Microbial diversity in sediments and soils is exceptionally high, and changes in their activity and physiological states play critical roles in the biogeochemical cycling of key nutrients, as well as in ecosystem resilience and recovery. Existing studies have revealed that sediments and soils contain a substantial number of dead cells, incompletely degraded extracellular DNA, and cells that are still alive but not physiologically active (dormant cells). Consequently, sequencing based on directly extracted environmental DNA (eDNA) can overestimate microbial diversity, potentially leading to biases in functional predictions and introducing significant uncertainty into assessments of the ecological impacts of global change.

    We have proposed a novel approach for parallel sequencing and integrated analysis of eDNA, eRNA, and propidium monoazide (PMA)-treated eDNA from environmental samples, termed the “Triple-Metabarcoding Analysis” (TMA), which is designed to identify the active, dormant, and dead microbes, as well as their community composition and dynamics in environmental samples (Deng et al. 2024, Environmental Microbiology). Application of the TMA method revealed that both dead and dormant eukaryotic microbes constitute a significant proportion in intertidal sediments. More recently, we investigated further the effects of warming on the diversity and dynamics of active and dormant bacteria and microeukaryotes using the TMA method and based on a laboratory-based warming simulation experiment of mangrove sediments. The main findings are as follows: