Articles | Volume 13, issue 7
https://doi.org/10.5194/bg-13-2207-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
https://doi.org/10.5194/bg-13-2207-2016
© Author(s) 2016. This work is distributed under
the Creative Commons Attribution 3.0 License.
the Creative Commons Attribution 3.0 License.
Research article
| 
15 Apr 2016
Research article |
| 15 Apr 2016
Metagenomic analyses of the late Pleistocene permafrost – additional tools for reconstruction of environmental conditions
Elizaveta Rivkina
CORRESPONDING AUTHOR
Institute of Physicochemical and Biological Problems in Soil Science,
Russian Academy of Sciences, Pushchino, Russia
Lada Petrovskaya
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian
Academy of Sciences, Moscow, Russia
Tatiana Vishnivetskaya
Institute of Physicochemical and Biological Problems in Soil Science,
Russian Academy of Sciences, Pushchino, Russia
University of Tennessee, Center for Environmental Biotechnology,
Knoxville, USA
Kirill Krivushin
Institute of Physicochemical and Biological Problems in Soil Science,
Russian Academy of Sciences, Pushchino, Russia
Lyubov Shmakova
Institute of Physicochemical and Biological Problems in Soil Science,
Russian Academy of Sciences, Pushchino, Russia
Maria Tutukina
Bioinformatics and Genomics Programme, Centre for Genomic
Regulation (CRG), Barcelona, Spain
Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino,
Russia
Arthur Meyers
University of Tennessee, Center for Environmental Biotechnology,
Knoxville, USA
Fyodor Kondrashov
Bioinformatics and Genomics Programme, Centre for Genomic
Regulation (CRG), Barcelona, Spain
Universitat Pompeu Fabra (UPF), Barcelona, Spain
Institució Catalana de Recerca i Estudis Avançats (ICREA),
Barcelona, Spain
Related subject area
Biodiversity and Ecosystem Function: Paleo
Comment on “The Volyn biota (Ukraine) – indications of 1.5 Gyr old eukaryotes in 3D preservation, a spotlight on the `boring billion' ” by Franz et al. (2023)
Rates of palaeoecological change can inform ecosystem restoration
Reply to Comment on Franz et al. (2023): A reinterpretation of the 1.5 billion year old Volyn ‘biota’ of Ukraine, and discussion of the evolution of the eukaryotes, by Head et al. (2023)
Ecological evolution in northern Iberia (SW Europe) during the Late Pleistocene through isotopic analysis on ungulate teeth
Paleoecology and evolutionary response of planktonic foraminifera to the mid-Pliocene Warm Period and Plio-Pleistocene bipolar ice sheet expansion
Late Neogene evolution of modern deep-dwelling plankton
Photosynthetic activity in Devonian Foraminifera
Microbial activity, methane production, and carbon storage in Early Holocene North Sea peats
Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology
Ecosystem regimes and responses in a coupled ancient lake system from MIS 5b to present: the diatom record of lakes Ohrid and Prespa
Differential resilience of ancient sister lakes Ohrid and Prespa to environmental disturbances during the Late Pleistocene
Stable isotope study of a new chondrichthyan fauna (Kimmeridgian, Porrentruy, Swiss Jura): an unusual freshwater-influenced isotopic composition for the hybodont shark Asteracanthus
Amelioration of marine environments at the Smithian–Spathian boundary, Early Triassic
Weathering by tree-root-associating fungi diminishes under simulated Cenozoic atmospheric CO2 decline
The impact of land-use change on floristic diversity at regional scale in southern Sweden 600 BC–AD 2008
Climate-related changes in peatland carbon accumulation during the last millennium
Stratigraphy and paleoenvironments of the early to middle Holocene Chipalamawamba Beds (Malawi Basin, Africa)
Experimental mineralization of crustacean eggs: new implications for the fossilization of Precambrian–Cambrian embryos
The last glacial-interglacial cycle in Lake Ohrid (Macedonia/Albania): testing diatom response to climate
Martin J. Head, James B. Riding, Jennifer M. K. O'Keefe, Julius Jeiter, and Julia Gravendyck
Biogeosciences, 21, 1773–1783, https://doi.org/10.5194/bg-21-1773-2024, https://doi.org/10.5194/bg-21-1773-2024, 2024
Short summary
Short summary
A diverse suite of “fossils” associated with the ~1.5 Ga Volyn (Ukraine) kerite was published recently. We show that at least some of them represent modern contamination including plant hairs, pollen, and likely later fungal growth. Comparable diversity is shown to exist in moderm museum dust, calling into question whether any part of the Volyn biota is of biological origin while emphasising the need for scrupulous care in collecting, analysing, and identifying Precambrian microfossils.
Walter Finsinger, Christian Bigler, Christoph Schwörer, and Willy Tinner
Biogeosciences, 21, 1629–1638, https://doi.org/10.5194/bg-21-1629-2024, https://doi.org/10.5194/bg-21-1629-2024, 2024
Short summary
Short summary
Rate-of-change records based on compositional data are ambiguous as they may rise irrespective of the underlying trajectory of ecosystems. We emphasize the importance of characterizing both the direction and the rate of palaeoecological changes in terms of key features of ecosystems rather than solely on community composition. Past accelerations of community transformation may document the potential of ecosystems to rapidly recover important ecological attributes and functions.
Gerhard Franz, Vladimir Khomenko, Peter Lyckberg, Vsevolod Chornousenko, and Ulrich Struck
EGUsphere, https://doi.org/10.5194/egusphere-2024-217, https://doi.org/10.5194/egusphere-2024-217, 2024
Short summary
Short summary
The Volyn biota (Ukraine), previously assumed to be an extreme case of natural, abiotic synthesis of organic matter, is more likely a diverse assemblage of fossils from the deep biosphere. Although contamination by modern organisms cannot completely be ruled out, it is unlikely, considering all aspects, i. e. their mode of occurrence in the deep biosphere, their fossilization and mature state of organic matter, their isotope signature, and their large morphological diversity.
Monica Fernández-Garcia, Sarah Pederzani, Kate Britton, Lucia Agudo-Pérez, Andrea Cicero, Jeanne Geiling, Joan Daura, Montse Sanz-Borrás, and Ana B. Marín-Arroyo
Biogeosciences Discuss., https://doi.org/10.5194/bg-2023-128, https://doi.org/10.5194/bg-2023-128, 2023
Revised manuscript accepted for BG
Short summary
Short summary
Significant climatic changes affected Europe's landscape, animals, and human groups during the Late Pleistocene. Reconstructing the local conditions humans faced is essential to understand adaptation processes and resilience. This study analyzed the chemical composition of animal teeth consumed by humans in northern Iberia, spanning 80,000 to 15,000 years, revealing the ecological changing conditios.
Adam Woodhouse, Frances A. Procter, Sophie L. Jackson, Robert A. Jamieson, Robert J. Newton, Philip F. Sexton, and Tracy Aze
Biogeosciences, 20, 121–139, https://doi.org/10.5194/bg-20-121-2023, https://doi.org/10.5194/bg-20-121-2023, 2023
Short summary
Short summary
This study looked into the regional and global response of planktonic foraminifera to the climate over the last 5 million years, when the Earth cooled significantly. These single celled organisms exhibit the best fossil record available to science. We document an abundance switch from warm water to cold water species as the Earth cooled. Moreover, a closer analysis of certain species may indicate higher fossil diversity than previously thought, which has implications for evolutionary studies.
Flavia Boscolo-Galazzo, Amy Jones, Tom Dunkley Jones, Katherine A. Crichton, Bridget S. Wade, and Paul N. Pearson
Biogeosciences, 19, 743–762, https://doi.org/10.5194/bg-19-743-2022, https://doi.org/10.5194/bg-19-743-2022, 2022
Short summary
Short summary
Deep-living organisms are a major yet poorly known component of ocean biomass. Here we reconstruct the evolution of deep-living zooplankton and phytoplankton. Deep-dwelling zooplankton and phytoplankton did not occur 15 Myr ago, when the ocean was several degrees warmer than today. Deep-dwelling species first evolve around 7.5 Myr ago, following global climate cooling. Their evolution was driven by colder ocean temperatures allowing more food, oxygen, and light at depth.
Zofia Dubicka, Maria Gajewska, Wojciech Kozłowski, Pamela Hallock, and Johann Hohenegger
Biogeosciences, 18, 5719–5728, https://doi.org/10.5194/bg-18-5719-2021, https://doi.org/10.5194/bg-18-5719-2021, 2021
Short summary
Short summary
Benthic foraminifera play a significant role in modern reefal ecosystems mainly due to their symbiosis with photosynthetic microorganisms. Foraminifera were also components of Devonian stromatoporoid coral reefs; however, whether they could have harbored symbionts has remained unclear. We show that Devonian foraminifera may have stayed photosynthetically active, which likely had an impact on their evolutionary radiation and possibly also on the functioning of Paleozoic shallow marine ecosystems.
Tanya J. R. Lippmann, Michiel H. in 't Zandt, Nathalie N. L. Van der Putten, Freek S. Busschers, Marc P. Hijma, Pieter van der Velden, Tim de Groot, Zicarlo van Aalderen, Ove H. Meisel, Caroline P. Slomp, Helge Niemann, Mike S. M. Jetten, Han A. J. Dolman, and Cornelia U. Welte
Biogeosciences, 18, 5491–5511, https://doi.org/10.5194/bg-18-5491-2021, https://doi.org/10.5194/bg-18-5491-2021, 2021
Short summary
Short summary
This paper is a step towards understanding the basal peat ecosystem beneath the North Sea. Plant remains followed parallel sequences. Methane concentrations were low with local exceptions, with the source likely being trapped pockets of millennia-old methane. Microbial community structure indicated the absence of a biofilter and was diverse across sites. Large carbon stores in the presence of methanogens and in the absence of methanotrophs have the potential to be metabolized into methane.
Raphaël Morard, Franck Lejzerowicz, Kate F. Darling, Béatrice Lecroq-Bennet, Mikkel Winther Pedersen, Ludovic Orlando, Jan Pawlowski, Stefan Mulitza, Colomban de Vargas, and Michal Kucera
Biogeosciences, 14, 2741–2754, https://doi.org/10.5194/bg-14-2741-2017, https://doi.org/10.5194/bg-14-2741-2017, 2017
Short summary
Short summary
The exploitation of deep-sea sedimentary archive relies on the recovery of mineralized skeletons of pelagic organisms. Planktonic groups leaving preserved remains represent only a fraction of the total marine diversity. Environmental DNA left by non-fossil organisms is a promising source of information for paleo-reconstructions. Here we show how planktonic-derived environmental DNA preserves ecological structure of planktonic communities. We use planktonic foraminifera as a case study.
Aleksandra Cvetkoska, Elena Jovanovska, Alexander Francke, Slavica Tofilovska, Hendrik Vogel, Zlatko Levkov, Timme H. Donders, Bernd Wagner, and Friederike Wagner-Cremer
Biogeosciences, 13, 3147–3162, https://doi.org/10.5194/bg-13-3147-2016, https://doi.org/10.5194/bg-13-3147-2016, 2016
Elena Jovanovska, Aleksandra Cvetkoska, Torsten Hauffe, Zlatko Levkov, Bernd Wagner, Roberto Sulpizio, Alexander Francke, Christian Albrecht, and Thomas Wilke
Biogeosciences, 13, 1149–1161, https://doi.org/10.5194/bg-13-1149-2016, https://doi.org/10.5194/bg-13-1149-2016, 2016
L. Leuzinger, L. Kocsis, J.-P. Billon-Bruyat, S. Spezzaferri, and T. Vennemann
Biogeosciences, 12, 6945–6954, https://doi.org/10.5194/bg-12-6945-2015, https://doi.org/10.5194/bg-12-6945-2015, 2015
Short summary
Short summary
We measured the oxygen isotopic composition of Late Jurassic chondrichthyan teeth (sharks, rays, chimaeras) from the Swiss Jura to get ecological information. The main finding is that the extinct shark Asteracanthus (Hybodontiformes) could inhabit reduced salinity areas, although previous studies on other European localities always resulted in a clear marine isotopic signal for this genus. We propose a mainly marine ecology coupled with excursions into areas of lower salinity in our study site.
L. Zhang, L. Zhao, Z.-Q. Chen, T. J. Algeo, Y. Li, and L. Cao
Biogeosciences, 12, 1597–1613, https://doi.org/10.5194/bg-12-1597-2015, https://doi.org/10.5194/bg-12-1597-2015, 2015
Short summary
Short summary
The Smithian--Spathian boundary was a key event in the recovery of marine environments and ecosystems following the end-Permian mass extinction ~1.5 million years earlier. Our analysis of the Shitouzhai section in South China reveals major changes in oceanographic conditions at the SSB intensification of oceanic circulation leading to enhanced upwelling of nutrient- and sulfide-rich deep waters and coinciding with an abrupt cooling that terminated the Early Triassic hothouse climate.
J. Quirk, J. R. Leake, S. A. Banwart, L. L. Taylor, and D. J. Beerling
Biogeosciences, 11, 321–331, https://doi.org/10.5194/bg-11-321-2014, https://doi.org/10.5194/bg-11-321-2014, 2014
D. Fredh, A. Broström, M. Rundgren, P. Lagerås, F. Mazier, and L. Zillén
Biogeosciences, 10, 3159–3173, https://doi.org/10.5194/bg-10-3159-2013, https://doi.org/10.5194/bg-10-3159-2013, 2013
D. J. Charman, D. W. Beilman, M. Blaauw, R. K. Booth, S. Brewer, F. M. Chambers, J. A. Christen, A. Gallego-Sala, S. P. Harrison, P. D. M. Hughes, S. T. Jackson, A. Korhola, D. Mauquoy, F. J. G. Mitchell, I. C. Prentice, M. van der Linden, F. De Vleeschouwer, Z. C. Yu, J. Alm, I. E. Bauer, Y. M. C. Corish, M. Garneau, V. Hohl, Y. Huang, E. Karofeld, G. Le Roux, J. Loisel, R. Moschen, J. E. Nichols, T. M. Nieminen, G. M. MacDonald, N. R. Phadtare, N. Rausch, Ü. Sillasoo, G. T. Swindles, E.-S. Tuittila, L. Ukonmaanaho, M. Väliranta, S. van Bellen, B. van Geel, D. H. Vitt, and Y. Zhao
Biogeosciences, 10, 929–944, https://doi.org/10.5194/bg-10-929-2013, https://doi.org/10.5194/bg-10-929-2013, 2013
B. Van Bocxlaer, W. Salenbien, N. Praet, and J. Verniers
Biogeosciences, 9, 4497–4512, https://doi.org/10.5194/bg-9-4497-2012, https://doi.org/10.5194/bg-9-4497-2012, 2012
D. Hippler, N. Hu, M. Steiner, G. Scholtz, and G. Franz
Biogeosciences, 9, 1765–1775, https://doi.org/10.5194/bg-9-1765-2012, https://doi.org/10.5194/bg-9-1765-2012, 2012
J. M. Reed, A. Cvetkoska, Z. Levkov, H. Vogel, and B. Wagner
Biogeosciences, 7, 3083–3094, https://doi.org/10.5194/bg-7-3083-2010, https://doi.org/10.5194/bg-7-3083-2010, 2010
Cited articles
Angly, F. E., Willner, D., Prieto-Davó, A., Edwards, R. A., Schmieder, R., Vega-Thurber, R., Antonopoulos, D. A., Barott, K., Cottrell, M. T., Desnues, C., Dinsdale, E. A., Furlan, M., Haynes, M., Henn, M. R., Hu, Y., Kirchman, D. L., McDole, T., McPherson, J. D., Meyer, F., Miller, R. M., Mundt, E., Naviaux, R. K., Rodriguez-Mueller, B., Stevens, R., Wegley, L., Zhang, L., Zhu, B., and Rohwer, F.: The GAAS metagenomic tool and its estimations of viraland microbial average genome size in four major biomes, PLoS Comput. Biol., 5, e1000593, https://doi.org/10.1371/journal.pcbi.1000593, 2009.
Anthony Walter, K. M., Zimov, S. A., Grosse, G., Jones, M. C., Anthony, P. M., Chapin III, F. S., Finlay, J. C., Mack, M. C., Davydov, S., Frenzel, P., and Frolking, S.: A shift of thermokarst lakes from carbon sources to sinks during the Holocene epoch, Nature, 511, 452–456, 2014.
Arp, D. J., Sayavedra-Soto, L. A., and Hommes, N. G.: Molecular biology and biochemistry of ammonia oxidation by Nitrosomonas europaea, Arch. Microbiol., 178, 250–255, 2002.
Bailly, J., Fraissinet-Tachet, L., Verner, M.-C., Debaud, J.-C., Lemaire, M., Wésolowski-Louvel, M., and Marmeisse, R.: Soil eukaryotic functional diversity, a metatranscriptomic approach, The ISME Journal, 1, 632–642, 2007.
Bischoff, J., Mangelsdorf, K., Gattinger, A., Schloter, M., Kurchatova, A.N., Herzschuh, U., and Wagner, D.: Response of methanogenic archaea to Late Pleistocene and Holocene climate changes in the Siberian Arctic, Global Biogeochem. Cy., 27, 305–317, 2013.
Brouchkov, A. and Fukuda, M.: Preliminary Measurements on Methane Content in Permafrost, Central Yakutia, and some Experimental Data 21, Permafrost. Periglac., 13, 187–197, 2002.
Chattopadhyay, M. K.: Mechanism of bacterial adaptation to low temperature, J. Biosciences, 31, 157–165, 2006.
Clegg, B. F., Clarke, G. H., Chipman, M. L., Chou, M., Walker, I. R., Tinner, W., and Hu, F. S.: Six millennia of summer temperature variation based on midge analysis of lake sediments from Alaska, Quaternary Sci. Rev., 29, 3308–3316, 2010.
D'Amico, S., Collins, T., Marx, J. C., Feller, G., and Gerday, C.: Psychrophilic microorganisms: challenges for life, EMBO Rep, 7, 385–389, 2006.
Ellenbroek, F. M. and Cappenberg, T. E.: DNA-synthesis and tritiated-thymidine incorporation by heterotrophic fresh-water bacteria in continuous culture, Appl. Environ. Microb., 57, 1675–1682, 1991.
Fierer, N., Leff, J. W., Adams, B. J., Nielsen, U. N., Bates, S. T., Lauber, C. L., Owens, S., Gilbert, J. A., and Caporaso, J. G.: Cross-biome metagenomic analyses of soil microbial communities and their functional attributes, P. Natl. Acad. Sci. USA, 109, 21390–21395, 2012.
Gilichinsky, D. and Rivkina, E.: Permafrost microbiology, in: Encyclopedia of Geobiology, edited by: Reitner, J. and Thiel, V., Springer, Dordrecht, the Netherlands, 726–732, 2011.
Glockner, F. O., Kube, M., Bauer, M., Teeling, H., Lombardot, T., and Ludwig, W., Gade, D., Beck, A., Borzym, K., Heitmann, K., Rabus, R., Schlesner, H., Amann, R., and Reinhardt,R.: Complete genome sequence of the marine planctomycete Pirellula sp. strain 1, P. Natl. Acad. Sci. USA, 100, 8298–8303, 2003.
Graham, D. E., Wallenstein, M. D., Vishnivetskaya, T. A., Waldrop, M. P., Phelps, T. J., Pfiffner, S. M., Onstott, T. C., Whyte, L. G., Rivkina, E. M., Gilichinsky, D. A., Elias, D. A., Mackelprang, R., VerBerkmoes, N. C., Hettich, R. L., Wagner, D., Wullschleger, S. D., and Jansson, J. K.: Microbes in thawing permafrost: the unknown variable in the climate change equation, ISME J., 6, 709–712, 2012.
Harmsen, H. J. M., Van Kuijk, B. L. M., Plugge, C. M., Akkermans, A. D. L., De Vos, W. M., and Stams, A. J. M.: Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfate-reducing bacterium, Int. J. Syst. Bacteriol., 48, 1383–1387, 1998.
Hazen, T. C., Rocha, A. M., and Techtmann, S. M.: Advances in monitoring environmental microbes, Curr. Opin. Biotech., 24, 526–533, 2013.
Holmes, A. J., Costello, A., Lidstrom, M. E., and Murrell, J. C.: Evidence that particulatemethane monooxygenase and ammonia monooxygenase may be evolutionarily related, FEMS Microbiol. Lett., 132, 203–208, 1995.
Jackson, B. E., Bhupathiraju, V. K., Tanner, R. S., Woese, C. R., and McInerney, M. J.: Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms, Arch. Microbiol., 171, 107–114, 1999.
Jansson, J. K. and Tas, N.: The microbial ecology of permafrost, Nature Rev. Microbiol., 12, 414–425, 2014.
Kanehisa, M. and Goto, S.: KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res., 28, 27–30, 2000.
Khmelenina, V. N., Makutina, V. A., Kalyuzhnaya, M. G., Rivkina, E. M., Gilichinsky, D. A., and Trotsenko, Y.: Discovery of viable methanotrophic bacteria in permafrost sediments of northeast Siberia, Dokl. Biol. Sci., 384, 235–237, 2002.
Konishchev, V. N. and Kolesnikov, S. F.: Specialities of structure and composition of late Cenozoic deposits in the section of Oyogossky Yar, in: Problems of Cryolithology, MGU Publishing, Moscow, 107–117, 1981 (in Russian).
Kraev, G. N., Schultze, E. D., and Rivkina, E. M.: Cryogenesis as a factor of methane distribution in layers of permafrost, Dokl. Earth Sci., 451, 882–885, 2013.
Krivushin, K. V., Shcherbakova, V. A., Petrovskaya, L. E., and Rivkina, E. M.: Methanobacterium veterum sp nov., from ancient Siberian permafrost, Int. J. Syst. Evol. Micr., 60, 455–459, 2010.
Krivushin, K., Kondrashov, F., Shmakova, L., Tutukina, M., Petrovskaya, L., and Rivkina, E.: Two metagenomes from Late Pleistocene northeast Siberian permafrost, Genome Announ., 3, e01380-14, https://doi.org/10.1128/genomeA.01380-14, 2015.
Larose, C., Dommergue, A., and Vogel, J. G.: Microbial nitrogen cycling in Arctic snowpacks, Environ. Res. Lett., 8, 035004, https://doi.org/10.1088/1748 9326/8/3/035004, 2013.
Lau, M. C. Y., Stackhouse, B. T., Layton, A. C., Chauhan, A., Vishnivetskaya, T. A., Chourey, K., Ronholm, J., Mykytczuk, N. C. S., Bennett, P. C., Lamarche-Gagnon, G., Burton, N., Pollard, W. H., Omelon, C. R., Medvigy, D. M., Hettich, R. L., Pfi ner, S. M., Whyte, L. G., and Onstott, T. C.: An active atmospheric methane sink in high Arctic mineral cryosols, ISME J., 9, 1880–1891, 2015.
Lay, C. Y., Mykytczuk, N. C., Yergeau, E., Lamarche-Gagnon, G., Greer, C. W., and Whyte, L. G.: Defining the functional potential and active community members of a sediment microbial community in a high-arctic hypersaline subzero spring, Appl. Environ. Microb., 79, 3637–3648, 2013.
Legendre, M., Bartoli, J., Shmakova, L., Jeudy, S., Labadie, K., Adrait, A., Lescot, M., Poirot, O., Bertaux, L., Bruley, C., Couté, Y., Rivkina, E., Abergel, C., and Claverie, J.-M.: Thirty thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology, P. Natl. Acad. Sci. USA, 111, 4274–4279, 2014.
Liebner, S. and Wagner, D.: Abundance, distribution and potential activity of methane oxidizing bacteria in permafrost soils from the Lena Delta, Siberia, Environ. Microbiol., 9, 107–117, 2007.
Mackelprang, R., Waldrop, M. P., DeAngelis, K. M., David, M. M., Chavarria, K. L., Blazewicz,S. J., Rubin, E. M., and Jansson, J. K.: Metagenomic analysis of a permafrost microbialcommunity reveals a rapid response to thaw, Nature, 480, 368–371, 2011.
Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., Wilkening, J., and Edwards, R. A.: The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes, BMC Bioinformatics, 9, 386, https://doi.org/10.1186/1471-2105-9-386, 2008.
Morozova, D. and Wagner D.: Stress response of methanogenic archaea from Siberian permafrost compared with methanogens from nonpermafrost habitats, FEMS Microbiol. Ecol., 61 , 16–25, 2007.
Newcombe, R. G.: Two-sided confidence intervals for the single proportion: comparison of seven methods, Stat. Med., 17, 857–872, 1998.
Overbeek, R., , Begley, T., Butler, R.M., Choudhuri, J.V., Chuang, H-Yu., Cohoon, M., Valérie de Crécy-Lagard, Diaz N., Disz, T., Edwards, R., Fonstein, M., Frank, E.D., Gerdes, S., Glass,E.M., Goesmann, A., Hanson, A. Iwata-Reuy, D., Jensen, R., Jamshidi, N., Krause L., Kuba, M., Larsen, L., Linke, B., McHardy, A.C., Meyer, F., Neuweger, H., Olsen, G., Olson, R., Osterman, A., Portnoy, V., Pusch, G.D., Rodionov, D.A., Ruckert, C., Steiner, J., Stevens, R., Thiele, I., Vassieva, O., Ye, Yu., Zagnitko, O., and Vonstein, V.: The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes, Nucleic Acids Res., 33, 5691–5702, 2005.
Parks, D. H. and Beiko, R. G.: Identifying biologically relevant di erences between metagenomic communities, Bioinformatics, 26, 715–721, 2010.
Raes, J., Korbel, J. O., Lercher, M. J., von Mering, C., and Bork, P.: Prediction of effective genome size in metagenomic samples, Genome Biol., 8, R10, https://doi.org/10.1186/gb-2007-8-1-r10, 2007.
Rivkina, E. and Kraev, G.: Permafrost degradation and influx of biogeogases into the atmosphere, Ninth International Conference on Permafrost, Fairbanks, USA, University of Alaska Fairbanks, 29 June–03 July, 1499–1504, 2008.
Rivkina, E., Laurinavichius, K., McGrath, J., Tiedje, J., Shcherbakova, V., and Gilichinsky, D.: Microbial life in permafrost, Adv. Space Res., 33, 1215–1221, 2004.
Rivkina, E., Kraev, G., Krivushin, K., Laurinavichius, K., Fyodorov-Davydov, D., Kholodov, A., Shcherbakova, V., and Gilichinsky, D.: Methane in permafrost of northeastern Arctic, Earth Cryosphere, 10, 23–41, 2006 (in Russian).
Rivkina, E., Shcherbakova, V., Laurinavichius, K., Petrovskaya, L., Krivushin, K., Kraev, G., Pecheritsina. S., and Gilichinsky, D.: Biogeochemistry of methane and methanogenic archaeain permafrost, FEMS Microbiol. Ecol., 61, 1–15, 2007.
Rivkina, E. M., Friedmann, E. I., McKay, C. P., and Gilichinsky, D. A.: Metabolic activity of permafrost bacteria below the freezing point, Appl. Environ. Microbiol., 66, 3230–3233, 2000.
Rozenbaum, G. E.: Special features of lithogenesis of the alluvial planes in the Eastern Subarctic as related to the problem of the Ice (Yedoma) Complex, in: Problems of Cryolithology, MSU Press, Moscow, 87–100, 1981 (in Russian).
Schirrmeister, L., Kunitsky, V., Grosse, G., Wetterich, S., Meyer, H., Schwamborn, G., Babiy, O., Derevyagin, A., and Siegert, C.: Sedimentary characteristics and origin of the Late Pleistocene Ice Complex on North-East Siberian Arctic coastal lowlands and islands – a review, Quatern. Int., 241, 3–25, 2011.
Schirrmeister, L., Froese, D., Tumskoy, V., Grosse, G., and Wetterich, S.: Yedoma: late Pleistocene ice-rich syngenetic permafrost of Beringia, in: Encyclopedia of Quaternary Science, 2nd Edn., edited by: Elias, S., Mock, C., and Murton, J., Elsevier, Amsterdam, 542–552, 2013.
Seifert, W. K. and Moldowan, J. M.: Paleoreconstruction by biological markers, Geochim. Cosmochim. Ac., 45, 783–794, 1981.
Shcherbakova, V., Rivkina, E., Pecheritsyna, S., Laurinavichius, K., Suzina, N., and Gilichinsky, D.: Methanobacterium arcticum sp. nov., a methanogenic archaeon from Holocene Arctic permafrost, Int. J. Syst. Evol. Micr., 61, 144–147, 2011.
Sher, A., Kaplina, T., and Ovander, M.: Unified regional stratigraphic chart for the Quaternary deposits in the Yana-Kolyma Lowland and its mountainous surroundings, Explanatory Note, Decisions of Interdepartmental Stratigraphic Conference on the Quaternary of the Eastern USSR, Magadan, 1982, USSR Academy of Sciences, Far-Eastern Branch, North-EasternComplex Research Institute, Magadan, USSR, 29–69, 1987 (in Russian).
Shi, T., Reeves, R. H., Gilichinsky, D. A., and Friedmann, E. I.: Characterization of viable bacteria from Siberian permafrost by 16S rDNA sequencing, Microb. Ecol., 33, 169–179, 1997.
Simon, C., Wiezer, A., Strittmatter, A. W., and Daniel, R.: Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome, Appl. Environ. Microb., 75, 7519–7526, 2009.
Stepanova, A. Y., Taldenkova, E. E., and Bauch, H. A.: Arctic quaternary ostracods and their use in paleoreconstructions, Paleontol. J., 44, 41–48, 2010.
Storey, J. D. and Tibshirani, R.: Statistical significance for genome wide studies, P. Natl. Acad. Sci. USA, 100, 9440–9445, 2003.
Storey, J. D., Taylor, J. E., and Siegmund, D.: Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach, J. Royal Stat. Soc. B, 66, 187–205, 2004.
Tomirdiaro, S. V. and Chernen'k'ii, B. I.: Cryogenic Deposits of East Arctic and Sub Arctic, ANSSSR Far-East-Science Center, Magadan, 1987.
Tomirdiaro, S. V., Arslanov, K. A., Chernen'kii, B. I., Tertychnaya, T. V., and Prokhorova, T. N.: New data on formation of loess-ice sequences in Northern Yakutia and ecological conditionsof mammoth fauna in the Arctic during the late Pleistocene, Reports Academy of Sciences USSR 278, 1446–1449, 1984 (in Russian).
Villemur, R., Lanthier, M., Beaudet, R., and Lepine, F.: The Desulfitobacterium genus, FEMS Microbiol. Rev., 30, 706–733, 2006.
Vishnivetskaya, T. A., Layton, A. C., Lau, M. C. Y., Chauhan, A., Cheng, K. R., Meyers, A. J., Murphy, J. R., Rogers, A.W., Saarunya, G. S., Williams, D. E., Pfi ner, S. M., Biggersta, J. P., Stackhouse, B. T., Phelps, T. J., Whyte, L., Sayler G. S., and Onstott, T. C.: Commercial DNA extraction kits impact observed microbial community composition in permafrost samples, FEMS Microbiol. Ecol., 87, 217–230, 2014.
Wagner, D., Schirmack, J., Ganzert L., Morozova D., and Mangelsdorf, K.: Methanosarcina soligelidi sp. nov., a desiccation- and freeze-thaw-resistant methanogenic archaeon from a Siberian permafrost-affected soil, Int. J. Syst. Evol. Microbiol., 63, 2986–2991, 2013.
Walter, K. M., Edwards, M. E., Grosse, G., Zimov, S. A., and Chapin, F. S.: Thermokarst lakes as a source of atmospheric CH4 during the last deglaciation, Science, 318, 633–636, 2007.
Wilke, A., Harrison, T., Wilkening, J., Field, D., Glass, E. M., Kyrpides, N., Mavrommatis, K., and Meyer, F.: The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools, BMC Bioinformatics, 13, 141, https://doi.org/10.1186/1471-2105-13-141, 2012.
Yergeau, E., Hogues, H., Whyte, L. G., and Greer, C. W.: The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses, ISME J., 4, 1–9, 2010.
Zimov, S. A., Schuur, E. A. G., and Chapin, F. S.: Permafrost and the global carbon budget, Science, 312, 1612–1613, 2006.
Short summary
A comparative analysis of the metagenomes from two 30,000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which are characterized by the absence of methane with lower values of redox potential and Fe2+ content) showed both a low abundance of methanogenic archaea and enzymes from the carbon, nitrogen, and sulfur cycles.
A comparative analysis of the metagenomes from two 30,000-year-old permafrost samples, one of...
Altmetrics
Final-revised paper
Preprint