Environmental DNA metabarcoding reveals the impacts of anthropogenic pollution on multitrophic aquatic communities across an urban river of western China

Xu, Xuming; Yuan, Yibin; Wang, Zhaoli; Zheng, Tong; Cai, Hetong; Yi, Malan; Li, Tianhong; Zhao, Zhonghua; Chen, Qian; Sun, Weiling

doi:10.1016/j.envres.2022.114512

Cited by 11 publications

(4 citation statements)

References 73 publications

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“…In general, sh species tend to be more mobile than freshwater macroinvertebrates, and so they may be able to spend some time in degraded habitats and then return to non-degraded habitats, thereby lowering their pollution exposure. A recent study in China found that urban pollutants were a primary driver of macroinvertebrate communities, but urban sh communities were instead driven by dispersal limitations (Xu et al 2023). Fish richness tended to be higher in river segments with a higher number of locks.…”

Section: Discussionmentioning

confidence: 95%

Inland navigation is a driver of freshwater biodiversity declines in Europe

Sexton,

Beisel,

Staentzel

et al. 2023

Preprint

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Freshwater navigation is expected to increase in the coming years, being promoted as a low-carbon form of transport. However, we currently lack knowledge on how this will impact biodiversity at large scales and interact with existing stressors. We addressed this knowledge gap by analyzing fish and macroinvertebrate community time series spanning the last 30 years across large European rivers comprising 19,592 observations from 4,049 sampling sites. We found ship traffic to be associated with biodiversity declines, i.e. decreases in fish and macroinvertebrate taxonomic richness and diversity, and trait richness. Shipping was also associated with increases in taxonomic evenness, which, in concert with richness decreases, can likely be attributed to losses in rare/smaller populations. In particular, shipping was especially harmful for benthic taxa and those preferring slow flows. These effects were often dependent on local land use and degradation. In fish, the negative impacts of shipping were highest in urban and agricultural landscapes. Regarding navigation infrastructure, the negative impact of channelization on macroinvertebrates was only evident when riparian degradation was also high. Our results demonstrate the risk of increasing inland navigation on freshwater biodiversity. Integrative waterway management accounting for riparian and landscape characteristics could help to mitigate these impacts.

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Section: Discussionmentioning

confidence: 95%

Inland navigation is a driver of freshwater biodiversity declines in Europe

Sexton,

Beisel,

Staentzel

et al. 2023

Preprint

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“…Ecological networks consist of nodes (individual taxa) and links (correlations in occurrence/abundance) and can be used to infer ecological interactions. 59 , 113 , 114 Co-occurrence networks of multitrophic communities in a habitat were inferred based on Spearman correlations (correlation coefficient | r | ≥0.75, adjusted p <0.05) between OTUs of the same and different taxonomic groups based on the RRA data, 23 using the corr.test function in the R package psych. 115 Cyanobacteria, diatoms, and invertebrates eDNA most likely reflect the occurrence of the corresponding taxa at the sampling sites, since living organisms themselves can be captured in the samples.…”

Section: Methodsmentioning

confidence: 99%

“… 20 , 21 More recently, eDNA has been integrated with ecological network analysis to reveal the organizational properties of ecological communities. 22 , 23 , 24 Highly efficient eDNA bioassessments using multi-marker metabarcoding techniques facilitate the reconstruction of multitrophic ecological networks at the ecosystem level and substantially enhance the ability of researchers to unveil hidden biotic interactions and detect ecosystem changes. 25 , 26 , 27 …”

Section: Introductionmentioning

confidence: 99%

Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau

Zhang,

Yan,

Zhao

et al. 2024

iScience

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“…Environmental metabarcoding has been used in different areas of research. For example, it has been used in food authentication (3), to understand plant-pollinator interactions (4), to detect invasive species in the environment (5), to monitor anthropogenic pollution (6), to reconstruct dietary components (7), and to reconstruct ancient ecosystems (8).…”

Section: Introductionmentioning

confidence: 99%

Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy

Sarhan,

Filosi,

Maixner

et al. 2024

Preprint

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Analyzing taxonomic diversity and identification in diverse ecological samples has become a crucial routine in various research and industrial fields. While DNA barcoding marker-gene approaches were once prevalent, the decreasing costs of next-generation sequencing have made metagenomic shotgun sequencing more popular and feasible. In contrast to DNA-barcoding, metagenomic shotgun sequencing offers possibilities for in-depth characterization of structural and functional diversity. However, analysis of such data is still considered a hurdle due to absence of taxa-specific databases. Here we present taxonize-gb, a command-line software tool to extract GenBank non-redundant nucleotide and protein databases, related to one or more input taxonomy identifier. Our tool allows the creation of taxa-specific reference databases tailored to specific research questions, which reduces search times and therefore represents a practical solution for researchers analyzing large metagenomic data on regular basis. Taxonize-gb is an open-source command-line Python-based tool freely available for installation at https://pypi.org/project/taxonize-gb/ and on GitHub https://github.com/msabrysarhan/taxonize_genbank. It is released under Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).

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Environmental DNA metabarcoding reveals the impacts of anthropogenic pollution on multitrophic aquatic communities across an urban river of western China

Cited by 11 publications

References 73 publications

Inland navigation is a driver of freshwater biodiversity declines in Europe

Inland navigation is a driver of freshwater biodiversity declines in Europe

Distinct multitrophic biodiversity composition and community organization in a freshwater lake and a hypersaline lake on the Tibetan Plateau

Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy

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