16S rRNA-based PCR-DGGE analysis of actinomycete communities in fields with continuous cotton cropping in Xinjiang, China.

The purpose of this study was to examine the variations in the microbial community structure of soil actinomycetes in fields with continuous cropping of cotton in Xinjiang Autonomous Region, China. Soil samples were collected from four depths in fields with 7-year continuous cotton cropping. The community structure of soil actinomycetes was examined using the 16S rRNA-based polymerase chain reaction-density gradient gel electrophoresis (PCR-DGGE) techniques. The microbial diversity indices of the soil samples from different depths generally decreased along with the period of continuous cotton cropping. When the period of continuous cropping of cotton reached 5 years, the diversity indices rose again and gradually stabilized at a level slightly lower than that of soils with original ecology (i.e., 0-year cotton cropping). Cluster analysis showed that at the 1-20-cm depth, the actinomycete community structure of the soil subjected to 1-year cotton cropping was similar to that of soil subjected to 0-year cotton cropping, whereas that of soils after 3-year continuous cotton cropping showed high similarity. At the 21-40-cm depth, the actinomycete community structure showed various changes but generally recovered to its original pattern after repeated fluctuations. Principal component analysis showed that at the 1-30-cm depth, the actinomycete community structure varied similarly regardless of the period of continuous cotton cropping. In contrast, there were no clear actinomycete community structure variation trends at the 31-40-cm soil depth. Homology comparison of sequences recovered from the DGGE bands showed that the obtained sequences shared similarities >88 %. Alignment with the known homologous sequences indicated a lack of microorganisms related to soil-borne cotton diseases. Continuous cotton cropping exerted significant influences on the community structure of soil actinomycetes in Xinjiang Autonomous Region, which were largely determined by the soil depth and the period of continuous cotton cropping. The microbial diversity of soil actinomycete communities gradually recovered after 5-year continuous cropping. Thereafter, a new actinomycete community structure that was beneficial for continuous cropping of cotton was formed and stabilized each year.