Sedimentary ancient DNA reveals rhizosphere-like plant–microbe association signals in a 2-million-year-old Arctic ecosystem

Plant–microbe interactions in the rhizosphere are central to nutrient cycling and ecosystem functioning. Sedimentary ancient DNA (sedaDNA) is a promising yet underexplored tool for reconstructing past microbial communities and investigating ecological interactions among plants, animals, and microorganisms. Here, we reanalyse the previously published Kap København Formation (Northern Greenland) sedaDNA dataset to move beyond taxonomic ecosystem reconstruction and test whether ancient sediments preserve structured, rhizosphere-compatible plant–microbe association signals. Our results show that this ancient boreal ecosystem hosted several rhizosphere-associated taxa, comparable to those in modern boreal soils. Several bacterial genera co-occurred repeatedly with specific plant families, forming a rhizosphere-like taxonomic core with predicted plant-growth-promoting traits related to nutrient acquisition, colonisation, and stress tolerance. Although sedaDNA co-occurrence cannot demonstrate direct symbiosis, the consistency of taxonomic, network, and functional signals suggests that ancient sediments preserve interconnected ecological structure. Our findings extend sedaDNA-based ecosystem reconstruction beyond taxonomy and provide a possibility for investigating plant–microbe association signals in deep time.