Application of Deep Pyrosequencing to the Analysis of Soil Microbial Communities in Different Lotus Fields

Fusarium oxyporum f. sp. nelumbicola is a very important plant pathogen that can cause lotus Fusarium wilt and lead to vast economic loss in Jiangxi Province, China. Sequencing data of 16S ribosomal RNA genes and internal transcribed spacer regions revealed that different bacterial and fungal communities were present in soil samples from healthy or Fusarium wilt-infected lotus fields with different years of continuous cropping, indicating that the long-term continuous cropping of lotus significantly altered the soil microbial communities. Fungal diversity indexes in the healthy soil samples increased with the years of monoculture, but decreased in the Fusarium wilt-infected soil samples, whereas bacterial community diversity in all the soil samples was relatively stable. A cluster analysis revealed that consecutive cropping time was a key factor for determining fungal community structure, but not for bacterial community structure. The relative abundances of Proteobacteria, Acidobacterial, Ascomycota, and Basidiomycota phyla decreased with the years of lotus monoculture. Compared with the healthy soil samples, the abundances of beneficial bacteria in the Fusarium wilt-infected soil samples significantly decreased with time. These observations indicate that soil weakness and lotus Fusarium wilt disease may be attributed to structural changes of soil microbial communities after long-term continuous cropping, and the changes include reduction of beneficial microorganisms and accumulation of fungal pathogens.