PacBio next-generation sequencing uncovers Apicomplexa diversity in different habitats

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Abstract The phylum Apicomplexacomprises a large group of protozoan organisms that are obligatory intracellular parasites and can infect various vertebrate and invertebrate hosts, leading to several significant medical and veterinary pathologies, including toxoplasmosis, cryptosporidiosis, theileriosis and eimeriosis. However, information on their diversity and distribution in nature is still limited, particularly in rivers. To address this gap, the study employed next-generation high-throughput 18S rRNA amplicon sequencing based on PacBio technology to determine the diversity and composition of the microeukaryotic parasitic taxa group (i.e., Apicomplexa). Principal component analysis (PCA) and principal coordinate analysis (PCoA) indicated the habitat heterogeneity for the physicochemical parameters and the Apicomplexa community. These results were supported by PERMANOVA (P < 0.001), ANOSIM (P < 0.001), Cluster analysis, and Venn diagram. Dominant apicomplexan parasites in inlet samples were Gregarina (38.54%), Cryptosporidium (32.29%), and Leidyana (11.90%). Outlet samples had Babesia, Cryptosporidium, and Theileria as dominant groups. Surface water samples had Toxoplasma(16%) and a lower relative abundance of Cryptosporidium (8.33%). The next-generation high throughput sequencing covered a wide range of parasites in Egypt for the first time to our knowledge, which could be useful for legislation of the standards for drinking water and wastewater reuse.

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