Isolates from ancient permafrost help to elucidate species boundaries in Acanthamoeba castellanii complex (Amoebozoa: Discosea)

Malavin, Stas; Shmakova, Lyubov

doi:10.1016/j.ejop.2020.125671

Cited by 12 publications

(8 citation statements)

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“…Since then, many more protozoa have been discovered in permanently frozen environments and further reactivated. These studies confirmed that microbes may survive for long periods of time (sometimes, up to one million years) at subzero temperatures, and in the absence of any oxygen and liquid water (Shatilovich et al 2009 , 2015 ; Stoupin et al 2012 ; Shmakova et al 2016 , 2018 ; Malavin and Shmakova 2020 ). Very recently, Malavin and co-workers reported on the isolation of 35 amoeboid protists from frozen sediments, a discovery that motivated them to propose the existence of a so-called “frozen zoo” (Malavin et al 2020 ).…”

Section: Cryosphere As Reservoir For Past and Present Human Pathogensmentioning

confidence: 75%

Climate change, melting cryosphere and frozen pathogens: Should we worry…?

Yarzábal

Salazar

Batista-García

2021

Environmental Sustainability

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Permanently frozen environments (glaciers, permafrost) are considered as natural reservoirs of huge amounts of microorganisms, mostly dormant, including human pathogens. Due to global warming, which increases the rate of ice-melting, approximately 4 × 10 21 of these microorganisms are released annually from their frozen confinement and enter natural ecosystems, in close proximity to human settlements. Some years ago, the hypothesis was put forward that this massive release of potentially-pathogenic microbes—many of which disappeared from the face of the Earth thousands and even millions of years ago—could give rise to epidemics. The recent anthrax outbreaks that occurred in Siberia, and the presence of bacterial and viral pathogens in glaciers worldwide, seem to confirm this hypothesis. In that context, the present review summarizes the currently available scientific evidence that allows us to imagine a near future in which epidemic outbreaks, similar to the abovementioned, could occur as a consequence of the resurrection and release of microbes from glaciers and permafrost. Supplementary Information The online version of this article (10.1007/s42398-021-00184-8) contains supplementary material, which is available to authorized users.

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Section: Cryosphere As Reservoir For Past and Present Human Pathogensmentioning

confidence: 75%

Climate change, melting cryosphere and frozen pathogens: Should we worry…?

Yarzábal

Salazar

Batista-García

2021

Environmental Sustainability

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“…Finally, it is also possible that the genomes of bacteriophages, like that of other viruses, are under-represented because of the use of an inadequate DNA extraction protocol. Regarding eukaryotic viruses, our results are nevertheless less surprising, since they show a predominance for families of viruses infecting protozoa whose presence in ancient permafrost is known (33, 34). In addition, some members of these viral families have been reactivated (23, 24).…”

Section: Discussionmentioning

confidence: 49%

“…7). Live amoeba are routinely isolated from permafrost (33, 34). Except for a small number of contigs associated to Asfarviridae and even less to Iridoviridae, almost no eukaryotic viruses were detected from the families known to infect metazoan organisms, although their metazoan DNA was readily detected in most samples (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…It was shown that ancient bacteria could be revived from even much older permafrost layers, up to 2 million years (29), although contaminations by modern bacteria have been suspected (30). A flower plant was also revived from 30,000 year old frozen tissues (31), as well as various fungi (from Antarctica) (32) and amoebal protozoans (33, 34).…”

Section: Introductionmentioning

confidence: 99%

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High prevalence and diversity of beta-lactamase-encoding bacteria in cryosoils and ancient permafrost

Rigou

Christo-Foroux

Santini

et al. 2021

Preprint

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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).

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“…At the present time there have been few loci other than the two small subunit rRNA genes for which a substantial number of isolates have been studied. Among the few regions with more than 20 sequences from various isolates are portions of the mitochondrial cytochrome C oxidase subunit I/II gene [ 47 , 48 , 49 , 50 ], the mitochondrial ND5 gene [ 47 ], the large subunit rRNA and the ITS region of the ribosomal RNA complex [ 51 ], the mannose and laminin binding proteins [ 52 ], and a set of 5 proteins: Beta Tubulin ( BETA ), Glycogen Phosphorylase ( GLYP ), Glyceraldehyde-3-phosphate dehydrogenase ( G3PD ), Elongation Factor 1 alpha ( ELF1 ), and RASC [ 53 ].…”

Section: How Reliable Is the Sequence Information For Standard Strain...mentioning

confidence: 99%

The Status of Molecular Analyses of Isolates of Acanthamoeba Maintained by International Culture Collections

Fuerst

2023

Microorganisms

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Acanthamoeba is among the most ubiquitous protistan groups in nature. Knowledge of the biological diversity of Acanthamoeba comes in part from the use of strains maintained by the major microbial culture collections, ATCC and CCAP. Standard strains are vital to ensure the comparability of research. The diversity of standard strains of Acanthamoeba in the culture collections is reviewed, emphasizing the extent of genotypic studies based on DNA sequencing of the small subunit ribosomal RNA from the nucleus (18S rRNA gene; Rns) or the mitochondria (16S-like rRNA gene; rns). Over 170 different strains have been maintained at some time by culture centers. DNA sequence information is available for more than 70% of these strains. Determination of the genotypic classification of standard strains within the genus indicates that frequencies of types within culture collections only roughly mirror that from clinical or environmental studies, with significant differences in the frequency of some genotypes. Culture collections include the type of isolate from almost all named species of Acanthamoeba, allowing an evaluation of the validity of species designations. Multiple species are found to share the same Sequence Type, while multiple Sequence Types have been identified for different strains that share the same species name. Issues of sequence reliability and the possibility that a small number of standard strains have been mislabeled when studied are also examined, leading to potential problems for comparative analyses. It is important that all species have reliable genotype designations. The culture collections should be encouraged to assist in completing the molecular inventory of standard strains, while workers in the Acanthamoeba research community should endeavor to ensure that strains representative of genotypes that are missing from the culture collection are provided to the culture centers for preservation.

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Isolates from ancient permafrost help to elucidate species boundaries in Acanthamoeba castellanii complex (Amoebozoa: Discosea)

Cited by 12 publications

References 67 publications

Climate change, melting cryosphere and frozen pathogens: Should we worry…?

Climate change, melting cryosphere and frozen pathogens: Should we worry…?

High prevalence and diversity of beta-lactamase-encoding bacteria in cryosoils and ancient permafrost

The Status of Molecular Analyses of Isolates of Acanthamoeba Maintained by International Culture Collections

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