Publications (2705)

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<i>Candidatus</i> Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution

Citation
Pessi et al. (2022). FEMS Microbes
Names
Ca. Nitrosopolaris
Subjects
General Medicine
Abstract
Abstract Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analysed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus “UBA10452”, an uncultured lineage of putative AOA in the order Nitrososphaerales (“terrestrial group I.1b”), phylum Thaumarchaeota. Analysis of other eight previously reported MAGs and publicly available amplicon sequencing data revealed that the UBA10452 lineage is predominantly found in acidic polar and alpine soils. In particular, UBA10452 MAGs were more abundant in highly oligotrophic environments such as mineral permafrost than in more nutrient-rich, vegetated tundra soils. UBA10452 MAGs harbour multiple copies of genes related to cold tolerance, particularly genes involved in DNA replication and repair. Based on the phylogenetic, biogeographical, and ecological characteristics of 12 UBA10452 MAGs, which include a high-quality MAG (90.8% complete, 3.9% redundant) with a nearly complete 16S rRNA gene, we propose a novel Candidatus genus, Ca. Nitrosopolaris, with four species representing clear biogeographical/habitat clusters.

The Upregulated Expression of the Citrus RIN4 Gene in HLB Diseased Citrus Aids Candidatus Liberibacter Asiaticus Infection

Citation
Cheng et al. (2022). International Journal of Molecular Sciences 23 (13)
Names
Ca. Liberibacter asiaticus Liberibacter
Subjects
Catalysis Computer Science Applications General Medicine Inorganic Chemistry Molecular Biology Organic Chemistry Physical and Theoretical Chemistry Spectroscopy
Abstract
The citrus industry has been threatened by Huanglongbing (HLB) for over a century. Here, an HLB-induced Arabidopsis RPM1-interacting protein 4 (RIN4) homologous gene was cloned from Citrus clementina, and its characteristics and function were analyzed to determine its role during citrus–Candidatus Liberibacter asiaticus (CLas) interactions. Quantitative real-time PCR showed that RIN4 was expressed in roots, stems, leaves and flowers, with the greatest expression level in leaves. Its expression was suppressed by gibberellic acid, indole-3-acetic acid, salicylic acid and jasmonic acid treatments, but was induced by abscisic acid and salt treatments, as well as wounding. The transient expression of a RIN4-GFP showed that RIN4 was localized in the cell membrane. RIN4-overexpressing transgenic C. maxima cv. ‘Shatianyou’ plants were obtained, and some transgenic plants showed greater sensitivity to CLas infection and earlier HLB symptoms appearance than non-transgenic controls. Results obtained in this study indicated that the upregulated expression of RIN4 in HLB diseased citrus may aid CLas infection.

Effect of the Symbiosis with Mycoplasma hominis and Candidatus Mycoplasma Girerdii on Trichomonas vaginalis Metronidazole Susceptibility

Citation
Margarita et al. (2022). Antibiotics 11 (6)
Names
Ca. Mycoplasma girerdii
Subjects
Biochemistry General Pharmacology, Toxicology and Pharmaceutics Infectious Diseases Microbiology Microbiology (medical) Pharmacology (medical)
Abstract
Trichomoniasis, the most common non-viral sexually transmitted infection worldwide, is caused by the protozoon Trichomonas vaginalis. The 5- nitroimidazole drugs, of which metronidazole is the most prescribed, are the only effective drugs to treat trichomoniasis. Resistance against metronidazole is increasingly reported among T. vaginalis isolates. T. vaginalis can establish an endosymbiosis with two Mycoplasma species, Mycoplasma hominis and Candidatus Mycoplasma girerdii, whose presence has been demonstrated to influence several aspects of the protozoan pathobiology. The role of M. hominis in T. vaginalis resistance to metronidazole is controversial, while the influence of Ca. M. girerdii has never been investigated. In this work, we investigate the possible correlation between the presence of Ca. M. girerdii and/or M. hominis and the in vitro drug susceptibility in a large group of T. vaginalis isolated in Italy and in Vietnam. We also evaluated, via RNA-seq analysis, the expression of protozoan genes involved in metronidazole resistance in a set of syngenic T. vaginalis strains, differing only for the presence/absence of the two Mycoplasmas. Our results show that the presence of M. hominis significantly increases the sensitivity to metronidazole in T. vaginalis and affects gene expression. On the contrary, the symbiosis with Candidatus Mycoplasma girerdii seems to have no effect on metronidazole resistance in T. vaginalis.

Devious Phloem Intruder <i>Candidatus</i> Liberibacter Species Causing Huanglongbing: History, Symptoms, Mechanism, and Current Strategies

Citation
Karuppaiya et al. (2022). Current and Emerging Challenges in the Diseases of Trees [Working Title]
Names
Ca. Liberibacter asiaticus Ca. Liberibacter americanus Ca. Liberibacter africanus Liberibacter
Abstract
Huanglongbing (HLB) or greening is a devastating phloem-intruding bacterial disease that generates various symptoms in leaves and fruits, threatening the global citrus industry. Candidatus Liberibacter asiaticus, Candidatus Liberibacter africanus, and Candidatus Liberibacter americanus are the causative agents of HLB in citrus-producing regions around many countries, and these proteobacteria are being vectorized by Diaphorina citri and Triozaerytreae. The lack of HLB-resistant citrus cultivars, the rapid spread of disease, and the fastidious nature of HLB-proteobacteria have made it difficult to mitigate HLB in the citrus field. There are numerous reports on the control of HLB disease using thermotherapy, chemotherapy, plant defense activators, brassinosteroids, and nanoemulsions. However, there is no evidence of such applicability of the methods mentioned above to complete the elimination or suppression of the pathogen to control HLB disease. We aim to provide an overall picture of HLB disease, its distribution, causal organism, pathogenic mechanism, and current and future strategies for combat against citrus Huanglongbing disease. This review may prompt the researchers toward an integrated and environmentally sustainable methodology for the mitigation/elimination of HLB pathogens.

Strain tracking of ‘<i>Candidatus</i> Liberibacter asiaticus’, citrus greening disease pathogen, enabled by high-resolution microbiome analysis of the Asian citrus psyllid

Citation
Higgins et al. (2022). Phytopathology®
Names
Ca. Liberibacter asiaticus
Subjects
Agronomy and Crop Science Plant Science
Abstract
The Asian citrus psyllid, Diaphorina citri, is an invasive insect and a vector of 'Candidatus Liberibacter asiaticus' (CLas), a bacterium whose growth in Citrus species results in huanglongbing (HLB), also known as citrus greening disease. Methods to enrich and sequence CLas from D. citri often rely on biased genome amplification and nevertheless contain significant quantities of host DNA. To overcome these hurdles, we developed a simple pre-treatment DNase and filtration (hereafter PDF) protocol to remove host DNA and directly sequence CLas and the complete, primarily uncultivable, microbiome from D. citri adults. The PDF protocol yielded CLas abundances upwards of 60% and facilitated direct measurement of CLas and endosymbiont replication rates in psyllids. The PDF protocol confirmed our strains derived from a progenitor Florida CLas strain and accumulated 156 genetic variants, underscoring the utility of this data for bacterial strain tracking. CLas genetic polymorphisms arising in lab-reared psyllid populations included prophage encoding regions with key functions in CLas pathogenesis, putative antibiotic resistance loci, and a single secreted effector. These variants suggest laboratory propagation of CLas may result in different phenotypic trajectories among laboratories, and may confound CLas physiology or therapeutic design and evaluation if these differences remain undocumented. Finally, we obtained genetic signatures affiliated with Citrus nuclear and organellar genomes, entomopathogenic fungal mitochondria, and commensal bacteria from laboratory-reared and field-collected D. citri adults. Hence, the PDF protocol can directly inform agricultural management strategies related to bacterial strain tracking, insect microbiome surveillance, and antibiotic resistance screening.

Molecular Identification and Characterization of Two Groups of Phytoplasma and Candidatus Liberibacter Asiaticus in Single or Mixed Infection of Citrus maxima on Hainan Island of China

Citation
Yu et al. (2022). Biology 11 (6)
Names
Ca. Liberibacter asiaticus Liberibacter
Subjects
General Agricultural and Biological Sciences General Biochemistry, Genetics and Molecular Biology General Immunology and Microbiology
Abstract
The pathogens associated with citrus Huanglongbing symptoms, including yellowing and mottled leaves in Citrus maxima, an important economic crop on Hainan Island of China, were identified and characterized. In the study, detection, genetic variation and phylogenetic relationship analysis of the pathogens were performed based on 16S rRNA and β-operon gene fragments specific to phytoplasma and Candidatus Liberibacter asiaticus. The results indicated that the pathogens—such as phytoplasma strains of CmPII-hn belonging to the 16SrII-V subgroup and CmPXXXII-hn belonging to the 16SrXXXII-D subgroup, as well as Candidatus Liberibacter asiaticus strains CmLas-hn—were identified in the diseased plant samples, with numbers of 12, 2 and 6 out of 54, respectively. Among them, mixed infection with the 16SrII-V subgroup phytoplasma and Candidatus Liberibacter asiaticus was found in the study, accounting for 7.4% (four samples). The phytoplasma strains of CmPII-hn—Tephrosia purpurea witches’ broom, Melochia corchorifolia witches’ broom and Emilia sonchifolia witches’ broom—were clustered into one clade belonging to the 16SrII-V subgroup, with a 99% bootstrap value. The phytoplasma strains of CmPXXXII-hn and Trema tomentosa witches’ broom belonging to 16SrXXXII-D, and the other 16SrXXXII subgroup strains were clustered into one clade belonging to the 16SrXXXII group with a 99% bootstrap value. There were 16 variable loci in the 16S rRNA gene sequences of the tested 16SrXXXII group phytoplasma strains, of which two bases had an insertion/deletion. The strains of Candidatus Liberibacter asiaticus, identified in the study and the strains that had been deposited in GenBank, were in one independent cluster with a 99% bootstrap value. To our knowledge, this is the first report showing that Citrus maxima can be infected by 16SrII-V and16SrXXXII-D subgroup phytoplasmas in China. Moreover, this is also the first report in which the plants are co-infected by 16SrII-V subgroup phytoplasmas and Candidatus Liberibacter asiaticus. More comprehensive and detailed identification and characterization of the pathogens associated with the diseased symptoms in Citrus maxima on the island in China would be beneficial for epidemic monitoring and for the effective prevention and control of related plant diseases.