Alteration of bacterial community composition in the sediments of an urban artificial river caused by sewage discharge

Abstract

Background: Urbanization has an ecological and evolutionary effect on urban microorganisms. Microorganisms are fundamental to ecosystem functions, such as global biogeochemical cycles, biodegradation and biotransformation of pollutants, and restoration and maintenance of ecosystems. Changes in microbial communities can disrupt these essential processes, leading to imbalances within ecosystems. Studying the impact of human activities on urban microbes is critical to protecting the environment, human health, and overall urban sustainability.

Methods: In this study, bacterial communities in the sediments of an urban artificial river were profiled by sequencing the 16S rRNA V3-V4 region. The samples collected from the eastern side of the Jiusha River were designated as the JHE group and were marked by persistent urban sewage discharges. The samples collected on the western side of the Jiusha River were categorized as the JHW group for comparative analysis.

Results: The calculated alpha diversity indices indicated that the bacterial community in the JHW group exhibited greater species diversity and evenness than that of the JHE group. Proteobacteria was the most dominant phylum between the two groups, followed by Bacteroidota. The relative abundance of Proteobacteria and Bacteroidota accumulated in the JHE group was higher than in the JHW group. Therefore, the estimated biomarkers in the JHE group were divided evenly between Proteobacteria and Bacteroidota, whereas the biomarkers in the JHW group mainly belonged to Proteobacteria. The Sulfuricurvum, MND1, and Thiobacillus genus were the major contributors to differences between the two groups. In contrast to JHW, JHE exhibited higher enzyme abundances related to hydrolases, oxidoreductases, and transferases, along with a prevalence of pathways associated with carbohydrate, energy, and amino acid metabolisms. Our study highlights the impact of human-induced water pollution on microorganisms in urban environments.

Keywords: 16S rRNA gene; Bacterial community; Function prediction; River sediment; Urban microbes.

Figure 1. The geographical and biological characteristics of the sampled sites.

(A) Location distribution map of sampling points on the eastern (JHE1-5) and western (JHW1-5) sides of Jiusha River. The blue arrows indicate the direction of river water flow. The yellow triangular symbols in the diagram represent the presence of sewage discharge outlets at these locations. The bar represents 500 m. (B) The similarity of sampling points based on the physicochemical properties and partial metal content listed in Table 1 as demonstrated by NMDS analysis. (C) Comparison analysis of alpha diversity indices between the eastern (JHE) and western (JHW) sides of the Jiusha River. The boxplots show median values and interquartile ranges. Map includes data from: Airbus, Imagery from 4/30/2023.

Figure 2. Distribution of species abundance in collected samples by phylum and genus classification.

(A) UPGMA tree based on weighted UniFrac distance at the phylum level. The left side is the UPGMA clustering tree structure, and the right side is the relative abundance distribution of the top 10 most abundant species in each sample at the phylum level. The remaining phyla are grouped as others. (B) Top 10 bacterial genera contributing most to the differences between the JHE and JHW groups based on similarity of percentages (Simper) analysis. The size of the bubble chart on the left represents the relative abundance of the species, and the length of the histogram on the right represents the contribution of the species to the difference between the two groups.

Figure 3. Key phylotypes of differently abundant taxa identified between the JHE and JHW groups using linear discriminant analysis (LDA) combined with effect size (LEfSe) algorithm.

(A) Histogram of the LDA scores (LDA score > 3, p value > 0.05) computed for differentially abundant bacterial taxa between the two groups. (B) Cladogram generated using the LEfSe method illustrating the significant phylogenetic distribution of bacteria associated with the JHE group (red) and JHW group (blue). Non-significant discriminant taxonomic nodes are colored yellow. The concentric circles radiating outward represent classification levels from phylum to species. The diameter of the circles is directly proportional to the relative abundance.

Figure 4. Differences in the abundances of enzymes (A) and pathways (B) inferred by PICRUSt2.

The bar plot shows mean proportions (%) of differential EC numbers and KEGG orthologs between the JHE and JHW groups. Sankey diagram on the left illustrates the enriched enzymes and metabolic pathways. The differences in proportions between groups are depicted with 95% confidence intervals on the right, and only Bonferroni-adjusted p-values ≤ 0.01 are shown.