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

Anna-Lotta Hiillos,Karelyn Emily Knott,Anne Thonig

doi:10.1002/ece3.8372

Anna-Lotta Hiillos, Karelyn Emily Knott + Show 1 more

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https://doi.org/10.1002/ece3.8372

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Abstract

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.

Highlights

Interactions between symbiotic organisms and their hosts dramatically influence organismal ecology and evolution, and the dynamics of entire ecosystems (Faust & Raes, 2012; Godfrey-Smith, 2015).For the majority of symbioses, we do not know how the interacting species affect each other, much less the broader consequences of the symbiosis for communities or ecosystems
We show that digital droplet PCR (ddPCR) can shed light on biological interactions with precise estimates of cryptic, unculturable symbionts in natural host populations, indicating that the method is useful in molecular ecology research
We developed a ddPCR assay to detect and quantify an undescribed agamococcidian based on its COX1 gene, and we demonstrated its use in studying infection dynamics by documenting the prevalence of the symbiont and the infection load in four seasonally sampled populations of its host, P. elegans. ddPCR can enable further investigation of cryptic symbiotic interactions that are difficult to carry out with other molecular methods and impossible with morphological methods alone

Summary

Introduction

Interactions between symbiotic organisms and their hosts dramatically influence organismal ecology and evolution, and the dynamics of entire ecosystems (Faust & Raes, 2012; Godfrey-Smith, 2015).For the majority of symbioses, we do not know how the interacting species affect each other, much less the broader consequences of the symbiosis for communities or ecosystems. Interactions between symbiotic organisms and their hosts dramatically influence organismal ecology and evolution, and the dynamics of entire ecosystems (Faust & Raes, 2012; Godfrey-Smith, 2015). It is the lack of tools for effectively monitoring or investigating symbiotic interactions that prohibits progress. . |2 about the symbiotic organisms can limit the development of these tools (Pawlowski et al, 2012), leaving much of the functional and species- level diversity understudied. Infecting majority of vertebrates and invertebrates in terrestrial and aquatic environments, apicomplexan species diversity is estimated to be over a million (Pawlowski et al, 2012). The bulk of apicomplexan diversity, especially in marine environments, is largely undescribed and contains many cryptic species (Janouškovec et al, 2015; Xavier et al, 2018). Even when the symbiont is cryptic, could help to shed light on the nature of their interaction with the host and their effect on host populations

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