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Vishnivetskaya TA, Mironov VA, Abramov AA, Shcherbakova VA, Rivkina EM. Biogeochemical Characteristics of Earth's Volcanic Permafrost: An Analog of Extraterrestrial Environments. ASTROBIOLOGY 2022; 22:812-828. [PMID: 35333595 DOI: 10.1089/ast.2021.0137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article describes a study of frozen volcanic deposits collected from volcanoes Tolbachik and Bezymianny on the Kamchatka Peninsula, Russia, and Deception Island volcano, Antarctica. In addition, we studied suprasnow ash layers deposited after the 2007 eruptions of volcanoes Shiveluch and Bezymianny on Kamchatka. The main objectives were to characterize the presence and survivability of thermophilic microorganisms in perennially frozen volcanic deposits. As opposed to permafrost from the polar regions, viable thermophiles were detected in volcanic permafrost by cultivation, microscopy, and sequencing. In the permafrost of Tolbachik volcano, we observed methane formation by both psychrophilic and thermophilic methanogenic archaea, while at 37°C, methane production was noticeably lower. Thermophilic bacteria isolated from volcanic permafrost from the Deception Island were 99.93% related to Geobacillus stearothermophilus. Our data showed biological sulfur reduction to sulfide at 85°C and even at 130°C, where hyperthermophilic archaea of the genus Thermoproteus were registered. Sequences of hyperthermophilic bacteria of the genus Caldicellulosiruptor were discovered in clone libraries from fresh volcanic ash deposited on snow. Microorganisms found in volcanic terrestrial permafrost may serve as a model for the alien inhabitants of Mars, a cryogenic planet with numerous volcanoes. Thermophiles and hyperthermophiles and their metabolic processes represent a guideline for the future exploration missions on Mars.
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Affiliation(s)
- Tatiana A Vishnivetskaya
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Vasiliy A Mironov
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
| | - Andrey A Abramov
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
| | - Viktoria A Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
| | - Elizaveta M Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
- Institute of Geography, Russian Academy of Sciences, Moscow, 119017, Russia
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2
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Shmakova L, Malavin S, Iakovenko N, Vishnivetskaya T, Shain D, Plewka M, Rivkina E. A living bdelloid rotifer from 24,000-year-old Arctic permafrost. Curr Biol 2021; 31:R712-R713. [PMID: 34102116 DOI: 10.1016/j.cub.2021.04.077] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In natural, permanently frozen habitats, some organisms may be preserved for hundreds to tens of thousands of years. For example, stems of Antarctic moss were successfully regrown from an over millennium-old sample covered by ice for about 400 years1. Likewise, whole campion plants were regenerated from seed tissue preserved in relict 32,000-year-old permafrost2, and nematodes were revived from the permafrost of two localities in northeastern Siberia, with source sediments dated over 30,000 years BP3. Bdelloid rotifers, microscopic multicellular animals, are known for their ability to survive extremely low temperatures4. Previous reports suggest survival after six to ten years when frozen between -20° to 0°C4-6. Here, we report the survival of an obligate parthenogenetic bdelloid rotifer, recovered from northeastern Siberian permafrost radiocarbon-dated to ∼24,000 years BP. This constitutes the longest reported case of rotifer survival in a frozen state. We confirmed the finding by identifying rotifer actin gene sequences in a metagenome obtained from the same sample. By morphological and molecular markers, the discovered rotifer belongs to the genus Adineta, and aligns with a contemporary Adineta vaga isolate collected in Belgium. Experiments demonstrated that the ancient rotifer withstands slow cooling and freezing (∼1°C min-1) for at least seven days. We also show that a clonal culture can continuously reproduce in the laboratory by parthenogenesis.
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Affiliation(s)
- Lyubov Shmakova
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya 2, 142290, Pushchino, Russia
| | - Stas Malavin
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya 2, 142290, Pushchino, Russia.
| | - Nataliia Iakovenko
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, CZ-16521, Praha 6 - Suchdol, Czech Republic
| | - Tatiana Vishnivetskaya
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya 2, 142290, Pushchino, Russia; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA
| | - Daniel Shain
- Department of Biology, Rutgers University, 200 Federal Street, Camden, NJ 08103, USA
| | - Michael Plewka
- Department of Biology, State Gymnasium, Ochsenkamp 100, 58285 Gevelsberg, Germany
| | - Elizaveta Rivkina
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya 2, 142290, Pushchino, Russia
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3
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Vishnivetskaya TA, Almatari AL, Spirina EV, Wu X, Williams DE, Pfiffner SM, Rivkina EM. Insights into community of photosynthetic microorganisms from permafrost. FEMS Microbiol Ecol 2021; 96:5979775. [PMID: 33181853 DOI: 10.1093/femsec/fiaa229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
This work integrates cultivation studies of Siberian permafrost and analyses of metagenomes from different locations in the Arctic with the aim of obtaining insights into the community of photosynthetic microorganisms in perennially frozen deposits. Cyanobacteria and microalgae have been described in Arctic aquatic and surface soil environments, but their diversity and ability to withstand harsh conditions within the permafrost are still largely unknown. Community structure of photosynthetic organisms in permafrost sediments was explored using Arctic metagenomes available through the MG-RAST. Sequences affiliated with cyanobacteria represented from 0.25 to 3.03% of total sequences, followed by sequences affiliated with Streptophyta (algae and vascular plants) 0.01-0.45% and Chlorophyta (green algae) 0.01-0.1%. Enrichment and cultivation approaches revealed that cyanobacteria and green algae survive in permafrost and they could be revived during prolonged incubation at low light intensity. Among photosynthetic microorganisms isolated from permafrost, the filamentous Oscillatoria-like cyanobacteria and unicellular green algae of the genus Chlorella were dominant. Our findings suggest that permafrost cyanobacteria and green algae are expected to be effective members of the re-assembled community after permafrost thawing and soil collapse.
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Affiliation(s)
- Tatiana A Vishnivetskaya
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA.,Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya Street, Bldg. 2, Pushchino, Russia
| | - Abraham L Almatari
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Elena V Spirina
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya Street, Bldg. 2, Pushchino, Russia
| | - Xiaofen Wu
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Daniel E Williams
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Susan M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, 676 Dabney Hall, 1416 Circle Drive, Knoxville, TN 37996-1605, USA
| | - Elizaveta M Rivkina
- Soil Cryology Laboratory, Institute of Physicochemical and Biological Problems in Soil Science, Institutskaya Street, Bldg. 2, Pushchino, Russia
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4
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Abramov A, Vishnivetskaya T, Rivkina E. Are permafrost microorganisms as old as permafrost? FEMS Microbiol Ecol 2021; 97:6143815. [PMID: 33601419 DOI: 10.1093/femsec/fiaa260] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022] Open
Abstract
Permafrost describes the condition of earth material (sand, ground, organic matter, etc.) cemented by ice when its temperature remains at or below 0°C continuously for longer than 2 years. Evidently, permafrost is as old as the time passed from freezing of the earth material. Permafrost is a unique phenomenon and may preserve life forms it encloses. Therefore, in order to talk confidently about the preservation of paleo-objects in permafrost, knowledge about the geological age of sediments, i.e. when the sediments were formed, and permafrost age, when those sediments became permanently frozen, is essential. There are two types of permafrost-syngenetic and epigenetic. The age of syngenetic permafrost corresponds to the geological age of its sediments, whereas the age of epigenetic permafrost is less than the geological age of its sediments. Both of these formations preserve microorganisms and their metabolic products; however, the interpretations of the microbiological and molecular-biological data are inconsistent. This paper reviews the current knowledge of time-temperature history and age of permafrost in relation to available microbiological and metagenomic data.
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Affiliation(s)
- Andrey Abramov
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Tatiana Vishnivetskaya
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino 142290, Russia.,University of Tennessee, Center for Environmental Biotechnology, Knoxville, TN 37996, USA
| | - Elizaveta Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino 142290, Russia
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Optimization of subsampling, decontamination, and DNA extraction of difficult peat and silt permafrost samples. Sci Rep 2020; 10:14295. [PMID: 32868827 PMCID: PMC7459103 DOI: 10.1038/s41598-020-71234-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022] Open
Abstract
This study aims to act as a methodological guide for contamination monitoring, decontamination, and DNA extraction for peaty and silty permafrost samples with low biomass or difficult to extract DNA. We applied a biological tracer, either only in the field or both in the field and in the lab, via either spraying or painting. Spraying in the field followed by painting in the lab resulted in a uniform layer of the tracer on the core sections. A combination of bleaching, washing, and scraping resulted in complete removal of the tracer leaving sufficient material for DNA extraction, while other widely used decontamination methods did not remove all detectable tracer. In addition, of four widely used commercially available DNA extraction kits, only a modified ZymoBIOMICS DNA Microprep kit was able to acquire PCR amplifiable DNA. Permafrost chemical parameters, age, and soil texture did not have an effect on decontamination efficacy; however, the permafrost type did influence DNA extraction. Based on these findings, we developed recommendations for permafrost researchers to acquire contaminant-free DNA from permafrost with low biomass.
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6
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Malavin S, Shmakova L, Claverie JM, Rivkina E. Frozen Zoo: a collection of permafrost samples containing viable protists and their viruses. Biodivers Data J 2020; 8:e51586. [PMID: 32733138 PMCID: PMC7367895 DOI: 10.3897/bdj.8.e51586] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 07/03/2020] [Indexed: 11/12/2022] Open
Abstract
Background Permafrost, frozen ground cemented with ice, occupies about a quarter of the Earth’s hard surface and reaches up to 1000 metres depth. Due to constant subzero temperatures, permafrost represents a unique record of past epochs, whenever it comes to accumulated methane, oxygen isotope ratio or stored mummies of animals. Permafrost is also a unique environment where cryptobiotic stages of different microorganisms are trapped and stored alive for up to hundreds of thousands of years. Several protist strains and two giant protist viruses isolated from permafrost cores have been already described. New information In this paper, we describe a collection of 35 amoeboid protist strains isolated from the samples of Holocene and Pleistocene permanently frozen sediments. These samples are stored at −18°C in the Soil Cryology Lab, Pushchino, Russia and may be used for further studies and isolation attempts. The collection strains are maintained in liquid media and may be available upon request. The paper also presents a dataset which consists of a table describing the samples and their properties (termed "Sampling events") and a table describing the isolated strains (termed "Occurrences"). The dataset is publicly available through the GBIF portal.
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Affiliation(s)
- Stas Malavin
- Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS, Pushchino, Russia Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS Pushchino Russia
| | - Lyubov Shmakova
- Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS, Pushchino, Russia Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS Pushchino Russia
| | - Jean-Michel Claverie
- Aix-Marseille University, CNRS, IGS (UMR7256), IMM (FR3479), Marseille, France Aix-Marseille University, CNRS, IGS (UMR7256), IMM (FR3479) Marseille France
| | - Elizaveta Rivkina
- Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS, Pushchino, Russia Soil Cryology Lab, Institute of Physicochemical and Biological Problems in Soil Science RAS Pushchino Russia
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7
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Isolates from ancient permafrost help to elucidate species boundaries in Acanthamoeba castellanii complex (Amoebozoa: Discosea). Eur J Protistol 2020; 73:125671. [DOI: 10.1016/j.ejop.2020.125671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 01/03/2020] [Accepted: 01/08/2020] [Indexed: 11/22/2022]
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8
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Rakitin A, Beletsky A, Mardanov A, Surgucheva N, Sorokin V, Cherbunina M, Brouchkov A, Mulyukin A, Filippova S. Prokaryotic community in Pleistocene ice wedges of Mammoth Mountain. Extremophiles 2019; 24:93-105. [PMID: 31606813 DOI: 10.1007/s00792-019-01138-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/30/2019] [Indexed: 01/21/2023]
Abstract
Ice wedges differ from other types of surface and underground glacial bodies and are widely spread in perennially frozen sub-Arctic regions, but the bacterial and archaeal diversity in these permafrost features remains poorly studied. Here, we compared the prokaryotic community composition in the active layer and ancient, 13-19 kyr BP and ~ 40 kyr BP, ice wedge horizons from the same exposure profile of the Mammoth Mountain, using pyrosequencing 16S rRNA gene. The most abundant OTUs in the active layer were affiliated with Acidobacteria (31.81%) followed by Actinobacteria (18.29%), Proteobacteria (18.14%), Gemmatimonadetes (7.3%), Parcubacteria (7.13%) and Bacteroidetes (6.49%). The prokaryotic community in 13-19 kyr BP ice wedge differed at the phylum level by the predominance of Actinobacteria (29.15%) over Acidobacteria (19.52%), Proteobacteria (18.45%), Verrumicrobia (5.88%), Firmicutes (2.98%) and Gemmatimonadetes (2.87%). In contrast, the oldest (~ 40 kyr BP) ice wedge prokaryotic community was rather poor, and only three phyla Firmicutes (54.48%), Proteobacteria (31.42%) and Bacteroidetes (7.92%) constituted the major fraction of reads. Archaeal sequences contributed with no more than 0.6% to total reads in all studied samples. Apparently, the Mammoth Mountain exposure profile harbors insular microbial communities with specific structure that reflects the stratigraphy, properties and age.
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Affiliation(s)
- Andrey Rakitin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia.
| | - Aleksey Beletsky
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Andrey Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Natalya Surgucheva
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Vladimir Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | | | - Anatoli Brouchkov
- Moscow State University, Leninskiye Gory 1, Moscow, 11999, Russia.,Tyumen State University, Volodarskogo St. 6, Tyumen, 625003, Russia
| | - Andrey Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
| | - Svetlana Filippova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp 33-2, Moscow, 119071, Russia
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9
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Roy RK, Augustine RA, Brown CH, Schwenke DO. Activation of oxytocin neurons in the paraventricular nucleus drives cardiac sympathetic nerve activation following myocardial infarction in rats. Commun Biol 2018; 1:160. [PMID: 30320228 PMCID: PMC6172223 DOI: 10.1038/s42003-018-0169-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 09/10/2018] [Indexed: 01/16/2023] Open
Abstract
Myocardial infarction (MI) initiates an increase in cardiac sympathetic nerve activity (SNA) that facilitates potentially fatal arrhythmias. The mechanism(s) underpinning sympathetic activation remain unclear. Some neuronal populations within the hypothalamic paraventricular nucleus (PVN) have been implicated in SNA. This study elucidated the role of the PVN in triggering cardiac SNA following MI (left anterior descending coronary artery ligation). By means of c-Fos, oxytocin, and vasopressin immunohistochemistry accompanied by retrograde tracing we showed that MI activates parvocellular oxytocin neurons projecting to the rostral ventral lateral medulla. Central inhibition of oxytocin receptors using atosiban (4.5 µg in 5 µl, i.c.v.), or retosiban (3 mg/kg, i.v.), prevented the MI-induced increase in SNA and reduced the incidence of ventricular arrhythmias and mortality. In conclusion, pre-autonomic oxytocin neurons can drive the increase in cardiac SNA following MI and peripheral administration of an oxytocin receptor blocker could be a plausible therapeutic strategy to improve outcomes for MI patients. Roy et al. showed that activation of parvocellular pre-autonomic oxytocin neurons increased sympathetic nerve activity following myocardial infarction. This and other aberrant physiological changes induced by acute myocardial infarction were decreased by oxytocin receptor antagonists, hinting to their potential therapeutic role.
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Affiliation(s)
- Ranjan K Roy
- Department of Physiology-HeartOtago, University of Otago, Dunedin, 9054, New Zealand
| | - Rachael A Augustine
- Department of Physiology-HeartOtago, University of Otago, Dunedin, 9054, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, 9054, New Zealand.,Centre for Neuroendocrinology, University of Otago, Dunedin, 9054, New Zealand
| | - Colin H Brown
- Department of Physiology-HeartOtago, University of Otago, Dunedin, 9054, New Zealand.,Brain Health Research Centre, University of Otago, Dunedin, 9054, New Zealand.,Centre for Neuroendocrinology, University of Otago, Dunedin, 9054, New Zealand
| | - Daryl O Schwenke
- Department of Physiology-HeartOtago, University of Otago, Dunedin, 9054, New Zealand.
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10
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Shmakova LA, Karpov SA, Malavin SA, Smirnov AV. Morphology, biology and phylogeny of Phalansterium arcticum sp. n. (Amoebozoa, Variosea), isolated from ancient Arctic permafrost. Eur J Protistol 2018; 63:117-129. [PMID: 29574284 DOI: 10.1016/j.ejop.2018.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 02/21/2018] [Accepted: 02/26/2018] [Indexed: 11/17/2022]
Abstract
A new species, Phalansterium arcticum sp. n., was isolated from an 8580-year-old Arctic permafrost layer. This organism typically lives as a sedentary uniflagellated cell enclosed in a thin flexible mucilaginous sheath, but can form naked swimming cells and amoeboid cells with eruptive pseudopodia accompanied with the formation of short, filopodia-like projections. In an SSU rDNA phylogenetic tree, it robustly groups with other species of this genus. Along with a description of the species, we also add new details to the description of the cell division of Phalansterium and the feeding process in this organism.
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Affiliation(s)
- Lyubov A Shmakova
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Institutskaya 2, 142290, Pushchino, Moscow Region, Russian Federation.
| | - Sergey A Karpov
- Zoological Institute, Russian Academy of Sciences, St. Petersburg 199034, Russian Federation; St. Petersburg State University, St. Petersburg 199034, Russian Federation
| | - Stanislav A Malavin
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Institutskaya 2, 142290, Pushchino, Moscow Region, Russian Federation
| | - Alexey V Smirnov
- St. Petersburg State University, St. Petersburg 199034, Russian Federation
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11
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Methods for Collection and Characterization of Samples From Icy Environments. METHODS IN MICROBIOLOGY 2018. [DOI: 10.1016/bs.mim.2018.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Potential microbial contamination during sampling of permafrost soil assessed by tracers. Sci Rep 2017; 7:43338. [PMID: 28230151 PMCID: PMC5322388 DOI: 10.1038/srep43338] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 01/25/2017] [Indexed: 11/08/2022] Open
Abstract
Drilling and handling of permanently frozen soil cores without microbial contamination is of concern because contamination e.g. from the active layer above may lead to incorrect interpretation of results in experiments investigating potential and actual microbial activity in these low microbial biomass environments. Here, we present an example of how microbial contamination from active layer soil affected analysis of the potentially active microbial community in permafrost soil. We also present the development and use of two tracers: (1) fluorescent plastic microspheres and (2) Pseudomonas putida genetically tagged with Green Fluorescent Protein production to mimic potential microbial contamination of two permafrost cores. A protocol with special emphasis on avoiding microbial contamination was developed and employed to examine how far microbial contamination can penetrate into permafrost cores. The quantity of tracer elements decreased with depth into the permafrost cores, but the tracers were detected as far as 17 mm from the surface of the cores. The results emphasize that caution should be taken to avoid microbial contamination of permafrost cores and that the application of tracers represents a useful tool to assess penetration of potential microbial contamination into permafrost cores.
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13
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Morgalev YN, Lushchaeva IV, Morgaleva TG, Kolesnichenko LG, Loiko SV, Krickov IV, Lim A, Raudina TV, Volkova II, Shirokova LS, Morgalev SY, Vorobyev SN, Kirpotin SN, Pokrovsky OS. Bacteria primarily metabolize at the active layer/permafrost border in the peat core from a permafrost region in western Siberia. Polar Biol 2017. [DOI: 10.1007/s00300-017-2088-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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14
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Abstract
Drilling is an integral part of subsurface exploration. Because almost all drilling operations require the use of a drill fluid, contamination by infiltration of drill fluid into the recovered core material cannot be avoided. Because it is impossible to maintain sterile conditions during drilling the drill fluid will contain surface microbes and other contaminants. As contamination cannot be avoided, it has to be tracked to identify those parts of the drill core that were not infiltrated by the drill fluid. This is done by the addition of tracer compounds. A great variety of tracers is available, and the choice depends on many factors. This review will first explain the basic principles of drilling before presenting the most common tracers and discussing their strengths and weaknesses. The final part of this review presents a number of key questions that have to be addressed in order to find the right tracer for a particular drilling operation.
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Affiliation(s)
- J Kallmeyer
- GFZ German Research Centre for Geosciences, Potsdam, Germany.
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15
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Barbato RA, Garcia-Reyero N, Foley K, Jones R, Courville Z, Douglas T, Perkins E, Reynolds CM. Removal of Exogenous Materials from the Outer Portion of Frozen Cores to Investigate the Ancient Biological Communities Harbored Inside. J Vis Exp 2016. [PMID: 27403572 DOI: 10.3791/54091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The cryosphere offers access to preserved organisms that persisted under past environmental conditions. In fact, these frozen materials could reflect conditions over vast time periods and investigation of biological materials harbored inside could provide insight of ancient environments. To appropriately analyze these ecosystems and extract meaningful biological information from frozen soils and ice, proper collection and processing of the frozen samples is necessary. This is especially critical for microbial and DNA analyses since the communities present may be so uniquely different from modern ones. Here, a protocol is presented to successfully collect and decontaminate frozen cores. Both the absence of the colonies used to dope the outer surface and exogenous DNA suggest that we successfully decontaminated the frozen cores and that the microorganisms detected were from the material, rather than contamination from drilling or processing the cores.
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Affiliation(s)
- Robyn A Barbato
- Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Hanover, NH;
| | - Natàlia Garcia-Reyero
- Environmental Processes Branch, Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS
| | - Karen Foley
- Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Hanover, NH
| | - Robert Jones
- Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Hanover, NH
| | - Zoe Courville
- Terrestrial and Cryospheric Scienes Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Hanover, NH
| | - Thomas Douglas
- Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Fairbanks, AK
| | - Edward Perkins
- Environmental Processes Branch, Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS
| | - Charles M Reynolds
- Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Fairbanks, AK
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16
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Shmakova L, Bondarenko N, Smirnov A. Viable Species of Flamella (Amoebozoa: Variosea) Isolated from Ancient Arctic Permafrost Sediments. Protist 2016; 167:13-30. [DOI: 10.1016/j.protis.2015.11.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 10/14/2015] [Accepted: 11/09/2015] [Indexed: 11/26/2022]
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17
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Microbial Community Composition, Functions, and Activities in the Gulf of Mexico 1 Year after the Deepwater Horizon Accident. Appl Environ Microbiol 2015; 81:5855-66. [PMID: 26092461 DOI: 10.1128/aem.01470-15] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 06/14/2015] [Indexed: 11/20/2022] Open
Abstract
Several studies have assessed the effects of the released oil on microbes, either during or immediately after the Deepwater Horizon accident. However, little is known about the potential longer-term persistent effects on microbial communities and their functions. In this study, one water column station near the wellhead (3.78 km southwest of the wellhead), one water column reference station outside the affected area (37.77 km southeast of the wellhead), and deep-sea sediments near the wellhead (3.66 km southeast of the wellhead) were sampled 1 year after the capping of the well. In order to analyze microbial community composition, function, and activity, we used metagenomics, metatranscriptomics, and mineralization assays. Mineralization of hexadecane was significantly higher at the wellhead station at a depth of ∼1,200 m than at the reference station. Community composition based on taxonomical or functional data showed that the samples taken at a depth of ∼1,200 m were significantly more dissimilar between the stations than at other depths (surface, 100 m, 750 m, and >1,500 m). Both Bacteria and Archaea showed reduced activity at depths of ∼1,200 m when the wellhead station was compared to the reference station, and their activity was significantly higher in surficial sediments than in 10-cm sediments. Surficial sediments also harbored significantly different active genera than did 5- and 10-cm sediments. For the remaining microbial parameters assessed, no significant differences could be observed between the wellhead and reference stations and between surface and 5- to 10-cm-deep sediments.
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18
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Perron GG, Whyte L, Turnbaugh PJ, Goordial J, Hanage WP, Dantas G, Desai MM. Functional characterization of bacteria isolated from ancient arctic soil exposes diverse resistance mechanisms to modern antibiotics. PLoS One 2015; 10:e0069533. [PMID: 25807523 PMCID: PMC4373940 DOI: 10.1371/journal.pone.0069533] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 01/14/2015] [Indexed: 12/03/2022] Open
Abstract
Using functional metagenomics to study the resistomes of bacterial communities isolated from different layers of the Canadian high Arctic permafrost, we show that microbial communities harbored diverse resistance mechanisms at least 5,000 years ago. Among bacteria sampled from the ancient layers of a permafrost core, we isolated eight genes conferring clinical levels of resistance against aminoglycoside, β-lactam and tetracycline antibiotics that are naturally produced by microorganisms. Among these resistance genes, four also conferred resistance against amikacin, a modern semi-synthetic antibiotic that does not naturally occur in microorganisms. In bacteria sampled from the overlaying active layer, we isolated ten different genes conferring resistance to all six antibiotics tested in this study, including aminoglycoside, β-lactam and tetracycline variants that are naturally produced by microorganisms as well as semi-synthetic variants produced in the laboratory. On average, we found that resistance genes found in permafrost bacteria conferred lower levels of resistance against clinically relevant antibiotics than resistance genes sampled from the active layer. Our results demonstrate that antibiotic resistance genes were functionally diverse prior to the anthropogenic use of antibiotics, contributing to the evolution of natural reservoirs of resistance genes.
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Affiliation(s)
- Gabriel G. Perron
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts, 02138, United States of America
- Department of Evolutionary and Organismic Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts, 02138, United States of America
- Biology Program, Bard College, 30 Campus Road, Annandale-on-Hudson, New York, 12504, United States of America
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, Macdonald Campus, 21,111 Lakeshore, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Peter J. Turnbaugh
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts, 02138, United States of America
- Department of Microbiology and Immunology, Hooper Foundation, University of California San Francisco, 513 Parnassus Ave, San Francisco, California, 94143, United States of America
| | - Jacqueline Goordial
- Department of Natural Resource Sciences, McGill University, Macdonald Campus, 21,111 Lakeshore, Ste-Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - William P. Hanage
- Department of Epidemiology, Harvard School of Public School, 677 Huntington Avenue, Boston, Massachusetts, 02115, United States of America
| | - Gautam Dantas
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 4444 Forest Park Avenue, St. Louis, Missouri, 63108, United States of America
- Department of Pathology and Immunology, Washington University School of Medicine, 4444 Park Forest Avenue, St. Louis, Missouri, 63108, United States of America
| | - Michael M. Desai
- FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts, 02138, United States of America
- Department of Evolutionary and Organismic Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts, 02138, United States of America
- Department of Physics, Harvard University, Cambridge, Massachusetts, 02138, United States of America
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19
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Pedersen MW, Overballe-Petersen S, Ermini L, Sarkissian CD, Haile J, Hellstrom M, Spens J, Thomsen PF, Bohmann K, Cappellini E, Schnell IB, Wales NA, Carøe C, Campos PF, Schmidt AMZ, Gilbert MTP, Hansen AJ, Orlando L, Willerslev E. Ancient and modern environmental DNA. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130383. [PMID: 25487334 PMCID: PMC4275890 DOI: 10.1098/rstb.2013.0383] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA obtained from environmental samples such as sediments, ice or water (environmental DNA, eDNA), represents an important source of information on past and present biodiversity. It has revealed an ancient forest in Greenland, extended by several thousand years the survival dates for mainland woolly mammoth in Alaska, and pushed back the dates for spruce survival in Scandinavian ice-free refugia during the last glaciation. More recently, eDNA was used to uncover the past 50 000 years of vegetation history in the Arctic, revealing massive vegetation turnover at the Pleistocene/Holocene transition, with implications for the extinction of megafauna. Furthermore, eDNA can reflect the biodiversity of extant flora and fauna, both qualitatively and quantitatively, allowing detection of rare species. As such, trace studies of plant and vertebrate DNA in the environment have revolutionized our knowledge of biogeography. However, the approach remains marred by biases related to DNA behaviour in environmental settings, incomplete reference databases and false positive results due to contamination. We provide a review of the field.
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Affiliation(s)
- Mikkel Winther Pedersen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Søren Overballe-Petersen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Luca Ermini
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - James Haile
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Trace and Environmental DNA Laboratory, Curtin University, Kent Street, Bentley, Perth, Western Australia 6102, Australia
| | - Micaela Hellstrom
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Johan Spens
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Department of Wildlife, Fish and Environmental Studies, SLU, Umeå S-901 83, Sweden
| | - Philip Francis Thomsen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Kristine Bohmann
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark School of Biological Sciences, University of Bristol, Woodland Road, Bristol BS8 1UG, UK
| | - Enrico Cappellini
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Ida Bærholm Schnell
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Nathan A Wales
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Christian Carøe
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Paula F Campos
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Astrid M Z Schmidt
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - M Thomas P Gilbert
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Anders J Hansen
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, The Natural History Museum of Denmark, Oester Voldgade 5-7, Copenhagen C 1350, Denmark
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20
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Orlando L, Cooper A. Using Ancient DNA to Understand Evolutionary and Ecological Processes. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091712] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of population genetics have revealed dynamic patterns of change in many large vertebrates, featuring localized extinctions, migrations, and population bottlenecks. The pronounced climate cycles of the Late Pleistocene have played a key role, reducing the taxonomic and genetic diversity of many taxa and shaping modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships in paleoecological systems. In the near future, genome-level surveys of ancient populations will play an increasingly important role in revealing, calibrating, and testing evolutionary processes.
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Affiliation(s)
- Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350K Copenhagen, Denmark;,
| | - Alan Cooper
- Australian Center for Ancient DNA, University of Adelaide, Adelaide, South Australia
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21
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Miteva V, Burlingame C, Sowers T, Brenchley J. Comparative evaluation of the indigenous microbial diversity vs. drilling fluid contaminants in the NEEM Greenland ice core. FEMS Microbiol Ecol 2014; 89:238-56. [DOI: 10.1111/1574-6941.12286] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 12/21/2013] [Accepted: 01/16/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Vanya Miteva
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park PA USA
| | - Caroline Burlingame
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park PA USA
| | - Todd Sowers
- Department of Geosciences; Earth and Environment Systems Institute; The Pennsylvania State University; University Park PA USA
| | - Jean Brenchley
- Department of Biochemistry and Molecular Biology; The Pennsylvania State University; University Park PA USA
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22
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Miteva V, Sowers T, Brenchley J. Penetration of fluorescent microspheres into the NEEM (North Eemian) Greenland ice core to assess the probability of microbial contamination. Polar Biol 2013. [DOI: 10.1007/s00300-013-1409-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Steven B, Lionard M, Kuske CR, Vincent WF. High bacterial diversity of biological soil crusts in water tracks over permafrost in the high arctic polar desert. PLoS One 2013; 8:e71489. [PMID: 23967218 PMCID: PMC3742766 DOI: 10.1371/journal.pone.0071489] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/05/2013] [Indexed: 11/18/2022] Open
Abstract
In this study we report the bacterial diversity of biological soil crusts (biocrusts) inhabiting polar desert soils at the northern land limit of the Arctic polar region (83° 05 N). Employing pyrosequencing of bacterial 16S rRNA genes this study demonstrated that these biocrusts harbor diverse bacterial communities, often as diverse as temperate latitude communities. The effect of wetting pulses on the composition of communities was also determined by collecting samples from soils outside and inside of permafrost water tracks, hill slope flow paths that drain permafrost-affected soils. The intermittent flow regime in the water tracks was correlated with altered relative abundance of phylum level taxonomic bins in the bacterial communities, but the alterations varied between individual sampling sites. Bacteria related to the Cyanobacteria and Acidobacteria demonstrated shifts in relative abundance based on their location either inside or outside of the water tracks. Among cyanobacterial sequences, the proportion of sequences belonging to the family Oscillatoriales consistently increased in relative abundance in the samples from inside the water tracks compared to those outside. Acidobacteria showed responses to wetting pulses in the water tracks, increasing in abundance at one site and decreasing at the other two sites. Subdivision 4 acidobacterial sequences tended to follow the trends in the total Acidobacteria relative abundance, suggesting these organisms were largely responsible for the changes observed in the Acidobacteria. Taken together, these data suggest that the bacterial communities of these high latitude polar biocrusts are diverse but do not show a consensus response to intermittent flow in water tracks over high Arctic permafrost.
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Affiliation(s)
- Blaire Steven
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Marie Lionard
- Département de biologie, Université Laval, Québec City, Québec, Canada
- Centre d’Études Nordiques, Université Laval, Québec City, Québec, Canada
| | - Cheryl R. Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Warwick F. Vincent
- Département de biologie, Université Laval, Québec City, Québec, Canada
- Centre d’Études Nordiques, Université Laval, Québec City, Québec, Canada
- * E-mail:
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24
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Mykytczuk NCS, Wilhelm RC, Whyte LG. Planococcus halocryophilus sp. nov., an extreme sub-zero species from high Arctic permafrost. Int J Syst Evol Microbiol 2012; 62:1937-1944. [DOI: 10.1099/ijs.0.035782-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel aerobic, Gram-positive, motile, coccoid bacterial strain, designated Or1T, was isolated from permafrost active-layer soil collected from the Canadian high Arctic. Strain Or1T was capable of growth over a broad temperature range, including sub-zero growth (below −10 to 37 °C), and at high salinity (0–19 % NaCl), growing optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % NaCl. Its taxonomic and phylogenetic position was determined by using a polyphasic approach, which indicated that strain Or1T was a member of the genus
Planococcus
. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Or1T belonged to the genus
Planococcus
, differing by 0.4–3.6 % from the type strains of all recognized
Planococcus
species, and was related most closely to
Planococcus antarcticus
CMS 26orT (98.8 % similarity) and
Planococcus donghaensis
JH1T (99.6 %). However, DNA–DNA hybridization experiments showed that strain Or1T had low genomic relatedness to
Planococcus antarcticus
CMS 26orT (18 %) and
Planococcus donghaensis
JH1T (46 %). The major menaquinones of strain Or1T were MK-7 (55 %), MK-8 (36 %) and MK-6 (9 %) and the major fatty acids were anteiso-C15 : 0, C16 : 1ω7c alcohol and anteiso-C17 : 0. The DNA G+C content of strain Or1T was 40.5 mol%. Differential phenotypic, phylogenetic and genomic data suggest that strain Or1T represents a novel species of the genus
Planococcus
, for which the name Planococcus halocryophilus sp. nov. is proposed. The type strain is Or1T ( = DSM 24743T = JCM 17719T).
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Affiliation(s)
| | - Roland C. Wilhelm
- Department of Natural Resource Sciences, McGill University, QC H9X 3V9, Canada
| | - Lyle G. Whyte
- Department of Natural Resource Sciences, McGill University, QC H9X 3V9, Canada
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25
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Wilhelm RC, Radtke KJ, Mykytczuk NCS, Greer CW, Whyte LG. Life at the wedge: the activity and diversity of arctic ice wedge microbial communities. ASTROBIOLOGY 2012; 12:347-360. [PMID: 22519974 DOI: 10.1089/ast.2011.0730] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The discovery of polygonal terrain on Mars underlain by ice heightens interest in the possibility that this water-bearing habitat may be, or may have been, a suitable habitat for extant life. The possibility is supported by the recurring detection of terrestrial microorganisms in subsurface ice environments, such as ice wedges found beneath tundra polygon features. A characterization of the microbial community of ice wedges from the high Arctic was performed to determine whether this ice environment can sustain actively respiring microorganisms and to assess the ecology of this extreme niche. We found that ice wedge samples contained a relatively abundant number of culturable cells compared to other ice habitats (∼10(5) CFU·mL(-1)). Respiration assays in which radio-labeled acetate and in situ measurement of CO(2) flux were used suggested low levels of microbial activity, though more sensitive techniques are required to confirm these findings. Based on 16S rRNA gene pyrosequencing, bacterial and archaeal ice wedge communities appeared to reflect surrounding soil communities. Two Pseudomonas sp. were the most abundant taxa in the ice wedge bacterial library (∼50%), while taxa related to ammonia-oxidizing Thaumarchaeota occupied 90% of the archaeal library. The tolerance of a variety of isolates to salinity and temperature revealed characteristics of a psychrotolerant, halotolerant community. Our findings support the hypothesis that ice wedges are capable of sustaining a diverse, plausibly active microbial community. As such, ice wedges, compared to other forms of less habitable ground ice, could serve as a reservoir for life on permanently cold, water-scarce, ice-rich extraterrestrial bodies and are therefore of interest to astrobiologists and ecologists alike. .
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Affiliation(s)
- Roland C Wilhelm
- Microbiology and Immunology, University of British Columbia, Vancouver, Canada
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26
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Wilhelm RC, Niederberger TD, Greer C, Whyte LG. Microbial diversity of active layer and permafrost in an acidic wetland from the Canadian High Arctic. Can J Microbiol 2012; 57:303-15. [PMID: 21491982 DOI: 10.1139/w11-004] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The abundance and structure of archaeal and bacterial communities from the active layer and the associated permafrost of a moderately acidic (pH < 5.0) High Arctic wetland (Axel Heiberg Island, Nunavut, Canada) were investigated using culture- and molecular-based methods. Aerobic viable cell counts from the active layer were ∼100-fold greater than those from the permafrost (2.5 × 10(5) CFU·(g soil dry mass)(-1)); however, a greater diversity of isolates were cultured from permafrost, as determined by 16S rRNA gene sequencing. Isolates from both layers demonstrated growth characteristics of a psychrotolerant, halotolerant, and acidotolerant community. Archaea constituted 0.1% of the total 16S rRNA gene copy number and, in the 16S rRNA gene clone library, predominantly (71% and 95%) consisted of Crenarchaeota related to Group I. 1b. In contrast, bacterial communities were diverse (Shannon's diversity index, H = ∼4), with Acidobacteria constituting the largest division of active layer clones (30%) and Actinobacteria most abundant in permafrost (28%). Direct comparisons of 16S rRNA gene sequence data highlighted significant differences between the bacterial communities of each layer, with the greatest differences occurring within Actinobacteria. Comparisons of 16S rRNA gene sequences with those from other Arctic permafrost and cold-temperature wetlands revealed commonly occurring taxa within the phyla Chloroflexi, Acidobacteria, and Actinobacteria (families Intrasporangiaceae and Rubrobacteraceae).
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Affiliation(s)
- Roland C Wilhelm
- Department of Natural Resource Sciences, McGill University, Ste. Anne de Bellevue, QC, Canada
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27
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The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME JOURNAL 2010; 4:1206-14. [DOI: 10.1038/ismej.2010.41] [Citation(s) in RCA: 238] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Niederberger TD, Steven B, Charvet S, Barbier B, Whyte LG. Virgibacillus arcticus sp. nov., a moderately halophilic, endospore-forming bacterium from permafrost in the Canadian high Arctic. Int J Syst Evol Microbiol 2009; 59:2219-25. [PMID: 19605723 DOI: 10.1099/ijs.0.002931-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, moderately halophilic, endospore-forming bacterial strain, designated Hal 1T, was isolated from a permafrost core collected from the Canadian high Arctic. The temperature for growth of strain Hal 1T was 0-30 degrees C with no growth observed at either -5 or 37 degrees C (optimum growth at about 25 degrees C). Strain Hal 1T was able to grow at NaCl concentrations of 0-20% (w/v) and did not have an absolute NaCl requirement for growth; optimal growth was at 5% (w/v) NaCl. The level of 16S rRNA gene sequence similarity between strain Hal 1T and the type strains of Virgibacillus carmonensis and Virgibacillus necropolis was 98.2%; values with respect to the type strains of other recognized Virgibacillus species were below 96.0%. The DNA G+C content of strain Hal 1T was 38.2 mol%. Levels of DNA-DNA relatedness between strain Hal 1T and the type strains of V. carmonensis and V. necropolis were 14.0 and 21.0%, respectively. The major fatty acid of strain Hal 1T was anteiso-C15:0, consistent with species of the genus Virgibacillus. The cell-wall peptidoglycan of strain Hal 1T was type A1alpha and the major respiratory quinone was MK-7. On the basis of genotypic and physiological results, strain Hal 1T (=DSM 19574T=JCM 14839T) is proposed as the type strain of a novel species of the genus Virgibacillus, namely Virgibacillus arcticus sp. nov.
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Affiliation(s)
- Thomas D Niederberger
- Department of Natural Resource Sciences, McGill University, 21,111 Lakeshore Rd, Ste-Anne de Bellevue, QC, Canada
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29
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Steven B, Pollard WH, Greer CW, Whyte LG. Microbial diversity and activity through a permafrost/ground ice core profile from the Canadian high Arctic. Environ Microbiol 2008; 10:3388-403. [PMID: 19025556 DOI: 10.1111/j.1462-2920.2008.01746.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Culture-dependent and culture-independent methods were used in an investigation of the microbial diversity in a permafrost/massive ground ice core from the Canadian high Arctic. Denaturing gradient gel electrophoresis as well as Bacteria and Archaea 16S rRNA gene clone libraries showed differences in the composition of the microbial communities in the distinct core horizons. Microbial diversity was similar in the active layer (surface) soil, permafrost table and permafrost horizons while the ground ice microbial community showed low diversity. Bacteria and Archaea sequences related to the Actinobacteria (54%) and Crenarchaeota (100%) respectively were predominant in the active layer while the majority of sequences in the permafrost were related to the Proteobacteria (57%) and Euryarchaeota (76%). The most abundant phyla in the ground ice clone libraries were the Firmicutes (59%) and Crenarchaeota (82%). Isolates from the permafrost were both less abundant and diverse than in the active layer soil, while no culturable cells were recovered from the ground ice. Mineralization of [1-(14)C] acetic acid and [2-(14)C] glucose was used to detect microbial activity in the different horizons in the core. Mineralization was detected at near ambient permafrost temperatures (-15 degrees C), indicating that permafrost may harbour an active microbial population, while the low microbial diversity, abundance and activity in ground ice suggests a less hospitable microbial habitat.
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Affiliation(s)
- Blaire Steven
- Department of Natural Resource Sciences, McGill University, Montreal, Quebec, Canada
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30
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31
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Vishnivetskaya TA. Viable Cyanobacteria and Green Algae from the Permafrost Darkness. SOIL BIOLOGY 2008. [DOI: 10.1007/978-3-540-69371-0_6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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32
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Pfiffner SM, Onstott TC, Ruskeeniemi T, Talikka M, Bakermans C, McGown D, Chan E, Johnson A, Phelps TJ, Le Puil M, Difurio SA, Pratt LM, Stotler R, Frape S, Telling J, Lollar BS, Neill I, Zerbin B. Challenges for coring deep permafrost on Earth and Mars. ASTROBIOLOGY 2008; 8:623-638. [PMID: 18680412 DOI: 10.1089/ast.2007.0159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A scientific drilling expedition to the High Lake region of Nunavut, Canada, was recently completed with the goals of collecting samples and delineating gradients in salinity, gas composition, pH, pe, and microbial abundance in a 400 m thick permafrost zone and accessing the underlying pristine subpermafrost brine. With a triple-barrel wireline tool and the use of stringent quality assurance and quality control (QA/QC) protocols, 200 m of frozen, Archean, mafic volcanic rock was collected from the lower boundary that separates the permafrost layer and subpermafrost saline water. Hot water was used to remove cuttings and prevent the drill rods from freezing in place. No cryopegs were detected during penetration through the permafrost. Coring stopped at the 535 m depth, and the drill water was bailed from the hole while saline water replaced it. Within 24 hours, the borehole iced closed at 125 m depth due to vapor condensation from atmospheric moisture and, initially, warm water leaking through the casing, which blocked further access. Preliminary data suggest that the recovered cores contain viable anaerobic microorganisms that are not contaminants even though isotopic analyses of the saline borehole water suggests that it is a residue of the drilling brine used to remove the ice from the upper, older portion of the borehole. Any proposed coring mission to Mars that seeks to access subpermafrost brine will not only require borehole stability but also a means by which to generate substantial heating along the borehole string to prevent closure of the borehole from condensation of water vapor generated by drilling.
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Affiliation(s)
- S M Pfiffner
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee 37932, USA.
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Rivkina E, Shcherbakova V, Laurinavichius K, Petrovskaya L, Krivushin K, Kraev G, Pecheritsina S, Gilichinsky D. Biogeochemistry of methane and methanogenic archaea in permafrost. FEMS Microbiol Ecol 2007; 61:1-15. [PMID: 17428301 DOI: 10.1111/j.1574-6941.2007.00315.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
This study summarizes the findings of our research on the genesis of methane, its content and distribution in permafrost horizons of different age and origin. Supported by reliable data from a broad geographical sweep, these findings confirm the presence of methane in permanently frozen fine-grained sediments. In contrast to the omnipresence of carbon dioxide in permafrost, methane-containing horizons (up to 40.0 mL kg(-1)) alternate with strata free of methane. Discrete methane-containing horizons representing over tens of thousands of years are indicative of the absence of methane diffusion through the frozen layers. Along with the isotopic composition of CH(4) carbon (delta(13)C -64 per thousand to -99 per thousand), this confirms its biological origin and points to in situ formation of this biogenic gas. Using (14)C-labeled substrates, the possibility of methane formation within permafrost was experimentally shown, as confirmed by delta(13)C values. Extremely low values (near -99 per thousand) indicate that the process of CH(4) formation is accompanied by the substantial fractionation of carbon isotopes. For the first time, cultures of methane-forming archaea, Methanosarcina mazei strain JL01 VKM B-2370, Methanobacterium sp. strain M2 VKM B-2371 and Methanobacterium sp. strain MK4 VKM B-2440 from permafrost, were isolated and described.
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Affiliation(s)
- Elizaveta Rivkina
- Institute of Physicochemical and Biological Problems in Soil Sciences, Russian Academy of Sciences, Moscow, Russian Federation.
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Gilichinsky DA, Wilson GS, Friedmann EI, McKay CP, Sletten RS, Rivkina EM, Vishnivetskaya TA, Erokhina LG, Ivanushkina NE, Kochkina GA, Shcherbakova VA, Soina VS, Spirina EV, Vorobyova EA, Fyodorov-Davydov DG, Hallet B, Ozerskaya SM, Sorokovikov VA, Laurinavichyus KS, Shatilovich AV, Chanton JP, Ostroumov VE, Tiedje JM. Microbial populations in Antarctic permafrost: biodiversity, state, age, and implication for astrobiology. ASTROBIOLOGY 2007; 7:275-311. [PMID: 17480161 DOI: 10.1089/ast.2006.0012] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Antarctic permafrost soils have not received as much geocryological and biological study as has been devoted to the ice sheet, though the permafrost is more stable and older and inhabited by more microbes. This makes these soils potentially more informative and a more significant microbial repository than ice sheets. Due to the stability of the subsurface physicochemical regime, Antarctic permafrost is not an extreme environment but a balanced natural one. Up to 10(4) viable cells/g, whose age presumably corresponds to the longevity of the permanently frozen state of the sediments, have been isolated from Antarctic permafrost. Along with the microbes, metabolic by-products are preserved. This presumed natural cryopreservation makes it possible to observe what may be the oldest microbial communities on Earth. Here, we describe the Antarctic permafrost habitat and biodiversity and provide a model for martian ecosystems.
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Affiliation(s)
- D A Gilichinsky
- Institutes of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, Russia. gilichin@online stack.net
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Steven B, Briggs G, McKay CP, Pollard WH, Greer CW, Whyte LG. Characterization of the microbial diversity in a permafrost sample from the Canadian high Arctic using culture-dependent and culture-independent methods. FEMS Microbiol Ecol 2007; 59:513-23. [PMID: 17313587 DOI: 10.1111/j.1574-6941.2006.00247.x] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
A combination of culture-dependent and culture-independent methodologies (Bacteria and Archaea 16S rRNA gene clone library analyses) was used to determine the microbial diversity present within a geographically distinct high Arctic permafrost sample. Culturable Bacteria isolates, identified by 16S rRNA gene sequencing, belonged to the phyla Firmicutes, Actinobacteria and Proteobacteria with spore-forming Firmicutes being the most abundant; the majority of the isolates (19/23) were psychrotolerant, some (11/23) were halotolerant, and three isolates grew at -5 degrees C. A Bacteria 16S rRNA gene library containing 101 clones was composed of 42 phylotypes related to diverse phylogenetic groups including the Actinobacteria, Proteobacteria, Firmicutes, Cytophaga - Flavobacteria - Bacteroides, Planctomyces and Gemmatimonadetes; the bacterial 16S rRNA gene phylotypes were dominated by Actinobacteria- and Proteobacteria-related sequences. An Archaea 16S rRNA gene clone library containing 56 clones was made up of 11 phylotypes and contained sequences related to both of the major Archaea domains (Euryarchaeota and Crenarchaeota); the majority of sequences in the Archaea library were related to halophilic Archaea. Characterization of the microbial diversity existing within permafrost environments is important as it will lead to a better understanding of how microorganisms function and survive in such extreme cryoenvironments.
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Affiliation(s)
- Blaire Steven
- Department of Natural Resource Sciences, McGill University, Montreal, Canada
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Vishnivetskaya TA, Petrova MA, Urbance J, Ponder M, Moyer CL, Gilichinsky DA, Tiedje JM. Bacterial community in ancient Siberian permafrost as characterized by culture and culture-independent methods. ASTROBIOLOGY 2006; 6:400-14. [PMID: 16805696 DOI: 10.1089/ast.2006.6.400] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The microbial composition of ancient permafrost sediments from the Kolyma lowland of Northeast Eurasia was examined through culture and culture-independent approaches. These sediments have been continuously frozen for 5,000 to 2-3 million years. A total of 265 Bacteria 16S rRNA gene sequences were amplified from the permafrost total-community genomic DNA and screened by amplified ribosomal 16S rRNA restriction analysis. Members of three major lineages were found: gamma-Proteobacteria (mostly Xanthomonadaceae), Actinobacteria, and Firmicutes. We also determined partial 16S rRNA gene sequences of 49 isolates from a collection of 462 aerobes isolated from these sediments. The bacteria included Actinomycetales (Arthrobacter and Microbacteriaceae); followed by the Firmicutes (Exiguobacterium and Planomicrobium); the Bacteroidetes (Flavobacterium); the gamma-Proteobacteria (Psychrobacter); and the alpha-Proteobacteria (Sphingomonas). Both culture and culture-independent approaches showed the presence of high and low G+C Gram-positive bacteria and gamma-Proteobacteria. Some of the 16S rRNA gene sequences of environmental clones matched those of Arthrobacter isolates. Two-thirds of the isolates grew at -2.5 degrees C, indicating that they are psychroactive, and all are closely related to phylogenetic groups with strains from other cold environments, mostly commonly from Antarctica. The culturable and non-culturable microorganisms found in the terrestrial permafrost provide a prototype for possible life on the cryogenic planets of the Solar System.
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Steven B, Léveillé R, Pollard WH, Whyte LG. Microbial ecology and biodiversity in permafrost. Extremophiles 2006; 10:259-67. [PMID: 16550305 DOI: 10.1007/s00792-006-0506-3] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Accepted: 11/18/2005] [Indexed: 11/29/2022]
Abstract
Permafrost represents 26% of terrestrial soil ecosystems; yet its biology, essentially microbiology, remains relatively unexplored. The permafrost environment is considered extreme because indigenous microorganisms must survive prolonged exposure to subzero temperatures and background radiation for geological time scales in a habitat with low water activity and extremely low rates of nutrient and metabolite transfer. Yet considerable numbers and biodiversity of bacteria exist in permafrost, some of which may be among the most ancient viable life on Earth. This review describes the permafrost environment as a microbial habitat and reviews recent studies examining microbial biodiversity found in permafrost as well as microbial growth and activity at ambient in situ subzero temperatures. These investigations suggest that functional microbial ecosystems exist within the permafrost environment and may have important implications on global biogeochemical processes as well as the search for past or extant life in permafrost presumably present on Mars and other bodies in our solar system.
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Affiliation(s)
- Blaire Steven
- Department of Natural Resource Sciences, McGill University, 21, 111 Lakeshore Rd, H9X 3V9, Ste-Anne de Bellevue, QC, Canada
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