Profiling population-level diversity and dynamics of Accumulibacter via high throughput sequencing of ppk1

  • Wei Song
  • Min Jia Zheng
  • Hao Li
  • Wei Zheng
  • Feng GuoEmail author
Environmental biotechnology


As the key organism for enhanced biological phosphorus removal, Accumulibacter has shown high intragenus diversity based on the phylogeny of polyphosphate kinase1 gene (ppk1) and many clade-specific features related to performance of wastewater treatment. However, the widely used molecular approaches are deficient or cost-inefficient in providing a comprehensive and quantitative population-level profile for Accumulibacter in complex community. In this study, we introduced a pipeline to analyze the population-level diversity and dynamics of Accumulibacter via high throughput sequencing (HTS) of ppk1 and 16S rRNA gene simultaneously. The HTS approach was assessed by testing primer coverage, performing sample replication, and comparing with a traditional clone library. Based on survey on full-scale activated sludge samples, unexpected high microdiversity in Accumulibacter and a tendency of exclusivity between two phylogenetic types were discovered. Moreover, the pipeline facilitated monitoring the population-level dynamics and co-occurrence pattern under various laboratory enriching conditions. The results revealed previously uncharacterized intraclade dynamics during enrichment, little effect of denitrifying process on the Accumulibacter diversity, and the niche adaption of Clade IIC on propionate as sole carbon source. Co-occurrence of Accumulibacter populations further partially supported the exclusivity of two types. A few bacterial taxa, including Cytophagaceae-, Prosthecobacter-, and Compteibacter-related taxa, showed co-occurrence with many Accumulibacter populations, suggesting their niche co-selection or potential metabolic interactions with Accumulibacter. The present pipeline is transplantable for studying microdiversity and niche differentiation of other functional microorganisms in complex microbial systems.


Enhanced biological phosphate removal Activated sludge Microdiversity Co-occurrence 



Prof. Xin Yu and Mr. Chengsong Ye are thanked for providing the activated sludge samples from WWTPs. Mr. Le Yang is thanked for his helps in operating partial bioreactors.

Funding information

The authors received financial supports from the National Natural Science Foundation of China (No. 31500100 and No. 31670492).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

253_2019_10183_MOESM1_ESM.pdf (471 kb)
ESM 1 (PDF 471 kb)


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Copyright information

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

Authors and Affiliations

  • Wei Song
    • 1
  • Min Jia Zheng
    • 1
  • Hao Li
    • 1
  • Wei Zheng
    • 1
  • Feng Guo
    • 1
    Email author
  1. 1.School of Life ScienceXiamen UniversityFujianPeople’s Republic of China

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