Quantitative stable isotope probing (qSIP) and cross-domain networks reveal bacterial-fungal interactions in the hyphosphere.

Background: Interactions between fungi and bacteria have the potential to substantially influence soil carbon dynamics in soil, but we have yet to fully identify these interactions and partners in their natural environment. In this study, we stacked two powerful methods, ¹³C quantitative stable isotope probing (qSIP) and cross-domain co-occurrence network, to identify interacting fungi and bacteria in a California grassland soil. We used in-field whole plant ¹³CO₂ labeling along with sand-filled ingrowth bags (that trap fungi and hyphae-associated bacteria) to amplify the signal of fungal-bacterial interactions, separate from the bulk soil background.

Results: We found a total of 54 bacterial ASVs and 9 fungal OTUs that were significantly ¹³C-enriched. These were saprotrophic and biotrophic fungi, and motile, sometimes predatory bacteria. Among these, 70% of all ¹³C-enriched bacteria identified were motile. Notably, we detected fungal-bacterial network links between a fungal OTU of the genus Alternaria and several bacterial ASVs of the genera Bacteriovorax, Mucilaginibacter, and Flavobacterium, providing empirical evidence of their direct interactions through C exchange. We observed a strong positive co-occurrence pattern between predatory bacteria of the phylum Bdellovibrionota and fungal OTUs, suggesting the transfer of C across the soil food web.

Conclusions: To date, our ability to associate microbial co-occurrence network patterns with biological interactions is limited, but the incorporation of qSIP allowed us to more precisely detect interacting partners by narrowing in on the taxa that were actively incorporating plant-fixed, fungal-transported labeled substrates. Together, these approaches can help build a mechanistic understanding of the complex nature of fungal-bacterial interactions in soil.