Environmental RNA can distinguish life stages in amphibian populations

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: 24(4)

Published: Aug. 18, 2023

Abstract Applications of environmental DNA (eDNA) analysis methods for biomonitoring have grown exponentially over the last decade and provide a wealth new information on distribution species. However, eDNA limited application estimating population‐level metrics. Environmental RNA (eRNA) has potential to address ecological questions by gathering population demographic from media but may be challenging detect analyze. We developed gene‐specific eRNA assays targeting keratin‐associated genes in two focal species, American bullfrogs ( Lithobates catesbeianus ) tiger salamanders Ambystoma mavortium answer an important question amphibian management: whether species detections represent breeding populations versus transitory adults. performed extensive laboratory validation with amphibians housed across development stages, where we collected 95 127 samples salamanders, respectively. Both were highly specific larval stage amplified high sensitivity (90% bullfrog 88.4% salamander samples). then applied our validated multiple natural systems. When larvae present, found 74.1% overall detection field 70.8% 48.5% ponds A. macrodactylum californiense larvae, correlating rates. only adults did not larvae‐specific ponds, despite Although much work is ahead optimizing assay design, sampling filtering methods, demonstrate that can successfully used discern life stages direct ecology conservation management.

Language: Английский

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Harnessing decay rates for coastal marine biosecurity applications: A review of environmental DNA and RNA fate

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(5), P. 960 - 972

Published: March 30, 2023

Abstract Marine nonindigenous species (NIS) are spreading at an alarming rate internationally through anthropogenic activities such as shipping and aquaculture, affecting local biodiversity negatively impacting the ecosystem human well‐being. Countries international organizations have recognized this global threat begun implementing biosecurity management programs to ensure early detection, effective surveillance, mitigation of marine NIS spread. Molecular techniques based on environmental DNA RNA (eDNA/eRNA), collectively referred nucleic acids (eNAs), become a popular noninvasive tool for detecting monitoring locally globally. However, uncertainties about eNAs detection probabilities location source population impede broad uptake in programs. It's been hypothesized that most these can be explained by studying molecules' dynamics within environment distribution models. To contribute further knowledge development area, our study reviews data from 20 recent reports degradation mechanisms fate environment. We classified critical factors influencing eNAs' persistence should considered practitioners, outlining complex interaction between processes particular conditions. help guide parameterization models, review also summarizes standardizes decay rates eDNA/eRNA literature. Finally, manuscript outlines guidelines calculate accurate build appropriate “fit‐for‐purpose” tools improved target detectability greater resolution assessing biodiversity.

Language: Английский

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Comparing eDNA and eRNA Sampling Methodologies From Pond Environments

Aquatic Conservation Marine and Freshwater Ecosystems, Journal Year: 2025, Volume and Issue: 35(2)

Published: Feb. 1, 2025

ABSTRACT Molecular traces are increasingly being applied to assess the presence of species and communities. Studies on environmental DNA (eDNA) have, a large extent, become common practice in detection, but less studies have compared biodiversity estimations with more temporary RNA (eRNA). This study compares metabarcoding results from pond water obtained both molecule types by sequencing V4 region 18S rRNA marker. Water was collected two depths, 20 80 cm, filtered sequentially through filter porosities, 0.45 0.22 μm. Each cut half before fixation either 96% ETOH or RNAlater. The showed no differences between fixatives for molecule. Overall, estimates eDNA significantly overperformed eRNA, likely due higher concentrations terrestrial sources. Comparisons depths variation only, increasing levels found at upper layer. Both pore sizes captured distinctive compositions taxa, where about 30% diversity uniquely identified second, finer filter. Taken together, these findings imply that choice molecular marker, depth size affects pond.

Language: Английский

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Environmental DNA and RNA in aquatic community ecology: Toward methodological standardization

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(6), P. 1133 - 1147

Published: Sept. 28, 2023

Abstract Molecular technologies have facilitated the expansion of biodiversity assessments across a broad range organisms and aquatic systems. Environmental DNA (eDNA) environmental RNA (eRNA), collectively referred to as nucleic acids (eNAs), revolutionized monitoring due their noninvasive nature high‐resolution capabilities when compared traditional survey methods. While eNA applications grown exponentially over past decade, methodological inconsistencies hinder reproducibility comparability. To assess current state methodologies in ecology, we conducted systematic review 300 peer‐reviewed studies that ecological communities diverse Of these papers, 291 examine eDNA, four eRNA, five consider both eDNA eRNA. The small number eRNA highlights field is its infancy. looked at, found clear geographic bias, with approximately 50% all occurring six high‐income countries, while less than 10% occur South America Africa. Further, report lack standardization studies, showing high variability water filtration volume, filter material, pore size, extraction method, marker choice, bioinformatic pipelines. We further highlight incomplete reference sequence databases for limit taxonomic assignment inferences. Finally, identify issue community ecology: missing details, which compromise reproducibility, especially newly emerging applications. facilitate systems permit integration monitoring, recommend improvement alongside guidelines encourage transparency.

Language: Английский

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Environmental RNA as a Noninvasive Tool for Assessing Toxic Effects in Fish: A Proof-of-concept Study Using Japanese Medaka Exposed to Pyrene

Environmental Science & Technology, Journal Year: 2023, Volume and Issue: 57(34), P. 12654 - 12662

Published: Aug. 16, 2023

Although environmental RNA (eRNA) is emerging as a noninvasive tool to assess the health status of aquatic macroorganisms, potential eRNA in assessing chemical hazards remain largely untested. In this study, we investigated ability detect changes gene expression Japanese medaka fish (Oryzias latipes) response sublethal pyrene exposure, model toxic chemical. We performed standardized acute toxicity tests and collected from tank water tissue after 96 h exposure. Our results showed that over 1000 genes were detected sequenced read counts these correlated with those (r = 0.50). Moreover, 86 differentially expressed pyrene, some which shared by RNA, including suppression collagen fiber genes. These suggest has stressors without need for sacrificing or causing pain fish. However, also found majority reads (>99%) not mapped reference genome they originated bacteria fungi, resulting low sequencing depth. addition, eRNA, particular nuclear genes, was highly degraded median transcript integrity number (TIN) <20. limitations highlight future studies improve analytical methods application.

Language: Английский

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Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms?

Molecular Ecology, Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 4, 2023

Abstract To safeguard biodiversity in a changing climate, taxonomic information about species turnover and insights into the health of organisms are required. Environmental DNA approaches increasingly used for identification, but cannot provide functional insights. Transcriptomic methods reveal physiological states macroorganisms, currently species‐specific require tissue sampling or animal sacrifice, making community‐wide assessments challenging. Here, we test whether broad (expression level transcribed genes) can be harnessed from environmental RNA (eRNA), which includes extra‐organismal macroorganisms along with whole microorganisms. We exposed Daphnia pulex as well phytoplankton prey microorganism colonizers to control (20°C) heat stress (28°C) conditions 7 days. sequenced eRNA tank water (after complete removal ) tissue, enabling comparisons organismal RNA‐based gene expression profiles. Both types detected similar responses . Using eRNA, identified 32 genes differentially expressed following stress. Of these, 17 were also exhibited levels relative RNA. In addition response, consisting distinct profiles 121 across eight taxa. Our study demonstrates that transcriptomics based on noninvasively changes, potential implications biomonitoring trophic chain.

Language: Английский

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Rapid, easy, sensitive, low‐cost and on‐site detection of environmental DNA and RNA using CRISPR‐Cas13

Methods in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 15(8), P. 1408 - 1421

Published: July 9, 2024

Abstract Environmental DNA (eDNA) monitoring of species distribution has become a critical tool in ecology, conservation biology and fisheries for identifying the presence diverse organisms, including important, threatened invasive species. However, eDNA detection still room improvement sensitivity, requiring time‐consuming real‐time polymerase chain reaction (qPCR) steps costly machines. In this study, we report CRISPR‐Cas13‐based method rapid, easy, sensitive, low‐cost on‐site eDNA. The assay common carp ( Cyprinus carpio ) medaka Oryzias latipes nucleic acid employs two‐step process, starting with recombinase amplification (RPA) followed by cleavage using Cas13 nuclease, to effectively identify mitochondrial or RNA. Our results showed that Cas13‐based higher sensitivity than qPCR‐based detecting tiny amounts When combined reverse transcription environmental RNA (eRNA), our increased approximately one order magnitude. could achieve quick extraction solution lateral flow strips. eRNA requires minimal training efforts can be performed 1 h, without need centrifugation qPCR portability method, along its accuracy relative ease designing primers CRISPR (crRNA), underscores potential broaden application various fields, biodiversity conservation.

Language: Английский

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Environmental Nucleic Acid Pollution: Characterization of Wastewater Generating False Positives in Molecular Ecological Surveys

ACS ES&T Water, Journal Year: 2023, Volume and Issue: 3(3), P. 756 - 764

Published: Feb. 15, 2023

Environmental nucleic acids (eDNA and eRNA) metabarcoding analyses have attracted considerable research attention as they non-invasively cost-effectively monitor ecosystems. For heretofore unknown reasons, however, often detect false positives. Here, we focused on domestic wastewater a possible source of positives characterized fish in the influent effluent treatment plant (WWTP). The analysis revealed that DNA RNA detected originated from over 120 species, most these were consumed fish. acid content was significantly higher than effluent, copy numbers those RNA. These findings corroborated by current literature indicated eRNA could effectively mitigate present study demonstrated rivers may be extensively contaminated acids, WWTPs substantially alter quantities ratios Therefore, near sampling points coverage sewage system enable us to select use appropriate type (DNA or RNA) for improve accuracy species detection identification.

Language: Английский

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Selecting Competent Reverse Transcription Strategies to Maximise Biodiversity Recovery With eRNA Metabarcoding

Molecular Ecology Resources, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 22, 2025

ABSTRACT Both environmental DNA (eDNA) and RNA (eRNA) have been widely adopted for biodiversity assessment. While eDNA often persists longer in environments, eRNA offers a more current view of biological activities. In metabarcoding, extracted is reverse transcribed into complementary (cDNA) metabarcoding. However, the efficacy various transcription strategies has not evaluated. Here we compared recovery efficiency three strategies: random priming with hexamers, oligo(dT) taxa‐specific using Mifish‐U fish both high‐ low‐biodiversity regions. Our results demonstrate that significantly impact recovery. Random consistently detected highest number taxa low‐ high‐biodiversity areas, performed comparably to hexamers; however, regions, hexamers outperformed oligo(dT), particularly recovering rare taxa. was comparable other high‐abundance taxa, it less effective thus limiting its utility comprehensive These differences are largely due multiple binding sites fewer or absent primers under high degradation. Combining improved recovery, especially low‐abundance species, supporting best practice eukaryotes. For prokaryotes genes lacking polyadenylation, favoured over taxa‐ gene‐specific priming. Collectively, these findings underscore critical importance selecting appropriate significant implications monitoring conservation efforts.

Language: Английский

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Release and degradation of dissolved environmental RNAs from zebrafish cells

RNA Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

The sources and degradation profiles of dissolved environmental RNAs from fish in water remain unknown. In this study, laboratory experiments mathematical modelling were conducted to investigate the permeability RNA extracted zebrafish cells through filters, release live dying cells, a non-sterile aqueous environment. This research aimed provide biological ecological insights into water. results showed that most was detected filtrates after passage 0.45 µm filters. Over course 6-day experiment, dynamic levels liquid environment containing or determined. rates calculated using modelling. degraded tubes, 2 months, more than 15% remained detectable. half-life tubes approximately 20 ~ 43 days. suggest natural waters aquariums could be so low it would difficult detect them current techniques. obtained study will help develop new methods for measuring dynamics determining their significance.

Language: Английский

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