Plant growth-promoting rhizobacteria suppressive to Phytophthora blight affect microbial activities and communities in the rhizosphere of pepper (Capsicum annuum L.) in the field

Two plant growth-promoting rhizobacteria, Pseudomonas corrugata CCR80 and Chryseobacterium indologenes ISE14, previously reported as suppressive to Phytophthora blight of pepper caused by Phytophthora capsici in the field were selected for use of this study. The effects of the strains on microbial activities, populations, and communities in pepper rhizosphere with or without pathogen inoculation were examined at 40, 80, and 120 days after transplanting (DAT) in the field in 2008 and 2009. To investigate the microbial effects, we used culture-dependent and -independent techniques such as plate counts on selective media, and fluorescein diacetate and denaturing gradient gel electrophoresis (DGGE) analyses. Root treatment with the strains increased total microbial activities in rhizosphere soil compared with controls (untreated, metalaxyl, or Escherichia coli DH5α) over the sampling time regardless of pathogen inoculation; however, microbial activities were greatly decreased in all treatments at 40–80 DAT. The strains also impacted the populations of bacterial and fungal functional groups. Eight fungal species, frequently observed on the medium for total fungi, were identified; these populations were significantly affected by the treatments: three species by metalaxyl, one by strain DH5α, one by strain ISE14, and none by strain CCR80 in both years. The DGGE analysis revealed that the strains affected bacterial and fungal community structure; the test strains increased the bacterial community composition, especially at 80 DAT, but had little effect on fungal community at later DAT. Taken together, strains CCR80 and ISE14 increased microbial activities and community composition, and affected certain microbial populations in the rhizosphere of pepper plants in the field, which might play significant roles in the suppression of Phytophthora blight of pepper.

► PGPR strains (ISE14 and CCR80) increased total microbial activities in pepper rhizosphere soil. ► These strains impacted populations of bacterial and fungal functional groups. ► The rhizosphere populations of eight fungal species were reduced by PGPR strains, metalaxyl, and DH5α. ► Three fungal species were affected by metalaxyl, one by DH5α, one by ISE14, and none by CCR80. ► DGGE analysis revealed that the PGPR strains affected bacterial and fungal community structure.