Changes in fungal community structure in bulk soil and spinach rhizosphere soil after chemical fumigation as revealed by 18S rDNA PCR-DGGE

Abstract To analyze the impact of chloropicrin and 1,3-dichloropropene on fungal community structure in bulk soil and spinach rhizosphere soil in a field, developed a new nested polymerase chain reaction (PCR) method to facilitate the detection of major fungal taxa and we used the method to monitor 18S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) profiles for 3 years. The cropping system consisted of soil fumigation in September and two subsequent consecutive spinach cultivations each year. The soil was treated with fumigants (chloropicrin at 20 mL m−2 or 1,3-dichloropropene at 32 mL m−2) and covered with polyethylene film for approximately 2 weeks. The nested PCR method with primer pairs AU2/AU4 and GC-FR1/FF390 successfully amplified sequences from all major fungal taxa, but not from plants or oomycetes, which were amplified from rhizosphere soil samples using direct PCR with the primer pair GC-FR1/FF390. The DGGE analysis of the nested PCR products indicated that the chloropicrin treatment h...