scholarly journals Let me see your iD: Impacts of Environmental Stressors on Aquatic Ecosystems Assessed by (e)DNA Metabarcoding

2018 ◽  
Vol 2 ◽  
pp. e25983
Author(s):  
Romana Salis ◽  
Arne Beermann ◽  
Jan Macher ◽  
Christoph Matthaei ◽  
Jeremy Piggott ◽  
...  
Keyword(s):  
Case Studies ◽  
Aquatic Ecosystems ◽  
Environmental Dna ◽  
Quantitative Information ◽  
Freshwater Ecosystems ◽  
Environmental Stressors ◽  
Macroinvertebrate Communities ◽  
Ecological Requirements ◽  
Dna Metabarcoding ◽  
The Impact

Traditionally, taxonomic characterisation of organisms has relied on their morphology; however, molecular methods are increasingly used to monitor and assess biodiversity and ecosystem health. Approaches such as DNA amplicon diversity assessments are a particularly useful tool when morphology-based taxonomy is difficult or taxa are morphologically ambiguous, for example for freshwater bacteria and fungi as well as many freshwater invertebrate species. DNA metabarcoding provides the ability to distinguish cryptic taxa (which can differ markedly in their ecological requirements and tolerances) and in addition it can provide valuable insights into the genetic and ecological diversity of taxa and ecosystems. While DNA metabarcoding has been used mostly on tissue of sampled specimens, recent years have seen an increased use of metabarcoding on environmental DNA samples: DNA extracted not from sampled specimens, but from the surrounding soil or water. However, the ability of metabarcoding of specimens and metabarcoding of environmental DNA (eDNA) to assess biodiversity and the impact of anthropogenic stressors on freshwater ecosystems is largely understudied. In this talk, several studies that document the advantages and still open challenges of (e)DNA metabarcoding for assessing impacts of environmental stressors on aquatic ecosystems will be presented. These studies, performed in Europe and New Zealand, integrate impacts across different biotic groups, i.e. look at stressor effects on bacterial, protist, fungal and macroinvertebrate communities. Specifically, we use various case studies from freshwater ecosystems to address the following questions: whether eDNA samples, which can be relatively quickly obtained from the water, can act as reliable proxies for catchment-level stressor impacts by comparing these to DNA obtained from local bulk samples, and whether DNA metabarcoding data can also provide quantitative information rather than only presence-absence data. In view of the case studies presented, a perspective on the urgent next steps that need to be taken in order to include genetic tools in routine biomonitoring will be derived and linked to the vision of the international network DNAqua-Net.

scholarly journals The Influence of Riparian Corridor Land Use on the Pesquería River’s Macroinvertebrate Community (N.E. Mexico)

Water ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 1930
Author(s):  
Daniel Castro-López ◽  
Pablo Rodríguez-Lozano ◽  
Rebeca Arias-Real ◽  
Víctor Guerra-Cobián ◽  
Narcís Prat
Keyword(s):  
Land Use ◽  
Agricultural Land ◽  
Land Use Changes ◽  
Freshwater Ecosystems ◽  
Urban Land Use ◽  
Macroinvertebrate Community ◽  
Biological Information ◽  
Macroinvertebrate Communities ◽  
Biological Metrics ◽  
The Impact

The Earth’s freshwater ecosystems are currently under threat, particularly in developing countries. In Mexico, intensive land use and inadequate monitoring policies have resulted in the severe degradation of the country’s freshwater ecosystems. This study assesses how the macroinvertebrate communities in the Pesquería River, located in Northeastern Mexico, are affected by riparian land use, in order to determine their potential use as bioindicators to evaluate the macroinvertebrate integrity of the Pesquería River. First, we characterized the land use cover in the riparian channel. Second, we sampled 16 sites for benthic macroinvertebrates along the main channel during the wet and dry seasons. Third, we evaluated the influence of the riparian channel land use on the macroinvertebrate community using 42 different biological metrics. The land use characterization depicted a riparian channel mainly influenced by agricultural and urban land use. Eighty-one invertebrate taxa were identified during the study. Permutational analysis of the variance analysis confirmed significant differences across the different land use classes and the macroinvertebrate community composition while no differences were found between seasons. The indicator species analysis revealed 31 representative taxa for natural land use, 1 for urban, and 4 for agricultural land use. Our modelling analysis showed that 28 of the 42 biological metrics tested responded significantly to land use disturbances, confirming the impact of land use changes on the Pesquería River’s macroinvertebrate communities and suggesting that these metrics may have a use as bioindicators. Finally, this study may provide significant biological information for further studies in similar conditions.

scholarly journals Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Giorgi Dal Pont ◽  
Camila Duarte Ritter ◽  
Andre Olivotto Agostinis ◽  
Paula Valeska Stica ◽  
Aline Horodesky ◽  
...  
Keyword(s):  
Fish Communities ◽  
Environmental Dna ◽  
Hydropower Plant ◽  
Southeastern Brazil ◽  
Fish Diversity ◽  
Pass System ◽  
Fish Pass ◽  
Dna Metabarcoding ◽  
The World ◽  
The Impact

AbstractThe Itaipu Hydroelectric Power Plant is the second largest in the world in power generation. The artificial barrier created by its dam imposes an obstacle for fish migration. Thus, in 2002, a fish pass system, named Piracema Channel, was built to allow fish to access areas upstream of the reservoir. We tested the potential of environmental DNA metabarcoding to monitor the impact of both the dam and associated fish pass system in the Paraná River fish communities and to compare it with traditional monitoring methods. Using a fragment of the 12S gene, we characterized richness and community composition based on amplicon sequence variants, operational taxonomic units, and zero-radius OTUs. We combined GenBank and in-house data for taxonomic assignment. We found that different bioinformatics approaches showed similar results. Also, we found a decrease in fish diversity from 2019 to 2020 probably due to the recent extreme drought experienced in southeastern Brazil. The highest alpha diversity was recorded in the mouth of the fish pass system, located in a protected valley with the highest environmental heterogeneity. Despite the clear indication that the reference databases need to be continuously improved, our results demonstrate the analytical efficiency of the metabarcoding to monitor fish species.

scholarly journals Artificial Light at Night Alleviates the Negative Effect of Pb on Freshwater Ecosystems

2019 ◽  
Vol 20 (6) ◽  
pp. 1343 ◽  
Author(s):  
Gaozhong Pu ◽  
Danjuan Zeng ◽  
Ling Mo ◽  
Jianxiong Liao ◽  
Xiaxia Chen
Keyword(s):  
Leaf Litter ◽  
Litter Decomposition ◽  
Decomposition Rate ◽  
Aquatic Ecosystems ◽  
Freshwater Ecosystems ◽  
Leaf Litter Decomposition ◽  
Artificial Light ◽  
Light At Night ◽  
Negative Effect ◽  
The Impact

Artificial light at night (ALAN) is an increasing phenomenon worldwide that can cause a series of biological and ecological effects, yet little is known about its potential interaction with other stressors in aquatic ecosystems. Here, we tested whether the impact of lead (Pb) on litter decomposition was altered by ALAN exposure using an indoor microcosm experiment. The results showed that ALAN exposure alone significantly increased leaf litter decomposition, decreased the lignin content of leaf litter, and altered fungal community composition and structure. The decomposition rate was 51% higher in Pb with ALAN exposure treatments than in Pb without ALAN treatments, resulting in increased microbial biomass, β-glucosidase (β-G) activity, and the enhanced correlation between β-G and litter decomposition rate. These results indicate that the negative effect of Pb on leaf litter decomposition in aquatic ecosystems may be alleviated by ALAN. In addition, ALAN exposure also alters the correlation among fungi associated with leaf litter decomposition. In summary, this study expands our understanding of Pb toxicity on litter decomposition in freshwater ecosystems and highlights the importance of considering ALAN when assessing environmental metal pollutions.

scholarly journals Parasite transmission in aquatic ecosystems under climate change: joint effects of temperature, host behavior and elimination of parasite larvae by predators

2019 ◽  
Author(s):  
M. Gopko ◽  
E. Mironova ◽  
A. Pasternak ◽  
V. Mikheev ◽  
J. Taskinen
Keyword(s):  
Climate Change ◽  
Aquatic Ecosystems ◽  
Disease Risk ◽  
Freshwater Ecosystems ◽  
Fish Host ◽  
Parasitic Infections ◽  
List Type ◽  
Filter Feeding ◽  
Increased Risk ◽  
The Impact

AbstractA moderate raise in temperature was suggested to enhance the impact of parasites on aquatic ecosystems. Under higher temperatures, poikilothermic animals (e.g. fish), increase their activity, which can result in a more frequent encounter with parasites. However, temperature increase may also trigger processes counteracting an increased risk of parasitic infections. For instance, removal of free-living stages of parasites by filter-feeding organisms can increase with temperature and potentially mitigate disease risk in ecosystems under climate change.In our study, we aimed to find out whether an increased infection transmission under higher temperatures can be, at least, partly compensated by the increased removal of parasitic larvae be aquatic predators. In addition, we planned to reveal the behavioral mechanism underlying the more successful transmission of the parasite at higher temperatures.We experimentally studied how temperature, the behavior of fish host (rainbow trout) and the presence of filter-feeding mussels in the environment influence transmission success of trematode larvae (Diplostomum pseudospathaceum cercariae) to fish host.We found that temperature raise increased, while presence of filter-feeding mussels in the environment decreased infection intensities in fish. However, the effect of mussel’s presence was constant within the tested range of water temperatures (15-23ºC), which suggests that it cannot compensate for the observed increased transmission of parasites under temperature raise. The difference in fish individual behavior (swimming activity) before the exposure to parasites was a substantial factor the affecting host’s vulnerability to infection. However, fish motor activity only weakly correlated with temperature, therefore, it is unlikely to be responsible for the increased infection success under warmer conditions. After exposure to parasites, fish strongly decreased their activity. This decrease was temperature-dependent and more pronounced in bolder (more active) fish, which leads to lower variability in activity of fish exposed to parasites compared with the safe environment. Post-exposure activity did not influence the infection intensity.In general, we showed that the elimination of trematode larvae by filter-feeders is unlikely to deter the potential effects of global warming on host-parasite interactions in temperate freshwater ecosystems.

scholarly journals The power of metabarcoding: Can we improve bioassessment and biodiversity surveys of stream macroinvertebrate communities?

2021 ◽  
Vol 5 ◽  
Author(s):  
Jarno Turunen ◽  
Heikki Mykrä ◽  
Vasco Elbrecht ◽  
Dirk Steinke ◽  
Thomas Braukmann ◽  
...  
Keyword(s):  
Species Identification ◽  
Cost Effective ◽  
Morphological Identification ◽  
Macroinvertebrate Communities ◽  
Dna Metabarcoding ◽  
Stream Macroinvertebrate ◽  
Data Deficient ◽  
Morphological Species ◽  
High Level ◽  
The Impact

Most stream bioassessment and biodiversity surveys are currently based on morphological identification of communities. However, DNA metabarcoding is emerging as a fast and cost-effective alternative for species identification. We compared both methods in a survey of benthic macroinvertebrate communities across 36 stream sites in northern Finland. We identified 291 taxa of which 62% were identified only by DNA metabarcoding. DNA metabarcoding produced extensive species level inventories for groups (Oligochaeta, Chironomidae, Simuliidae, Limoniidae and Limnephilidae), for which morphological identification was not feasible due to the high level of expertise needed. Metabarcoding also provided more insightful taxonomic information on the occurrence of three red-listed vulnerable or data deficient species, the discovery of two likely cryptic and potentially new species to Finland and species information of insect genera at an early larval stage that could not be separated morphologically. However, it systematically failed to reliably detect the occurrence of gastropods that were easily identified morphologically. The impact of mining on community structure could only be shown using DNA metabarcoding data which suggests that the finer taxonomic detail can improve detection of subtle impacts. Both methods generally exhibited similar strength of community-environment relationships, but DNA metabarcoding showed better performance with presence/absence data than with relative DNA sequence abundances. Our results suggest that DNA metabarcoding holds a promise for future anthropogenic impact assessments, although, in our case, the performance did not improve much from the morphological species identification. The key advantage of DNA metabarcoding lies in efficient biodiversity surveys, taxonomical studies and applications in conservation biology.

scholarly journals Integration of DNA-Based Approaches in Aquatic Ecological Assessment Using Benthic Macroinvertebrates

Water ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 331
Author(s):  
Sofia Duarte ◽  
Barbara R. Leite ◽  
Maria João Feio ◽  
Filipe O. Costa ◽  
Ana Filipa Filipe
Keyword(s):  
Benthic Macroinvertebrates ◽  
Aquatic Ecosystems ◽  
Ecological Status ◽  
Environmental Dna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Dna Metabarcoding ◽  
Marine Current ◽  
Increased Sensitivity ◽  
Commercial Kits

Benthic macroinvertebrates are among the most used biological quality elements for assessing the condition of all types of aquatic ecosystems worldwide (i.e., fresh water, transitional, and marine). Current morphology-based assessments have several limitations that may be circumvented by using DNA-based approaches. Here, we present a comprehensive review of 90 publications on the use of DNA metabarcoding of benthic macroinvertebrates in aquatic ecosystems bioassessments. Metabarcoding of bulk macrozoobenthos has been preferentially used in fresh waters, whereas in marine waters, environmental DNA (eDNA) from sediment and bulk communities from deployed artificial structures has been favored. DNA extraction has been done predominantly through commercial kits, and cytochrome c oxidase subunit I (COI) has been, by far, the most used marker, occasionally combined with others, namely, the 18S rRNA gene. Current limitations include the lack of standardized protocols and broad-coverage primers, the incompleteness of reference libraries, and the inability to reliably extrapolate abundance data. In addition, morphology versus DNA benchmarking of ecological status and biotic indexes are required to allow general worldwide implementation and higher end-user confidence. The increased sensitivity, high throughput, and faster execution of DNA metabarcoding can provide much higher spatial and temporal data resolution on aquatic ecological status, thereby being more responsive to immediate management needs.

scholarly journals Evaluating early-warning indicators of critical transitions in natural aquatic ecosystems

2016 ◽  
Vol 113 (50) ◽  
pp. E8089-E8095 ◽  
Author(s):  
Alena Sonia Gsell ◽  
Ulrike Scharfenberger ◽  
Deniz Özkundakci ◽  
Annika Walters ◽  
Lars-Anders Hansson ◽  
...  
Keyword(s):  
Time Series ◽  
Case Studies ◽  
Early Warning ◽  
Aquatic Ecosystems ◽  
Theoretical Models ◽  
Freshwater Ecosystems ◽  
State Variables ◽  
Critical Transitions ◽  
Early Warning Indicators ◽  
Warning Indicators

Ecosystems can show sudden and persistent changes in state despite only incremental changes in drivers. Such critical transitions are difficult to predict, because the state of the system often shows little change before the transition. Early-warning indicators (EWIs) are hypothesized to signal the loss of system resilience and have been shown to precede critical transitions in theoretical models, paleo-climate time series, and in laboratory as well as whole lake experiments. The generalizability of EWIs for detecting critical transitions in empirical time series of natural aquatic ecosystems remains largely untested, however. Here we assessed four commonly used EWIs on long-term datasets of five freshwater ecosystems that have experienced sudden, persistent transitions and for which the relevant ecological mechanisms and drivers are well understood. These case studies were categorized by three mechanisms that can generate critical transitions between alternative states: competition, trophic cascade, and intraguild predation. Although EWIs could be detected in most of the case studies, agreement among the four indicators was low. In some cases, EWIs were detected considerably ahead of the transition. Nonetheless, our results show that at present, EWIs do not provide reliable and consistent signals of impending critical transitions despite using some of the best routinely monitored freshwater ecosystems. Our analysis strongly suggests that a priori knowledge of the underlying mechanisms driving ecosystem transitions is necessary to identify relevant state variables for successfully monitoring EWIs.

scholarly journals Fresh insights into Mediterranean biodiversity: environmental DNA reveals spatio-temporal patterns of stream invertebrate communities on Sicily

Hydrobiologia ◽  
2021 ◽  
Author(s):  
Kamil Hupało ◽  
Saskia Schmidt ◽  
Till-Hendrik Macher ◽  
Martina Weiss ◽  
Florian Leese
Keyword(s):  
Global Climate ◽  
Environmental Dna ◽  
Spatial Diversity ◽  
Freshwater Ecosystems ◽  
High Rate ◽  
Sequence Variant ◽  
Macroinvertebrate Communities ◽  
Freshwater Biodiversity ◽  
Anthropogenic Pressures ◽  
Spatio Temporal

AbstractThe Mediterranean region with its islands is among the top biodiversity hotspots. It houses numerous freshwater taxa with a high rate of endemism, but is heavily impacted by anthropogenic pressures and global climate change. To conserve biodiversity, reliable data on species and genetic diversity are needed especially for the scarcely known insular freshwater ecosystems. Environmental DNA (eDNA) metabarcoding provides a straight-forward opportunity to assess aquatic biodiversity. Therefore, we conducted the first eDNA metabarcoding study in one stream catchment on Sicily. Specifically, we aimed to (i) investigate spatial diversity patterns of macroinvertebrate communities, (ii) assess seasonal changes (autumn and winter), and (iii) check if dispersal barriers can be identified. Water samples were taken at 27 different sites in two seasons and eDNA metabarcoding was performed using a fragment of the mitochondrial cytochrome c oxidase subunit I gene as a marker. In total, we detected 98 macroinvertebrate species, including 28 taxa potentially new to Sicily. Exact sequence variant and species composition data showed that diversity differed between seasons with less taxa detected in winter. We also detected a dispersal barrier, which had a stronger effect in autumn. Our findings show that eDNA metabarcoding provides valuable information on Sicilian freshwater biodiversity. We therefore encourage its application for understudied regions to better understand the state and dynamics of freshwater biodiversity.

scholarly journals Complexity matters: Evaluating the impact of bioinformatics parameters on eukaryotic MOTU delimitation and taxonomy assignment

2021 ◽  
Vol 4 ◽  
Author(s):  
Holly Bik
Keyword(s):  
Recent Work ◽  
Marine Sediment ◽  
Dna Sequences ◽  
Environmental Dna ◽  
Microbial Eukaryotes ◽  
Dna Metabarcoding ◽  
Animal Phyla ◽  
Global Biodiversity ◽  
Intragenomic Variation ◽  
The Impact

Microbial metazoans (e.g. nematodes, copepods, tardigrades and other 'minor' animal phyla < 1mm in size) are ubiquitous and abundant across most ecosystems on earth. In marine sediment habitats, microbial metazoa exhibit high biodiversity but suffer from poor taxonomy and an ongoing lack of reference DNA sequences in public databases. Environmental DNA metabarcoding thus represents an increasingly critical tool for rapidly assessing the global biodiversity and phylogeographic patterns of such neglected metazoan groups. However, there are significant bioinformatics hurdles facing the study of microbial eukaryotes. Most software pipelines and databases have been designed and optimized for smaller (e.g. bacteria/archaea) or larger (e.g. vertebrate) taxa, and emphasize "standard" metabarcoding loci such as COI which are not useful for groups such as nematodes which lack universal COI primer binding regions. In addition, the sparsity of public reference barcodes for microbial metazoa often precludes accurate taxonomy assignments for unknown MOTUs in metabarcoding datasets. Here, I will present recent work focused on the refinement of bionformatics workflows for microbial metazoan groups, including efforts to account for intragenomic variation observed in rRNA loci, discrepancies in results across OTU vs. ASV generation pipelines, and biases in sequence-based taxonomhy assignment methods.

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