Removal of organic biomass in Eucalyptus plantations has a greater impact on fungal than on bacterial networks

Complex and stable soil microbial networks are essential for productivity in plantation forestry, but their response to disturbances from harvesting and replanting is not well understood. This study assessed the impact of treatments designed to mitigate these disturbances on microbial biodiversity and networks in Eucalyptus plantation soils at three South African sites. We used high-throughput sequencing to catalogue fungal and bacterial biodiversity from 108 soil samples across three treatments: (i) retention of harvest residues (retained), (ii) removal of residues (removed), and (iii) removal of residues with added fertilizer (fertilized). Bioinformatic and statistical analyses of the sequence data revealed treatment-specific variations in microbial OTU richness, network structure and taxon associations at order-level. Microbiome richness was highest in ‘retained’ plots, and treatment-specific microbial diversity was evident in both fungal and bacterial communities. Network comparisons revealed that treatments to mitigate disturbances caused by harvesting significantly affected fungal networks but not bacterial networks. Fungal networks in ‘retained’ plots exhibited the highest complexity and stability compared to plots where the entire crop was removed. However, bacterial networks did not show significant differences in network structure among treatments. The associations between fungal and bacterial nodes were consistent in the three treatments, as indicated by similar Jaccard indices. However, distinct fungal hub nodes were found when comparing the 'retained' and 'removed' treatments. These findings highlight that retaining harvest residues enhances microbial richness and stabilizes fungal networks, making it a better strategy for managing soil disturbances than residue removal or fertilization. • Retaining residues enhances fungal diversity more than removal or fertilization. • Fungal networks respond strongly to treatment; bacterial ones remain stable. • Residue retention fosters complex, stable fungal networks vs. residue removal. • Bacterial networks show minimal structural shifts across all treatments. • Fungal hub nodes differ by treatment; bacterial associations stay consistent.