A large area of desert land in the desert-oasis ecotone in northwestern China is being reclaimed for continuous cotton production for several decades. However, little is known about the possible effect of reclamation and long-term monocultural cotton cultivation on soil properties and microbial communities in the desert-oasis ecotone area.

Soil samples were collected from the 0–20-cm mineral soil from croplands that had been continuously planted cotton for 5, 25, and 50 years after reclamation, as well as a desert land (t?=?0, before reclamation, used as the control). Soil physical and chemical properties, enzyme activities, and bacterial and fungal community diversities were determined.

Soil organic carbon, total nitrogen, and enzyme activities increased up to 25 years after reclamation, and further monocultural cotton cropping was not beneficial to improve soil quality. Soil urease, alkaline phosphatase, and sucrase activities increased by 121~205%, 100~167%, and 206~719% in croplands as compared with the desert land, respectively, after reclamation with the highest value at 25 years of cotton cultivation. Bacterial richness and diversity increased from desert land to the 5-year-old cropland and then remained stable after 5 years of cotton cropping, and soil fungal richness and diversity were not affected by reclamation and cropping years.

Crop rotation or fallow should be considered to maintain or improve soil quality over the long-term monocultural cropping.