Shifts in Straw-Associated Functional Microbiomes Under Long-Term Soil Management

Long-term soil fertility is governed by the metabolic plasticity of microbial communities, particularly during the decomposition of crop residues. This study investigated the straw-associated functional microbial profile associated with straw decomposition under the influence of 62 years of continuous management with mineral fertilization and liming. Using the Biolog EcoPlateTM approach combined with a modified litter-bag protocol, we assessed shifts in metabolic activity patterns of functional guilds and groups. PERMANOVA results revealed that the interaction between liming and fertilization (p < 0.05) was the primary driver of divergence in functional communities, rather than the individual effect of factors. Long-term treatments induced a significant reconfiguration of the functional niche, shifting from the native, generalist microbiome to specialized communities in treated variants, with carbohydrate (CH) guilds as dominant and indicators of community performance. Moderate levels of liming (L1) stimulated metabolic activity and maintained higher functional diversity across amino acid (AA) and polymers (Px) guilds. Intensive liming (L2), in contrast, restricted the activity of most microbial functional groups and favored amine (AM) and carboxylic acid (CX) guilds. Shifts from a generalist microbiome in native soil to specialized communities in treated soils show the capacity of microorganisms to adapt efficiently under agronomic management.