Although there are adequate DNA sequence differences among plant-associated and plant-pathogenic bacteria to facilitate molecular approaches for their identification, identification at a taxonomic level that is predictive of their phenotype is a challenge. The problem is the absence of a taxonomy that describes genetic variation at a biologically relevant resolution and of a database containing reference strains for comparison. Moreover, molecular evolution, population genetics, ecology, and epidemiology of many plant-pathogenic and plant-associated bacteria are still poorly understood. To address these challenges, a database with web interface was specifically designed for plant-associated and plant-pathogenic microorganisms. The Plant-Associated Microbes Database (PAMDB) comprises, thus far, data from multilocus sequence typing and analysis (MLST/MLSA) studies of Acidovorax citrulli, Pseudomonas syringae, Ralstonia solanacearum, and Xanthomonas spp. Using data deposited in PAMDB, a robust phylogeny of Xanthomonas axonopodis and related bacteria has been inferred, and the diversity existing in the Xanthomonas genus and in described Xanthomonas spp. has been compared with the diversity in P. syringae and R. solanacearum. Moreover, we show how PAMDB makes it easy to distinguish between different pathogens that cause almost identical diseases. The scalable design of PAMDB will make it easy to add more plant pathogens in the future.

Myxobacteria are soil dwelling gram-negative gliding bacteria that form fruiting bodies containing myxospores. Although myxobacteria produce a wide range of antibiotics and lytic enzymes that assist in their ability to prey on other microorganisms, their role in agriculture has received little attention. Myxococcus spp. were isolated from soils in organic and conventionally managed strawberry production and transplant fields in the absence of soil fumigation. Fumigation with methyl bromide and chloropicrin virtually eliminated these organisms from soil. However, soil fumigation had no effect on the frequency of isolation of Myxococcus spp. from strawberry roots. Six Myxococcus spp. were tested in vitro against eight soilborne plant pathogenic fungi (Cylindrocarpon spp., Fusarium oxysporum f. sp. apii, Phytophthora capsici, Pythium ultimum, Rhizoctonia spp., Sclerotinia minor, Verticillium albo-atrum, and V. dahliae) and against two fungal biological control agents (Gliocladium virens and Trichoderma viride). Phytophthora capsici, Pythium ultimum, Rhizoctonia spp., S. minor, and T. viride were completely inhibited by all of the Myxococcus spp. tested. F. oxysporum f. sp. apii was the least sensitive to the myxobacteria, and no inhibition occurred with some Myxococcus spp. Inhibition of the other fungi tested was variable. Myxococcus coralloides inhibited nearly all the fungi tested. The ability of bacterial biological control agents to produce antibiotics and other secondary metabolites determined whether or not they were lysed by myxobacteria. Secondary metabolite production regulated by gacS protected Pseudomonas fluorescens strain CHA0 from lysis by myxobacteria. More specifically, phenazine antibiotics produced by Pseudomonas aureofaciens strain 30–84 protected it from lysis.

Since 2002, severe leaf spotting on parsley (Petroselinum crispum) has occurred in Monterey County, CA. Either of two different pathovars of Pseudomonas syringae sensu lato were isolated from diseased leaves from eight distinct outbreaks and once from the same outbreak. Fragment analysis of DNA amplified between repetitive sequence polymerase chain reaction; 16S rDNA sequence analysis; and biochemical, physiological, and host range tests identified the pathogens as Pseudomonas syringae pv. apii and P. syringae pv. coriandricola. Koch's postulates were completed for the isolates from parsley, and host range tests with parsley isolates and pathotype strains demonstrated that P. syringae pv. apii and P. syringae pv. coriandricola cause leaf spot diseases on parsley, celery, and coriander or cilantro. In a multilocus sequence typing (MLST) approach, four housekeeping gene fragments were sequenced from 10 strains isolated from parsley and 56 pathotype strains of P. syringae. Allele sequences were uploaded to the Plant-Associated Microbes Database and a phylogenetic tree was built based on concatenated sequences. Tree topology directly corresponded to P. syringae genomospecies and P. syringae pv. apii was allocated appropriately to genomospecies 3. This is the first demonstration that MLST can accurately allocate new pathogens directly to P. syringae sensu lato genomospecies. According to MLST, P. syringae pv. coriandricola is a member of genomospecies 9, P. cannabina. In a blind test, both P. syringae pv. coriandricola and P. syringae pv. apii isolates from parsley were correctly identified to pathovar. In both cases, MLST described diversity within each pathovar that was previously unknown.