Metagenomic insights into microbial diversity in a groundwater basin impacted by a variety of anthropogenic activities

  • Prinpida SonthiphandEmail author
  • Siwat Ruangroengkulrith
  • Wuttichai Mhuantong
  • Varodom Charoensawan
  • Srilert Chotpantarat
  • Satika Boonkaewwan
Research Article


Microbial communities in groundwater are diverse and each may respond differently to environmental change. The goal of this study was to investigate the diversity, abundance, and dynamics of microbial communities in impacted groundwater and correlate them to the corresponding land use and groundwater geochemistry, using an Illumina MiSeq platform targeting the V3 and V4 regions of the 16S rRNA gene. The resulting MiSeq sequencing revealed the co-occurrence patterns of both abundant and rare microbial taxa within an impacted groundwater basin. Proteobacteria were the most common groundwater-associated bacterial phylum, mainly composed of the classes Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria. The phyla detected at less abundances were the Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, OD1, and Nitrospirae. The members of detected groundwater microorganisms involved in natural biogeochemical processes such as nitrification, anammox, methane oxidation, sulfate reduction, and arsenic transformation. Some of the detected microorganisms were able to perform anaerobic degradation of organic pollutants. The resulting PCA indicates that major land usage within the sampling area seemed to be significantly linked to the groundwater microbial distributions. The distinct microbial pattern was observed in the groundwater collected from a landfill area. This study suggests that the combinations of anthropogenic and natural effects possibly led to a unique pattern of microbial diversity across different locations at the impacted groundwater basin.


Microbial diversity Groundwater Anthropogenic activities Land use Groundwater microbiome Metagenomics analysis 


Funding information

This research was supported by Mahidol University through the New Researcher Grant and the Faculty of Science, Mahidol University. V.C. lab is supported by the Thailand Research Fund (TRF) Grant for New Scholar (MRG6080235); the Faculty of Science, Mahidol University; and the Crown Property Bureau Foundation. The authors also received financial support from the research program on controls of hazardous contaminants in raw water resources for water scarcity resilience.

Supplementary material

11356_2019_5905_MOESM1_ESM.docx (870 kb)
ESM 1 (DOCX 869 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Biology, Faculty of ScienceMahidol UniversityBangkokThailand
  2. 2.Department of Biochemistry, Faculty of ScienceMahidol UniversityBangkokThailand
  3. 3.Enzyme Technology LaboratoryNational Center for Genetic Engineering and BiotechnologyPathum ThaniThailand
  4. 4.Integrative Computational BioScience (ICBS) CenterMahidol UniversityNakhon PathomThailand
  5. 5.Systems Biology of Diseases Research Unit, Faculty of ScienceMahidol UniversityNakhon PathomThailand
  6. 6.Department of Geology, Faculty of ScienceChulalongkorn UniversityBangkokThailand
  7. 7.Research Program on Controls of Hazardous Contaminants in Raw Water Resources for Water Scarcity Resilience, Center of Excellence on Hazardous Substance Management (HSM)Chulalongkorn UniversityBangkokThailand
  8. 8.Research Unit of Green Mining (GMM)Chulalongkorn UniversityBangkokThailand
  9. 9.International Postgraduate Program in Hazardous Substance and Environmental ManagementChulalongkorn UniversityBangkokThailand

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