Shift in the microbial community composition of surface water and sediment along an urban river
Graphical abstract
Introduction
Rivers or streams flowing through cities always serve as an important sink for waste materials, urban sewage, and storm water run-off. They are also the main source of drinking or industrial water in cities, especially those along the river. Microorganisms inhabiting these ecosystems are one of the crucial players in the biogeochemical cycling of organic matter and nutrients, biodegradation and biotransformation of pollutants, and the recovery and maintenance of ecosystem health and balance (Bai et al., 2014; Kirchman, 1994; Ruiz-González et al., 2015). Although there has been an increasing awareness of water quality and great efforts are being taken to ensure greater sustainability of urban rivers, the accelerating development of cities, commonly in developing countries, inevitably leads to an increase in river deterioration (Suthar et al., 2010) due to high-load discharge and water front construction. Meanwhile, the water microbial properties, particularly the diversity and community structure, could be susceptibly influenced by the spatial variability of the physicochemical and biotic parameters, which can be used as an indicator of environmental conditions (Kostanjsek et al., 2005; Lundgaard et al., 2017; Tiquia, 2010). Most previous laboratory and field studies assessing the impact of urban human activity on surface water and sediments have focused on physicochemical indexes such as heavy metals (Vink et al., 1999; Zheng et al., 2008), hydrocarbons (Yunker et al., 2002) or nutrients (Howarth et al., 2000), and algal characters (Biggs, 2000; Flynn et al., 2013). The in-depth understanding of microbial community diversity in the flowing urban river is still lacking, and is less explored than that of marine or lake ecosystems (Zinger et al., 2012).
It is well-understood that microbial communities are taxonomically distinct at different spatial and temporal scales in river systems (Garcia-Armisen et al., 2014; Savio et al., 2015; Zhi et al., 2015). Urban rivers are rather spatially heterogeneous ecosystems that are mainly influenced by the terrestrial environment. Sewage from the residential areas containing organic and inorganic pollutants notably alters the basic parameters of freshwater, such as pH, temperature, dissolved oxygen content, and light penetration, which could further reshape the bacterial community structure (Garcia-Armisen et al., 2014; Lindström et al., 2005; Mark Ibekwe et al., 2012). The sewage system seems to be an eutrophic environment for stimulating the growth of microorganisms which are likely to be physiologically adapted to this environment. In addition, sewage also introduces microbiological contamination to the river which can have a key impact on the diversity and function of the bacterial community (Drury et al., 2013). To some degree, the spatial distribution of river bacterial communities is also associated with the landscape topography and hydrology (Crump et al., 2007; Lindström and Bergström, 2004). The variations in valley width, hydrologic connections, and flow can directly influence the water residence time and water dilution capacity. These factors are related to the balance process between the bacteria from terrestrial or sewage source, and indigenous communities, and the stabilization of the communities by predation or competition (Crump et al., 2007; Lozupone and Knight, 2007; Read et al., 2015; Székely et al., 2013), which might indirectly or directly affect the microbial community function. As a result, it is essential to understand the microbial communities in the context of their spatial distribution and microbial diversity in a river to monitor the ecosystem health and function. Recently, a growing number of nations have highlighted the development of small hydropower resources (Karki, 2007; Li et al., 2009; Yüksel, 2007). The construction of hydropower stations could exert a significant influence on altering the upstream and downstream water quality (Zhang et al., 2005). These changes can greatly affect the microbial communities in the aquatic system (Sekiguchi et al., 2002; Yan et al., 2015). Several studies have described the impact of hydropower stations on phytoplankton (Sow et al., 2016; Ye et al., 2006; Zhou et al., 2011) and other related environmental changes (Zhang et al., 2005). However, there exists little data regarding their effects on microorganisms. Therefore, an attempt to determine the shift in microbial communities caused by hydropower projects has also been emphasized in the present study.
We hypothesized that addition of high nutrient elements from anthropogenic sources associated with urbanization is an important impetus for altering the microbial communities in the surface water and sediment of urban rivers. In the current study, the Jialing River (Nanchong section), which is the second longest tributary of the Yangtze River impacted by urbanization and a small hydropower station, was chosen as a model to gain insight into the variation of bacterial communities in the urban river. We performed 16S rRNA gene-based high-throughput sequencing on the microbial communities of eight surface water samples (two of which were collected from the urban branches) and three representative sediments. The objectives of the study are as follows: (i) to study the spatial variations in bacterial communities along the urban river; (ii) to reveal the main environmental factors leading to the altered dynamics change of microbial communities; and (iii) to identify the response of microbial communities to urban discharge and the construction of a hydropower station in terms of microbial composition and metabolic prediction analysis.
Section snippets
Description of sampling sites
The Jialing River is the second longest tributary of the YangtZe River in China, and stretches over 1120 km from Qinling Mountain to Chong Qing city (Zhang et al., 2008). Nanchong is located in the low reach of the Jialing River, and the river runs through Nanchong city. The flow direction throughout Nanchong City is from the north to the south. The area is highly urbanized with a population of over 7.6 million. Jialing River is the main source of drinking and household water, and also the main
Physicochemical properties of water and sediment samples
The physicochemical characteristics of the water and sediment samples collected from each sampling site are shown in Table 1. Temperature and pH ranged from 25.0 to 28.0 °C and 7.91 to 8.22 in all water samples, respectively. Significant differences in water NO3− and NO2− content among samples were observed (P < 0.05). The hydropower station built between the 2W and 3W did not affect the chemical characters measured in this study. The NO3−and TP contents in branch 5BW were higher than those in
Discussion
There is a large degree of variation in the freshwater bacterial community in terms of taxonomic composition and spatial distribution among or within different rivers (Bai et al., 2014; Garcia-Armisen et al., 2014; Ibekwe et al., 2016; Ouattara et al., 2014; Ruiz-González et al., 2015), how and where the shift of microbial communities occurs in a certain urban river remains largely unexplored. The shifts in aquatic and sediment bacterial communities were determined by Illumina Miseq sequencing
Conclusion
In conclusion, our study demonstrates the spatial shift in microbial communities of freshwater and sediments in an integral urban river, shaped by environmental variables like TP, NO3−, DO, metals (Fe, Zn) and a hydropower station. We also demonstrate significant differences in the bacterial and archaeal community composition between the branches and the main river within the same district. The construction of the hydropower station led to the high abundance of Cyanobacteria in the upstream
Acknowledgments
This work was financially supported by the National Science Foundation of China (41606142) and the Fundamental Research Funds of China West Normal University (463140 and 412554). We thank Tao Hou for the sample collection, and Mingli Liao, Xiao Xu for their assistance in chemical analysis. We are grateful to the two anonymous reviewers for the great comments that improved the manuscript greatly.
References (103)
- et al.
Antibiotics and antibiotic resistance in water environments
Curr. Opin. Biotechnol.
(2008) - et al.
Phytoplankton composition, growth and production in the Guadiana estuary (SW Iberia): unraveling changes induced after dam construction
Sci. Total Environ.
(2012) - et al.
River damming leads to decreased phytoplankton biomass and disappearance of cyanobacteria blooms
Estuar. Coast. Shelf Sci.
(2014) - et al.
Modeling the lateral variation of bottom-attached algae in rivers
Ecol. Model.
(2013) - et al.
Microbial community structures in different wastewater treatment plants as revealed by 454-pyrosequencing analysis
Bioresour. Technol.
(2012) - et al.
Bacterial community composition and structure in an Urban River impacted by different pollutant sources
Sci. Total Environ.
(2016) The ecology of Cytophaga–Flavobacteria in aquatic environments
FEMS Microbiol. Ecol.
(2002)- et al.
Long-term survey of heavy-metal pollution, biofilm contamination and diatom community structure in the Riou Mort watershed, South-West France
J. Environ. Pollut.
(2008) - et al.
The use of ozone in the remediation of polycyclic aromatic hydrocarbon contaminated soil
Chemosphere
(2006) - et al.
Contamination of rivers in Tianjin, China by polycyclic aromatic hydrocarbons
J. Environ. Pollut.
(2005)
PAHs contamination and bacterial communities in mangrove surface sediments of the Jiulong River Estuary, China
Mar. Pollut. Bull.
Metabolic diversity of the heterotrophic microorganisms and potential link to pollution of the Rouge River
J. Environ. Pollut.
Development of the heavy metal pollution trends in several European rivers: an analysis of point and diffuse sources
Water Sci. Technol.
Behaviour of pathogenic and indicator bacteria during urban wastewater treatment and sludge composting, as revealed by quantitative PCR
J. Water Res.
Delivery and cycling of phosphorus in rivers: a review
Sci. Total Environ.
Sources and significance of alkane and PAH hydrocarbons in Canadian arctic rivers
Estuar. Coast. Shelf Sci.
Characterization of heavy metal concentrations in the sediments of three freshwater rivers in Huludao City, Northeast China
J. Environ. Pollut.
Using high-throughput sequencing to assess the impacts of treated and untreatewastewater discharge on prokaryotic communities in an urban river
Appl. Environ. Microbiol.
Molecular phylogenetic analysis of a bacterial community in an oligotrophic cave environment
Geomicrobiol J.
Aminoglycoside antibiotic-inactivating enzymes in actinomycetes similar to those present in clinical isolates of antibiotic-resistant bacteria
PNAS
Eutrophication of streams and rivers: dissolved nutrient-chlorophyll relationships for benthic algae
J. N. Am. Benthol. Soc.
Galaxy: a web-based genome analysis tool for experimentalists
Curr. Protoc. Mol. Biol.
High taxonomic level fingerprint of the human intestinal microbiota by ligase detection reaction - universal array approach
BMC Microbiol.
Distribution and ecosystem risk assessment of polycyclic aromatic hydrocarbons in the Luan River, China
Ecotoxicology
PyNAST: a flexible tool for aligning sequences to a template alignment
Bioinformatics
QIIME allows analysis of high-throughput community sequencing data
Nat. Methods
Unexpected occurrence of plasmid-mediated quinolone resistance determinants in environmental Aeromonas spp
Emerg. Infect. Dis.
Nonparametric estimation of the number of classes in a population
Scand. J. Stat.
Estimating the number of classes via sample coverage
J. Am. Stat. Assoc.
Primer v6: User Manual/Tutorial Plymouth UK
Biogeography of bacterioplankton in lakes and streams of an arctic tundra catchment
J. Ecol.
Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)
BMC Microbiol.
Wastewater treatment effluent reduces the abundance and diversity of benthic bacterial communities in urban and suburban rivers
Appl. Environ. Microbiol.
Search and clustering orders of magnitude faster than BLAST
Bioinformatics
Seasonal dynamics of shallow-hyporheic-zone microbial community structure along a heavy-metal contamination gradient
Appl. Environ. Microbiol.
Methanospirillum, a new genus of methanogenic bacteria, and characterization of Methanospirillum hungatii sp. nov
Int. J. Syst. Evol. Microbiol.
Toward an ecological classification of soil bacteria
J. Ecol.
Ecological tools for the management of cyanobacteria blooms in the Guadiana River watershed, Southwest Iberia
Seasonal variations and resilience of bacterial communities in a sewage polluted urban river
PLoS One
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
Genome Biol.
Ecology of actinomycetes
Annu. Rev. Microbiol.
Microbial diversity and community structure along a lake elevation gradient in Yosemite National Park, California, USA
Environ. Microbiol.
Issues in Ecology: Nutrient Pollution of Coastal Rivers, Bays, and Seas
Diversity and quantity of ammonia-oxidizing archaea and bacteria in sediment of the Pearl River Estuary, China
J. Appl. Microbiol. Biotechnol.
Bisphenol A degradation by bacteria isolated from river water
Arch. Environ. Contam. Toxicol.
Bisphenol A in the aquatic environment and its endocrine-disruptive effects on aquatic organisms
Crit. Rev. Toxicol.
Microcystin-LR biodegradation by Bacillus sp.: reaction rates and possible genes involved in the degradation
Water
Implications of Small Hydropower Plants in Power Sector Development: A Case of Nepal
The uptake of inorganic nutrients by heterotrophic bacteria
J. Microb. Ecol.
Changes in bacterial activity and community structure in response to dissolved organic matter in the Hudson River, New York
Aquat. Microb. Ecol.
Cited by (188)
Response of microbial communities to exogenous nitrate nitrogen input in black and odorous sediment
2024, Environmental Research