Objective In order to provide scientific basis for ecological control and soil health management in continuous cotton cropping in the Xinjiang region, this study evaluated the ecological and health status of cotton fields based on soil properties and microbial community structure under different continuous cropping years.

Methods Based on the field survey, soil samples were collected in cotton fields with continuous cropping years of of 5, 7, 12, 20, 25 and 30 years in Jiashi County, Kashgar, Xinjiang. Soil physicochemical properties, extracellular enzyme activities, microbial community diversity, and plant pathogen abundance were analyzed. A minimum data set was constructed by principal component analysis to assess soil health by SHI-area method, and the relationship between plant pathogens and soil health was explored.

Results With the increase of continuous cropping years, soil electrical conductivity (EC) and salinity kept increasing, while available Fe and Mn contents and the activities of β-glucosidase, cellobiose hydrolase, leucine aminopeptidase, and alkaline phosphatase that were involved in carbon, nitrogen and phosphorus cycles enhanced as well. Soil microbial diversity indices were significantly affected by continuous cropping years, with α-diversity decreasing to a lower level after 7 years of continuous cropping. Based on the principal component analysis, soil total nitrogen, β-glucosidase, available Mn, salinity and fungal α-diversity (Simpson index) were identified as key factors to construct the minimum data set for soil health evaluation. The soil health index (SHI) calculated based on this data set decreased first (SHI_Y7 = 0.07) and then recovered gradually with the extension of continuous cropping years, and recovered to the highest point at 20 years (SHI_Y20 = 0.53), but did not exceed the level of 5 years of continuous cropping (SHI_Y5 = 0.58). Based on the minimum data set, plant pathogen abundance was found significantly and negatively correlated with SHI (y = −0.0727x+ 0.561, R² = 0.46, P = 0.002). Besides, correlation analysis showed that total N was the most important factor affecting plant pathogens abundance (r = −0.912, P<0.001). At the level of dominant fungal genera, Pseudogymnoascus, Gymnoascus and Canariomyces showed significant negative correlations with soil health index (r<−0.612, P<0.01).

Conclusions The soil health index decreased in the first 5 to 7 years of continuous cropping. Although the SHI showed a increasing trend thereafter, it did not reach the level observed at 5 years. Total nitrogen, salinity, available manganese, β-glucosidase activity and fungal diversity are the key indicators to evaluate soil health. The abundance of plant pathogens was suppressed by total nitrogen, which increased with the extension of continuous cropping years and became the most significant factor contributing to the restorative improvement of the soil health index. However, the increase of EC and salinity should be monitored as well.