Synergistic Application of Molecular Markers and Community-Based Microbial Source Tracking Methods for Identification of Fecal Pollution in River Water During Dry and Wet Seasons

Hongxia Liang; Zhisheng Yu; Bobo Wang; Fabrice Ndayisenga; Ruyin Liu; Hongxun Zhang; Gang Wu

doi:10.3389/fmicb.2021.660368

Synergistic Application of Molecular Markers and Community-Based Microbial Source Tracking Methods for Identification of Fecal Pollution in River Water During Dry and Wet Seasons

Front Microbiol. 2021 Jun 14:12:660368. doi: 10.3389/fmicb.2021.660368. eCollection 2021.

Authors

Hongxia Liang¹, Zhisheng Yu^{1

2}, Bobo Wang¹, Fabrice Ndayisenga¹, Ruyin Liu¹, Hongxun Zhang¹, Gang Wu^{3

4}

Affiliations

¹ College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
² RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, China.
³ State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, University of Chinese Academy of Sciences, Beijing, China.
⁴ University of Chinese Academy of Sciences, Beijing, China.

Abstract

It is important to track fecal sources from humans and animals that negatively influence the water quality of rural rivers and human health. In this study, microbial source tracking (MST) methods using molecular markers and the community-based FEAST (fast expectation-maximization microbial source tracking) program were synergistically applied to distinguish the fecal contributions of multiple sources in a rural river located in Beijing, China. The performance of eight markers were evaluated using 133 fecal samples based on real-time quantitative (qPCR) technique. Among them, six markers, including universal (BacUni), human-associated (HF183-1 and BacH), swine-associated (Pig-2-Bac), ruminant-associated (Rum-2-Bac), and avian-associated (AV4143) markers, performed well in the study. A total of 96 water samples from the river and outfalls showed a coordinated composition of fecal pollution, which revealed that outfall water might be a potential input of the Fsq River. In the FEAST program, bacterial 16S rRNA genes of 58 fecal and 12 water samples were sequenced to build the "source" library and "sink," respectively. The relative contribution (<4.01% of sequence reads) of each source (i.e., human, swine, bovine, or sheep) was calculated based on simultaneous screening of the operational taxonomic units (OTUs) of sources and sinks, which indicated that community-based MST methods could be promising tools for identifying fecal sources from a more comprehensive perspective. Results of the qPCR assays indicated that fecal contamination from human was dominant during dry weather and that fecal sources from swine and ruminant were more prevalent in samples during the wet season than in those during the dry season, which were consistent with the findings predicted by the FEAST program using a very small sample size. Information from the study could be valuable for the development of improved regulation policies to reduce the levels of fecal contamination in rural rivers.

Keywords: FEAST program; dry and wet seasons; fecal pollution; high-throughput sequencing; microbial source tracking; molecular markers; real-time quantitative PCR.