Succession of Bacteria and Archaea Within the Soil Micro-Food Web Shifts Soil Respiration Dynamics

Bacterivorous nematodes are important grazers in the soil micro-food web. Their trophic regulation shapes the composition and ecosystem services of the soil microbiome, but the underlying population dynamics of bacteria and archaea are poorly understood. We followed soil respiration and 221 dominant bacterial and archaeal 16S rRNA gene amplicon sequencing variants (ASVs) in response to top-down control by a common bacterivorous soil nematode, Acrobeloides buetschlii, bottom-up control by maize litter amendment and their combination over 32 days. Maize litter amendment significantly increased soil respiration, while A. buetschlii addition caused an earlier peak in soil respiration. Underlying bacterial and archaeal population dynamics separated into five major response types, differentiating in their temporal abundance maxima and minima. In-depth analysis of these population dynamics identified a broad imprint of A. buetschlii grazing on dominant bacterial (Acidobacteriota, Bacteroidota, Gemmatimonadota, Pseudomonadota) and archaeal (Nitrososphaerota) ASVs. Combined bottom-up control by maize litter and top-down control by A. buetschlii grazing caused a succession of soil microbiota, driven by population changes first in the Bacteroidota, then in the Pseudomonadota and finally in the Acidobacteriota and Nitrososphaerota. Our results are an essential step forward in understanding trophic modulation of soil microbiota and its feedback on soil respiration.