Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework

Frontiers in Microbiology

Raquel Rodríguez-Martínez¹  Thomas A. Richards¹  Patrick J. Keeling²  Javier del Campo³  Ramon Massana⁴  Alexandra Z. Worden⁵  Thierry J. Heger⁶ 

[1] Department of Biosciences, Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom;Department of Botany, University of British Columbia, Vancouver, BC, Canada;Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States;Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Barcelona, Spain;GEOMAR – Helmholtz Centre for Ocean Research Kiel, Kiel, Germany;Soil Science Group, CHANGINS, University of Applied Sciences and Arts Western Switzerland, Nyon, Switzerland;

关键词: apicomplexans;    diversity;    distribution;    phylogeny;    classification;    metabarcoding;   

DOI  :  10.3389/fmicb.2019.02373

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown