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Unique microbiome in organic matter-polluted urban rivers

Cite this dataset

Liang, Zhiwei; Wang, Shanquan (2022). Unique microbiome in organic matter-polluted urban rivers [Dataset]. Dryad.


Approximately half of the global annual production of wastewater is released untreated into aquatic environments, which results in worldwide organic matter pollution in urban rivers, especially in highly populated developing countries. Nonetheless, information on microbial community assembly and assembly-driving processes in organic matter-polluted urban rivers remains elusive. In this study, a field study based on water and sediment samples collected from 200 organic matter-polluted urban rivers of 82 cities in China and Indonesia is combined with laboratory water-sediment column experiments. Our findings demonstrate a unique microbiome in these urban rivers. Among the community assembly-regulating factors, both organic matter and geographic conditions play major roles in determining prokaryotic and eukaryotic community assemblies, especially regarding the critical role of organic matter in regulating taxonomic composition. Using a dissimilarity-overlap approach, we found universality in the dynamics of water and sediment community assembly in organic matter-polluted urban rivers, which is distinctively different from patterns in eutrophic and oligotrophic waters. The prokaryotic and eukaryotic communities are dominated by deterministic and stochastic processes, respectively. Interestingly, water prokaryotic communities showed a three-phase cyclic succession of the community assembly process before, during, and after organic matter pollution. Our study provides the first large-scale and comprehensive insight into the prokaryotic and eukaryotic community assembly in organic matter-polluted urban rivers and supports their future sustainable management.


To have a comprehensive insight into microbiomes of black-odorous urban rivers, 186 mediumly and highly polluted urban rivers of 78 cities in China (June to September 2018) were selected based on the cities’ black-odorous urban river number and the water quality criteria, including DOC, redox potential and SS (NURPG, 2015; MOHURD, 2018; Liang et al., 2021) (Figure S1). In addition, water and sediment samples from 14 highly polluted urban rivers in four cities in Indonesia (May 2019) were also collected to confirm the impact of variances in geography and pollution ingredients on the urban river microbiome (Figure S1). For each sampling location, water samples (500 ml) were collected from the middle layers of urban rivers, and surface sediment samples (approximately 200 g, top layer, <30 cm) were acquired using a customized sediment sampler, as previously described (Liang et al., 2021; Lu et al., 2021). The water samples were further divided into two subsamples, one for physicochemical tests and the other for microbial community assembly analyses. The water samples for total genomic DNA extraction were filtered with a 0.22 µm membrane filter to preserve microbial cells. All samples were preserved in ice boxes and then shipped to the laboratory as previously described (Wang et al., 2013; Liang et al., 2021). After arriving at laboratory, the samples were stored at -80◦C prior to subsequent analyses.

Water temperature and pH were monitored in situ using portable probes (SG2; Mettler-Toledo, Greifensee, Switzerland). All liquid samples were filtered through 0.22 µm membrane filters prior to the analytical tests. Suspended solids (SS), ammonium, total nitrogen (TN) and total phosphorus (TP) in the water samples were measured according to standard methods (Baird et al., 2017). Nitrate and sulfate concentrations were determined using an ICS-600 ion chromatography (Thermo Scientific, Carlsbad, CA, USA), as previously described (Fang et al., 2020). Dissolved organic carbon (DOC) was measured using a TOC-VCPH analyzer (Shimadzu, Kyoto, Japan). To perform sediment pH measurements, approximately 10 g of sediment samples were mixed with 25 ml deionized water (25 mL), and then equilibrated for 20 min prior to subsequent pH tests. The total organic carbon (TOC) in the sediment samples was measured as previously described (Schumacher et al., 2002). Briefly, the sediment samples were oxidized with hydrochloric acid to remove carbonate and then measured using an elemental analyzer (Vario EL, Elementar, GmbH, Germany). 


National Natural Science Foundation of China, Award: 42161160306

National Natural Science Foundation of China, Award: 42107129

National Natural Science Foundation of China, Award: 41922049

China Postdoctoral Science Foundation, Award: 2022M713632

Natural Science and Engineering Research Council of Canada, Award: RGPIN-2017-06210

National Council for Scientific and Technological Development