| 1. |
- Bighiu, Maria, et al.
(författare)
-
Limited effects of pesticides on stream macroinvertebrates, biofilm nematodes, and algae in intensive agricultural landscapes in Sweden
- 2020
-
Ingår i: Water Research. - : Elsevier BV. - 0043-1354 .- 1879-2448. ; 174
-
Tidskriftsartikel (refereegranskat)abstract
- Pesticides are frequently detected in surface waters, sometimes at levels exceeding ecotoxicological guidelines. We screened for almost 100 pesticides in 32 streams from intense agricultural areas in Southern Sweden, in concert with water chemistry parameters. In addition, we investigated the communities of benthic macroinvertebrates, biofilm nematodes and algae and calculated multiple bioassessment metrics. The number of pesticides found in each stream ranged between 2 and 52, but the sum of Toxic Units (Sigma TU) for the mixtures was generally low, and exceeded the European Uniform Principles only in a single sample for algae and in 2% of the samples for Daphnia. Only nematode communities were significantly correlated with the Sigma TU, potentially due to their higher pesticide exposure in biofilms. Diatom metrics showed that most streams were impacted by eutrophication and macroinvertebrate metrics showed good status in most streams, whereas the SPEAR(pesticides) (SPEcies At Risk) index, specifically designed to indicate pesticide effects, showed that about half of the samples were at risk. Interestingly, SPEAR(pesticides) was not correlated to Sigma TUDaphnia and this discrepancy suggests that redefining the boundaries for quality classes might be necessary for this index. Moreover, SPEAR(pesticides) was positively correlated with the commonly used macroinvertebrate index ASPT, although disparate results were found for several streams. We argue that this questions the scaling of both metrics and the specificity of their responses. We discuss that the overall good/moderate status of the streams, despite the intense agriculture in the catchments, can be due to the fact that i) a sampling strategy with repeated grab samples did not capture peak pesticide concentrations, thus underestimating acute exposure, ii) pesticide run-off indeed was low, due to measures such as buffer strips, and iii) the nutrient-rich conditions and high sediment loads counteracted pesticide toxicity. We conclude that agricultural land use was the overriding stressor in the investigated streams, including strong effects of nutrients, less apparent effects of pesticides and likely impact of hydromorphological alterations (not specifically addressed in this study). (C) 2020 The Authors. Published by Elsevier Ltd.
|
|
| 2. |
- Drakare, Stina, et al.
(författare)
-
EuropaBON EBV workflow templates
- 2024
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The information provided here represents the EBV workflow templates collected during the EuropaBON online workshop on Essential Biodiversity Variable (EBV) workflows from 22–24 February 2023. The templates were designed to capture comprehensive descriptions about the three workflow components (data collection and sampling, data integration, and modelling) that are typical for generating EBVs. Recognising the potential value of those EBV templates for European biodiversity monitoring, our objective is to share them for enhancing transparency, knowledge exchange and collaboration, and promoting the operationalisation of EBVs across Europe.EuropaBON (https://europabon.org/) is a Horizon 2020 research and innovation action funded by the European Commission that seeks to co-design a European Biodiversity Observation Network. This network aims to bridge the gap between the biodiversity data needs of policy-makers and authorities on the one hand and the existing reporting streams and available data sources on the other hand, considering both present obligations and forthcoming policy needs. Essential Biodiversity Variables (EBVs) are a central concept of EuropaBON as they provide a standardised framework for biodiversity monitoring and reporting. In 2023, EuropaBON had identified 70 EBVs (Junker et al., 2023) that are policy-relevant for the EU, and measurable with available and existing technologies and with a proven track record of feasibility in ongoing initiatives. EBVs require workflows to process the raw data (primary observations) through data integration and modelling into spatially-explicit EBV data products (Kissling et al., 2018; Schmeller et al., 2017). These workflows can be broken down into three main components (data collection and sampling, data integration, and modelling), with additional aspects of data interoperability and IT infrastructure being recognised as crucial for transnational data streams (Kissling & Lumbierres, 2023).To capture information about the EBV workflows, an online workshop was held on 22–24 February 2023 with 520 registered participants from 49 countries, covering a large range of expertise (Lumbierres & Kissling, 2023). Participants contributed information on EBV workflow components and advanced monitoring techniques, discussed initiatives, and identified tools and requirements for implementing 70 proposed EBVs. The information from the workshop participants was collected through pre-defined EBV workflow templates (provided as Google Docs). Templates were organised into rows representing the workflow components (‘Data collection and sampling’, ‘Data integration’, and ‘Modelling’) and columns reflecting the levels of maturity ('Current initiatives', 'Emerging tools and projects' or 'Future needs'). Prior to the workshop, some information on existing workflows was pre-filled based on previous EuropaBON deliverables, namely an assessment of the current biodiversity monitoring gaps in the EU (Santana et al., 2023) and an assessment of current EU monitoring workflows and bottlenecks (Morán-Ordóñez et al., 2023).After the workshop, the EBV workflow templates were processed to ensure the accuracy and relevance of the information. Each listed initiative was verified to be part of an active biodiversity monitoring scheme and pertinent to the specific EBV under consideration, cross-referencing with the initiative’s websites and other data collected by the EuropaBON deliverables (Morán-Ordóñez et al., 2023; Santana et al., 2023). Moreover, we ensured correct alignment of each initiative and listed requirements and needs with the appropriate workflow components and maturity levels.The EBV workflow templates provide insights into the current biodiversity monitoring landscape in Europe and how EBV production could be operationalized at the EU level. They offer detailed information about ongoing initiatives and projects, methodologies, and technologies that can be used to generate EBVs at a continental scale. Nevertheless, it is important to note that they do not encompass an exhaustive list of all ongoing or proposed initiatives of biodiversity monitoring in all member states of the EU. It is suggested to use them as a starting point and baseline for the further development of EBVs in a European context.
|
|
| 3. |
|
|
| 4. |
- Kahlert, Maria, et al.
(författare)
-
Benthic Diatom Communities in Urban Streams and the Role of Riparian Buffers
- 2020
-
Ingår i: Water. - : MDPI AG. - 2073-4441. ; 12
-
Tidskriftsartikel (refereegranskat)abstract
- Urbanization impacts stream ecosystems globally through degraded water quality, altered hydrology, and landscape disturbances at the catchment and riparian scales, causing biodiversity losses and altered system functioning. Addressing the "urban stream syndrome" requires multiple mitigation tools, and rehabilitation of riparian vegetation may help improve stream ecological status and provide key ecosystem services. However, the extent to which forested riparian buffers can help support stream biodiversity in the face of numerous environmental contingencies remains uncertain. We assessed how a key indicator of stream ecological status, benthic diatoms, respond to riparian habitat conditions using 10 urban site pairs (each comprising of one unbuffered and one buffered reach), and additional urban downstream and forest reference upstream sites in the Oslo Fjord basin. Diatom communities were structured by multiple drivers including spatial location, land use, water quality, and instream habitat. Among these, riparian habitat condition independently explained 16% of variation in community composition among site pairs. Changes in community structure and indicator taxa, along with a reduction in pollution-tolerant diatoms, suggested tangible benefits of forested riparian buffers for stream biodiversity in urban environments. Managing urban impacts requires multiple solutions, with forested riparian zones providing a potential tool to help improve biodiversity and ecosystem services.
|
|
| 5. |
- Kahlert, Maria, et al.
(författare)
-
Biodiversity patterns of Arctic diatom assemblages in lakes and streams: Current reference conditions and historical context for biomonitoring
- 2022
-
Ingår i: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 67, s. 116-140
-
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.
|
|
| 6. |
- Kahlert, Maria
(författare)
-
Co-occurrence, ecological profiles and geographical distribution based on unique molecular identifiers of the common freshwater diatoms Fragilaria and Ulnaria
- 2022
-
Ingår i: Ecological Indicators. - : Elsevier BV. - 1470-160X .- 1872-7034. ; 141
-
Tidskriftsartikel (refereegranskat)abstract
- Diatom taxonomy has evolved in recent years, with many new species described and new approaches such as molecular genetics showing the existence of cryptic diversity within currently accepted species. This cryptic diversity is not well understood even for common freshwater genera such as Fragilaria and Ulnaria. The purpose of our study was to define taxon-specific ecological profiles and geographical distributions for unique molecular identifiers (amplicon sequence variants, ASVs) linked to curated taxonomy for these genera. Our goal is to contribute to the development of ecological assessment methods, and to the understanding why we often observe so many diatom species co-occurring in a single sample. We filtered a large (770 samples) metabarcoding dataset with linked environmental data covering several countries in Europe for genetic variants (ASVs) assigned to currently accepted species of our target genera. We studied the geographical distribution of the ASVs, and tested for ASV-pair co-occurrence. We modelled ASV-specific preferences for pH, alkalinity, total nitrogen, total phosphorus and conductivity, and analysed their preference for lakes or streams as habitat. Our study confirmed that there seems to be no general geographical barrier for the distribution of freshwater benthic diatom ASVs in Europe, but that dispersal is not rapid enough to hide historical events. The Fragilaria and Ulnaria ASVs in our study showed considerable overlap in geographical distribution, habitat and ecological preferences. We found evidence that only large differences in preferences for the analysed water chemistry variables prevented the cooccurrence of ASVs at the same sites. Instead, Fragilaria and Ulnaria ASVs co-occurred frequently in samples. We found subtle differences in ecological preferences for some ASV pairs, which might in part explain the cooccurrence by the avoidance of direct competition. However, the great overlap in distribution and ecological preferences suggests that other factors not studied here were also responsible for the observed co-occurrences and high richness of ASVs found at many sites. To our knowledge, we are the first to use ASVs in combination with a curated taxonomy to understand co-occurrence, specific ecological profiles and large-scale geographical distribution for unique identifiers not biased by the quality of reference databases, clustering methods, or non-harmonized morphological identification. Thus, our results can now be used in subsequent projects to interpret ASV occurrences, e.g. for development of ecological assessment methods.
|
|
| 7. |
- Kahlert, Maria
(författare)
-
Delimitation of Some Taxa of Ulnaria and Fragilaria (Bacillariophyceae) Based on Genetic, Morphological Data and Mating Compatibility
- 2023
-
Ingår i: Diversity. - : MDPI AG. - 1424-2818. ; 15
-
Tidskriftsartikel (refereegranskat)abstract
- Fragilaria and Ulnaria are two closely related diatom genera for which the delimitation and circumscription of several species is unclear. We studied strains isolated from Lake Baikal and compared them with the species from freshwater reservoirs in Europe and Asia using phylogenetic and species delimitation methods, microscopy and interclonal crossing experiments. The results of the phylogenetic analyses of the fragments of rbcL and 18S rRNA genes revealed that baikalian F. radians clade was independent from the representatives of the genus from other localities. Among Ulnaria we found the following 18S rRNA phylogenetic tree groups at species level: U. acus, U. ulna and U. danica. Genetic distance between genera varied between 3.9-10.2% substitutions in rbcL gene and 3.2-11.5% in 18S rRNA. The boundary between intraspecies and interspecies polymorphism for studied species of Ulnaria and Fragilaria in these marker genes was around 0.8% substitutions. Morphometric characters of individual strains showed their variability and division into F. radians, U. acus and U. ulna together with U. danica. Strains of U. acus and U. danica from different localities of Europe and Asia were sexually compatible inside the species. Sexual reproduction has never been observed in monoclonal cultures, either between this species or with strains of the Fragilaria.
|
|
| 8. |
- Kahlert, Maria, et al.
(författare)
-
Diatom DNA metabarcoding for ecological assessment: Comparison among bioinformatics pipelines used in six European countries reveals the need for standardization
- 2020
-
Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 745
-
Tidskriftsartikel (refereegranskat)abstract
- Ecological assessment of lakes and rivers using benthic diatom assemblages currently requires considerable taxonomic expertise to identify species using light microscopy. This traditional approach is also time-consuming. Diatom metabarcoding is a promising alternative and there is increasing interest in using this approach for routine assessment. However, until now, analysis protocols for diatom metabarcoding have been developed and optimised by research groups working in isolation. The diversity of existing bioinformatics methods highlights the need for an assessment of the performance and comparability of results of different methods. The aim of this study was to test the correspondence of outputs from six bioinformatics pipelines currently in use for diatom metabarcoding in different European countries. Raw sequence data from 29 biofilm samples were treated by each of the bioinformatics pipelines, five of them using the same curated reference database. The outputs of the pipelines were compared in terms of sequence unit assemblages, taxonomic assignment, biotic index score and ecological assessment outcomes. The three last components were also compared to outputs from traditional light microscopy, which is currently accepted for ecological assessment of phytobenthos, as required by the Water Framework Directive. We also tested the performance of the pipelines on the two DNA markers (rbcL and 185-V4) that are currently used by the working groups participating in this study. The sequence unit assemblages produced by different pipelines showed significant differences in terms of assigned and unassigned read numbers and sequence unit numbers. When comparing the taxonomic assignments at genus and species level, correspondence of the taxonomic assemblages between pipelines was weak. Most discrepancies were linked to differential detection or quantification of taxa, despite the use of the same reference database. Subsequent calculation of biotic index scores also showed significant differences between approaches, which were reflected in the final ecological assessment. Use of the rbcL marker always resulted in better correlation among molecular datasets and also in results closer to these generated using traditional microscopy. This study shows that decisions made in pipeline design have implications for the dataset's structure and the taxonomic assemblage, which in turn may affect biotic index calculation and ecological assessment. There is a need to define best-practice bioinformatics parameters in order to ensure the best representation of diatom assemblages. Only the use of similar parameters will ensure the compatibility of data from different working groups. The future of diatom metabarcoding for ecological assessment may also lie in the development of new metrics using, for example, presence/absence instead of relative abundance data. (C) 2020 The Authors. Published by Elsevier B.V.
|
|
| 9. |
- Kahlert, Maria, et al.
(författare)
-
Ecological correlates of riverine diatom and macroinvertebrate alpha and beta diversity across Arctic Fennoscandia
- 2022
-
Ingår i: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 67, s. 49-63
-
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.
|
|
| 10. |
- Kahlert, Maria
(författare)
-
European river typologies fail to capture diatom, fish, and macrophyte community composition
- 2023
-
Ingår i: Science of the Total Environment. - 0048-9697 .- 1879-1026. ; 896
-
Tidskriftsartikel (refereegranskat)abstract
- Typology systems are frequently used in applied and fundamental ecology and are relevant for environmental moni-toring and conservation. They aggregate ecosystems into discrete types based on biotic and abiotic variables, assuming that ecosystems of the same type are more alike than ecosystems of different types with regard to a specific property of interest. We evaluated whether this assumption is met by the Broad River Types (BRT), a recently proposed European river typology system, that classifies river segments based on abiotic variables, when it is used to group biological com-munities. We compiled data on the community composition of diatoms, fishes, and aquatic macrophytes throughout Europe and evaluated whether the composition is more similar in site groups with the same river type than in site groups of different river types using analysis of similarities, classification strength, typical species analysis, and the area under zeta diversity decline curves. We compared the performance of the BRT with those of four region-based ty-pology systems, namely, Illies Freshwater Ecoregions, the Biogeographic Regions, the Freshwater Ecoregions of the World, and the Environmental Zones, as well as spatial autocorrelation (SA) classifications.All typology systems received low scores from most evaluation methods, relative to predefined thresholds and the SA classifications. The BRT often scored lowest of all typology systems. Within each typology system, community compo-sition overlapped considerably between site groups defined by the types of the systems. The overlap tended to be the lowest for fishes and between Illies Freshwater Ecoregions.In conclusion, we found that existing broad-scale river typology systems fail to delineate site groups with distinct and compositionally homogeneous communities of diatoms, fishes, and macrophytes. A way to improve the fit between typology systems and biological communities might be to combine segment-based and region-based typology systems to simultaneously account for local environmental variation and historical distribution patterns, thus potentially im-proving the utility of broad-scale typology systems for freshwater biota.
|
|
| 11. |
- Kahlert, Maria, et al.
(författare)
-
Gaps in current Baltic Sea environmental monitoring – Science versus management perspectives
- 2020
-
Ingår i: Marine Pollution Bulletin. - London : Elsevier. - 0025-326X .- 1879-3363. ; 160
-
Tidskriftsartikel (refereegranskat)abstract
- Legislations and commitments regulate Baltic Sea status assessments and monitoring. These assessments suffer from monitoring gaps that need prioritization. We used three sources of information; scientific articles, projectreports and a stakeholder survey to identify gaps in relation to requirements set by the HELCOM's Baltic SeaAction Plan, the Marine Strategy Framework Directive and the Water Framework Directive. The most frequentlymentioned gap was that key requirements are not sufficiently monitored in space and time. Biodiversity monitoringwas the category containing most gaps. However, whereas more than half of the gaps in reports related tobiodiversity, scientific articles pointed out many gaps in the monitoring of pollution and water quality. Animportant finding was that the three sources differed notably with respect to which gaps were mentioned mostoften. Thus, conclusions about gap prioritization for management should be drawn after carefully consideringthe different viewpoints of scientists and stakeholders. © 2020 The Authors. Published by Elsevier Ltd.
|
|
| 12. |
- Kahlert, Maria
(författare)
-
Kiselalger i svenska vattendrag och sjöar : Utvärdering av det gemensamma delprogrammet 2021
- 2022
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Rapporten redovisar den tredje och sista gemensamma utvärderingen av regional och nationell miljöövervakning inom det gemensamma delprogrammet ”Kiselalger i vattendrag”. Delprogrammet startade 2009 och är ett frivilligt samarbete mellan ett stort antal länsstyrelser i Sverige. Rapporten omfattar en utvärdering av tidsseriedata för kiselalger i vattendrag från 2007–2020. Vidare omfattar uppdraget en första utvärdering av kiselalger i sjöar och en kort lägesrapport om aktuella projekt kring eDNA-teknik för kiselalgsanalys.
|
|
| 13. |
- Kahlert, Maria
(författare)
-
Marine monitoring in transition: On the verge of technological revolution?
- 2022
-
Ingår i: Frontiers in marine science. - : Frontiers Media SA. - 2296-7745. ; 9
-
Forskningsöversikt (refereegranskat)abstract
- Efforts to renew marine ecosystem monitoring to include advanced technology and cost-effective methods have been repeatedly called for. The current environmental legislation in European Union (EU) requires also ecosystem monitoring beyond the scope of conventional methods and sampling strategies. Despite several studies showing the benefits of new methods, the progress to adopt the methods in national monitoring programmes under legal requirements has been slow. In this study, we have reviewed the current use of a set of methods in marine monitoring programmes under the EU marine strategy framework directive (MSFD), which calls for a holistic view of the marine environment and thus requires tens of monitoring parameters by different methods. Here we assess how widely the new methods are being adopted in the EU member states implementing the MSFD. Our results show a relatively high adoption rate for certain methods, while others are widely ignored. We compare the results also with the monitoring strategies of the four regional sea conventions. We argue that the adoption of methods in European and regional programmes may positively influence the national use of new methods.
|
|
| 14. |
- Kahlert, Maria
(författare)
-
Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life
- 2021
-
Ingår i: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 5, s. 17-33
-
Tidskriftsartikel (refereegranskat)abstract
- DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data.
|
|
| 15. |
- Kahlert, Maria
(författare)
-
Recommendations for the preservation of environmental samples in diatom metabarcoding studies
- 2022
-
Ingår i: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6, s. 349-365
-
Tidskriftsartikel (refereegranskat)abstract
- Implementation of DNA metabarcoding for diatoms for environmental monitoring is now moving from a research to an operational phase, requiring rigorous guidelines and standards. In particular, the first steps of the diatom metabarcoding process, which consist of sampling and storage, have been addressed in various ways in scientific and pilot studies and now need to be rationalised. The objective of this study was to compare three currently applied preservation protocols through different storage durations (ranging from one day to one year) for phytobenthos and phytoplankton samples intended for diatom DNA metabarcoding analysis. The experimental design used samples from four freshwater and two marine sites of diverse ecological characteristics. The impact of the sample preservation and storage duration was assessed through diatom metabarcoding endpoints: DNA quality and quantity, diversity and richness, diatom assemblage composition and ecological index values (for freshwater samples). The yield and quality of extracted DNA only decreased for freshwater phytobenthos samples preserved with ethanol. Diatom diversity was not affected and their taxonomic composition predominantly reflected the site origin. Only rare taxa (< 100 reads) differed among preservation methods and storage durations. For biomonitoring purposes, freshwater ecological index values were not affected by the preservation method and storage duration tested (including ethanol preservation), all treatments returning the same ecological status for a site. This study contributes to consolidating diatom metabarcoding. Thus, accompanied by operational standards, the method will be ready to be confidently deployed and prescribed in future regulatory monitoring.
|
|
| 16. |
- Kahlert, Maria, et al.
(författare)
-
Revisiting global diversity and biogeography of freshwater diatoms: New insights from molecular data
- 2023
-
Ingår i: Environmental DNA. - 2637-4943. ; 5, s. 1505-1515
-
Tidskriftsartikel (refereegranskat)abstract
- The distribution of microorganisms has long been assumed to be cosmopolitan and primarily controlled by the environment, but recent studies suggest that microbes may also exhibit strong biogeographical patterns driven by dispersal limitation. Past attempts to study the global biogeography of freshwater diatoms have always encountered the great difficulty of collecting taxonomically harmonized large-scale data. However, developments in molecular techniques and DNA metabarcoding provide a unique opportunity to overcome these limitations and to disclose diatom biodiversity at an unprecedented scale and resolution. Here, we assembled DNA metabarcoding data of freshwater benthic diatom communities sampled in seven geographic regions across the world to investigate how diatom diversity varies along latitude and to assess the proportion of genetic variants of these microorganisms which are exclusive or shared across regions. We observed significant differences in assemblages among climate zones and found that genetic richness is not affected by latitude, but by an island effect. The genetic resolution directly impacts the proportion of variants shared across regions; however, the majority of taxa remained specific to a single geographic region. Freshwater diatoms disperse over long distances and across oceans but at rates that allow the appearance of local genetic variants and the regionalization of assemblages. Future work should focus on putting these diversity dynamics into a temporal context, an approach that should be possible by bringing together new sequencing techniques and phylogeography.
|
|
| 17. |
- Kahlert, Maria, et al.
(författare)
-
Same same, but different: The response of diatoms to environmental gradients in Fennoscandian streams and lakes-barcodes, traits and microscope data compared
- 2021
-
Ingår i: Ecological Indicators. - : Elsevier BV. - 1470-160X .- 1872-7034. ; 130
-
Tidskriftsartikel (refereegranskat)abstract
- We developed and compared the performance of freshwater benthic diatom indices calculated from (i) traditional morphological species identification, (ii) Amplicon Sequence Variants (ASVs) obtained via DNA metabarcoding, and (iii) morphological traits to indicate eutrophication in rivers and lakes in Fennoscandia. Based on the results, we provided recommendations for the future routine use of diatom bioassessment tools in environmental monitoring and assessment. Our results show that ASVs are the most promising candidates to be used in environmental assessment. Indices based on ASVs correlated better with TotP concentrations than morphological taxa data, whereas the trait indices correlated least. We could see by studying the taxonomic assignments of the ASVs that traditional morphotaxa were divided up into several ASVs with different ecological profiles, which explained part of the better index performance and also encourages further studies on diatom diversity and ecological preferences. In general, ASV- and morphotaxon-specific optima differed slightly between streams and lakes, but were significantly correlated with each other. This means that it should be possible to develop a common index that is applicable in both streams and lakes, but boundary values with respect to TotP might need to be set separately for them. More knowledge on diatom traits is required to enable their use for environmental assessment.
|
|
| 18. |
- Kahlert, Maria
(författare)
-
Stream diatom assemblages as environmental indicators - A cross-regional assessment
- 2020
-
Ingår i: Ecological Indicators. - : Elsevier BV. - 1470-160X .- 1872-7034. ; 113
-
Tidskriftsartikel (refereegranskat)abstract
- Ongoing climatic change and anthropogenic pressure highlight the importance of reliable assessment of the ecological status of freshwaters. Bioindicators are used widely in ecological assessments as biotic assemblages reflect the environmental conditions in current ecosystems. However, the robustness of bioindicators relies on the transferability of indices and models outside the regions they were derived from. We tested the reliability of stream diatom assemblages as indicators of water chemistry and climatic factors in a cross-regional assessment by developing a predictive model with diatom assemblage data from Sweden and using it to model stream conditions in Finland. The inference models and predictions were performed using the Boosted Regression Trees (BRT) method, separately in species and genus levels. The predictive performance of the calibration models in Sweden were good or moderate for both water chemistry and climatic variables, both at species and genus levels. The most important climatic (growing degree days, r(2) = 0.57) and water chemistry variables (pH, r(2) = 0.65; and total phosphorus (TP), r(2) = 0.52) could be inferred from diatom assemblages relatively well. However, predictive performances of the cross-regional models were low (r(2) <= 0.13). Nevertheless, water chemistry variables, conductivity (r(2) = 0.13) and TP (r(2) = 0.12), were predicted the best. The most important diatom indicators for climatic and environmental variables varied between Sweden and Finland. The study showed that diatom assemblages can be robust indicators of water chemistry and climatic variables within the region where the inference models are calibrated. However, their indicator ability may be weak between regions. The reason for the low transferability of the diatom inference models may stem from between-region differences in species realized niches, species pools and/or ecosystems, local adaptation or species identification. Hence, models should only be used with caution in geographical contexts other than the one where they were developed. The calibration data should cover as large geographical area as possible to give reliable predictions when applied in smaller regions.
|
|
| 19. |
- Kahlert, Maria
(författare)
-
A strategy for successful integration of DNA-based methods in aquatic monitoring
- 2022
-
Ingår i: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6, s. 215-226
-
Tidskriftsartikel (refereegranskat)abstract
- Recent advances in molecular biomonitoring open new horizons for aquatic ecosystem assessment. Rapid and cost-effective methods based on organismal DNA or environmental DNA (eDNA) now offer the opportunity to produce inventories of indicator taxa that can subsequently be used to assess biodiversity and ecological quality. However, the integration of these new DNA-based methods into current monitoring practices is not straightforward, and will require coordinated actions in the coming years at national and international levels. To plan and stimulate such an integration, the European network DNAqua-Net (COST Action CA15219) brought together international experts from academia, as well as key environmental biomonitoring stakeholders from different European countries. Together, this transdisciplinary consortium developed a roadmap for implementing DNA-based methods with a focus on inland waters assessed by the EU Water Framework Directive (2000/60/EC). This was done through a series of online workshops held in April 2020, which included fifty participants, followed by extensive synthesis work. The roadmap is organised around six objectives: 1) to highlight the effectiveness and benefits of DNA-based methods, 2) develop an adaptive approach for the implementation of new methods, 3) provide guidelines and standards for best practice, 4) engage stakeholders and ensure effective knowledge transfer, 5) support the environmental biomonitoring sector to achieve the required changes, 6) steer the process and harmonise efforts at the European level. This paper provides an overview of the forum discussions and the common European views that have emerged from them, while reflecting the diversity of situations in different countries. It highlights important actions required for a successful implementation of DNA-based biomonitoring of aquatic ecosystems by 2030.
|
|
| 20. |
- Lau, Danny C. P., et al.
(författare)
-
Multitrophic biodiversity patterns and environmental descriptors of sub‐Arctic lakes in northern Europe
- 2022
-
Ingår i: Freshwater Biology. - : John Wiley & Sons. - 0046-5070 .- 1365-2427. ; 67:1, s. 30-48
-
Tidskriftsartikel (refereegranskat)abstract
- 1. Arctic and sub‐Arctic lakes in northern Europe are increasingly threatened by climate change, which can affect their biodiversity directly by shifting thermal and hydrological regimes, and indirectly by altering landscape processes and catchment vegetation. Most previous studies of northern lake biodiversity responses to environmental changes have focused on only a single organismal group. Investigations at whole‐lake scales that integrate different habitats and trophic levels are currently rare, but highly necessary for future lake monitoring and management.2. We analysed spatial biodiversity patterns of 74 sub‐Arctic lakes in Norway, Sweden, Finland, and the Faroe Islands with monitoring data for at least three biological focal ecosystem components (FECs)—benthic diatoms, macrophytes, phytoplankton, littoral benthic macroinvertebrates, zooplankton, and fish—that covered both pelagic and benthic habitats and multiple trophic levels.3. We calculated the richnessrelative (i.e. taxon richness of a FEC in the lake divided by the total richness of that FEC in all 74 lakes) and the biodiversity metrics (i.e. taxon richness, inverse Simpson index (diversity), and taxon evenness) of individual FECs using presence–absence and abundance data, respectively. We then investigated whether the FEC richnessrelative and biodiversity metrics were correlated with lake abiotic and geospatial variables. We hypothesised that (1) individual FECs would be more diverse in a warmer and wetter climate (e.g. at lower latitudes and/or elevations), and in hydrobasins with greater forest cover that could enhance the supply of terrestrial organic matter and nutrients that stimulated lake productivity; and (2) patterns in FEC responses would be coupled among trophic levels.4. Results from redundancy analyses showed that the richnessrelative of phytoplankton, macrophytes, and fish decreased, but those of the intermediate trophic levels (i.e. macroinvertebrates and zooplankton) increased with decreasing latitude and/or elevation. Fish richnessrelative and diversity increased with increasing temporal variation in climate (temperature and/or precipitation), ambient nutrient concentrations (e.g. total nitrogen) in lakes, and woody vegetation (e.g. taiga forest) cover in hydrobasins, whereas taxon richness of macroinvertebrates and zooplankton decreased with increasing temporal variation in climate.5. The similar patterns detected for richnessrelative of fish, macrophytes, and phytoplankton could be caused by similar responses to the environmental descriptors, and/or the beneficial effects of macrophytes as habitat structure. By creating habitat, macrophytes may increase fish diversity and production, which in turn may promote higher densities and probably more diverse assemblages of phytoplankton through trophic cascades. Lakes with greater fish richnessrelative tended to have greater average richnessrelative among FECs, suggesting that fish are a potential indicator for overall lake biodiversity.6. Overall, the biodiversity patterns observed along the environmental gradients were trophic‐level specific, indicating that an integrated food‐web perspective may lead to a more holistic understanding of ecosystem biodiversity in future monitoring and management of high‐latitude lakes. In future, monitoring should also focus on collecting more abundance data for fish and lower trophic levels in both benthic and pelagic habitats. This may require more concentrated sampling effort on fewer lakes at smaller spatial scales, while continuing to sample lakes distributed along environmental gradients.
|
|
| 21. |
- Mack, Leoni, et al.
(författare)
-
A Synthesis of Marine Monitoring Methods With the Potential to Enhance the Status Assessment of the Baltic Sea
- 2020
-
Ingår i: Frontiers in Marine Science. - Lausanne : Frontiers Media S.A.. - 2296-7745. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- A multitude of anthropogenic pressures deteriorate the Baltic Sea, resulting in theneed to protect and restore its marine ecosystem. For an efficient conservation,comprehensive monitoring and assessment of all ecosystem elements is of fundamentalimportance. The Baltic Marine Environment Protection Commission HELCOMcoordinates conservation measures regulated by several European directives. However,this holistic assessment is hindered by gaps within the current monitoring schemes.Here, twenty-two novel methods with the potential to fill some of these gaps andimprove the monitoring of the Baltic marine environment are examined. We asked keystakeholders to point out methods likely to improve current Baltic Sea monitoring. Wethen described these methods in a comparable way and evaluated them based ontheir costs and applicability potential (i.e., possibility to make them operational). Twelvemethods require low to very low costs, while five require moderate and two high costs.Seventeen methods were rated with a high to very high applicability, whereas fourmethods had moderate and one low applicability for Baltic Sea monitoring. Methodswith both low costs and a high applicability include the Manta Trawl, Rocket, SedimentCorer, Argo Float, Artificial Substrates, Citizen Observation, Earth Observation, theHydroFIARpH system, DNA Metabarcoding and Stable Isotope Analysis. © 2020 Mack, Attila, Aylagas, Beermann, Borja, Hering, Kahlert, Leese, Lenz, Lehtiniemi, Liess, Lips, Mattila, Meissner, Pyhälahti, Setälä, Strehse, Uusitalo, Willstrand Wranne and Birk.
|
|
| 22. |
- Truchy, Amélie, et al.
(författare)
-
Responses of multiple structural and functional indicators along three contrasting disturbance gradients
- 2022
-
Ingår i: Ecological Indicators. - : Elsevier. - 1470-160X .- 1872-7034. ; 135
-
Tidskriftsartikel (refereegranskat)abstract
- Ecosystem functioning and community structure are recognized as key components of ecosystem integrity, but comprehensive, standardized studies of the responses of both structural and functional indicators to different types of anthropogenic pressures remain rare. Consequently, we lack an empirical basis for (i) identifying when monitoring ecosystem structure alone misses important changes in ecosystem functioning, (ii) recommending sets of structural and functional metrics best suited for detecting ecological change driven by different anthropogenic pressures, and (iii) understanding the cumulative effects of multiple, co-occurring stressors on structure and function. We investigated variation in community structure and ecosystem functioning of stream ecosystems along three gradients (10–16 independent stream sites each) of increasing impact arising from agriculture, forestry and river regulation for hydropower, respectively. For each stream, we quantified variation in (i) the abiotic environment, (ii) community composition of four organism groups and (iii) three basal ecosystem processes underpinning carbon and nutrient cycling in streams. We assessed the responsiveness of multiple biodiversity, community structure and ecosystem functioning indicators based on variance explained and effect size metrics. Along a gradient of increasing agricultural impact, diatoms and fish were the most responsive groups overall, but significant variation was detected in at least one aspect of community composition, abundance and/or biodiversity of every organism group. In contrast, most of our functional metrics did not vary significantly along the agricultural gradient, possibly due to contrasting, antagonistic effects of increasing nutrient concentrations and turbidity on ecosystem process rates. The exception was detritivore-mediated litter decomposition which increased up to moderate levels of nutrient. Impacts of river regulation were most marked for diatoms, which were responsive to both increasingly frequent hydropeaking and to increasing seasonal river regulation. Among functional indicators, both litter decomposition and algal biomass accrual declined significantly with increasing hydropeaking. Few structural or functional metrics varied with forest management, with macroinvertebrate diversity increasing along the forestry gradient, as did algal and fungal biomass accrual. Together, these findings highlight the challenges of making inferences about the impacts of anthropogenic disturbances at the ecosystem level based on community data alone, and pinpoint the need to identify optimal sets of functional and structural indicators best suited for detecting ecological changes associated with different human activities.
|
|
