Hydrogenotrophic methanogenesis and distinct microbial assemblages fostered by dauciform roots of Cladium jamaicense

Nutrient availability regulates ecosystem processes, and plant roots strongly influence nutrient cycling through microbial interaction in the rhizosphere. In the extremely phosphorus-limited Florida Everglades, Cladium jamaicense (sawgrass) develops specialized roots, called dauciform roots, which release carboxylates that mobilize soil-bound nutrients. Although methanogenesis is a well-documented process in wetlands, the composition of methanogenic communities across separate root-associated compartments is not as well characterized. We investigated microbial community composition and predicted functional pathways across bulk soil, the general rhizosphere soil, and the rhizosphere of dauciform roots in calcareous (marl) soils near Everglades National Park. Functional predictions were inferred from 16SrRNA gene data using PICRUSt2 with taxonomic assignments referenced against SILVA v138.2 using rANOMALY. Alpha and beta community analyses revealed significant differences among compartments. Dauciform roots harbored the lowest Shannon diversity, whereas bulk soils supported the most distinct assemblages. Microbial communities clustered strongly by compartments, with compartment identity explaining 66% of the variation (p = 0.001). Pairwise comparisons showed the strongest separation between bulk and dauciform soils. Furthermore, functional predictions showed enrichment of hydrogenotrophic methanogenesis sequences in dauciform roots, while acetoclastic methanogenesis was most abundant in rhizosphere soils further emphasizing their distinct communities. Our preliminary results demonstrate that root-associated compartments foster distinct microbial assemblages with implications for key ecosystem processes, including methanogenesis. These findings highlight how root traits in oligotrophic systems influence carbon cycling and potential methane pathways, contributing to broader insights into microbial community assembly and ecosystem processes in nutrient-limited wetlands. HighlightsO_LIFirst genomic investigation of the dauciform root rhizosphere. C_LIO_LIRoot & dauciform rhizosphere harbor microbial communities distinct from bulk soil. C_LIO_LIPredicted enrichment of hydrogenotrophic methanogens in dauciform roots. C_LI