A Framework to Unify the Relationship Between Numerical Abundance, Biomass, and Environmental DNA DOI Creative Commons
Matthew C. Yates, Taylor M. Wilcox, Shannon L. Kay

et al.

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Does environmental DNA (eDNA) concentration correlate with numerical abundance ( N ) or biomass in aquatic organisms? We hypothesize that eDNA can be adjusted to simultaneously reflect both. Building on frameworks developed from the Metabolic Theory of Ecology, we derive two equations adjust data both and using population size structure allometric scaling coefficients. also demonstrate these share model parameters, necessitating joint estimation regressions between eDNA, , biomass. Furthermore, our framework extended how other variables (temperature, taxa, diet, trophic level, etc.) might impact relationships natural ecosystems. applied previously published studies correlating Brook Trout Salvelinus fontinalis In case studies, point estimates coefficient b reflected processes = 0.51 0.37 for Case Study 1 2, respectively), credible intervals indicating likely differed zero (i.e., scales one biomass). Directly estimating value improved relative assuming equals 0, which particularly affected capacity estimate However, models production scaled 1) were largely similar implying linearly a sufficient approximation some systems. Nevertheless, demonstrates directly either (as is commonly done many studies) inherently necessitates an adjustment infer metric if populations exhibit variation. Collectively, quantitative unlikely correspond exactly but

Language: Английский

Linking the state of environmental DNA to its application for biomonitoring and stock assessment: Targeting mitochondrial/nuclear genes, and different DNA fragment lengths and particle sizes DOI Creative Commons
Toshiaki Jo,

Kenta Takao,

Toshifumi Minamoto

et al.

Environmental DNA, Journal Year: 2021, Volume and Issue: 4(2), P. 271 - 283

Published: Sept. 27, 2021

Abstract Environmental DNA (eDNA) analysis is a revolutionary tool for non‐invasive, cost‐effective, and highly sensitive monitoring of species distribution abundance; however, there remain some uncertainties related to eDNA detection quantification, as well limitations in terms its ecological interpretation. Although these may be elucidated by better understanding the characteristics dynamics eDNA, insight into such basic information has been limited this decade, contrary advancements applications targeting various taxa environments. This review compiled previous findings regarding macrobial provides insights how knowledge can contribute refinement development biomonitoring stock assessment. A literature survey revealed that studies on cellular molecular state were particularly lacking (18/728 papers from 2008 2020), resulting process transport degradation. highlighted number types beyond short mitochondrial fragments (nuclear longer fragments, larger particles) show improves reliability accuracy abundance estimation, provide more detailed individuals other than their presence abundance. Linking application will advance improve biodiversity, ecosystem function, fisheries resources.

Language: Английский

Citations

72
DNA Metabarcoding for the Characterization of Terrestrial Microbiota—Pitfalls and Solutions DOI Creative Commons
Davide Francioli, Guillaume Lentendu, Simon Lewin

et al.

Microorganisms, Journal Year: 2021, Volume and Issue: 9(2), P. 361 - 361

Published: Feb. 12, 2021

Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth health. Therefore, the identification, taxonomic characterization determination of role members soil microbial communities have become topics interest. The development continuous improvement high-throughput sequencing platforms further stimulated study complex microbiota soils plants. most frequently used approach to composition, diversity dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with subsequent amplicons. This methodological called DNA metabarcoding. Over last decade, metabarcoding has rapidly emerged as a powerful cost-effective method for description environmental samples. However, this involves several processing steps, each which might introduce significant biases that can considerably compromise reliability output. aim review provide state-of-the-art background knowledge needed make appropriate decisions at step workflow, highlighting crucial steps that, if considered, ensures an accurate standardized studies.

Language: Английский

Citations

68
Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries DOI Creative Commons
Raman P. Nagarajan,

Mallory Bedwell,

Ann E. Holmes

et al.

Estuaries and Coasts, Journal Year: 2022, Volume and Issue: 45(7), P. 2254 - 2273

Published: June 25, 2022

Abstract Environmental DNA (eDNA) detection methods can complement traditional biomonitoring to yield new ecological insights in aquatic systems. However, the conceptual and methodological frameworks for eDNA interpretation were developed primarily freshwater environments have not been well established estuaries marine that are by nature dynamic, turbid, hydrologically complex. context species life history critical successful application of methods, challenges associated with subject a symposium held at University California Davis on January 29, 2020 ( https://marinescience.ucdavis.edu/engagement/past-events/edna ). Here, we elaborate upon topics addressed evaluate monitoring biodiversity studies estuaries. We first provide concise overview science then examine San Francisco Estuary (SFE) as case study illustrate how programs regional guidance future potential applications. Additionally, offer recommendations enhancing communication between scientists natural resource managers, which is essential integrating into existing programs. Our intent create accessible those outside field eDNA, especially without oversimplifying or advantages these methods.

Language: Английский

Citations

58
Methodology for fish biodiversity monitoring with environmental DNA metabarcoding: The primers, databases and bioinformatic pipelines DOI Creative Commons
Fan Xiong, Lu Shu, Honghui Zeng

et al.

Water Biology and Security, Journal Year: 2022, Volume and Issue: 1(1), P. 100007 - 100007

Published: Jan. 19, 2022

Environmental DNA (eDNA) originates from cellular material shed by organisms into aquatic or terrestrial environments and can be sampled monitored using metabarcoding technology, which is revolutionizing fish biodiversity monitoring. Several reviews concerning eDNA have focused on standard sampling methods its applications, though a systematic review marker genes, databases, bioinformatic pipelines has not yet been published. Here, we present comprehensive literature of studies applying technology to for the purpose We systematically provide available universal primers used amplify barcoding sequences eDNA, then discuss reference relevant analyses, as well developed pipelines. The performances their databases are summarized. Combined use multiple primer pairs targeted more than one gene (e.g., 12S, 16S, Cytb, COI), both local public recommended approaches improve sensitivity reliability analyses. also compare effectiveness traditional monitoring highlight challenges future perspectives associated with this new tool. Ultimately, advocate greater incorporation analysis assessments assist environmental managers.

Language: Английский

Citations

55
Why eDNA fractions need consideration in biomonitoring DOI
Magdalena Nagler, Sabine Marie Podmirseg, Judith Ascher‐Jenull

et al.

Molecular Ecology Resources, Journal Year: 2022, Volume and Issue: 22(7), P. 2458 - 2470

Published: June 2, 2022

Abstract The analysis of environmental DNA (eDNA) is revolutionizing the monitoring biodiversity as it allows to assess organismic diversity at large scale and unprecedented taxonomic detail. However, eDNA consists an extracellular intracellular fraction, each characterized by particular properties that determine retrievable information on when where organisms live or have been living. Here, we review fractions eDNA, describe how obtain them from samples present a four‐scenario concept aims enhancing spatial temporal resolution eDNA‐based monitoring. Importantly, highlight appropriate choice precludes misinterpretation data. Finally, future avenues research towards fraction‐specific analyses are outlined unravel full potential studies targeting micro‐ macro‐organisms.

Language: Английский

Citations

46
Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs DOI Creative Commons
Florian Altermatt, Luca Carraro, Manuel Antonetti

et al.

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(4), P. 671 - 682

Published: May 16, 2023

Abstract Reliable and comparable estimates of biodiversity are the foundation for understanding ecological systems informing policy decision‐making, especially in an era massive anthropogenic impacts on biodiversity. Environmental DNA (eDNA) metabarcoding is at forefront technological advances monitoring, last few years have seen major progress solutions to technical challenges from laboratory bioinformatics. Water eDNA has been shown allow fast efficient recovery signals, but rapid pace development meant that some important principles regarding sampling design, which well established traditional inventories, neglected. Using a spatially explicit river flow model, we illustrate how must be adjusted size watercourse increase quality signal recovered. We additionally investigate effect parameters (volume, number sites, sequencing depth) detection probability empirical data set. Based principles, propose aquatic replication volume scaled match organisms' ecosystems' properties provide reliable estimates. present generalizable conceptual equation describing features as function ecosystem monitored, abundance target organisms, procedure. The aim this formalization enhance standardization critical steps design inventory studies using eDNA. More robust standards will generate more eDNA, necessary method's long‐term plausibility comparability.

Language: Английский

Citations

40
Groundwater is a hidden global keystone ecosystem DOI Creative Commons
Mattia Saccò, Stefano Mammola, Florian Altermatt

et al.

Global Change Biology, Journal Year: 2023, Volume and Issue: 30(1)

Published: Dec. 12, 2023

Abstract Groundwater is a vital ecosystem of the global water cycle, hosting unique biodiversity and providing essential services to societies. Despite being largest unfrozen freshwater resource, in period depletion by extraction pollution, groundwater environments have been repeatedly overlooked conservation agendas. Disregarding importance as an ignores its critical role preserving surface biomes. To foster timely groundwater, we propose elevating concept keystone species into realm ecosystems, claiming that influences integrity many dependent ecosystems. Our analysis shows over half land areas (52.6%) has medium‐to‐high interaction with reaching up 74.9% when deserts high mountains are excluded. We postulate intrinsic transboundary features for shifting perspectives towards more holistic approaches aquatic ecology beyond. Furthermore, eight key themes develop science‐policy integrated agenda. Given ecosystems above below ground intersect at levels, considering component planetary health pivotal reduce loss buffer against climate change.

Language: Английский

Citations

39
Novel community data in ecology-properties and prospects DOI
Florian Härtig, Nerea Abrego, Alex Bush

et al.

Trends in Ecology & Evolution, Journal Year: 2023, Volume and Issue: 39(3), P. 280 - 293

Published: Nov. 8, 2023

Language: Английский

Citations

38
Environmental DNA as an emerging tool in botanical research DOI Creative Commons
Mark D. Johnson, Joanna R. Freeland, Laura Parducci

et al.

American Journal of Botany, Journal Year: 2023, Volume and Issue: 110(2)

Published: Jan. 12, 2023

Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species communities), means of elucidating biological interaction networks, window into understanding patterns biodiversity. However, only recently potential eDNA realized in botanical world. Here we synthesize state applications systems with emphases on aquatic, ancient, contemporary sediment, airborne systems, focusing both single-species approaches multispecies community metabarcoding. Further, describe how abiotic biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, relative abundance influence utilization interpretation results. Lastly, explore several areas opportunities for further development tools plants, advancing our knowledge efficacy, utility, cost-effectiveness, ultimately facilitating increased adoption analyses systems.

Language: Английский

Citations

25
Current status and topical issues on the use of eDNA-based targeted detection of rare animal species DOI
Sofia Duarte, Luara Aparecida Simões, Filipe O. Costa

et al.

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 904, P. 166675 - 166675

Published: Aug. 29, 2023

Language: Английский

Citations

24