High-throughput amplicon sequencing of microscopic kelp gametophytes from benthic eDNA samples

Kelps have a complex life-history where the microscopic gametophyte phase alternates with the forest-forming sporophyte phase. Though microscopic, gametophytes are shown to be resilient to environmental stressors. However, gametophytes are notoriously hard to study in-situ, which creates many uncertainties surrounding their life expectancy and their ability to create a long-lived seed bank that could preserve a population. We have developed a genetic monitoring tool that estimates gametophyte densities through the collection of environmental DNA (eDNA) and high-throughput amplicon sequencing. Because eDNA methods can only estimate species presence-absence, we have devised a numerical maximum likelihood approach to estimate the number of gametophytes most likely to have produced observed counts of unique microsatellite alleles. The method is akin to forensic analyses of crime scenes, where multiple suspects are identified from contaminated DNA.