Integrating pyrogenic carbon, organic residues, and soil fauna offers a promising strategy to improve soil fertility in tropical agroecosystems, inspired by the persistent fertility of Terra Preta de Índio (TPI; Amazonian Dark Earth). Here, we evaluated the individual and combined effects of biochar, manure, and the earthworm Pontoscolex corethrurus on bacterial communities across bulk soil, maize roots, and earthworm gut in a factorial pot experiment using an acidic, inherently nutrient-poor tropical Latosol as a model soil. High-throughput 16S rRNA gene sequencing revealed strong compartmentalisation of bacterial communities, while also identifying a prevalence-defined core shared across compartments that accounted for 75.4% of total sequence abundance despite limited taxonomic overlap.
Responses to experimental factors were strongly compartment-dependent. In bulk soil, manure was the principal driver of bacterial community composition through shifts in pH and nutrient availability, whereas earthworms increased exchangeable Fe and restructured microbial networks toward greater modularity. Root-associated communities were comparatively buffered, whereas the earthworm gut remained responsive to manure, and biochar altered gut network topology. Crucially, the stacked TPI-inspired treatment (TPI mix), combining biochar, manure, earthworms, and maize, generated non-additive microbial trajectories and emergent community states across compartments. These microbial shifts were accompanied by improved functional outcomes: while manure was the only individual factor to enhance maize growth, the stacked TPI mix produced the strongest overall response. Bradyrhizobium emerged as a key indicator taxon, reaching high relative abundance in both soil and earthworm gut under the integrated treatment. Our findings show that TPI-inspired amendment strategies can reorganise microbiomes across the soil–root–fauna continuum, with implications for soil biological functioning and fertility improvement in low-fertility soils.
