Reactivation of dormant and nonculturable bacterial forms from paleosoils and subsoil permafrost

Kryazhevskikh, N. A.; Demkina, E. V.; Manucharova, N. A.; Soina, V. S.; Гальченко, В. Ф.; Эль-Регистан, Г. И.

doi:10.1134/s0026261712040108

Cited by 24 publications

(10 citation statements)

References 22 publications

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“…The subjects of this work were Acinetobacter lwoffii strain ЕК30А, Arthrobacter oxydans strain К14, and Arthrobacter sulfonivorans strain K15 isolated from frozen subsoil deposits [16], Acinetobacter lwoffii strain BSW 27 (Saratov State Medical School Collection), Corynebacterium pseudodiphtheriticum strain 090497 (State Research Institute SKMBP Collection), Rhodococcus opacus strain 1cp (Collection of the Institute of Microbial Biochemistry and Physiology, Russian Academy of Sciences), E. coli strain MG 1655 (Collection of the Institute of Molecular Genetics, Russian Academy of Sciences), and a mutant strain, Escherichia coli dsp 250, which contains a plasmid with inserted fimA and lacZ genes controlled by the same promoter; its variants differed in terms of their ability to form type 1 pili that are associated with bac terial virulence.…”

Section: Methodsmentioning

confidence: 99%

Applicability of MALDI mass spectrometry for diagnostics of phase variants in bacterial populations

et al. 2015

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Efficiency of MALDI mass spectrometry for differentiation between phenotypic phase variants (in colony morphology and virulence/avirulence) was investigated for saprotrophic and opportunistically pathogenic bacteria of five genera (Acinetobacter, Arthrobacter, Rhodococcus, Corynebacterium, and Escheri chia). Analysis of MALDI spectra (on the SA and HCCA matrices) included (1) determination of similarity of the protein spectra as a percentage of the common protein peaks to the total amount of proteins, which reflects the phylogenetic relationships of the objects and has been recommended for identification of closely related species; (2) comparison of intensities of the common peaks; and (3) the presence of specific peaks as determinative characteristics of the variants. Under the standard analytical conditions, the similarity between the MALDI profiles was shown to increase in the row: genus-species-strain-variant. Assessment of inten sities of the common peaks was most applicable for differentiation between phase variants, especially in the case of high similarity of their profiles. Phase variants (A. oxydans strain K14) with similar colony morpho types (S, R, M, and S m ) grown on different media (LB agar, TSA, and TGYg) exhibited differences in their protein profiles reflecting the differences in their physiological characteristics. This finding is in agreement with our previous results on screening of the R. opacus with similar colony morphology and different substrate specificity in decomposition of chlorinated phenols. Analysis of MALDI spectra is probably the only efficient method for detection of such variants.

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Section: Methodsmentioning

confidence: 99%

Applicability of MALDI mass spectrometry for diagnostics of phase variants in bacterial populations

et al. 2015

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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). Many spore-forming bacteria within the classes Clostridia and Bacilli have been cultivated frequently from ancient permafrost in Siberia (16)(17)(18)(19), Canada (20), and northern Norway (21).…”

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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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“…The constant low thermal energy and water availability make metabolic activity, such as enzymatic degradation, a difficult task in these ecosystems. As a response to these conditions, microorganisms may be induced into a state of dormancy as a means for their long-term survival (44, 47–49). One of the most recent examples of microbial resilience involved the resurrection of a 30,000-year-old Pithovirus sibericum sample preserved in Siberian permafrost, the oldest eukaryote-infecting virus isolated to date, which also retained its infectivity in spite of such an extended dormant state (50).…”

Section: Sources Of Ancient Microbial Dnamentioning

confidence: 99%

“…Microbial population studies of ancient permafrost are also important for determining the mechanisms by which microbial communities survive thousands of years in these ecosystems (26, 51–55). Furthermore, ancient variants of cold acclimation and cold shock proteins, as well as other key components of microbial activities, would provide valuable information regarding the evolution of metabolic processes and survival mechanisms for temperatures below 0°C (47, 52, 53, 56). …”

Section: Sources Of Ancient Microbial Dnamentioning

confidence: 99%

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology

2016

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Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.

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Reactivation of dormant and nonculturable bacterial forms from paleosoils and subsoil permafrost

Cited by 24 publications

References 22 publications

Applicability of MALDI mass spectrometry for diagnostics of phase variants in bacterial populations

Applicability of MALDI mass spectrometry for diagnostics of phase variants in bacterial populations

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

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology

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