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A flow cytometric method to measure prokaryotic records in ice cores: an example from the West Antarctic Ice Sheet Divide drilling site


Microorganisms were the earliest inhabitants on our planet that occupy nearly every environment, and play a major role in biogeochemical cycles. Despite their global importance, there remains a paucity of data on microbial responses to long-term environmental and climatic changes. Microorganisms are known to be immured in glacial ice, but no high-resolution temporal records of their density exist, owing in large part to the lack of appropriate clean methodology that allows for rapid analysis of samples over depth. We describe a clean and time efficient method that can produce a high-temporal resolution record of prokaryotic density archived in ice cores. The method combines acquisition of discrete samples using a continuous ice-core melting system coupled with flow cytometry (FCM) of DNA-stained samples. Specifically, we evaluate the performance of the FCM measurement technique in terms of specificity, precision, accuracy and minimum detection limits. Examples from the West Antarctic Ice Sheet Divide ice core are included to show the efficacy of the method.

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      A flow cytometric method to measure prokaryotic records in ice cores: an example from the West Antarctic Ice Sheet Divide drilling site
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      A flow cytometric method to measure prokaryotic records in ice cores: an example from the West Antarctic Ice Sheet Divide drilling site
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This is an Open Access article, distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives licence (, which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is unaltered and is properly cited. The written permission of Cambridge University Press must be obtained for commercial re-use or in order to create a derivative work.
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Correspondence: Pamela A. Santibáñez <>
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This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.

JR Banta , JR McConnell , MM Frey , RC Bales and K Taylor (2008) Spatial and temporal variability in snow accumulation at the West Antarctic Ice Sheet Divide over recent centuries. J. Geophys. Res., 113(D23), 18 (doi: 10.1029/2008JD010235)

KD Bidle , S Lee , DR Marchant and PG Falkowski (2007) Fossil genes and microbes in the oldest ice on earth. Proc. Natl. Acad. Sci. U. S. A., 104(33), 1345513460 (doi: 10.1073/pnas.0702196104)

R Bojsen , R Torbensen , CE Larsen , A Folkesson and B Regenberg (2013) The synthetic amphipathic peptidomimetic ltx109 is a potent fungicide that disturbs plasma membrane integrity in a sphingolipid dependent manner. PLoS ONE, 8(7) (doi: 10.1371/journal.pone.0069483)

SL Burnett and LR Beuchat (2002) Comparison of methods for fluorescent detection of viable, dead, and total Escherichia coli O157:H7 cells in suspensions and on apples using confocal scanning laser microscopy following treatment with sanitizers. Int. J. Food Microbiol., 74, 3745 (doi: 10.1016/S0168-1605(01)00714-0)

SM Burrows and 6 others (2009b) Bacteria in the global atmosphere – part 2: modelling of emissions and transport between different ecosystems. Atmos. Chem. Phys. Discuss., 9, 1082910881 (doi: 10.5194/acp-9-9281-2009)

PH Calcott and RA MacLeod (1974) Survival of Escherichia coli from freeze-thaw damage: influence of nutritional status and growth rate. Can. J. Microbiol., 20, 683689 (doi: 10.1139/m74-104)

PH Calcott and RA MacLeod (1975) The survival of Escherichia coli from freeze-thaw damage: the relative importance of wall and membrane damage. Can. J. Microbiol., 21, 19601968 (doi: 10.1139/m75-253)

BC Christner and 5 others (2000) Recovery and identification of viable bacteria immured in glacial ice. Icarus, 144, 479485 (doi: 10.1006/1999.6288)

BC Christner , E Mosley-Thompson , LG Thompson and JN Reeve (2003) Bacterial recovery from ancient glacial ice. Env. Microb., 5, 433436 (doi: 10.1046/j.1462-2920.2003.00422.x)

RS de Groot , MA Wilson and RM Boumans (2002) Typology for the classification, description and valuation of ecosystem functions, goods and services. Ecol. Econ., 41(3), 393408 (doi: 10.1016/S0921-8009(02)00089-7)

B Delmonte and 5 others (2004) Dust size evidence for opposite regional atmospheric circulation changes over east Antarctica during the last climatic transition. Clim. Dyn., 23, 427438 (doi: 10.1007/s00382-004-0450-9)

M Dieser , M Greenwood and CM Foreman (2010) Carotenoid pigmentation in antarctic heterotrophic bacteria as a strategy to withstand environmental stresses. Arct. Antarct. Alp. Res., 42(4), 396405 (doi: 10.1657/1938-4246-42.4.396)

CB Field (1998) Primary production of the biosphere: integrating terrestrial and oceanic components. Science, 281(5374), 237240 (doi: 10.1126/science.281.5374.237)

BJ Finlay , SC Maberly and JI Cooper (1997) Microbial diversity and ecosystem function. Oikos, 80, 209213 (doi: 10.2307/3546587)

JM Gasol and PA del Giorgio (2000) Using flow cytometry for counting natural planktonic bacteria and understanding the structure of planktonic bacterial communities. Sci. Mar., 64(2), 197224 (doi: 10.3989/scimar.2000.64n2197)

DW Griffin and 5 others (2003) Atmospheric microbiology in the northern Caribbean during African dust events. Aerobiologia, 19, 143157 (doi: 10.1023/B:AERO.0000006530.32845.8d)

RH Hadfield (2009) Single-photon detectors for optical quantum information applications. Nat. Photonics, 3(12), 696705 (doi: 10.1038/nphoton.2009.230)

K Hara and D Zhang (2012) Bacterial abundance and viability in long-range transported dust. Atm. Env., 47, 2025 (doi: 10.1016/j.atmosenv.2011.11.050)

CM Harris and DB Kell (1985) The estimation of microbial biomass. Biosensors J., 1, 1784 (doi: 10.1016/0265-928X(85)85005-7)

EW Henningson , M Lundquist , E Larsson , G Sandström and M Forsman (1997) A comparative study of different methods to determine the total number and the survival ratio of bacteria in aerobiological samples. J. Aerosol Sci., 28(3), 459469 (doi: 10.1016/S0021-8502(96)00447-8)

D Hopwood (1969) Fixatives and fixation: a review. Histochem. J., 1, 323360 (doi: 10.1007/BF01003278)

JBC Jackson and DH Erwin (2006) What can we learn about ecology and evolution from the fossil record? Trends Ecol. Evol., 21(6), 322328 (doi: 10.1016/j.tree.2006.03.017)

EJ Javaux , CP Marshall and A Bekker (2010) Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic deposits. Nature, 463(7283), 934938 (doi: 10.1038/nature08793)

LJ Jones and VL Singer (2001) Fluorescence microplate-based assay for tumor necrosis factor activity using SYTOX green stain. Anal. Biochem., 293(1), 815 (doi: 10.1006/abio.2001.5116)

P Klauth , R Wilhelm , E Klumpp , L Poschen and J Groeneweg (2004) Enumeration of soil bacteria with the green fluorescent nucleic acid dye SYTOX green in the presence of soil particles. J. Microbiol. Methods, 59(2), 189198 (doi: 10.1016/j.mimet.2004.07.004)

RE Kopp , JL Kirschvink , IA Hilburn and CZ Nash (2005) The Paleoproterozoic snowball Earth: a climate disaster triggered by the evolution of oxygenic photosynthesis. Proc. Natl. Acad. Sci. U. S. A., 102(32), 11131–6 (doi: 10.1073/pnas.0504878102)

F Lambert and 9 others (2008) Dust-climate couplings over the past 800,000 years from the EPICA Dome C ice core. Nature, 452(7187), 616619 (doi: 10.1038/nature06763)

P Lebaron and 5 others (2001) Does the high nucleic acid content of individual bacterial cells allow us to discriminate between active cells and inactive cells in aquatic systems? Appl. Environ. Microbiol., 67(4), 1775 (doi: 10.1128/AEM.67.4.1775)

P Lebaron and 5 others (2002) Variations of bacterial-specific activity with cell size and nucleic acid content assessed by flow cytometry. Aquat. Microb. Ecol., 28, 131140 (doi: 10.3354/ame028131)

D Lüthi and 10 others (2008) High-resolution carbon dioxide concentration record 650,000–800,000 years before present. Nature, 453(7193), 379382 (doi: 10.1038/nature06949)

EL Madsen (2011) Microorganisms and their roles in fundamental biogeochemical cycles. Curr. Opin. Biotechnol., 22(3), 456464 (doi: 10.1016/j.copbio.2011.01.008)

PA Mayewski and 13 others (1996) Climate change during the last deglaciation in Antarctica. Science, 272(5268), 16361638 (doi: 10.1126/science.272.5268.1636)

P Mazur (1966) Theoretical and experimental effects of cooling and warming velocity on the survival of frozen and thawed cells. Cryobiology, 2(1), 181192 (doi: 10.1016/S0011-2240(66)80165-7)

P Mazur (1977) The role of intracellular freezing in the death of cells cooled at supraoptimal rates. Cryobiology, 14, 251272 (doi: 10.1016/0011-2240(77)90175-4)

P Mazur and JJ Schmidt (1968) Interactions of cooling velocity, temperature, and warming velocity on the survival of frozen and thawed yeast. Cryobiology, 5, 117 (doi: 10.1016/S0011-2240(68)80138-5)

JF McManus , R Francois , J-M Gherardi , LD Keigwin and S Brown-Leger (2004) Collapse and rapid resumption of Atlantic meridional circulation linked to deglacial climate changes. Nature, 428(6985), 834837 (doi: 10.1038/nature02494)

PS Meadows (1971) The attachment of bacteria to solid surfaces. Arch. fr Mikrobiol., 75, 374381 (doi: 10.1007/BF00407699)

FC Mortimer , DJ Mason and VA Gant (2000) Flow cytometric monitoring of antibiotic-induced injury in Escherichia coli using cell-impermeant fluorescent probes. Antimicrob. Agents Chemother., 44(3), 676681 (doi: 10.1128/AAC.44.3.676-681.2000)

S Müller and G Nebe-von-Caron (2010) Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities. FEMS Microbiol. Rev., 34(4), 554587 (doi: 10.1111/j.1574-6976.2010.00214)

G Nebe-von-Caron , PJ Stephens , CJ Hewitt , JR Powell and RA Badley (2000) Analysis of bacterial function by multi-colour fluorescence flow cytometry and single cell sorting. J. Microbiol. Methods, 42(1), 97114 (doi: 10.1016/S0167-7012(00)00181-0)

N Noffke , KA Eriksson , RM Hazen and EL Simpson (2006) A new window into early Archean life: microbial mats in Earth's oldest siliciclastic tidal deposits (3.2 Ga Moodies Group, South Africa). Geology, 34(4), 253 (doi: 10.1130/G22246.1)

A Perfumo and R Marchant (2010) Global transport of thermophilic bacteria in atmospheric dust. Env. Microb. Rep., 2, 333339 (doi: 10.1111/j.1758-2229.2010.00143.x)

KA Pratt and 8 others (2009) In situ detection of biological particles in cloud ice-crystals. Nat. Geosci., 2, 398401 (doi: 10.1038/ngeo521)

JC Priscu and B Christner (2004) Earth's icy biosphere. In Microbial diversity and bioprospecting. American Society for Microbiology, Washington, DC

JC Priscu and 11 others (1999) Geomicrobiology of subglacial ice above lake Vostok, Antarctica. Science, 286(5447), 21412144 (doi: 10.1126/science.286.5447.2141)

H Puchtler and SN Meloan (1985) On the chemistry of formaldehyde fixation and its effects on immune histochemical reactions. Histochemistry, 82, 201204 (doi: 10.1007/BF00501395)

B Rasmussen (2000) Filamentous microfossils in a 3,235-million-year-old volcanogenic massive sulphide deposit. Nature, 405, 676679 (doi: 10.1038/35015063)

T Segawa , K Ushida , H Narita , H Kanda and S Kohshima (2010) Bacterial communities in two Antarctic ice cores analyzed by 16S rRNA gene sequencing analysis. Polar Sci., 4(2), 215227 (doi: 10.1016/j.polar.2010.05.003)

HM Shapiro (2003) Practical flow cytometry, 4th edn. Wiley-Liss, New Jersey

HM Shapiro (2004) Lasers for flow cytometry in current protocols in cytometry. John Wiley and Sons, New York (doi: 10.1002/0471142956.cy0109s27)

BK Singh , RD Bardgett , P Smith and DS Reay (2010) Microorganisms and climate change: terrestrial feedbacks and mitigation options. Nat. Rev. Microbiol., 8(11), 779790 (doi: 10.1038/nrmicro2439)

HB Steen (1992) Noise, sensitivity, and resolution of flow cytometers. Cytometry, 13(8), 822830 (doi: 10.1002/cyto.990130804)

HB Steen (2000) Flow cytometry of bacteria: glimpses from the past with a view to the future. J. Microbiol. Methods, 42(1), 6574 (doi: 10.1016/S0167-7012(00)00177-9)

T Sun and H Morgan (2010) Single-cell microfluidic Impedance cytometry: a review. Microfluid. Nanofluidics, 8(4), 423443 (doi: 10.1007/s10404-010-0580-9)

J Vives-Rego , P Lebaron and G Nebe-von Caron (2000) Current and future applications of flow cytometry in aquatic microbiology. FEMS Microbiol. Rev., 24(4), 429448 (doi:

VK Walker , GR Palmer and G Voordouw (2006) Freeze-thaw tolerance and clues to the winter survival of a soil community. Appl. Environ. Microbiol., 72(3), 17841792 (doi: 10.1128/AEM.72.3.1784-1792.2006)

Y Wang , F Hammes , K De Roy , W Verstraete and N Boon (2010) Past, present and future applications of flow cytometry in aquatic microbiology. Trends Biotechnol., 28(8), 416424 (doi: 10.1016/j.tibtech.2010.04.006)

KJ Willis and HJB Birks (2006) What is natural? The need for a long-term perspective in biodiversity conservation. Science, 314, 12611265 (doi: 10.1126/science.1122667)

KJ Willis , RM Bailey , SA Bhagwat and HJB Birks (2010) Biodiversity baselines, thresholds and resilience: testing predictions and assumptions using palaeoecological data. Trends Ecol. Evol., 25, 583591 (doi: 10.1016/j.tree.2010.07.006)

A Wobus and 6 others (2003) Microbial diversity and functional characterization of sediments from reservoirs of different trophic state. FEMS Microbiol. Ecol., 46(3), 331347 (doi: 10.1016/S0168-6496(03)00249-6)

EW Wolff and 29 others (2010) Changes in environment over the last 800,000 years from chemical analysis of the EPICA Dome C ice core. Quat. Sci. Rev., 29(1–2), 285295 (doi: 10.1016/j.quascirev.2009.06.013)

JC Wood (1998) Fundamental flow cytometer properties governing sensitivity and resolution. Cytometry, 33, 260266 (doi: 10.1002/(SICI)1097-0320(19981001)33:2<260::AID-CYTO23>3.0.CO;2-R)

SR Xiang , TC Shang , Y Chen and TD Yao (2009) Deposition and postdeposition mechanisms as possible drivers of microbial population variability in glacier ice: minireview. FEMS Microbiol. Ecol., 70, 165176 (doi: 10.1111/j.1574-6941.2009.00759.x)

E Yergeau and 6 others (2012) Shifts in soil microorganisms in response to warming are consistent across a range of Antarctic environments. ISME J., 6(3), 692702 (doi: 10.1038/ismej.2011.124)

U Zimmermann , G Pilwat and F Riemann (1974) Dielectric breakdown of cell membranes. Biophys. J., 14, 881899 (doi: 10.1016/S0006-3495(74)85956-4)

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