Deciphering the impact of decabromodiphenyl ether (BDE-209) on benthic foraminiferal communities: Insights from Cell-Tracker Green staining and eDNA metabarcoding

Journal of Hazardous Materials, Journal Year: 2024, Volume and Issue: 466, P. 133652 - 133652

Published: Jan. 29, 2024

Language: Английский

---

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

---

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

---

Metabarcoding by Combining Environmental DNA with Environmental RNA to Monitor Fish Species in the Han River, Korea

Fishes, Journal Year: 2023, Volume and Issue: 8(11), P. 550 - 550

Published: Nov. 15, 2023

Fishes are ecologically important organisms that have long lifespans, high mobilities, and diverse trophic levels. Due to their importance, fishes used as bioindicators for monitoring aquatic environments. One method is based on environmental DNA (eDNA), which the deoxynucleic acids released by into environment. However, there has been a problem with false positives because eDNA relatively stable in environment could even likely represent dead or non-inhabiting organisms. To address this weakness, RNA (eRNA), degrades more rapidly than environment, can be utilized complement eDNA. But, date, few studies eRNA freshwater fish monitoring. In study, determine relative usefulness of metabarcoding fishes, we performed 12S rRNA targeting using water samples were collected from three locations Han River. We then calculated sensitivity positive predictivity approach comparing our data previous specimen capture survey (PSCS) last six years. The results showed 42 species detected 19 at locations. At all locations, compared PSCS data, average was higher (46.1%) (34.6%), (31.7%) (20.7%). This confirmed advantage broadly determining presence absence (including those no longer present dead), but it also generates positives; meanwhile, reports living species, detects fewer Combining therefore emphasizes advantages compensates disadvantages, conducting may useful identifying actually technique future provide insights fisheries.

Language: Английский

---

rCRUX: A rapid and versatile tool for generating metabarcoding reference libraries in R

Environmental DNA, Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 29, 2023

The sequencing revolution requires accurate taxonomic classification of DNA sequences. Key to making assignments are curated, comprehensive reference barcode databases. However, the generation and curation such databases has remained challenging given large continuously growing volumes both sequence data novel targets. Monitoring research applications require a greater diversity specialized gene regions targeted taxa then currently curated by professional staff. Thus there is need for an easy implement computational tool that can generate metabarcoding libraries any bespoke locus. We address this reimagining CRUX from Anacapa Toolkit present rCRUX package in R which, like it's predecessor, relies on homology PCR primer compatibility instead keyword-searches avoid limitations user-defined metadata. typical workflow involves searching plausible seed amplicons (

Language: Английский

---