Evaluation of Mediterranean sponges as natural samplers for environmental DNA (eDNA)

Open Research Europe, Journal Year: 2025, Volume and Issue: 5, P. 69 - 69

Published: March 17, 2025

Marine sponges have emerged as effective natural samplers of environmental DNA (eDNA), offering a promising alternative for biodiversity monitoring. By filtering large volumes seawater, accumulate eDNA from surrounding communities, potentially enhancing species detection in marine environments where conventional water sampling is limited. In this study, we evaluated the recovery efficiency seven Mediterranean sponge to identify optimal candidates biomonitoring. Axinella verrucosa outperformed other tested species, highlighting its potential long-term assessments. Our results align with previous findings that low microbial abundance (LMA) recover more than high (HMA) reinforcing need targeted selection future studies. Detected fish taxa were all bottom dwelling, supporting relevance monitoring cryptic and benthic habitats. As eDNA-based advances, offers valuable complement surveys, particularly habitats challenging.

Language: Английский

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CRISPR‐Based Environmental Biosurveillance Assisted via Artificial Intelligence Design of Guide‐RNAs

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(3)

Published: May 1, 2025

ABSTRACT Environmental biosecurity challenges are intensifying as climate change and human activities accelerate the spread of invasive species, disrupting ecosystem composition, function, essential services. DNA (eDNA) has transformed traditional biosurveillance by detecting trace fragments left organisms in their surroundings, primarily applying quantitative polymerase chain reaction (qPCR) methods. However, qPCR presents challenges, including limited portability, reliance on precise thermal cycling, susceptibility to inhibitors. To address these enable field‐deployable monitoring, isothermal amplification techniques such recombinase (RPA) paired with clustered regularly interspaced short palindromic repeats associated proteins (CRISPR‐Cas) have been proposed promising alternatives. CRISPR‐Cas technology also searching optimizing a guide RNA (gRNA) that is highly sensitive no off‐target interactions for use an effective environmental tool. We present here development SENTINEL ( S mart E nvironmental N ucleic‐acid T racking using I nference from eural‐networks arly‐warning L ocalization) harnesses programmability, specificity sensitivity one‐pot RPA‐CRISPR‐Cas13a integrating accessible pre‐trained neural network assay design rapid deployment. challenged waterborne eDNA two marine sites invaded species not native New Zealand proof‐of‐concept fluorescence‐based tests: Sabella spallanzanii (Mediterranean fanworm) Undaria pinnatifida (Wakame). Off‐target effects were explored challenging assays gDNA suite co‐occurring species. presented robust, streamlined method incorporating trained network, achieving down 10 attomolar recombinant ~0.34 copies/μL samples 1 h, costing 3.5 USD per sample. There was 100% agreement between results qPCR‐based analysis samples. displayed activity when against 23 Thus, our study showcases SENTINEL's potential robust platform screening applications.

Language: Английский

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The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data

Metabarcoding and Metagenomics, Journal Year: 2024, Volume and Issue: 8

Published: Dec. 30, 2024

Environmental DNA (eDNA) and RNA (eRNA) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data metadata makes results difficult to reproduce synthesise. A working group scientists have collaborated produce set minimum reporting guidelines the constituent steps workflows, physical layout laboratories through archiving. We emphasise how suite should adhere findable, accessible, interoperable reproducible (FAIR) standards, thereby providing context evaluating understanding study results. An overview considerations each workflow step is presented then summarised in checklist that can accompany published or report. Ensuring workflows are transparent documented critical research allow more efficient uptake into management decision-making.

Language: Английский

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DNA State Influences the Uptake and Persistence of Environmental DNA by Marine Sponge Natural Samplers

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(5)

Published: May 1, 2025

ABSTRACT Marine sponges as natural samplers of environmental DNA (eDNA) are receiving growing attention an untapped source biodiversity data. However, little is known about the state (e.g., cellular or extracellular) that captured by these samples and how this compares to conventional aquatic eDNA samples. Here, we present artificial spiking experiment where in extracellular states was added into tanks containing two sponge species. Aquatic sampler (nsDNA) were collected over 7 days from quantified each sample using quantitative real‐time PCR (qPCR). We found there a significant interaction between type (eDNA nsDNA), with lower detection concentration DNA, compared nsDNA also rate significantly than overall. During methodological testing, inhibition observed both species; prohibitive one Further work investigate degree during metabarcoding important understand its impact on communities resolved methods. Synthesis applications . show may originate subset media, potentially providing more stable picture local communities. Natural provide promising option for hard‐to‐reach environments retrieving data archived samples; however, further optimization required what not well represented widely applied approaches.

Language: Английский

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Long-distance Southern Ocean environmental DNA (eDNA) transect provides insights into spatial marine biota and invasion pathways for non-native species

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 951, P. 175657 - 175657

Published: Aug. 22, 2024

The Southern Ocean surrounding Antarctica harbours some of the most pristine marine environments remaining, but is increasingly vulnerable to anthropogenic pressures, climate change, and invasion by non-native species. Monitoring biotic responses cumulative impacts requires temporal spatial baselines ongoing monitoring - traditionally, this has been obtained continuous plankton recorder (CPR) surveys. Here, we conduct one longest environmental DNA (eDNA) transects yet, spanning over 3000 nautical miles from Hobart (Australia) Davis Station (Antarctica). We evaluate eDNA sampling strategies for long-term open ocean biomonitoring comparing two water volume filter pore size combinations: large (12 l with 20 μm) small (2 0.45 μm). Employing a broad COI metabarcoding assay, found sample/pore combination was better suited monitoring, detecting more target rare or low abundance Comparisons four simultaneously conducted CPR revealed that detections were diverse than CPR, 7 (4 unique) 4 (1 phyla respectively. While both methods effectively delineated biodiversity patterns across Ocean, enables surveys in presence sea-ice where cannot be conducted. Accordingly, 16 species concern detected along transect using eDNA, notably Antarctic region (south 60°S). These largely attributed hull biofouling, recognized pathway introductions into Antarctica. Given vulnerability potential warming work underscores importance continued biosecurity vigilance. advocate integrating emphasising urgency its implementation. anticipate interweaving biophysical data will generate nuanced picture ecosystems, significant implications conservation preservation ecosystems.

Language: Английский

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Unlocking Antarctic molecular time-capsules – recovering historical environmental DNA from museum-preserved sponges

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

Published: April 28, 2024

ABSTRACT Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of to accumulate eDNA provides an exciting opportunity reconstruct contemporary communities and ecosystems with high temporal spatial precision. However, the use historical (heDNA), trapped within vast number specimens stored in scientific collections, opens up begin past. Here, using a variety Antarctic sponge extensive marine invertebrate collection, we were able recover information on fish biodiversity from 20 years old. We successfully recovered 64 heDNA signals 27 specimens. Alpha diversity measures did not differ among preservation methods, but frozen had significantly different community composition compared those dry or ethanol. Our results show that consistently reliably extract specimens, thereby enabling reconstruction investigation recent past resolution previously unattainable. Future research into extraction other well impact specimen age collection method will strengthen expand opportunities for this novel resource access new knowledge ecological change during last century.

Language: Английский

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Unlocking Antarctic molecular time‐capsules – Recovering historical environmental DNA from museum‐preserved sponges

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(7)

Published: July 25, 2024

Abstract Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of to accumulate eDNA provides an exciting opportunity reconstruct contemporary communities and ecosystems with high temporal spatial precision. However, the use historical eDNA, trapped within vast number specimens stored in scientific collections, opens up begin past. Here, we define term ‘heDNA’ denote that can be obtained from recent past accuracy. Using a variety Antarctic sponge extensive marine invertebrate collection, were able recover information on fish biodiversity 20 years old. We successfully recovered 64 heDNA signals 27 specimens. Alpha diversity measures did not differ among preservation methods, but frozen had significantly different community composition compared those dry or ethanol. Our results show consistently reliably extract specimens, thereby enabling reconstruction investigation resolution previously unattainable. Future research into extraction other well impact specimen age collection method, will strengthen expand opportunities for this novel resource access new knowledge ecological change during last century.

Language: Английский

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Unlocking Antarctic molecular time-capsules -- recovering historical environmental DNA from museum-preserved sponges

Authorea (Authorea), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 15, 2024

Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of to accumulate eDNA provides an exciting opportunity reconstruct contemporary communities and ecosystems with high temporal spatial precision. However, the use historical (heDNA), trapped within vast number specimens stored in scientific collections, opens up begin past. Here, using a variety Antarctic sponge extensive marine invertebrate collection, we were able recover information on fish biodiversity from 20 years old. We successfully recovered 64 heDNA signals 27 specimens. Alpha diversity measures did not differ among preservation methods, but frozen had significantly different community composition compared those dry or ethanol. Our results show that consistently reliably extract specimens, thereby enabling reconstruction investigation recent past resolution previously unattainable. Future research into extraction other well impact specimen age collection method will strengthen expand opportunities for this novel resource access new knowledge ecological change during last century.

Language: Английский

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CRISPR-based environmental biosurveillance assisted via artificial intelligence design of guide-RNAs

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

Published: Dec. 11, 2024

Abstract Environmental biosecurity challenges are worsening for aquatic ecosystems as climate change and increased anthropogenic pressures facilitate the spread of invasive species, thereby broadly impacting ecosystem composition, functioning, services. DNA (eDNA) has transformed traditional biomonitoring through detection trace fragments left by organisms in their surroundings, primarily application quantitative polymerase chain reaction (qPCR). However, qPCR presents challenges, including limited portability, reliance on precise thermal cycling, susceptibility to inhibitors. To address these enable field-deployable monitoring, isothermal amplification techniques such Recombinase Polymerase Amplification (RPA) paired with Clustered Regularly Interspaced Short Palindromic Repeats associated proteins (CRISPR-Cas) have been proposed alternatives. We report here development CORSAIR ( C RISPR-based envir O nmental biosu R veillance a S sisted via A rtificial I ntelligence guide- NAs), that harnesses programmability CRISPR-Cas technology, RPA artificial intelligence (AI)-based tool Activity-informed Design All-inclusive Patrolling Targets (ADAPT) deploy swift RPA-CRISPR-Cas13a-based method detects eDNA from two species proof concept: Sabella spallanzanii Undaria pinnatifida . showcased robust, streamlined augmented ADAPT, reaching high specificity when tested against co-occurring 100% agreement 12 PCR-benchmarked samples, sensitivity 0.34 copies uL -1 1 hour cost 3.5 USD per sample; thus highlighting powerful environmental biosurveillance platform nucleic acid detection. Graphical abstract

Language: Английский

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