Rootstock Genotype Interactions with Rhizosphere Microbial Consortia, and Associated Responses to Apple Replant Disease

For 20 years we have investigated biological methods for managing apple replant disease (ARD), a common soil-borne disease complex with variable causes in New York orchards.  Initially we evaluated different preplant cover crops and soil amendments in more than 30 orchards over many years. No preplant cover crops or soil amendments provided consistent ARD control across different sites and soil types, so we began searching for genetic sources of ARD resistance or tolerance in various Malus species and rootstocks.  Testing some 1000 different accessions representing 19 species of Malus, we found several rootstocks (G.30 and CG.6210) from the Cornell-Geneva rootstock breeding program, and some M. sieversii seedlings that were resistant or tolerant to ARD in a composite mixture of soils from five NY orchards with known histories of severe ARD.  When G.30 and CG6210 were later planted in an ARD orchard following preplant soil fumigation with Telone C-17, or soil compost amendments, 'Empire' apple trees on those two rootstocks grew and yielded substantially more than trees on M.7, M.26, or G.16 rootstock, and performed equally well in fumigated or non-fumigated locations, and in or out of the previous orchard tree rows.  Molecular fingerprint studies (DGGE based on 16s rRNA) of root-zone soil samples from the different rootstock genotypes showed that G.30 and CG.6210 had different rhizosphere microbial communities than the Malling rootstocks. More recently we have investigated root-zone soil microbial consortia and severity of ARD on seven rootstock genotypes (M.9, M.26, G.30, G.41, G.65, G.935, and CG.6210) planted in soil where trees on four of those same rootstocks (M.9, M.26, G.30 and CG.6210) had grown for the previous 15 years. Rootstock genotyping showed that genetic distances among these rootstocks were correlated with their differential responses to ARD. Root-zone fungal and bacterial community composition (assessed with T-RFLP molecular analyses) differed between ARD resistant and susceptible rootstocks, and sequences matching with the Burkholderia cepacia complex (a putative disease-suppressive soil microbe) in the GENBANK database were obtained only from CG.6210 root-zone samples. Rootstock genotypes previously grown in the soil affected subsequent ARD severity differentially among these replant rootstocks, but replanting with the same rootstocks did not consistently exacerbate ARD severity. These results indicate that CG.6210 induces an ARD-suppressive microbial consortium in its rhizosphere, which may represent a novel mechanism for controlling this disease in orchards.