Environmental DNA Metabarcoding of Cephalopod Diversity in the Tyrrhenian Deep Sea DOI Creative Commons
M. Torre, Alex Cussigh, Valentina Crobe

et al.

Journal of Marine Science and Engineering, Journal Year: 2024, Volume and Issue: 12(11), P. 1897 - 1897

Published: Oct. 23, 2024

The deep sea, the largest biome on Earth, is least explored and understood. This lack of knowledge hampers our ability to understand protect this important environment. In study, water sediment samples were collected at different depths in central Mediterranean (224–780 m), specifically, within Dohrn Canyon Palinuro Seamount, investigate diversity cephalopods establish a baseline their distribution these sites preserve habitats estimate impacts human-driven environmental changes. Key taxa identified included Heteroteuthis sp., Loligo Histioteuthis which most abundant across all sampling stations. A low overlap species detection was observed between samples, confirming previous findings that typology matrices used eDNA metabarcoding has significant impact organisms detected and, therefore, integrated use better represent local biodiversity recommended. Furthermore, study highlights limitations posed by gaps reference databases, particularly for deep-sea organisms, addresses emphasising need improved multi-marker approaches expanded databases enhance accuracy eDNA-based assessment.

Language: Английский

Metagenomic profiling of rhizosphere microbiota: Unraveling the plant-soil dynamics DOI
Atif Khurshid Wani, Farida Rahayu, Abdullah M. Alkahtani

et al.

Physiological and Molecular Plant Pathology, Journal Year: 2024, Volume and Issue: 133, P. 102381 - 102381

Published: Aug. 20, 2024

Language: Английский

Citations

7
Reconstruction of Marimo Population Dynamics Over 200 Years Using Molecular Markers and Fossil Plankton Remains DOI Creative Commons
Jotaro Urabe, Isamu Wakana, Hajime Ohtsuki

et al.

Environmental DNA, Journal Year: 2025, Volume and Issue: 7(2)

Published: March 1, 2025

ABSTRACT Recent efforts have focused on reconstructing the historical abundance of unfossilized organisms using environmental DNA preserved in sediments (sedDNA). This information is crucial for understanding long‐term changes ecosystems. However, because sedDNA prone to degradation, its quantification may not always provide accurate estimates past abundances. To address this issue, we developed a novel method correct degradation by incorporating plankton remains and applied it estimate marimo—large spherical colonies green alga Aegagropila brownii (formerly A. linnaei )—in Lake Akan, Japan, which only known habitat large marimo. We first quantified marimo lake dating back over 200 years. then used our new their from sedDNA. Analyses revealed that were historically 10–100 times more abundant than they are today, but declined early 20th century when influxes muddy water level fluctuations occurred due deforestation operation hydroelectric power plant. These findings align with eyewitness accounts, indicating that, corrected fossilized remains, can be powerful tool organisms.

Language: Английский

Citations

0
Parasite sedimentary DNA reveals fish introduction into a European high-mountain lake by the seventh century DOI Creative Commons
Elena Fagín, Marisol Felip, Anton Brancelj

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: April 8, 2025

High-mountain lakes were historically fishless due to natural barriers, but human introductions have led widespread fish presence. Although particularly intensive during the last decades, historical documents indicate in European high mountains already 14th and 15th centuries, they could occurred before, provided land use of mountain had started earlier. We used ancient environmental DNA from lake sediments (sedDNA) investigate this hypothesis. Fish ectoparasites various clades identified using 18S rRNA gene sediment record a deep, high-mountain Pyrenean lake, with Ichthyobodo (Kinetoplastea) being particular interest its consistent occurrence. The study shows continued presence parasites since 7th century, which coincides Late-Roman Visigothic extensive for sheep pasturing as supported by nearby archeological remains increased primary production evidenced photosynthetic pigments.

Language: Английский

Citations

0
Aquatic eDNA outperforms sedimentary eDNA for the detection of estuarine fish communities in subtropical coastal vegetated ecosystems DOI Creative Commons
Emma Isabelle Rossouw, Sophie von der Heyden, Nasreen Peer

et al.

Journal of Fish Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 14, 2025

Abstract In South Africa, mangrove forests and seagrass meadows often co‐occur in estuarine systems combination host rich, endemic biodiversity. There is an urgent need to explore community diversity coastal vegetated ecosystems, given the degrading effects of climate change anthropogenic pressures. Environmental DNA metabarcoding a promising biomonitoring tool African although studies highlight optimise standardise sampling protocols. This study aimed contribute developing protocols by understanding applicability environmental (eDNA) within habitats investigating using two different sample types. Aquatic sedimentary samples from three estuaries along east coast with MiFish metabarcoding, detected 148 operational taxonomic units (OTUs) representing 67 fish genera 50 families, only 16% were resolved species. We observed that aquatic eDNA 97% total diversity, suggesting this efficient comprehensively detect ichthyofaunal diversity. did not communities between mangroves seagrasses our findings underscore importance taking hydrological connectivity into consideration for design. Overall, work reinforces key considerations future focused on fauna estuaries, therefore contributes optimising support

Language: Английский

Citations

0
qPCR-based eDNA workflow for humic-rich lake sediments: Combined use of sedimentary DNA (sedDNA) and Indigenous Knowledge in reconstructing historical fish records DOI Creative Commons
Mark Louie D. Lopez,

Matthew Bonderud,

Michael J. Allison

et al.

Ecological Indicators, Journal Year: 2023, Volume and Issue: 155, P. 111014 - 111014

Published: Oct. 7, 2023

Lake sediment serves as a natural archive of historical biological information. The use sedimentary DNA (sedDNA), form environmental (eDNA) shed by aquatic organisms and preserved in sediment, has been instrumental reconstructing past faunal composition communities. However, the low abundance fish sedDNA often humic-rich nature lake sediments create methodological challenges for accurate detection target using quantitative polymerase chain reaction (qPCR)-based approaches. Herein, we present consolidated qPCR-based eDNA workflow to reconstruct current fauna Cowpar located Oil Sands region Alberta (Canada), which were then validated Indigenous Knowledge from Chipewyan Prairie First Nation community members. study highlights importance combining column- precipitation-based PCR inhibitor clean-up, nucleic acid concentration, incorporating endogenous chloroplast sample integrity control. Robust assays also useful preventing false-negative copies DNA. presence Northern pike (1905 2019) Cisco (1919 1942) was confirmed based on detected core. reconstructed records sedDNA-inferred data aligned with accounts human-mediated changes land around lake. Overall, addresses common concerns processing samples demonstrates great potential combined eDNA-inferred

Language: Английский

Citations

10
Using DNA archived in lake sediments to reconstruct past ecosystems DOI
Maïlys Picard, Jordan Von Eggers, Katie A. Brasell

et al.

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown, P. 673 - 690

Published: Feb. 24, 2024

Language: Английский

Citations

2
The Sources and Fates of Lake Sedimentary DNA DOI
Charline Giguet‐Covex, Stanislav Jelavić, Anthony Foucher

et al.

Developments in paleoenvironmental research, Journal Year: 2023, Volume and Issue: unknown, P. 9 - 52

Published: Jan. 1, 2023

Language: Английский

Citations

4
Metal ions limit or enhance environmental DNA detectability in marine sediments DOI Creative Commons
L. Dumoulin, Marion Chevrinais,

Richard St‐Louis

et al.

Environmental DNA, Journal Year: 2024, Volume and Issue: 6(3)

Published: May 1, 2024

Abstract Natural matrices affect environmental DNA (eDNA) detections. Effects of matrix‐eluted compounds on the polymerase chain reaction (PCR) step have been focus most inhibition studies. Factors affecting eDNA detections in a typical laboratory workflow, i.e., extraction and PCR steps, are mostly unknown. Here, we assessed effect four metal ions (Ca 2+ , Fe 3+ Mn Cu ) present marine sediments detectability for both detection steps. A single ion exogenous were added to treated chemically remove inhibitors. Our results showed that natural concentrations calcium, iron, manganese surface can impede completely Alternatively, copper matrix increased by 7.7%. We also observed bimodal inhibitory effects calcium iron detectability, suggesting steps affected. findings highlight new limitations Avenues optimize protocols applicable multiple discussed.

Language: Английский

Citations

0
Reconstructing historical fish occurrence and documenting human-mediated introductions in lakes using sedimentary DNA DOI Creative Commons
Mark Louie D. Lopez,

Matthew Bonderud,

Michael J. Allison

et al.

Global Ecology and Conservation, Journal Year: 2024, Volume and Issue: 54, P. e03040 - e03040

Published: June 21, 2024

The recovery of DNA preserved in the sediment aquatic systems (sedDNA) has provided short-term and long-term data on biological groups (e.g., bacteria, phytoplankton, zooplankton, fishes) advanced our understanding how environmental changes have affected communities. Here, we demonstrate use fish sedDNA from lake cores reconstructing history occurrences four lakes within Oil Sands region Alberta, Canada. A general eight targeted qPCR-based eDNA assays for freshwater species (cisco, whitefish, northern pike, chain pickerel, burbot, rainbow trout, walleye) were rigorously designed validated. Utilizing these assays, detected several spanning over a century, which aligned with conventional surveys historical records human-mediated introductions. greater temporal resolution into faunal records, bridging knowledge gap that spanned 100- to 150-year-old data. present study also allowed documentation introductions populations examined lakes. These findings can be used refine native ranges clarify influence diversity lakes, providing essential baseline conservation management impact assessments.

Language: Английский

Citations

0
Deciphering the Chronological Dynamics of Azolla invasion in Dal Lake, Srinagar: Insights from Sediment eDNA and 210Pb/137Cs Dating Techniques DOI

Zulaykha Khurshid,

Ravi Bhushan,

A. K. Sudheer

et al.

Earth Systems and Environment, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 16, 2024

Language: Английский

Citations

0