Publications

4641

A novel, strictly anaerobic, slightly alkaliphilic, halotolerant, peptide- and amino acid-utilizing bacterial strain, SD1T, was isolated from a hypersaline lake in Western Australia. The strain stained Gram-negative and was a motile, spore-forming rod. The strain grew between 15 and 50 °C (optimum 40 °C), 1–15% w/v sodium chloride (optimum 5%) and pH 6.0–10.0 (optimum 9.0). Major fatty acids included anteiso-C15 : 0 (24.9%), C14 : 0 dimethyl acetyl (13.2%), anteiso-C15 : 0 dimethyl acetyl (11.5%) and iso-C15 : 0 (10.4%). The DNA G+C content was 30.3 mol%. The isolate did not grow using any tested sugars but grew well on arginine and glycine. It is capable of using elemental sulfur and thiosulfate as alternate electron acceptors, but not sulfide, sulfate, nitrate or nitrite. 16S rRNA gene similarity indicates that the isolate is related to Sporosalibacterium tautonense MRo-4T (94.33% identity). SD1T showed 76.18%–76.31% average nucleotide identity with other strains within the family Thermohalobacteraceae. Phylogenetics, based on the 16S rRNA gene and whole-genome sequence, as well as phenotypic analysis, differentiates the isolate from close neighbors. We propose that SD1T represents a novel species in a new genus, which we have named Dethiothermospora halolimnae gen. nov., sp. nov., type strain SD1T (DSM 117405T = TSD-443T). From this work, we also propose repositioning of the genus Anaeromonas to the family Thermohalobacteraceae.

Abstract A new distribution map is provided for Candidatus Liberibacter solanacearum (Liefting et al.) Alphaproteobacteria: Rhizobiales: Rhizobiaceae Hosts: Solanaceae, including potato (Solanum tuberosum), tomato (S. lycopersicum), pepper (Capsicum annuum), tobacco (Nicotiana tabacum), Solanum melongena (eggplant), also Apiaceae, including carrot (Daucus carota), celery (Apium graveolens) and parsnip (Pastinaca saliva).

ABSTRACT The Coxiellaceae bacterial family, within the order Legionellales, is defined by a collection of poorly characterized obligate intracellular bacteria. The zoonotic pathogen and causative agent of human Q fever, Coxiella burnetii , represents the best-characterized member of this family. Coxiellaceae establish replicative niches within diverse host cells and rely on their host for survival, making them challenging to isolate and cultivate within a laboratory setting. Here, we describe a new genus within the Coxiellaceae family that has been previously shown to infect economically significant freshwater crayfish. Using culture-independent long-read metagenomics, we reconstructed the complete genome of this novel organism and demonstrate that the species previously referred to as Candidatus Coxiella cheraxi represents a novel genus within this family, herein denoted Candidatus Paracoxiella cheracis . Interestingly, we demonstrate that Candidatus P. cheracis encodes a complete, putatively functional Dot/Icm type 4 secretion system that likely mediates the intracellular success of this pathogen. In silico analysis defined a unique repertoire of Dot/Icm effector proteins and highlighted homologs of several important C. burnetii effectors, including a homolog of CpeB that was demonstrated to be a Dot/Icm substrate in C. burnetii . IMPORTANCE Using long-read sequencing technology, we have uncovered the full genome sequence of Candidatus Paracoxiella cheracis , a pathogen of economic importance in aquaculture. Analysis of this sequence has revealed new insights into this novel member of the Coxiellaceae family, demonstrating that it represents a new genus within this poorly characterized family of intracellular organisms. Importantly, the genome sequence reveals invaluable information that will support diagnostics and potentially both preventative and treatment strategies within crayfish breeding facilities. Candidatus P. cheracis also represents a new member of Dot/Icm pathogens that rely on this system to establish an intracellular niche. Candidatus P. cheracis possesses a unique cohort of putative Dot/Icm substrates that constitute a collection of new eukaryotic cell biology-manipulating effector proteins.

Phytoplasmas (genus ‘Candidatus Phytoplasma’) encompass a group of uncultivated bacteria affecting numerous plant species and causing significant damage in agriculture worldwide. They have a dual parasitic cycle, including colonization of both plant phloem and insect cells. Their genomes are small, diverse, repetitive, prone to rearrangements and harbour transposon-like elements known as potential mobile units (PMUs). In the Euro-Mediterranean region, ‘Ca. P. solani’ is an important species due to its broad range of plant hosts and insect vectors. To provide insights into the genomic diversity of this species, particularly the repertoire of putative effectors and PMUs, this study conducted genome sequencing and analyses of two ‘Ca. P. solani’ strains originating from different plants and transmitted by different insects. Based on de novo assembly, we obtained 19 contigs totalling 656 141 bp for strain STOL and 28 contigs totalling 707 036 bp for strain ST19. The prevalence of repetitive sequences and PMUs contributed to the fragmentation of these draft assemblies. The annotation identified 28 and 26 genes that encode putative secreted proteins in these two strains, respectively, including several homologues of previously characterized phytoplasma effectors. Our comparative analyses further identified species- and strain-specific genes. Frequently, genes that encode putative secreted proteins and effectors were found within PMU-like regions in both genomes. Moreover, strain STOL showed characteristics of a more reduced genome, having fewer PMU-like repetitive elements and genome rearrangements, while strain ST19 exhibited a higher level of sequence divergence in its PMU genes. The high levels of genomic diversity among ‘Ca. P. solani’ strains suggested rapid evolution of this species, which may contribute to its wide host range and adaptability potential. This study provides novel data on the diversification of ‘Ca. P. solani’ genomes. These results provide a foundation for future functional studies of putative effectors and their interactions with host targets, which could facilitate deciphering the pathogenicity strategies of this successful and versatile pathogen.

A Gram-stain-negative, aerobic, rod-shaped bacterial strain, SYSU D60014T, was isolated from a sandy soil sample collected from the Gurbantunggut Desert in Xinjiang, PR China. Colonies of SYSU D60014T were pink-coloured, crystalline, irregular edge with a rough surface. Phylogenetic analyses based on both the 16S rRNA gene and whole-genome sequences assigned strain SYSU D60014T belonged to the family Rhodospirillaceae, formed a distinct lineage and showed 92.5–91.0% similarity to closely related strains. Digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values between strain SYSU D60014T and members of its related species were 17.2–19.6%, 70.8–74.4% and 48.9–64.5%, respectively. The complete genome of strain SYSU D60014T was 5,100,926 bp with a DNA G+C content of 65.1%. Cells were oxidase-positive and catalase-negative. The strain could grow at 28–40 °C (optimum, 37 °C), pH 5.0–8.0 (optimum, pH 7.0), and in the presence of up to 3% NaCl (optimum, 1–1.5%, w/v) on R2A. The predominant menaquinone was Q-10. The main polar lipids were phosphatidylethanolamine, phosphatidylmethyl ethanolamine, diphosphatidylglycerol, unidentified aminophospholipid, unidentified aminolipid, unidentified phospholipid, four unidentified polar lipids and two unidentified phosphoglycolipids. Major cellular fatty acids were C19 : 0 cyclo ω8c, summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and C16 : 0. Based on the results obtained through genotypic and phenotypic analyses, we propose that strain SYSU D60014T represents a novel species and genus within the family Rhodospirillaceae, for which we propose the name Virgifigura deserti gen. nov., sp. nov. (type strain SYSU D60014T=NBRC 112951T=CPCC 101030T).