Meiofauna investigation and taxonomic identification through imaging—a game of compromise

Abstract Imaging methods have developed rapidly in recent decades, opening new opportunities for taxonomy and biodiversity studies of marine organisms. In particular, the microscopic size range, which used to be challenging to study due to time‐consuming preparation and observation steps, now benefits from high‐throughput quantitative imaging methods and the development of fast high‐resolution microscopy approaches. Meiofauna, interstitial sediment animals ranging from 20 μ m to 1 mm, are important components of ecosystems. These organisms can serve as bioindicators, and the group as a whole holds immense potential for the discovery of new species. However, protocols for studying meiobenthos are highly time‐consuming, which helps explain why this group is understudied. We tested five imaging techniques, ranging from low to high resolution, that could accelerate hard‐bodied meiofauna studies, both for ecology and species description, and address the gap in our understanding of this part of marine life. Thus, two flow imaging modalities (in line holographic microscopy and classic optic microscopy), a semi‐automated microscopy acquisition procedure, and two three‐dimensional (3D) fluorescence microscopy protocols were used. We examined the classic compromises of imaging, including resolution, throughput, and data volume, to evaluate the potential benefits of using such techniques for meiofaunal studies. For ecological surveys, flow imaging could benefit meiobenthos studies, but resolution remains a limiting factor. For taxonomic description, 3D fluorescent imaging added relevant information, considering the time required for preparation and acquisition. The semi‐automated motorized microscopy procedure could be used for both purposes according to the versatility of the system.