Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream

PeerJ, Journal Year: 2024, Volume and Issue: 12, P. e18016 - e18016

Published: Oct. 24, 2024

Environmental DNA (eDNA) metabarcoding has emerged as a promising approach to assess biodiversity and derive ecological status classes from water samples. However, limitation of eDNA surveys is that detected molecules may originate other places or even dead organisms, distorting local assessments. RNA (eRNA) recently been proposed complementary tool for more localized assessments the biological community. In this study, we evaluated effectiveness eRNA inferring richness species distribution patterns vertebrates invertebrates in Central European lowland river. We collected samples analyzed them using 12S marker COI invertebrates. 31 fish, 16 mammal, 10 bird one lamprey vertebrate dataset. While results were largely consistent, higher number when analysing (mean = 30.89) than 26.16). Also, detections had stronger signature compared against traditional fish monitoring data. For invertebrates, 109 arthropod, 22 annelid, 12 rotiferan, eight molluscan four cnidarian species. contrast pattern richness, 41.37) 22.42). Our findings primarily show eRNA-based are comparable invertebrate taxa. Biological replication was important both template studied. Signal eDNA. Overall, advantages extra steps needed analyses depend on study question but methods provide data research.

Language: Английский

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Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context

Environmental DNA, Journal Year: 2023, Volume and Issue: 5(5), P. 1016 - 1031

Published: June 6, 2023

Abstract Molecular tools of species identification based on eNAs (environmental nucleic acids; environmental DNA [eDNA] and RNA [eRNA]) have the potential to greatly transform biodiversity science. However, ability obtain “real‐time” estimates may be complicated by differential persistence degradation dynamics molecular template (eDNA or eRNA) barcode marker used. Here, we collected water samples over a 28‐day period comparatively assess detection using eDNA eRNA metabarcoding two distinct markers—a mitochondrial mRNA (COI) nuclear rRNA (18S)—following complete removal Arthropoda taxa in semi‐natural freshwater system. Our findings demonstrate that community composition was largely influenced choice, rather than template, individual microcosm, sampling time point. Furthermore, although capture similar diversity as established method, this finding marker‐dependent. Although found little no difference decay rates observed among sample groups (COI eDNA, COI eRNA, 18S eRNA), result is likely due limitations eNA‐based provide strong correlation between true eNA copy numbers present environment final read counts obtained (following workflow). Collectively, our further support for use multi‐marker assessments surveys unravel broadest taxonomic possible, highlight methods providing accurate rate estimates, well establish need comparative studies both single‐species diverse range taxa.

Language: Английский

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Detection and Management of Freshwater Invasive Alien Species through Environmental DNA Analysis and Geographic Information Systems: A Review

Sustainability, Journal Year: 2023, Volume and Issue: 15(12), P. 9497 - 9497

Published: June 13, 2023

Freshwater invasive alien species (IAS) are non-native organisms that were intentionally or unintentionally released into local water bodies and later harmed the invaded habitat by disrupting ecological processes. Over last few years, environmental deoxyribonucleic acid (eDNA) analyses have been used in many studies to detect IAS, with positive results. However, help of geographic information systems (GIS), efforts presence IAS can be made faster more efficiently. In this paper, we review background Southeast Asia management undertaken involving input known habitat-specific geographical parameters GIS mapping. Via strategy, it is possible identify distinguish areas fit features from those do not. eDNA analysis applied confirm detected areas, enabling further actions. The certain as an indicator assess integrity native waterways. This combined method likely first approach detection freshwater bodies. Apart saving energy resources, embedding study not only benefits ecosystem but also assists locals authorities managing taking necessary enforcement actions curb spread.

Language: Английский

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Utilizing environmental DNA and imaging to study the deep-sea fish community of Takuyo-Daigo Seamount

npj Biodiversity, Journal Year: 2024, Volume and Issue: 3(1)

Published: May 31, 2024

Abstract The increase in interest of mining at seamounts means there is a critical need to establish baseline inventories through environmental survey, with the aim promoting conservation and stewardship these remote habitats. To efficiently evaluate fish biodiversity around seamount, we compared DNA (eDNA) methods using seawater sponge samples against imagery obtained remotely operated vehicle (ROV) free-fall deep-sea camera lander called Edokko Mark I on Takuyo-Daigo Seamount (153.0°E, 23.5°N) northwestern Pacific Ocean. We detected total 18 families by methods. fauna seamount included many commonly found areas were similar other located latitudes Pacific. Significant differences patterns detection between eDNA imaging attributed differing powers some groups (related primer compatibility size). For fish, difference composition family level was not significant, but ROV significant; latter likely due whether or bait used attract fish. Although workflow implemented here requires improvements, use combination provided better insight into fishes where our knowledge has been extremely limited. Our recovery from demonstrates potential for facilitating surveys impact assessments activities obtain results previously possible visual only.

Language: Английский

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The Definition of RNA Age Related to RNA Sequence Changes

Wiley Interdisciplinary Reviews - RNA, Journal Year: 2024, Volume and Issue: 15(6)

Published: Nov. 1, 2024

ABSTRACT Ribonucleic acid (RNA) undergoes dynamic changes in its structure and function under various intracellular extracellular conditions over time. However, there is a lack of research on the concept RNA age to describe diverse fates. This study proposes definition address this issue. was defined as sequence numbers wherein elements were nucleotide ages ribonucleotide residues RNA. Mean used represent age. describes temporal properties RNAs that have undergone life histories reflects state each residue, which can be expressed mathematically. Notably, events (including base insertions, deletions, substitutions) are likely cause become younger or older when using mean Although information, including presence added markers RNA, chemical modification excision introns mRNA cells, may provide basis for identifying age, little known about determining wild. Nonetheless, we believe has an important relationship with biological conditions. Therefore, our proposed offers new perspectives studying function, aging, ancient environmental other biomolecules.

Language: Английский

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