Journal Article

Unraveling Long‐Term Microsporidia Diversity and Dynamics in Lake Aydat (France) Through Paleogenomics

Monjot, Arthur, Chauvet, Marina, Lepère, Cécile, Combes, Léa, Moreau, Carol, Moné, Anne‐Isabelle, Pont, Caroline, Diogon, Marie

2026

Overview

Despite their ubiquity, the diversity and dynamics of Microsporidia in aquatic ecosystems have long been overlooked. Here, we applied 18S rRNA gene metabarcoding targeting the V1‐V3 region for Microsporidia and V4 region for other eukaryotes to sedimentary ancient DNA to reconstruct the temporal dynamics of Microsporidia and their eukaryotic hosts over the past 138 years in Lake Aydat (France). We detected remarkably high microsporidian diversity, with 1976 Operational Taxonomic Units (OTUs). However, 54% of these OTUs could not be assigned at the genus level, indicating substantial, as yet undescribed diversity. The remaining OTUs were affiliated predominantly with three genera: Crispospora, Pseudoberwaldia, and Vittaforma. Despite only one formally described species in each of these genera, we show a high species‐level diversity forming putative freshwater lake‐specific clades, which are likely associated with new hosts. Using co‐occurrence network analysis combined with published host records, we identify rotifers as candidate reservoirs for lacustrine Microsporidia. The microsporidian community underwent substantial temporal changes, marked by a major turnover in the early 2000s. This shift coincides with decades of strong anthropogenic pressure on Lake Aydat, including untreated sewage inputs, nutrient enrichment from agro‐pastoral activities, and wetland destruction. As obligate intracellular parasites, Microsporidia are tightly linked to the ecology and population dynamics of their hosts, suggesting that the observed community shifts primarily reflect changes in host communities. Sedimentary ancient DNA study revealed 138 years of hidden microsporidian (unicellular eukaryotic parasite) diversity and host–parasite dynamics in a freshwater lake. A major community shift in the 2000s, linked to anthropogenic pressures, shows how paleogenomics reveals the diversity and long‐term ecological trajectories of these previously overlooked aquatic parasites.

• Publisher: John Wiley & Sons, Inc,John Wiley & Sons Inc,Wiley
• Subject: Aquatic ecosystems / Biodiversity and Ecology / Deoxyribonucleic acid / DNA / Dynamics / Ecology, environment / Environmental Sciences / Eukaryotes / Freshwater lakes / Genera / lake / Life Sciences / metabarcoding / Microbiology and Parasitology / Microsporidia / Network analysis / Nutrient enrichment / paleogenomics / Parasites / Parasitology / Plankton / Population dynamics / rRNA 18S / SedaDNA / Sediments / Sewage / Species diversity / Symbiosis