Xanthomonas euroxanthea sp. nov., a new xanthomonad species including pathogenic and non-pathogenic strains of walnut

Abstract

We describe a novel species isolated from walnut (Juglans regia) which comprises non-pathogenic and pathogenic strains on walnut. The isolates, obtained from a single ornamental walnut tree showing disease symptoms, grew on yeast extract–dextrose–carbonate agar as mucoid yellow colonies characteristic of Xanthomonas species. Pathogenicity assays showed that while strain CPBF 424T causes disease in walnut, strain CPBF 367 was non-pathogenic on walnut leaves. Biolog GEN III metabolic profiles disclosed some differences between strains CPBF 367 and CPBF 424T and other xanthomonads. Multilocus sequence analysis with seven housekeeping genes (fyuA, gyrB, rpoD, atpD, dnaK, efp, glnA) grouped these strains in a distinct cluster from Xanthomonas arboricola pv. juglandis and closer to Xanthomonas prunicola and Xanthomonas arboricola pv. populi. Average nucleotide identity (ANI) analysis results displayed similarity values below 93 % to X. arboricola strains. Meanwhile ANI and digital DNA–DNA hybridization similarity values were below 89 and 50 % to non-arboricola Xanthomonas strains, respectively, revealing that they do not belong to any previously described Xanthomonas species. Furthermore, the two strains show over 98 % similarity to each other. Genomic analysis shows that strain CPBF 424T harbours a complete type III secretion system and several type III effector proteins, in contrast with strain CPBF 367, shown to be non-pathogenic in plant bioassays. Taking these data altogether, we propose that strains CPBF 367 and CPBF 424T belong to a new species herein named Xanthomonas euroxanthea sp. nov., with CPBF 424T (=LMG 31037T=CCOS 1891T=NCPPB 4675T) as the type strain.

Complete Genome Sequences of Walnut-Associated Xanthomonas euroxanthea Strains CPBF 367 and CPBF 426 Obtained by Illumina/Nanopore Hybrid Assembly

“…OrthoANI v1.40 (12) indicates an average nucleotide identity value higher than 97%, assigning these strains to X. euroxanthea, together with a previously reported strain, CPBF 424 (13,14). Interestingly, while X. euroxanthea CPBF 424 holds an apparently functional T3SS and was shown to be pathogenic in walnut plantlets, X. euroxanthea strains CPBF 367 and CPBF 426 were deficient for most T3SS operon genes, suggesting that these strains are nonpathogenic in walnut, which was confirmed in walnut pathogenicity assays for strain CPBF 367 (6). Altogether, the distinct genomic repertoires of these X. euroxanthea strains (CPBF 367 and CPBF 426), in comparison to those of X. arboricola pv.…”

“…juglandis ( 5 ). More recently, based on phenotypic and genomic analyses, such as average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), it has been proposed that some of these bacteria are members of a new species designated Xanthomonas euroxanthea , which includes both pathogenic and nonpathogenic strains on walnut ( 6 ). Here, we sequenced the whole genome of two strains belonging to this new Xanthomonas species, CPBF 367 (LMG 31036 = CCOS 1890) and CPBF 426 (LMG 31038 = CCOS1892).…”

Comprehensive diversity assessment of walnut‐associated xanthomonads reveal the occurrence of distinct Xanthomonas arboricola lineages and of a new species (Xanthomonas euroxanthea) within the same tree

“…Most of the 19 isolates evaluated from Clusters VII to X could be assigned to nonpathogenic groups, and it was possible to prove this for CPBF 75, CPBF 1488, CPBF 1514, and CPBF 367 (Fernandes, 2019; Martins et al, 2020). In contrast, CPBF 424 (and CPBF 78), which was proved to be pathogenic on walnut (Martins et al, 2020), displayed a different pattern of T3E genes (presence of xopR and xopF1 ; absence of avrbs2 and xopN ) when compared with X . arboricola pathogenic strains.…”

“…arboricola isolates ( n = 4), and Lin21 to Lin31 were represented by Xanthomonas sp. isolates ( n = 15), including the strains CPBF 367, CPBF 424, and CPBF 426, recently characterized as members of the new species Xanthomonas euroxanthea (Martins et al, 2020).…”

“…campestris (CN14, JX), and to the recently proposed X . euroxanthea that includes strain CPBF 424, a walnut pathogen, and the nonpathogenic strains CPBF 367 and CPBF 426 (Martins et al, 2020), all assigned to MLSA Cluster X.…”