Publications

4715

Summary Thermoplasmata is a widely distributed and ecologically important archaeal class in the phylum Euryarchaeota. Because few cultures and genomes are available, uncharacterized Thermoplasmata metabolisms remain unexplored. In this study, we obtained four medium‐ to high‐quality archaeal metagenome‐assembled genomes (MAGs) from the filamentous fragments of black‐odorous aquatic sediments (Foshan, Guangdong, China). Based on their 16S rRNA gene and ribosomal protein phylogenies, the four MAGs belong to the previously unnamed Thermoplasmata UBA10834 clade. We propose that this clade (five reference genomes from the Genome Taxonomy Database (GTDB) and four MAGs from this study) be considered a new order, Candidatus Gimiplasmatales. Metabolic pathway reconstructions indicated that the Ca . Gimiplasmatales MAGs can biosynthesize isoprenoids and nucleotides de novo . Additionally, some taxa have genes for formaldehyde and acetate assimilation, and the Wood–Ljungdahl CO 2 ‐fixation pathway, indicating a mixotrophic lifestyle. Sulfur reduction, hydrogen metabolism, and arsenic detoxification pathways were predicted, indicating sulfur‐, hydrogen‐, and arsenic‐transformation potentials. Comparative genomics indicated that the H 4 F Wood–Ljungdahl pathway of both Ca . Gimiplasmatales and Methanomassiliicoccales was likely obtained by the interdomain lateral gene transfer from the Firmicutes. Collectively, this study elucidates the taxonomic and potential metabolic diversity of the new order Ca . Gimiplasmatales and the evolution of this subgroup and its sister lineage Methanomassiliicoccales.

‘Candidatus Liberibacter asiaticus’ (CLas) is the predominant causal agent of citrus huanglongbing, the most devastating citrus disease worldwide. CLas colonizes phloem tissue and causes phloem dysfunction. The pathogen population size in local tissues and in the whole plant is critical for the development of disease symptoms by determining the load of pathogenicity factors and metabolic burden to the host. However, the total population size of CLas in a whole plant and the ratio of CLas to citrus cells in local tissues have not been addressed previously. The total CLas population size for 2.5-year-old ‘Valencia’ sweet orange on ‘Kuharske’ citrange rootstock trees was quantified using quantitative PCR to be approximately 1.74 × 109 cells/tree, whereas 7- and 20-year-old sweet orange trees were estimated to be 4.3 × 1010 cells/tree, and 6.0 × 1010 cells/tree, respectively. The majority of CLas cells were distributed in leaf tissues (55.58%), followed by those in branch (36.78%), feeder root (4.75%), trunk (2.39%), and structural root (0.51%) tissues. The ratios of citrus cells to CLas cells for branch, leaf, trunk, feeder root, and structural root samples were within approximately 39 to 79, 44 to 124, 153 to 1,355, 191 to 1,054, and 561 to 3,760, respectively, representing the metabolic burden of CLas in different organs. It was estimated that the ratios of phloem cells to CLas cells for branch, leaf, trunk, feeder root, and structural root samples are approximately 0.39 to 0.79, 0.44 to 1.24, 1.53 to 13.55, 1.91 to 10.54, and 5.61 to 37.60, respectively. Approximately 0.01% of the total citrus phloem volume was estimated to be occupied by CLas, explaining the difficulty to observe CLas in most tissues under transmission electron microscopy. The CLas titer inside the leaf was estimated to be approximately 1.64 × 106 cells/leaf or 9.2 × 104 cells cm–2 in leaves, approximately 104 times less than that of typical apoplastic bacterial pathogens. This study provides quantitative estimates of phloem colonization by bacterial pathogens and furthers the understanding of the biology and virulence mechanisms of CLas.

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

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.

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