Soil microbial communities shift from plant- to microorganism-derived resources under resource limitation

Soil microorganisms are central for soil functioning and decomposition in the biosphere, but trophic positions of microorganisms in soil food webs are still poorly understood due to methodological challenges. Here, we designed a microbial decomposition experiment with detritus of different quality (based on C and N stoichiometry) and quantified the trophic position and resource use of saprotrophic microbial communities growing on high-quality detritus acquired essential amino acids primarily from autotrophic (plant) sources, while communities using compound-specific amino acid stable isotope analysis. Contrary to the common assumption of saprotrophic microorganisms as primary decomposers at trophic position two, both bacteria and fungi consistently occupied higher trophic positions (on average: 2.36 ± 0.21) which further increased under nutrient-limited soil conditions. microorganisms growing on low-quality detritus derived most amino acids from heterotrophic (microbial) sources. Bacteria relied more on plant-derived compounds than fungi (44.1% vs. 18.1%), indicating less de novo synthesis of amino acids. Overall, our study emphasizes that saprotrophic microorganisms in soil food webs should not be viewed merely as primary decomposers relying exclusively on leaf litter. Rather, their trophic position depends on the shifting between plant- and microbe-derived resources across the gradient of detritus quality, which needs to be considered when modelling soil food webs.