Environmental DNA (eDNA) detects temporal and habitat effects on community composition and endangered species in ephemeral ecosystems: A case study in vernal pools

Abstract

AbstractVernal pools are temporary wetlands that can form during a rainy season, often in Mediterranean climates, and serve as ideal testing grounds to understand species detection using eDNA and how biological communities may shift across time and spatial and environmental heterogeneity. Most vernal pools exhibit high plant and animal diversity and endemism, but due to their ephemeral nature, they are understudied, especially their microorganisms. Habitat destruction and fragmentation creates an urgent need to monitor their biodiversity, but traditional species surveys require time and taxonomic expertise. We conducted a community science‐enabled examination of soil environmental DNA (eDNA) in California's Great Central Valley and assessed the capacity of eDNA to aid biomonitoring. We used metabarcoding of16S,ITS1,CO1,18S, andITS2marker regions to quantify and compare differences in pool communities across two sampling periods (during years with disparate precipitation) and to estimate variation among pools and inundation zones (vernal pool bottom, transitional edge, and grassland upland). We found differences in beta diversity among sampling periods, pools, and inundation zones; alpha diversity was mainly affected by sampling period and zone, but this differed by marker. Numerous taxonomic families varied in abundance and composition among samples, yet vernal pool communities remained distinct from upland grass communities, even between sampling periods differing by 1 year. Turnover in ecologically co‐occurring taxon pairs varied by over 90% between sampling periods in all metabarcodes but plants, which were more stable. Finally, we confirmed substantial concordance between eDNA and traditional inventories of the reserve's plants and presented a case in which we detected one endangered plant species, Colusa grass (Neostapfia colusana), in advance of its emergence. This initial study adds hundreds of new taxon records for California vernal pools and discusses benefits and challenges of using eDNA for biomonitoring within stressful, temporary, or otherwise challenging ecosystems.