Abundance, viability and diversity of the indigenous microbial populations at different depths of the NEEM Greenland ice core

References

• Abyzov S.S. Friedman E.I. Microorganisms in the Antarctic ice. Antarctic microbiology. 1993; New York: Wiley. 265–295.
   Google Scholar
• Ashelford K.E., Chuzhanova N.A., Fry J.C., Jones A.J., Weightman A.J. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Applied and Environmental Microbiology. 2006; 72: 5734–5741. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Baker G.C., Smith J.J., Cowan D.A. Review and re-analysis of domain-specific 16S primers. Journal of Microbiological Methods. 2003; 55: 541–555. [PubMed Abstract].
   Google Scholar
• Binder T., Garbe C.S., Wagenbach D., Freitag J., Kipfstuhl S. Extraction and parametrization of grain boundary networks in glacier ice using a dedicated method of automatic image analysis. Journal of Microscopy. 2013; 2502: 130–141.
   Google Scholar
• Binder T., Weikusat I., Freitag J., Garbe C.S., Wagenbach D., Kipfstuhl S. Microstructure through an ice sheet. Materials Science Forum. 2013; 753: 481–484.
   Google Scholar
• Buzzini P., Branda E., Goretti M., Turchetti B. Psychrophilic yeasts from worldwide glacial habitats: diversity, adaptation strategies and biotechnological potential. FEMS Microbiology Ecology. 2012; 82: 217–241. [PubMed Abstract].
   Google Scholar
• Castello J., Rogers S., Starmer W., Catranis C., Ma L., Bachand W.G., Zhao Y., Smith J. Detection of tomato mosaic tobamovirus RNA in ancient glacial ice. Polar Biology. 1999; 22: 207–212.
   Web of Science ®Google Scholar
• Catranis C., Starmer W. Microorganisms entrapped in glacier ice. Antarctic Journal of the United States. 1991; 26: 234–236.
   Google Scholar
• Choudhari S., Smith S., Owens S., Gilbert J.A., Shain D.H., Dial R.J., Grigoriev A. Metagenome sequencing of prokaryotic microbiota collected from Byron Glacier, Alaska. Genome Announcements. 2013; 1(2): 00099–13.
   Google Scholar
• Christner B.C., Montross G.G., Priscu J.C. Dissolved gases in frozen basal water from the NGRIP borehole, implications for biogeochemical processes beneath the Greenland ice sheet. Polar Biology. 2012; 35: 1735–1741.
   Web of Science ®Google Scholar
• Christner B.C., Mosley-Thompson E., Thompson L.G., Zagorodnov V., Sandman K., Reeve J.N. Recovery and identification of viable bacteria immured in glacial ice. Icarus. 2000; 144: 479–485.
   Web of Science ®Google Scholar
• Chu J.-N., Arun A.B., Chen W.-M., Chou J.-H., Shen F.-T., Rekha P.D., Kämpfer P., Young L.-S., Lin S.-Y., Young C.-C. Agaricicola taiwanensis gen. nov., sp. nov., an alphaproteobacterium isolated from the edible mushroom Agaricus blazei. International Journal of Systematic and Evolutionary Microbiology. 2010; 60: 2032–2035. [PubMed Abstract].
   Google Scholar
• Dani K.G.S., Mader H.M., Wolff E.W., Wadham J.L. Modeling the liquid-water veins system within polar ice sheets as a potential microbial habitat. Earth and Planetary Science Letters. 2012; 333–334: 238–249.
   Web of Science ®Google Scholar
• De Sousa T., Bhosle S. Satyanarayana T. Microbial denitrification and its ecological implications in the marine system. Microorganisms in environmental management, microbes and environment. 2012; New York: Springer. 683–700.
   Google Scholar
• Doronina N., Trotsenko Y.A., Tourova T.P., Boris B., Kuznetsov B.B., Leisinger T. Albibacter methylovorans gen. nov., sp. nov., a novel aerobic, facultatively autotrophic and methylotrophic bacterium that utilizes dichloromethane. International Journal of Systematic and Evolutionary Microbiology. 2001; 51: 1051–1058. [PubMed Abstract].
   Google Scholar
• Durand G., Weiss J., Lipenkov V., Barnola J., Krinner G., Parrenin F., Delmonte B., Ritz C., Duval P., Röthlisberger R., Bigler M. Effect of impurities on grain growth in cold ice sheets. Journal of Geophysical Research—Earth Surface. 2006; 111: 01015.
   Web of Science ®Google Scholar
• Edgar R.C., Haas B.J., Clemente J.C., Quince C., Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011; 27: 2194–2200. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Faria S.H., Freitag J., Kipfstuhl S. Polar ice structure and the integrity of ice-core paleoclimate records. Quaternary Science Reviews. 2010; 29: 338–351.
   Web of Science ®Google Scholar
• Goeke F., Thiel V., Wiese J., Labes A., Imhoff J.F. Algae as an important environment for bacteria—phylogenetic relationships among new bacterial species isolated from algae. Phycologia. 2013; 52: 14–24.
   Web of Science ®Google Scholar
• Guillevic M., Bazin L., Landais A., Kindler P., Orsi A., Masson-Delmotte V., Blunier T., Buchardt S.L., Capron E., Leuenberger M., Martinerie P., Prie F., Vinther B.M. Spatial gradient of temperature, accumulation and δ18O-ice in Greenland over a series of Dansgaard-Oeschger events. Climate of the Past. 2012; 8: 5209–5261.
   Google Scholar
• Hamilton T.L., Peters J.W., Skidmore M.L., Boyd E.S. Molecular evidence for an active endogenous microbiome beneath glacial ice. The ISME Journal. 2013; 7: 1402–1412. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Hashizume A., Fudou R., Jojima Y., Nakai R., Hiraishi A., Tabuchi A., Sen K., Shibai H. Rare bacterium of a new genus isolated with prolonged enrichment culture. Bioscience, Biotechnology and Biochemistry. 2004; 681: 28–35.
   Google Scholar
• Hell K., Edwards A., Zarsky J., Podmirseg S.M., Girdwood S., Pachebat J.A., Insam H., Sattler B. The dynamic bacterial communities of a melting High Arctic glacier snowpack. The ISME Journal. 2013; 7: 1814–1826. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Hemp J. The search for ancestrally anoxygenic or non-phototrophic Cyanobacteria. 2012. Accessed on the internet at www.mbl.edu/microbialdiversity/files/2012/08/Jim-Hemp.pdf on 28 April 2014.
   Google Scholar
• Hong S.H., Bunge J., Leslin C., Jeon S., Epstein S.S. Polymerase chain reaction primers miss half of rRNA microbial diversity. The ISME Journal. 2009; 3: 1365–1373. [PubMed Abstract].
   Google Scholar
• Isenbarger T.A., Carr C.E., Johnson S.S., Finney M., Church G.M., Gilbert W., Zuber M.T., Ruvkun G. The most conserved genome segments for life detection on Earth and other planets. Origins of Life and Evolution of Biospheres. 2008; 38: 517–533.
   PubMed Web of Science ®Google Scholar
• Ivanova E., Doronina N., Trotsenko Y. Hansshlegelia plantiphila gen. nov. sp. nov., a new aerobic restricted facultative methylotrophic bacterium associated with plants. Systematic and Applied Microbiology. 2007; 30: 444–452. [PubMed Abstract].
   Google Scholar
• Junge K., Christner B., Staley J.T. Horikoshi K. Diversity of psychrophilic bacteria from sea ice and glacial ice communities. Extremophiles handbook. 2011; New York: Springer. 794–815.
   Google Scholar
• Kasalicky V., Jezbera J., Hahn M.W., Simek K. The diversity of the Limnohabitans genus, an important group of freshwater bacterioplankton, by characterization of 35 isolated strains. PLoS One. 2013; 83: 58209.
   Google Scholar
• Komárek J., Nedbalová L., Hauer T. Phylogenetic position and taxonomy of three heterocytous cyanobacteria dominating the littoral of deglaciated lakes, James Ross Island, Antarctica. Polar Biology. 2012; 35: 759–774.
   Web of Science ®Google Scholar
• Knowlton C., Veerapaneni R., D'Elia T., Rogers S.O. Microbial analyses of ancient ice core sections from Greenland and Antarctica. Biology. 2013; 2: 206–232. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Larkin M.A., Blackshields N.P., Brown R.C., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez A.R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 2321: 2947–2948.
   Web of Science ®Google Scholar
• Leibeling S., Schmidt F., Jehmlich N., von Bergen M., Muller R.H., Harms H. Declining capacity of starving Delftia acidovorans MC1 to degrade phenoxypropionate herbicides correlates with oxidative modification of the initial enzyme. Environmental Science & Technology. 2010; 44: 3793–3799. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Li L., Zheng J.-W., Hang B.-J., Doronina N.V., Trotsenko Y.A., He J., Li S.-P. Methylopila jiangsuensis sp. nov., an aerobic, facultatively methylotrophic bacterium. International Journal of Systematic and Evolutionary Microbiology. 2011; 61: 1561–1566. [PubMed Abstract].
   Google Scholar
• Liu Z., DeSantis T.Z., Andersen G.L., Knight R. Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucleic Acids Research. 2008; 36: 120.
   PubMed Web of Science ®Google Scholar
• Loveland-Curtze J., Miteva V., Brenchley J. Herminiimonas glaciei sp. nov., a novel ultramicrobacterium from 3042 m deep Greenland glacial ice. International Journal of Systematic and Evolutionary Microbiology. 2008; 59: 1272–1277.
   Web of Science ®Google Scholar
• Loveland-Curtze J., Miteva V., Brenchley J. Novel ultramicrobacterial isolates from a deep Greenland ice core represent a proposed new species, Chryseobacterium greenlandense sp. nov. Extremophiles. 2010; 14: 61–69. [PubMed Abstract].
   Google Scholar
• Miteva V. Margesin R. Bacteria in snow and glacier ice. Psychrophiles, from biodiversity to biotechnology. 2008; Berlin: Springer. 31–50.
   Google Scholar
• Miteva V., Burlingame C., Sowers T., Brenchley J. Comparative evaluation of the indigenous microbial diversity versus drilling fluid contaminants in the NEEM Greenland ice core. FEMS Microbiology Ecology. 2014; 89: 238–256. [PubMed Abstract].
   Google Scholar
• 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 Biology. 2014; 37: 47–59.
   Web of Science ®Google Scholar
• Miteva V., Teacher C., Sowers T., Brenchley J. Comparison of microbial diversity at different depths of the GISP2 Greenland ice core in relation to deposition climate. Environmental Microbiology. 2009; 11: 640–656. [PubMed Abstract].
   Google Scholar
• Miteva V.I., Brenchley J.B. Detection and isolation of ultrasmall microorganisms from a 120,000 years old Greenland glacier ice core. Applied and Environmental Microbiology. 2005; 71: 7806–7818. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Miteva V.I., Sheridan P.P., Brenchley J.B. Phylogenetic and physiological diversity of microorganisms isolated from a deep Greenland ice core. Applied and Environmental Microbiology. 2004; 70: 202–213. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Montagnat M., Azuma N., Dahl-Jensen D., Eichler J., Fujita S., Gillet-Chaulet F., Kipfstuhl S., Samyn D., Svensson A., Weikusat I. Fabric measurement along the NEEM ice core, Greenland, and comparison with GRIP and NGRIP ice cores. The Cryosphere Discussions. 2014; 8: 307–335.
   Web of Science ®Google Scholar
• Nakai R., Shibuya E., Justel A., Rico E., Quesada A., Kobayashi F., Iwasaka Y., Shi G.-Y., Amano Y., Iwatsuki T., Naganuma T. Phylogeographic analysis of filterable bacteria with special reference to Rhizobiales strains that occur in cryospheric habitats. Antarctic Science. 2013; 25: 219–228.
   Web of Science ®Google Scholar
• NEEM Community Members. Eemian interglacial reconstructed from a Greenland folded ice core. Nature. 2013; 493(7433): 489–494.
   Web of Science ®Google Scholar
• Nubel U., Garcia-Pichel F., Muyzer G. PCR primers to amplify 16S rRNA genes from cyanobacteria. Applied and Environmental Microbiology. 1997; 63: 3327–3332. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Quesada A., Vincent W.F. Whitton B.A. Cyanobacteria in the cryosphere, snow, ice and extreme cold. Ecology of cyanobacteria. II. Their diversity in space and time. 2012; New York: Springer. 387–399.
   Google Scholar
• Pinard R., de Winter A., Sarkis G.J., Gerstein M.B., Tartaro K.R., Plant R.N., Egholm M., Rothberg J.M., Leamon J.H. Assessment of whole genome amplification-induced bias through high-throughput, massively parallel whole genome sequencing. BMC Genomics. 2006; 7: 216–237. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Price P.B. A habitat for psychrophiles in deep Antarctic ice. Proceedings of the National Academy of Sciences of the United States of America. 2000; 97: 1247–1251. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Price P.B. Microbial life in glacier ice and implications for a cold origin of life. FEMS Microbiology Ecology. 2007; 59: 217–231. [PubMed Abstract].
   Google Scholar
• Price P.B., Bay R.C. Marine bacteria in deep Arctic and Antarctic ice cores, a proxy for evolution in oceans over 300 million generations. Biogeosciences. 2012; 9: 3799–3815.
   Web of Science ®Google Scholar
• Pruesse E., Quast C., Knittel K., Fuchs B.M., Ludwig W., Peplies J., Glöckner F.O. SILVA, a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Research. 2007; 35: 7188–7196. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Qiagen. Qiagen supplementary protocol. Purification of DNA amplified with REPLI-g kits (RG21 Nov-12). 2012; Hilden, Germany: Qiagen.
   Google Scholar
• Rasmussen S.O., Abbott P., Blunier T., Bourne A., Brook E., Buchardt S.L., Buizert C., Chappellaz J., Clausen H.B., Cook E., Davies S., Guillevic M., Kipfstuhl S., Laepple T., Dahl-Jensen D., Seierstad I.K., Severinghaus J.P., Steffensen J.P., Stowasser C., Svensson A., Vallelonga P., Vinther B.M., Wilhelms F., Winstrup M. A first chronology for the NEEM ice core. Climate Past Discussions. 2013; 9: 2967–3013.
   Google Scholar
• Reysenbach A.-L., Pace N.R. Robb F.T. Reliable amplification of hyperthermophilic Archaeal 16S rRNA genes by the polymerase chain reaction. Archaea: a laboratory manual. 1995; Cold Spring Harbor: Cold Spring Harbor Laboratory Press. 101–105.
   Google Scholar
• Rogers S.O., Theraisnathan V., Ma L.J., Zhao Y., Zhang G., Shin S., Castelo J.D., Starmer W.T. Comparisons of protocols for decontamination of environmental ice samples for biological and molecular examinations. Applied and Environmental Microbiology. 2004; 70: 2540–2544. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Rohde R.A., Price P.B., Bay R.C., Bramall N.E. In-situ microbial metabolism as a cause of gas artifacts in ice. Proceedings of the National Academy of Sciences of the United States of America. 2008; 105: 8667–8672. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Schloss P.D., Westcott S.L., Ryabin T., Hall J.R., Hartmann M., Hollister E.B., Lesniewski R.A., Oakley B.B., Parks D.H., Robinson C.J., Sahl J.W., Stres B., Thallinger G.G., Van Horn D.J., Weber C.F. Introducing mothur, open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology. 2009; 75: 7537–7541. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Sheridan P.P., Miteva V.I., Brenchley J.B. Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a Greenland ice core. Applied and Environmental Microbiology. 2003; 69: 2153–2160. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Shtarkman Y.M., Kocer Z.A., Edgar R., Veerapaneni R.S., D'Elia T., Morris P.F., Rogers S.O. Subglacial Lake Vostok Antarctica. Accretion ice contains a diverse set of sequences from aquatic, marine and sediment-inhabiting Bacteria and Eukarya. PLoS One. 2013; 8: 67221.
   Web of Science ®Google Scholar
• Sihvonen L.M., Lyra C., Fewer D.P., Rajaniemi-Wacklin P., Lehtimaki J.M., Wahlsten M., Sivonen K. Strains of the cyanobacterial genera Calothrix and Rivularia isolated from the Baltic Sea display cryptic diversity and are distantly related to Gloeotrichia and Tolypothrix. FEMS Microbiology Ecology. 2007; 61: 74–84. [PubMed Abstract].
   Google Scholar
• Simon C., Strittmatter A.W., Daniel R. Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Applied and Environmental Microbiology. 2009; 75: 7519–7526. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Skidmore M., Anderson S.P., Sharp M., Foght J., Lanoil B.D. Comparison of microbial community compositions of two subglacial environments reveals a possible role for microbes in chemical weathering processes. Applied and Environmental Microbiology. 2005; 71: 6986–6997. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Soo R.M., Skennerton C.T., Sekiguchi Y., Imelfort M., Paech S.J., Dennis P.G., Steen J.A., Parks D.H., Tyson G.W., Hugenholtz P. Photosynthesis is not a universal feature of the phylum Cyanobacteria. Peer Journal PrePrints. 2014; 2: 204v2.
   Google Scholar
• Starmer W., Fell J., Catranis C., Aberdeen V., Ma L.-J., Zhou S., Rogers S. Castello J.D., Rogers S.O. Yeasts in the genus Rhodotorula recovered from the Greenland ice sheet. Life in ancient ice. 2005; Princeton: Princeton University Press. 181–196.
   Google Scholar
• Stibal M., Hasan F., Wadham J.L., Sharp M.J., Anesio A.M. Prokaryotic diversity in sediments beneath two polar glaciers with contrasting organic carbon substrates. Extremophiles. 2012; 16: 255–265. [PubMed Abstract].
   Google Scholar
• Strunecky O., Elster J., Komarek J. Molecular clock evidence for survival of Antarctic cyanobacteria Oscillatoriales, Phormidium autumnale. from Paleozoic times. FEMS Microbiology Ecology. 2012; 82: 482–490. [PubMed Abstract].
   Google Scholar
• Vincent W.F. Seckbach J. Cold tolerance in cyanobacteria and life in the cryosphere. Algae and cyanobacteria in extreme environments. 2007; Berlin: Springer. 287–301.
   Google Scholar
• Vishnivetskaya T.A. Margesin R. Viable cyanobacteria and green algae from the permafrost darkness. Permafrost soils. 2009; Berlin: Springer. 73–84.
   Google Scholar
• Wang Y., Qianh P.Y. Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. PLoS One. 2009; 4: 7401.
   PubMed Web of Science ®Google Scholar
• Willerslev E., Hansen A., Christensen B., Steffensen J.P., Arctander P. Diversity of Holocene life forms in fossil glacier ice. Proceedings of the National Academy of Sciences of the United States of America. 1999; 96: 8017–8021. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Wright E.S., Yilmaz L.S., Noguera D.R. DECIPHER, a search-based approach to chimera identification for 16S rRNA Sequences. Applied and Environmental Microbiology. 2012; 78: 717–725. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Xiang S., Yao T., An L., Xu B., Wang J. 16S rRNA sequences and difference in bacteria isolated Muztag Ata Glacier at increasing depths. Applied and Environmental Microbiology. 2005; 71: 4619–4627. [PubMed Abstract] [PubMed CentralFull Text].
   Google Scholar
• Xiang S.R., Shang T.C., Chen Y., Yao T.D. Deposition and post-deposition mechanisms as possible drivers of microbial population variability in glacier ice. FEMS Microbiology Ecology. 2009; 70: 165–176.
   Web of Science ®Google Scholar
• Yao T., Xiang S., Zhang X., Wang N. Microorganisms in the Malan ice core and their relation to climatic and environmental changes. Global Biogeochemical Cycles. 2006; 20: 1004.
   Web of Science ®Google Scholar
• Yde J.C., Finster K.W., Raiswell R., Steffensen J.P., Heinemeier J., Olsen J., Gunnlaugsson H.P., Nielsen O.B. Basal ice microbiology at the margin of the Greenland ice sheet. Annals of Glaciology. 2010; 51: 71–79.
   Web of Science ®Google Scholar
• Yung P.T., Shafaat H.S., Connon S.A., Ponce A. Quantification of viable endospores from a Greenland ice core. FEMS Microbiology Ecology. 2007; 59: 300–306. [PubMed Abstract].
   Google Scholar
• Zeng Y., Yan M., Yu Y., Li H., He J., Sun K., Zhang F. Diversity of bacteria in surface ice of Austre Lovenbreen glacier, Svalbard. Archives of Microbiology. 2013; 195: 313–322. [PubMed Abstract].
   Google Scholar
• Zhang S., Yang G., Wang Y., Hou S. Abundance and community of snow bacteria from three glaciers in the Tibetan Plateau. Journal of Environmental Science China. 2010; 22: 1418–1424.
   PubMed Web of Science ®Google Scholar