Unique microbiome in organic matter-polluted urban rivers.

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.

Sources and drivers of contamination along an urban tropical river (Ciliwung, Indonesia): Insights from microbial DNA, isotopes and water chemistry.

Wastewater treatment infrastructure is lacking in many developing countries, often resulting in high loads of contaminants discharged to urban rivers. In these countries, targeted pollution mitigation requires an understanding of where, how and when contaminants enter water bodies. Here we report on contamination of the Ciliwung River, a dynamic, tropical system flowing through the Jakarta metropolitan area (Indonesia). We measured a set of isotopic, chemical and microbial tracers in representative water and contamination sources, as well as longitudinally within the river, to assess the spatial and temporal variations in contaminant levels in and pathways to the river. In the dry season, we observed a tight coupling between locally recharged groundwater sources and the river, whereas in the wet season, one single water source originating from the fractured headwaters predominantly contributed to river flow. Yet, the flushing of upstream waters in the wet season did not always lead to the dilution of contaminants downstream. We delineated several contamination hotspots along the river, particularly active during the wet season due to higher hydrological connectivity between sources and the river. These hotspots may originate from septic tank leakage, as supported by metal ratios and dominant microbial communities, although we could not rule out other potential sources such as urban runoff or sediment resuspension. Bayesian source tracking on the whole microbial community proved useful in outlining processes that conventional tracers did not capture, such as the occurrence of a localised domestic contamination in the upper catchment, and the inflow of agricultural runoff all along the river profile during the wet season. Our study emphasises the role of rivers as biogeochemical reactors that constantly process and transform contaminants and microbial communities. We also demonstrate the value of using isotopic, chemical and microbial tools together to trace the movement of water and contaminants through urban rivers.