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. 2025 Apr 12;14(4):410.
doi: 10.3390/biology14040410.

A Study on the Community and Ecological Characteristics of Benthic Invertebrates in the Ulungu River, Xinjiang, via eDNA Metabarcoding and Morphological Methods

Qiang Huo  1   2 , Yuying Ma  1 , Linghui Hu  1   2 , Qi Liu  1   2 , Chengxin Wang  1   2 , Jiaxuan Liu  1   2 , Daoquan Ren  1 , Zhichao Wang  1 , Baoqiang Wang  3 , Honghui Zeng  3 , Yong Song  1   2 , Sheng'ao Chen  1   2
Affiliations

A Study on the Community and Ecological Characteristics of Benthic Invertebrates in the Ulungu River, Xinjiang, via eDNA Metabarcoding and Morphological Methods

Qiang Huo et al. Biology (Basel). .

Abstract

eDNA metabarcoding has been used for the biomonitoring of benthic invertebrates, but the correct steps to achieve its effectiveness, the stability of the results, and comparisons with morphological methods are still understudied. In this study, morphology and eDNA were studied for benthic invertebrate samples collected at six sites in the Ulungu River Basin. A Mantel test and NMDS analyses were used to test the correlations of the communities obtained via the two methods, the Shannon index was calculated to evaluate the ecological status, and the correlation of the evaluation results was analyzed. The results revealed that eDNA metabarcoding did not detect a greater number of species than the morphological method, that the results from the two methods shared fewer taxa at the family level and below, and that only five taxa were shared at the genus level. The Mantel test and NMDS analyses revealed very significant differences between the communities monitored by the two methods (PERMANOVA, p = 0.0056), but eDNA metabarcoding provided richness and abundance data for species that are difficult to identify morphologically, and these findings can be used to supplement the morphological data. The cor.test revealed that there was no significant correlation between the diversity and ecological assessment results of the two methods, and the ecological assessment results of eDNA metabarcoding cannot represent accurate and true ecological conditions. The water sample eDNA-based method and morphological method exhibited low consistency and high complementarity in monitoring benthic invertebrate communities and diversity. More research is still needed on the key links of eDNA sampling, the control of the degradation rate, data utilization, and index development to provide more environmentally friendly and effective monitoring methods for ecological protection, more reliable support for ecological decision-making, and to more adequately respond to the challenges of global environmental change.

Keywords: Ulungu River; benthic invertebrates; eDNA; ecological assessment; morphology.

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Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Figures

Figure 1
Figure 1
Distribution of eDNA and morphological sample collection sites in the Ulungu River Basin.
Figure 2
Figure 2
Benthic invertebrate richness at each site detected by eDNA metabarcoding and morphological methods at the genus (a) and phylum levels (b) and the number of genus-level taxa (c) and relative abundance (d) of shared phyla detected by both methods; * denote p ≤ 0.05.
Figure 3
Figure 3
Relative abundance (%) of benthic invertebrates at the genus level (a,b) and phylum level (c,d) at each site using eDNA metabarcoding (a,c) or morphological methods (b,d).
Figure 4
Figure 4
Number of taxa shared between the eDNA metabarcoding and morphology results at different taxonomic levels.
Figure 5
Figure 5
NMDS analysis of different benthic invertebrate communities monitored by eDNA metabarcoding and morphological methods.
Figure 6
Figure 6
Shannon index and ecological status assessment at each site via eDNA metabarcoding and morphological methods.
See this image and copyright information in PMC

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