Droplet digital PCR as a tool for investigating dynamics of cryptic symbionts

Anna Lotta Hiillos*, Anne Thonig, Karelyn Emily Knott

*Corresponding author

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review


Interactions among symbiotic organisms and their hosts are major drivers of ecological and evolutionary processes. Monitoring the infection patterns among natural populations and identifying factors affecting these interactions are critical for understanding symbiont–host relationships. However, many of these interactions remain understudied since the knowledge about the symbiont species is lacking, which hinders the development of appropriate tools. In this study, we developed a digital droplet PCR (ddPCR) assay based on apicomplexan COX1 gene to detect an undescribed agamococcidian symbiont. We show that the method gives precise and reproducible results and enables detecting cryptic symbionts in low target concentration. We further exemplify the assay's use to survey seasonally sampled natural host (Pygospio elegans) populations for symbiont infection dynamics. We found that symbiont prevalence differs spatially but does not show seasonal changes. Infection load differed between populations and was low in spring and significantly increased towards fall in all populations. We also found that the symbiont prevalence is affected by host length and population density. Larger hosts were more likely to be infected, and high host densities were found to have a lower probability of infection. The observed variations could be due to characteristics of both symbiont and host biology, especially the seasonal variation in encounter rates. Our findings show that the developed ddPCR assay is a robust tool for detecting undescribed symbionts that are otherwise difficult to quantify, enabling further insight into the impact cryptic symbionts have on their hosts.
TidsskriftEcology and Evolution
Udgave nummer23
Sider (fra-til)17381-17396
Antal sider16
StatusUdgivet - dec. 2021

Bibliografisk note

Funding Information:
This work was funded by the University of Jyväskylä Graduate School for Doctoral Studies (Department of Biological and Environmental Science) and Emil Aaltonen Foundation grant to ALH (grant number a6a412). We would like to thank Su Houyi for working on the ddPCR assay, Gita Paskerova for providing the gregarine samples, and Joel Kostensalo for helping with the modeling of missing data. We thank Hanna Hartikainen, an anonymous reviewer, and the editors for their detailed and supportive reviews and comments.

Publisher Copyright:
© 2021 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.


  • apicomplexa
  • cryptic symbiosis
  • droplet digital PCR
  • infection dynamics

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