Publications

4516

AbstractIn recent years, empty or poor grain bearing corn plants with leaf reddening symptoms have been observed in some commercial maize production areas in the Adana province of Turkey. The disease is increasing and causing economic losses. To verify the possible presence of phytoplasmas, leaf samples were tested with P1/Tint and R16F2n/R2 phytoplasma‐specific primer pairs after DNA extraction. The 16S ribosomal gene sequence analysis followed by sequence in silico enzyme digestions and phylogenetic analyses allowed the identification of ‘Candidatus Phytoplasma solani’, subgroup of 16SrXII‐A related‐strain in all symptomatic samples. The positive samples were characterized using tuf and vmp1 genes. In silico restriction fragment length polymorphism and sequence analyses allowed the inclusion of all the positive samples into tuf‐type b and V15 molecular types. The sequence analysis indicated the presence of a single genotype in all the tested samples (n = 12). This is the first molecular characterization of a ‘Ca. P. solani’ strain infecting maize plants in Turkey. The identified pathogen is listed in the EPPO A2 list.

Abstract Background Rickettsia spp. are human pathogens that cause a number of diseases and are transmitted by arthropods, such as ixodid ticks. Estonia is one of few regions where the distribution area of two medically important tick species, Ixodes persulcatus and I. ricinus, overlaps. The nidicolous rodent-associated Ixodestrianguliceps has also recently been shown to be present in Estonia. Although no data are available on human disease(s) caused by tick-borne Rickettsia spp. in Estonia, the presence of three Rickettsia species in non-nidicolous ticks has been previously reported. The aim of this study was to detect, identify and partially characterize Rickettsia species in nidicolous and non-nidicolous ticks attached to rodents in Estonia. Results Larvae and nymphs of I.ricinus (n = 1004), I. persulcatus (n = 75) and I.trianguliceps (n = 117), all removed from rodents and shrews caught in different parts of Estonia, were studied for the presence of Rickettsia spp. by nested PCR. Ticks were collected from 314 small animals of five species [Myodes glareolus (bank voles), Apodemus flavicollis (yellow necked mice), A.agrarius (striped field mice), Microtus subterranius (pine voles) and Sorex araneus (common shrews)]. Rickettsial DNA was detected in 8.7% (103/1186) of the studied ticks. In addition to identifying R.helvetica, which had been previously found in questing ticks, we report here the first time that the recently described I.trianguliceps-associated Candidatus Rickettsia uralica has been identified west of the Ural Mountains. Graphical Abstract

Autophagy, also known as type II programmed cell death, is a cellular mechanism of “self-eating”. Autophagy plays an important role against pathogen infection in numerous organisms. Recently, it has been demonstrated that autophagy can be activated and even manipulated by plant viruses to facilitate their transmission within insect vectors. However, little is known about the role of autophagy in the interactions of insect vectors with plant bacterial pathogens. ‘Candidatus Liberibacter solanacearum’ (Lso) is a phloem-limited Gram-negative bacterium that infects crops worldwide. Two Lso haplotypes, LsoA and LsoB, are transmitted by the potato psyllid, Bactericera cockerelli and cause damaging diseases in solanaceous plants (e.g., zebra chip in potatoes). Both LsoA and LsoB are transmitted by the potato psyllid in a persistent circulative manner: they colonize and replicate within psyllid tissues. Following acquisition, the gut is the first organ Lso encounters and could be a barrier for transmission. In this study, we annotated autophagy-related genes (ATGs) from the potato psyllid transcriptome and evaluated their expression in response to Lso infection at the gut interface. In total, 19 ATGs belonging to 17 different families were identified. The comprehensive expression profile analysis revealed that the majority of the ATGs were regulated in the psyllid gut following the exposure or infection to each Lso haplotype, LsoA and LsoB, suggesting a potential role of autophagy in response to Lso at the psyllid gut interface.

Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.

Biological foaming or scumming is a sludge separation problem that has become the subject of major concern for long-term stable activated sludge operation in decades. Biological foaming was considered induced by foaming bacteria.

Resolving metabolisms of deep-sea microorganisms is crucial for understanding ocean energy cycling. Here, a strictly anaerobic, Gram-negative strain NS-1 was isolated from the deep-sea cold seep in the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain NS-1 was most closely related to the type strain Halocella cellulosilytica DSM 7362T (with 92.52% similarity). A combination of phylogenetic, genomic, and physiological traits with strain NS-1, was proposed to be representative of a novel genus in the family Halanaerobiaceae, for which Iocasia fonsfrigidae NS-1 was named. It is noteworthy that I. fonsfrigidae NS-1 could metabolize multiple carbohydrates including xylan, alginate, starch, and lignin, and thereby produce diverse fermentation products such as hydrogen, lactate, butyrate, and ethanol. The expressions of the key genes responsible for carbohydrate degradation as well as the production of the above small molecular substrates when strain NS-1 cultured under different conditions, were further analyzed by transcriptomic methods. We thus predicted that part of the ecological role of Iocasia sp. is likely in the fermentation of products from the degradation of diverse carbohydrates to produce hydrogen as well as other small molecules, which are in turn utilized by other members of cold seep microbes.