. We exposed biofilms in artificial channels to a nominal concentration of 30 mg.L-1 of DDBAC and/or ALAN for 10 days. ALAN modified DDBAC exposure, decreasing concentrations in the water but not accumulation in biofilms. DDBAC had negative impacts on biofilm functioning and structure. Photosynthetic activity was inhibited by > 90% after 2 days of exposure, compared to the controls, and did not recover over the duration of the experiment. Biofilm composition was also impacted, with a marked decrease in green algae and the disappearance of microfauna under DDBAC exposure. The integrity of algal cells was compromised where DDBAC exposure altered the chloroplasts and chlorophyll content. Impacts on autotrophs were also observed through a shift in lipid profiles, in particular a strong decrease in glycolipid content was noted. We found no significant interactive effect of ALAN and DDBAC on the studied endpoints.

Teratogenic effects of environmental concentration of plastic particles on freshwater organisms

Given the widespread presence of plastics, especially in micro- and nanoscale sizes, in freshwater systems, it is crucial to identify a suitable model organism for assessing the potential toxic and teratogenic effects of exposure to plastic particles. Until now, the early life stage of freshwater organisms and the regeneration capacity in relation to plastic particles exposure is a still poorly investigated topic. In this study, we examine the teratogenic effect on diatom Cocconeis placentula and cnidarian Hydra vulgaris under controlled exposure conditions of poly(styrene-co-methyl methacrylate) (P(S-co-MMA)) particles. Significant effects were observed at the lowest concentrations (0.1 μg/L). A significant increase in the teratological frequency in C. placentula and a significant decrease in the regeneration rate in H. vulgaris were found at the lowest concentration. The delay in hydra regeneration impaired the feeding capacity and tentacles reactivity at 96 h of exposure. No effects on diatom growth were observed upon exposure to P(S-co-MMA) particles (0.1, 1, 100, 10,000 μg/L) for 28 days and these findings agree with other studies investigating algal growth. The application of the Teratogenic Risk Index, modified for diatoms, highlighted a moderate risk for the lowest concentration evaluating C. placentula and low risk at the lowest and the highest concentrations considering H. vulgaris. This study suggests the importance of testing organisms belonging to different trophic levels as diverse teratogenic effects can be found and the need to evaluate environmentally relevant concentrations of plastic particles.

Qualitative and quantitative assessment of diatom deformities and protoplasmic condition under metal and metalloid stress

Metals and metalloids are toxic, persistent, and non-biodegradable and can be biomagnified (e.g., Hg), and therefore pose a serious threat to the algal flora of aquatic ecosystems. This laboratory study tested the effects of metals (Zn, Fe, and Hg) and a metalloid (As) on the cell wall morphology and protoplasmic content of living cells of six widespread diatom genera over 28 days. Diatoms exposed to Zn and Fe had a higher frequency of deformed diatom frustules (> 1%) compared to the As, Hg, and control treatments (< 1%). Deformities in the valve outline and striae were found in all treatments, including the control, whereas deformed raphes and more than one type of deformity were more prevalent under Zn and Hg stress. The order of toxicity is as follows: Zn > Fe > Hg≈As. Deformities were more frequent in Achnanthes and Diploneis (adnate forms) than in the motile genera of Nitzschia and Navicula. The correlation between the % healthy diatoms and % deformities in all six genera showed a negative relationship with the integrity of protoplasmic content (i.e., greater alteration in protoplasmic content was associated with greater frustule deformation). We conclude that diatom deformities can be a good indicator of metal and metalloid stress in waterbodies and are very useful in the rapid biomonitoring of aquatic ecosystems.

Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring

Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.

Emerging challenges of the impacts of pharmaceuticals on aquatic ecosystems: A diatom perspective

Pharmaceuticals are a ubiquitous group of emerging pollutants of considerable importance due to their biological potency and potential to elicit effects in wildlife and humans. Pharmaceuticals have been quantified in terrestrial, marine, fresh, and transitional waters, as well as the fauna and macro-flora that inhabit them. Pharmaceuticals can enter water ways through different human and veterinary pathways with traditional wastewater treatment, unable to completely remove pharmaceuticals, discharging often unknown quantities to aquatic ecosystems. However, there is a paucity of available information regarding the effects of pharmaceuticals on species at the base of aquatic food webs, especially on phytoplankton, with research typically focussing on fish and aquatic invertebrates. Diatoms are one of the main classes of phytoplankton and are some of the most abundant and important organisms in aquatic systems. As primary producers, diatoms generate ∼40 % of the world's oxygen and are a vital food source for primary consumers. Diatoms can also be used for bioremediation of polluted water bodies but perhaps are best known as bio-indicators for water quality studies. However, this keystone, non-target group is often ignored during ecotoxicological studies to assess the effects of pollutants of concern. Observed effects of pharmaceuticals on diatoms have the potential to be used as an indicator of pharmaceutical-induced impacts on higher trophic level organisms and wider ecosystem effects. The aim of this review is to present a synthesis of research on pharmaceutical exposure to diatoms, considering ecotoxicity, bioremediation and the role of diatoms as bio-indicators. We highlight significant omissions and knowledge gaps which need addressing to realise the potential role of diatoms in future risk assessment approaches and help evaluate the impacts of pharmaceuticals in the aquatic environment at local and global scales.

Diatom DNA metabarcoding to assess the effect of natural radioactivity in mineral springs on ASV of benthic diatom communities

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, ²³⁸U 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 ²³⁸U, suggesting its high tolerance to this particular radionuclide. This diatom species may therefore represent a bio-indicator of high natural levels of uranium.

Combined effects of microplastics and warming enhance algal carbon and nitrogen storage

Algae dominate primary production in groundwater and oceans and play a critical role in global carbon dioxide fixation and climate change but are threatened by ongoing global warming events (such as heatwaves) and increasing microplastic (MP) pollution. However, whether and how ecologically important phytoplankton respond to the combined effects of warming and MPs remain poorly understood. We thus investigated the combined effects of these factors on carbon and nitrogen storage and the mechanisms underlying the alterations in the physiological performance of a model diatom, Phaeodactylum tricornutum, exposed to a warming stressor (25 °C compared with 21 °C) and polystyrene MP acclimation. Although warmer conditions decreased the cell viability, the diatoms subjected to the synergistic effects of MPs and warming showed significant increases in the growth rate (1.10-fold) and nitrogen uptake rate (1.26-fold). Metabolomics and transcriptomic analyses revealed that MPs and warming mainly promoted fatty acid metabolism, the urea cycle, glutamine and glutamate production, and the tricarboxylic acid (TCA) cycle due to an increased level of 2-oxoglutarate, which is the hub of carbon and nitrogen metabolism and accounts for the acquisition and utilization of carbon and nitrogen. Our findings emphasize the nonnegligible effects of MPs and HWs on the algal carbon and nitrogen cycles in waters.

A lentic microcosm approach to determine the toxicity of DDT and deltamethrin on diatom communities

Worldwide the use of pesticides has increased, especially in the industry and agriculture sector even though they contain highly toxic substances. The use of pesticides has various negative effects on the aquatic ecosystem and organisms within these ecosystems. The paper aimed to assess the effects of increased concentrations of malaria vector control insecticides (Dichlorodiphenyltrichloroethane (DDT) and Deltamethrin (DTM)) on the freshwater diatom community structure using a microcosm approach as well as determine whether a mixture (DDT 1:1 Deltamethrin) exposure will have a greater influence on the diatom community when compared to single exposures of these insecticides. Diatoms were exposed to a high and low concentration (based on LC50 data for freshwater Xenopus laevis from the USEPA Ecotox database) of DDT, DTM and a mixture in lentic microcosms over a total period of 28 days. Results indicated that irrespective of exposure concentrations, DDT, DTM and a mixture had negative effects on the diatom community including functionality and vitality as these insecticides induced changes to their chloroplasts. There was an increased percentage dead cells for all exposures compared to the control, with the insecticides having a phototoxic effect on the diatom community. Exposure to the selected insecticides caused a significant decrease in some diatom metrics indicating the negative effects these insecticides have on the diatom metrics. Therefore, diatoms may prove to be useful as bio-indicators in ecotoxicology studies when assessing the effects of any insecticide exposures.

Toxic Effect of Metal Doping on Diatoms as Probed by Broadband Terahertz Time-Domain Spectroscopy

The global marine environment is increasingly affected by human activities causing climate change, eutrophication, and pollution. These factors influence the metabolic mechanisms of phytoplankton species, such as diatoms. Among other pollutant agents, heavy metals can have dramatic effects on diatom viability. Detailed knowledge of the interaction of diatoms with metals is essential from both a fundamental and applicative point of view. To this aim, we assess terahertz time-domain spectroscopy as a tool for sensing the diatoms in aqueous systems which mimic their natural environment. Despite the strong absorption of terahertz radiation in water, we show that diatoms can be sensed by probing the water absorption enhancement in the terahertz range caused by the water–diatom interaction. We reveal that the addition of metal dopants affects this absorption enhancement, thus enabling the monitoring of the toxic effects of metals on diatoms using terahertz spectroscopy. We demonstrate that this technique can detect the detrimental effects of heavy metals earlier than conventional methods such as microscopy, enzymatic assays, and molecular analyses aimed at assessing the overexpression of genes involved in the heavy metal-stress response.

Diatoms as indicators in running waters: trends of studies on biological assessment and monitoring

Despite the biodiversity and ecosystem services provided by lotic ecosystems, they are strongly affected by anthropogenic activities. Therefore, biological monitoring and assessment strategies are crucial in helping maintain these ecosystems and developing mitigation policies. We provide a global overview of the use of benthic diatoms as bioindicators in lotic environments, by analyzing 764 articles published in the past 20 years. We analyzed the influence of substrate type on samplings, which species have been highlighted as indicators and for which type of impacts, which anthropogenic impacts have been most commonly evaluated, and which metrics have been commonly used in studies using diatoms to assess and monitor the quality of lotic environments. We found that the most studied anthropogenic impact is artificial eutrophication and that some species, especially Nitzschia palea, have been thoroughly mentioned as indicators of this impact. Indicator species related to other types of impact are less common, demonstrating the need for studies on this issue. Moreover, we verified that traditional taxonomic metrics, such as diversity and diatom indices, have been widely used. Some alternative metrics have been used recently, such as those based on teratological valves, lipid bodies, valve size, and DNA metabarcoding. The number of biomonitoring and assessment studies based on diatoms has increased considerably in the past 20 years. Nonetheless, the demand for natural resources and consequently the degradation of lotic ecosystems have accelerated significantly. Thus, the development of low-cost and time-efficient biological assessment and monitoring strategies is essential for evaluating the health of lotic environments.

Novel Approach to Freshwater Diatom Profiling and Identification Using Raman Spectroscopy and Chemometric Analysis

(1) An approach with great potential for fast and cost-effective profiling and identification of diatoms in lake ecosystems is presented herein. This approach takes advantage of Raman spectroscopy. (2) The study was based on the analysis of 790 Raman spectra from 29 species, belonging to 15 genera, 12 families, 9 orders and 4 subclasses, which were analysed using chemometric methods. The Raman data were first analysed by a partial least squares regression discriminant analysis (PLS-DA) to characterise the diatom species. Furthermore, a method was developed to streamline the integrated interpretation of PLS-DA when a high number of significant components is extracted. Subsequently, an artificial neural network (ANN) was used for taxa identification from Raman data. (3) The PLS interpretation produced a Raman profile for each species reflecting its biochemical composition. The ANN models were useful to identify various taxa with high accuracy. (4) Compared to studies in the literature, involving huge datasets one to four orders of magnitude larger than ours, high sensitivity was found for the identification of Achnanthidium exiguum (67%), Fragilaria pararumpens (67%), Amphora pediculus (71%), Achnanthidium minutissimum (80%) and Melosira varians (82%).

Reducing nutrient increases diatom biomass in a subtropical eutrophic lake, China-Do the ammonium concentration and nitrate to ammonium ratio play a role?

Response of aquatic organisms to eutrophication have been well reported, while less studies are available for the recovery of eutrophic lakes following a reduction in the external loading, especially for systems where nitrogen is reduced but the phosphorus concentration is maintained high due to internal loading. Diatoms are nitrate (NO₃-N) opportunists but can also use ammonium (NH₄-N). They may, therefore, be more sensitive to nitrogen reduction than other algae that typically prefer NH₄-N. We document the variations of nutrients and diatoms in subtropical, eutrophic Lake Taihu over 28 yr during which a reduction of the external loading resulted from lake management. According to the results of change point analysis, data on environmental variables were divided into two periods (P1: 1992-2006; P2: 2007-2019) with two different seasons (WS: Winter-Spring; SA: Summer-Autumn), respectively. Compared with P1-WS, the concentration of NH₄-N decreased significantly whereas NO₃-N showed no significant change in P2-WS. In contrast, NH₄-N concentrations were low and showed no significant changes in P1-SA and P2-SA and NO₃-N decreased significantly in the latter period. Accordingly, NO₃-N: NH₄-N mass ratios in P1-SA and P2-WS were all significantly higher than those in P2-SA and P1-WS, respectively. The biomass of WS diatom increased significantly and the timing of the peak biomass shifted from P1-SA to P2-WS since 2007. The SEM analysis showed that NO₃-N was retained as a statistically significant predictor for diatom biomass in P1-SA and significant effects of windspeed, zooplankton and NH₄-N on diatom biomass in P2-WS. Windspeed and zooplankton have further changed the biomass of diatoms in the case of declining inorganic nitrogen. We conclude that the magnitude of vernal suppression or stimulation of diatom assemblages has increased, concomitant with the variations of NH₄-N and NO₃-N: NH₄-N mass ratios. Diatoms response to NH₄-N or NO₃-N is apparently changing in response to water temperature in this eutrophic shallow lake. Thus, parallel reductions in external nitrogen loading, along with variations in dominant inorganic nitrogen, will stimulate the growth of diatom and therefore increase the total biomass of phytoplankton in still high internal phosphorus loading, which is should be regarded as a good sign of restoration measures.

Benthic diatoms and macroinvertebrates status with relevant to sediment quality of islands shores in the Nile River, Egypt

Sediments are utilized as a marker for events that endure long enough to manifest their environmental impacts and determine the contamination levels. The purpose of the present study was to highlight the current sediment quality of four Nile islands shores by utilizing a variety of physical, chemical, and biological aspects and indices. In addition, the status of benthic diatoms and macroinvertebrates, as well as their responses to sediment variables were investigated. The metals followed a decreasing concentration order: Al > Fe > Mn > Zn > Ni ≈ Cr > Cu > Co > Pb > Cd. The outcomes of metal pollution indices revealed some localized contaminated sites, by mostly Ni and Cd. In addition, a moderate toxic risk from metals was observed for El-Keratten shores, while the sediments of El-Warraq, El-Zamalek, and El-Manial islands shores were at low toxic risk. A total of 112 diatom species belonging to 24 genera were identified in the total sample set, where most of the diatoms encountered were cosmopolitan. Metals had a remarkable impact on the composition, distribution, and dominance of diatom assemblages, but had little effect on diatom diversity, while there was a noticeable effect of grain size on diatom distribution and diversity. Thirty-four species of benthic invertebrates were identified in the collected samples from the islands shores. The dominant taxa and groups of benthic invertebrates at different islands were affected by various sediment parameters, where the levels and types of such variables differed from one species to another.

Graphical abstract

Biogeochemical indicators (waters/diatoms) of acid mine drainage pollution in the Odiel river (Iberian Pyritic Belt, SW Spain)

Odiel river basin is located in the Iberian Pyritic Belt (IPB) and mostly of its tributaries are severely affected by acid mine drainage (AMD). It is originated when pyritic minerals from abandoned mines, especially mineral residues from waste rock dams, get in contact with air and water. Fifteen sampling points were chosen to analyze interactions between diatom communities and water hydrogeochemistry. Considering physicochemical characteristics, sampling points were assigned as highly, moderately, and unpolluted by AMD. No correlation was observed between ecological diversity indexes and physico-chemical parameters. However, a dependency relationship between diatom species distribution and specific pH, conductivity, redox potential, sulfate, and metal concentrations was observed. Cluster analysis based on Pearson correlation and rs values of the non-parametric Spearman correlation allowed to identify Pinnularia acidophila, Pinnularia subcapitata var. elongata, and Eunotia exigua as the main bioindicators of AMD-polluted Odiel streams. Finally, a principal component analysis led to associate the most abundant diatoms species to specific physico-chemical parameters.

Environmental diagnosis with Raman Spectroscopy applied to diatoms

Freshwater quality has been changing due to the ever greater use of water resources and the contamination load resulting from human activities. Management of these systems, thus, requires constant diagnose of water quality with fast and efficient methodologies. The conventional methods adopted are, however, time-consuming, often very expensive, and require specialised expertise. Raman spectroscopy (RS) is a simple, fast and label-free technique that can be applied to environmental diagnosis using diatoms. Here, we developed a diagnostic method based on Raman spectroscopy applied to freshwater diatoms. For this, Raman spectra were recorded from diatoms of three lakes of a natural city park. The data acquired was analysed by chemometrics methods to describe the data (Partial Least Squares Regression), infer relationships in the dataset (Cluster Analysis) and produce classification models (Artificial Neural Network). The classification models developed diagnosed the lakes with excellent accuracy (89%) without requiring taxonomic information about the diatom species recorded. This study provides a proof-of-concept for the application of diatom Raman spectroscopy to diagnosing water quality, laying an important foundation for future environmental studies aiming at assessing freshwater systems, to be replicated at larger scales and to varied geographic settings.

Consideration of Multitrophic Biodiversity and Ecosystem Functions Improves Indices on River Ecological Status

Biological quality elements have been developed worldwide to assess whether a water body is in a good status or not. However, current studies mainly focus on a single taxonomic group or a small set of species, often limited by methods of morphological identification, and lack further aspects of biodiversity (e.g., across taxa and multiple attributes) and ecosystem functions. Here, we advance a framework for assessing the river's ecological status based on complete biodiversity data measured by environmental DNA (eDNA) metabarcoding and measurements of ecosystem functions in addition to physicochemical elements across a large riverine system in China. We identified 40 indicators of biodiversity and ecosystem functions, covering five taxonomic groups from bacteria to invertebrates, and associated with multiple attributes of biodiversity and ecosystem functions. Our data show that human impact on ecosystems could be accurately predicted by these eDNA-based indicators and ecosystem functions, using cross-validation with a known stressor gradient. Moreover, indices based on these indicators of biodiversity and ecosystem functions not only distinguish the physicochemical characteristics of the sites but also improve the assessment accuracy of 20-30% for the river's ecological status. Overall, by incorporating eDNA-based biodiversity with physicochemical and ecosystem functional elements, the multidimensional perspectives of ecosystem states provide additional information to protect and maintain a good ecological status of rivers.

Transient effect of bisphenol A (BPA) and di-(2-ethylhexyl) phthalate (DEHP) on the cosmopolitan marine diatom Chaetoceros decipiens-lorenzianus

Incubation under controlled laboratory conditions were performed to assess the toxic effects of two plastic derived chemicals, bisphenol A (BPA) and di-(2-ethylhexyl) phthalate (DEHP), on the growth, photosynthetic efficiency and photosynthetic activity of the cosmopolitan diatom Chaetoceros decipiens-lorenzianus. Non-axenic diatom cells were exposed to concentrations of BPA and DEHP (separately and in mixture), mimicking concentrations observed in contaminated marine ecosystems, for seven days. Upon short-term exposure (i.e., during the first 48 h), BPA and DEHP induced a slight but significant stimulation of biomass and photosynthetic activity relative to the control, whereas, no significant impact was observed on the photosynthetic efficiency. Nevertheless, this pattern was transient. The stimulation was followed by a return to control conditions for all treatments at the end of incubation. These results showed that the cosmopolitan diatom Chaetoceros was not impacted by representative in situ concentrations of plastic derivatives, thus confirming its ability to thrive in coastal anthropogenic environments.

How can integrated morphotaxonomy- and metabarcoding-based diatom assemblage analyses best contribute to the ecological assessment of streams?

Environmental conditions, such as nutrient concentrations, salinity, elevation etc., shape diatom assemblages of periphytic biofilms. These assemblages respond rapidly to environmental changes, a fact which makes diatoms valuable bioindicators. Hence, freshwater biomonitoring programmes currently use diatom indices (e.g. EU Water Framework Directive - WFD). To date, microscopy-based assessments require high taxonomic expertise for diatom identification at the species level. High-throughput technologies now provide cost-effective identification approaches that are promising, complementary or alternative tools for bioassessment. The suitability of the metabarcoding method is evaluated for the first time in the Cyprus streams WFD monitoring network, an eastern Mediterranean country with many endemic species and results are compared to the results acquired from the morphotaxonomic analysis. Morphotaxonomic identification was conducted microscopically, using the most updated taxonomic concepts, literature and online resources. At the same time, DNA metabarcoding involved the use of the rbcL 312 bp barcode, high-throughput sequencing and bioinformatic analysis. The ecological status was calculated using the IPS Index. Results show a positive correlation between morpho-taxonomic and molecular IPS scores. Discrepancies between the two methodologies are related to the limitations of both techniques. This study confirmed that Fistulifera saprophila can have a crucial role in key differences observed, as it negatively influences IPS scores and microscopy methods frequently overlook it. Importantly, gaps in the DNA barcoding reference databases lead to a positive overestimation in IPS scores. Overall, we conclude that DNA metabarcoding offsets the morphotaxonomic methodology for the ecological quality assessment of freshwaters.

Raman spectroscopy applied to diatoms (microalgae, Bacillariophyta): Prospective use in the environmental diagnosis of freshwater ecosystems

Diatom species are good pollution bioindicators due to their large distribution, fast response to changes in environmental parameters and different tolerance ranges. These organisms are used in ecological water assessment all over the world using autoecological indices. Such assessments commonly rely on the taxonomic identification of diatom species-specific shape and frustule ornaments, from which cell counts, species richness and diversity indices can be estimated. Taxonomic identification is, however, time-consuming and requires years of expertise. Additionally, though the diatom autoecological indices are region-specific, they are often applied indiscriminately across regions. Raman spectroscopy is a simpler, fast and label-free technique that can be applied to environmental diagnosis with diatoms. However, this approach has been poorly explored. This work reviews Raman spectroscopy studies involving the structure, location and conformation of diatom cell components and their variation under different conditions. A critical appreciation of the pros and cons of its application to environmental diagnosis is also given. This knowledge provides a strong foundation for the development of environmental protocols using Raman spectroscopy in diatoms. Our work aims at stimulating further research on the application of Raman spectroscopy as a tool to assess physiological changes and water quality under a changing climate.

Benthic Diatoms in River Biomonitoring—Present and Future Perspectives within the Water Framework Directive

The European Water Framework Directive 2000/60/EC (WFD) has been implemented over the past 20 years, using physicochemical, biological and hydromorphological elements to assess the ecological status of surface waters. Benthic diatoms (i.e., phytobenthos) are one of the most common biological quality elements (BQEs) used in surface water monitoring and are particularly successful in detecting eutrophication, organic pollution and acidification. Herein, we reviewed their implementation in river biomonitoring for the purposes of the WFD, highlighting their advantages and disadvantages over other BQEs, and we discuss recent advances that could be applied in future biomonitoring. Until now, phytobenthos have been intercalibrated by the vast majority (26 out of 28) of EU Member States (MS) in 54% of the total water bodies assessed and was the most commonly used BQE after benthic invertebrates (85% of water bodies), followed by fish (53%), macrophytes (27%) and phytoplankton (4%). To meet the WFD demands, numerous taxonomy-based quality indices have been developed among MS, presenting, however, uncertainties possibly related to species biogeography. Recent development of different types of quality indices (trait-based, DNA sequencing and predictive modeling) could provide more accurate results in biomonitoring, but should be validated and intercalibrated among MS before their wide application in water quality assessments.

Diatoms recovery from wastewater: Overview from an ecological and economic perspective

Alarming water pollution is toxic to the aquatic ecosystem leading to a sharp decline in species diversity. Diatoms have great potency to survive in contaminated water bodies, hence they can be compelling bioindicators to monitor the change in the environmental matrices effectively. Around the globe, researchers are intended to evaluate the impact of pollution on the diatoms recovery and techniques used for the assessment. The diatoms are precious for futuristic need viz. value-added products, energy generation, pharmaceuticals, and aquaculture feedstocks. All these applications led to a significant rise in diatoms research among the scientific community. This review presents different isolation practices, cultivation, and other challenges associated with the diatoms. A precise focus is given to diatoms isolation techniques from highly polluted water bodies with the main thrust towards obtaining an axenic culture to elucidate the significance of pure diatom cultures. Recovery of "jewels of the sea" from polluted water signifies the prospective ecological and economic aspects.

Assessment of five live-cell characteristics in periphytic diatoms as a measure of copper stress

Metal pollution of fluvial systems remains a major problem and biomonitoring can be a useful tool for assessing the metal contamination. To assess their potential as new bioindicators of copper stress, we treated a field-collected live periphytic diatom community (dominated by Amphora, Navicula, and Nitzschia) with dissolved Cu under optimal growth conditions. We studied the effects of Cu on five live-cell attributes: motility, protoplasmic content, lipid body number and biovolume, and frustule morphology. In all three genera, motility and protoplasmic content decreased, whereas the LB number, biovolume and deformity increased when Cu and exposure time increased. The sensitivity to Cu was highest for % MF, % CPC and % BCLB in Navicula and the LB number and deformity in Nitzschia. Amphora appeared to be more tolerant to Cu in comparison with other genera. The five cell attributes were inter-related. A heatmap showed that a recommended indicator for rapid screening of Cu toxicity was % BCLB for Amphora and % MF for Navicula and Nitzschia. % MF might be the most common representative indicator that can be applied to all three genera to evaluate the lethal effects of Cu stress if only one of the five cell attributes must be selected.

Diatom motility and nuclear alterations are affected by sediment elutriates of agricultural streams

Diatoms respond to toxicants in lotic systems, and they are commonly considered to be sensitive indicators in environmental safety assessment. In addition to the structural characteristics of the algal populations, recent studies have shown that endpoints such as nuclear anomalies or diatom motility measures can be affected quickly by environmental changes. We sought to determine if cell density, cell size, nuclear anomalies and motility of the diatom Nitzschia palea were useful indicators of sediment quality from agricultural streams. For this purpose, we exposed cultures of the diatom to elutriates from sediments of a stream that flows through an intensive agricultural area, and measured the responses of the populations for 7 days in laboratory tests. The bioassays showed that motility measures in Nitzschia palea and the condition of their nuclear membranes rapidly reflected the effects of sediment quality after only 48 h of exposure; mean cell density and length were affected by day 7. The sediment elutriates affected cell movements by shortening the total path length and decreasing cell velocity; they also increased the number of cells with nuclear membrane breakage. Our results from these bioassays show that diatom motility measurements and the condition of the nuclei might be indicators that respond faster to impacts than the traditional structural parameters, such as cell density, specific composition of the assemblage or diversity metrics of the algal communities more often used in biomonitoring.

Freshwater diatom biomonitoring through benthic kick-net metabarcoding

Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status. However, multi-substrate periphyton collection, a common diatom sampling practice, is time-consuming and thus costly in terms of labour. This study examined whether the benthic kick-net technique used for macroinvertebrate biomonitoring could be applied to bulk-sample diatoms for metabarcoding. To test this approach, we collected samples using both conventional multi-substrate microhabitat periphyton collections and bulk-tissue kick-net methodologies in parallel from replicated sites with different habitat status (good/fair). We found there was no significant difference in community assemblages between conventional periphyton collection and kick-net methodologies or site status, but there was significant difference between diatom communities depending on site (P = 0.042). These results show the diatom taxonomic coverage achieved through DNA metabarcoding of kick-net is suitable for ecological biomonitoring applications. The shift to a more robust sampling approach and capturing diatoms as well as macroinvertebrates in a single sampling event has the potential to significantly improve efficiency of biomonitoring programmes that currently only use the kick-net technique to sample macroinvertebrates.

Diatoms as indicators of environmental health on Korean islands

Diatoms are highly sensitive to perturbations in their environment and are thus useful as bioindicators for anthropogenic impacts such as pollution. However, there is no consensus about what aspects of diatom populations to measure (e.g., diversity, physiology, or morphology) and efficient and reliable survey protocols are lacking. Here, we evaluated the ecological status of diatom communities using both traditional and relatively novel methods on two islands (Deokjeok island and Daeijak island) affected by anthropogenic activities due to extensive agricultural practices and exploitation and that are under consideration for representative touristic sites in South Korea. Dissolved concentrations of metals and metalloid (As, Cu, Cr, Cd, Ni, Hg, Pb, and Zn) were below the ecological screening and toxicity reference values in water fractions but were above these values for sediment, particularly at one island, Deokjeok. The tested methods were generally consistent in finding little evidence for disruption of diatom communities, with dominance by Navicula and Gyrosigma, relatively high diversity, and typical abundance of lipid bodies and morphological deformities. However, analysis of lipid bodies and morphological deformities suggested greater potential anthropogenic disturbance at one site in Deokjeok. Future planning is required to ensure the maintenance of the near-pristine environments present on these islands.

Excess of nitrogen reduces temporal variability of stream diatom assemblages

Nutrient enrichment degrades water quality and threatens aquatic biota. However, our knowledge on (dis)similarities in temporal patterns of biota among sites of varying level of nutrient stress is limited. We addressed this gap by assessing temporal (among seasons) variation in algal biomass, species diversity and composition of diatom assemblages in three streams that differ in nutrient stress, but are otherwise similar and share the same regional species pool. We monitored three riffle sections in each stream bi-weekly from May to October in 2014. Temporal variation in water chemistry and other environmental variables was mainly synchronous among riffles within streams and often also among streams, indicating shared environmental forcing through time. We found significant differences in diatom assemblage composition among streams and, albeit less so, also among riffles within streams. Diatom assemblages in the two nutrient-enriched streams were more similar to each other than to those in the nutrient-poor stream. Taxa richness did not differ consistently among the streams, and did not vary synchronously at any spatial scale. Temporal variation in diatom assemblage composition decreased with increasing DIN:TotP ratio, likely via a negative effect on sensitive taxa while maintaining favorable conditions for certain tolerant taxa, irrespective of season. This relationship weakened but remained significant even after controlling for stochastic effects, suggesting deterministic mechanisms between nutrient levels and diatom assemblage stability. After controlling for stochastic effects temporal variability was best explained by DIN suggesting that excess of nitrogen reduces temporal variability(intra-annual beta diversity) of diatom assemblages. The high temporal variation, and especially the lack of temporal synchrony at the within streams scale, suggests that single sampling at a single site may be insufficient to reliably assess and monitor a complete stream water body. Our results also showed that measures including species identity outperform traditional diversity metrics in detecting nutrient stress in streams.

Biotic and Abiotic Factors Influencing Arsenic Biogeochemistry and Toxicity in Fluvial Ecosystems: A Review

This review is focused on the biogeochemistry of arsenic in freshwaters and, especially, on the key role that benthic microalgae and prokaryotic communities from biofilms play together in through speciation, distribution, and cycling. These microorganisms incorporate the dominant iAs (inorganic arsenic) form and may transform it to other arsenic forms through metabolic or detoxifying processes. These transformations have a big impact on the environmental behavior of arsenic because different chemical forms exhibit differences in mobility and toxicity. Moreover, exposure to toxicants may alter the physiology and structure of biofilms, leading to changes in ecosystem function and trophic relations. In this review we also explain how microorganisms (i.e., biofilms) can influence the effects of arsenic exposure on other key constituents of aquatic ecosystems such as fish. At the end, we present two real cases of fluvial systems with different origins of arsenic exposure (natural vs. anthropogenic) that have improved our comprehension of arsenic biogeochemistry and toxicity in freshwaters, the Pampean streams (Argentina) and the Anllóns River (Galicia, Spain). We finish with a briefly discussion of what we consider as future research needs on this topic. This work especially contributes to the general understanding of biofilms influencing arsenic biogeochemistry and highlights the strong impact of nutrient availability on arsenic toxicity for freshwater (micro) organisms.

Diatoms as indicators of the effects of river impoundment at multiple spatial scales

River impoundment constitutes one of the most important anthropogenic impacts on the World's rivers. An increasing number of studies have tried to quantify the effects of river impoundment on riverine ecosystems over the past two decades, often focusing on the effects of individual large reservoirs. This study is one of the first to use a large-scale, multi-year diatom dataset from a routine biomonitoring network to analyse sample sites downstream of a large number of water supply reservoirs (n = 77) and to compare them with paired unregulated control sites. We analysed benthic diatom assemblage structure and a set of derived indices, including ecological guilds, in tandem with multiple spatio-temporal variables to disclose patterns of ecological responses to reservoirs beyond the site-specific scale. Diatom assemblage structure at sites downstream of water supply reservoirs was significantly different to control sites, with the effect being most evident at the regional scale. We found that regional influences were important drivers of differences in assemblage structure at the national scale, although this effect was weaker at downstream sites, indicating the homogenising effect of river impoundment on diatom assemblages. Sites downstream of reservoirs typically exhibited a higher taxonomic richness, with the strongest increases found within the motile guild. In addition, Trophic Diatom Index (TDI) values were typically higher at downstream sites. Water quality gradients appeared to be an important driver of diatom assemblages, but the influence of other abiotic factors could not be ruled out and should be investigated further. Our results demonstrate the value of diatom assemblage data from national-scale biomonitoring networks to detect the effects of water supply reservoirs on instream communities at large spatial scales. This information may assist water resource managers with the future implementation of mitigation measures such as setting environmental flow targets.

Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France water framework directive networks

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.

DNA metabarcoding adds valuable information for management of biodiversity in roadside stormwater ponds

ABSTRACT

Stormwater ponds are used to compensate for the adverse effects that road runoff might have on the natural environment. Depending on their design and placement, stormwater ponds can act as both refugia and traps for local biodiversity. To evaluate the impact of stormwater ponds on biodiversity, it is critical to use effective and precise methods for identification of life associated with the water body. DNA metabarcoding has recently become a promising tool for identification and assessment of freshwater biodiversity.Using both morphology and DNA metabarcoding, we analyze species richness and biological composition of samples from 12 stormwater ponds and investigate the impact of pond size and pollution levels in the sediments and water column on the macroinvertebrate community structure.DNA metabarcoding captured and identified more than twice the number of taxa compared to morphological identification. The (dis)similarity of macroinvertebrate community composition in different ponds showed that the ponds appear better separated in the results obtained by DNA metabarcoding, but that the explained variation is higher for the results obtained by morphologically identification, since it provides abundance data.The reliance on morphological methods has limited our perception of the aquatic biodiversity in response to anthropogenic stressors, thereby providing inaccurate information for appropriate design and management of stormwater ponds; these drawbacks can be overcome by DNA metabarcoding. Synthesis and applications. The results indicate that DNA metabarcoding is a useful tool in identifying species, especially Diptera, which are difficult to determine. Application of DNA metabarcoding greatly increases the number of species identified at each sampling site, thereby providing a more accurate information regarding the way the ponds function and how they are affected by management.

OPEN PRACTICES

This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://www.ebi.ac.uk/ena/data/view/PRJEB30841.

Benthic Diatom Communities in an Alpine River Impacted by Waste Water Treatment Effluents as Revealed Using DNA Metabarcoding

Freshwater ecosystems are continuously affected by anthropogenic pressure. One of the main sources of contamination comes from wastewater treatment plant (WWTP) effluents that contain wide range of micro- and macropollutants. Chemical composition, toxicity levels and impact of treated effluents (TEs) on the recipient aquatic ecosystems may strongly differ depending on the wastewater origin. Compared to urban TEs, hospital ones may contain more active pharmaceutical substances. Benthic diatoms are relevant ecological indicators because of their high species and ecological diversity and rapid response to human pressure. They are routinely used for water quality monitoring. However, there is a knowledge gap on diatom communities’ development and behavior in treated wastewater in relation to prevailing micro- and macropollutants. In this study, we aim to (1) investigate the response of diatom communities to urban and hospital TEs, and (2) evaluate TEs effect on communities in the recipient river. Environmental biofilms were colonized in TEs and the recipient river up- and downstream from the WWTP output to study benthic diatoms using DNA metabarcoding combined with high-throughput sequencing (HTS). In parallel, concentrations of nutrients, pharmaceuticals and seasonal conditions were recorded. Diatom metabarcoding showed that benthic communities differed strongly in their diversity and structure depending on the habitat. TE sites were generally dominated by few genera with polysaprobic preferences belonging to the motile guild, while river sites favored diverse communities from oligotrophic and oligosaprobic groups. Seasonal changes were visible to lower extent. To categorize parameters important for diatom changes we performed redundancy analysis which suggested that communities within TE sites were associated to higher concentrations of beta-blockers and non-steroidal anti-inflammatory drugs in urban effluents vs. antibiotics and orthophosphate in hospital effluents. Furthermore, indicator species analysis showed that 27% of OTUs detected in river downstream communities were indicator for urban or hospital TE sites and were absent in the river upstream. Finally, biological diatom index (BDI) calculated to evaluate the ecological status of the recipient river suggested water quality decrease linked to the release of TEs. Thus, in-depth assessment of diatom community composition using DNA metabarcoding is proposed as a promising technique to highlight the disturbing effect of pollutants in Alpine rivers.

Multiple stressor effects on biodiversity and ecosystem functioning in a Mediterranean temporary river

The hydrological and biological complexity of temporary rivers as well as their importance in providing goods and services is increasingly recognized, as much as it is the vulnerability of the biotic communities in view of climate change and increased anthropogenic pressures. However, the effects of flow intermittency (resulting from both seasonal variations and rising hydrological pressure) and pollution on biodiversity and ecosystem functioning have been overlooked in these ecosystems. We explore the way multiple stressors affect biodiversity and ecosystem functioning, as well as the biodiversity-ecosystem functioning (B-EF) relationship in a Mediterranean temporary river. We measured diversity of benthic communities (i.e. diatoms and macroinvertebrates) and related ecosystem processes (i.e. resource use efficiency-RUE and organic matter breakdown-OMB) across a pollution and flow intermittency gradient. Our results showed decreases in macroinvertebrate diversity and the opposite trend in diatom assemblages, whereas ecosystem functioning was negatively affected by both pollution and flow intermittency. The explored B-EF relationships showed contrasting results: RUE decreased with higher diatom diversity, whereas OMB increased with increased macroinvertebrate diversity. The different responses suggest contrasting operating mechanisms, selection effects possibly driving the B-EF relationship in diatoms and complementarity effects driving the B-EF relationship in macroinvertebrates. The understanding of multiple stressor effects on diversity and ecosystem functioning, as well as the B-EF relationship in temporary rivers could provide insights on the risks affecting ecosystem functioning under global change.

Metal toxicity and recovery response of riverine periphytic algae

In the present study, in situ assessment of metal (Cu and Zn) toxicity followed by their recovery response was examined in periphyton dominated by diatoms. For doing so, metal diffusing substrates (MDS) were constructed and deployed in the river water for 6 weeks (3 weeks stress and 3 weeks recovery after replacing metal solution from the MDS). The use of MDS ensured that colonised periphyton on metal diffusing and control substrates were exposed to similar environmental conditions. The metal toxicity and recovery response of the community was examined in terms of traditional algal community parameters (biovolume, species richness, Shannon index, relative abundance) as well as with the newer non-taxonomical parameters (deformities and lipid bodies in diatoms). Both traditional and non-taxonomical parameters indicated complete recovery (from metal toxicity) of periphytic communities after 3 weeks following the withdrawal of Cu and Zn solution from the diffusing substrates. Newer non-taxonomical parameters, such as, deformities and lipid bodies, provide a new insight to understand metal toxicity and recovery response of diatom assemblages (the dominant autotrophs in the periphyton community) because these features are directly visible in live frustules, need no expertise in identification of diatoms and can be globally assessed with simple protocol. The experimental loss of metal pollutants and the constant immigration of algae (not previously exposed to high levels of metals) in fluvial systems aided periphyton recovery. Lastly, it is found that periphytic biofilms (dominated by diatoms) proved to be good bioindicators of metal toxicity and recovery in fluvial ecosystem.

Application of Environmental DNA Metabarcoding for Predicting Anthropogenic Pollution in Rivers

Rivers are among the most threatened freshwater ecosystems, and anthropogenic activities are affecting both river structures and water quality. While assessing the organisms can provide a comprehensive measure of a river's ecological status, it is limited by the traditional morphotaxonomy-based biomonitoring. Recent advances in environmental DNA (eDNA) metabarcoding allow to identify prokaryotes and eukaryotes in one sequencing run, and could thus allow unprecedented resolution. Whether such eDNA-based data can be used directly to predict the pollution status of rivers as a complementation of environmental data remains unknown. Here we used eDNA metabarcoding to explore the main stressors of rivers along which community structure changes, and to identify the method's potential for predicting pollution status based on eDNA data. We showed that a broad range of taxa in bacterial, protistan, and metazoan communities could be profiled with eDNA. Nutrients were the main driving stressor affecting communities' structure, alpha diversity, and the ecological network. We specifically observed that the relative abundance of indicative OTUs was significantly correlated with nutrient levels. These OTUs data could be used to predict the nutrient status up to 79% accuracy on testing data sets. Thus, our study gives a novel approach to predicting the pollution status of rivers by eDNA data.

Morphological, physiological and molecular responses of Nitzschia palea under cadmium stress

The impact of cadmium on the diatom Nitzschia palea (Kützing) W. Smith 1856 was studied by examining the relation between valve deformities and response through biological processes and genetic expression. Cultures of N. palea were exposed to two Cd treatments (C₁ = 2.4 ± 0.6 and C₂ = 42.6 ± 4.2 µg Cd/L) along with a control (C₀ = 0 µg Cd/L) for 28 days. Cadmium bioaccumulation, diatoms growth, photosynthetic efficiencies, valve deformities and genetic expression were investigated during the course of the experiment. Cadmium exposure had significant effects on bioaccumulation, growth, valve deformities and genetic expression. Maximal effects for all studied endpoints were recorded after 7 days of exposure for the C₂ treatment, which corresponded to the sampling time and condition with maximum cadmium bioaccumulation. Abnormal raphe formations (deviation from its lateral position) were significantly more abundant in the C₂ treatment compared to the control. Molecular responses were related to cadmium level based on the number of genes impacted, intensity of the response and the frequency of observations. The expression of genes involved in the regulation of mitochondrial metabolism, photosynthesis, oxidative stress and silica metabolism was affected by cadmium exposure.

A freshwater diatom challenged by Zn: Biochemical, physiological and metabolomic responses of Tabellaria flocculosa(Roth) Kützing

Freshwater ecosystems are under threatening anthropogenic pressures worldwide, namely by metals. Diatoms are used as water quality indicators, but the influence of micronutrients such as Zn and its impacts are poorly understood. Thus, our study aimed to elucidate the tolerance level, the cellular targets and the responses to counteract Zn toxicity of freshwater diatoms by exposing Tabellaria flocculosa, isolated from a Zn contaminated stream. Biochemical, physiological and metabolomic approaches were used. It was demonstrated that Zn is toxic to T. flocculosa at concentrations occurring in contaminated environments. At low stress (30 μg Zn/L) few alterations in the metabolome were observed, but the enzymatic (SOD, CAT) and molecular (GSH, GSSG) antioxidant systems were induced, protecting cells from oxidative stress. At moderate stress (500 μg Zn/L) the main changes occurred in the metabolome (increases in fatty acids, amino acids, terpenoids, glycerol and phosphate, decreases in sucrose and lumichrome) with a moderate increase in cell damage (LPO and PC). The concerted action of all these mechanisms resulted in a non-significant decrease of growth, explaining the survival of this T. flocculosa strain in an environment with this Zn concentration. At the highest stress level (1000 μg Zn/L) the metabolome was identical to 500 μg Zn/L, and the induction of antioxidant systems and extracellular ion chelation (exopolysaccharides, frustulins) were the main responses to the increase of Zn toxicity. However, these mechanisms were unable to effectively abrogate cellular damage and growth reduction was observed. Moreover, the decrease in sucrose and especially in lumichrome should be tested as new specific markers of Zn toxicity. The information obtained in this study can assist in environmental risk assessment policies, support the prediction of diatom behaviour in highly impacted Zn environments, such as mining scenarios, and may help develop new indices, which include alterations induced by metals.

Use the predictive models to explore the key factors affecting phytoplankton succession in Lake Erhai, China

Increasing algae in Lake Erhai has resulted in frequent blooms that have not only led to water ecosystem degeneration but also seriously influenced the quality of the water supply and caused extensive damage to the local people, as the lake is a water resource for Dali City. Exploring the key factors affecting phytoplankton succession and developing predictive models with easily detectable parameters for phytoplankton have been proven to be practical ways to improve water quality. To this end, a systematic survey focused on phytoplankton succession was conducted over 2 years in Lake Erhai. The data from the first study year were used to develop predictive models, and the data from the second year were used for model verification. The seasonal succession of phytoplankton in Lake Erhai was obvious. The dominant groups were Cyanobacteria in the summer, Chlorophyta in the autumn and Bacillariophyta in the winter. The developments and verification of predictive models indicated that compared to phytoplankton biomass, phytoplankton density is more effective for estimating phytoplankton variation in Lake Erhai. CCA (canonical correlation analysis) indicated that TN (total nitrogen), TP (total phosphorus), DO (dissolved oxygen), SD (Secchi depth), Cond (conductivity), T (water temperature), and ORP (oxidation reduction potential) had significant influences (p < 0.05) on the phytoplankton community. The CCA of the dominant species found that Microcystis was significantly influenced by T. The dominant Chlorophyta, Psephonema aenigmaticum and Mougeotia, were significantly influenced by TN. All results indicated that TN and T were the two key factors driving phytoplankton succession in Lake Erhai.

Evaluating features of periphytic diatom communities as biomonitoring tools in fresh, brackish and marine waters

The aims of this study were to assess the biodiversity of periphytic diatom assemblages in fresh, brackish and marine waterbodies of Korea, and to assess the effect of environmental and anthropogenic factors on parameters such as the quantity and biovolume of lipid bodies and deformations of diatoms as early warning measures of anthropogenic impact. Diatom samples were collected from 31 sites (14 freshwater, 10 brackish and 7 marine), which included less impacted (upstream) and impacted (downstream) sites in each water type. Our results showed higher abundance and biodiversity of periphytic diatoms at the less impacted sites in terms of species richness, Shannon index, cell count and biovolume of the communities than at the impacted sites for freshwater and estuarine sites, but not for marine sites. 84 diatom species were noted in freshwater, 80 in brackish water and 40 in marine waters. In comparison to diatoms of the impacted sites, those of less impacted freshwater, brackish and marine sites had less lipid bodies (also less biovolume) and a lower percentage of teratological frustules, and showed more mobile forms in the community. Principal component analysis (PCA) also showed clear segregation of impacted from less impacted sites by the extent of the presence of lipid bodies (higher both in number and biovolume) and deformities in diatom frustules. Pearson correlation analysis revealed that lipid body induction and deformities were positively correlated with metals (Cd, Co, Cr, Cu, Fe, Pb and Zn) and nutrients (total phosphorus and total nitrogen), whereas they showed negative correlation with salinity, dissolved oxygen, suspended solutes and pH. Life-forms, lipid bodies and deformities in diatoms may be an effective biomonitoring tool for assessing biological effects of pollutants in non-marine aquatic ecosystems in Korea.