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. 2024 Jul 29;12(8):1551.
doi: 10.3390/microorganisms12081551.

Microbial Metagenomics Revealed the Diversity and Distribution Characteristics of Groundwater Microorganisms in the Middle and Lower Reaches of the Yangtze River Basin

Yue Wang  1 , Ming-Yu Weng  2 , Ji-Wen Zhong  1 , Liang He  1 , De-Jun Guo  1 , Dong Luo  3 , Jia-Yu Xue  2
Affiliations

Microbial Metagenomics Revealed the Diversity and Distribution Characteristics of Groundwater Microorganisms in the Middle and Lower Reaches of the Yangtze River Basin

Yue Wang et al. Microorganisms. .

Abstract

Groundwater is one of the important freshwater resources on Earth and is closely related to human activities. As a good biological vector, a more diverse repertory of antibiotic resistance genes in the water environment would have a profound impact on human medical health. Therefore, this study conducted a metagenomic sequencing analysis of water samples from groundwater monitoring points in the middle and lower reaches of the Yangtze River to characterize microbial community composition and antibiotic resistance in the groundwater environment. Our results show that different microbial communities and community composition were the driving factors in the groundwater environment, and a diversity of antibiotic resistance genes in the groundwater environment was detected. The main source of antibiotic resistance gene host was determined by correlation tests and analyses. In this study, metagenomics was used for the first time to comprehensively analyze microbial communities in groundwater systems in the middle and lower reaches of the Yangtze River basin. The data obtained from this study serve as an invaluable resource and represent the basic metagenomic characteristics of groundwater microbial communities in the middle and lower reaches of the Yangtze River basin. These findings will be useful tools and provide a basis for future research on water microbial community and quality, greatly expanding the depth and breadth of our understanding of groundwater.

Keywords: antibiotic-resistant bacteria; diversity; groundwater; metagenomics; microorganisms.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Geographic distribution of metagenomic samples from groundwater sampling points in Jiangxi and Jiangsu.
Figure 2
Figure 2
Composition of groundwater microbial communities. (a) Overview of microbial community structure at phylum level; (b) overview of microbial community structure at class level.
Figure 3
Figure 3
(a) Heatmap displaying cluster analysis based on distance matrix of species abundance, The difference in color represents the degree of similarity in species abundance between sample sites; (b) NMDS plot of groundwater microbial communities.
Figure 4
Figure 4
The response of groundwater microbial communities to environmental factors. (a) NCM (Neutral Community Model) fit of the groundwater microbial communities in Jiangxi and Jiangsu. The solid blue line represents the best fit with the NCM, and the dashed blue lines represent the 95% confidence interval predicted by the model. Microbial communities that occur more or less frequently than predicted by the NCM are shown in different colors. Nm represents the number of species in the groundwater microbial community, and BCTC (bacterial community total count) indicates the degree of model fit. (b) An ecological network diagram (MENs, microbial ecology networks) of groundwater microbial communities in Jiangxi and Jiangsu, constructed using Spearman correlation coefficients of relative abundance at the class level using kraken2 (version 2.1.2) (c) Redundancy analysis (RDA) of microbial communities at the phylum level and chemical factors in groundwater samples, with red dots representing Bray–Curtis distances between samples. The arrows indicate chemical factors influencing the composition of groundwater microbial communities. (d) A heatmap showing the correlation between physicochemical factors and microbial communities in groundwater.
Figure 5
Figure 5
The occurrence of antibiotic resistance mechanisms. (a) The distribution of ARGs (antibiotic resistance genes) in groundwater samples from Jiangxi and Jiangsu. The lines and their thicknesses represent the types and quantities of ARGs detected at the sampling sites. (b) A box plot showing the number of different types of ARGs detected in groundwater samples; (c) species abundance of various resistance genes in groundwater samples; (d) the mechanisms of antibiotic resistance genes.
Figure 6
Figure 6
(a) Network analysis revealing co-occurrence of groundwater microbes and ARG subtypes. Node colors distinguish between microbial and ARG types, with line thickness and color indicating strength and nature of correlations. (b) Distribution and abundance of ARGs in plasmids and chromosomes within groundwater environment. (c) Correlation analysis between antibiotic resistance genes and their host microbial communities at phylum level in groundwater.
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