Publications

3843

SummaryLarge amounts of detrital organic matter and osmolytes accumulate in the sediments of hadal trenches (>6000 m depth) due to the funnelling effect. It is still unknown whether there are novel active microbes that depend on specific carbon sources in extreme and isolated environments. In this study, we present a novel active bacterial phylum, Candidatus Tianyabacteria in the FCB superphylum, which was enriched in sediments collected from the Challenger Deep. Genome binning resulted in high‐quality Ca. Tianyabacteria genomes representing two Ca. Tianyabacteria lineages (L1 and L2) in sediments 0–21 cm below the surface (cmbsf); L1 tends to be abundant in the upper layers (0–9 cmbsf), and L2 seems to be more prevalent in the deeper layers (12–21 cmbsf). Gene annotation and transcriptomics results indicate that the two lineages might import and catalyse amino acids and myo‐inositol into central carbon metabolism for a heterotrophic lifestyle. Probably due to differences in environmental oxygen levels, the L2 genomes harbour gene clusters responsible for denitrification and fermentation, while the L1 genomes encode octahaem cytochrome c and multicopper oxidase using unknown substrates. The Ca. Tianyabacteria are thus novel heterotrophic organisms that participate in processes of carbon, nitrogen and organic osmolyte cycling in hadal sediments.

SummaryAn 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.

‘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.

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. Proteobacteria / Oligoflexia / Silvanigrellales / Silvanigrellaceae / Silvanigrella 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 .

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.

AbstractAsgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca. Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero-organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of bacteria and eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.