Identification of microorganisms associated with soil suppressiveness against Heterodera schachtii and Phytophthora cinnamomi using ribosomal RNA gene analyses and examination of bacterial functional redundancy along a soil reclamation gradient using in s

To obtain a better understanding of the mechanisms responsible for suppressiveness against the plant-parasitic nematode Heterodera schachtii in a Southern California soil, we investigated the distribution of fungal and bacterial rDNA associated with H. schachtii cysts that developed in that particular soil. The biological nature of the suppressiveness can be transferred to fumigated, non-suppressive soil by cysts that developed in the suppressive soil. This makes the cyst a valuable target for identifying the microorganisms involved in the suppressiveness. Five soils, containing varying levels of suppressiveness, were established by mixing different amounts of the suppressive soil and fumigated, non-suppressive soil. The soils were planted with mustard greens and infested with H. schachtii. After two nematode generations, cysts were extracted from these soils and the fungal and bacterial rDNA associated with the cysts were identified using the culture-independent oligonucleotide fingerprinting of ribosomal RNA genes (OFRG) method. For cyst-associated fungi, rDNA with high sequence identity to Cephaliophora muscicola was found predominately in the cysts from soils possessing high levels of suppressiveness. Fungal rDNA with high sequence identity to Fusarium oxysporum were found mostly in the cysts from moderately suppressive soils. Few fungal rDNA were identified in the fumigated, non-suppressive soil. Sequence-selective primers were developed and used to examine fungal rDNA from H. schachtii cysts from several sources. The C. muscicola-like rDNA was the only fungal rDNA consistently detected in highly suppressive soils. For cyst-associated bacteria, five major taxonomic groups were identified: Actinobacteria, Cytophaga-Flexibacter-Bacteroides, alpha-Proteobacteria , beta-Proteobacteria, and gamma-Proteobacteria . Among these bacteria, three rDNA groups correlated with high levels of suppressiveness. When group-specific PCR analysis was used to examine these bacterial rDNA from H. schachtii cysts from different sources, only a Rhizobium-like rDNA group (alpha- Proteobacteria) was consistently detected in the highly suppressive soils. A competitive PCR analysis confirmed the association of this bacterial rDNA group with H. schachtii suppressiveness.