Seasonally and niche-differentiated diversity of active, dormant and dead microbes in coastal waters and surface sediments

Metabarcoding surveys have rarely discriminated metabolically active, dormant, and dead microbes in environmental samples. This study employed a triple metabarcoding approach targeting environmental 16S and 18S rRNA genes and their transcripts to investigate the diversity of these physiologically distinct assemblages in the water column and surface sediments of a tropical coastal region. We found that dead bacteria, archaea, and microeukaryotes (relic DNA) accounted for ≤5% of the planktonic DNA pools but significantly contributed to ASV richness (53%, 50%, and 32%, respectively), while dominating in sediments (44% of sequence, 80% of richness). In viable assemblages, dormant microbes were rarer but enriched richness, particularly in the water (20%, 62%, and 28%, respectively). Collectively, the proportions of microbes in different physiological states exhibited niche-specific and seasonal patterns, primarily driven by pH and temperature. Significant differences in richness and assemblage composition were observed between water, sediment, and seasons for all physiological fractions. Active microbial communities responded to distinct environmental drivers compared to DNA-characterized assemblages, suggesting that DNA-based methods may misidentify factors driving functional diversity in biogeochemical cycles. Dormant taxa exhibited a broader taxonomic distribution than previously recognized, underscoring the need for further research on microbial ecophysiology, function, and biogeography across temporal and spatial scales.