Phytoplankton Communities Show Low Spatial Congruence Between Morphology‐Based Identification and DNA Metabarcoding

Monitoring tropical freshwater biodiversity is particularly challenging due to the remoteness of many sites, the shortage of trained taxonomists, and the rapid pace of environmental change. To overcome these limitations, it is essential to combine complementary techniques for assessing biological communities.

In this study, we applied DNA metabarcoding and traditional microscopy to investigate phytoplankton communities in floodplain lakes of Central Brazil (Araguaia River), using morphological identification (excluding cyanobacteria) and DNA metabarcoding targeting the 18S rRNA V4 region. We aimed to evaluate spatial congruence between morphology‐based identification and DNA metabarcoding results.

The morphological approach recovered a diverse flora spanning several phyla, with Cryptista and Chlorophyta frequently dominant. Comparisons between methods revealed limited taxonomic overlap at both species and genus levels, with DNA metabarcode detecting many taxa absent from microscopy records, while morphology identified others not recovered molecularly. Ordination‐based analyses showed only modest spatial congruence between the two datasets, despite both targeting the same communities.

Our findings demonstrate that DNA metabarcoding and morphology are not interchangeable surrogates, but rather complementary perspectives on phytoplankton diversity. Integrating both approaches can increase sensitivity to ecological change, broaden taxonomic coverage, and strengthen inferences about the environmental and spatial processes structuring communities in dynamic tropical floodplains. We therefore recommend incorporating DNA techniques based alongside traditional microscopy, while improving reference databases and standardising protocols, to advance tropical freshwater biomonitoring.