Résumé
In tropical marine ecosystems, cyanobacteria are key components of phytoplankton communities, yet their diversity and spatio-temporal dynamics in tropical lagoons remain poorly documented. Here, we use the Nouméa lagoon (New Caledonia) as a model system to genetically characterize cyanobacterial communities in a subtropical lagoon subjected to both natural and anthropogenic pressures. Using metabarcoding, we investigated seasonal and spatial variations along environmental gradients, spanning from estuarine zones to oligotrophic reef areas. A single Synechococcus ASV dominated most communities, particularly in nutrient-enriched coastal waters. Beyond this dominant lineage, we uncovered a diverse “minor cyanosphere,” which comprised Synechococcus subclusters 5.1, 5.2, and 5.3, several Prochlorococcus ecotypes, an as-yet-uncultivated group of picocyanobacteria, and various diazotrophic cyanobacteria. This assemblage exhibited spatial structuring, suggesting environmental filtering and thereby underscoring its potential as a bioindicator of water masses in lagoon systems. We also assessed the impact of Cyclone Uesi (February 2020), which triggered shifts in community composition. Floodwaters resulted in an atypical surge of fast-growing estuarine Synechococcus strains, which were subsequently transported to offshore reef zones, as confirmed by buoy tracking. These findings suggest that increasingly frequent cyclones could influence plankton dynamics and, consequently, reef health under climate change scenarios. Overall, this study highlights the complex structuring of cyanobacterial communities in the Nouméa lagoon, shaped by spatial gradients, seasonal changes, and episodic extreme disturbances, and emphasizes the ecological significance of reef passages, which help maintain the trophic gradient within the lagoon following cyclonic events.