| 1. |
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| 2. |
- Corcoll, Natàlia, 1981, et al.
(author)
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Linking pesticide pollution with periphyton quality in agricultural streams: a fatty-acids approach
- 2018
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In: SETAC Europe 28th Annual Meeting 13−17 May 2018 | Rome, Italy. Abstract Book.. - 2309-8031.
-
Conference paper (peer-reviewed)abstract
- Although the environmental risks associated with pesticide pollution in agricultural streams are quite well documented, little is know about its potential effects on periphyton quality. Periphyton provides many of the essential polyunsaturated fatty acids (PUFA) that are needed for organisms at higher trophic levels in river food webs. This study aims to assess the effects of pesticide mixtures on periphyton quality in situ. Three streams (Höje å, Skivarpsån and M42) located in the agriculturally dominated region of Skåne (SE Sweden) were sampled in September and October 2016. The effects of pesticide pollution were assessed by passive field sampling coupled with laboratory ecotoxicity tests, by mixture toxicity modelling to predict which chemical stressors were potentially driving the toxicity, and by examining the fatty acid profiles, pigment content and algal diversity of periphyton communities. Results from water chemical analyses clearly showed higher levels of nutrients and pesticide pollution in Skivarpsån and M42 than in Höje å. Ecotoxicity tests using the passive sampler extracts demonstrated that the pesticide mixtures ocurring at Skivarpsån and M42 were toxic for periphyton communities from Höje å, causing an inhibition of the photosynthetic activity up to 63% and 53%, respectively. Cluster and principal component analyses based on pigments content, algal diversity and fatty acid profiles, clearly separated the periphyton from the three river sites studied. Algal biomass from periphyton of pesticide polluted streams (Skivarpsån and M42) was higher than in Höje å. The nutritive quality of the periphyton differed among streams, and fatty acids considered high-quality such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) were also more abundant in pesticide polluted streams (Skivarpsån and M42). Overal, even though results from the lab show that the mixture of pesticides pollution in the studied streams might be toxic for periphyton (i.e. inhibiting the photosynthetic activity), being herbicides the driving chemical stressors. Results from the field, indicate that when the levels of pesticide pollution are low and co-occur with high levels of nutrients pollution, nutrients migh mask pesticides effects on periphyton quantity and quality because compensatory effects from nutrients
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| 3. |
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| 4. |
- Diehl, Sebastian, et al.
(author)
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Inverse relationship of epilithic algae and pelagic phosphorusin unproductive lakes : Roles of N2 fixers and light
- 2018
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In: Freshwater Biology. - Chichester : Wiley-Blackwell Publishing Inc.. - 0046-5070 .- 1365-2427. ; 63:7, s. 662-675
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Journal article (peer-reviewed)abstract
- 1. Phosphorus (P) often limits the biomass of primary producers in freshwater lakes. However, in unproductive northern lakes, where anthropogenic nitrogen (N) deposition is low, N instead of P can limit primary producers. In addition, light can be limiting to primary producers at high concentrations of coloured dissolved organic matter (cDOM), as cDOM is the major determinant of light penetration in these lakes.2. To address resource limitation of epilithic algal biomass, we repeatedly sampled epilithon (periphyton on stony substrata) in 20 lakes covering a large, correlated cDOM and N-deposition gradient across boreal and subarctic Sweden. Across these lakes, pelagic total N (TN) and total P (TP) were positively correlated, and benthic light supply was negatively correlated, with cDOM. Microscopically determined algal biovolume and epilithic carbon (C), N and P were subsequently regressed against benthic light supply and pelagic TN and TP.3. Patterns in epilithic biovolume were driven by N2-fixing cyanobacteria, which accounted for 2%–90% of total epilithic biovolume. Averaged over the growing season, epilithic algal biovolume, C and N were negatively related to TP and positively to TN, and were highest in the clearest, most phosphorus-poor lakes, where epilithon was heavily dominated by potentially N2-fixing cyanobacteria.4. A structural equation model supports the hypothesis that cDOM had two counteracting effects on total epilithic algal biovolume: a positive one by providing N to algae that depend on dissolved N for growth, and a negative one by shading N2-fixing cyanobacteria, with the negative effect being somewhat stronger.5. Together, these findings suggest that (1) light and N are the main resources limiting epilithic algal biomass in boreal to subarctic Swedish lakes, (2) epilithic cyanobacteria are more competitive in high-light and low-nitrogen environments, where their N2-fixing ability allows them to reach high biomass, and (3) epilithic N increases with N2 fixer biomass and is—seemingly paradoxically—highest in the most oligotrophic lakes. © 2018 John Wiley & Sons Ltd
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| 5. |
- Drakare, Stina, et al.
(author)
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Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive
- 2018
-
In: Water Research. - : Elsevier BV. - 0043-1354 .- 1879-2448. ; 138, s. 192-205
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Research review (peer-reviewed)abstract
- Assessment of ecological status for the European Water Framework Directive (WFD) is based on “Biological Quality Elements” (BQEs), namely phytoplankton, benthic flora, benthic invertebrates and fish. Morphological identification of these organisms is a time-consuming and expensive procedure. Here, we assess the options for complementing and, perhaps, replacing morphological identification with procedures using eDNA, metabarcoding or similar approaches. We rate the applicability of DNA-based identification for the individual BQEs and water categories (rivers, lakes, transitional and coastal waters) against eleven criteria, summarised under the headlines representativeness (for example suitability of current sampling methods for DNA-based identification, errors from DNA-based species detection), sensitivity (for example capability to detect sensitive taxa, unassigned reads), precision of DNA-based identification (knowledge about uncertainty), comparability with conventional approaches (for example sensitivity of metrics to differences in DNA-based identification), cost effectiveness and environmental impact. Overall, suitability of DNA-based identification is particularly high for fish, as eDNA is a well-suited sampling approach which can replace expensive and potentially harmful methods such as gill-netting, trawling or electrofishing. Furthermore, there are attempts to replace absolute by relative abundance in metric calculations. For invertebrates and phytobenthos, the main challenges include the modification of indices and completing barcode libraries. For phytoplankton, the barcode libraries are even more problematic, due to the high taxonomic diversity in plankton samples. If current assessment concepts are kept, DNA-based identification is least appropriate for macrophytes (rivers, lakes) and angiosperms/macroalgae (transitional and coastal waters), which are surveyed rather than sampled. We discuss general implications of implementing DNA-based identification into standard ecological assessment, in particular considering any adaptations to the WFD that may be required to facilitate the transition to molecular data.
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| 6. |
- Drakare, Stina, et al.
(author)
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Redundancy in the ecological assessment of lakes: Are phytoplankton, macrophytes and phytobenthos all necessary?
- 2016
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In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 568, s. 594-602
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Journal article (peer-reviewed)abstract
- Although the Water Framework Directive specifies that macrophytes and phytobenthos should be used for the ecological assessment of lakes and rivers, practice varies widely throughout the EU. Most countries have separate methods for macrophytes and phytobenthos in rivers; however, the situation is very different for lakes. Here, 16 countries do not have dedicated phytobenthos methods, some include filamentous algae within macrophyte survey methods whilst others use diatoms as proxies for phytobenthos. The most widely-cited justification for not having a dedicated phytobenthos method is redundancy, i.e. that macrophyte and phytoplankton assessments alone are sufficient to detect nutrient impacts. Evidence from those European Union Member States that have dedicated phytobenthos methods supports this for high level overviews of lake condition and classification; however, there are a number of situations where phytobenthos may contribute valuable information for the management of lakes. (C) 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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| 7. |
- Epp, Alexandra, et al.
(author)
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Sialylation of IgG antibodies inhibits IgG-mediated allergic reactions
- 2018
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In: Journal of Allergy and Clinical Immunology. - : Elsevier BV. - 1097-6825 .- 0091-6749. ; 141:1, s. 8-402
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Journal article (peer-reviewed)abstract
- In presence of high allergen dosis besides IgE also IgG antibodies can induce allergic reactions, whose severity is dependent on the induced type of IgG Fc glycosylation, what should be considered for new AIT protocols containing new adjuvants.
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| 8. |
- Feckler, Alexander, et al.
(author)
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Blinded by the light: Increased chlorophyll fluorescence of herbicide-exposed periphyton masks unfavorable structural responses during exposure and recovery
- 2018
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In: Aquatic Toxicology. - : Elsevier BV. - 0166-445X .- 1879-1514. ; 203, s. 187-193
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Journal article (peer-reviewed)abstract
- In surface waters within agricultural catchments, periphyton - i.e., biofilms containing algae, heterotrophs, and associated detritus - is subjected to multiple stressors including herbicides. Although herbicide effects on periphyton are frequently studied, the focus has been on photosynthesis-inhibiting herbicides while other modes of toxic action have received little attention. Against this background, a 21-days-lasting bioassay was conducted, during which mature periphytic communities were exposed to the carotenoid-biosynthesis-inhibiting herbicide diflufenican for 12 days (up to 10 mu g/L; n = 4), followed by a 9-days-lasting recovery phase in herbicide-free medium. Variables related to periphytic functioning (photosynthetic efficiency and non-photochemical quenching) and structure (pigment concentrations, biomass, and algal community structure) were quantified every third day during both experimental phases. Exposure to >= 0.2 mu g diflufenican/L resulted in 20-25% and 25-30% lowered carotenoid and chlorophyll a concentrations, respectively, likely explained by a reduced algal biovolume as well as diflufenican's mode of toxic action and thus a shift towards a higher heterotrophy of the communities. Despite these adverse effects on the photosynthetic apparatus, the photosynthetic efficiency increased by up to similar to 15% under diflufenican exposure judged on higher chlorophyll fluorescence. This may be explained by an up to similar to 60% reduced non-photochemical quenching as well as binding of diflufenican to the pigment-protein membrane complex of the photosystem II, two processes causing higher chlorophyll fluorescence. Additionally, phototrophs may have actively increased energy assimilation to cope with higher energy demands under chemical stress. Although periphyton showed some recovery potential following the exposure phase, observed as increasing chlorophyll a concentrations and non-photochemical quenching, periphyton may not be able to quickly recover from stress given the persistent increase in the photosynthetic efficiency. While the processes underlying the observed effects yet remain speculative, the results suggest a shift towards a higher degree of heterotrophy in periphytic communities ultimately increasing the importance of heterotrophic ecosystem functions at impacted sites over the long term.
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| 9. |
- Feckler, Alexander, et al.
(author)
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Impacts of Contaminants on the Ecological Role of Lotic Biofilms
- 2015
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In: Bulletin of Environmental Contamination and Toxicology. - : Springer Science and Business Media LLC. - 0007-4861 .- 1432-0800. ; 95, s. 421-427
-
Research review (peer-reviewed)abstract
- Biofilms play a fundamental ecological role in freshwater ecosystems as they contribute to ecosystem function(s) such as autotrophic primary production, organic matter decomposition and the bottom-up directed energy transfer in the food web. The present focused review summarizes the scientific knowledge on how the roles of autotrophic and heterotrophic biofilms can be modulated as a response to chemical (i.e., pesticide) stress. We discuss how horizontal effects (alterations in the structure of biofilms) can affect the physiological fitness and life history strategy of the next trophic level (vertical effects), namely primary consumers. Since the literature indicates that heterotrophic biofilms are currently at risk as a result of pesticide stress, the protectiveness of environmental risk assessment in Europe as well as North America is questioned. By briefly outlining substantial knowledge gaps, we provide ideas on how the identified uncertainties may be empirically addressed.
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| 10. |
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| 11. |
- Goedkoop, Willem, et al.
(author)
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CAFF Circumpolar Biodiversity Monitoring Program State of Arctic Freshwater Biodiversity Report
- 2019
-
Reports (other academic/artistic)abstract
- Arctic freshwater ecosystems (lakes, rivers, and associated wetlands) are threatened by climate change and human development that can affect freshwater biodiversity. Such effects will change not only the distributions and abundances of aquatic species, but also the lives of Arctic Peoples that are dependent on the ecosystem services supplied by lakes and rivers. Thus, the freshwater biodiversity program of the Circumpolar Biodiversity Monitoring Program (Freshwater-CBMP) focuses on lake and river ecosystems and has established a long-term monitoring framework for these Arctic freshwaters. Developed for the Conservation of Arctic Flora and Fauna (CAFF; the biodiversity Working Group of the Arctic Council), this framework facilitates more accurate and rapid detection, communication and response to significant trends in Arctic water quality and biodiversity. Freshwater-CBMP goals are addressed in the “Arctic Freshwater Biodiversity Monitoring Plan”, which describes an integrated, ecosystem-based approach for monitoring Arctic freshwaters.
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| 12. |
- Goedkoop, Willem, et al.
(author)
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Undersökning av pesticidorsakade effekter på bentiska organismsamhällen i jordbrukspåverkade vattendrag
- 2018
-
Reports (other academic/artistic)abstract
- Under 2015 och 2016 provtogs sammanlagt 32 respektive 13 vattendrag i jordbruksbygder med avseende paett antal biologiska variabler (pavaxtalger, meiofauna och makroskopisk bottenfauna) bottenfauna och medavseende pa oorganisk vattenkemi (narsalter, metaller, alkalinitet, m.m.). Proverna togs och analyserades avackrediterad personal vid SLU. Backarna ingick i det screeninguppdrag som SLU fick av Naturvardsverket2015–2016, utom 4 som utgor del av det nationella miljoovervakningsprogrammet (M42, N34, O18, E21).Undersokningen en unik mojlighet att fa ett dataunderlag som innefattar bade kvantifieringar av exponeringenmed bekampningsmedel (beraknat som toxiska enheter, ΣTU, med akuta EC50-varden) och den biologiskaresponsen hos olika organismgrupper i jordbrukspaverkade vattendrag.Generellt var det svart att koppla analyser av de biologiska samhallena till exponeringen medbekampningsmedel (ΣTU). Det beror framst pa att toppar med kraftiga fororeningar med bekampningsmedelnoterades endast i enstaka fall. Analyserna visade att exponeringen for alger oftast overskred EU:s uniformprinciples, en regulatorisk koncentration for vilken inga effekter ska forekomma for enskilda substanser.Pavaxtalgerna har dock en kort generationstid och en snabb tillvaxt och torde visa en snabb aterhamtning efteren exponering.Analys av algssamhallena uppvisade en stor variation i biomassa och artsammansattning blandvattendragen. Tradformiga gronalger och tradformiga rodalger var vanligt forekommande, och kiselalger,framforallt arter som lever som enstaka celler, fanns pa alla lokaler. De flesta algtaxa ar typiska for naringsrikavattendrag och vatten med neutralt eller hogt pH. Forekomsten av rodalger tyder pa en mojlig begransningmed ljus i vissa backar, och forekomsten av kiselalgstaxon Diadesmis contenta var. contenta tyder pa starkavattenstandsforandringar i andra. Den ekologiska statusklassningen med fastsittande kiselalger bekraftade attde flesta vattendrag var naringsrika, framforallt rika pa fosfor, samt att nagra aven var mattligt eller starktpaverkade av organiska, syretarande fororeningar. De flesta av vattendragen klassades som mattlig ekologiskstatus. Andelen deformerade kiselalgsskal overskred 1% pa en tredjedel av lokalerna vilket kan tyda pa enpaverkan av miljogifter sasom metaller eller bekampningsmedel. Redundansanalys for kiselalger visade intepa en signifikant paverkan fran herbiciderna. Daremot paverkades kiselalgernas artsammansattning signifikantav aluminium-, jarn- och kvavekoncentrationerna i vattnet.Bottenfaunadata visade att alla vattendrag utom O18 uppnar hog eller god ekologisk status narbedomningen gors med ASPT. For SPEARpesticides-indexet lag samtliga varden utom fyra under 33, vilket i denvetenskapliga litteraturen anges som grans for god-mattlig status, utan att ha en formell sadan status iTyskland. SPEARpesticides visar med andra ord en helt annan bild an ASPT som ingar i de svenskabedomningsgrunderna. Bade ASPT och SPEARpesticides visar dock, liksom i tidigare analyser, ett starktstatistiskt samband (R2 = 0,62). Det starka sambandet tyder pa att de bada indexen i stort satt mater sammapaverkan, fast i olika skalor. Tidigare analyser har ocksa visat att bada indexen visar ett starkt samband medandelen jordbruksmark i vattendragens avrinningsomrade. Varken ASPT eller SPEARpesticides visar ett tydligtsamband med den maximalt uppmatta ΣTUDaphnia under sasongen, vilket kan beror pa de generellt laga vardenfor ΣTUDaphnia.Redundansanalys visade att ΣTUDaphnia inte paverkade bottenfaunasamhallena signifikant. Daremot fannvi att meiofaunasamhallen i biofilmerna pa stenarna signifikant paverkades av ΣTUDaphnia. Resultatet kan beropa att denna mindre fauna lever mer exponerat och att vissa bekampningsmedel kan ackumulera i biofilmerna.Nematodfaunan i biofilmerna visade pa nema-SPEAR-varden under gransen for god status i Kavlingean,Segea och M42. Atta vattendrag hade en sa pass rik nematodfauna med manga fororeningskansliganematodarter att Nema-SPEAR indikerade hog ekologisk status.Analysen visar att vattendrag som erfar en stark jordbrukspaverkan och fysisk paverkan haller enoverraskande god status med avseende pa pavaxtalger och bottenfauna. En kombination av hoganasaltskoncentrationer, en god syresattning som foljd av stromforhallandena, samt en god tillgang till fodakan bidra till att vattendragen far en rik bottenfauna och forhallandevist hoga indexvarden. Aven det faktumatt provtagning gors pa de sparsamma steniga bottnarna (dar mojligt) i de annars sand/lerbottendomineradevattendragen kan bidra till att de visar forhallandevis hog status.
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| 13. |
- Goncalves, Sara, et al.
(author)
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A freshwater diatom challenged by Zn: Biochemical, physiological and metabolomic responses of Tabellaria flocculosa(Roth) Kutzing
- 2018
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In: Environmental Pollution. - : Elsevier BV. - 0269-7491 .- 1873-6424. ; 238, s. 959-971
-
Journal article (peer-reviewed)abstract
- 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 mu g 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 mu g 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 mu g Zn/L) the metabolome was identical to 500 mu g 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. (C) 2018 Elsevier Ltd. All rights reserved.
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| 14. |
- Goncalves, Sara, et al.
(author)
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Assessing Cu impacts on freshwater diatoms: biochemical and metabolomic responses of Tabellaria flocculosa (Roth) Kutzing
- 2018
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In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 625, s. 1234-1246
-
Journal article (peer-reviewed)abstract
- Metals are a recognised threat to aquatic organisms but the impact of metals such as copper (Cu) on benthic freshwater diatoms is poorly understood, even if diatoms are commonly used as water quality indicators. Our study aimed to elucidate the cellular targets of Cu toxicity and the mechanisms cells resort to counteract toxicity and to increase tolerance to Cu. A concerted approach analysing the biochemical, physiological and metabolome alterations in diatom cells was conducted by exposing the freshwater diatom Tabellaria flocattosa to 0, 0.3, 6 and 10 mu g Cu/L. Cu was already toxic to T. flocculosa at concentrations common in environments and which are not usually considered to be contaminated (0.3 mu g Cu/L). Under Cu impact, the metabolome of T. flocculosa changed significantly, especially at high concentrations (6 and 10 mu g Cu/L). Cu toxicity was counteracted by increasing extracellular immobilization (EPS, frustulins), antioxidant (SOD, CAT) and detoxifying (GSTs) enzymes activity and low molecular weight antioxidants (GSH). These mechanisms were fuelled by higher energy production (increased ETS activity). At the highest Cu concentration (10 mu g/L), these processes were specially enhanced in an attempt to restrain the oxidative stress generated by high intracellular Cu concentrations. However, these mechanisms were not able to fully protect cells, and damage in membranes and proteins increased. Moreover, the decrease of hydroxylamine and unsaturated fatty acids and the increase of saturated fatty acids, 2-palmiloylglycerol, glycerol and diterpenoid compounds should be tested as new specific markers of Cu toxicity in future studies. This information can support the prediction of diatom behaviour in different Cu contamination levels, including highly impacted environments, such as mining scenarios, and may assist in environmental risk assessment policies and restoration programs. (C) 2018 Elsevier B.V. All rights reserved.
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| 15. |
- Goncalves, Sara, et al.
(author)
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Valve teratologies and Chl c in the freshwater diatom Tabellaria flocculosa as biomarkers for metal contamination
- 2019
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In: Ecological Indicators. - : Elsevier BV. - 1470-160X .- 1872-7034. ; 101, s. 476-485
-
Journal article (peer-reviewed)abstract
- Freshwater benthic diatoms, routinely used for bioassessment, are potential metal indicators because of their known capacity to reflect changes in water chemistry. Nevertheless, the effect of metals on benthic freshwater diatoms is still poorly understood. Metals, such as Zn and Cu, are not only essential as micronutrients, but also one of the main anthropogenic pressures in aquatic ecosystems. However, metal stress cannot be detected with the current European standard methods using bioindicators for environmental assessment, so new tools need to be developed. We studied the effects of Zn and Cu on the freshwater diatom Tabellaria flocculosa. This diatom isolated from a Zn and Cu contaminated stream, was exposed to different concentrations of Zn and Cu, and the metal effects were assessed by measuring physiological ((growth, fluorescence, pigments' content (Chl a, c, carotenoids)) and morphological parameters (teratological forms). We found that at environmental concentrations occurring in European streams, Zn and Cu showed toxic effects on T. flocculosa. Toxic effects induced by Zn were only observed at high concentrations (500 and 1000 mu g/L), resulting in fluorescence changes, an increase of Chl c cellular content and an increase of teratological forms (with an increase of more heavily deformed valves with increasing metal concentrations). Increasing Cu exposure induced several changes, such as increasing the cellular content of Chl a and c, while carotenoids' cellular content decreased. Cu also increased the number of T. flocculosa frustule deformations. Cu did not affect the cellular fluorescence. Our results thus show that the frequency of diatom teratologies could potentially be used to assess metal stress for the studied metals Zn and Cu. Additionally, the analysis of algal pigments could potentially separate the effects of different metals.
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| 16. |
- Hasselquist, Eliza Maher, et al.
(author)
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Contrasting Responses among Aquatic Organism Groups to Changes in Geomorphic Complexity Along a Gradient of Stream Habitat Restoration : Implications for Restoration Planning and Assessment
- 2018
-
In: Water. - : MDPI. - 2073-4441. ; 10:10
-
Journal article (peer-reviewed)abstract
- Many stream restoration projects aim to increase geomorphic complexity, assuming that this increases habitat heterogeneity and, thus, biodiversity. However, empirical data supporting these linkages remain scant. Previous assessments of stream restoration suffer from incomplete quantification of habitat complexity, or a narrow focus on only one organism group and/or one restoration measure, limiting learning. Based on a comprehensive quantification of geomorphic complexity in 20 stream reaches in northern Sweden, ranging from streams channelized for timber floating to restored and reference reaches, we investigated responses of macroinvertebrates, diatoms, and macrophytes to multiple geomorphic metrics. Sediment size heterogeneity, which was generally improved in restored sites, favored macroinvertebrate and diatom diversity and macroinvertebrate abundance. In contrast, macrophyte diversity responded to increased variation along the longitudinal stream profile (e.g., step-pools), which was not consistently improved by the restoration. Our analyses highlight the value of learning across multiple restoration projects, both in identifying which aspects of restoration have succeeded, and pinpointing other measures that might be targeted during adaptive management or future restoration. Given our results, a combination of restoration measures targeting not only sediment size heterogeneity, but also features such as step-pools and instream wood, is most likely to benefit benthic biota in streams.
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| 17. |
- Kahlert, Maria
(author)
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Application of high-throughput sequencing (HTS) metabarcoding to diatom biomonitoring: Do DNA extraction methods matter?
- 2017
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In: Freshwater Science. - : University of Chicago Press. - 2161-9549 .- 2161-9565. ; 36, s. 162-177
-
Journal article (peer-reviewed)abstract
- Current freshwater biomonitoring with diatoms is based on microscopic examination of the morphology of their silica skeleton. This standardized approach is time consuming and requires a high degree of taxonomic expertise. Metabarcoding combined with high-throughput sequencing (HTS) has great potential for next-generation biomonitoring applications but requires standardization. Molecular inventories are strongly influenced by the DNA extraction method used, but the effect of extraction protocols has not been tested to enable selection of the best DNA extraction method for HTS metabarcoding. We used 5 DNA extraction methods combining various types of cell lysis and DNA purification to extract DNA from 8 pure diatom cultures and 8 samples from streams and lakes with differing water quality. We compared the methods based on: 1) quality and purity of the extracted DNA, 2) community inventories obtained from HTS targeting the ribulose-1, 5-bisphosphate carboxylase (rbcL) barcode, and 3) similarity between molecular and microscopy-based inventories of community composition and the Specific Pollution sensitivity Index [SPI]. A method based on GenEluteTM-LPA had higher extraction efficiency than the 4 commercial kits but had the highest polymerase chain reaction inhibition level. All 5 methods were efficient for HTS, and method did not affect operational taxonomic unit richness. We observed variations in the relative abundance of some taxa within Nitzschia, Amphora, Encyonerna, Gomphonema, and Navicula between 2 of the 5 methods, but method did not affect global diatom community composition or SPI values. SPI values calculated from microscopy-based inventories and molecular inventories based on all 5 extraction methods were strongly correlated. For convenience purposes (high DNA quantity and low cost), we encourage standardization of FITS diatom biomonitoring based on the SA-Gen method.
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| 18. |
- Kahlert, Maria
(author)
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Applied use of taxonomy: lessons learned from the first German intercalibration exercise for benthic diatoms
- 2015
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In: Acta Botanica Croatica. - : Walter de Gruyter GmbH. - 0365-0588. ; 74, s. 211-232
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Journal article (peer-reviewed)abstract
- The first German intercalibration exercise for benthic diatoms was conducted to improve the application of the implementation of the European Water Framework Directive for running waters and lakes in Germany. The intercalibration exercise revealed several taxonomic problems. Among others, considerable problems occurred with identifying and differentiating species of the following four groups: (I) Amphora indistincta Levkov and A. pediculus (Kutzing) Grunow, (II) Cocconeis placentula var. euglypta Ehrenberg and C. placentula var. lineata (Ehrenberg) Van Heurck, (III) Navicula cryptotenella Lange-Bertalot and N. cryptotenelloides Lange-Bertalot and (IV) N. reichardtiana Lange-Bertalot and N. caterva Hohn & Hellermann. The taxonomic problems that emerged occurred due to both insufficient use of given taxonomic details (by limnologists) and ambiguous species descriptions and documentation (by taxonomists). Thus, we recommend to the applied limnologist to use the mandatory identification literature and to document any ambiguous valves during routine counts. Also, it would be desirable to further investigate certain species by taxonomists and, in general, to provide more basic data with species descriptions or in identification manuals. These measures will improve the use of diatoms as bioindicators and consequently benefit both applied limnologists and taxonomists.
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| 19. |
- Kahlert, Maria
(author)
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Benthic diatoms in streams and lakes
- 2016
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In: Ecological Assessment of Swedish Water Bodies; development, harmonisation and integration of biological indicators. Final report of the research programme WATERS. Deliverable 1.1-4. - 9789163920981 ; 2016:10:2016:10, s. 44-50
-
Book chapter (other academic/artistic)abstract
- The Water Framework Directive was incorporated into Swedish legislation in 2004. Its aim is to develop sustainable management of European surface- and groundwater and with the implementation of the directive there was a need for development of monitoring programmes and tools for assessing water quality. In response to these needs the Swedish Environmental Protection Agency opened a call for research on "Biological assessment criteria in aquatic environments". As a result of this call, a consortium of 11 partners, was granted a total budget of 47 million SEK funded by the Swedish Environmental Protection Agency's Environmental Research Grant, to pursue the research programme WATERS during 5 years. WATERS has developed better indicators and methods for classification and references in Swedish lakes, streams and coastal waters. This provides a valuable basis for a new generation of biological assessment criteria to be defined by the authorities. WATERS has also developed general methods for assessing and reducing uncertainty in classification of ecological status, as well as harmonised and transparent methods for integrated assessment. In combination, these results are expected to improve and simplify future status assessments according to the Water Framework Directive. Several teams of ecologists specialised in limnic and marine waters have contributed, led by Jacob Carstensen, Aarhus university, Richard Johnson, Swedish university of agricultural sciences, Leif Pihl, University of Gothenburg and Sofia A Wikström, Stockholm university. The programme has been coordinated by Mats Lindegarth at the Swedish institute for the marine environment. We wish to express our sincere gratitude to everyone that has contributed to the success of the programme. WATERS steering group has consisted of the coordinator, team leaders and responsible contacts at the Swedish Agency for Marine and Water Management and the Swedish Environmental Protection Agency. These have been represented by Mats Svensson and Cecilia Lindblad respectively. The authors alone are responsible for the content of this report.
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| 20. |
- Kahlert, Maria, et al.
(author)
-
Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)
- 2019
-
In: Journal of Phycology. - : Wiley. - 0022-3646 .- 1529-8817. ; 55, s. 948-970
-
Journal article (peer-reviewed)abstract
- This paper explores the diversity and taxonomy of species within Fragilaria sensu stricto, an abundant and ecologically important diatom genus, taking advantage of cultured and DNA-barcoded material. The goal is to facilitate the identification of European taxa within this complex, providing a unified view on morphological and molecular diversity. There is a general agreement that the separation of species within the group of Fragilaria is difficult because morphological descriptions of species are not consistent between authorities, ongoing taxonomic revisions have resulted in species described with standards of the late 20th and 21st centuries alongside descriptions based on 19th century (light microscopical) criteria, and because not all diagnostic characters can be seen in all specimens encountered in routine analyses. Consequent confusion could blur potentially important ecological distinctions between species. Our study demonstrated that some species defined on morphological criteria could be confirmed using the rbcL chloroplast gene as a genetic marker, for example, Fragilaria gracilis, Fragilaria tenera, Fragilaria perminuta, and Fragilaria subconstricta. However, even for those species, preliminary identifications based on morphology often differed from identifications based on phylogenetic clustering combined with detailed morphological study. Clades were well-defined by rbcL, but based on morphology, the terminal taxa of these clades did not match the currently described Fragilaria species. To clarify recognition of these taxa, we describe three new species: Fragilaria agnesiae, Fragilaria heatherae, and Fragilaria joachimii.
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| 21. |
- Kahlert, Maria, et al.
(author)
-
Diatom teratologies as biomarkers of contamination: are all deformities ecologically meaningful?
- 2017
-
In: Ecological Indicators. - : Elsevier BV. - 1470-160X .- 1872-7034. ; 82, s. 539-550
-
Journal article (peer-reviewed)abstract
- Contaminant-related stress on aquatic biota is difficult to assess when lethal impacts are not observed. Diatoms, by displaying deformities (teratologies) in their valves, have the potential to reflect sub-lethal responses to environmental stressors such as metals and organic compounds. For this reason, there is great interest in using diatom morphological aberrations in biomonitoring. However, the detection and mostly the quantification of teratologies is still a challenge; not all studies have succeeded in showing a relationship between the proportion of abnormal valves and contamination level along a gradient of exposure. This limitation in part reflects the loss of ecological information from diatom teratologies during analyses when all deformities are considered. The type of deformity, the severity of aberration, species proneness to deformity formation, and propagation of deformities throughout the population are key components and constraints in quantifying teratologies. Before a metric based on diatom deformities can be used as an indicator of contamination, it is important to better understand the "ecological signal" provided by this biomarker. Using the overall abundance of teratologies has proved to be an excellent tool for identifying contaminated and non-contaminated environments (presence/absence), but refining this biomonitoring approach may bring additional insights allowing for a better assessment of contamination level along a gradient. The dilemma: are all teratologies significant, equal and/or meaningful in assessing changing levels of contamination? This viewpoint article examines numerous interrogatives relative to the use of diatom teratologies in water quality monitoring, provides selected examples of differential responses to contamination, and proposes solutions that may refine our understanding and quantification of the stress. This paper highlights the logistical problems associated with accurately evaluating and interpreting teratologies and stimulates more discussion and research on the subject to enhance the sensitivity of this metric in bioassessments.
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| 22. |
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| 23. |
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| 24. |
- Kahlert, Maria, et al.
(author)
-
DNA-streckkodning – nytt verktyg i miljöövervakningen
- 2018
-
In: Sötvatten 2017. - 9789188727022 ; , s. 17-19
-
Book chapter (pop. science, debate, etc.)abstract
- Enligt EU:s ramdirektiv för vatten ska bland annat den biologiska mångfalden i vatten kartläggas och rapporteras. Resultaten bildar underlag för bedömning av ett vattendrags ekologiska status med målet att alla vattendrag ska nå god ekologisk status till år 2021. Att kartlägga olika arter av exempelvis plankton, kiselalger och bottenfauna kan vara tidskrävande och komplicerat, och därigenom dyrt. Nu öppnar ny teknik med hjälp av DNA-streckkoder upp dörren för en snabbare och säkrare artbestämning, spårning av till exempel främmande arter och övervakning av olika vattenorganismer.
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| 25. |
- Kahlert, Maria, et al.
(author)
-
DNAqua-Net: developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe
- 2016
-
In: Research Ideas and Outcomes. - : Pensoft Publishers. - 2367-7163. ; 2
-
Journal article (peer-reviewed)abstract
- The protection, preservation and restoration of aquatic ecosystems and their functions are of global importance. For European states it became legally binding mainly through the EUWater Framework Directive (WFD). In order to assess the ecological status of a given water body, aquatic biodiversity data are obtained and compared to a reference water body. The quantified mismatch obtained determines the extent of potential management actions. The current approach to biodiversity assessment is based on morpho-taxonomy. This approach has many drawbacks such as being time consuming, limited in temporal and spatial resolution, and error-prone due to the varying individual taxonomic expertise of the analysts. Novel genomic tools can overcome many of the aforementioned problems and could complement or even replace traditional bioassessment. Yet, a plethora of approaches are independently developed in different institutions, thereby hampering any concerted routine application. The goal of this Action is to nucleate a group of researchers across disciplines with the task to identify gold-standard genomic tools and novel ecogenomic indices for routine application in biodiversity assessments of European fresh- and marine water bodies. Furthermore, DNAqua-Net will provide a platform for training of the next generation of European researchers preparing them for the new technologies. Jointly with water managers, politicians, and other stakeholders, the group will develop a DNAqua-Net: Developing new genetic tools for bioassessment and monitoring conceptual framework for the standard application of eco-genomic tools as part of legally binding assessments.
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| 26. |
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| 27. |
- Kahlert, Maria, et al.
(author)
-
Kiselalger i vattendrag : Utvärdering av det gemensamma delprogrammet
- 2015
-
Reports (other academic/artistic)abstract
- Rapporten redovisar den andra gemensamma utvärderingen av regional och nationell miljöövervakning inom det gemensamma delprogrammet ・Kiselalger i vattendrag.Den nationella provtagningen har fokus på vatten med hög status (Delprogram Trendvattendrag) och försurning (Delprogram IKEU). Därför fattas bland annat lokaler med måttlig status eller sämre och vattendrag med högt pH. Sammanlagt provtas drygt 90 vattendrag i dessa program, vilket innebär att inte alla vattendragstyper är väl representerade. De regionala programmen kompletterar med många fler vattendrag som har en ganska bra geografisk spridning i framförallt södra Sverige. Tyvärr fattas fjällregionen fortfarande helt i båda programmen. De regionala programmen kompletterar framförallt med lokaler med låg humushalt i regionerna 2-6, med hög alkalinitet i regionerna 4-6, med vatten som har god och måttlig ekologisk status samt med neutrala och alkaliska vatten (se figur 3 för regionindelning). För att kunna följa även starkt förorenade vattendrag bör även fler vatten med dålig eller otillfredsställande status ingå i det gemensamma delprogrammetUtvärderingen av de nationella programmen visar att Sveriges kiselalgsindex ACID och IPS uppvisar signifikanta trender i vattendrag med trender för surhet respektive totalfosfor. Det gäller även när dessa trender är svaga. Sambandet mellan index och påverkanstrender är lägre för de regionala programmen med sin glesare provtagning men fortfarande tydlig och signifikant för ACID. För IPS är variationen dock så stor i de regionala programmen att sambandet försvinner i bruset av variationen. Det har tidigare beräknats att variationskoefficienten för IPS i genomsnitt är 2,4 % och standardavvikelsen 0,37. Samtidigt har det visats att variationen är större i näringsrika (totalfosfor > 25 μg P/l) vattendrag ä i näingsfattiga. Det innebä att man i genomsnitt måte ha lägre tidsserier eller täare provtagning i måga av de regionala programmen med sina näingsrika vattendrag fö att upptäka en varaktig signifikant (signifikansnivåp=0,01) fösäring frå god till måtlig status med 80 % sannolikhet (Kahlert 2011). Eftersom de flesta regionala program istälet har glesare provtagning ä i det nationella programmet måte man räna med störe variationer och att föädringar kommer att upptäkas senare. Öerlag speglar de svenska kiselalgsindex korrekt att varken pH eller TP i de undersöta vattendragen uppvisar nåra störe föädringar öer de senaste tio åen.
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| 28. |
- Kahlert, Maria, et al.
(author)
-
Knowledge and monitoring gap analysis with respect to the EU Directives
- 2019
-
Reports (other academic/artistic)abstract
- This report presents the results of a review on gaps in Baltic Sea monitoring based on two different information sources: peer-reviewed scientific articles, and BONUS and HELCOM project reports. The reviews are part of the BONUS project FUMARI. Our main questions are:(1) does the current monitoring of the Baltic Sea sufficiently address the requirements set by the Marine Strategy Framework Directive, the Water Framework Directive and the HELCOM´s Baltic Sea Action Plan?(2) what are the most critical shortcomings (gaps) in the current Baltic Sea monitoring programs?We found that scientific articles dealing with Baltic Sea monitoring present a view on main monitoring gap occurrence, that differs from the view presented in reports dealing with the same topic. Both scientific articles and reports agreed that many thematic assessment categories are not monitored sufficiently, often due to insufficient spatial coverage. However, whereas articles often highlight both that a category is not sufficiently monitored, and that there is a lack of indicators, the reports focused more on gaps in data storage or handling, coordination of monitoring, or highlighted plans for new but non-operational indicators. Articles mainly mentioned gaps in relation to Eutrophication, Contaminants, Biodiversity, Commercial fish and shellfish, Food webs, Hydrographical conditions, and No alien species. Reports however indicated primarily Biodiversity gaps, followed by Contaminants and Healthy wildlife, Marine litter, and Sea-floor integrity. Our review also showed that certain categories are underrepresented in the scientific literature, i.e. with few scientists developing indicators or assessing data related to them, potentially indicating a knowledge gap in these fields.
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| 29. |
- Kahlert, Maria, et al.
(author)
-
Molecular versus morphological data for benthic diatoms biomonitoring in Northern Europe freshwater and consequences for ecological status
- 2019
-
In: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 3, s. 21-35
-
Journal article (peer-reviewed)abstract
- Diatoms are known to be efficient bioindicators for water quality assessment because of their rapid response to environmental pressures and their omnipresence in water bodies. The identification of benthic diatoms communities in the biofilm, coupled with quality indices such as the Indice de polluosensibilité spécifique (IPS) can be used for biomonitoring purposes in freshwater. However, the morphological identification and counting of diatoms species under the microscope is time-consuming and requires extensive expertise to deal with a constantly evolving taxonomy. In response, a molecular-based and potentially more cost-effective method has been developed, coupling high-throughput sequencing and DNA metabarcoding. The method has already been tested for water quality assessment with diatoms in Central Europe. In this study, we applied both the traditional and molecular methods on 180 biofilms samples from Northern Europe (rivers and lakes of Fennoscandia and Iceland). The DNA metabarcoding data were obtained on two different DNA markers, the 18S-V4 and rbcL barcodes, with the NucleoSpin Soil kit for DNA extraction and sequenced on an Ion Torrent PGM platform. We assessed the ability of the molecular method to produce species inventories, IPS scores and ecological status class comparable to the ones generated by the traditional morphology-based approach. The two methods generated correlated but significantly different IPS scores and ecological status assessment. The observed deviations are explained by presence/absence and abundance discrepancies in the species inventories, mainly due to the incompleteness of the barcodes reference databases, primer bias and strictness of the bioinformatic pipeline. Abundance discrepancies are less common than presence/absence discrepancies but have a greater effect on the ecological assessment. Missing species in the reference databases are mostly acidophilic benthic diatoms species, typical of the low pH waters of Northern Europe. The two different DNA markers also generated significantly different ecological status assessments. The use of the 18S-V4 marker generates more species inventories discrepancies, but achieves an ecological assessment more similar to the traditional morphology-based method. Further development of the metabarcoding method is needed for its use in environmental assessment. For its application in Northern Europe, completion and curation of reference databases are necessary, as well as evaluation of the currently available bioinformatics pipelines. New indices, fitted for environmental biomonitoring, should also be developed directly from molecular data.
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| 30. |
- Kahlert, Maria, et al.
(author)
-
New molecular methods to assess biodiversity. Potentials and pitfalls of DNA metabarcoding: a workshop report
- 2019
-
In: Research Ideas and Outcomes. - : Pensoft Publishers. - 2367-7163. ; 5
-
Journal article (other academic/artistic)abstract
- This report presents the outcome of the joint work of PhD students and senior researchers working with DNA-based biodiversity assessment approaches with the goal to facilitate others the access to definitions and explanations about novel DNA-based methods. The work was performed during a PhD course (SLU PNS0169) at the Swedish University of Agricultural Sciences (SLU) in Uppsala, Sweden. The course was co-organized by the EU COST research network DNAqua-Net and the SLU Research Schools Focus on Soils and Water (FoSW) and Ecology - basics and applications. DNAqua-Net (COST Action CA15219, 2016-2020) is a network connecting researchers, water managers, politicians and other stakeholders with the aim to develop new genetic tools for bioassessment of aquatic ecosystems in Europe and beyond. The PhD course offered a comprehensive overview of the paradigm shift from traditional morphology-based species identification to novel identification approaches based on molecular markers. We covered the use of molecular tools in both basic research and applied use with a focus on aquatic ecosystem assessment, from species collection to the use of diversity in environmental legislation. The focus of the course was on DNA (meta)barcoding and aquatic organisms. The knowledge gained was shared with the general public by creating Wikipedia pages and through this collaborative Open Access publication, co-authored by all course participants.
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| 31. |
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| 32. |
- Kahlert, Maria
(author)
-
Quality assurance of diatom counts in Europe: towards harmonized datasets
- 2016
-
In: Hydrobiologia. - : Springer Science and Business Media LLC. - 0018-8158 .- 1573-5117. ; 772, s. 1-14
-
Journal article (peer-reviewed)abstract
- Investigations on organism ecology, biodiversity and biogeography often use large compiled datasets to extract information on species ecological preferences, which then can be used in environmental assessment. Freshwater benthic diatoms are commonly used in this context. However, it is important that the taxonomic information of the separate diatom datasets is compatible. At present, inconsistencies between diatom datasets, mainly due to differences and uncertainties in diatom identification, may misinform diatom taxon-specific ecological preferences, geographical distribution and water quality assessment. It is our opinion that these inconsistencies in diatom datasets can be reduced with quality assurance (QA), such as identification exercises. However, the results of these exercises must be well documented and well communicated; otherwise, gained knowledge may not spread inter-regionally or internationally. As a first step to reach greater consistency in QA/harmonization studies, this article (1) presents and compares information of existing diatom identification and counting QA from published and grey (non-peer reviewed) European literature to identify advantages and drawbacks of each approach; (2) summarizes taxa that can easily be misidentified according to European identification exercises; and (3) suggests a consistent design of identification exercises for diatom dataset QA.
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| 33. |
- Kahlert, Maria, et al.
(author)
-
Similar small-scale variation of diatom assemblages on different substrates in a mesotrophic stream
- 2015
-
In: Acta Botanica Croatica. - : Walter de Gruyter GmbH. - 0365-0588. ; 74, s. 363-376
-
Journal article (peer-reviewed)abstract
- The aim of the present study was to analyze if small-scale spatial variation of benthic diatom assemblages has consequences for biomonitoring. Benthic diatom samples were collected at one sampling site in a mesotrophic stream in Middle-Sweden from stone and plant (macrophytes and mosses) substrate. Our results showed that spatial variation of both the diatom species composition and the calculated bioindices were similar on both small (distance of centimeter) and medium (distance of decimeters) scales. Spatial variation was also similar on both studied substrates. This implies that it does not matter if a small or a larger area is sampled for biomonitoring as long as no major environmental factors impact certain sites systematically. Diatom assemblages and indices were significantly different between substrates. Spatial variation did not contribute much to this variation, and variation on a slide was unimportant. These results confirm earlier findings that smallscale spatial variation is not a problem when using diatoms to detect anthropogenic impacts to a stream or lake.
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| 34. |
- Kahlert, Maria
(author)
-
Taming the Wild West of Molecular Tools Application in Aquatic Research and Biomonitoring
- 2019
-
In: Biodiversity Information Science and Standards. - : Pensoft Publishers. - 2535-0897. ; 3
-
Conference paper (other academic/artistic)abstract
- Modern high-throughput sequencing technologies are becoming a game changer in many fields of aquatic research and biomonitoring. To unfold their full potential, however, the independent development of approaches has to be streamlined. This discussion must be fuelled by stakeholders and practitioners and, scientific results collaboratively filtered to identify the most promising avenues. Furthermore, aspects such as time, budget, skills and the application context have to be considered, finally communicating good practice strategies to target audiences.
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| 35. |
- Kahlert, Maria
(author)
-
The best of both worlds: a combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods
- 2017
-
In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 12
-
Journal article (peer-reviewed)abstract
- An increasing number of studies use next generation sequencing (NGS) to analyze complex communities, but is the method sensitive enough when it comes to identification and quantification of species? We compared NGS with morphology-based identification methods in an analysis of microalgal (periphyton) communities. We conducted a mesocosm experiment in which we allowed two benthic grazer species to feed upon benthic biofilms, which resulted in altered periphyton communities. Morphology-based identification and 454 (Roche) pyro-sequencing of the V4 region in the small ribosomal unit (18S) rDNA gene were used to investigate the community change caused by grazing. Both the NGS-based data and the morphology-based method detected a marked shift in the biofilm composition, though the two methods varied strongly in their abilities to detect and quantify specific taxa, and neither method was able to detect all species in the biofilms. For quantitative analysis, we therefore recommend using both metabarcoding and microscopic identification when assessing the community composition of eukaryotic microorganisms.
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| 36. |
- Kahlert, Maria
(author)
-
The future of biotic indices in the ecogenomic era: Integrating (e) DNA metabarcoding in biological assessment of aquatic ecosystems
- 2018
-
In: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 637-638, s. 1295-1310
-
Research review (peer-reviewed)abstract
- The bioassessment of aquatic ecosystems is currently based on various biotic indices that use the occurrence and/or abundance of selected taxonomic groups to define ecological status. These conventional indices have some limitations, often related to difficulties in morphological identification of bioindicator taxa. Recent development of DNA barcoding and metabarcoding could potentially alleviate some of these limitations, by using DNA sequences instead of morphology to identify organisms and to characterize a given ecosystem. In this paper, we review the structure of conventional biotic indices, and we present the results of pilot metabarcoding studies using environmental DNA to infer biotic indices. We discuss the main advantages and pitfalls of metabarcoding approaches to assess parameters such as richness, abundance, taxonomic composition and species ecological values, to be used for calculation of biotic indices. We present some future developments to fully exploit the potential of metabarcoding data and improve the accuracy and precision of their analysis. We also propose some recommendations for the future integration of DNA metabarcoding to routine biomonitoring programs. (C) 2018 The Authors. Published by Elsevier B.V.
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| 37. |
- Kahlert, Maria, et al.
(author)
-
The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes
- 2018
-
In: Fottea. - : Palacky University Olomouc. - 1802-5439 .- 1805-4927. ; 18, s. 37-54
-
Journal article (peer-reviewed)abstract
- Diatoms are used routinely to assess pollution level in rivers and lakes. Current methods are based on identification by light microscopy, which is laborious. An alternative is to identify species based on short DNA fragments and High-Throughput Sequencing (HTS). However a potential limitation is the incomplete coverage of species in reference barcode libraries. Usually these libraries are compiled by isolating cells, before culturing and sequencing them, which is tedious and often unsuccessful. Here we propose the use of rbcL sequences from environmental samples analysed by HTS. We set several criteria to ensure good sequence quality and correspondence with the target species observed in microscopy: the sequence needed to be abundant in the sample, and with no insertions nor deletions or stop codon, phylogenetic neighbour taxa had to correspond to neighbour taxonomic taxa expected from morphological observations. Four species from tropical rivers are given as examples, including one that is new to science.
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| 38. |
- Kahlert, Maria
(author)
-
Why We Need Sustainable Networks Bridging Countries, Disciplines, Cultures and Generations for Aquatic Biomonitoring 2.0: A Perspective Derived From the DNAqua-Net COST Action
- 2018
-
In: Advances in Ecological Research. - : Elsevier. - 0065-2504. ; 58, s. 63-99
-
Research review (peer-reviewed)abstract
- Aquatic biomonitoring has become an essential task in Europe and many other regions as a consequence of strong anthropogenic pressures affecting the health of lakes, rivers, oceans and groundwater. A typical assessment of the environmental quality status, such as it is required by European but also North American and other legislation, relies on matching the composition of assemblages of organisms identified using morphological criteria present in aquatic ecosystems to those expected in the absence of anthropogenic pressures. Through decade-long and difficult intercalibration exercises among networks of regulators and scientists in European countries, a pragmatic biomonitoring approach was developed and adopted, which now produces invaluable information. Nonetheless, this approach is based on several hundred different protocols, making it susceptible to issues with comparability, scale and resolution. Furthermore, data acquisition is often slow due to a lack of taxonomic experts for many taxa and regions and time-consuming morphological identification of organisms. High-throughput genetic screening methods such as (e)DNA metabarcoding have been proposed as a possible solution to these shortcomings. Such "next-generation biomonitoring", also termed "biomonitoring 2.0", has many advantages over the traditional approach in terms of speed, comparability and costs. It also creates the potential to include new bioindicators and thereby further improves the assessment of aquatic ecosystem health. However, several major conceptual and technological challenges still hinder its implementation into legal and regulatory frameworks. Academic scientists sometimes tend to overlook legal or socioeconomic constraints, which regulators have to consider on a regular basis. Moreover, quantification of species abundance or biomass remains a significant bottleneck to releasing the full potential of these approaches. Here, we highlight the main challenges for next-generation aquatic biomonitoring and outline principles and good practices to address these with an emphasis on bridging traditional disciplinary boundaries between academics, regulators, stakeholders and industry.
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| 39. |
- Keck, Francois, et al.
(author)
-
Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles
- 2018
-
In: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 18, s. 1299-1309
-
Journal article (peer-reviewed)abstract
- DNA metabarcoding has been introduced as a revolutionary way to identify organisms and monitor ecosystems. However, the potential of this approach for biomonitoring remains partially unfulfilled because a significant part of the sampled DNA cannot be affiliated to species due to incomplete reference libraries. Thus, biotic indices, which are based on the estimated abundances of species in a community and their ecological profiles, can be inaccurate. We propose to compute biotic indices using phylogenetic imputation of operational taxonomic units (OTUs') ecological profiles (OTU-PITI approach). First, OTUs sequences are inserted within a reference phylogeny. Second, OTUs' ecological profiles are estimated on the basis of their phylogenetic relationships with reference species whose ecology is known. Based on these ecological profiles, biotic indices can be computed using all available OTUs. Using freshwater diatoms as a case study, we show that short DNA barcodes can be placed accurately within a phylogeny and their ecological preferences estimated with a satisfactory level of precision. In the light of these results, we tested the approach with a data set of 139 environmental samples of benthic river diatoms for which the same biotic index (specific sensitivity index) was calculated using (a) traditional microscopy, (b) OTUs with taxonomic assignment approach, (c) OTUs with phylogenetic estimation of ecological profiles (OTU-PITI) and (d) OTU with taxonomic assignment completed by the phylogenetic approach (OTU-PITI) for unclassified OTUs. Using traditional microscopy as a reference, we found that the combination of the OTUs' taxonomic assignment completed by the phylogenetic method performed satisfactorily and substantially better than the other methods tested.
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| 40. |
- Keck, Francois, et al.
(author)
-
Community phylogenetic structure reveals the imprint of dispersal-related dynamics and environmental filtering by nutrient availability in freshwater diatoms
- 2019
-
In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
-
Journal article (peer-reviewed)abstract
- Despite important progress, uncertainty persists regarding the ecological forces driving microbial community assembly. Here, we present the first study to use phylogenetic information to interpret the structure and diversity of diatom communities. We examined local phylogenetic divergence and beta-phylogenetic diversity in a large dataset of 595 freshwater benthic diatom communities and we investigated how this diversity is influenced by gradients in nutrients, pH, organic matter and catchment size. Overall, we found that diatom communities were phylogenetically clustered, i.e. species within communities were more closely related than expected by chance. Phylogenetic clustering was stronger in nutrient-poor environments and in sites with a small catchment area. The variation of the phylogenetic beta-diversity index was much better explained by space and environment than the variation of the taxonomic index was. Both approaches detected a significant effect of environment and space on diatom community turnover. Our results support the view that diatom communities are primarily shaped by environmental filtering, in particular by nutrient availability. Moreover, they highlight the importance of considering dispersal-related processes and the depth of phylogenetic signal in functional traits when interpreting patterns of diversity.
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| 41. |
- Keck, Francois, et al.
(author)
-
Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities
- 2019
-
In: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 7
-
Journal article (peer-reviewed)abstract
- Recent 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.
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| 42. |
- Keck, Francois, et al.
(author)
-
Disentangling the processes driving the biogeography of freshwater diatoms: a multiscale approach
- 2018
-
In: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 45, s. 1582-1592
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Journal article (peer-reviewed)abstract
- Aim1. To disentangle the effects of local environmental conditions and space at multiple scales in order to uncover and explain biogeographical signals in microbial communities of freshwater diatoms. 2. To assess the role of species traits related to dispersal capacities in diatom biogeography.Location Rivers and streams of Sweden sampled over a total area of 450,000km(2).MethodsWe used partial redundancy analyses and variation partitioning coupled with spatial eigenfunctions analyses to separate the effects of environment and space at three different scales on diatoms community structure. As community analyses might give limited insight into species-specific mechanisms, we also performed species by species variation partitioning and the amount of variance explained by each fraction was related to species cell length and attachment to the substrate.Results We found a strong effect of environment and space at a large scale suggesting environmental filtering and dispersal limitation over large distances. Additionally, species-based analyses uncovered an effect of space at fine scale suggesting possible species-specific mass effect dynamic or species sorting driven by missing environmental factors varying at fine scale. Environmental and spatial effects varied strongly among species, but this variation was not explained by cell length and attachment to the substrate.Main conclusions Our results confirm the importance of both environment and dispersal-related processes in controlling diatom community structure and bring new perspectives on the role of dispersal in shaping microbial communities at biogeographical scale. Dispersal being a species-specific mechanism, species associations are not necessarily conserved from site to site and species-based approaches can detect different spatial patterns than those derived from traditional community analyses. Contrary to the conclusions of small-scale analysis of connected metacommunities, interspecific trait variation seems to be of limited importance for long-distance overland dispersal in diatoms.
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- Keck, Francois, et al.
(author)
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R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring
- 2016
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In: Database. - : Oxford University Press (OUP). - 1758-0463. ; 2016, s. baw016-
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Journal article (peer-reviewed)abstract
- Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst.inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts...), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom.
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