Changes in the Level of Biofilm Development Significantly Affect the Persistence of Edna in Flowing Water DOI
Jianmin Zhang, Lei Huang,

Wang Yu-rong

et al.

Published: Jan. 1, 2023

As one of the powerful tools species biomonitoring, utilization environmental DNA (eDNA) technology is progressively expanding in both scope and frequency within field ecology. Nonetheless, growing dissemination this has brought to light a multitude intricate issues. The complex effects factors on persistence eDNA unknown transport transformation mechanism biological water have many challenges interpretation information. This study examined how changes development biofilms influence characteristics grass carp diverse sediment types flow conditions, encompassing aspects degradation resuspension. results showed that variations level biofilm significantly impact (eDNA), which further intensified by disruptive flow. Notably, when levels are held constant, differences underlying do not engender statistically significant biofilms. Moreover, investigation did detect any instances phenomenon likely attributable rapid its heterogeneous distribution, influenced various including electrostatic interactions between or sediments, coupled with dearth large-particle forms aquatic milieu, constitute pivotal contributing these observed outcomes. conclusions drawn from will offer theoretical underpinning for application technology.

Language: Английский

A Hierarchical Model for eDNA Fate and Transport Dynamics Accommodating Low Concentration Samples DOI Creative Commons
Ben C. Augustine, Patrick R. Hutchins, Devin N. Jones

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 2, 2024

Abstract Environmental DNA (eDNA) sampling is an increasingly important tool for answering ecological questions and informing aquatic species management; however, several factors currently limit the reliability of inference from eDNA sampling. Two particular challenges are 1) determining source location(s) 2) accurately precisely measuring low concentration samples in presence multiple sources measurement variability. The recently introduced Integrating Transport Hydrology (eDITH) model provides a framework relating measurements to locations riverine networks, but little empirical work has been done test refine assumptions or accommodate samples, that can be systematically undermeasured. To better understand fate transport dynamics our ability reliably quantify we developed hierarchical used it evaluate experiment. Our addresses by modeling number copies each PCR replicate as latent variable with count distribution conditioning detection quantification on copy number. We provide evidence removal rate declined through time, estimating over 80% was removed first 10 meters, traversed 41 seconds. After this initial period rapid decay, decayed slowly consistent farthest site 1km release location, 250 further allowed us detect extra-Poisson variation allocation replicates. extended continuous effect inhibitors inhibitor hypothesis explore potential implications. While not panacea all faced when quantifying low-concentration more complete accounting uncertainty.

Language: Английский

Citations

2
Environmental DNA dynamics of three species of unionid freshwater mussels DOI Creative Commons
Dannise V. Ruiz‐Ramos, Nathan L. Thompson, Catherine A. Richter

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(2)

Published: March 1, 2024

Abstract North American freshwater mussels are of special conservation concern due to their high endemism and the multiple anthropogenic stressors affecting them. Of over 300 species in America, nearly one third these federally listed as threatened or endangered. Environmental DNA (eDNA) analysis has been successful detecting could aid monitoring populations. Production degradation rates eDNA for interest needed inform interpretation detections, allow possible modeling relative abundance population location, mussel through identification. Here, we designed tested qPCR assays three species, mucket ( Ortmanniana ligamentina ), fatmucket Lampsilis siliquoidea endangered spectaclecase Cumberlandia monodonta ). We performed laboratory experiments under controlled conditions measure shedding each species. Different biomasses, temperatures, food regimens were independently determine if factors influence amount produced by mussels. Degradation measured from experimental tank water after removed. Overall, observed low compared previous studies fish rates. Furthermore, temperature feeding showed limited no significant effects studied. consistent with those reported literature other taxa. Collectively, our results will be useful designing studies, dispersal, interpreting help efforts.

Language: Английский

Citations

2
Changes in the level of biofilm development significantly affect the persistence of environmental DNA in flowing water DOI
Jianmin Zhang, Lei Huang, Yurong Wang

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 917, P. 170162 - 170162

Published: Jan. 18, 2024

Language: Английский

Citations

1
Environmental DNA Particle Size Distribution and Quantity Differ Across Taxa and Organelles DOI Creative Commons
Héloïse Verdier, Thibault Datry, Maxime Logez

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(5)

Published: Sept. 1, 2024

ABSTRACT The use of environmental DNA to detect species is now widespread in freshwater ecology. However, the detectability depends on many factors, such as quantity eDNA particles available environment and their state (e.g., free fragments, organellar, or aggregated particles). To date, most advanced knowledge production concerns teleosts. Most often, these studies target mitochondrial genes, since they are present multiple copies a cell. it likely that characteristics molecules vary greatly among taxa genetic compartments, with direct consequences for detection. Using an indoor mesocosm experiment, we compared rate nuclear particle size distribution (PSD) four distinct common aquatic (zebrafish, tadpole, isopod mollusk). tank water was filtered through series filters decreasing porosity at each fraction were quantified by qPCR. We found varied compartments. For taxa, number released higher than origin. PSD mt‐eDNA showed pattern all taxa: relative increased from smallest fractions (0.2 μm less) largest (over 1.2 μm), while nu‐eDNA very different one taxon another. also observed high temporal variability PSD, although latter more complex model. These results call caution how sample analyze environments, particularly organisms emit small quantities isopods.

Language: Английский

Citations

1
Evaluation of Fish Biodiversity in Estuaries Through Environmental DNA Metabarcoding: A Comprehensive Review DOI Creative Commons
Asma Massad Alenzi

Fishes, Journal Year: 2024, Volume and Issue: 9(11), P. 422 - 422

Published: Oct. 22, 2024

Traditional methods face difficulties in capturing elusive species and navigating the complexities of estuarine environments. The adoption eDNA metabarcoding has revolutionized biodiversity assessment, offering non-invasive comprehensive sampling. Challenges specific to estuaries, such as sediment loads salinity fluctuations, were initially addressed through improved DNA extraction, optimized primers, specialized bioinformatics tools. integration multiple genetic markers quantitative approaches enhanced resolution, enabling detection rare cryptic species. Standardized sampling protocols validation traditional contribute reliability metabarcoding. This technology holds promise for informing conservation management strategies ecosystems by providing timely cost-effective data.

Language: Английский

Citations

1
Key Environmental Factors Influencing eDNA Quantitative Detection of Golden Mussel (Limnoperna fortunei) in a Long-Distance Water Diversion Project DOI Creative Commons

Yao Yang,

Kai Liu, Jiahao Zhang

et al.

Environmental Technology & Innovation, Journal Year: 2024, Volume and Issue: unknown, P. 103998 - 103998

Published: Dec. 1, 2024

Language: Английский

Citations

1
Environmental DNA Transport at an Offshore Mesophotic Bank in the Northwestern Gulf of Mexico DOI Open Access
Luke McCartin, Annette F. Govindarajan, Jill M. McDermott

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 27, 2024

Accurately constraining the transport of environmental DNA (eDNA) after it is shed from an animal vital to appropriately geolocate species detections and biodiversity measurements eDNA sequencing data. Modeling studies predict horizontal at concentrations detectable using quantitative PCR over scales tens kilometers, but more limited vertical transport. Field routinely find that metabarcoding data distinguishes biological communities small spatial scales, meters. Here, we leverage unique bathymetry offshore, mesophotic bank benthic invertebrate community supports determine extent which may affect interpretation We found in a stratified water column, invertebrates was vertically constrained depths close seafloor thermocline versus surface mixed layer above. However, when primers are taxonomically specific corals, evidence for coral distances least ~1.5 km where they can be reasonably expected occur. On contrary, there minimal generated broadly targeted sequences eukaryotes. These results highlight importance as well considering methodological details, like taxonomic specificity primers, interpreting

Language: Английский

Citations

0
Assessing the Potential of Environmental DNA for Monitoring Nature‐Like Bypasses: Erroneous Surveillance Owing to DNA Flow‐Through DOI Creative Commons
Kimmo Tolonen,

Anne Lehtinen,

Tiina Laamanen

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(5)

Published: Sept. 1, 2024

ABSTRACT Nature‐like bypasses refer to fishways that simulate natural streams. Apart from facilitating fish migrations, possess the capacity enhance biodiversity in dammed rivers. Feasibility of environmental DNA (eDNA) as a tool for bypass assessments is unknown. This study investigated eDNA 10 and their main channels. Initially, relative flow‐through was estimated bypasses. Subsequently, impact factors on assemblages evaluated, robustness electrofishing methods assessed pertaining monitoring. The computed using an equation estimate residual at specified distances downstream source site. lowest longest with low flow rate highest shortest higher dependent decay coefficient used. redundancy analysis revealed significant effects spatial location, agriculture, catchment area, length species composition. within‐river analyses indicated nonsignificant composition total richness, respectively. Higher richness abundance migratory threatened were observed than samples displayed compared electrofishing. intermediate between channel samples, which further corroborated performance Therefore, represented variable mixtures local assemblages, indicating relatively quantitative spatially accurate assessments. Nevertheless, these results demonstrate practical applicability surveying presence desired evidence benefits supporting by damming.

Language: Английский

Citations

0
Identifying Key Environmental Drivers of Reach‐Scale Salmonid eDNA Recovery With Random Forest DOI Creative Commons
Shawn A. Melendy, John R. Olson

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(5)

Published: Sept. 1, 2024

ABSTRACT Environmental DNA (eDNA) sampling from rivers has emerged as a promising new method for monitoring freshwater organisms of management concern. However, eDNA cannot yet offer reliable estimates target species' abundance/biomass or confident determinations absence river segment. To unlock these abilities—and thereby greatly improve tool decision‐making—the influence local environmental factors on fate must be better understood. At nine sites across the central California coast, we added known quantity novel (Brook Trout, Salvelinus fontinalis ) and collected at sequential downstream distances qPCR analysis. We then used random forest modeling to identify most important reach‐scale (≤ 200 m) outcomes characterize salmonid fate. Our final model identified six outcomes, including five (discharge, catchment calcium oxide content, average depth cross‐section, presence pools, impervious cover watershed) one factor regarding our experimental design (the number technical replicates). results highlight notable effects cross‐sectional area, turbulence, geology fate, suggest discharge pools useful proxies evaluating site's favorability recovery.

Language: Английский

Citations

0
Spatial and seasonal biodiversity variation in a large Mediterranean lagoon using environmental DNA metabarcoding through sponge tissue collection DOI Open Access
Andrea Corral‐Lou, Ana Ramón‐Laca,

Lourdes Alcaraz

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 18, 2024

Abstract Ecosystem monitoring is a fundamental tool to avert biodiversity loss, gathering valuable information that can be used develop conservation policies, evaluating management outcomes, and guiding science-based decision-making. The Mar Menor costal lagoon (South-East of Spain) has experienced episodes eutrophication due intensive agriculture other human activities, causing mass mortalities marine fauna. In this scenario, crucial evaluate the status fauna flora take appropriate measures. Here, our main objective was assess faunal composition its spatial temporal structure associated with pillars support built recreational well-being facilities along Menor. We capitalised on many sea sponges settle these structures by collecting tissue samples for subsequent extraction filtered environmental DNA (i.e. ‘natural sampler DNA’, nsDNA) in northern southern areas lagoon, both spring summer. metabarcoded all at cytochrome oxidase subunit I gene ( COI ), reliably identified 76 taxa belonging nine different phyla, annelids, poriferans, molluscs cnidarians being richest groups. detected emblematic species threatened status, such as pipefishes (genus Syngnathus ) piddock clam, Pholas dactylus , others known become invasive, ascidians Styela canopus Botrylloides niger barnacle Amphibalanus amphitrite polychaetes Branchiomma bairdi boholense . use common widely distributed natural eDNA samplers allowed us characterise diversity, further emphasizing importance low-cost approach biological communities shallow coastal ecosystems.

Language: Английский

Citations

0