scholarly journals Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Luca Carraro ◽  
Elvira Mächler ◽  
Remo Wüthrich ◽  
Florian Altermatt
Keyword(s):  
Spatial Patterns ◽  
Environmental Dna ◽  
Freshwater Ecosystems

scholarly journals Monitoring spawning migrations of potamodromous fish species via eDNA

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Bettina Thalinger ◽  
Elisabeth Wolf ◽  
Michael Traugott ◽  
Josef Wanzenböck
Keyword(s):  
Fish Species ◽  
Anthropogenic Impacts ◽  
Environmental Dna ◽  
Signal Strength ◽  
Digital Pcr ◽  
Freshwater Ecosystems ◽  
Non Invasive ◽  
River Stretch ◽  
Daily Discharge ◽  
Invasive Techniques

Abstract Potamodromous fish are considered important indicators of habitat connectivity in freshwater ecosystems, but they are globally threatened by anthropogenic impacts. Hence, non-invasive techniques are necessary for monitoring during spawning migrations. The use of environmental DNA (eDNA) potentially facilitates these efforts, albeit quantitative examinations of spawning migrations remain so far mostly uncharted. Here, we investigated spawning migrations of Danube bleak, Alburnus mento, and Vimba bream, Vimba vimba, and found a strong correlation between daily visual fish counts and downstream eDNA signals obtained from filtered water samples analysed with digital PCR and end-point PCR coupled with capillary electrophoresis. By accounting for daily discharge fluctuations, it was possible to predict eDNA signal strength from the number of migrating fish: first, the whole spawning reach was taken into account. Second, the model was validated using eDNA signals and fish counts obtained from the upper half of the examined river stretch. Consequently, fish counts and their day-to-day changes could be described via an eDNA-based time series model for the whole migration period. Our findings highlight the capability of eDNA beyond delivering simple presence/absence data towards efficient and informative monitoring of highly dynamic aquatic processes such as spawning migrations of potamodromous fish species.

scholarly journals Fish community assessment with eDNA metabarcoding: effects of sampling design and bioinformatic filtering

2017 ◽  
Vol 74 (9) ◽  
pp. 1362-1374 ◽  
Author(s):  
Nathan T. Evans ◽  
Yiyuan Li ◽  
Mark A. Renshaw ◽  
Brett P. Olds ◽  
Kristy Deiner ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Species Richness ◽  
Spatial Resolution ◽  
Spatial Patterns ◽  
Water Body ◽  
Fish Community ◽  
Sampling Design ◽  
Environmental Dna ◽  
Body Type ◽  
Multiple Samples

Species richness is a metric of biodiversity that represents the number of species present in a community. Traditional fisheries assessments that rely on capture of organisms often underestimate true species richness. Environmental DNA (eDNA) metabarcoding is an alternative tool that infers species richness by collecting and sequencing DNA present in the ecosystem. Our objective was to determine how spatial distribution of samples and “bioinformatic stringency” affected eDNA-metabarcoding estimates of species richness compared with capture-based estimates in a 2.2 ha reservoir. When bioinformatic criteria required species to be detected only in a single sample, eDNA metabarcoding detected all species captured with traditional methods plus an additional 11 noncaptured species. However, when we required species to be detected with multiple markers and in multiple samples, eDNA metabarcoding detected only seven of the captured species. Our analysis of the spatial patterns of species detection indicated that eDNA was distributed relatively homogeneously throughout the reservoir, except near the inflowing stream. We suggest that interpretation of eDNA metabarcoding data must consider the potential effects of water body type, spatial resolution, and bioinformatic stringency.

scholarly journals Effective removal of the American bullfrog (Lithobates catesbeianus) on a landscape level: long term monitoring and removal efforts in Yosemite Valley, Yosemite National Park

2019 ◽  
Vol 22 (2) ◽  
pp. 617-626 ◽  
Author(s):  
Colleen Kamoroff ◽  
Ninette Daniele ◽  
Robert L. Grasso ◽  
Rebecca Rising ◽  
Travis Espinoza ◽  
...  
Keyword(s):  
Invasive Species ◽  
National Parks ◽  
National Park ◽  
Environmental Dna ◽  
Freshwater Ecosystems ◽  
Yosemite National Park ◽  
American Bullfrog ◽  
Yosemite Valley ◽  
Park Service ◽  
Landscape Level

Abstract Invasive alien species are a major threat to freshwater ecosystems, and American bullfrogs are among the world’s 100 most prominent aquatic invasive species causing negative direct and indirect effect on native aquatic fauna worldwide. Bullfrogs were intentionally introduced into Yosemite Valley, Yosemite National Park in the 1950s where they became well established in the subsequent years. Starting in 2005, the National Park Service (NPS) began bullfrog removal, targeting various life stages using hand, net, and spear techniques. Starting in 2015, the NPS conducted environmental DNA (eDNA) surveys and deployed audio recordings devices to ensure adequate detection of bullfrogs. During the first year of cencerted effort in the Valley in 2005, the NPS removed 86% of all recorded bullfrog. The subsequent decade was spent searching for individuals with lower return on effort. In 2012, the NPS removed the last observed signs of bullfrog breeding, and the last observed bullfrog in 2019. Following removal of the breeding bullfrog population, the NPS began restoration projects for species of special concern. The NPS introduced the federally threatened California red-legged frogs (Rana draytonii) into Yosemite Valley beginning in 2016. This is the first published successful eradication of bullfrogs on a landscape level. National Parks and Monuments often provide refuges for imperiled wildlife and should be managed to remove invasive species. Our work highlights effective bullfrog removal is obtainable and can lead to local recovery of endangered species.

scholarly journals Evidence for self-organization in determining spatial patterns of stream nutrients, despite primacy of the geomorphic template

2017 ◽  
Vol 114 (24) ◽  
pp. E4744-E4752 ◽  
Author(s):  
Xiaoli Dong ◽  
Albert Ruhí ◽  
Nancy B. Grimm
Keyword(s):  
Surface Water ◽  
Spatial Heterogeneity ◽  
Spatial Patterns ◽  
Vascular Plant ◽  
Freshwater Ecosystems ◽  
Self Organization ◽  
Major Influence ◽  
Spatial And Temporal Scales ◽  
Riverine Ecosystems ◽  
Wide Range

Nutrients in freshwater ecosystems are highly variable in space and time. Nevertheless, the variety of processes contributing to nutrient patchiness, and the wide range of spatial and temporal scales at which these processes operate, obfuscate how this spatial heterogeneity is generated. Here, we describe the spatial structure of stream nutrient concentration, quantify the relative importance of the physical template and biological processes, and detect and evaluate the role of self-organization in driving such patterns. We examined nutrient spatial patterns in Sycamore Creek, an intermittent desert stream in Arizona that experienced an ecosystem regime shift [from a gravel/algae-dominated to a vascular plant-dominated (hereafter, “wetland”) system] in 2000 when cattle grazing ceased. We conducted high-resolution nutrient surveys in surface water along a 10-km stream reach over four visits spanning 18 y (1995–2013) that represent different successional stages and prewetland stage vs. postwetland state. As expected, groundwater upwelling had a major influence on nutrient spatial patterns. However, self-organization realized by the mechanism of spatial feedbacks also was significant and intensified over ecosystem succession, as a resource (nitrogen) became increasingly limiting. By late succession, the effects of internal spatial feedbacks and groundwater upwelling were approximately equal in magnitude. Wetland establishment influenced nutrient spatial patterns only indirectly, by modifying the extent of surface water/groundwater exchange. This study illustrates that multiple mechanisms interact in a dynamic way to create spatial heterogeneity in riverine ecosystems, and provides a means to detect spatial self-organization against physical template heterogeneity as a dominant driver of spatial patterns.

scholarly journals Ethanol eDNA Reveals Unique Community Composition of Aquatic Macroinvertebrates Compared to Bulk Tissue Metabarcoding in a Biomonitoring Sampling Scheme

Diversity ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 34
Author(s):  
Sadhna Fiona Persaud ◽  
Karl Cottenie ◽  
Jennifer Erin Gleason
Keyword(s):  
Land Use ◽  
Community Composition ◽  
Agricultural Land ◽  
Environmental Dna ◽  
Ecological Condition ◽  
Freshwater Ecosystems ◽  
Aquatic Macroinvertebrates ◽  
Biological Communities ◽  
Non Destructive ◽  
Bulk Tissue

Freshwater ecosystems provide essential ecosystem services and support biodiversity; however, their water quality and biological communities are influenced by adjacent agricultural land use. Aquatic macroinvertebrates are commonly used as bioindicators of stream conditions in freshwater biomonitoring programs. Sorting benthic samples for molecular identification is a time-consuming process, and this study investigates the potential of ethanol-collected environmental DNA (eDNA) for metabarcoding macroinvertebrates, especially for common bioindicator groups. The objective of this study was to compare macroinvertebrate composition between paired bulk tissue and ethanol eDNA samples, as eDNA could provide a less time-consuming and non-destructive method of sampling macroinvertebrates. We collected benthic samples from streams in Ontario, Canada, and found that community composition varied greatly between sampling methods and that few taxa were shared between paired tissue and ethanol samples, suggesting that ethanol eDNA is not an acceptable substitute. It is unclear why we did not detect all the organisms that were preserved in the ethanol, or the origin of the DNA we did detect. Furthermore, we also detected no difference in community composition for bioindicator taxa due to surrounding land use or water chemistry, suggesting sites were similar in ecological condition.

scholarly journals Using environmental DNA to monitor the reintroduction success of the Rhine sculpin (Cottus rhenanus) in a restored stream

2019 ◽  
Author(s):  
Christopher A Hempel ◽  
Bianca Peinert ◽  
Arne J Beermann ◽  
Vasco Elbrecht ◽  
Jan-Niklas Macher ◽  
...  
Keyword(s):  
False Negative ◽  
Ecological Status ◽  
Environmental Dna ◽  
Freshwater Ecosystems ◽  
Freshwater Ecosystem ◽  
Ecosystem Monitoring ◽  
Modern Approach ◽  
Negative Results ◽  
False Negative Results ◽  
Good Ecological Status

As a consequence of the strong human impact on freshwater ecosystems, restoration measures are increasingly applied to restore and maintain their good ecological status. The ecological status of freshwaters can be inferred by assessing the presence of indicator species, such as the Rhine sculpin (Cottus rhenanus). However, traditional methods of monitoring fish, such as electrofishing, are often challenging and invasive. To augment or even replace the traditional fish monitoring approach, the analysis of environmental DNA (eDNA) has recently been proposed as an alternative, sensitive approach. The present study employed this modern approach to monitor the Rhine sculpin, a species that has been reintroduced into a recently restored stream within the Emscher catchment in Germany, in order to validate the success of the restorations. We monitored the dispersal of the Rhine sculpin using replicated 12S end-point PCR eDNA surveillance at a fine spatial and temporal scale to investigate the applicability of analyzing eDNA for freshwater ecosystem monitoring. We also performed traditional electrofishing in one instance to compare visual and eDNA-based assessments. We could track the dispersal of the Rhine sculpin and showed a higher dispersal potential of the species than we assumed. Furthermore, the eDNA analysis showed higher sensitivity for detecting the species than traditional electrofishing, although false negative results occurred at early reintroduction stages. Our results show that analyzing eDNA is capable of validating and tracking ecological reintroductions and contribute to the assessment and modelling of ecological status of streams.

scholarly journals An assessment of environmental metabarcoding protocols aiming at favouring contemporary biodiversity in inventories of deep-sea communities

2019 ◽  
Author(s):  
Miriam I. Brandt ◽  
Blandine Trouche ◽  
Nicolas Henry ◽  
Cathy Liautard-Haag ◽  
Lois Maignien ◽  
...  
Keyword(s):  
Spatial Patterns ◽  
Ancient Dna ◽  
Deep Sea ◽  
Messenger Rna ◽  
Environmental Dna ◽  
List Type ◽  
Dna Fragments ◽  
Large Reservoir ◽  
Alpha And Beta Diversity ◽  
Dna And Rna

ABSTRACTThe abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly under target of resource-extraction industries although being drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased towards describing past rather than present communities as sediments contain both contemporary and ancient DNA.Using commercially available kits, we investigated the impacts of five molecular processing methods on DNA metabarcoding biodiversity inventories targeting prokaryotes (16S-V4V5), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed towards small fragments, we evaluated the effect of removing short DNA fragments via size-selection and ethanol reconcentration using DNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by DNA and RNA co-extracted from 2 g of sediment at the same sites.Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using environmental RNA (eRNA). With ribosomal loci, RNA, while resolving similar spatial patterns than co-extracted DNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to over-abundance of rRNA and RNA release. With the mitochondrial locus, RNA detected lower metazoan richness and resolved less spatial patterns than co-extracted DNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (≥10 g) for accurately surveying eukaryotic diversity.We conclude that DNA should be favoured over RNA for logistically realistic, repeatable, and reliable surveys, and confirm that large sediment samples (≥10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.

scholarly journals Effects of Microbial Activity and Environmental Parameters on the Degradation of Extracellular Environmental DNA from a Eutrophic Lake

2019 ◽  
Vol 16 (18) ◽  
pp. 3339 ◽  
Author(s):  
Nur Syahidah Zulkefli ◽  
Keon-Hee Kim ◽  
Soon-Jin Hwang
Keyword(s):  
Microbial Activity ◽  
Degradation Rate ◽  
Abiotic Factors ◽  
Environmental Parameters ◽  
Environmental Dna ◽  
Eutrophic Lake ◽  
Freshwater Ecosystems ◽  
Extracellular Dna ◽  
Biotic And Abiotic Factors ◽  
Positive Effects

Extracellular DNA (exDNA) pool in aquatic environments is a valuable source for biomonitoring and bioassessment. However, degradation under particular environmental conditions can hamper exDNA detectability over time. In this study, we analyzed how different biotic and abiotic factors affect the degradation rate of extracellular environmental DNA using 16S rDNA sequences extracted from the sediment of a eutrophic lake and Anabaena variabilis cultured in the laboratory. We exposed the extracted exDNA to different levels of temperature, light, pH, and bacterial activity, and quantitatively analyzed the concentration of exDNA during 4 days. The solution containing bacteria for microbial activity treatment was obtained from the lake sediment using four consecutive steps of filtration; two mesh filters (100 μm and 60 μm mesh) and two glass fiber filters (2.7 μm and 1.2 μm pore-sized). We found that temperature individually and in combination with bacterial abundance had significant positive effects on the degradation of exDNA. The highest degradation rate was observed in samples exposed to high microbial activity, where exDNA was completely degraded within 1 day at a rate of 3.27 day−1. Light intensity and pH had no significant effects on degradation rate of exDNA. Our results indicate that degradation of exDNA in freshwater ecosystems is driven by the combination of both biotic and abiotic factors and it may occur very fast under particular conditions.

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