General Medicine

The decision by the International Committee on Systematics of Prokaryotes (ICSP) to place the rank of phylum under the rules of the International Code of Nomenclature of Prokaryotes (ICNP), with phylum names ending in –ota based on the name of a type genus, enables the valid publication of the phylum name Cyanobacteriota with Cyanobacterium as the type genus. The names Cyanobacterium and its type species Cyanobacterium stanieri were effectively published in 1983 by Rippka and Cohen-Bazire, but the names were not validly published under the rules of the ICNP (then named the International Code of Nomenclature of Bacteria) or the rules of the ICN (International Code of Nomenclature for algae, fungi, and plants, then named the International Code of Botanical Nomenclature). We here propose the names Cyanobacterium gen. nov and Cyanobacterium stanieri sp. nov. for valid publication under the provisions of the ICN. Upon validation these names are also validly published under the ICNP according to General Consideration 5 and Rule 30. We also propose the phylum name Cyanobacteriota phyl. nov. under the rules of the ICNP.

The morphology, 16S rRNA gene phylogeny and 16S–23S rRNA gene ITS secondary structures of three strains of marine Cyanobacteria, isolated from inter- and subtidal environments from north Portugal were studied, resulting in the description of Zarconia navalis gen. nov., sp. nov. (Oscillatoriales incertae sedis), Romeriopsis navalis gen. nov., sp. nov. (Leptolyngbyaceae) and Romeriopsis marina sp. nov., named under the International Code of Nomenclature for algae, fungi, and plants. No diacritical morphological characters were found for the new genera and species. The 16S rRNA gene maximum-likelihood and Bayesian phylogenies supported that the genus Zarconia is a member of the Oscillatoriales, morphologically similar to the genera Microcoleus and Phormidium, but distant from them. The genus Romeriopsis is positioned within the Leptolyngbyaceae (Synechococcales) and is closely related to Alkalinema . The secondary structures of the D1-D1′, Box B, V2 and V3 helices corroborate the phylogenetic results. Furthermore, our study supports previous observations of polyphyletic Oscillatoriales families and reinforces the need for their taxonomic revision.

AbstractAmmonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analyzed 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, biogeographic, 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 biogeographic/habitat clusters.

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.

“Candidatus Liberibacter asiaticus” (CLas) is the causal agent of citrus Huanglongbing (HLB, also called citrus greening disease), a highly destructive disease threatening citrus production worldwide. A novel Microviridae phage (named CLasMV1) has been found to infect CLas, providing a potential therapeutic strategy for CLas/HLB control. However, little is known about the CLasMV1 biology. In this study, we analyzed the population dynamics of CLasMV1 between the insect vector of CLas, the Asian citrus psyllid (ACP, Diaphorina citri Kuwayama) and the holoparasitic dodder plant (Cuscuta campestris Yunck.); both acquired CLasMV1-infected CLas from an HLB citrus. All CLas-positive dodder samples were CLasMV1-positive, whereas only 32% of CLas-positive ACP samples were identified as CLasMV1-positive. Quantitative analyses showed a similar distribution pattern of CLasMV1 phage and CLas among eight citrus cultivars by presenting at highest abundance in the fruit pith and/or the center axis of the fruit. Transcriptome analyses revealed the possible lytic activity of CLasMV1 on CLas in fruit pith as evidenced by high-level expressions of CLasMV1 genes, and CLas genes related to cell wall biogenesis and remodeling to maintain the CLas cell envelope integrity. The up-regulation of CLas genes were involved in restriction–modification system that could involve possible phage resistance for CLas during CLasMV1 infection. In addition, the regulation of CLas genes involved in cell surface components and Sec pathway by CLasMV1 phage could be beneficial for phage infection. This study expanded our knowledge of CLasMV1 phage that will benefit further CLas phage research and HLB control.

AbstractZebra chip disease (ZC), associated with the plant pathogenic bacterium ‘Candidatus Liberibacter solanacearum’ (psyllaurous) (CLso), is a major threat to global potato production. In addition to yield loss, CLso infection causes discoloration in the tubers, rendering them unmarketable. CLso is transmitted by the potato psyllid, Bactericera cockerelli (Šulc) (Hemiptera: Triozidae). ZC is managed by prophylactic insecticide applications to control the vector, which is costly and carries environmental and human health risks. Given the expense, difficulty, and unsustainability of managing vector‐borne diseases with insecticides, identifying sources of resistance to CLso and developing varieties that are resistant or tolerant to CLso and/or potato psyllids has become a major goal of breeding efforts. These efforts include field and laboratory evaluations of noncultivated germplasm and cultivars, studies of tubers in cold storage, detailed quantifications of biochemical responses to infection with CLso, possible mechanisms underlying insect resistance, and traditional examination of potato quality following infections. This review provides a brief history of ZC and potato psyllid, a summary of currently available tools to manage ZC, and a comprehensive review of breeding efforts for ZC and potato psyllid management within the greater context of Integrated Pest Management (IPM) strategies. © 2022 Society of Chemical Industry. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.

Huanglongbing (otherwise known as HLB or greening) is currently the most devastating citrus disease worldwide. HLB is primarily associated with the phloem-inhabiting bacterium ‘Candidatus Liberibacter asiaticus’ (CLas). Currently, there are no citrus species resistant to CLas. Genetic transformation is one of the most effective approaches used to induce resistance against plant diseases. Antimicrobial peptides (AMPs) have shown potential breakthroughs to improve resistance to bacterial diseases in plants. In this paper, we confirm the Agrobacterium-mediated transformation of Pera sweet orange expressing the AMP sarcotoxin IA (stx IA) gene isolated from the flesh fly Sarcophaga peregrina and its reaction to CLas, involving plant performance and fruit quality assessments. Four independent transgenic lines, STX-5, STX-11, STX-12, and STX-13, and a non-transgenic control, were graft-inoculated with CLas. Based on our findings, none of the transgenic plants were immune to CLas. However, the STX-5 and STX-11 lines showed reduced susceptibility to HLB with mild disease symptoms and low incidence of plants with the presence of CLas. Fruit and juice quality were not affected by the genetic transformation. Further, no residues of the sarcotoxin IA protein were found in the juice of the STX-11 and STX-12 fruits, though detected in the juice of the STX-5 and STX-13 lines, as revealed by the immunoblotting test. However, juices from all transgenic lines showed low traces of sarcotoxin IA peptide in its composition. The accumulation of this peptide did not cause any deleterious effects on plants or in fruit/juice. Our findings reinforce the challenges of identifying novel approaches to managing HLB.

A co-culture of a novel thermoacidophilic, obligate symbiotic archaeon, designated as strain MJ1T, with its specific host archaeon Metallosphaera sedula strain MJ1HA was obtained from a terrestrial hot spring in Japan. Strain MJ1T grew in the co-culture under aerobic conditions. Coccoid cells of strain MJ1T were 200–500 nm in diameter, and attached to the MJ1HA cells in the co-culture. The ranges and optima of the growth temperature and pH of strain MJ1T in the co-culture were 60–75 °C (optimum, 65–70 °C) and pH 1.0–4.0 (optimum, pH 2.5), respectively. Core lipids of dialkyl glycerol tetraethers (GDGT)−3 and GDGT-4 were highly abundant in MJ1T cells concentrated from the co-culture. Strain MJ1T has a small genome (0.67 Mbp) lacking genes for biosynthesis of essential biomolecules, such as nucleotides, lipids and ATP. The genomic DNA G+C content was 24.9 mol%. The 16S rRNA gene sequence of strain MJ1T was most closely related to that of the cultivated species, ‘Nanopusillus acidilobi’ strain N7A (85.8 % similarity). Based on phylogenetic and physiological characteristics, we propose the name Nanobdella aerobiophila gen. nov., sp. nov. to accommodate the strain MJ1T (=JCM 33616T=DSM 111728T). In addition, we propose the names Nanobdellaceae fam. nov., Nanobdellales ord. nov., and Nanobdellia class. nov. to accommodate the novel genus.