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Chapter Ten - Microorganisms in cryoturbated organic matter of Arctic permafrost soils

from Part III - Life in extreme environments and the responses to change: the example of polar environments

Published online by Cambridge University Press:  28 September 2020

Guido di Prisco
Affiliation:
National Research Council of Italy
Howell G. M. Edwards
Affiliation:
University of Bradford
Josef Elster
Affiliation:
University of South Bohemia, Czech Republic
Ad H. L. Huiskes
Affiliation:
Royal Netherlands Institute for Sea Research
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Summary

Cryosols (permafrost-affected soils) cover more than 90% of the continuous permafrost zone in the Arctic (Tarnocai & Bockheim, 2011). They represent the dominant soil in the arctic and sub-arctic regions in Canada, Alaska and Russia but also occur in boreal and alpine regions. They can be classified into the static or organic Cryosols which develop on mineral or organic deposits, respectively.

Type
Chapter
Information
Life in Extreme Environments
Insights in Biological Capability
, pp. 234 - 250
Publisher: Cambridge University Press
Print publication year: 2020

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References

Ausec, L., van Elsas, J.D., Mandic-Mulec, I. (2011). Two- and three-domain bacterial laccase-like genes are present in drained peat soils. Soil Biology and Biochemistry. Soil Biology and Biochemistry, 43(5), 975983.CrossRefGoogle Scholar
Bailey, V.L., Smith, J.L., Bolton, H. (2002). Fungal-to-bacterial ratios in soils investigated for enhanced C sequestration. Soil Biology and Biochemistry, 34(7), 9971007.Google Scholar
Bakermans, C., Tsapin, A.I., Souza-Egipsy, V., Gilichinsky, D.A., Nealson, K.H. (2003). Reproduction and metabolism at -10°C of bacteria isolated from Siberian permafrost. Environmental Microbiology, 5(4), 321326.CrossRefGoogle Scholar
Baldrian, P., Valášková, V. (2008). Degradation of cellulose by basidiomycetous fungi. FEMS Microbiology Reviews, 32(3), 501521.Google Scholar
Barka, E.A., Vatsa, P., Sanchez, L., et al. (2016). Taxonomy, physiology, and natural products of actinobacteria. Microbiology and Molecular Biology Reviews, 80(1), 143.CrossRefGoogle ScholarPubMed
Bellemain, E., Davey, M.L., Kauserud, H., et al. (2013). Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. Environmental Microbiology, 15(4), 11761189.Google Scholar
Bugg, T.D.H., Ahmad, M., Hardiman, E.M., Rahmanpour, R. (2011). Pathways for degradation of lignin in bacteria and fungi. Natural Product Reports, 28(12), 18831896.Google Scholar
Čapek, P., Diáková, K., Dickopp, J.-E., et al. (2015). The effect of warming on the vulnerability of subducted organic carbon in arctic soils. Soil Biology and Biochemistry, 90, 1929.CrossRefGoogle Scholar
Coolen, M.J.L., Orsi, W.D. (2015). The transcriptional response of microbial communities in thawing Alaskan permafrost soils. Frontiers in Microbiology, 6, 197. doi:10.3389/fmicb.2015.00197Google Scholar
Costa, O.Y.A., Raaijmakers, J.M., Kuramae, E.E. (2018). Microbial extracellular polymeric substances: Ecological function and impact on soil aggregation. Frontiers in Microbiology, 9, 1636. doi:10.3389/fmicb.2018.01636Google Scholar
Czapski, T.R., Trun, N. (2014). Expression of csp genes in E. Coli K-12 in defined rich and defined minimal media during normal growth, and after cold-shock. Gene, 547(1), 9197. doi:10.1016/j.gene.2014.06.033Google Scholar
Dao, T.T., Gentsch, N., Mikutta, R., et al. (2018). Fate of carbohydrates and lignin in north-east Siberian permafrost soils. Soil Biology and Biochemistry, 116, 311322.Google Scholar
Davidson, E.A., Janssens, I.A. (2006). Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature, 440(7081), 165173.CrossRefGoogle ScholarPubMed
De Boer, W., Folman, L.B., Summerbell, R.C., Boddy, L. (2005). Living in a fungal world: Impact of fungi on soil bacterial niche development. FEMS Microbiology Reviews, 29(4), 795811.CrossRefGoogle Scholar
DeAngelis, K.M., Allgaier, M., Chavarria, Y., et al. (2011). Characterization of trapped lignin-degrading microbes in tropical forest soil. PLoS ONE, 6(4), e19306.Google Scholar
Dungait, J.A.J., Hopkins, D.W., Gregory, A.S., Whitmore, A.P. (2012). Soil organic matter turnover is governed by accessibility not recalcitrance. Global Change Biology, 18(6), 17811796.Google Scholar
Eilers, K.G., Debenport, S., Anderson, S., Fierer, N. (2012). Digging deeper to find unique microbial communities: The strong effect of depth on the structure of bacterial and archaeal communities in soil. Soil Biology and Biochemistry, 50, 5865.Google Scholar
Fierer, N., Allen, A.S., Schimel, J.P., Holden, P.A. (2003a). Controls on microbial CO2 production: A comparison of surface and subsurface soil horizons. Global Change Biology, 9(9), 13221332.CrossRefGoogle Scholar
Fierer, N., Schimel, J.P., Holden, P.A. (2003b). Variations in microbial community composition through two soil depth profiles. Soil Biology and Biochemistry, 35(1), 167176.Google Scholar
Finore, I., Di Donato, P., Mastascusa, V., Nicolaus, B., Poli, A. (2014). Fermentation technologies for the optimization of marine microbial exopolysaccharide production. Marine Drugs, 12(5), 30053024.Google Scholar
Frey, B., Rime, T., Phillips, M., et al. (2016). Microbial diversity in European alpine permafrost and active layers. FEMS Microbiology Ecology, 92(3).Google Scholar
Gentsch, N., Mikutta, R., Alves, R.J.E., et al. (2015). Storage and transformation of organic matter fractions in cryoturbated permafrost soils across the Siberian Arctic. Biogeosciences, 12(14), 45254542.Google Scholar
Gentsch, N., Wild, B., Mikutta, R., et al. (2018). Temperature response of permafrost soil carbon is attenuated by mineral protection. Global Change Biology, 24, 34013415. doi:10.1111/gcb.14316CrossRefGoogle Scholar
Gilichinsky, D., Rivkina, E., Bakermans, C., et al. (2005). Biodiversity of cryopegs in permafrost. FEMS Microbiology Ecology, 53, 117128. doi:10.1016/j.femsec.2005.02.003Google Scholar
Gittel, A., Bárta, J., Kohoutová¡, I., et al. (2014a). Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland. Frontiers in Microbiology, 5. doi:10.3389/fmicb.2014.00541CrossRefGoogle ScholarPubMed
Gittel, A., Bárta, J., Kohoutová, I., et al. (2014b). Distinct microbial communities associated with buried soils in the Siberian tundra. ISME Journal, 8(4), 841853. doi:10.1038/ismej.2013.219Google Scholar
Orwin, K.H., Kirschbaum, M.U.F., St John, M.G., Dickie, I.A. (2011). Organic nutrient uptake by mycorrhizal fungi enhances ecosystem carbon storage: a model‐based assessment. Ecology Letters, 14, 493502. doi:10.1111/j.1461-0248.2011.01611.xCrossRefGoogle Scholar
Harden, J.W., Koven, C.D., Ping, C.L., et al. (2012). Field information links permafrost carbon to physical vulnerabilities of thawing. Geophysical Research Letters, 39(15). doi:10.1029/2012GL051958Google Scholar
Hartmann, M., Lee, S., Hallam, S.J., Mohn, W.W. (2009). Bacterial, archaeal and eukaryal community structures throughout soil horizons of harvested and naturally disturbed forest stands. Environmental Microbiology, 11(12), 30453062. doi:10.1111/j.1462-2920.2009.02008.xCrossRefGoogle ScholarPubMed
Hibbett, D.S., Ohman, A., Glotzer, D., et al. (2011). Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biology Reviews, 25(1), 3847. doi:10.1016/j.fbr.2011.01.001CrossRefGoogle Scholar
Hobbie, J.E., Hobbie, E.A. (2013). Microbes in nature are limited by carbon and energy: The starving-survival lifestyle in soil and consequences for estimating microbial rates. Frontiers in Microbiology, 4. doi:10.3389/fmicb.2013.00324Google Scholar
Hodge, A., Campbell, C.D., Fitter, A.H. (2001). An arbuscular mycorrhizal fungus accelerates decomposition and acquires nitrogen directly from organic material. Nature, 413(6853), 297299.Google Scholar
Hoshino, T., Xiao, N., Tkachenko, O.B. (2009). Cold adaptation in the phytopathogenic fungi causing snow molds. Mycoscience, 50(1), 2638.CrossRefGoogle Scholar
Hu, W., Zhang, Q., Li, D., et al. (2014). Diversity and community structure of fungi through a permafrost core profile from the Qinghai-Tibet Plateau of China. Journal of Basic Microbiology, 54(12), 13311341.CrossRefGoogle ScholarPubMed
Hugelius, G., Kuhry, P., Tarnocai, C. (2016). Ideas and perspectives: Holocene thermokarst sediments of the Yedoma permafrost region do not increase the northern peatland carbon pool. Biogeosciences, 13(7), 20032010.CrossRefGoogle Scholar
IPCC (2014). AR5 Climate Change 2014: Impacts, Adaptation, and Vulnerability. www.ipcc.ch/report/ar5/wg2/Google Scholar
Iversen, C.M., Sloan, V.L., Sullivan, P.F., et al. (2015). The unseen iceberg: Plant roots in arctic tundra. New Phytologist, 205(1), 3458.CrossRefGoogle ScholarPubMed
Jansson, J.K., Taş, N. (2014). The microbial ecology of permafrost. Nature Reviews Microbiology, 12(6), 414425.Google Scholar
Jobbágy, E.G., Jackson, R.B. (2000). The vertical distribution of soil organic carbon and its relation to climate and vegetation. Ecological Applications, 10(2), 423436.Google Scholar
Johnson, S.S., Hebsgaard, M.B., Christensen, T.R., et al. (2007). Ancient bacteria show evidence of DNA repair. Proceedings of the National Academy of Sciences of the United States of America, 104(36), 1440114405.Google Scholar
Kaiser, C., Meyer, H., Biasi, C., et al. (2007). Conservation of soil organic matter through cryoturbation in arctic soils in Siberia. Journal of Geophysical Research: Biogeosciences, 112(2).Google Scholar
Kochkina, G., Ivanushkina, N., Ozerskaya, S., et al. (2012). Ancient fungi in Antarctic permafrost environments. FEMS Microbiology Ecology, 82(2), 501509.Google Scholar
Koven, C.D., Ringeval, B., Friedlingstein, P., et al. (2011). Permafrost carbon-climate feedbacks accelerate global warming. Proceedings of the National Academy of Sciences of the United States of America, 108(36), 1476914774.CrossRefGoogle ScholarPubMed
Lawrence, D.M., Koven, C.D., Swenson, S.C., Riley, W.J., Slater, A.G. (2015). Permafrost thaw and resulting soil moisture changes regulate projected high-latitude CO2 and CH4 emissions. Environmental Research Letters, 10(9). doi:10.1088/1748-9326/10/9/094011Google Scholar
Le Roes-Hill, M., Khan, N., Burton, S.G. (2011). Actinobacterial peroxidases: An unexplored resource for biocatalysis. Applied Biochemistry and Biotechnology, 164(5), 681713.CrossRefGoogle ScholarPubMed
Lipson, D.A., Haggerty, J.M., Srinivas, A., et al. (2013). metagenomic insights into anaerobic metabolism along an arctic peat soil profile. PLoS ONE, 8(5). doi:10.1371/journal.pone.0064659Google Scholar
Lydolph, M.C., Jacobsen, J., Arctander, P., et al. (2005). Beringian paleoecology inferred from permafrost-preserved fungal DNA. Applied and Environmental Microbiology, 71(2), 10121017.Google Scholar
Lykidis, A., Mavromatis, K., Ivanova, N., et al. (2007). Genome sequence and analysis of the soil cellulolytic actinomycete Thermobifida fusca YX. Journal of Bacteriology, 189(6), 24772486.CrossRefGoogle ScholarPubMed
MacKelprang, R., Waldrop, M.P., Deangelis, K.M., et al. (2011). Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature, 480(7377), 368371. doi:10.1038/nature10576Google Scholar
MacKelprang, R., Burkert, A., Haw, M., et al. (2017). Microbial survival strategies in ancient permafrost: Insights from metagenomics. ISME Journal, 11(10), 23052318.CrossRefGoogle ScholarPubMed
McCarthy, A.J. (1987). Lignocellulose-degrading actinomycetes. FEMS Microbiology Letters, 46(2), 145163.Google Scholar
McMahon, S.K., Wallenstein, M.D., Schimel, J.P. (2011). A cross-seasonal comparison of active and total bacterial community composition in Arctic tundra soil using bromodeoxyuridine labeling. Soil Biology and Biochemistry, 43(2), 287295.Google Scholar
Mondav, R., McCalley, C.K., Hodgkins, S.B., et al. (2017). Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient. Environmental Microbiology, 19(8), 32013218.Google Scholar
Mueller, G.M., Schmit, J.P. (2007). Fungal biodiversity: What do we know? What can we predict? Biodiversity and Conservation, 16(1), 15.Google Scholar
Ozerskaya, S., Kochkina, G., Ivanushkina, N., Gilichinsky, D.A. (2009). Fungi in permafrost. In: Margesin, R. (ed.) Permafrost Soils. Soil Biology, vol 16. Springer, Berlin, Heidelberg.Google Scholar
Phadtare, S. (2004). Recent developments in bacterial cold-shock response. Current Issues in Molecular Biology, 6(2), 125136.Google Scholar
Ping, C.L., Jastrow, J.D., Jorgenson, M.T., Michaelson, G.J., Shur, Y.L. (2015). Permafrost soils and carbon cycling. Soil, 1(1), 147171.Google Scholar
Rivkina, E.M., Kraev, G.N., Krivushin, K.V., et al. (2006). Methane in permafrost of Northeastern Arctic. Earth’s Cryosphere, 10(3), 2341.Google Scholar
Robinson, C.H. (2001). Cold adaptation in Arctic and Antarctic fungi. New Phytologist, 151(2), 341353.Google Scholar
Šantrůčková, H., Kotas, P., Bárta, J., et al. (2018). Significance of dark CO2 fixation in arctic soils. Soil Biology and Biochemistry, 119. doi:10.1016/j.soilbio.2017.12.021Google Scholar
Schellenberger, S., Kolb, S., Drake, H.L. (2010). Metabolic responses of novel cellulolytic and saccharolytic agricultural soil Bacteria to oxygen. Environmental Microbiology, 12(4), 845861.Google Scholar
Schmidt, G. (2011). Climate change and climate modeling. Eos, Transactions American Geophysical Union, 92(23), 198199.Google Scholar
Schnecker, J., Wild, B., Hofhansl, F., et al. (2014). Effects of soil organic matter properties and microbial community composition on enzyme activities in cryoturbated arctic soils. PLoS ONE, 9(4).Google Scholar
Schuur, E.A.G., Abbott, B. (2011). Climate change: High risk of permafrost thaw. Nature, 480(7375), 3233.Google Scholar
Schuur, E.A.G., Bockheim, J., Canadell, J.G., et al. (2008). Vulnerability of permafrost carbon to climate change: Implications for the global carbon cycle. BioScience, 58(8), 701714.CrossRefGoogle Scholar
Soil Survey Staff (2010). Keys to Soil Taxonomy, 11th ed. USDA-NRCS, Washington DC.Google Scholar
Soina, V.S., Vorobiova, E.A., Zvyagintsev, D.G., Gilichinsky, D.A. (1995). Preservation of cell structures in permafrost: A model for exobiology. Advances in Space Research, 15, 237242. doi:10.1016/S0273-1177(99)80090-8Google Scholar
Talbot, J.M., Treseder, K.K. (2010). Controls over mycorrhizal uptake of organic nitrogen. Pedobiologia, 53(3), 169179. doi:10.1016/j.pedobi.2009.12.001Google Scholar
Talbot, J.M., Allison, S.D., Treseder, K.K. (2008). Decomposers in disguise: Mycorrhizal fungi as regulators of soil C dynamics in ecosystems under global change. Functional Ecology, 22(6), 955963.Google Scholar
Tarnocai, C. (2018). The amount of organic carbon in various soil orders and Ecological Provinces in Canada. In: Harms, D., Korschens, M., Olson, G., et al. (eds) Soil Processes and the Carbon Cycle. CRC Press, Boca Raton, FL. doi:10.1201/9780203739273Google Scholar
Tarnocai, C. (2006). The effect of climate change on carbon in Canadian peatlands. Global and Planetary Change 53(4), 222232.Google Scholar
Tarnocai, C., Bockheim, J. (2011). Cryosolic soils of Canada: Genesis, distribution, and classification. Canadian Journal of Soil Science, 91(5), 749762.CrossRefGoogle Scholar
Tibbett, M., Sanders, F.E., Cairney, J.W.G. (2002). Low-temperature-induced changes in trehalose, mannitol and arabitol associated with enhanced tolerance to freezing in ectomycorrhizal basidiomycetes (Hebeloma spp.). Mycorrhiza, 12(5), 249255.Google Scholar
Tisdall, J.M., Oades, J.M. (1982). Organic matter and water‐stable aggregates in soils. Journal of Soil Science, 33(2), 141163.Google Scholar
Toljander, J.F., Lindahl, D., Paul, L.R., Elfstrand, M., Finlay, R.D. (2007). Influence of arbuscular mycorrhizal mycelial exudates on soil bacterial growth and community structure. FEMS Microbiology Ecology, 61, 295304. doi:10.1111/j.1574-6941.2007.00337.xGoogle Scholar
Tveit, A., Schwacke, R., Svenning, M.M., Urich, T. (2013). Organic carbon transformations in high-Arctic peat soils: Key functions and microorganisms. ISME Journal, 7(2), 299311.Google Scholar
Tveit, A.T., Urich, T., Frenzel, P., Svenning, M.M. (2015). Metabolic and trophic interactions modulate methane production by Arctic peat microbiota in response to warming. Proceedings of the National Academy of Sciences of the United States of America, 112(19), E2507–2516.Google Scholar
Uchimura, H., Enjoji, H., Seki, T., et al. (2002). Nitrate reductase-formate dehydrogenase couple involved in the fungal denitrification by Fusarium oxysporum. Journal of Biochemistry, 131(4), 579586.Google Scholar
Van Der Heul, H.U., Bilyk, B.L., McDowall, K.J., Seipke, R.F., Van Wezel, G.P. (2018). Regulation of antibiotic production in Actinobacteria: New perspectives from the post-genomic era. Natural Product Reports, 35(6), 575604.Google Scholar
Weinstein, R.N., Montiel, P.O., Johnstone, K. (2007). Influence of growth temperature on lipid and soluble carbohydrate synthesis by fungi isolated from Fellfield Soil in the Maritime Antarctic. Mycologia, 92(2), 222229.Google Scholar
Wild, B., Schnecker, J., Bárta, J., et al. (2013). Nitrogen dynamics in Turbic Cryosols from Siberia and Greenland. Soil Biology and Biochemistry, 67. doi:10.1016/j.soilbio.2013.08.004Google Scholar
Wild, B., Schnecker, J., Alves, R.J.E., et al. (2014). Input of easily available organic C and N stimulates microbial decomposition of soil organic matter in arctic permafrost soil. Soil Biology and Biochemistry, 75, 143151. doi:10.1016/j.soilbio.2014.04.014Google Scholar
Wild, B., Schnecker, J., Knoltsch, A., et al. (2015). Microbial nitrogen dynamics in organic and mineral soil horizons along a latitudinal transect in western Siberia. Global Biogeochemical Cycles, 29(5), 567582. doi:10.1002/2015GB005084CrossRefGoogle ScholarPubMed
Wild, B., Gentsch, N., Capek, P., et al. (2016). Plant-derived compounds stimulate the decomposition of organic matter in arctic permafrost soils. Scientific Reports, 6. doi:10.1038/srep25607Google Scholar
Wild, B., Alves, R.J.E., Bárta, J., et al. (2018). Amino acid production exceeds plant nitrogen demand in Siberian tundra. Environmental Research Letters, 13. doi:10.1088/1748-9326/aaa4faGoogle Scholar
Wilhelm, R.C., Niederberger, T.D., Greer, C., Whyte, L.G. (2011). Microbial diversity of active layer and permafrost in an acidic wetland from the Canadian High Arctic. Canadian Journal of Microbiology, 57(4), 303315.Google Scholar
Xiao, D., Peng, S.P., Wang, E.Y. (2015). Fermentation enhancement of methanogenic archaea consortia from an Illinois basin coalbed via DOL emulsion nutrition. PLoS ONE, 10(4).Google Scholar
Yergeau, E., Hogues, H., Whyte, L.G., Greer, C.W. (2010). The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. ISME Journal, 4(9), 12061214.Google Scholar
Yong‐Liang, C., Ye, D., Jin‐Zhi, D., et al. (2017). Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau. Molecular Ecology, 26, 66086620. doi:10.1111/mec.14396Google Scholar
Zhou, L., Xing, X., Peng, B., Fang, G. (2016). Extracellular polymeric substance (EPS) characteristics and comparison of suspended and attached activated sludge at low temperatures. Qinghua Daxue Xuebao/Journal of Tsinghua University, 56(9), 10091015.Google Scholar

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