Navigating diversity: primer impact on arthropod recovery in molecular environmental monitoring in tropical Amazon DOI Creative Commons
Fernanda Valente Penner, Christina Lynggaard, Leandro Araújo Argôlo

et al.

Frontiers in Ecology and Evolution, Journal Year: 2024, Volume and Issue: 12

Published: Dec. 4, 2024

Introduction The urgent need for effective environmental monitoring amid the escalating biodiversity crisis has prompted adoption of molecular techniques like DNA metabarcoding. Through sequencing taxonomically informative mitochondrial markers in bulk arthropod samples, metabarcoding allows assessment diversity, which is crucial ecosystem health evaluations, especially threatened regions Amazon. However, challenges such as primer biases and reference database limitations persist. Methods Here, we assess performance four sets, two COI (ZBJ-ArtF1c/ZBJ-ArtR2c [Zeale]: 157bp, targeting arthropods, mlCOIintF/jgHCO2198 [Leray]: 313bp, metazoans) 16S (Ins16S_1shortF/Ins16S_1shortR [Ins16S]: 150bp, insects, Coleop_16Sc/Coleop_16Sd [EPP]: 105bp, mainly Coleoptera) amplifying taxonomic constituents collected across different natural anthropogenic habitats from Brazilian Amazon biome. To evaluate performance, used indicators (i) amplification efficiency, (ii) specificity, i.e., amount non-target sequences, (iii) detected OTU richness, (iv) group coverage (v) resolution. Finally, (vi) estimated refinement taxa recovery by additional amplifications. Results Despite lower specificity contrasting results regarding pairs returning larger fragments showed higher resolution (Ins16S) broader (Leray) than Zeale EPP did. Furthermore, demonstrated complementarity Leray Ins16S sets taxon-dependent studies. Conclusions limitations, combining these primers could enhance region. Considering incomplete gene banks, maximizing richness (EPP Leray) may be best choice taxon-independent surveys. These findings underscore importance selection highlight ongoing efforts to refine robust assessments.

Language: Английский

Microeukaryotic plankton community dynamics under ecological water replenishment: Insights from eDNA metabarcoding DOI Creative Commons
Shuping Wang, Songsong Gu,

Yaqun Zhang

et al.

Environmental Science and Ecotechnology, Journal Year: 2024, Volume and Issue: 20, P. 100409 - 100409

Published: March 7, 2024

Ecological water replenishment (EWR) is an important strategy for river restoration globally, but timely evaluation of its ecological effects at a large spatiotemporal scale to further adjust the EWR schemes great challenge. Here, we examine impact on microeukaryotic plankton communities in three distinct ecosystems through environmental DNA (eDNA) metabarcoding. The include long-term cut-off river, short-term connected after EWR, and rivers. We analyzed community stability by investigating species composition, stochastic deterministic dynamics interplay, network robustness. found that markedly reduced diversity complexity plankton, altered their dynamics, lessened variation within community. Moreover, disrupted patterns organization, favoring dispersal constraints, aligning with trends observed naturally shift from isolated temporarily appeared transition structuring mechanisms dominance, whereas, permanently rivers, both forces concurrently influenced assembly. rivers post-EWR demonstrated significantly greater intricacy compared other systems. This bolstered resilience network. eDNA metabarcoding insights offer novel understanding ecosystem under interventions, which could be critical assessing projects throughout life cycle.

Language: Английский

Citations

7
Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau DOI Creative Commons
Siyu Zhang, Yan Qi, Jindong Zhao

et al.

iScience, Journal Year: 2024, Volume and Issue: 27(6), P. 110124 - 110124

Published: May 27, 2024

Alpine lakes play pivotal roles in plateau hydrological processes but are highly sensitive to climate change, yet we lack comprehensive knowledge of their multitrophic biodiversity patterns. Here, compared the characteristics diverse taxonomic groups across water depths and surface sediments from a freshwater lake hypersaline on northwestern Tibetan Plateau. Using multi-marker environmental DNA metabarcoding, detected 134 cyanobacteria, 443 diatom, 1,519 invertebrate, 28 vertebrate taxa. Each group had substantially different community composition two lakes, differences were also found between within each lake. Cooccurrence network analysis revealed higher complexity, lower modularity, fewer negative cohesions lake, suggesting that high salinity may destabilize ecological networks. Our results provide first holistic view under contrasting levels reveal structural networks impact ecosystem resilience.

Language: Английский

Citations

4
Environmental heterogeneity drives the spatial distribution of macrobenthos in the Yellow River Delta wetland DOI

Qinglu Fu,

Jiao Wang, Debin Sun

et al.

Aquatic Sciences, Journal Year: 2025, Volume and Issue: 87(2)

Published: Feb. 21, 2025

Language: Английский

Citations

0
Environmental DNA (eDNA): an eco-friendly approach for conservation of Indian freshwater diversity—a review DOI
Ashish Sahu, Mahender Singh, Rishikesh Krishan Laxmi

et al.

Environmental Science and Pollution Research, Journal Year: 2025, Volume and Issue: unknown

Published: March 25, 2025

Language: Английский

Citations

0
Revealing the Structure and Biodiversity Patterns of Fish Communities in River Networks Based on Environmental DNA DOI Creative Commons
Ziyu Liu, Yongsheng Wu,

Wenhui You

et al.

Fishes, Journal Year: 2025, Volume and Issue: 10(4), P. 175 - 175

Published: April 13, 2025

Revealing taxonomic, functional, and phylogenetic dimensions of biodiversity is critical for the effective conservation management aquatic organisms in freshwater ecosystems subjected to multiple threats. Fish patterns river exhibit complex spatiotemporal variation influenced by hydrological connectivity dispersal ability species within network. This study utilized eDNA metabarcoding investigate fish communities three subtropical mountain rivers, aiming uncover community structure dynamics multidimensional across varying positions The indices at confluence were significantly greater than those mainstream dry season, whereas diversity tributaries during wet season was that mainstream. likely reflected unique spatial configuration confluences seasonal results this highlighted important role networks fact they need be prioritized conserve riverine diversity.

Language: Английский

Citations

0
eDNA Metabarcoding Reveals the Depth-Structured Variation of Coral Reef Fish DOI Creative Commons

Jinfa Zhao,

Lin Lin, Yong Liu

et al.

Fishes, Journal Year: 2025, Volume and Issue: 10(5), P. 209 - 209

Published: May 2, 2025

Global coral reef ecosystems face various levels of disturbance pressure. Understanding the depth-structured variation in fish communities can help us to better grasp and predict adaptive changes ecosystem under different stressors. This study applied eDNA metabarcoding technology analyze spatial distribution at depths (0 m, 5 10 15 20 30 40 50 60 m) within Xisha Islands China. The results indicated that detected a total 213 amplicon sequence variants (ASVs), including 33 species were not identified using traditional methods. Herbivorous generally dominated relative abundance across depths. Moreover, similarity among depth groups was largely absent, significant differences existed assemblages gradients, consistent with unique preferences microhabitats. Importantly, our findings revealed distinct functional fish. Large carnivorous initially increased then decreased along gradient from 0 turning point around while large herbivorous displayed opposite trend. Small small consistently declined same gradient. Additionally, Margalef index (D) Function richness (FRic) both downward trend increasing depth, Shannon–Wiener (H′), Pielou (J′), Quadratic entropy (RaoQ), Functional dispersion (FDis), evenness (FEve) decreased, peaking m. is an effective tool for evaluating biodiversity, community composition, distribution. It enhances understanding dynamics offers valuable insights conservation restoration efforts.

Language: Английский

Citations

0
Dynamic response of fish community to hydrologic regime alteration in the upper reaches of the Yangtze River DOI
Shandian Zhe, Wenjie Li, Yu Wan

et al.

Environmental Monitoring and Assessment, Journal Year: 2025, Volume and Issue: 197(6)

Published: May 8, 2025

Language: Английский

Citations

0
Comparison of Environmental DNA Metabarcoding and a Traditional Survey Method for Assessing Fish Diversity and Distribution Along Salinity Gradient in an Urban Brackish Reservoir, China DOI Creative Commons
Wang Xu, Jiaqiao Wang,

Lin Lin

et al.

Biology, Journal Year: 2024, Volume and Issue: 13(11), P. 930 - 930

Published: Nov. 15, 2024

With the decrease in fish diversity, monitoring of has become a current research hotspot. Here, diversity and spatial distribution along salinity gradient (0.28‱-3.32‱) Xinglinwan Reservoir, China, were investigated using eDNA TSM. combination both methods, 12 species from 6 orders, 9 families, 11 genera observed. The invasive

Language: Английский

Citations

3
Comparison Between Environmental DNA Metabarcoding and Traditional Survey Method to Identify Community Composition and Assembly of Stream Fish DOI Creative Commons
Ziyu Liu, Cong Hu,

Wenhui You

et al.

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(11)

Published: Nov. 1, 2024

Environmental DNA (eDNA) metabarcoding has been widely used in freshwater systems, contributing to the advancements monitoring of fish diversity and community species composition. Nevertheless, accuracy reliability eDNA assessing functional structures revealing mechanisms underlying assembly remain unclear. In this study, we combined a traditional survey method (electrofishing) conduct stock upper reaches Huishui stream. We assessed taxonomic structures, as well mechanisms, during dry wet seasons. The results revealed that, compared with electrofishing surveys, detected greater number higher richness both Despite significant differences composition between seasons, methods indicated that environmental filtering dominated process showed is comparable stream can accurately reliably determine mechanisms. Combining traits robust approach for uncertainty.

Language: Английский

Citations

3
Environmental DNA Metabarcoding Reveals the Influence of Environmental Heterogeneity on Microeukaryotic Plankton in the Offshore Waters of East China Sea DOI

Li JiangNan,

Shuping Wang,

Pengxia Liu

et al.

Environmental Research, Journal Year: 2024, Volume and Issue: 262, P. 119921 - 119921

Published: Sept. 2, 2024

Language: Английский

Citations

1