Anthropogenic activities drive the microbial community and its function in urban river sediment

Zhang, Xu; Gu, Qing; Long, Xiaojing; Li, Zhao-Lei; Liu, Dong-Xiu; Ye, Dan-Hua; He, Chaohui; Liu, Xiaoyan; Väänänen, Kristiina; Chen, Xueping

doi:10.1007/s11368-015-1246-8

Cited by 41 publications

(17 citation statements)

References 38 publications

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“…Thus, the attribute in this result may be that the nitrifiers were inhibited by low DO concentration in the urban rivers, which was induced by excessive NH 4 + . Meanwhile, this result may be also attributed to other pollutants, such as heavy metals and permanent organic pollutants, as reported in previous studies in urban river ecosystems [35,36,37,38]. In addition, Firmicutes is the Gram-positive heterotrophic bacteria for nutrient cycling, the richness of Firmicutes was thus affected by the fecal pollution [8], and the Firmicutes community was the indicator of NH 4 + and NO 3 – derived from anthropogenic activities [38].…”

Section: Discussionsupporting

confidence: 62%

Bacterial Community Shifts Driven by Nitrogen Pollution in River Sediments of a Highly Urbanized City

Lin

Gao

et al. 2019

IJERPH

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Effects of nitrogen pollution on bacterial community shifts in river sediments remain barely understood. Here, we investigated the bacterial communities in sediments of urban and suburban rivers in a highly urbanized city, Shanghai. Sediment nitrate (NO3−) and ammonia (NH4+) were highly accumulated in urban river. Operation Taxonomic Units (OTUs), Abundance-based Coverage Estimators (ACEs) and Chao 1 estimator in urban rivers were slightly lower than those in suburban rivers, while Shannon and Simpson indices were higher in urban rivers than those in suburban rivers. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phylum communities, accounting for 68.5–84.9% of all communities. In particular, the relative abundances of Firmicutes and Nitrospirae were significantly higher in suburban rivers than in urban rivers, while relative abundances of Bacteroidetes, Verrucomicrobia, and Spirochaetes were significantly lower in suburban rivers than in urban rivers. NH4+ was significantly and negatively correlated with abundances of Firmicutes, Nitrospirae, and Actinobacteria. Importantly, the significant and negative effects of sediment NH4+ on bacterial richness and diversity suggested that nitrogen pollution likely contribute to the decrease in the bacterial richness and diversity. The results highlight that nitrogen enrichment could drive the shifts of bacterial abundance and diversity in the urban river sediments where are strongly influenced by human activities under the rapid urbanization stress.

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Section: Discussionsupporting

confidence: 62%

Bacterial Community Shifts Driven by Nitrogen Pollution in River Sediments of a Highly Urbanized City

Lin

Gao

et al. 2019

IJERPH

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“…Recent developments include: the use of the natural and artificially-applied DNA-markers (e.g., Mahler et al, 1998;Granger et al, 2007) associated with contrasting source materials; and the use of plantassociated fatty-acids and compound-specific stable isotopes (e.g., Reiffarth et al, 2016). Other studies (e.g., Zhang et al, 2016) have also demonstrated the potential of using microbial communities to identify sediment derived from different land use activities.…”

Section: Organic Tracers: Identification Of Contributions From Differmentioning

confidence: 99%

Fingerprinting and tracing the sources of soils and sediments: Earth and ocean science, geoarchaeological, forensic, and human health applications

Owens

Blake

Gaspar

et al. 2016

Earth-Science Reviews

200

120

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“…It is possible that mussels had the most impact on nitrification genes because their biodeposition products increase porewater NH 3 concentrations (Bril et al, 2014) and enhanced the flux of NO − 3 from water to sediment (Hoellein, Zarnoch, Bruesewitz, & DeMartini, 2017). Other studies have found significantly greater AOB amoA genes corresponding with a higher NH 3 load (Zhang et al, 2016) and aerophilic conditions (Wang et al, 2015). The most distinct nitrification genes were most closely related to NOB Nitrospira and comammox Nitrospira.…”

Section: Nitrification Biomarkers In Sediments With Musselsmentioning

confidence: 99%

Metagenomic analysis of nitrogen‐cycling genes in upper Mississippi river sediment with mussel assemblages

2018

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We investigated the impact of native freshwater mussel assemblages (order Unionoida) on the abundance and composition of nitrogen‐cycling genes in sediment of an upper Mississippi river habitat. We hypothesized that the genomic potential for ammonia and nitrite oxidation would be greater in the sediment with mussel assemblages, presumably due to mussel biodeposition products, namely ammonia and organic carbon. Regardless of the presence of mussels, upper Mississippi river sediment microbial communities had the largest genomic potential for nitrogen fixation followed by urea catabolism, nitrate metabolism, and nitrate assimilation, as evidenced by analysis of nitrogen cycling pathway abundances. However, genes encoding nitrate and nitrite redox reactions, nar GHI and nxr AB , were the most abundant functional genes of the nitrogen cycling gene families. Using linear discriminant analysis ( LDA ), we found nitrification genes were the most important biomarkers for nitrogen cycling genomic potential when mussels were present, and this presented an opposing effect on the abundance of genes encoding nitric oxide reduction. The genes involved in nitrification that increased the most were amoA associated with comammox Nitrospira and nxr homologs associated with Nitrospira . On the other hand, the most distinctive biomarkers of microbial communities without mussels were norB and nrfA , as part of denitrification and dissimilatory nitrate reduction to ammonium pathways, respectively. Ultimately, this research demonstrates the impact of native mollusks on microbial nitrogen cycling in an aquatic agroecosystem.

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Anthropogenic activities drive the microbial community and its function in urban river sediment

Cited by 41 publications

References 38 publications

Bacterial Community Shifts Driven by Nitrogen Pollution in River Sediments of a Highly Urbanized City

Bacterial Community Shifts Driven by Nitrogen Pollution in River Sediments of a Highly Urbanized City

Fingerprinting and tracing the sources of soils and sediments: Earth and ocean science, geoarchaeological, forensic, and human health applications

Metagenomic analysis of nitrogen‐cycling genes in upper Mississippi river sediment with mussel assemblages

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