Spatial structuring dominates over seasonality in tropical coastal microbiomes: Insights from New Caledonia's Indo‐Pacific lagoon

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Abstract Tropical coastal ecosystems harbor diverse microbes essential for biogeochemical cycling and serve as sentinels of environmental change. However, microbial community profiles remain largely undocumented across the Southwest Pacific. We investigated bacterial communities in coastal and lagoonal waters surrounding Nouméa, New Caledonia, an area under increasing urban pressure. Our objective was to determine whether spatial heterogeneity or seasonal variation primarily structures these communities and how anthropogenic activities shape microbial diversity. Forty‐two seawater samples were collected from seven sites spanning anthropized bays, mangrove estuaries, and offshore lagoon waters during hot and cold seasons. We found that spatial gradients explained significantly more variation in community structure ( R 2 = 0.25) than seasonal changes ( R 2 = 0.04), revealing distinct microbial signatures along the land‐to‐sea continuum. Coastal and mangrove sites harbored more copiotrophic taxa and elevated levels of predicted pathogen‐associated functional pathways, though these predictions are based on 16S rRNA data, and require validation with metagenomic or functional assays. Seasonal shifts mainly involved Cyanobacteria ( Synechococcus ↑, Prochlorococcus ↓ in warm season) and archaeal Marine Group II, reflecting temperature‐mediated niche partitioning. This study establishes the first spatial and seasonal microbial inventory for New Caledonian coastal ecosystems, suggesting associations between anthropogenic influence and microbial community health. Spatial dominance highlights the potential value of local management, while temperature sensitivity of key taxa underscores the importance of integrating microbial monitoring into coastal conservation and One Health frameworks.

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