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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Microbiol. | doi: 10.3389/fmicb.2019.02373

Assessing the diversity and distribution of apicomplexans in host and free-living environments using high-throughput amplicon data and a phylogenetically informed reference framework

 Javier del Campo1, 2*,  Thierry Heger2, 3,  Raquel Rodríguez-Martínez4, Alexandra Z. Worden5,  Thomas A. Richards4,  Ramon Massana6 and Patrick J. Keeling2
  • 1Rosenstiel School of Marine and Atmospheric Science, University of Miami, United States
  • 2University of British Columbia, Canada
  • 3University of Applied Sciences and Arts of Western Switzerland, Switzerland
  • 4University of Exeter, United Kingdom
  • 5Monterey Bay Aquarium Research Institute (MBARI), United States
  • 6Institute of Marine Sciences, Superior Council of Scientific Investigations, Spain

Apicomplexans are a group of microbial eukaryotes that contain some of the most well-studied parasites, including the causing agents of toxoplasmosis and malaria, and emergent diseases like cryptosporidiosis or babesiosis. Decades of research have illuminated the pathogenic mechanisms, molecular biology, and genomics of model apicomplexans, but we know little about their diversity and distribution in natural environments. In this study we analyze the distribution of apicomplexans across a range of both host-associated and free-living environments. Using publicly available small subunit (SSU) rRNA gene databases, high-throughput environmental sequencing (HTES) surveys, and our own generated HTES data, we developed an apicomplexan reference database, which includes the largest apicomplexan SSU rRNA tree available to date and encompasses comprehensive sampling of this group and their closest relatives. This tree allowed us to identify and correct incongruences in the molecular identification of apicomplexan sequences. Analyzing the diversity and distribution of apicomplexans in HTES studies with this curated reference database also showed a widespread, and quantitatively important, presence of apicomplexans across a variety of free-living environments. These data allow us to describe a remarkable molecular diversity of this group compared with our current knowledge, especially when compared with that identified from described apicomplexan species. This is most striking in marine environments, where potentially the most diverse apicomplexans apparently exist, but have not yet been formally recognized. The new database will be useful for microbial ecology and epidemiological studies, and provide valuable reference for medical and veterinary diagnosis especially in cases of emerging, zoonotic, and cryptic infections.

Keywords: Apicomplexa, diversity, distribution, phylogeny, Classification, metabarcoding, Environmental sequencing, reference database

Received: 20 Mar 2019; Accepted: 30 Sep 2019.

Copyright: © 2019 del Campo, Heger, Rodríguez-Martínez, Worden, Richards, Massana and Keeling. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Javier del Campo, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, United States,