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Validation of Bacteroidales-based microbial source tracking markers for pig fecal pollution and their application in two rivers of North China

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Abstract

In China, pig feces is the predominant source of excrement produced by animal husbandry. Improper use or direct discharge of pig feces can result in contamination of natural water systems. Microbial source tracking (MST) technology can identify the sources of fecal pollution in environmental water, and contribute to the management of pig fecal pollution by local environmental protection agencies. However, the accuracy of such assays can be context-dependent, and they have not been comprehensively evaluated under Chinese conditions. We aimed to compare the performance of five previously reported pig-specific MST assays (PF, Pig-Bac1SYBR, Pig-Bac2SYBR, Pig-1-BacTaqMan, and Pig-2-BacTaqMan, which are based on Bacteroidales 16S rRNA gene markers) and apply them in two rivers of North China. We collected a total of 173 fecal samples from pigs, cows, goats, chickens, humans, and horses across China. The PF assay optimized in this study showed outstanding qualitative performance and achieved 100% specificity and sensitivity. However, the two SYBR green qPCR assays (Pig-Bac1SYBR and Pig-Bac2SYBR) cross-reacted with most non-pig fecal samples. In contrast, both the Pig-1-BacTaqMan and Pig-2-BacTaqMan assays gave 100% specificity and sensitivity. Of these, the Pig-2-BacTaqMan assay showed higher reproducibility. Our results regarding the specificity of these pig-specific MST assays differ from those reported in Thailand, Japan, and America. Using the PF and Pig-2-BacTaqMan assays, a field test comparing the levels of pig fecal pollution in rivers near a pig farm before and after comprehensive environmental pollution governance indicated that pig fecal pollution was effectively controlled at this location.

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Acknowledgements

This work was supported by the National Key Research and Development Program of China (No.2016YFC0503601), and Excellent Young Teachers’ Scientific Research Ability Improvement Project of University of Chinese Academy of Sciences (No. Y95401FXX2).

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Authors and Affiliations

  1. College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China

    Youfen Xu, Zong Li, Ruyin Liu, Hongxia Liang, Zhisheng Yu & Hongxun Zhang

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  1. Youfen Xu
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  2. Zong Li
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  3. Ruyin Liu
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  4. Hongxia Liang
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  5. Zhisheng Yu
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  6. Hongxun Zhang
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Correspondence to Ruyin Liu.

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Highlights

• Pig feces is the predominant excrement produced by animal husbandry in China.

• The PF, Pig-1-BacTaqMan, and Pig-2-BacTaqMan MST assays showed better performance.

• The pig-specific MST assays can contribute to managing the pig fecal pollution.

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Xu, Y., Li, Z., Liu, R. et al. Validation of Bacteroidales-based microbial source tracking markers for pig fecal pollution and their application in two rivers of North China. Front. Environ. Sci. Eng. 14, 67 (2020). https://doi.org/10.1007/s11783-020-1246-9

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  • DOI: https://doi.org/10.1007/s11783-020-1246-9

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