Agricultural expansion in Sub-Saharan Africa is characterized by different farm ages in smallholder communities. This study investigated changes in microbial indices broadly (i) at the reconnaissance survey level in four agro-ecological zones and (ii) in different farms at the forest (Dompem) and forest–savanna transition (Adansam) zones, as influenced by the duration of cultivation. Soils from one-year (first cultivation of cleared forest/fallow), three-year, five-year, and ten-year farms were analyzed for basic soil properties, active or labile carbon (POXC), basal respiration (BR), microbial biomass (Cmic) using permanganate oxidizable C, alkali trap, and chloroform fumigation incubation. In both study levels, POXC content was <1% of soil organic carbon (SOC) in all zones, higher in the wet agro-ecological zones, and positively correlated with SOC (r = 0.70, 0.81; p < 0.01, p < 0.001). Dompem SOC and BR declined by 1–23% and 6–25% (p < 0.001), respectively, in the first three years; Cmic (p = 0.002) and %Cmic/SOC (p = 0.610) decreased from three-year farms onwards. Conversely, the Adansam SOC, BR, Cmic, and %Cmic/SOC rather had irregular trends. The microbial indices were influenced by exchangeable acidity, the sum of exchangeable bases, and effective cation exchangeable capacity negatively or positively, followed by SOC, pedogenic compounds, particularly dithionite-citrate iron (Fed), oxalate iron (Feox), and lastly, soil pH. Therefore, understanding the degree, direction, and changing aspects of these drivers of soil ecosystem services is necessary for sustainable soil management practices in different agro-ecological zones.
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