Microbial diversity, functional potential, and antimicrobial resistance across soil depth in fire-affected rotational shifting cultivation soils

Information from the abstract

Abstract Charcoal-rich surface hosts distinct, low-evenness microbiome. Nitrogen-fixing taxa peak in the nutrient-leaching layer. Sharp vertical shift from copiotrophs to oligotrophs with depth. Surface soils act as hotspots of methane and nitrogen transformations. AMR genes persist across depths without anthropogenic inputs. Fire is a recurring disturbance in rotational shifting cultivation (RSC) system, yet the depth-related organization of soil microbial communities in these systems remains poorly understood. This study investigated microbial diversity, functional potential, and antimicrobial resistance (AMR) in relation to soil depth and fire legacy in fire-affected RSC soils of northern Thailand using metagenomic sequencing. Soil samples were collected from three depth layers: the charcoal-mixed surface (CS, 0–2 cm), nutrient-leaching (N, 10–20 cm), and deep (D, 100 cm) horizons. Results revealed significant depth-dependent variation in soil physicochemical properties, microbial diversity, and taxonomic composition. The CS layer exhibited higher nutrient content and metabolic activity but lower Shannon diversity and evenness compared with deeper soils. Actinomycetota and Bacillota dominated surface soils, while Acidobacteriota and Pseudomonadota were enriched in subsoils, indicating a transition from copiotrophic to oligotrophic communities with increasing depth. Functional gene profiles (COG and KEGG) demonstrated strong vertical differentiation: surface soils were enriched in genes for amino acid metabolism, nutrient transport, and energy production, whereas deeper layers showed higher abundances of genes associated with DNA repair, replication, and stress tolerance. Functional genes linked to carbon, nitrogen, sulfur, and phosphorus cycles displayed clear stratification, with surface layers supporting greater biogeochemical activity. AMR genes, particularly those conferring resistance to Rifamycin, Macrolide , and Glycopeptide antibiotics, were most abundant in the D horizon. These patterns were observed in fire-affected RSC soils and are associated with both soil depth and fire legacy, and may reflect microbial responses to environmental stress conditions.

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Related topics: Soil Carbon and Nitrogen Dynamics · Fire effects on ecosystems · Microbial Community Ecology and Physiology