Bridging the Gap: Integrating DNA Metabarcoding and Microscopy to Assess Benthic Diatoms and Their Environmental Drivers in a Mountain Lake of the Alps

Metabarcoding is increasingly used for monitoring, but its usefulness for assessing benthic diatom diversity in mountain lakes is poorly understood, especially for Italy. We assessed benthic diatom diversity in Upper Lake Balma (2204 m asl; North-Western Alps; Italy) using microscopy and metabarcoding (amplicon sequence variants—ASVs—of the rbcL gene) during July and October 2021. We found a higher diversity with metabarcoding than with microscopy but metabarcoding missed taxa detected with microscopy and vice versa. The application of a correction factor based on biovolume to the metabarcoding dataset did not markedly improve the similarity between the methods. With metabarcoding, only 53% of ASVs were identified to the species level. Metabarcoding indicated good water quality, whereas microscopy indicated high quality. Among ecological guilds, diatoms of the guild high-profile dominated in July and October with both methods. Similarly, monthly differences linked to similar environmental variables (pH, temperature, conductivity) were indicated by multivariate ordination based on the abundance of ASVs and taxa-MICROSCOPY, respectively. The vast occurrence of diatom taxa classified as worthy of protection emphasized the ecological value of the lake. Unless reference databases reflect diversity of the mountain lakes, we suggest the complementary use of both methods to comprehensively assess benthic diatom diversity.