eDNA Metabarcoding Provides Accurate Quantitative Surveys of Sponge Communities
Here, we evaluated DNA barcoding and environmental DNA (eDNA) metabarcoding of the internal transcribed spacer 2 (ITS2) region as a non-invasive alternative to traditional collection-based surveys for freshwater sponge monitoring in a Piedmont watershed in northern Virginia, USA. We conducted parallel surveys by 1) collecting small tissue samples for morphology-based identification and DNA barcoding from 184 sponges and 2) collecting 33 contemporaneous eDNA water samples from the same sites. Only 27 (14.7%) possessed the gemmules necessary to identify species by morphology, whereas nearly all 182 (98.9%) were successfully identified by DNA barcoding. eDNA and collection-based surveys recovered highly similar community composition (Mantel r = 0.722, p = 0.0015), while eDNA typically detected greater species richness at each site. Notably, eDNA detected Trochospongilla horrida at five sites despite its complete absence from the collected specimens, highlighting the ability of eDNA to reveal rare or cryptic taxa. Sequence read proportions were strongly correlated with observed relative sponge abundance across species and sites (Nakagawa R2 = 0.94, p < 0.001), demonstrating that metabarcoding provides informative estimates of relative species abundances. Turbidity was a strong ecological correlate of sponge diversity and composition, regardless of survey method. A conspicuous lack of sponges was observed immediately downstream of a historic pyrite mining site, though cause could not be determined from available data. Environmental DNA metabarcoding provides a rapid, non-destructive, and effective alternative to traditional freshwater sponge surveys, yielding comparable or improved species detection while accurately reflecting quantitative sponge community composition.