Abundant taxa can better indicate seasonal and depth variations of pelagic microbial communities in the tropical open ocean

Understanding seasonal and depth variations of microbial communities is essential to predict the impact of climate change on pelagic ecosystem. Unfortunately, a major barrier to this knowledge is that long-term deployed automated equipment meets the low-cost requirement for obtaining time-series data in pelagic oceans far from land, but these techniques hardly obtain diversity data covering the whole community. To test whether monitoring abundant taxa can better capture variations of pelagic microbial communities in the tropical open ocean, the seasonal and depth variations of prokaryotic and microeukaryotic communities throughout the water column over three seasons were studied using 16S rRNA and 18S rRNA gene amplicon sequencing in the western Pacific Warm Pool, where is the most stable open ocean marine environment on earth. Our results showed that photic and aphotic layers were comprised of distinct microbes, and seasonal changes of microbes occurred at all depths, which were strongest at 200 m. Specificity and occupancy indicated that most of seasonal or depth specialists were abundant taxa. The community similarity distributions of abundant taxa and the whole microbial community were similar, while that of rare taxa was completely different. These results suggested abundant taxa can better indicate seasonal and depth variations of pelagic microbial communities compared to rare taxa, which provide a basis for the future development of autonomous platforms for long time-series monitoring of microbial community dynamics using a minimal number of taxa.