Analysis Of Bacteria During Different Cotton Rhizosphere Soil Developmental Stages

The rhizosphere constitutes a complex niche that may be exploited by a wide variety of bacteria. The effect of developing cotton or invaded by the pathogenic fungus Verticillium dahliae roots on the presence and activity of bacterial populations in the rhizosphere was examined by using culture-independent methods, such as T-RFLP, 16S rDNA clone library and DGGE.TRF community profiles show bacterial community structure in rhizosphere soil of healthy and diseased cotton is dynamic and changing after a growing season. Cotton rhizospheric bacterial community is consist of Proteobacteria, Firmicutes, Bacteroidetes and Acidobacterteria. The diversity index of each sample was calculated by software Bio-Dap. 3h sample has the highest Shannon-Weaver diversity index (H′) and the the reciprocal of Simson's index of diversity (1/D), but 4y sample has the highest evenness (E).The primers 27F and 1492R were used to constructed six 16S rDNA clone librares, namely, healthy cotton rhizosphere soil sample in squaring period, diseased cotton rhizosphere soil sample in squaring period, healthy cotton rhizosphere soil sample in flowering and boll-forming period, diseased cotton rhizosphere soil sample in flowering and boll-forming period, healthy cotton rhizosphere soil sample in squaring period and diseased cotton rhizosphere soil sample in squaring period. Subsequent sequence analysis revealed that, on the basis of the about 1500-bp sequence information, 79.2% has the highest similarity with uncultured bacteria. Acidobacteria and Proteobacteria are predominant phylua. Within Proteobacteria, the predominant subgroups are the alpha, beta or gamma subgroup. The other phyla are found in cotton rhizosphere, WS3, Deinococcus-Thermus, Verrucomicrobia, Firmicutes ,Bacteroidetes, Actinobacteria, Thermomicrobia, Gemmatimonadetes, Planctomycetes, Proteobacteria, Acidobacteria, Cyanobacteria. There are also 3%-8% of unclassified bacteria.Analysis of DGGE profiles by QuantityOne, it is showed that all samples are fell into two main clusters. Namely, healthy samples are clustered one category and diseased samples are clustered another category. Three sequences from the excised prominent DGGE bands with about 550-bp length were obtained. They have the highest similarity with alpha or beta proteobacteria. It proved that the predominant phyla from 16S rDNA clone libraries are accurate.In different growth stage of cotton, bacterial diversity is the highest in flowering and boll-forming period. Sometimes root activity dominance effect the cotton rhizosphere soil bacterial community, sometimes pathogen invading influence is dominant.