Publications

4866

We report the complete genome sequence and annotation of “ Candidatus Nardonella dryophthoridicola” strain NardRF, obtained by sequencing its host bacteriome, Rhynchophorus ferrugineus , using Oxford Nanopore technology.

AbstractBACKGROUNDDiaphorina citri is a vector of ‘Candidatus Liberibacter asiaticus’ (CLas), which is associated with citrus huanglongbing (HLB). In this study, the adaptability and CLas titres of D. citri adults on three weed species, namely, Ageratum conyzoides, Solanum nigrum and Praxelis clematidea, which are widely distributed in citrus orchards in China, were determined.RESULTSD. citri selected S. nigrum preferentially over the other weed species. The longest survival times of D. citri adults on A. conyzoides, S. nigrum and P. clematidea were 48, 41 and 11 days, respectively. On S. nigrum, the survivorship of females was significantly higher than that of males. The CLas titres of D. citri adults feeding on the three weeds for 1 week increased significantly during autumn but did not change significantly during spring. Conversely, the titres of adults on citrus increased significantly during spring but did not change significantly during autumn.CONCLUSIOND. citri exhibited different adaptabilities to the three weed species, but the CLas titres of D. citri adults did not decrease on any of the weeds. These results suggested that the three weed species could help dispersing of D. citri and transmission of CLas while ideal host conditions were scarce or absent. © 2021 Society of Chemical Industry.

Summary An anaerobic enrichment with CO from sediments of hypersaline soda lakes resulted in a methane‐forming binary culture, whereby CO was utilized by a bacterium and not the methanogenic partner. The bacterial isolate ANCO1 forms a deep‐branching phylogenetic lineage at the level of a new family within the class ‘ Natranaerobiia ’. It is an extreme haloalkaliphilic and moderate thermophilic acetogen utilizing CO, formate, pyruvate and lactate as electron donors and thiosulfate, nitrate (reduced to ammonia) and fumarate as electron acceptors. The genome of ANCO1 encodes a full Wood–Ljungdahl pathway allowing for CO oxidation and acetogenic conversion of pyruvate. A locus encoding Nap nitrate reductase/NrfA ammonifying nitrite reductase is also present. Thiosulfate respiration is encoded by a Phs/Psr‐like operon. The organism obviously relies on Na‐based bioenergetics, since the genome encodes for the Na + ‐Rnf complex, Na + ‐F1F0 ATPase and Na + ‐translocating decarboxylase. Glycine betaine serves as a compatible solute. ANCO1 has an unusual membrane polar lipid composition dominated by diethers, more common among archaea, probably a result of adaptation to multiple extremophilic conditions. Overall, ANCO1 represents a unique example of a triple extremophilic CO‐oxidizing anaerobe and is classified as a novel genus and species Natranaerofaba carboxydovora in a novel family Natranaerofabacea .

Abstract Na.no.ha.lo'bi.um. Gr. masc. n. nanos a dwarf; Gr. masc. n. hals , halos salt; Gr. masc. n. bios life; N.L. neut. n. Nanohalobium small organism living in salt. The genus Candidatus Nanohalobium was established based on a genome sequence found after the enrichment, cultivation, and characterization of a binary association with its chitinolytic host, obtained from a crystallizer pond brine collected in the marine solar saltern Saline della Laguna of Trapani, Italy. Ca . Nanohalobium is phylogenetically affiliated with members of the Ca . Nanohaloarchaeota ( Candidatus Haloredivivus, Candidatus Nanosalina, and Candidatus Nanosalinicola) of the archaeal DPANN superphylum. Cultivation experiments and analysis of the 0.97 Mb genome of Ca . Nanohalobium constans LC1Nh revealed that the organism has an organoheterotrophic, sugar‐fermenting lifestyle, lacking key anabolic machinery and any respiratory complexes. Additionally, the cultivation experiments revealed a remarkable mutualism of a nanohaloarchaeon–haloarchaeon association, namely the nanohaloarchaeon's ability to hydrolyze glycogen and starch to glucose, enabling the growth of Halomicrobium sp. LC1Hm in the absence of chitin. The low‐median isoelectric point for the predicted proteins suggests a “salt‐in” strategy used by the nanohaloarchaeon for osmotic balance. 16S rRNA gene sequences affiliated with Ca . Nanohalobium were recovered from other saltern ponds and hypersaline lakes worldwide. DNA G + C content (mol%) : 43.2 (genome). Type species : Candidatus Nanohalobium constans , La Cono et al. 2020. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nanohalobium is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Nanobdellati / Candidatus Nanohalarchaeota / Candidatus Nanohalobiia / Candidatus Nanohalobiales / Candidatus Nanohalobiaceae / Candidatus Nanohalobium The genus Candidatus Nanohalobium can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nanohalobium (version v220) ** . GTDB classification: d__Archaea / p__Nanohaloarchaeota / c__Nanosalinia / o__Nanosalinales / f__Nanosalinaceae / g__Nanohalobium * 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 Sil.va.ni.grel'la. N.L. fem. dim. n. Silvanigrella named after Silva nigra the Latin geographic name of the Schwarzwald (Black Forest) mountains located in the south‐west of Germany. The genus Silvanigrella accommodates heterotrophic freshwater bacteria isolated from the water column of circumneutral or slightly acidic (pH 5–7) lakes and ponds with low ion concentrations (conductivity < 30 μS/cm). So far, only the two species Silvanigrella aquatica and Silvanigrella paludirubra have been described. Cells of the type strains have in common red pigmentation, motility, and pleomorphic morphology. In both species, the cell morphology ranges from rod‐shaped cells to filamentous forms, the cell size is variable in length and width. The type strain of S. aquatica in addition forms, densely coiled spirals. The type strains of both species grow at temperatures above 30°C, but only the type strain of S. paludirubra grows at temperatures below 10°C. Growth occurred up to supplementary NaCl concentrations of 1.0–1.1% (w/v). Both type strains utilized various organic substrates including carbohydrates, amino acids, and short‐chain fatty acids; however, the substrate spectra of the two strains differed. The most abundant fatty acid was iso‐C 15:0 for both type strains, contributing 33% to the total fatty acid content. The major respiratory quinone of S. paludirubra is menaquinone MK‐8, while the quinones of S. aquatica remained unidentified. The type strains of S. aquatica and S. paludirubra were both characterized by medium‐sized genomes (3.5 and 3.9 Mb, respectively) with low G + C content (32.6 and 29.3 mol%, respectively). DNA G + C content (mol%) : 29–33 (genome sequencing). Type species : Silvanigrella aquatica Hahn et al. 2017 VP . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Silvanigrella is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Pseudomonadati / Pseudomonadota / Oligoflexia / Silvanigrellales / Silvanigrellaceae / Silvanigrella The genus Silvanigrella can also be recovered in the Genome Taxonomy Database (GTDB) as g__Silvanigrella (version v220) ** . GTDB classification: d__Bacteria / p__Bdellovibrionota / c__Oligoflexia / o__Silvanigrellales / f__Silvanigrellaceae / g__Silvanigrella * 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 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

La papa Solanum tuberosum L pertenece a la familia de las solanáceas, es el cuarto cultivo sembrado en más de 100 países incluyendo Nicaragua, en este país existe un consumo por persona de hasta unos 8 kg anuales, la papa se cultiva en Nicaragua entre 800 a 1 200 hectáreas y se obtiene una producción que representa de 35 % a 40 % de la demanda nacional. El objetivo del presente estudio fue determinar la fluctuación poblacional de  Bactericera cockerelli e incidencia de punta morada (Candidatus liberibacter, Solanacearum) en lotes comerciales de papa en el municipio de Estelí entre los meses de enero a noviembre de 2014,  la toma de datos se realizó en lotes de papa en las localidades de Miraflor y El Tisey, los lotes fueron seleccionados con similitud en condiciones climáticas y de manejo del cultivo, en cada lote seleccionado se colocaron trampas amarillas con pegamento para la captura de adultos de B. cockerelli, de igual manera se realizaron muestreos aleatorios en 100 plantas por lote para medir la fluctuación poblacional de ninfas y adultos del vector, así como para medir la incidencia de síntomas similares a Candidatus liberibacter, solanacearum  de las cuales se seleccionaron cinco plantas para análisis y detección del patógeno a través de la técnica de PCR en el Centro Nacional de Diagnostico Fitosanitario del IPSA.  Los resultados indican que el insecto estuvo presente desde el inicio del estudio siendo las mayores capturas en los meses febrero a mayo; julio, agosto y octubre con 0.84 insectos promedio por trampa, de igual manera los meses de marzo, abril, julio y octubre fueron donde se expresaron más plantas con síntomas de 3 al 4% incidencia, así mismo de las muestras tomadas solamente el 20% resultó positivas a la enfermedad coincidiendo con baja poblaciones del insecto vector.

Our results suggest that Midichloria mitochondrii , the intramitochondrial bacterium, does not invade mitochondria like predatory bacteria do but instead moves from mitochondrion to mitochondrion within the oocytes of Ixodes ricinus . A better understanding of the lifestyle of M. mitochondrii will allow us to better define the role of this bacterial symbiont in the host physiology.

Citrus production is facing an unprecedented problem because of huanglongbing (HLB) disease. Presently, no effective HLB-easing method is available when citrus becomes infected. Guanosine 5′-monophosphate synthetase (GMPS) is a key protein in the de novo synthesis of guanine nucleotides. GMPS is used as an attractive target for developing agents that are effective against the patogen infection. In this research, homology modeling, structure-based virtual screening, and molecular docking were used to discover the new inhibitors against CLas GMPS. Enzyme assay showed that folic acid and AZD1152 showed high inhibition at micromole concentrations, with AZD1152 being the most potent molecule. The inhibition constant (Ki) value of folic acid and AZD1152 was 51.98 µM and 4.05 µM, respectively. These results suggested that folic acid and AZD1152 could be considered as promising candidates for the development of CLas agents.