| 1. |
- Kahlert, Maria, et al.
(författare)
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Biodiversity patterns of Arctic diatom assemblages in lakes and streams: Current reference conditions and historical context for biomonitoring
- 2022
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Ingår i: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 67, s. 116-140
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Tidskriftsartikel (refereegranskat)abstract
- Comprehensive assessments of contemporary diatom distributions across the Arctic remain scarce. Furthermore, studies tracking species compositional differences across space and time, as well as diatom responses to climate warming, are mainly limited to paleolimnological studies due to a lack of routine monitoring in lakes and streams across vast areas of the Arctic. The study aims to provide a spatial assessment of contemporary species distributions across the circum-Arctic, establish contemporary biodiversity patterns of diatom assemblages to use as reference conditions for future biomonitoring assessments, and determine pre-industrial baseline conditions to provide historical context for modern diatom distributions. Diatom assemblages were assessed using information from ongoing regulatory monitoring programmes, individual research projects, and from surface sediment layers obtained from lake cores. Pre-industrial baseline conditions as well as the nature, direction and magnitude of changes in diatom assemblages over the pastc.200 years were determined by comparing surface sediment samples (i.e. containing modern assemblages) with a sediment interval deposited prior to the onset of significant anthropogenic activities (i.e. containing pre-1850 assemblages), together with an examination of diatoms preserved in contiguous samples from dated sediment cores. We identified several biotypes with distinct diatom assemblages using contemporary diatom data from both lakes and streams, including a biotype typical for High Arctic regions. Differences in diatom assemblage composition across circum-Arctic regions were gradual rather than abrupt. Species richness was lowest in High Arctic regions compared to Low Arctic and sub-Arctic regions, and higher in lakes than in streams. Dominant diatom taxa were not endemic to the Arctic. Species richness in both lakes and streams reached maximum values between 60 degrees N and 75 degrees N but was highly variable, probably reflecting differences in local and regional environmental factors and possibly sampling effort. We found clear taxon-specific differences between contemporary and pre-industrial samples that were often specific to both ecozone and lake depth. Regional patterns of species turnover (beta-diversity) in the pastc.200 years revealed that regions of the Canadian High Arctic and the Hudson Bay Lowlands to the south showed most compositional change, whereas the easternmost regions of the Canadian Arctic changed least. As shown in previous Arctic diatom studies, global warming has already affected these remote high latitude ecosystems. Our results provide reference conditions for future environmental monitoring programmes in the Arctic. Furthermore, diatom taxa identification and harmonisation require improvement, starting with circum-Arctic intercalibrations. Despite the challenges posed by the remoteness of the Arctic, our study shows the need for routine monitoring programmes that have a wide geographical coverage for both streams and lakes.
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| 2. |
- Kahlert, Maria, et al.
(författare)
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Connecting the morphological and molecular species concepts to facilitate species identification within the genus Fragilaria (Bacillariophyta)
- 2019
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Ingår i: Journal of Phycology. - : Wiley. - 0022-3646 .- 1529-8817. ; 55, s. 948-970
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Tidskriftsartikel (refereegranskat)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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| 3. |
- Kahlert, Maria, et al.
(författare)
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DNA-streckkodning – nytt verktyg i miljöövervakningen
- 2018
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Ingår i: Sötvatten 2017. - 9789188727022 ; , s. 17-19
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Bokkapitel (populärvet., debatt m.m.)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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| 4. |
- Kahlert, Maria, et al.
(författare)
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Ecological correlates of riverine diatom and macroinvertebrate alpha and beta diversity across Arctic Fennoscandia
- 2022
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Ingår i: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 67, s. 49-63
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Tidskriftsartikel (refereegranskat)abstract
- Arctic freshwaters support biota adapted to the harsh conditions at these latitudes, but the climate is changing rapidly and so are the underlying environmental filters. Currently, we have limited understanding of broad-scale patterns of Arctic riverine biodiversity and the correlates of alpha- and beta-diversity. Using information from a database set up within the scope of the Arctic Council's Conservation of Arctic Flora and Fauna Circumpolar Biodiversity Monitoring Plan, we analysed patterns and correlates of alpha- and beta-diversity in benthic diatom and macroinvertebrate communities across northern Norway, Sweden, and Finland. We analysed variation in total beta-diversity and its replacement and richness difference components in relation to location of the river reach and its drainage basin (Baltic Sea in the south, the Barents Sea in the east and the north, and the Norwegian Sea in the west), in addition to climate and environmental variables. In both macroinvertebrates and diatoms, the replacement and richness difference components showed wide variation. For macroinvertebrates, the richness difference component was the more important, whereas for diatoms, the replacement component was the more important in contributing to variation in beta-diversity. There was no significant difference in beta-diversity between the three main drainage basins, but species composition differed among the drainage basins. Based on the richness difference component of beta-diversity, climate variables were most strongly associated with community variation in macroinvertebrates. In diatoms, both environmental and climate variables were strongly correlated with community compositional variation. In both groups, there were also significant differences in alpha-diversity among the three main drainage basins, and several taxa were significant indicators of one of these drainage basins. Alpha diversity was greater in areas with a continental climate, while the oceanic areas in the west harboured greatly reduced flora and fauna. The correlates of biodiversity were relatively similar in macroinvertebrates and diatoms. Climate variables, in particular temperature, were the most strongly associated with biodiversity patterns in the Arctic rivers of Fennoscandia. Sedimentary geology may be associated with increased productivity and, to a lesser extent, with sensitivity to acidification. There was considerable variation in community composition across Arctic Fennoscandia, indicating the necessity of protecting several stream reaches or even whole catchments within each region to conserve total riverine biodiversity. Furthermore, it is likely that the predicted changes in temperature in Arctic areas will influence riverine diversity patterns across Fennoscandia.
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| 5. |
- Kahlert, Maria, et al.
(författare)
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The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes
- 2018
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Ingår i: Fottea. - : Palacky University Olomouc. - 1802-5439 .- 1805-4927. ; 18, s. 37-54
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Tidskriftsartikel (refereegranskat)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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| 6. |
- Keck, Francois
(författare)
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Benthic Diatom Communities in an Alpine River Impacted by Waste Water Treatment Effluents as Revealed Using DNA Metabarcoding
- 2019
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 7. |
- Keck, Francois, et al.
(författare)
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Boosting DNA metabarcoding for biomonitoring with phylogenetic estimation of operational taxonomic units' ecological profiles
- 2018
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Ingår i: Molecular Ecology Resources. - : Wiley. - 1755-098X .- 1755-0998. ; 18, s. 1299-1309
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Tidskriftsartikel (refereegranskat)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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| 8. |
- Keck, Francois, et al.
(författare)
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Community phylogenetic structure reveals the imprint of dispersal-related dynamics and environmental filtering by nutrient availability in freshwater diatoms
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 9
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Tidskriftsartikel (refereegranskat)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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| 9. |
- Keck, Francois, et al.
(författare)
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Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities
- 2019
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Ingår i: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 7
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Tidskriftsartikel (refereegranskat)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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| 10. |
- Keck, Francois, et al.
(författare)
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Disentangling the processes driving the biogeography of freshwater diatoms: a multiscale approach
- 2018
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 45, s. 1582-1592
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Tidskriftsartikel (refereegranskat)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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