Abstract
Illumina sequencing is a representative tool for understanding the massive diversity of microbial eukaryotes in natural ecosystems. Here, we investigated the eukaryotic community in a pond (salinity of 2–4) on Dokdo (island) in the East Sea, Korea, using Illumina sequencing with primer sets for the V4 and V9 regions of 18S rDNA from 2016 to 2018 for the first time. Totally, 1,413 operational taxonomic units (OTUs) and 915 OTUs were detected using the V9 and V4 primer sets, respectively. Taxonomic analyses of these OTUs revealed that although the V4 primer set failed to describe the extant diversity for some major sub-division groups, the V9 primer set represented their diversity. Moreover, the rare taxa with <1% of total reads were exclusively detected using V9 primer set. Hence, the diversity of the eukaryotic community can vary depending on the choice of primers. The Illumina sequencing data of the V9 region of 18S rDNA may be advantageous for estimating the richness of the eukaryotic community including a rare biosphere, whereas the simultaneous application of two biomarkers may be suitable for understanding the molecular phylogenetic relationships. We strongly recommend both biomarkers be used to assess the diversity and phylogenetic relationship within the eukaryotic community in natural samples.
Highlights
Illumina sequencing is a representative tool for understanding the massive diversity of microbial eukaryotes in natural ecosystems
Several studies on the diversity of eukaryotes noted that the V1–V2, V3, V4, and V9 regions of 18S rDNA have been used for better understanding the massive diversity of microbial community[9,10,11]
Based on an in silico analysis, the V9 region of 18S rDNA offers the advantage to reveal the extant diversity of eukaryotes, whereas the V4 region of 18S rDNA is commonly used for studying the phylogenetic relationship of eukaryotes[14]
Summary
Illumina sequencing is a representative tool for understanding the massive diversity of microbial eukaryotes in natural ecosystems. Based on an in silico analysis, the V9 region of 18S rDNA offers the advantage to reveal the extant diversity of eukaryotes, whereas the V4 region of 18S rDNA is commonly used for studying the phylogenetic relationship of eukaryotes[14] Despite these advantages of both V4 and V9 regions of 18S rDNA, multiple primer sets have been employed rarely for environmental samples[15,16,17]. Fundamental interrogations remain unanswered regarding the region of 18S rDNA that is appropriate to describe the diversity and phylogenetic relationship of the dominant or rare eukaryotic groups using the Illumina platform in field surveys, of brackish water. The V4 region that is longer than the V9 region is appropriate to explain the previous evolutionary relationship of eukaryotes
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
