NatureMetrics has detected European otter (Lutra lutra), neotropical otter (Lontra longicaudis), and giant river otter (Pteronura brasiliensis) from water samples using our vertebrate or mammal metabarcoding assays. We have also identified otters from their spraints, and can analyse spraints to understand otter diet (including vertebrate and invertebrate prey) using metabarcoding.
However, detection rates for these species are low relative to how much time they spend in water. Otters deposit spraint outside of water on riverbanks, logs and rocks, and use latrines associated with caves and dens. Spraint may get washed into water if heavy rainfall occurs and/or water levels rise, but the likelihood of this is unknown. Furthermore, otter fur is very dense so they may not shed much hair into the water either. Although otters hunt in water, they tend to take their prey back to shore to eat, so DNA from saliva/prey remains is also unlikely to be deposited in water. Finally, these mammals have large territories and tend to be solitary apart from mating and rearing pups.
High sampling effort across a number of waterbodies and in different seasons is needed to maximise chances of otter detection.