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Phytogenic nebkhas formed by shrubs, widely distributed in arid and semiarid ecosystems, commonly results in the patchiness of vegetation and strongly affect the spatial distribution of soil resources. In this study, we investigated the soil nutrient contents (organic matter, total N and P, and available N, P, and K), enzymatic activities (polyphenol oxidase, phosphomonoesterase, dehydrogenase, urease, and protease), and microbial community level physiological profiles for carbon source utilization in varying soil depths in different microsites within nabkhas, under the crown, and outside nabkhas of Caragana microphylla, Atraphaxis manshurica, and Salix gordejevii nebkhas in the western Horqin Sandy Land in Northeast China. Our main objectives were to determine whether "islands of fertility" developed both within and under the crown of the three nabkha types, to test whether the effects of islands of fertility differ among nebkha types, and to study the spatial heterogeneities of soil microbiological properties. Soil nutrients decreased with soil depth and with the distances from the center of each nebkha. The three nebkha types all created spatially heterogeneous patterns of soil nutrient within and around the nebkhas. Island of fertility effect varied among the nebkha types. C. microphylla nebkha had the highest enrichment ratios in soil organic matter and available N and P, whereas A. manshurica had the highest ratios in total N and P, and S. gordejevii had the highest ratio in available K. Phytogenic nebkhas also increased soil enzymatic activities and functional diversity for carbon source utilization of soil microflora. Enzyme activities among the microsites varied with enzyme type and shrub species. Phytogenic nebkhas can be considered major sources of soil nutrient and heterogeneity in microbiological property in the semi-arid ecosystem. Thus, more attentions to the management of phytogenic nebkhas should be considered in ecological restoration practices in semi-arid regions. (C) 2016 Elsevier B.V. All rights reserved.