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Abstract Ni.tro.so.pe.la'gi.cus. N.L. masc. adj. nitrosus nitrous; L. masc. adj. pelagicus of the open sea; N.L. masc. n. Nitrosopelagicus a nitrite producer of the open sea. The genus Candidatus Nitrosopelagicus is composed of marine ammonia‐oxidizing archaea, almost all of which are uncultivated. They are found in shallow waters (<200 m depth) of the oligotrophic tropical, subtropical, and temperate open oceans. A single species has been described, Candidatus Nitrosopelagicus brevis, which couples growth with the oxidation of ammonia to nitrite. One described strain ( Ca . N. brevis U25) is capable of hydrolyzing urea to supply the ammonia required for growth. Cells are obligately aerobic, small, and nonmotile rods. They grow free‐living, not associated with surfaces. No growth enhancement has been observed in the presence of organic carbon compounds; a reduction in the lag phase of growth has been observed with addition of α‐ketoacids, potentially serving as radical oxygen scavengers. Organisms are mesophilic and obligately marine. Lipid composition distinguishes Ca . Nitrosopelagicus from Nitrosopumilus using glycerol dibiphytanyl glycerol tetraether (GDGT) distributions, with lower amounts of GDGT‐2 and higher amounts of GDGT‐0 and GDGT‐1 found in Ca . Nitrosopelagicus. Abundance of Ca . Nitrospelagicus‐like organisms is correlated with nitrification rates, suggesting that these organisms are the dominant ammonia oxidizers in epipelagic and upper mesopelagic environments of the low‐ and mid‐latitude open oceans. DNA G + C content (mol%) : 33.1. Type species : Candidatus Nitrosopelagicus brevis Santoro et al. 2015. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nitrosopelagicus is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / Nitrososphaeria / Nitrosopumilales / incertae sedis / Candidatus Nitrosopelagicus The genus Candidatus Nitrosopelagicus can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nitrosopelagicus (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales / f__Nitrosopumilaceae / g__Nitrosopelagicus * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

In Iran, polyphasic studies of unicellular cyanobacteria are still scarce, with more emphasis being placed on filamentous cyanobacteria in paddy fields and fresh water regions. In an effort to increase the knowledge of the diversity of unicellular cyanobacteria from paddy fields in Iran, we have isolated and characterized a new unicellular cyanobacterium strain. The strain was studied using a polyphasic approach based on morphological, ecological and phylogenetic analyses of the 16S–23S ITS rRNA gene region. Complementarily, we have searched for the presence of cyanotoxin genes and analysed the pigment content of the strain. Results showed that the strain was morphologically indistinguishable from the genus Chroococcus , but phylogenetic analyses based on the Bayesian inference and maximum-likelihood methods placed the strain in a separated monophyletic and highly supported (0.99/98, posterior probability/maximum-likelihood) genus-level cluster, distant from Chroococcus sensu stricto and with Chalicogloea cavernicola as sister taxa. The calculated p-distance for the 16S rRNA gene also reinforced the presence of a new genus, by showing 92 % similarity to C. cavernicola . The D1–D1′, Box-B and V3 ITS secondary structures showed the uniqueness of this strain, as it shared no similar pattern with closest genera within the Chroococcales. For all these reasons, and in accordance with the International Code of Nomenclature for Algae, Fungi and Plants, we here proposed the description of a new genus with the name Alborzia gen. nov. along with the description of a new species, Alborzia kermanshahica sp. nov. (holotype: CCC1399-a; reference strains CCC1399-b; MCC 4116).

The actinobacterial strain 15G-AUS-rotT was isolated from an artificial pond located near Salzburg, Austria. The strain showed 16S rRNA gene sequence similarities of 98.7 % to Candidatus Aquiluna rubra and of 96.6 and 96.7 % to the two validly described species of the genus Rhodoluna . Phylogenetic reconstructions based on 16S rRNA gene sequences and genome-based on amino acid sequences of 118 single copy genes referred strain 15G-AUS-rotT to the family Microbacteriaceae and therein to the so-called subcluster Luna-1. The genome-based phylogenetic tree showed that the new strain represents a putative new genus. Cultures of strain 15G-AUS-rotT were light red pigmented and comprised very small, rod-shaped cells. They metabolized a broad variety of substrates. Major fatty acids (>10 %) of cells were iso-C16 : 0, antiso-C15 : 0 and iso-C14 : 0. The major respiratory quinone was MK-11 and a minor component was MK-10. The peptidoglycan structure belonged to an unusual B type. The closed genome sequence of the strain was very small (1.4 Mbp) and had a DNA G+C content of 54.8 mol%. An interesting feature was the presence of genes putatively encoding the complete light-driven proton pumping actinorhodopsin/retinal system, which were located at three different positions of the genome. Based on the characteristics of the strain, a new genus and a new species termed Aquiluna borgnonia is proposed for strain 15G-AUS-rotT (=DSM 107803T=JCM 32974T).

Abstract Presence of glycogen granules in anaerobic ammonium-oxidizing (anammox) bacteria has been reported so far. However, very little is known about their glycogen metabolism and the exact roles. Here, we studied the glycogen metabolism in “Ca. Brocadia sinica” growing in continuous retentostat cultures with bicarbonate as a carbon source. The effect of the culture growth phase was investigated. During the growing phase, intracellular glycogen content increased up to 32.6 mg-glucose (g-biomass dry wt)−1 while the specific growth rate and ATP/ADP ratio decreased. The accumulated glycogen begun to decrease at the onset of entering the near-zero growth phase and was consumed rapidly when substrates were depleted. This clearly indicates that glycogen was synthesized and utilized as an energy storage. The proteomic analysis revealed that “Ca. B. sinica” synthesized glycogen via three known glycogen biosynthesis pathways and simultaneously degraded during the progress of active anammox, implying that glycogen is being continuously recycled. When cells were starved, a part of stored glycogen was converted to trehalose, a potential stress protectant. This suggests that glycogen serves at least as a primary carbon source of trehalose synthesis for survival. This study provides the first physiological evidence of glycogen metabolism in anammox bacteria and its significance in survival under natural substrate-limited habitat.

Abstract Hal.ec.to.sym.bi.o'ta. Gr. masc. n. hals , halos salt, salt water; Gr. prep. ektos outside; N.L. masc. n. symbiota (from Gr. n. symbiotes ) one who lives with a companion, partner; N.L. masc. n. Halectosymbiota an ectosymbiont from salt water organisms. The genus Candidatus Halectosymbiota corrig., originally described as Ca . Haloectosymbiotes, was established based on a 16S rRNA taxonomic marker gene sequence of the only identified species in this genus, Candidatus Halectosymbiota riaformosensis. Ca . Halectosymbiota riaformosensis was observed to live as ectosymbiont on a halophile scuticociliate, which was isolated from a thalassohaline solar saltern pond (12% salinity) in Faro, Portugal. Comparisons of 16S rRNA gene sequences showed that Ca . Halectosymbiota is phylogenetically affiliated to the genera Halolamina (sequence similarity to H. pelagica : 87%) and Halobaculum (sequence similarity to H. magnesiiphilum 85%). Based on scanning electron microscopy micrographs and fluorescence in situ hybridization, cells are rod‐shaped and approximately 1.8 × 0.6 μm in size. Cells are densely covering the surface of the host, with approximately 0.52 epibiotic cells per μm 2 . Free‐living forms were not observed. Candidatus Halectosymbiota riaformosensis is sensitive to anisomycin. Known habitats are aquatic hypersaline environments. Type species : Not applicable. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Halectosymbiota is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Halobacteria / Halobacteriales / Halobacteriaceae / Candidatus Halectosymbiota Candidatus Halectosymbiota could not be recovered in GTDB ** . * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Me.tha.no.tri.cha'les. N.L. fem. n. Methanothrix type genus of the order; suff. ‐ ales the ending to denote an order; N.L. fem. pl. n. Methanotrichales the order of Methanothrix . Cells are nonmotile, sheathed rods with flat ends. Gram‐stain negative. Lipids contain myo ‐inositol, ethanolamine, and galactose as the polar head groups. Species are oxygen‐tolerant anaerobe. However, growth and methanogenesis can only occur in strictly anaerobic and highly reducing conditions. Energy is obtained by splitting acetate into methane and CO 2 . When cocultured with electrogenic Geobacter spp., CO 2 is reduced to methane via direct interspecies electron transfer (DIET). Optimum growth pH range is 7.0–7.8. Mesophilic and thermophilic. Optimum growth temperatures are 34–37°C for mesophilic strains and 55–60°C for thermophilic strains. They occupy a wide range of anoxic habitats including anaerobic river mud, paddy field soil, hot springs, thermal lakes, thermophilic, and mesophilic anaerobic wastewater digesters treating domestic wastes; granular sludge, anaerobic fixed‐bed reactors, and other types of anaerobic systems. Genome sequences have been determined for strains of all three of the described species in the order, and the genome size ranges from 1.9 to 3.0 Mb. The order Methanotrichales consists of one family Methanotrichaceae . Although all three described species are currently classified in a single genus Methanothrix , phylogenomic analyses suggest that two species should be transferred to novel genera. DNA G + C content (mol%) : 51–61 (Genome). Type genus : Methanothrix Huser et al. 1982, VL10. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Methanotrichales is: synonym (and no standing) (last update, February 2025) * . Correct name: Methanosarcinales LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Methanosarcinia / Methanosarcinales The order Methanotrichales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Methanotrichales (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Methanosarcinia / o__Methanotrichales * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Ther.mo.ha.lo.bac.te.ra.ce'ae. N.L. masc. n. Thermohalobacter , type genus of the family; suff. ‐aceae , ending to denote a family; N.L. fem. pl. n. Thermohalobacteraceae , the Thermohalobacter family. Free‐living bacteria that mainly occur in anoxic saline environments. Cells are not pigmented and have a Gram‐positive type of cell wall. Gram‐stain reaction can be negative or positive. Typically slender rod‐shaped cells that are motile by flagella. Several strains form heat‐resistant spores. Mainly euryhaline, moderately thermophilic and halophilic. Members of the family are strictly anaerobic bacteria that utilize carbohydrates or peptides by fermentation. Cellular fatty acid patterns are dominated by iso ‐C 15:0 and iso ‐C 15:0 DMA. The family currently accommodates members of the genera Thermohalobacter , Caldisalinibacter , Caloranaerobacter , Brassicibacter , Sporosalibacterium , and Clostridiisalibacter , which were previously affiliated with the family Clostridiaceae . The affiliation of novel species to this family depends on the phylogenetic position, which should be determined on the basis of comparative sequence analyses of 16S rRNA genes or genomes. DNA G + C content (mol%): 28–33. Type genus: Thermohalobacter Cayol et al. 2000. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Thermohalobacteraceae is: synonym (last update, February 2025) * . Correct name: Clostridiaceae LPSN classification: Bacteria / Bacillati / Bacillota / Clostridia / Eubacteriales / Clostridiaceae The family Thermohalobacteraceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__Thermohalobacteraceae (version v220) ** . GTDB classification: d__Bacteria / p__Bacillota_A / c__Clostridia / o__Tissierellales / f__Thermohalobacteraceae * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

Abstract Phy.to.plas‐ma. Gr. masc. n. phytos a plant; N.L. neut. n. Phytoplasma a form from a plant. Phytoplasmas are wall‐less, nutritionally fastidious, and phytopathogenic prokaryotes 0.2–0.8 μm in diameter that morphologically resemble nonhelical members of the class Mollicutes . Sequencing of nearly full‐length PCR‐amplified 16S rRNA genes, combined with earlier studies, provided the first comprehensive phylogeny of the organisms and showed that they constitute a unique, monophyletic clade within the Mollicutes . These organisms are most closely related to members of the genus Acholeplasma within the Anaeroplasma clade as defined by Weisburg et al. Despite decades of efforts and recent progress, sustained pure culture in cell‐free media has not yet been demonstrated for any phytoplasma. Their genome sizes have been estimated to range from 530 to 1,350 kb, and the DNA G + C content is about 23–30 mol%. The presence of a characteristic oligonucleotide sequence in the 16S rRNA gene, CAA GAY BAT KAT GTK TAG CYG GDC T, and standard codon usage indicate that phytoplasmas represent a distinct genus‐level taxon for which the name ‘ Candidatus Phytoplasma’ has been adopted. At present, for any subtaxa within the provisional genus, the designation ‘ Candidatus ’ must still be used. DNA G + C content (mol%) : 23–29. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Phytoplasma is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Bacteria / Bacillati / Mycoplasmatota / Mollicutes / Acholeplasmatales / Acholeplasmataceae / Candidatus Phytoplasma Candidatus Phytoplasma could not be recovered in GTDB ** . * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776

‘Candidatus Liberibacter asiaticus’ (CLas) is the pathogenic bacterium that causes the disease Huanglongbing (HLB) in citrus and some model plants, such as Nicotiana benthamiana. After infection, CLas releases a set of effectors to modulate host responses. One of these critical effectors is Sec-delivered effector 1 (SDE1), which induces chlorosis and cell death in N. benthamiana. In this study, we revealed the DEAD-box RNA helicase (DDX3) interacts with SDE1. Gene silencing study revealed that knockdown of the NbDDX3 gene triggers leaf chlorosis, mimicking the primary symptom of CLas infection in N. benthamiana. The interactions between SDE1 and NbDDX3 were localized in the cell membrane. Overexpression of SDE1 resulted in suppression of NbDDX3 gene expression in N. benthamiana, which suggests a critical role of SDE1 in modulating NbDDX3 expression. Furthermore, we verified the interaction of SDE1 with citrus DDX3 (CsDDX3), and demonstrated that the expression of the CsDDX3 gene was significantly reduced in HLB-affected yellowing and mottled leaves of citrus. Thus, we provide molecular evidence that the downregulation of the host DDX3 gene is a crucial mechanism of leaf chlorosis in HLB-affected plants. The identification of CsDDX3 as a critical target of SDE1 and its association with HLB symptom development indicates that the DDX3 gene is an important target for gene editing, to interrupt the interaction between DDX3 and SDE1, and therefore interfere host susceptibility.

Abstract Me.tha'no.thrix. N.L. neut. n. methanum methane; Gr. fem. n. thrix , hair; N.L. fem. n. Methanothrix , methane (‐producing) hair. Straight, rod‐shaped cells with flat ends, usually 0.8–1.3 μm wide by 2.0–6.0 μm long enclosed in a tubular sheath. Forms short (∼5–25 μm) to long (>150 μm) flexible chains of cells within the sheath. Nonmotile. Gram‐stain‐negative. Lipids contain myo ‐inositol, ethanolamine, and galactose as the polar head groups. Oxygen‐tolerant anaerobe. Organotrophic, splitting acetate into methane and CO 2 for energy generation. Some strains split formate into H 2 and CO 2 without producing methane. CO 2 can be reduced to methane in coculture with Geobacter spp. via direct interspecies electron transfer (DIET). Growth factors such as vitamins are stimulatory. Yeast extract is required, stimulatory or inhibitory, depending on the strain. NaCl is not required for growth. Optimal temperatures range from 34 to 37°C for mesophilic strains and 55 to 60°C for thermophilic strains; optimal pH range is 7.0–7.8. Gas vacuoles are generally found in thermophilic strains. Occur in both mesophilic and thermophilic anaerobic sludge digesters as well as anaerobic sediments. Synonymous with the genus Methanosaeta . DNA G + C content (mol%) : 51–61 (genome). Type species : Methanothrix soehngenii Huser et al. 1982, VL10. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Methanothrix is: correct name (last update, February 2025) * . LPSN classification: Archaea / Methanobacteriati / Methanobacteriota / Methanosarcinia / Methanosarcinales / Methanotrichaceae / Methanothrix The genus Methanothrix can also be recovered in the Genome Taxonomy Database (GTDB) as g__Methanothrix (version v220) ** . GTDB classification: d__Archaea / p__Halobacteriota / c__Methanosarcinia / o__Methanotrichales / f__Methanotrichaceae / g__Methanothrix * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776