Why eDNA fractions need consideration in biomonitoring

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

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Ecosystem type drives soil eukaryotic diversity and composition in Europe

Global Change Biology, Journal Year: 2023, Volume and Issue: 29(19), P. 5706 - 5719

Published: July 14, 2023

Soil eukaryotes play a crucial role in maintaining ecosystem functions and services, yet the factors driving their diversity distribution remain poorly understood. While many studies focus on some eukaryotic groups (mostly fungi), they are limited spatial scale. Here, we analyzed an unprecedented amount of observational data soil eukaryomes at continental scale (787 sites across Europe) to gain further insights into impact wide range environmental conditions (climatic edaphic) community composition structure. We found that fungi, protists, rotifers, tardigrades, nematodes, arthropods, annelids was predominantly shaped by type (annual permanent croplands, managed unmanaged grasslands, coniferous broadleaved woodlands), higher observed croplands than less intensively systems, such as woodlands. Also more specialized eukaryotes, while between homogeneous compared other ecosystems. The high proportion overlapping taxa ecosystems also indicates DNA has accumulated from previous land uses, hence mimicking transformations occurring Europe last decades. This strong ecosystem-type influence linked properties, particularly, pH richness annelids, plant-available phosphorus drove nematodes. Furthermore, organic carbon total nitrogen ratio crucially explained possibly decades agricultural inputs. Our results highlighted importance long-term variables rather measured time sampling shaping communities, which reinforces need include those addition future monitoring programs conservation efforts.

Language: Английский

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Particle size influences decay rates of environmental DNA in aquatic systems

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 23(4), P. 756 - 770

Published: Jan. 12, 2023

Environmental DNA (eDNA) analysis is a powerful tool for remote detection of target organisms. However, obtaining quantitative and longitudinal information from eDNA data challenging, requiring deep understanding ecology. Notably, if the various size components decay at different rates, we can separate them within sample, their changing proportions could be used to obtain dynamics on targets. To test this possibility, conducted an aquatic mesocosm experiment in which separated fish-derived using sequential filtration evaluate rate proportion particle sizes over time. We then fit four alternative mathematical models data, building towards predictive framework interpret sizes. found that medium-sized particles (1-10 μm) decayed more slowly than other classes (i.e., <1 > 10 μm), thus made up increasing also observed distinct distribution (PSD) between our Common carp Rainbow trout samples, suggesting target-specific assays are required determine starting PSDs. Additionally, evidence do not independently, with conversion replenishing smaller Nonetheless, parsimonious model where independently best explained data. Given these results, suggest discern distance abundance by applying filtration, theoretically has both metabarcoding single-target applications.

Language: Английский

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Biocides as Drivers of Antibiotic Resistance: A Critical Review of Environmental Implications and Public Health Risks

Environmental Science and Ecotechnology, Journal Year: 2025, Volume and Issue: unknown, P. 100557 - 100557

Published: March 1, 2025

The widespread and indiscriminate use of biocides poses significant threats to global health, socioeconomic development, environmental sustainability by accelerating antibiotic resistance. Bacterial resistance development is highly complex influenced significantly factors. Increased biocide usage in households, agriculture, livestock farming, industrial settings, hospitals produces persistent chemical residues that pollute soil aquatic environments. Such contaminants contribute the selection proliferation resistant bacteria antimicrobial genes (ARGs), facilitating their dissemination among humans, animals, ecosystems. In this review, we conduct a critical assessment four issues pertaining topic. Specifically, (i) role exerting selective pressure within resistome, thereby promoting microbial populations contributing spread (ARGs); (ii) triggering transient phenotypic adaptations bacteria, including efflux pump overexpression, membrane alterations, reduced porin expression, which often result cross-resistance multiple antibiotics; (iii) capacity disrupt make genetic content accessible, releasing DNA into environment remains intact under certain conditions, horizontal gene transfer determinants; (iv) bacterial cells, enhancing interactions between biofilms environment, strengthening biofilm cohesion, inducing mechanisms, creating reservoirs for microorganisms ARG dissemination. Collectively, review highlights public health implications use, emphasizing an urgent need strategic interventions mitigate proliferation.

Language: Английский

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Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2023, Volume and Issue: 290(1999)

Published: May 30, 2023

Environmental DNA (eDNA) analysis allows cost-effective and non-destructive biomonitoring with a high detection sensitivity in terrestrial aquatic environments. However, the eDNA results can sometimes include false-positive inferences of target organisms owing to aged that has long since been released from individual is more likely be detected at site further away its source. In order address issue, this manuscript focuses on state eDNA, proposing new methodologies estimate age eDNA: (1) damage rate, (2) particle size distribution, (3) viable cell-derived eDNA. addition, also shorter persistence environmental RNA (eRNA) compared highlighting application eRNA nucleic acid ratio for assessing genetic materials water. Although substantial research essential support feasibility these methodologies, incorporating time-scale information into would update current analysis, improve accuracy reliability eDNA-based monitoring, refine as useful monitoring tool ecology, fisheries various sciences.

Language: Английский

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Environmental DNA (eDNA) removal rates in streams differ by particle size under varying substrate and light conditions

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 903, P. 166469 - 166469

Published: Aug. 24, 2023

Language: Английский

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Sorting states of environmental DNA: Effects of isolation method and water matrix on the recovery of membrane‐bound, dissolved, and adsorbed states of eDNA

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(3), P. 582 - 596

Published: April 10, 2023

Abstract Environmental DNA (eDNA) once shed can exist in numerous states with varying behaviors including degradation rates and transport potential. In this study, we consider three of eDNA: (1) a membrane‐bound state referring to enveloped cellular or organellar membrane, (2) dissolved defined as the extracellular molecule environment without any interaction other particles, (3) an adsorbed particle surface environment. Capturing, isolating, analyzing target eDNA provides utility for better interpretation While methods separating different have been developed, they remain poorly evaluated due lack state‐controlled experimentation. We from single sample by spiking species represent state‐specific controls. used chicken state, cultured mouse cells salmon clay particles state. performed separation water matrices, two environmental one synthetic, spiked states. The was only that isolated minimal contamination nontarget also had highest recovery (54.11 ± 19.24%), followed (5.08 2.28%), lowest total (2.21 2.36%). This study highlights potential sort independently analyze them more informed biodiversity assessments. However, further method development is needed improve reduce cross‐contamination.

Language: Английский

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Predicting downstream transport distance of fish eDNA in lotic environments

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(4)

Published: Feb. 6, 2024

Abstract Environmental DNA (eDNA) is an effective tool for describing fish biodiversity in lotic environments, but the downstream transport of eDNA released by organisms makes it difficult to interpret species detection at local scale. In addition biophysical degradation and exchanges water–sediment interface, hydrological conditions control distance. A new model described this paper considers retention processes combination with hydraulic assumes that sedimentation rate very fine particles a correct estimate deposition rate. Based on meta‐analyses available studies, particle size distribution (PSD), relationship between suspension, influence temperature were successively modelled. After combining results mechanistic‐based model, uptake distances (distance required retain 63.21% riverbed) observed compilation previous experimental studies correctly simulated. negligible low flow has comparable background transfer when allow long The wide prediction intervals associated simulations reflect complexity acting after shedding. This can be useful estimating distance from source point discussing possibility false positive samples, as shown example.

Language: Английский

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Suspended Materials Affect Particle Size Distribution and Removal of Environmental DNA in Flowing Waters

Environmental Science & Technology, Journal Year: 2023, Volume and Issue: 57(35), P. 13161 - 13171

Published: Aug. 23, 2023

Environmental DNA (eDNA) in aquatic systems is a complex mixture that includes dissolved DNA, intracellular and particle-adsorbed DNA. Information about the various components of eDNA their relative proportions could be used to discern target organism abundance location. However, limited knowledge adsorption dynamics interactions with other materials hinders these applications. To address this gap, we recirculating stream mesocosms investigate impact suspended (fine particulate organic matter, plankton, clay, titanium dioxide) on concentration particle size distribution (PSD) from two fish species flowing water. Our findings revealed rapidly adsorbs water column, affecting its PSD. Nonetheless, only matter affected removal rate after 30 h. Moreover, observed larger (≥10 μm) was more strongly influenced by physical processes, whereas smaller driven biological degradation. This disparity mechanisms between explain changes composition over time space, which have implications for modeling spatial optimizing detection high turbidity systems.

Language: Английский

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Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(6), P. 1449 - 1472

Published: Aug. 28, 2023

Abstract Environmental DNA studies have proliferated over the last decade, with promising data describing diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery present in sediment systems (sedDNA) has provided short‐ long‐term on a wide range biological groups (e.g., photosynthetic organisms, zooplankton species) advanced our understanding how environmental changes affected communities. However, substantial challenges remain for recovering genetic material macro‐organisms fish) from sediments, preventing complete reconstructions past ecosystems, limiting historic, higher trophic level interactions. In this review, we outline biotic abiotic factors affecting production, persistence, transport fish water column to address questions regarding preservation sediment. We identify sources uncertainties around sedDNA arising during workflow. This includes methodological issues related experimental design, extraction procedures, selected molecular method (quantitative PCR, digital metabarcoding, metagenomics). By evaluating previous efforts (published unpublished works) recover signals, provide suggestions future research propose troubleshooting workflows effective detection quantification sedDNA. With further research, use potential be powerful tool inferring presence time reconstructing their population community dynamics.

Language: Английский

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