Intact DNA in ancient permafrost

Lewis, Kim; Epstein, Slava E.; Godoy, Veronica G.; Hong, Sun Hee

doi:10.1016/j.tim.2008.01.002

Cited by 12 publications

(10 citation statements)

References 26 publications

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“…Based on a report of viable fungal cells being recovered from permafrost samples that are thousands of years old (Ozerskaya et al, 2009;Yashima et al, 2012), the DNA recovered from permafrost sediments may represent a mixture of DNA from cryopreserved cells and extracellular DNA adsorbed to soil particles (Trevors, 1996;Pietramellara et al, 2009). However, there has been some debate whether viable microbial cells and intact DNA recovered from ancient permafrost truly represent ancient organisms; it has rather been hypothesized that permafrost soils and glacial ice could actually host living, metabolizing communities of extremophiles (Lewis et al, 2008). This hypothesis is supported by a growing body of research suggesting that a diverse group of microorganisms, including many fungi, are psychrotrophic or psychrophilic and capable of not just survival, but active metabolism and growth at temperatures below 0°C (Steven et al, 2008;McMahon et al, 2009;Yergeau et al, 2010).…”

Section: Mixed Communities Of Modern and Ancient Dna?mentioning

confidence: 99%

Fungal palaeodiversity revealed using high‐throughput metabarcoding of ancient DNA from arctic permafrost

Bellemain

Davey

Kauserud

et al. 2012

Environmental Microbiology

121

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The taxonomic and ecological diversity of ancient fungal communities was assessed by combining next generation sequencing and metabarcoding of DNA preserved in permafrost. Twenty-six sediment samples dated 16 000-32 000 radiocarbon years old from two localities in Siberia were analysed for fungal ITS. We detected 75 fungal OTUs from 21 orders representing three phyla, although rarefaction analyses suggested that the full diversity was not recovered despite generating an average of 6677 ± 3811 (mean ± SD) sequences per sample and that preservation bias likely has considerable effect on the recovered DNA. Most OTUs (75.4%) represented ascomycetes. Due to insufficient sequencing depth, DNA degradation and putative preservation biases in our samples, the recovered taxa probably do not represent the complete historic fungal community, and it is difficult to determine whether the fungal communities varied geographically or experienced a composition shift within the period of 16 000-32 000 bp. However, annotation of OTUs to functional ecological groups provided a wealth of information on the historic communities. About one-third of the OTUs are presumed plant-associates (pathogens, saprotrophs and endophytes) typical of graminoid- and forb-rich habitats. We also detected putative insect pathogens, coprophiles and keratinophiles likely associated with ancient insect and herbivore faunas. The detection of putative insect pathogens, mycoparasites, aquatic fungi and endophytes broadens our previous knowledge of the diversity of fungi present in Beringian palaeoecosystems. A large group of putatively psychrophilic/psychrotolerant fungi was also detected, most likely representing a modern, metabolically active fungal community.

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Section: Mixed Communities Of Modern and Ancient Dna?mentioning

confidence: 99%

Fungal palaeodiversity revealed using high‐throughput metabarcoding of ancient DNA from arctic permafrost

Bellemain

Davey

Kauserud

et al. 2012

Environmental Microbiology

121

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“…If the notion that DNA may persist over geological timespans (>1 My) is gaining a progressive acceptance, the fact that cellular organisms might survive that long remains a contentious issue (10,11). Because of its neutral pH and reducing and anaerobic properties, northeast Siberian permafrost is among the most suitable environments to look for long-term surviving microorganisms (12) or even plants (13).…”

Section: Resultsmentioning

confidence: 99%

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology

Legendre

Bartoli

Shmakova

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

441

522

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Significance Giant DNA viruses are visible under a light microscope and their genomes encode more proteins than some bacteria or intracellular parasitic eukaryotes. There are two very distinct types and infect unicellular protists such as Acanthamoeba . On one hand, Megaviridae possess large pseudoicosahedral capsids enclosing a megabase-sized adenine–thymine-rich genome, and on the other, the recently discovered Pandoraviruses exhibit micron-sized amphora-shaped particles and guanine–cytosine-rich genomes of up to 2.8 Mb. While initiating a survey of the Siberian permafrost, we isolated a third type of giant virus combining the Pandoravirus morphology with a gene content more similar to that of icosahedral DNA viruses. This suggests that pandoravirus-like particles may correspond to an unexplored diversity of unconventional DNA virus families.

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“…The mechanisms for the long-term survival strategies of cold-adapted microorganisms in ancient permafrost have been investigated in several studies (3,(11)(12)(13)(14). Given the harsh conditions in ancient permafrost, microbial dormancy is considered to be a major mechanism to maintain long-term viability over geological time (15).…”

mentioning

confidence: 99%

“…Although non-spore-forming bacteria, such as Actinobacteria, were more frequently isolated from Siberian permafrost sediments ranging in age from 10 kyr to 3 million years (3 Ma), the cultivation of spore formers capable of growth at subzero temperatures has been reported from 3-Ma-old permafrost (16)(17)(18)(19). It has been hypothesized previously that the spore formers in ancient permafrost might be present as active vegetative cells instead of being in a dormant state (14).…”

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confidence: 99%

Predominance of Anaerobic, Spore-Forming Bacteria in Metabolically Active Microbial Communities from Ancient Siberian Permafrost

Liang

Lau

Vishnivetskaya

et al. 2019

Appl Environ Microbiol

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The prevalence of microbial life in permafrost up to several million years (Ma) old has been well documented. However, the long-term survivability, evolution, and metabolic activity of the entombed microbes over this time span remain underexplored. We integrated aspartic acid (Asp) racemization assays with metagenomic sequencing to characterize the microbial activity, phylogenetic diversity, and metabolic functions of indigenous microbial communities across a ∼0.01- to 1.1-Ma chronosequence of continuously frozen permafrost from northeastern Siberia. Although Asp in the older bulk sediments (0.8 to 1.1 Ma) underwent severe racemization relative to that in the youngest sediment (∼0.01 Ma), the much lower d-Asp/l-Asp ratio (0.05 to 0.14) in the separated cells from all samples suggested that indigenous microbial communities were viable and metabolically active in ancient permafrost up to 1.1 Ma. The microbial community in the youngest sediment was the most diverse and was dominated by the phyla Actinobacteria and Proteobacteria. In contrast, microbial diversity decreased dramatically in the older sediments, and anaerobic, spore-forming bacteria within Firmicutes became overwhelmingly dominant. In addition to the enrichment of sporulation-related genes, functional genes involved in anaerobic metabolic pathways such as fermentation, sulfate reduction, and methanogenesis were more abundant in the older sediments. Taken together, the predominance of spore-forming bacteria and associated anaerobic metabolism in the older sediments suggest that a subset of the original indigenous microbial community entrapped in the permafrost survived burial over geological time. IMPORTANCE Understanding the long-term survivability and associated metabolic traits of microorganisms in ancient permafrost frozen millions of years ago provides a unique window into the burial and preservation processes experienced in general by subsurface microorganisms in sedimentary deposits because of permafrost’s hydrological isolation and exceptional DNA preservation. We employed aspartic acid racemization modeling and metagenomics to determine which microbial communities were metabolically active in the 1.1-Ma permafrost from northeastern Siberia. The simultaneous sequencing of extracellular and intracellular genomic DNA provided insight into the metabolic potential distinguishing extinct from extant microorganisms under frozen conditions over this time interval. This in-depth metagenomic sequencing advances our understanding of the microbial diversity and metabolic functions of extant microbiomes from early Pleistocene permafrost. Therefore, these findings extend our knowledge of the survivability of microbes in permafrost from 33,000 years to 1.1 Ma.

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Intact DNA in ancient permafrost

Cited by 12 publications

References 26 publications

Fungal palaeodiversity revealed using high‐throughput metabarcoding of ancient DNA from arctic permafrost

Fungal palaeodiversity revealed using high‐throughput metabarcoding of ancient DNA from arctic permafrost

Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology

Predominance of Anaerobic, Spore-Forming Bacteria in Metabolically Active Microbial Communities from Ancient Siberian Permafrost

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