DOI: 10.5061/dryad.31zcrjdq4
title: Unique microbiome in organic matter-polluted urban rivers

description: 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.
description: 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, &lt;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).