Publications

4774

Citrus Huanglongbing, caused by ‘ Candidatus Liberibacter asiaticus’ (CLas), is the most devastating citrus disease worldwide. The CLas genome is much smaller than those of its relatives, such as Sinorhizobium meliloti, due to its reductive evolution. Because CLas has not been cultured in artificial media, despite some progress in co-cultivating, and because genetic manipulation of CLas remains impossible, the understanding of CLas biology is very limited. Usually, 10% of total genes in bacteria are regulatory genes, but only 2% of CLas genes encode transcriptional factors. Here, 20 transcriptional regulators were predicted, including nine genes ( lsrB, ldtR, rem, visR, visN, ctrA, mucR, pelD, and atoC) directly or indirectly involved in regulating motility, and five genes ( rpoH, prbP, phrR, rirA, and lsrB) involved in oxidative stress response. We demonstrated that rem, lsrB, and visNR of CLas can complement the corresponding mutants of S. meliloti in their reduced motility. We further investigated traits controlled by Rem in S. meliloti and CLas using RNA sequencing analyses of rem mutant versus complementation strains with remSmc or remLas. Transcriptomic analysis showed that RemLas significantly regulates the expression of genes in S. meliloti, which was used to infer its regulation of CLas genes by identification of homologous genes. We found that Rem is involved in regulating motility, chemotaxis, transporters, and oxidative phosphorylation in S. meliloti and regulating flagellar and transporter genes in CLas. Among the 39 putative RemLas-regulated genes in CLas, 16 contain the Rem-binding motif, including 10 genes involved in flagellar assembly. Taken together, this study offers valuable insights regarding CLas regulatory genes, with many of them involved in regulating motility and oxidative stress response. The regulation of flagellar genes by Rem in CLas unravels critical information regarding motility in CLas infection of hosts.

Diaphorina citri (Hemiptera: Liviidae) is the main vector for the bacterium ‘ Candidatus Liberibacter asiaticus’, which is associated with citrus greening, also known as Huanglongbing. D. citri transmits ‘ Ca. L. asiaticus’ during its feeding on citrus phloem sap. Transmission occurs in a circulative, propagative, and persistent manner. ‘ Ca. L. asiaticus’ has a small genome (1.2 Mb). Therefore, it acquires most of its nutrients and energetic nucleotides from its hosts. The objective of this study was to assess the effect of ‘ Ca. L. asiaticus’ infection on the level of the free fatty acids in its vector. The fatty acids were extracted from adult D. citri using ethyl acetate, derivatized with boron trifluoride-methanol, and analyzed using gas chromatography-mass spectrometry. Nine fatty acids were identified in the D. citri extracts. Oleic acid was the most predominant fatty acid, followed by stearic and palmitic acid, whereas the rest of the fatty acids were present in low amounts. In general, the levels of the detected fatty acids in ‘ Ca. L. asiaticus’-infected D. citri were lower than those found in healthy psyllids. Our findings showed that the reduction of fatty acids in ‘ Ca. L. asiaticus’-infected psyllids resulted from the higher activity of β-oxidation to generate acetyl-coenzyme A, which causes more production of ATP. Our results indicated that ‘ Ca. L. asiaticus’ may enhance the β-oxidation of fatty acids in its vector insect to fulfill its nutrient and energetic nucleotide requirements.

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.