Benefits of combined environmental DNA and microscopy for diversity monitoring in rotifer community: A mesocosm experiment

Abstract

Rotifers are crucial for the monitoring of aquatic ecosystems because of the sensitive response of rotifer community structure to environmental changes. Comparisons and combinations of meta-barcoding (sequence analysis) and traditional morphological identification for rotifer community responses are rare. To better understand the differences between the two approaches, we conducted a study using 48 mesocosms (2500 L) and a combination of warming, nutrient loading, and pesticide to evaluate the applicability of both methods to rotifer communities in order to better understand how rotifer communities respond to multiple environmental stressors. The findings demonstrated that the degree of matching between both techniques was limited, despite the fact that there was a substantial positive association between the morphology abundance determined by morphological identification and the sequence abundances determined by eDNA metabarcoding. Although the two methods had similar responses to various environmental stresses, sequence analysis can identify rotifers that are difficult to identify with traditional methods such as Bdelloidea, while classical morphological methods were more suitable for assessing the effects of various environmental changes on rotifer communities. This study provided valuable implications for monitoring and managing aquatic ecosystems since it enables us to spot changes in the rotifer community structure early on and take the necessary precautions to safeguard these sensitive ecosystems.