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Meneghel J, Passot S, Dupont S, Fonseca F. Biophysical characterization of the Lactobacillus delbrueckii subsp. bulgaricus membrane during cold and osmotic stress and its relevance for cryopreservation. Appl Microbiol Biotechnol 2016; 101:1427-1441. [DOI: 10.1007/s00253-016-7935-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/08/2016] [Accepted: 10/12/2016] [Indexed: 10/20/2022]
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A single mutation Gln142Lys doubles the catalytic activity of VPR, a cold adapted subtilisin-like serine proteinase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1436-43. [PMID: 27456266 DOI: 10.1016/j.bbapap.2016.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 07/11/2016] [Accepted: 07/15/2016] [Indexed: 11/20/2022]
Abstract
Structural comparisons of the cold adapted subtilase VPR and its thermophilic homologue, aqualysin I (AQUI) indicated the presence of additional salt bridges in the latter. Few of those appear to contribute significantly to thermal stability of AQUI. This includes a putative salt bridge between residues Lys142 and Glu172 as its deletion did not have any significant effect on its stability or activity (Jónsdóttir et al. (2014)). Insertion of this putative salt bridge into the structure of VPR, in a double mutant (VPRΔC_Q142K/S172E), however was detrimental to the stability of the enzyme. Incorporation of either the Q142K or S172E mutations into VPR, were found to significantly affect the catalytic properties of the enzyme. The single mutation Q142K was highly effective, as it increased the kcat and kcat/Km more than twofold. When the Q142K mutation was inserted into a thermostabilized, but a low activity mutant of VPR (VPRΔC_N3P/I5P), the activity increased about tenfold in terms of kcat and kcat/Km, while retaining the stability of the mutant. Molecular dynamics simulations of the single mutants were carried out to provide structural rationale for these experimental observations. Based on root mean square fluctuation (RMSF) profiles, the two mutants were more flexible in certain regions of the structure and the Q142K mutant had the highest overall flexibility of the three enzymes. The results suggest that weakening of specific H-bonds resulting from the mutations may be propagated over some distance giving rise to higher flexibility in the active site regions of the enzyme, causing higher catalytic activity in the mutants.
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Kilbride P, Gonzalez-Molina J, Maurmann N, Mendonça da Silva J, Gibbons S, Selden C, Fuller B, Morris J. Impact of Storage at -80°C on Encapsulated Liver Spheroids After Liquid Nitrogen Storage. Biores Open Access 2016; 5:146-54. [PMID: 27298755 PMCID: PMC4900228 DOI: 10.1089/biores.2016.0017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
For many bioengineered tissues to have practical clinical application, cryopreservation for use on demand is essential. This study examined different thermal histories on warming and short holding periods at different subzero temperatures on subsequent functional recoveries of alginate encapsulated liver spheroids (ELS) for use in a bioartificial liver device. This mimicked transport at liquid nitrogen (−196°C) or dry ice (∼−80°C) temperatures. Holding at −80°C on warming after −196°C storage resulted in ELS expressing significant (p < 0.001) damage compared with direct thaw from liquid nitrogen, with viable cell number falling from 74.0 ± 8.4 million viable cells/mL without −80°C storage to 1.9 ± 0.6 million viable cells/mL 72 h post-thaw after 8 days storage at −80°C. Even 1 day at −80°C after −196°C storage resulted in lower viability (down 21% 24 h post-thaw), viable cell count (down 29% 24 h post-thaw), glucose, and alpha-1-fetoprotein production (reduced by 59% and 95% 24 h from 1 day post-thaw, respectively). Storage at −80°C was determined to be harmful only during the warming cycle. Chemical measurements of the alginate component of ELS were unchanged by cryogenic exposure in either condition.
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Affiliation(s)
- Peter Kilbride
- Asymptote Ltd., St. John's Innovation Centre, Cambridge, United Kingdom.; UCL Institute for Liver and Digestive Health, Royal Free Hospital Campus, London, United Kingdom
| | - Jordi Gonzalez-Molina
- UCL Institute for Liver and Digestive Health , Royal Free Hospital Campus, London, United Kingdom
| | - Natasha Maurmann
- UCL Institute for Liver and Digestive Health, Royal Free Hospital Campus, London, United Kingdom.; UCL Department of Surgery, Royal Free Hospital Campus, London, United Kingdom
| | - Joana Mendonça da Silva
- UCL Institute for Liver and Digestive Health , Royal Free Hospital Campus, London, United Kingdom
| | - Stephanie Gibbons
- UCL Institute for Liver and Digestive Health , Royal Free Hospital Campus, London, United Kingdom
| | - Clare Selden
- UCL Institute for Liver and Digestive Health , Royal Free Hospital Campus, London, United Kingdom
| | - Barry Fuller
- UCL Department of Surgery , Royal Free Hospital Campus, London, United Kingdom
| | - John Morris
- Asymptote Ltd. , St. John's Innovation Centre, Cambridge, United Kingdom
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54
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Schuerger AC, Nicholson WL. Twenty-Three Species of Hypobarophilic Bacteria Recovered from Diverse Ecosystems Exhibit Growth under Simulated Martian Conditions at 0.7 kPa. ASTROBIOLOGY 2016; 16:335-47. [PMID: 27135839 PMCID: PMC4876496 DOI: 10.1089/ast.2015.1394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
UNLABELLED Bacterial growth at low pressure is a new research area with implications for predicting microbial activity in clouds and the bulk atmosphere on Earth, and for modeling the forward contamination of planetary surfaces like Mars. Here, we describe experiments on the recovery and identification of 23 species of bacterial hypobarophiles (def., growth under hypobaric conditions of approximately 1-2 kPa) in 11 genera capable of growth at 0.7 kPa. Hypobarophilic bacteria, but not archaea or fungi, were recovered from soil and non-soil ecosystems. The highest numbers of hypobarophiles were recovered from Arctic soil, Siberian permafrost, and human saliva. Isolates were identified through 16S rRNA sequencing to belong to the genera Carnobacterium, Exiguobacterium, Leuconostoc, Paenibacillus, and Trichococcus. The highest population of culturable hypobarophilic bacteria (5.1 × 10(4) cfu/g) was recovered from Colour Lake soils from Axel Heiberg Island in the Canadian Arctic. In addition, we extend the number of hypobarophilic species in the genus Serratia to six type-strains that include S. ficaria, S. fonticola, S. grimesii, S. liquefaciens, S. plymuthica, and S. quinivorans. Microbial growth at 0.7 kPa suggests that pressure alone will not be growth-limiting on the martian surface or in Earth's atmosphere up to an altitude of 34 km. KEY WORDS Planetary protection-Simulated martian atmosphere-Piezophile-Habitability-Extremophilic microorganisms. Astrobiology 16, 335-347.
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Affiliation(s)
| | - Wayne L. Nicholson
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida
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55
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Proline hydration at low temperatures: its role in the protection of cell from freeze-induced stress. Amino Acids 2016; 48:1685-94. [DOI: 10.1007/s00726-016-2232-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/05/2016] [Indexed: 11/26/2022]
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56
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Fonseca F, Meneghel J, Cenard S, Passot S, Morris GJ. Determination of Intracellular Vitrification Temperatures for Unicellular Micro Organisms under Conditions Relevant for Cryopreservation. PLoS One 2016; 11:e0152939. [PMID: 27055246 PMCID: PMC4824440 DOI: 10.1371/journal.pone.0152939] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/20/2016] [Indexed: 11/18/2022] Open
Abstract
During cryopreservation ice nucleation and crystal growth may occur within cells or the intracellular compartment may vitrify. Whilst previous literature describes intracellular vitrification in a qualitative manner, here we measure the intracellular vitrification temperature of bacteria and yeasts under conditions relevant to cryopreservation, including the addition of high levels of permeating and nonpermeating additives and the application of rapid rates of cooling. The effects of growth conditions that are known to modify cellular freezing resistance on the intracellular vitrification temperature are also examined. For bacteria a plot of the activity on thawing against intracellular glass transition of the maximally freeze-concentrated matrix (Tg’) shows that cells with the lowest value of intracellular Tg’ survive the freezing process better than cells with a higher intracellular Tg’. This paper demonstrates the role of the physical state of the intracellular environment in determining the response of microbial cells to preservation and could be a powerful tool to be manipulated to allow the optimization of methods for the preservation of microorganisms.
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Affiliation(s)
- Fernanda Fonseca
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
- * E-mail:
| | - Julie Meneghel
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Stéphanie Cenard
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - Stéphanie Passot
- UMR GMPA, AgroParisTech, INRA, Université Paris-Saclay, Thiverval-Grignon, France
| | - G. John Morris
- Asymptote Ltd, St John’s Innovation Centre, Cambridge CB4 0WS, United Kingdom
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57
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Chrismas NAM, Anesio AM, Sánchez-Baracaldo P. Multiple adaptations to polar and alpine environments within cyanobacteria: a phylogenomic and Bayesian approach. Front Microbiol 2015; 6:1070. [PMID: 26528250 PMCID: PMC4602134 DOI: 10.3389/fmicb.2015.01070] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/17/2015] [Indexed: 01/15/2023] Open
Abstract
Cyanobacteria are major primary producers in the polar and alpine regions contributing significantly to nitrogen and carbon cycles in the cryosphere. Recent advancements in environmental sequencing techniques have revealed great molecular diversity of microorganisms in cold environments. However, there are no comprehensive phylogenetic analyses including the entire known diversity of cyanobacteria from these extreme environments. We present here a global phylogenetic analysis of cyanobacteria including an extensive dataset comprised of available small subunit (SSU) rRNA gene sequences of cyanobacteria from polar and high altitude environments. Furthermore, we used a large-scale multi-gene (135 proteins and 2 ribosomal RNAs) genome constraint including 57 cyanobacterial genomes. Our analyses produced the first phylogeny of cold cyanobacteria exhibiting robust deep branching relationships implementing a phylogenomic approach. We recovered several clades common to Arctic, Antarctic and alpine sites suggesting that the traits necessary for survival in the cold have been acquired by a range of different mechanisms in all major cyanobacteria lineages. Bayesian ancestral state reconstruction revealed that 20 clades each have common ancestors with high probabilities of being capable of surviving in cold environments.
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Affiliation(s)
- Nathan A M Chrismas
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol Bristol, UK
| | - Alexandre M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol Bristol, UK
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58
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Bailey TL, Wang M, Solocinski J, Nathan BP, Chakraborty N, Menze MA. Protective effects of osmolytes in cryopreserving adherent neuroblastoma (Neuro-2a) cells. Cryobiology 2015; 71:472-80. [PMID: 26408850 DOI: 10.1016/j.cryobiol.2015.08.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 08/12/2015] [Accepted: 08/26/2015] [Indexed: 12/13/2022]
Abstract
A simple method to cryopreserve adherent monolayers of neuronal cells is currently not available, but the development of this technique could facilitate numerous applications in the field of biomedical engineering, cell line development, and drug screening. However, complex tissues of some exceptional animals survive freezing in nature. These animals are known to accumulate several small molecular weight solutes prior to freezing. Following a similar strategy, we investigated the effects of osmolytes such as trehalose, proline, and sucrose as additives to the traditional cryoprotectant dimethyl sulfoxide (Me2SO) in modulating the cryopreservation outcome of mouse neuroblastoma (Neuro-2a) cells. Neuro-2a cells adhered to cell culture plates were incubated for 24 h at varying concentrations of trehalose, proline, sucrose and combinations of these compounds. Cells were cryopreserved for 24 h and cell viability post-freezing and thawing was quantified by trypan blue exclusion assay. On average, only 13.5% of adherent cells survived freezing in the presence of 10% Me2SO alone (control). Pre-incubation of cells with medium containing both trehalose and proline severely decreased cell proliferation, but increased cell recovery to about 53% of control. Furthermore, characterization using Raman microspectroscopy revealed that the addition of both trehalose and proline to 10% Me2SO substantially increased the size, and altered the nature, of ice crystals formed during freezing. Our results suggest that pre-incubation of Neuro-2a cells with trehalose and proline in combination provides cell protection along with alterations of ice structure in order to increase cell survival post-freezing.
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Affiliation(s)
- Trisha L Bailey
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA
| | - Mian Wang
- Department of Mechanical Engineering, University of Michigan, Dearborn, MI 48128, USA
| | - Jason Solocinski
- Department of Mechanical Engineering, University of Michigan, Dearborn, MI 48128, USA
| | - Britto P Nathan
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA
| | - Nilay Chakraborty
- Department of Mechanical Engineering, University of Michigan, Dearborn, MI 48128, USA
| | - Michael A Menze
- Department of Biological Sciences, Eastern Illinois University, Charleston, IL 61920, USA.
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59
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Bains W, Xiao Y, Yu C. Prediction of the maximum temperature for life based on the stability of metabolites to decomposition in water. Life (Basel) 2015; 5:1054-100. [PMID: 25821932 PMCID: PMC4500130 DOI: 10.3390/life5021054] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/03/2015] [Accepted: 03/05/2015] [Indexed: 12/01/2022] Open
Abstract
The components of life must survive in a cell long enough to perform their function in that cell. Because the rate of attack by water increases with temperature, we can, in principle, predict a maximum temperature above which an active terrestrial metabolism cannot function by analysis of the decomposition rates of the components of life, and comparison of those rates with the metabolites' minimum metabolic half-lives. The present study is a first step in this direction, providing an analytical framework and method, and analyzing the stability of 63 small molecule metabolites based on literature data. Assuming that attack by water follows a first order rate equation, we extracted decomposition rate constants from literature data and estimated their statistical reliability. The resulting rate equations were then used to give a measure of confidence in the half-life of the metabolite concerned at different temperatures. There is little reliable data on metabolite decomposition or hydrolysis rates in the literature, the data is mostly confined to a small number of classes of chemicals, and the data available are sometimes mutually contradictory because of varying reaction conditions. However, a preliminary analysis suggests that terrestrial biochemistry is limited to environments below ~150-180 °C. We comment briefly on why pressure is likely to have a small effect on this.
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Affiliation(s)
- William Bains
- Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Mass. Avenue, Cambridge, MA 02139, USA.
| | - Yao Xiao
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK.
| | - Changyong Yu
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK.
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60
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Snow surface microbiome on the High Antarctic Plateau (DOME C). PLoS One 2014; 9:e104505. [PMID: 25101779 PMCID: PMC4125213 DOI: 10.1371/journal.pone.0104505] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/14/2014] [Indexed: 12/22/2022] Open
Abstract
The cryosphere is an integral part of the global climate system and one of the major habitable ecosystems of Earth's biosphere. These permanently frozen environments harbor diverse, viable and metabolically active microbial populations that represent almost all the major phylogenetic groups. In this study, we investigated the microbial diversity in the surface snow surrounding the Concordia Research Station on the High Antarctic Plateau through a polyphasic approach, including direct prokaryotic quantification by flow cytometry and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and phylogenetic identification by 16S RNA gene clone library sequencing and 454 16S amplicon pyrosequencing. Although the microbial abundance was low (<103 cells/ml of snowmelt), concordant results were obtained with the different techniques. The microbial community was mainly composed of members of the Alpha-proteobacteria class (e.g. Kiloniellaceae and Rhodobacteraceae), which is one of the most well-represented bacterial groups in marine habitats, Bacteroidetes (e.g. Cryomorphaceae and Flavobacteriaceae) and Cyanobacteria. Based on our results, polar microorganisms could not only be considered as deposited airborne particles, but as an active component of the snowpack ecology of the High Antarctic Plateau.
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61
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Everatt MJ, Convey P, Bale JS, Worland MR, Hayward SAL. Responses of invertebrates to temperature and water stress: A polar perspective. J Therm Biol 2014; 54:118-32. [PMID: 26615734 DOI: 10.1016/j.jtherbio.2014.05.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/20/2014] [Accepted: 05/20/2014] [Indexed: 10/25/2022]
Abstract
As small bodied poikilothermic ectotherms, invertebrates, more so than any other animal group, are susceptible to extremes of temperature and low water availability. In few places is this more apparent than in the Arctic and Antarctic, where low temperatures predominate and water is unusable during winter and unavailable for parts of summer. Polar terrestrial invertebrates express a suite of physiological, biochemical and genomic features in response to these stressors. However, the situation is not as simple as responding to each stressor in isolation, as they are often faced in combination. We consider how polar terrestrial invertebrates manage this scenario in light of their physiology and ecology. Climate change is also leading to warmer summers in parts of the polar regions, concomitantly increasing the potential for drought. The interaction between high temperature and low water availability, and the invertebrates' response to them, are therefore also explored.
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Affiliation(s)
- Matthew J Everatt
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Pete Convey
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK; National Antarctic Research Center, IPS Building, University Malaya, 50603 Kuala Lumpur, Malaysia; Gateway Antarctica, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Jeffrey S Bale
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - M Roger Worland
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Scott A L Hayward
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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62
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De Maayer P, Anderson D, Cary C, Cowan DA. Some like it cold: understanding the survival strategies of psychrophiles. EMBO Rep 2014; 15:508-17. [PMID: 24671034 DOI: 10.1002/embr.201338170] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Much of the Earth's surface, both marine and terrestrial, is either periodically or permanently cold. Although habitats that are largely or continuously frozen are generally considered to be inhospitable to life, psychrophilic organisms have managed to survive in these environments. This is attributed to their innate adaptive capacity to cope with cold and its associated stresses. Here, we review the various environmental, physiological and molecular adaptations that psychrophilic microorganisms use to thrive under adverse conditions. We also discuss the impact of modern "omic" technologies in developing an improved understanding of these adaptations, highlighting recent work in this growing field.
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Affiliation(s)
- Pieter De Maayer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
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63
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Smith DJ. Microbes in the upper atmosphere and unique opportunities for astrobiology research. ASTROBIOLOGY 2013; 13:981-90. [PMID: 24106911 DOI: 10.1089/ast.2013.1074] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Microbial taxa from every major biological lineage have been detected in Earth's upper atmosphere. The goal of this review is to communicate (1) relevant astrobiology questions that can be addressed with upper atmosphere microbiology studies and (2) available sampling methods for collecting microbes at extreme altitudes. Precipitation, mountain stations, airplanes, balloons, rockets, and satellites are all feasible routes for conducting aerobiology research. However, more efficient air samplers are needed, and contamination is also a pervasive problem in the field. Measuring microbial signatures without false positives in the upper atmosphere might contribute to sterilization and bioburden reduction methods for proposed astrobiology missions. Intriguingly, environmental conditions in the upper atmosphere resemble the surface conditions of Mars (extreme cold, hypobaria, desiccation, and irradiation). Whether terrestrial microbes are active in the upper atmosphere is an area of intense research interest. If, in fact, microbial metabolism, growth, or replication is achievable independent of Earth's surface, then the search for habitable zones on other worlds should be broadened to include atmospheres (e.g., the high-altitude clouds of Venus). Furthermore, viable cells in the heavily irradiated upper atmosphere of Earth could help identify microbial genes or enzymes that bestow radiation resistance. Compelling astrobiology questions on the origin of life (if the atmosphere synthesized organic aerosols), evolution (if airborne transport influenced microbial mutation rates and speciation), and panspermia (outbound or inbound) are also testable in Earth's upper atmosphere.
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Affiliation(s)
- David J Smith
- NASA John F. Kennedy Space Center , Surface Systems Office, Kennedy Space Center, Florida
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