Acinetobacter baumannii is a gram-negative, non-fermenting aerobic bacterium which is often associated with hospital-acquired infections and known for its ability to develop resistance to antibiotics, form biofilms, and survive for long periods in hospital environments. In this study, we present two novel viruses, vB_AbaP_AS11 and vB_AbaP_AS12, specifically infecting and lysing distinct multidrug-resistant clinical A. baumannii strains with K19 and K27 capsular polysaccharide structures, respectively. Both phages demonstrate rapid adsorption, short latent periods, and high burst sizes in one-step growth experiments. The AS11 and AS12 linear double-stranded DNA genomes of 41,642 base pairs (bp) and 41,402 bp share 86% nucleotide sequence identity with the most variable regions falling in host receptor–recognition genes. These genes encode tail spikes possessing depolymerizing activities towards corresponding capsular polysaccharides which are the primary bacterial receptors. We described AS11 and AS12 genome organization and discuss the possible regulation of transcription. The overall genomic architecture and gene homology analyses showed that the phages are new representatives of the recently designated Fri1virus genus of the Autographivirinae subfamily within the Podoviridae family.

A partial carcass of an adult woolly mammoth (Mammuthus primigenius) found in 2012 on Maly Lyakhovsky Island presents a new opportunity to retrieve associated anatomical, morphological, and life history data on this important component of Pleistocene biotas. In addition, we address hematological, histological, and microbiological issues that relate directly to quality of preservation. Recovered by staff from North-Eastern Federal University in Yakutsk, this individual is a relatively old female preserving soft tissue of the anteroventral portion of the head, most of both fore-quarters, and the ventral aspect of much of the rest of the body. Both tusks were recovered and subjected to computed tomographic analysis in which annual dentin increments were revealed as cycles of variation in X-ray attenuation. Measurements of annual increment areas (in longitudinal section) display a pulsed pattern of tusk growth showing cycles of growth rate variation over periods of 3e5 years. These intervals are interpreted as calving cycles reflecting regular shifts in calcium and phosphate demand for tusk growth vs. fetal ossification and lactation. Brown liquid associated with the frozen carcass turned out to include remains of hemolyzed blood, and blood samples examined microscopically included white blood cells with preserved nuclei. Muscle tissue from the trunk was unusually well preserved, even at the histological level. Intestinal contents and tissue samples were investigated microbiologically, and several strains of lacticacid bacteria (e.g., Enterococcus faecium, Enterococcus hirae) that are widely distributed as commensal organisms in the intestines of herbivores were isolated.

One quarter of the Northern hemisphere is underlain by permanently frozen ground, referred to as permafrost. Due to climate warming, irreversibly thawing permafrost is releasing organic matter frozen for up to a million years, most of which decomposes into carbon dioxide and methane, further enhancing the greenhouse effect. Part of this organic matter also consists of revived cellular microbes (prokaryotes, unicellular eukaryotes) as well as viruses that have remained dormant since prehistorical times. While the literature abounds on descriptions of the rich and diverse prokaryotic microbiomes found in permafrost, no additional report about “live” viruses have been published since the two original studies describing pithovirus (in 2014) and mollivirus (in 2015). This wrongly suggests that such occurrences are rare and that “zombie viruses” are not a public health threat. To restore an appreciation closer to reality, we report the preliminary characterizations of 13 new viruses isolated from seven different ancient Siberian permafrost samples, one from the Lena river and one from Kamchatka cryosol. As expected from the host specificity imposed by our protocol, these viruses belong to five different clades infecting Acanthamoeba spp. but not previously revived from permafrost: Pandoravirus, Cedratvirus, Megavirus, and Pacmanvirus, in addition to a new Pithovirus strain.

Enterococcus faecium 58m is a putative ancient nonpathogenic strain isolated from the intestinal content of an adult woolly mammoth (Mammuthus primigenius). Here, we report its draft genome sequence, consisting of 60 contigs. In silico genomic analysis was performed to determine the genetic features and pathogenic potential of this microorganism.

In the context of global warming, the melting of arctic permafrost raises the threat of a re-emergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here we present a metagenomics analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia, and Kamchatka, including 9 permafrost samples collected at various depths. These large datasets (9.2 1011 total bp) were assembled (525,313 contigs > 5kb), their encoded protein contents predicted, then used to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of β-lactamase genes, almost 0.9 copy/bacterial genome. In addition of known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. β-lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations.

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Extracts of Aconitum septentrionale Koelle roots obtained using chloroform, isopropanol, and ethanol were purified using chloroform and basic γ-Al 2 O 3 . Ballast materials were selectively adsorbed by γ-Al 2 O 3 , increasing the mass fraction of lappaconitine in the extract. The ethanol extract was purified most. The degree of lappaconitine extraction by chloroform was unaffected by the presence of γ-Al 2 O 3 . However, the mass fraction in the extract and lappaconitine extraction from Aconitum septentrionale were increased more than twice.Aconitum septentrionale Koelle roots are a source of lappaconitine, the hydrobromide of which is a pharmacopeic preparation for antiarrhythmia [1,2].At present various separations of this alkaloid from the plant raw materials have been developed. However, the basic principles have not changed. Plant raw material is suitably extracted with benzene [3], chloroform [4], methanol [5], acetone:water [6], ethanol:water [7], or diluted aqueous acids [8]. The resulting extract contains the total alkaloids and a complex mixture of ballast materials. Isolation and purification of lappaconitine is a multi-step extraction procedure that leads to losses of the product.Use of a mechanical chemical method that consists of preliminary vigorous mechanical processing of plant raw material together with an added solid [9, 10] (oxide adsorbents, mineral salts, organic acids, sugar, urea) increased the yield, rate, and selectivity of the extraction of the product.In the present work, the role of γ-Al 2 O 3 on the degree and selectivity of lappaconitine extraction from A. septentrionale roots by CHCl 3 was studied in greater detail.Raw material was extracted with CHCl 3 , CHCl 3 with γ-Al 2 O 3 , isopropanol, and ethanol. Table 1 lists the analytical results from UV spectroscopy of the resulting extracts.Quantitative analysis of the ethanol extract showed that the lappaconitine content per mass of air-dried raw material was less than 3.6% according to HPLC and 3.8% according to UV spectroscopy.Comparison of the analytical data of extracts obtained using CHCl 3 found that the presence of γ-Al 2 O 3 in the extraction system with CHCl 3 had no effect on the degree of lappaconitine extraction. However, it decreased the amount of ballast materials in the extract owing to their adsorption on γ-Al 2 O 3 . In this instance the adsorbent could not be regenerated because of the complexity of separating it from the processed raw material.The yield of extractive substances increased sharply if the solvent polarity was increased in the order CHCl 3 -i-PrOHEtOH. The amount of extracted lappaconitine also increased. However, the selectivity of the extraction decreased. This indicated that most of the ballast materials were polar.

SummaryBackgroundAntimicrobial resistance is one of the major challenges affecting public health. It is mostly due to the continuous emergence of extended-spectrum β-lactamase from various environments followed by their rapid dissemination and selection in clinical settings. The warming of Earth’s climate is the other global threat facing human society, in particular with the Arctic regions experiencing a twice faster warming than the global average and permafrost affected by widespread thawing. A potentially dreadful combination of these two threats would be the release and dispersion of harmful microbes that have remained confined to largely uninhabited Arctic regions, or are stored dormant in permafrost.MethodsEnvironmental DNA was isolated from 12 soil samples from various Arctic and subarctic pristine regions in Siberia (Yakutia and Kamchatka), including nine permafrost samples collected at various depths. The large datasets obtained from high throughput sequencing was assembled in contigs and their protein-gene contents predicted. We used exhaustive similarity searches to perform taxonomical assignments of bacterial, archaeal, and eukaryotic organisms, as well as DNA viruses. In addition, we specifically identified β-lactamase genes and their prevalence per bacterial genome estimated through the detection of two universal single copy genes.FindingsA total of 9.217 1011 bp were exploited, leading to a total of 525,313 contigs at least 5kb in size. The DNA content of the various samples was found to be highly variable, not strictly correlated with the depth or radio-carbon-based deposit age, and most likely linked to the global density of microbes trapped in the corresponding permafrost layers. Bacteria account for more than 90% of the contigs in most samples, followed by Eukaryotes and Archaea (always lower than 10%). Viruses represented less than 2% of all contigs in all samples. The taxonomic profiles of surface cryosoils and deep permafrost samples exhibited a high diversity, including between permafrost samples originating from various depths in the same borehole. In all samples, bacterial contigs carrying different β-lactamases from class A to D were identified.InterpretationNo clear common taxonomic feature could be found shared by surface cryosoils or ancient permafrost layers. However, most samples (9/12) exhibited a high frequency of β-lactamase genes, with an estimated average close to 1 copy/bacterial genome. In addition to the well-documented reactivation of infectious ancient pathogens (bacteria, viruses, protozoa), we show now that global warming could contribute to the emergence of new antibiotic resistances through the mobilization by contemporary bacteria of ancient DNA released from thawing permafrost.FundingCNRS PRC research grant (PRC1484-2018) to C.A. E C-F was supported by a PhD grant (DGA/DS/MRIS) #2017 60 0004. GG and JS were funded by ERC PETA-CARB (#338335) and the HGF Impulse and Networking Fund (ERC-0013).