Ecological influence of sediment bypass tunnels on macroinvertebrates in dam-fragmented rivers by DNA metabarcoding.
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ABSTRACT:
SUBMITTER: Serrana JM
PROVIDER: S-EPMC6033945 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Rivers are crucial ecosystems supporting biodiversity and human well-being, yet they face increasing degradation globally. Traditional river biomonitoring methods based on morphological identification of macroinvertebrates present challenges in terms of taxonomic resolution and scalability. This study explores the application of DNA metabarcoding analysis in both bulk and environmental DNA (eDNA) samples for comprehensive assessment of macrozoobenthic biodiversity, detection of invasive and endangered species, and evaluation of river ecological status in northwestern Spain. DNA metabarcoding of homogenized bulk samples and water eDNA revealed a mean of 100 and 87 macrozoobenthos species per sample respectively. However, the specific composition was significantly different with only 27.3% of the total species being shared. It was not possible to identify all the OTUs to species level; only 17.43% and 49.4% of the OTUs generated could be identified to species level in the bulk and eDNA samples, respectively. Additionally, a total of 11 exotic species (two first records for the Iberian Peninsula and another three first records for Asturias region) and one endangered species were detected by molecular tools. Molecular methods showed significant correlations with morphological identification for EQR values (Ecological Quality Ratio) of IBMWP index, yet differences in inferred river ecological status were noted, with bulk samples tending to indicate higher status. Overall, DNA metabarcoding offers a promising approach for river biomonitoring, providing insights into biodiversity, invasive species, and ecological status within a single analysis. Further optimization and intercalibration are required for its implementation in routine biomonitoring programmes, but its scalability and multi-tasking capabilities position it as a valuable tool for integrated monitoring of river ecosystems.
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Project description:The marine environment contains suspended particulate matter which originates from natural and anthropogenic sources. Settlement of this material can leave benthic organisms susceptible to smothering, especially if burial is sudden i.e. following storms or activities such as dredging. Their survival will depend on their tolerance to, and their ability to escape from burial. Here we present data from a multi-factorial experiment measuring burial responses incorporating duration, sediment fraction and depth. Six macroinvertebrates commonly found in sediment rich environments were selected for their commercial and/or conservation importance. Assessments revealed that the brittle star (Ophiura ophiura), the queen scallop (Aequipecten opercularis) and the sea squirt (Ciona intestinalis) were all highly intolerant to burial whilst the green urchin (Psammichinus miliaris) and the anemone (Sagartiogeton laceratus), showed intermediate and low intolerance respectively, to burial. The least intolerant, with very high survival was the Ross worm (Sabellaria spinulosa). With the exception of C. intestinalis, increasing duration and depth of burial with finer sediment fractions resulted in increased mortality for all species assessed. For C. intestinalis depth of burial and sediment fraction were found to be inconsequential since there was complete mortality of all specimens buried for more than one day. When burial emergence was assessed O. ophiura emerged most frequently, followed by P. miliaris. The former emerged most frequently from the medium and fine sediments whereas P. miliaris emerged more frequently from coarse sediment. Both A. opercularis and S. laceratus showed similar emergence responses over time, with A. opercularis emerging more frequently under coarse sediments. The frequency of emergence of S. laceratus increased with progressively finer sediment and C. intestinalis did not emerge from burial irrespective of sediment fraction or depth. Finally, and perhaps unsurprisingly, the greatest ability to emerge from burial in all other species was from shallow (2 cm) burial. Although survival was consistently highly dependent on duration and depth of burial as expected, emergence behaviour was not as easily predictable thereby confounding predictions. We conclude that responses to burial are highly species specific and therefore tolerance generalisations are likely to be oversimplifications. These data may be used to inform environmental impact models that allow forecasting of the cumulative impacts of seabed disturbance and may provide mitigation measures for the sustainable use of the seabed.
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Project description:DNA-based identification through the use of metabarcoding has been proposed as the next step in the monitoring of biological communities, such as those assessed under the Water Framework Directive (WFD). Advances have been made in the field of metabarcoding, but challenges remain when using complex samples. Uneven biomass distributions, preferential amplification and reference database deficiencies can all lead to discrepancies between morphological and DNA-based taxa lists. The effects of different taxonomic groups on these issues remain understudied. By metabarcoding WFD monitoring samples, we analyzed six different taxonomic groups of freshwater organisms, both separately and combined. Identifications based on metabarcoding data were compared directly to morphological assessments performed under the WFD. The diversity of taxa for both morphological and DNA-based assessments was similar, although large differences were observed in some samples. The overlap between the two taxon lists was 56.8% on average across all taxa, and was highest for Crustacea, Heteroptera, and Coleoptera, and lowest for Annelida and Mollusca. Taxonomic sorting in six basic groups before DNA extraction and amplification improved taxon recovery by 46.5%. The impact on ecological quality ratio (EQR) scoring was considerable when replacing morphology with DNA-based identifications, but there was a high correlation when only replacing a single taxonomic group with molecular data. Different taxonomic groups provide their own challenges and benefits. Some groups might benefit from a more consistent and robust method of identification. Others present difficulties in molecular processing, due to uneven biomass distributions, large genetic diversity or shortcomings of the reference database. Sorting samples into basic taxonomic groups that require little taxonomic knowledge greatly improves the recovery of taxa with metabarcoding. Current standards for EQR monitoring may not be easily replaced completely with molecular strategies, but the effectiveness of molecular methods opens up the way for a paradigm shift in biomonitoring.
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Project description:Rivers are a vital resource for human wellbeing. To reduce human impact on water bodies, the European Union has established an essential regulatory framework for protection and sustainable management (WFD; 2000/60/EC). In this strategy, reliable and economic bioindicators are a fundamental component. Benthic macroinvertebrates are the group most commonly used as bioindicators through all European countries. However, their conventional assessment currently entails serious cost-efficiency limitations. In this study, we have tested the reliability of metabarcoding as a tool to record river macroinvertebrates using samples from a mock community (in vitro validation) and eDNA extracted for field validation from water from six sites within a north Iberian river (River Nalón, Asturias, Spain). Two markers (V4 region within the nuclear 18S rDNA and a fragment of the mitochondrial COI gene) were amplified and sequenced using an Illumina platform. The molecular technique has proven to be more sensitive than the visual one. A cost-benefit analysis shows that the metabarcoding approach is more expensive than conventional techniques for determining macroinvertebrate communities but requires fewer sampling and identification efforts. Our results suggest metabarcoding is a useful tool for alternative assessment of freshwater quality.
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Project description:Understanding how rivers adjust to the sediment load they carry is critical to predicting the evolution of landscapes. Presently, however, no physically based model reliably captures the dependence of basic river properties, such as its shape or slope, on the discharge of sediment, even in the simple case of laboratory rivers. Here, we show how the balance between fluid stress and gravity acting on the sediment grains, along with cross-stream diffusion of sediment, determines the shape and sediment flux profile of laminar laboratory rivers that carry sediment as bedload. Using this model, which reliably reproduces the experiments without any tuning, we confirm the hypothesis, originally proposed by Parker [G. Parker, J. Fluid Mech 89, 127-146 (1978)], that rivers are restricted to exist close to the threshold of sediment motion (within about 20%). This limit is set by the fluid-sediment interaction and is independent of the water and sediment load carried by the river. Thus, as the total sediment discharge increases, the intensity of sediment flux (sediment discharge per unit width) in a river saturates, and the river can transport more sediment only by widening. In this large discharge regime, the cross-stream diffusion of momentum in the flow permits sediment transport. Conversely, in the weak transport regime, the transported sediment concentrates around the river center without significantly altering the river shape. If this theory holds for natural rivers, the aspect ratio of a river could become a proxy for sediment discharge-a quantity notoriously difficult to measure in the field.
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Project description:Organophosphate esters (OPEs) are synthetic chemicals widely used as e.g., flame retardants and plasticisers in various consumer products. Due to the toxicity of OPEs in aquatic ecosystems, exposure of fauna and flora to these compounds is of potential concern. In this study, the concentrations, profiles, sources, and ecological risk of eight OPEs were investigated in the sediments from the two major rivers in southwest Nigeria. Concentrations of ∑OPEs in surface sediments were in the range 13.1 - 2110 ng/g dry weight (dw) (median: 378 ng/g dw) in the Ogun River and 24.7-589 ng/g dw (median: 174 ng/g dw) in the Osun River. These concentrations are broadly within the range of those reported in surface sediment in previous studies conducted in other locations around the world. Tris (2-butoxyethyl) phosphate (TBOEP) was the dominant OPE in the sediment samples with a median concentration of 337 and 126 ng/g dw for the Ogun and Osun Rivers respectively, while tri-n-butyl phosphate (TnBP) was not detected in any sample. Excluding TBOEP, the chlorinated organophosphate esters: tris(2-chloroethyl) phosphate (TCEP), tris(2-chloro-propyl) phosphate (TCIPP), and tris(1,3-dichloro-2-propyl) phosphate (TDCIPP) were the dominant OPEs in the Osun River, while the aryl-OPEs: triphenyl phosphate (TPHP), 2-ethylhexyl diphenyl phosphate (EHDPP), and tri-m-tolyl phosphate (TMTP) were dominant in the Ogun River. Under a median exposure scenario, moderate ecological risk was predicted from exposure to TCIPP in the Osun River. In contrast, under a high exposure scenario, concentrations of TDCIPP (risk quotient, RQ = 5.33-5.37) constituted a high ecological risk in both rivers, with moderate risks observed for TBOEP (RQ = 0.022-0.18) and TCIPP (RQ = 0.097 - 0.16). Therefore, the risk to aquatic organisms from concomitant exposure to mixtures of OPEs in freshwater ecosystems requires further investigation.
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Project description:In many gravel-bedded rivers, floods that fill the channel banks create just enough shear stress to move the median-sized gravel particles on the bed surface (D50). Because this observation is common and is supported by theory, the coincidence of bankfull flow and the incipient motion of D50 has become a commonly used assumption. However, not all natural gravel channels actually conform to this simple relationship; some channels maintain bankfull stresses far in excess of the critical stress required to initiate sediment transport. We use a database of >300 gravel-bedded rivers and >600 10Be-derived erosion rates from across North America to explore the hypothesis that sediment supply drives the magnitude of bankfull shear stress relative to the critical stress required to mobilize the median bed surface grain size ([Formula: see text]). We find that [Formula: see text] is significantly higher in West Coast river reaches (2.35, n = 96) than in river reaches elsewhere on the continent (1.03, n = 245). This pattern parallels patterns in erosion rates (and hence sediment supplies). Supporting our hypothesis, we find a significant correlation between upstream erosion rate and local [Formula: see text] at sites where this comparison is possible. Our analysis reveals a decrease in bed surface armoring with increasing [Formula: see text], suggesting channels accommodate changes in sediment supply through adjustments in bed surface grain size, as also shown through numerical modeling. Our findings demonstrate that sediment supply is encoded in the bankfull hydraulic geometry of gravel bedded channels through its control on bed surface grain size.
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Project description:Dam removal is an increasingly important method of stream restoration, but most removal efforts are under-studied in their effects. In order to better understand the effects of such removals on the stream ecosystem, we examined changes in stream macroinvertebrate communities from 2011-2016. Comparisons were focused above, below, and before and after the October 2012 removal of the Brown Bridge Dam on the Boardman River in Michigan (USA), as well as to new channel sites created in its former reservoir (2013-2015). Using linear mixed-effect models on the percent abundance of ecologically sensitive taxa (% Ephemeroptera, Plecoptera, Trichoptera (EPT)), total density of all macroinvertebrates, overall taxa richness, and Functional Feeding Groups, along with multivariate analyses on the community matrix, we examined differences in community composition among sites and years. EPT declined downstream of the dam immediately after dam removal, but recovered in the second year, becoming dominant within 2-4 years. Downstream sites before removal had different community composition than upstream sites and downstream sites after removal (p<0.001), while upstream and downstream sites after removal converged towards similarity. New channel (restored) %EPT, density, and taxa richness were not different from upstream sites in any year following removal, but new channel sites were the most distinct in community composition, possessing multiple indicator taxa characteristic of unique new conditions. The invasive New Zealand mud snail (Potamopyrgus antipodarum) was absent from all sites prior to dam removal, but appeared at low densities in upstream sites in 2013, had spread to all sites by 2015, and showed large increases at all sites by 2016. Managers employing dam removal for stream restoration should include post-removal monitoring for multiple years following removal and conduct risk analysis regarding potential effects on colonization of invasive invertebrate species.
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Project description:Due to the great possibility of water contamination of many rivers by human activities in Iran, the study of water quality is crucial for water resource protection and human health. High level of phosphorous is the main reason for eutrophication of freshwater systems. The main aim of this study was to investigate the concentration of phosphorus in the rivers feeding into Taham dam in Zanjan, using GIS software. 40 sampling stations were selected along Taham and Ghalharod Rivers with respect to sewage discharge points and feeding characteristics of water entering to Taham dam. In total, 160 water samples were taken from rivers with regard to precipitation season in two different periods from winter 2014 to spring 2015. The obtained data were analyzed using SPSS and ArcView GIS. The findings showed that 15% of the studied stations had phosphorous levels higher than acceptable levels set by EPA. The highest levels of phosphorous contamination were observed in stations No. 145, 154, 155, 161, 166 and 168. The elevated concentrations of phosphorous in the rivers can be responsible for the eutrophication of Taham dam reservoir.
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Project description:Sediment pulses can cause widespread, complex changes to rivers and coastal regions. Quantifying landscape response to sediment-supply changes is a long-standing problem in geomorphology, but the unanticipated nature of most sediment pulses rarely allows for detailed measurement of associated landscape processes and evolution. The intentional removal of two large dams on the Elwha River (Washington, USA) exposed ~30?Mt of impounded sediment to fluvial erosion, presenting a unique opportunity to quantify source-to-sink river and coastal responses to a massive sediment-source perturbation. Here we evaluate geomorphic evolution during and after the sediment pulse, presenting a 5-year sediment budget and morphodynamic analysis of the Elwha River and its delta. Approximately 65% of the sediment was eroded, of which only ~10% was deposited in the fluvial system. This restored fluvial supply of sand, gravel, and wood substantially changed the channel morphology. The remaining ~90% of the released sediment was transported to the coast, causing ~60?ha of delta growth. Although metrics of geomorphic change did not follow simple time-coherent paths, many signals peaked 1-2 years after the start of dam removal, indicating combined impulse and step-change disturbance responses.
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