ABSTRACT. Understanding how microbial community composition and diversity respond to continuous cropping obstacle is not well understood. However, determining the community composition vs assessing the diversity of molecular operational taxonomic units is often difficult. In this study, we focused on the microbial diversity and niche differentiation in rhizosphere soils between healthy and diseased cotton using a molecular approach based on a culture-independent method. A total of 124 operational taxonomic units (OTUs) from 1076 DNA fragments were detected, including 46, 57, and 21 OTUs from fungi, bacteria, and actinomycetes, respectively. The identified OTUs were confirmed by sequencing after polymerase chain reaction-restriction 1603 Microflora of healthy/diseased cotton rhizosphere soil ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (1): 1602-1611 (2015) fragment length polymorphism analysis. The number of OTUs from Fusarium species in diseased rhizosphere soils was higher than that in healthy rhizosphere, which was consistent with field observations. Overall, the results showed that microbes in healthy rhizosphere soils were more diverse and occupied a wider niche in the healthy rhizosphere soil environment of the cotton field. Beneficial microbes should further be analyzed in studies examining the soil ecology of fields in which continuous cropping of cotton takes place.

The Southern Xinjiang is the main productive area of cotton, which is in long continuous cropping due to the limited land resources. The community structures of cultural fungi were analyzed in the rhizosphere soil from healthy and diseased cotton fields. A total of 236 soil fungal isolates were obtained by means of the soil plating and dilution plating method. Based on morphological characteristics and internal transcribed spacers (ITS) sequences, these fungal isolates were grouped into sixteen genera. Of these genera, Aspergillus was the dominant genus in these rhizosphere soils, followed by Fusarium. The isolates of Trichoderma species in the rhizosphere soils with healthy cotton significantly outnumbered those with diseased cotton, while the genera of Fusarium and Verticillium showed the opposite trend. The biocontrol potential of the soil fungi, especially the Trichoderma isolates, was evaluated in vitro against Fusarium oxysporum and Verticillium dahliae using the dual culture technique. The fungal isolates from different soils showed different antagonistic potential, which came mostly from Aspergillus. Moreover, 10 isolates of Trichoderma spp. were shown to have a marked inhibitory effect on the tested pathogens in vitro. All together, these data indicate that the biocontrol fungi on the plant pathogens can contribute significantly in sustaining and improving soil quality.