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Processes governing the drinking water microbiome


  • Sandy Chan

Summary, in English

Safe drinking water is far from sterile and can contain 10^3-10^5 bacteria/mL. This water microbiome can be altered through various treatment processes in the drinking water treatment plant (DWTP), particularity when it comes in contact with biofilms. Biofilms cover surfaces in the drinking water systems and contain diverse bacterial communities that interact with the water. In this thesis, the bacterial communities in biofilms living on surfaces in a full-scale drinking water distribution system (DWDS), and within different slow sand filters (SSFs), were investigated to understand how they shape and interact with the water microbiome.

The installation of ultrafiltration (UF) in a DWTP resulted in extensive removal of bacteria from the distributed water. This permitted the addition of bacteria to the water from the DWDS biofilm to be quantitated in a full-scale system, and was estimated using flow cytometry to account for 58 % of the total bacterial content in the water. Using this estimate and bacterial counts from before UF was installed, when many more bacteria originated from the DWTP, the biofilm then contributed only 0.5 % of bacteria to the water microbiome. DESeq2 analysis of 16S rRNA gene sequences identified specific bacterial taxa released from the biofilm including genera Nitrospira, Sphingomonas and Hyphomicrobium. This study showed that the origin of the water microbiome is complex as it can include dynamic contributions from both the DWTP and the DWDS biofilm.

In a DWTP, biofilters alter the water microbiome in ways that can persist throughout the DWDS. To identify factors in these filters that govern this transformation of the water microbiome, different SSFs were compared using flow cytometry with cytometric histogram image comparison (CHIC), and 16S rRNA gene sequencing. In contrast to that seen for new SSFs, removal of the top layer of sand, including the Schmutzdecke, did not affect the removal of E. coli and coliforms, or the transformation of the water microbiome by an established SSF. Using washed sand as an inoculum for new SSF gave a more rapid development of the surface sand community towards that was observed in the established filter. A specific transformation of the water microbiome, including an increase in intact bacteria, and bacteria with low nucleic acid (LNA) content, higher community evenness, and higher abundance of certain bacterial taxa, including Planctomycetes and Pseudomonas, are proposed as a microbial signature for desirable SSF function. This thesis has demonstrated how several technological alterations in DWTPs altered the water microbiome, and contributed to the understanding of how processes can govern the microbiome of drinking water, which is essential for control and management of this important resource.

Publishing year




Document type



Department of Chemistry, Lund University


  • Engineering and Technology


  • Drinking water microbiome
  • Biofilm
  • Slow sand filters
  • Ultrafiltration
  • Bacterial community
  • Flow cytometry
  • Next generation sequencing




  • ISBN: 978-91-7422-598-3

Defence date

26 October 2018

Defence time


Defence place

Lecture hall B, Kemicentrum, Naturvetarvägen 14, Faculty of Engineering LTH, Lund University, Lund


  • Frederik Hammes (Doctor)