Examination of Soil Microbial Communities After Permafrost Thaw Subsequent to an Active Layer Detachment in the High Arctic

References Cited

• Abrams, E. S. , and Stanton, V. P., Jr. , 1992: Use of denaturing gradient gel electrophoresis to study conformational transitions in nucleic acids. Methods in Enzymology , 212: 71–104, doi: http://dx.doi.org/10.1016/0076-6879(92)12006-c.
   PubMed Web of Science ®Google Scholar
• Allan, J. , Ronholm, J. , Mykytczuk, N. , Greer, C. , Onstott, T. , and Whyte, L. , 2014: Methanogen community composition and rates of methane consumption in Canadian High Arctic permafrost soils. Environmental Microbiology Reports , 6: 136–144, doi: http://dx.doi.org/10.1111/1758-2229.12139.
   Google Scholar
• Bai, Y. , Sun, Q. , Wen, D. , and Tang, X. , 2012: Abundance of ammonia-oxidizing bacteria and archaea in industrial and domestic wastewater treatment systems. FEMS Microbiology Ecology , 80: 323–330, doi: http://dx.doi.org/10.1111/j.1574-6941.2012.01296.x.
   PubMed Web of Science ®Google Scholar
• Bailey, M. T. , Dowd, S. E. , Parry, N. M. , Galley, J. D. , Schauer, D. B. , and Lyte, M. , 2010: Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium. Infection and Immunity , 784: 1509–1519, doi: http://dx.doi.org/10.1128/iai.00862-09.
   Google Scholar
• Boon, N. , Windt, W. , Verstraete, W. , and Top, E. M. , 2002: Evaluation of nested PCR-DGGE (denaturing gradient gel electrophoresis) with group-specific 16S rRNA primers for the analysis of bacterial communities from different wastewater treatment plants. FEMS Microbiology Ecology , 39: 101–112, doi: http://dx.doi.org/10.1111/j.1574-6941.2002.tb00911.x.
   PubMed Web of Science ®Google Scholar
• Bosquet, L. M. , 2011: The Effects of Observed and Experimental Climate Change and Permafrost Disturbance on Tundra Vegetation in the Western Canadian High Arctic. Master's thesis, Queen's University, Kingston, Ontario, 114 pp.
   Google Scholar
• Brookes, P. , Kragt, J. F. , Powlson, D. S. , and Jenkinson, D. S. , 1985: Chloroform fumigation and the release of soil nitrogen: the effects of fumigation time and temperature. Soil Biology and Biochemistry , 17: 831–835, doi: http://dx.doi.org/10.1016/0038-0717(85)90143-9.
   Web of Science ®Google Scholar
• Brown, E. , and Allen-Vercoe, E. , 2011: Analysis of the fungal, archaeal and bacteriophage diversity in the human distal gut. Studies by Undergraduate Researchers at Guelph , 4: 75–82.
   Google Scholar
• Buckeridge, K. M. , and Grogan, P. , 2010: Deepened snow increases late thaw biogeochemical pulses in mesic low arctic tundra. Biogeochemistry , 101: 105–121, doi: http://dx.doi.org/10.1007/s10533-010-9426-5.
   Web of Science ®Google Scholar
• Buckeridge, K. M. , Banerjee, S. , Siciliano, S. D. , and Grogan, P. , 2013: The seasonal pattern of soil microbial community structure in mesic Low Arctic tundra. Soil Biology & Biochemistry , 65: 338–347, doi: http://dx.doi.org/10.1016/j.soilbio.2013.06.012.
   Google Scholar
• Christiansen, C. T. , Svendsen, S. H. , Schmidt, N. M. , and Michelsen, A. , 2012: High arctic heath soil respiration and biogeochemical dynamics during summer and autumn freeze-in—Effects of long-term enhanced water and nutrient supply. Global Change Biology , 18(10): 3224–3236, doi: http://dx.doi.org/10.1111/j.1365-2486.2012.02770.x.
   Google Scholar
• Chu, H. , Neufeld, J. D. , Walker, V. K. , and Grogan, P. , 2011: The influence of vegetation type on the dominant soil bacteria, archaea, and fungi in a low arctic tundra landscape. Soil Science Society of America Journal , 75: 1756–1765, doi: http://dx.doi.org/10.2136/sssaj2011.0057.
   Web of Science ®Google Scholar
• Cole, J. R. , Wang, Q. , Cardenas, E. , Fish, J. , Chai, B. , Farris, R. J. , Kulam-Syed-Mohideen, A. S. , McGarrell, D. M. , Marsh, T. , Garrity, G. M. , and Tiedje, J. M. , 2009: The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Research , 37: D141–D145, doi: http://dx.doi.org/10.1093/nar/gkn879.
   PubMed Web of Science ®Google Scholar
• Delidow, B. C. , Lynch, J. P. , Peluso, J. J. , and White, B. A. , 1993: Polymerase chain reaction: basic protocols. In White, B. A. (ed.), PCR Protocols: Current Methods and Applications. New York: Humana Press.
   Google Scholar
• Dowd, S. E. , Zaragoza, J. , Rodriguez, J. R. , Oliver, M. J. , and Payton, P. R. , 2005: Windows .NET network distributed basic local alignment search toolkit (W.ND-BLAST). BMC Bioinformatics , 6: 93, doi: http://dx.doi.org/10.1186/1471-2105-6-93.
   PubMed Web of Science ®Google Scholar
• Dowd, S. E. , Callaway, T. R. , Wolcott, R. D. , Sun, Y. , McKeehan, T. , Hagevoort, R. G. , and Edrington, T. S. , 2008: Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP). BMC Microbiology , 8: 125, doi: http://dx.doi.org/10.1186/1471-2180-8-125.
   PubMed Web of Science ®Google Scholar
• Foster, M. L. , Dowd, S. E. , Stephenson, C. , Steiner, J. M. , and Suchodolski, J. S. , 2013: Characterization of the fungal microbiome (mycobiome) in fecal samples from dogs. Veterinary Medicine International , 2013: 658373, doi: http://dx.doi.org/10.1155/2013/658373.
   Google Scholar
• Francis, C. A. , Roberts, K. J. , Beman, J. M. , Santoro, A. E. , and Oakley, B. B. , 2005: Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences of the United States of America , 102: 14683–14688, doi: http://dx.doi.org/10.1073/pnas.0506625102.
   PubMed Web of Science ®Google Scholar
• Fujimura, K. E. , and Egger, K. N. , 2012: Host plant and environment influence community assembly of High Arctic root-associated fungal communities. Fungal Ecology , 5: 409–418.
   Web of Science ®Google Scholar
• Geml, J. , Morgado, L. N. , Semenova, T. A. , Welker, J. M. , Walker, M. D. , and Smets, E. , 2015: Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi. FEMS Microbiology Ecology , 91(8): fiv095, doi: http://dx.doi.org/10.1093/femsec/fiv095.
   Google Scholar
• Gontcharova, V. , Youn, E. , Wolcott, R. D. , Hollister, E. B. , Gentry, T. J. , and Dowd, S. E. , 2010: Black Box Chimera Check (B2C2): a Windows-based software for batch depletion of chimeras from bacterial 16S rRNA gene datasets. The Open Microbiology Journal , 4: 47–52, doi: http://dx.doi.org/10.2174/1874285801004010047.
   PubMedGoogle Scholar
• IPCC, 2007: Climate change 2007: the physical science basis. In Solomon, S. , Qin, D. , Manning, M. , Chen, Z. , Marquis, M. , Averyt, K. B. , Tignor, M. , and Miller, H. L. (eds.), Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge and New York: Cambridge University Press , 1–383.
   Google Scholar
• Jones, B. M. , Amundson, C. L. , and Koch, J. C. , 2013: Thermokarst and thaw-related landscape dynamics: an annotated bibliography with an emphasis on potential effects on habitat and wildlife. U.S. Geological Survey Open-File Report 2013-1161.
   Google Scholar
• Kokelj, S. V. , and Burn, C. R. , 2005: Geochemistry of the active layer and near-surface permafrost, Mackenzie delta region, Northwest Territories, Canada. Canadian Journal of Earth Sciences , 42: 37–48, doi: http://dx.doi.org/10.1139/e04-089.
   Web of Science ®Google Scholar
• Koyama, A. , Wallenstein, M. D. , Simpson, R. T. , and Moore, J. C. , 2014: Soil bacterial community composition altered by increased nutrient availability in arctic tundra soils. Frontiers in Microbiology , 5: 516, doi: http://dx.doi.org/10.3389/fmicb.2014.00516.
   Google Scholar
• Kumar, N. , Grogan, P. , Chu, H. , Christiansen, C. T. , and Walker, V. K. , 2012: The effect of freeze-thaw conditions on arctic soil bacterial communities. Biology , 2: 356–377, doi: http://dx.doi.org/10.3390/biology2010356.
   Google Scholar
• Kuo, S. , 1996: Phosphorus. In Methods of Soil Analysis. Part 3: Chemical Methods. Madison, Wisconsin: Soil Science Society of America and American Society of Agronomy, 869–919.
   Google Scholar
• Lamhonwah, D. , Lafrenière, M. J. , Lamoureux, S. F. , and Wolfe, B. B. , 2016: Multi-year impacts of permafrost disturbance and thermal perturbation on High Arctic stream chemistry. Arctic Science , 3(2): 1–23, doi: https://dx.doi.org/10.1139/as-2016-0024.
   Google Scholar
• Lamoureux, S. F. , and Lafrenière, M. J. , 2009: Fluvial impact of extensive active layer detachments, Cape Bounty, Melville Island, Canada. Arctic, Antarctic, and Alpine Research , 41: 59–68, doi: http://dx.doi.org/10.1657/1938-4246(08-030).
   Web of Science ®Google Scholar
• Lewis, T. , and Lamoureux, S. F. , 2010: Twenty-first century discharge and sediment yield predictions in a small High Arctic watershed. Global Planet Change , 71: 27–41, doi: http://dx.doi.org/10.1016/j.gloplacha.2009.12.006.
   Web of Science ®Google Scholar
• Lewis, T. , Lafrenière, M. J. , and Lamoureux, S. F. , 2012: Hydrochemical and sedimentary responses of paired High Arctic watersheds to unusual climate and permafrost disturbance, Cape Bounty, Melville Island, Canada. Hydrological Processes , 26: 2003–2018, doi: http://dx.doi.org/10.1002/hyp.8335.
   Web of Science ®Google Scholar
• Louiseize, N. L. , Lafrenière, M. J. , and Hastings, M. G. , 2014: Stable isotopic evidence of enhanced export of microbially derived nitrate following active layer slope disturbance in the Canadian High Arctic. Biogeochemistry , 121: 565–580, doi: http://dx.doi.org/10.1007/s10533-014-0023.
   Google Scholar
• Mack, M. C. , Schuur, E. G. , Bret-Harte, M. S. , Shaver, G. R. , and Chapin, F. S. , 2004: Ecosystem carbon storage in arctic tundra reduced by long-term nutrient fertilization. Nature , 431: 440–443, doi: http://dx.doi.org/10.1038/nature02887.
   PubMed Web of Science ®Google Scholar
• McCune, B. , Grace, J. B. , and Urban, D. L. , 2002: In Analysis of Ecological Communities. Gleneden Beach, Oregon: MjM Software.
   Google Scholar
• McMurdie, P. J. , and Holmes, S. , 2014: Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Computational Biology , 10(4): e1003531, doi: https://dx.doi.org/10.1371/journal.pcbi.1003531.
   PubMed Web of Science ®Google Scholar
• Mulvaney, R. , 1996: Nitrogen-inorganic forms. In Methods of Soil Analysis. Part 3: Chemical Methods. Madison, Wisconsin: Soil Science Society of America and American Society of Agronomy, 1123–1184.
   Google Scholar
• Muyzer, G. , de Waal, E. C. , and Uitterlinden, A. G. , 1993: Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology , 59: 695–700.
   PubMed Web of Science ®Google Scholar
• Myers, R. M. , Sheffield, V. , and Cox, D. R. , 1988: Detection of single base changes in DNA: ribonuclease cleavage and denaturing gradient gel electrophoresis. In Davies, K. E. (ed.), Genome Analysis: a Practical Approach. Oxford, England: IRL Press Limited, 95–139.
   Google Scholar
• Nelson, D. W. , and Sommers, L. E. , 1996: Total carbon, organic carbon and organic matter. In Methods of Soil Analysis. Part 3: Chemical Methods. Madison, Wisconsin: Soil Science Society of America and American Society of Agronomy, 961–1010.
   Google Scholar
• Nowinski, N. , Trumbore, S. , Schuur, E. G. , Mack, M. , and Shaver, G. , 2008: Nutrient addition prompts rapid destabilization of organic matter in an arctic tundra ecosystem. Ecosystems , 11: 16–25, doi: http://dx.doi.org/10.1007/s10021-007-9104-1.
   Google Scholar
• Øvreås, L. , Forney, L. , Daae, F. L. , and Torsvik, V. , 1997: Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Applied and Environmental Microbiology , 63: 3367–3373.
   PubMed Web of Science ®Google Scholar
• Pautler, B. G. , Simpson, A. J. , Mcnally, D. J. , Lamoureux, S. F. , and Simpson, M. J. , 2010: Arctic permafrost active layer detachments stimulate microbial activity and degradation of soil organic matter. Environmental Science and Technology , 44: 4076–4082, doi: http://dx.doi.org/10.1021/es903685j.
   Google Scholar
• Rillig, M. C. , and Mummey, D. L. , 2006: Mycorrhizas and soil structure. New Phytologist , 171: 41–53, doi: http://dx.doi.org/10.1111/j.1469-8137.2006.01750.x.
   PubMed Web of Science ®Google Scholar
• Schadt, C. W. , Martin, A. P. , Lipson, D. A. , and Schmidt, S. K. , 2003: Seasonal dynamics of previously unknown fungal lineages in tundra soils. Science , 301: 1359–1361, doi: http://dx.doi.org/10.1126/science.1086940.
   PubMed Web of Science ®Google Scholar
• Shi, Y. , Xiang, X. , Shen, C. , Chu, H. , Neufeld, J. D. , Walker, V. K. , and Grogan, P. , 2015: Vegetation-associated impacts on arctic tundra bacterial and microeukaryotic communities. Applied and Environmental Microbiology , 81: 492–501.
   PubMed Web of Science ®Google Scholar
• Stajich, J. E. , Berbee, M. L. , Blackwell, M. , Hibbett, D. S. , James, T. Y. , Spatafora, J. W. , and Taylor, J. W. , 2009: The fungi. Current Biology , 19: R840-5, doi: http://dx.doi.org/10.1016/j.cub.2009.07.004.
   Google Scholar
• Steven, B. , Briggs, G. , McKay, C. P. , Pollard, W. H. , Greer, C. W. , and Whyte, L. G. , 2007: Characterization of the microbial diversity in a permafrost sample from the Canadian High Arctic using culture-dependent and culture-independent methods. FEMS Microbiology Ecology , 59: 513–523, doi: http://dx.doi.org/10.1111/j.1574-6941.2006.00247.x.
   PubMed Web of Science ®Google Scholar
• Timling, I. , and Taylor, D. L. , 2012: Peeking through a frosty window: molecular insights into the ecology of arctic soil fungi. Fungal Ecology , 5: 419–429, doi: http://dx.doi.org/10.1016/j.funeco.2012.01.009.
   Web of Science ®Google Scholar
• Timling, I. , Walker, D. A. , Nusbaum, C. , Lennon, N. J. , and Taylor, D. L. , 2014: Rich and cold: diversity, distribution and drivers of fungal communities in patterned-ground ecosystems of the North American Arctic. Molecular Ecology , 23: 3258–3272, doi: http://dx.doi.org/10.1111/mec.12743.
   PubMed Web of Science ®Google Scholar
• Tisdall, J. M. , 1994: Possible role of soil microorganisms in aggregation in soils. Plant and Soil , 159: 115–121.
   Web of Science ®Google Scholar
• Tourna, M. , Freitag, T. E. , Nicol, G. W. , and Prosser, J. I. , 2008: Growth, activity and temperature responses of ammonia-oxidizing archaea and bacteria in soil microcosms. Environmental Microbiology , 10: 1357–1364, doi: http://dx.doi.org/10.1111/j.1462-2920.2007.01563.x.
   PubMed Web of Science ®Google Scholar
• Vissers, E. W. , Bodelier, P. L. , Muyzer, G. , and Laanbroek, H. J. , 2009: A nested PCR approach for improved recovery of archaeal 16S rRNA gene fragments from freshwater samples. FEMS Microbiology Letters , 298: 193–198, doi: http://dx.doi.org/10.1111/j.1574-6968.2009.01718.x.
   PubMed Web of Science ®Google Scholar
• Wagner, D. , 2008: Microbial communities and processes in arctic permafrost environments. Soil Biology , 13: 133–154.
   Google Scholar
• Walker, J. F. , Aldrich-Wolfe, L. , Riffel, A. , Barbare, H. , Simpson, N. B. , Trowbridge, J. , and Jumpponen, A. , 2011: Diverse Helotiales associated with the roots of three species of arctic Ericaceae provide no evidence for host specificity. New Phytologist , 191: 515–527, doi: http://dx.doi.org/10.1111/j.1469-8137.2011.03703.x.
   PubMed Web of Science ®Google Scholar
• Wilhelm, R. C. , Niederberger, T. D. , Greer, C. , and 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: 303–315, doi: http://dx.doi.org/10.1139/W11-004.
   PubMed Web of Science ®Google Scholar
• Yergeau, E. , Hogues, H. , Whyte, L. G. , and Greer, C. W. , 2010: The functional potential of High Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses. International Society for Microbial Ecology Journal , 4: 1206–1214, doi: http://dx.doi.org/10.1038/ismej.2010.41.
   Google Scholar
• Zhang, L. , Offre, P. R. , He, J. , Verhamme, D. T. , Nicol, G. W. , and Prosser, J. I. , 2010: Autotrophic ammonia oxidation by soil thaumarchaea. Proceedings of the National Academy of Sciences of the United States of America , 107: 17240–17245, doi: http://dx.doi.org/10.1073/pnas.1004947107.
   PubMed Web of Science ®Google Scholar