Downloaded from www.microbiologyresearch.org by IP: 54.70.40.11 On: Fri, 28 Dec 2018 03:27:49 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. Isolde M. Francis, 1 Kenneth N. Jochimsen, 2 3 Paul De Vos 3 and Ariena H. C. van Bruggen 2 4 Correspondence Ariena H.C. van Bruggen ahcvanbruggen@ufl.edu 1 Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA 2 Department of Plant Pathology, University of California, Davis, CA 95616, USA 3 Laboratory of Microbiology, Ghent University, 9000 Ghent, Belgium 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, CA1 T 5LMG 17323 T 5ATCC 49355 T ), 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 NL9 T (5LMG 12560 T 5ATCC 51296 T ), WI4 T (5LMG 11032 T 5ATCC 51292 T ) and SP1 T (5LMG 12581 T 5ATCC 51289 T ), respectively. Several strains isolated from lettuce roots belonged to the genus Sphingomonas, but none of them were pathogenic. The genus Rhizomonas was created for strains of Gram- negative bacteria causing corky root of lettuce (van Bruggen et al., 1990), a widespread and important lettuce disease in various parts of the USA, Europe and Australia (Datnoff & Nagata, 1990; van Bruggen & Jochimsen, 1992, 1993; van Bruggen et al., 1988, 1989). Only one species of the genus Rhizomonas was described, Rhizomonas suberifaciens, con- taining most pathogenic strains isolated in the USA, except for strain WI4 T which was presumed to belong to a separate species of the genus Rhizomonas (van Bruggen et al., 1990). A non-pathogenic strain isolated from lettuce roots in California, strain CA16, was shown to be related to strain WI4 T and was presumed to belong to the same unnamed species (van Bruggen et al., 1993). 3Present address: Zuckermann Farms, Stockton, California 95201, USA. 4Present address: Department of Plant Pathology and the Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA. Abbreviations: DDH, DNA–DNA hybridization; FAME, fatty acid methyl ester; PHB, polyhydroxybutyrate. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of Sphingobium mellinum WI4 T , Rhizorhapis suberifaciens CA1 T , Rhizorhabdus argentea SP1 T and Sphingobium xanthum NL9 T are KF437546, KF437561, KF437572 and KF437579, respectively, and those of other strains determined in this study are listed in Table S1. Four supplementary figures and three supplementary tables are available with the online version of this paper. International Journal of Systematic and Evolutionary Microbiology (2014), 64, 1340–1350 DOI 10.1099/ijs.0.058909-0 1340 058909 G 2014 IUMS Printed in Great Britain