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Globally, Jatropha curcas is a potential bio‐fuel crop and can grow on wastelands without competition with food crops. However, little is known about its fertilizer management and soil quality. This study investigated the effects of nitrogen (N) applied through urea fertilizers and organic manures (farm yard manure (FYM) and Jatropha cake) on soil nutrient availability, microbial communities, and enzymes activities in Jatropha plantation. Treatments examined were 140 kg N ha−1 through (i) urea (100% N); (ii) Jatropha cake (100% N Jatropha cake); (iii) FYM (100% N FYM) and (iv) 70 kg N ha−1 through urea (50% N) during four years. A 100% nitrogen addition by urea fertilizers significantly increased available N, whereas available phosphorus was significantly higher in cake‐amended soil. Phospholipid fatty acid (PLFA) analysis was used to assess changes in microbial biomass and soil microbial community structure. Higher concentrations of total PLFA, Gram‐positive, Gram‐negative bacterial, and actinomycetes PLFAs were observed in cake, FYM, and 50% N treatments compared to 100% N by urea fertilizers. The fungal PLFA concentration was significantly greater with cake‐amended soil. Nonmetric multidimensional scaling analysis of PLFA profiles for soil microbial community shift showed that 100% N urea fertilizer treatment was significantly different from other treatments. Microbial biomass C and enzyme activities (β‐glucosidase and alkaline phosphatase enzymes) were significantly enhanced by organic manure amendments (cake and FYM) compared to urea fertilizers (50 and 100% N). The study shows that N supplied by organic manures significantly affected the soil microbial community, and had positive effects in enhancing the microbial diversity and activity.

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