Publications

4364

Genomic information can yield new insights into the molecular and physiological mechanisms that underpin pathogen virulence and transmission. We decode the genome of Spirobacillus cienkowskii Metchnikoff 1889, a gram-negative bacterium and one of the first described parasites of Daphnia. We use long-read sequencing and extensive annotation to assemble the complete circular genome of 2.81 Mbp with 2,486 protein-coding genes. In addition to antiviral systems, including CRISPR-Cas and restriction-modification systems, we describe the likely molecular basis of the unusual red phenotype of S. cienkowskii, which results from carotenoid production. We further describe genetic modules that may mediate this bacterium’s interactions with its host and environment. Our study provides insight into the metabolic and functional capacities of a parasite through the assessment of its genome. More generally, it demonstrates what can be learnt by applying recent advances in high-throughput sequencing to the study of parasites.

ABSTRACT The stolbur disease associated with “ Candidatus Phytoplasma solani” (CaPsol) is very common in Europe and the Mediterranean regions and adversely affects perennial or annual plants but is rarely reported on cucurbits. We report the first multilocus genetic characterisation of CaPsol strains infecting cucurbit plants and the presence of some RNA viruses prevalent in cucurbits. Between 2019 and 2020, 156 symptomatic and nine asymptomatic plant samples were collected during surveys in cucurbit‐growing areas. Symptomatic plants exhibited leaf deformation, growth retardation, yellowing, flower deformation and other virus‐like symptoms. Molecular testing detected potyviruses, tobamoviruses and Cucumis melo endornavirus (CmEV) as single and double infections in 108 samples, but CaPsol was determined only in seven plants as a single infection. CaPsol strains infecting squash and watermelon in the Marmara region of Türkiye were genetically characterised by describing their tuf, vmp1 and stamp gene sequences. All cucurbit‐associated CaPsol strains were of the tuf ‐b1 genotype and five different stamp genotypes previously reported in other crops and wild plant reservoirs in Europe. Cucurbit CaPsol strains had vmp1 gene sequences corresponding to RFLP types V4 and V14, previously detected in the Mediterranean basin. These strains were not novel cucurbit‐specific genotypes but shared similarities with genotypes from diverse plant hosts across Europe. This indicated that CaPsol is not restricted to cucurbits and may persist in alternative plant hosts. Thus, disease management should include monitoring alternative plant reservoirs, rather than focusing solely on cucurbit production areas. Viral infections showed significantly higher prevalence compared to phytoplasma infections in the region.

[Pasteurella] langaaensis has been found to be polyphyletic in relation to the type species Pasteurella multocida, as endicated by 16S rRNA gene sequence comparisons and a number of other comparisons (enclosing the genus name in brackets). 16S rRNA gene sequence-based phylogeny confirmed that [P.] langaaensis is unrelated to other members of Pasteurellaceae at the genus level and may be a candidate for a new genus with 95% 16S rRNA gene sequence identity to the closest related sequence belonging to the type strain of [Actinobacillus] rossii. The highest digital DNA–DNA hybridization value predicted from the whole-genomic sequence of the type strain of [P.] langaaensis was to the type strain of Acinobacillus suis with 26%, confirming a separate taxonomic status at the species level. The phylogenetic comparison of concatenated conserved protein sequences determined in a previous study showed a unique position of the taxon investigated, which qualified for the status of a new genus since the highest conserved protein sequence identity was found to [A.] rossii with 86%. A new genus with one species, Alitibacter langaaensis gen. nov., comb. nov., is proposed. The genus can be separated from other genera in the family Pasteurellaceae by from 1 up to 12 phenotypic characters, and it is monotypic from other genera with respect to analysis of 16S rRNA gene sequences as well as of predicted core genomic proteins. The type strain of Alitibacter langaaensis is F73T (=NCTC 11411T=CCUG 15566T=DSM 22999T=CPI 102678T=ATCC 43328T).