Publications

4721

Summary Uncultivated microbial clades (‘microbial dark matter’) are inferred to play important but uncharacterized roles in nutrient cycling. Using Antarctic lake (Ace Lake, Vestfold Hills) metagenomes, 12 metagenome‐assembled genomes (MAGs; 88%–100% complete) were generated for four ‘dark matter’ phyla: six MAGs from Candidatus Auribacterota (=Aureabacteria, SURF‐CP‐2), inferred to be hydrogen‐ and sulfide‐producing fermentative heterotrophs, with individual MAGs encoding bacterial microcompartments (BMCs), gas vesicles, and type IV pili; one MAG (100% complete) from Candidatus Hinthialibacterota (=OLB16), inferred to be a facultative anaerobe capable of dissimilatory nitrate reduction to ammonia, specialized for mineralization of complex organic matter (e.g. sulfated polysaccharides), and encoding BMCs, flagella, and Tad pili; three MAGs from Candidatus Electryoneota (=AABM5‐125‐24), previously reported to include facultative anaerobes capable of dissimilatory sulfate reduction, and here inferred to perform sulfite oxidation, reverse tricarboxylic acid cycle for autotrophy, and possess numerous proteolytic enzymes; two MAGs from Candidatus Lernaellota (=FEN‐1099), inferred to be capable of formate oxidation, amino acid fermentation, and possess numerous enzymes for protein and polysaccharide degradation. The presence of 16S rRNA gene sequences in public metagenome datasets (88%–100% identity) suggests these ‘dark matter’ phyla contribute to sulfur cycling, degradation of complex organic matter, ammonification and/or chemolithoautotrophic CO 2 fixation in diverse global environments.

Summary The KTK 4A‐related Thermoplasmata thrives in the sediment of saline lakes; however, systematic research on its taxonomy, environmental adaptation and metabolism is lacking. Here, we detected this abundant lineage in the sediment of five artificially separated ponds (salinity 7.0%–33.0%) within a Chinese soda‐saline lake using culture‐independent metagenomics and archaeal 16S rRNA gene amplicons. The phylogenies based on the 16S rRNA gene, and 122 archaeal ubiquitous single‐copy proteins and genome‐level identity analyses among the metagenome‐assembled genomes demonstrate this lineage forming a novel order, Candidatus Haloplasmatales, comprising four genera affiliated with the identical family. Isoelectric point profiles of predicted proteomes suggest that most members adopt the energetically favourable ‘salt‐in’ strategy. Functional prediction indicates the lithoheterotrophic nature with the versatile metabolic potentials for carbohydrate and organic acids as well as carbon monoxide and hydrogen utilization. Additionally, hydrogenase genes hdrABC ‐ mvhADG are linked with incomplete reductive citrate cycle genes in the genomes, suggesting their functional connection. Comparison with the coupling of HdrABC‐MvhADG and methanogenesis pathway provides new insights into the compatibility of laterally acquired methanogenesis with energy metabolism in the related order Methanomassiliicoccales . Globally, our research sheds light on the taxonomy, environmental adaptative mechanisms, metabolic potentials and evolutional significance of Ca . Haloplasmatales.

AbstractCandidatus Liberibacter solanacearum (CLso) transmitted by the carrot psyllid, Bactericera trigonica causes carrot yellows in Israel, and has recently gained much importance due to the excessive economical loss. Understanding the interactions between CLso and the psyllid at the cellular level is fundamental for the disease management. Here, we demonstrate the role of calcium ATPase, cytosolic calcium and most importantly Beclin1 in regulating autophagy and its association with Liberibacter. Presence of CLso generates reactive oxygen species and induces the expression of the detoxification enzymes in the psyllid midguts. CLso also induces the expression of both sarco/endoplasmic reticulum Ca2+ pump (SERCA) and 1,4,5-trisphosphate receptors (ITPR) in the midguts, followed by high levels of calcium in the cytosol. Silencing these proteins individually disrupted the calcium levels in the cytosol leading to direct effects on autophagy and thus on Liberibacter. On the other hand, inhibiting Beclin1-phosphorylation through different calcium induced kinases altered the expression of autophagy and CLso abundance. This study establishes a direct correlation between cytosolic calcium levels, autophagy and CLso in the carrot psyllid midgut.

The genus ‘Candidatus Phytoplasma’ was proposed to accommodate cell wall-less bacteria that are molecularly and biochemically incompletely characterized, and colonize plant phloem and insect vector tissues. This provisional classification is highly relevant due to its application in epidemiological and ecological studies, mainly aimed at keeping the severe phytoplasma plant diseases under control worldwide. Given the increasing discovery of molecular diversity within the genus ‘Ca. Phytoplasma’, the proposed guidelines were revised and clarified to accommodate those ‘Ca. Phytoplasma’ species strains sharing >98.65 % sequence identity of their full or nearly full 16S rRNA gene sequences, obtained with at least twofold coverage of the sequence, compared with those of the reference strain of such species. Strains sharing <98.65 % sequence identity with the reference strain but >98.65 % with other strain(s) within the same ‘Ca. Phytoplasma’ species should be considered related strains to that ‘Ca. Phytoplasma’ species. The guidelines herein, keep the original published reference strains. However, to improve ‘Ca. Phytoplasma’ species assignment, complementary strains are suggested as an alternative to the reference strains. This will be implemented when only a partial 16S rRNA gene and/or a few other genes have been sequenced, or the strain is no longer available for further molecular characterization. Lists of ‘Ca. Phytoplasma’ species and alternative reference strains described are reported. For new ‘Ca. Phytoplasma’ species that will be assigned with identity ≥98.65 % of their 16S rRNA gene sequences, a threshold of 95 % genome-wide average nucleotide identity is suggested. When the whole genome sequences are unavailable, two among conserved housekeeping genes could be used. There are 49 officially published ‘Candidatus Phytoplasma’ species, including ‘Ca. P. cocostanzaniae’ and ‘Ca. P. palmae’ described in this manuscript.

The deep ocean microbiota represents the unexplored majority of global ocean waters. The phylum Chloroflexi is abundant and broadly distributed in various deep-sea ecosystems.

Manganese (Mn) is an abundant redox-active metal that cycles in many of Earth’s biomes. While diverse bacteria and archaea have been demonstrated to respire Mn(III/IV), only recently have bacteria been implicated in Mn(II) oxidation-dependent growth.

El trabajo se llevó a cabo en tres localidades, Salache, Machachi y Saquisilí, donde se determinó el comportamiento y hábitos del psílido (Bactericera cockerelli.), responsable de la transmisión del fitoplasma conocido como punta morada en el cultivo de papa (Solanum tuberosum). Se observó el desarrollo del insecto, alimentándolo con follaje fresco de plantas de papa, mantenidos en cámaras artesanales de cría; para Salache la temperatura promedio fue de 21 ºC y una humedad relativa del 68% con un ciclo total de 31 días; para Saquisilí se mantuvieron con una humedad relativa promedio de 75%, y una temperatura de 13,9°C con un ciclo total de 33 días y en Machachi se mantuvo una temperatura alrededor de 17°C y una humedad relativa de 74% con un ciclo total de 34 días.  Los datos registrados en todo el proceso fueron: número de huevos depositados, tiempo de desarrollo de cada estado ninfal y duración de la etapa adulto. Las observaciones se realizaron durante los meses de octubre, noviembre y diciembre, en donde se registraron los datos de los primeros instares de B. cockerelli hasta su última etapa, logrando determinar que la localidad Saquisilí tuvo un desarrollo oval rápido promedio de 2 a 6 días y la localidad más longeva en etapa adulta de B. cockerelli fue Salache, la misma que además obtuvo el mejor desarrollo en el ciclo biológico total de la especie.