Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov.

The genus Rhizorhapis gen. nov. (to replace the illegitimate genus name Rhizomonas ) is proposed for strains of Gram-negative bacteria causing corky root of lettuce, a widespread and important lettuce disease worldwide. Only one species of the genus Rhizomonas was described, Rhizomonas suberifaciens , which was subsequently reclassified as Sphingomonas suberifaciens based on 16S rRNA gene sequences and the presence of sphingoglycolipid in the cell envelope. However, the genus Sphingomonas is so diverse that further reclassification was deemed necessary. Twenty new Rhizorhapis gen. nov.- and Sphingomonas -like isolates were obtained from lettuce or sow thistle roots, or from soil using lettuce seedlings as bait. These and previously reported isolates were characterized in a polyphasic study including 16S rRNA gene sequencing, DNA–DNA hybridization, DNA G+C content, whole-cell fatty acid composition, morphology, substrate oxidation, temperature and pH sensitivity, and pathogenicity to lettuce. The isolates causing lettuce corky root belonged to the genera Rhizorhapis gen. nov., Sphingobium , Sphingopyxis and Rhizorhabdus gen. nov. More specifically, we propose to reclassify Rhizomonas suberifaciens as Rhizorhapis suberifaciens gen. nov., comb. nov. (type strain, CA1T = LMG 17323T = ATCC 49355T), and also propose the novel species Sphingobium xanthum sp. nov., Sphingobium mellinum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov. with the type strains NL9T ( = LMG 12560T = ATCC 51296T), WI4T ( = LMG 11032T = ATCC 51292T) and SP1T ( = LMG 12581T = ATCC 51289T), respectively. Several strains isolated from lettuce roots belonged to the genus Sphingomonas , but none of them were pathogenic.

SNP-based codominant markers for a recessive gene conferring resistance to corky root rot (Rhizomonas suberifaciens) in lettuce (Lactuca sativa)

The analysis of F2 progeny and derived F3 families of Lactuca sativa segregating for resistance to corky root rot caused by Rhizomonas suberifaciens permitted the identification of restriction fragment length polymorphism (RFLP) and single nucleotide polymorphism (SNP) markers linked to the recessive resistance gene cor. PCR-based markers were identified by bulked segregant analysis (BSA). Allele-specific primers were generally designed with the 3´ terminal base coinciding with an SNP, matching one of the alleles and mismatching the other, and with an additional subterminal 3´ base mismatching both alleles. Codominant, robust, and inexpensive molecular markers were obtained that used standardized PCR conditions. Some of the markers could be analyzed in multiple Lactuca mapping populations that did not segregate for disease resistance allowing the cor locus to be located on several maps. The consistent low density of markers around cor in these maps suggests that cor may be in an area with an elevated rate of recombination. Evaluation of these markers in a large sample of cultivars and landraces identified pairs of flanking polymorphic markers that can be used for marker-assisted selection of corky root resistance.Key words: single nucleotide polymorphism (SNP), sequence characterized amplified region (SCAR), marker-assisted selection (MAS), genetic map, resistance gene.

Relationship between Corky Root Disease and Yield of Crisphead Lettuce

The effects of corky root (CR) disease, caused by Rhizomonas suberifaciens(van Bruggen, Jochimsen, and Brown) on fresh and marketable weights of lettuce (Lactuca sativa L.) were assessed during the 1988 and 1989 cropping seasons in several commercial lettuce fields. The resistant crisphead cultivars Raleigh and South Bay and the susceptible cultivars Ithaca and Shawnee produced similar yields in fields either planted in lettuce for the first time or in continuous lettuce production for three cropping cycles. Average yields of the resistant cultivars, from two fields cropped for six cycles naturally infested with CR, ranged from 875 to 1062 g/head fresh weight and 674 to 907 g/head marketable weight. The average yields of the susceptible cultivars in these infested fields ranged from 419.8 to 668.7 g/head fresh weight (37% to 52% yield loss) and 317.5 to 488.2 g/head marketable weight (46% to 53% yield loss). CR severity ratings were highly negatively correlated with root dry matter accumulation and whole and marketable head weights of-lettuce.

Crop Rotation Minimizes Losses from Corky Root in Florida Lettuce

The severity of corky root disease (Rhizomonas suberifaciens Van Bruggen et al.) increases with continuous lettuce (Lactuca sativa L.) cropping and exerts a negative impact on the quantity and quality of the lettuce produced. Experimental data from commercial fields were used to analyze profitability outcomes resulting from various management strategies, including cultivars, locations, and field cropping history, to control corky root. Regardless of the field cropping history, net returns were not negatively affected when resistant cultivars were planted. For susceptible cultivars, even when considering land development costs, producers maximize net returns by planting lettuce following sugarcane in land not previously cropped to lettuce. After the first crop of lettuce following sugarcane, yields slowly decreased but remained profitable for three to four crop cycles.

Distinction Between Infectious and Noninfectious Corky Root of Lettuce in Relation to Nitrogen Fertilizer

In growth chamber experiments with five concentrations of NH4NO3 and inoculation of lettuce (Lactuca sativa L.) cv. Salinas with Rhizomonas suberifaciens, the causal agent of corky root (CR), symptoms of noninfectious corky root induced by high rates of N were distinct from those of infectious corky root (ICR). Nitrogen toxicity was observed at 350 kg·ha-1 and above, and was not affected by inoculation with R. suberifaciens. There was a curvilinear relationship between concentration of NH4NO3 applied and ICR severity with a maximum at 525 kg·ha-1. In a similar growth chamber experiment with NH4NO3 plus urea, ICR severity decreased and N toxicity increased at increasing N levels (N at 160 to 650 kg·ha-1). In microplots at Davis, Calif., sidedressing with NH4NO3 (N at 170 kg·ha-1) increased ICR severity on `Salinas' lettuce over the nonfertilized control. There was a significant interaction between N fertilization and soil-infestation with R. suberifaciens with respect to head fresh weight: sidedressing with NH4NO3 increased head weight in noninfested plots, but decreased head weight in infested plots. In four field experiments at Salinas, Calif., sidedressing with N at 78 to 213 kg·ha-1, with N as (NH4)1SO4, NH4NO3, urea, or Ca(NO3)2, increased ICR over the control, but there were no significant differences between the forms of N. Head fresh and dry weights were either increased or unaffected by sidedressing with N fertilizers, depending on the residual concentrations of N in the soil. The increase in ICR was likely related to concentrations of soil NO3 rather than NH4.