Hydrological seasonality shapes microbial biomass and diversity in an equatorial estuarine mangrove

Abstract Mangroves are pantropical marine forests rooted in soft sediments and subject to pronounced seasonal variability. However, the effects of these hydrological fluctuations on root‐associated prokaryotic communities remain poorly understood, particularly in underexplored regions like the Guianas. In light of increasing climatic extremes, we investigated microbial responses to contrasting hydrological regimes in the Cayenne Estuary (French Guiana), using the exceptionally warm 2017 dry season and the record‐wet 2022 La Niña season as case studies. We combined sediment biogeochemical profiling with 16S rRNA gene amplicon sequencing, quantification of bacterial and archaeal 16S rRNA gene copies, and molecular microbial biomass. Results revealed pronounced seasonal shifts. Wet‐season sediments were highly reduced and supported up to three times microbial biomass and a tenfold increase in bacterial abundances. Contrastingly, they showed a steep decline in archaeal abundances. Functional shifts affected core taxa, including methanogens and anammox‐bacteria. Redundancy analysis notably revealed linear relationships between prokaryotic beta‐diversity and meiofauna density. In contrast, dry‐season sediments harbored more spatially structured communities dominated by archaeal taxa adapted to nutrient‐limited, stable microhabitats. Co‐occurrence network topology highlighted seasonally distinct ecological structures: a larger, interconnected network in the wet season vs. modular, site‐specific communities during the dry season. These findings indicate reduced microbial dispersal and increased niche partitioning under tidally dominated conditions. This study offers new insights into the response of prokaryotic assemblages to hydrological dynamics modulated by seasonality in estuarine mangroves of the Guiana Shield and has broader implications for understanding microbial dynamics in global estuarine systems under future climate change scenarios.