Bacterial communities in ancient permafrost profiles of Svalbard, Arctic

Singh, Purnima; Singh, Shiv Mohan; Singh, Ram; Naik, Simantini; Roy, Utpal; Srivastava, Alok Kumar; Bölter, Manfred

doi:10.1002/jobm.201700061

Cited by 32 publications

(17 citation statements)

References 70 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Microbial cell counts ranged from 2.3 10 7 to 4.7 10 7 cells gdw -1 and were consistent with previous studies from Arctic and sub-Arctic permafrost (1) (14) (15) (64) (65), but were one to two orders of magnitude lower than is commonly observed in temperate soils (66) (67) (68). Among the three age categories the intermediate had the highest number of live, dead, and total cells and the highest proportion of live cells.…”

Section: Discussionsupporting

confidence: 89%

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

Burkert

Douglas

Waldrop

et al. 2018

Preprint

View full text Add to dashboard Cite

29Permafrost hosts a community of microorganisms that survive and reproduce for 30 millennia despite extreme environmental conditions such as water stress, subzero 31 temperatures, high salinity, and low nutrient availability. Many studies focused on 32 permafrost microbial community composition use DNA-based methods such as 33 metagenomic and 16S rRNA gene sequencing. However, these methods do not 34 distinguish between active, dead, and dormant cells. This is of particular concern in 35 ancient permafrost where constant subzero temperatures preserve DNA from dead 36 organisms and dormancy may be a common survival strategy. To circumvent this 37 we applied: (i) live/dead differential staining coupled with microscopy, (ii) 38 endospore enrichment, and (iii) selective depletion of DNA from dead cells to 39 permafrost microbial communities across a Pleistocene permafrost chronosequence 40 (19K, 27K, and 33K). Cell counts and analysis of 16S rRNA gene amplicons from 41 live, dead, and dormant cells revealed how communities differ between these pools 42 and how they change over geologic time. We found clear evidence that cells capable 43 of forming endospores are not necessarily dormant and that the propensity to form 44 endospores differed among taxa. Specifically, Bacilli are more likely to form 45 endospores in response to long-term stressors associated with permafrost 46 environmental conditions than members of Clostridia, which are more likely to 47 content largely control microbial community diversity and cell abundances. 52 53 IMPORTANCE 54 The study of permafrost transcends the study of climate change and 55 exobiology. Permafrost soils store more than half earth's soil carbon despite 56 covering ~15% of the land area (Tarnocai et al 2009). This permafrost carbon is 57 rapidly degraded following thaw (Tarnocai C et al 2009, Schuur et al 2015) . 58 Understanding microbial communities in permafrost will contribute to the 59 knowledge base necessary to understand the rates and forms of permafrost C and N 60 cycling post thaw. Permafrost is also an analog for frozen extraterrestrial 61 environments and evidence of viable organisms in ancient permafrost is of interest 62 to those searching for potential life on distant worlds. If we can identify strategies 63 microbial communities utilize to survive permafrost we can focus efforts searching 64 for evidence of life on cryogenic cosmic bodies. Our work is significant because it 65 contributes to an understanding of how microbial life adapts and survives in the 66 extreme environmental conditions in permafrost terrains across geologic timescales. 67 68 drastically alter estimates of diversity and abundance. Furthermore, because many 75 communities host dormant cells, DNA-based approaches may not represent active 76 members. In temperate soils, up to 40% of DNA is from dead or compromised cells (3). 77In permafrost, the amount of 'relic' DNA may be even higher because frozen conditions 78 preserve DNA from dead cells. In non-permafrost environments, multi-omic approac...

show abstract

Section: Discussionsupporting

confidence: 89%

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

Burkert

Douglas

Waldrop

et al. 2018

Preprint

View full text Add to dashboard Cite

show abstract

“…Microbial cell counts ranged from 2.3 × 10 7 to 4.7 × 10 7 cells g (dry weight) −1 and were consistent with previous studies from Arctic and sub-Arctic permafrost (1, 16, 17, 26, 34) but were 1 to 2 orders of magnitude lower than is commonly observed in temperate soils (35–37). Among the three age categories, the intermediate-age category had the highest numbers of live, dead, and total cells and the highest proportion of live cells.…”

Section: Discussionsupporting

confidence: 88%

Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

Burkert

Douglas

Waldrop

et al. 2019

Appl Environ Microbiol

View full text Add to dashboard Cite

Permafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

show abstract

“…The obtained Chao1 index value is comparable with the corresponding indices, obtained for the Greenland ice samples [68], and for the Svalbard permafrost samples [69]. Representatives of all genera isolated by us were previously isolated from permafrost or frozen environments [10,46,[70][71][72][73][74][75][76][77][78][79][80][81][82][83][84].…”

Section: Discussionsupporting

confidence: 82%

Bacterial Communities of Novaya Zemlya Archipelago Ice and Permafrost

et al. 2020

View full text Add to dashboard Cite

The study of bacterial communities associated with extreme ecosystems is one of the most important tasks in modern microbial ecology. Despite a large number of studies being performed, the ecosystems that have not been sufficiently explored from the microbiological point of view still exist. Such research is needed for improving the understanding of the limits and mechanisms of bacterial survival under extreme conditions, and for revealing previously undescribed species and their role in global biospheric processes and their functional specifics. The results of the complex microbiological characteristics of permafrost and ice—collected on the Severniy Island in the northern part of the Novaya Zemlya archipelago—which have not previously been described from microbiological point of view, are presented in this article. The analysis included both culture-independent and culture-dependent methods, in particular, the spectra of metabolic activity range analysis in vitro under different temperature, pH and salinity conditions. High values for the total number of prokaryotes in situ (1.9 × 108–3.5 × 108 cells/g), a significant part of which was able to return to a metabolically active state after thawing, and moderate numbers of culturable bacteria (3.3 × 106–7.8 × 107 CFU/g) were revealed. Representatives of Proteobacteria, Actinobacteria, and Bacteroidetes were dominant in situ; Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes were the most abundant phyla in vitro. Physiological assays revealed the mesophilic and neutrophilic optima of temperature and pH of culturing conditions, respectively, and wide temperature and pH ranges of culturable communities’ reproduction activity. Isolated strains were characterized by moderate halotolerant properties and antibiotic resistance, including multiple antibiotic resistance. It was found that almost all cultured bacterial diversity revealed (not just a few resistant species) had extremotolerant properties regarding a number of stress factors. This indicates the high adaptive potential of the studied microbial communities and their high sustainability and capability to retain functional activity under changing environmental (including climatic) conditions in wide ranges.

show abstract

Bacterial communities in ancient permafrost profiles of Svalbard, Arctic

Cited by 32 publications

References 70 publications

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

Changes in the Active, Dead, and Dormant Microbial Community Structure Across a Pleistocene Permafrost Chronosequence

Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

Bacterial Communities of Novaya Zemlya Archipelago Ice and Permafrost

Contact Info

Product

Resources

About