skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates: High resolution permafrost microbial profile

Abstract

Thawing permafrost can stimulate microbial activity, leading to faster decomposition of formerly preserved organic matter and CO 2 release. Detailed knowledge about the vertical distribution of the responsible microbial community that is changing with increasing soil depth is limited. In this study, we determined the microbial community composition from cores sampled in a high Arctic heath at Svalbard, Norway; spanning from the active layer (AL) into the permafrost layer (PL). A special aim has been on identifying a layer of recently thawed soil, the transition zone (TZ), which might provide new insights into the fate of thawing permafrost. A unique sampling strategy allowed us to observe a diverse and gradually shifting microbial community in the AL, a Bacteroidetes dominated community in the TZ and throughout the PL, a community strongly dominated by a single Actinobacteria family (Intrasporangiaceae). The contrasting abundances of these two taxa caused a community difference of about 60%, just within 3 cm from TZ to PL. We incubated subsamples at about 5°C and measured highest CO 2 production rates under aerobic incubations, yet contrasting for five different layers and correlating to the microbial community composition. This high resolution strategy provides new insights on how microbial communities aremore » structured in permafrost and a better understanding of how they respond to thaw.« less

Authors:
ORCiD logo [1];  [2];  [3];  [4];  [5];  [5];  [3];  [6]
  1. Bergen Univ. (Norway). Department of Biological Sciences
  2. Aarhus University, Roskilde (Denmark). Department of Environmental Science; Copenhagen Univ. (Denmark). Department of Biology
  3. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
  4. Copenhagen Univ. (Denmark). Department of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM)
  5. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  6. Bergen Univ. (Norway). Department of Biological Sciences; University Center in Svalbard, UNIS, Longyearbyen (Norway)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1476599
DOE Contract Number:  
AC02-05CH11231; AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Environmental Microbiology
Additional Journal Information:
Journal Volume: 20; Journal Issue: 12; Journal ID: ISSN 1462-2912
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
58 GEOSCIENCES

Citation Formats

Müller, Oliver, Bang-Andreasen, Toke, White, Richard Allen, Elberling, Bo, Taş, Neslihan, Kneafsey, Timothy, Jansson, Janet K., and Øvreås, Lise. Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates: High resolution permafrost microbial profile. United States: N. p., 2018. Web. doi:10.1111/1462-2920.14348.
Müller, Oliver, Bang-Andreasen, Toke, White, Richard Allen, Elberling, Bo, Taş, Neslihan, Kneafsey, Timothy, Jansson, Janet K., & Øvreås, Lise. Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates: High resolution permafrost microbial profile. United States. doi:10.1111/1462-2920.14348.
Müller, Oliver, Bang-Andreasen, Toke, White, Richard Allen, Elberling, Bo, Taş, Neslihan, Kneafsey, Timothy, Jansson, Janet K., and Øvreås, Lise. Tue . "Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates: High resolution permafrost microbial profile". United States. doi:10.1111/1462-2920.14348. https://www.osti.gov/servlets/purl/1476599.
@article{osti_1476599,
title = {Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates: High resolution permafrost microbial profile},
author = {Müller, Oliver and Bang-Andreasen, Toke and White, Richard Allen and Elberling, Bo and Taş, Neslihan and Kneafsey, Timothy and Jansson, Janet K. and Øvreås, Lise},
abstractNote = {Thawing permafrost can stimulate microbial activity, leading to faster decomposition of formerly preserved organic matter and CO2 release. Detailed knowledge about the vertical distribution of the responsible microbial community that is changing with increasing soil depth is limited. In this study, we determined the microbial community composition from cores sampled in a high Arctic heath at Svalbard, Norway; spanning from the active layer (AL) into the permafrost layer (PL). A special aim has been on identifying a layer of recently thawed soil, the transition zone (TZ), which might provide new insights into the fate of thawing permafrost. A unique sampling strategy allowed us to observe a diverse and gradually shifting microbial community in the AL, a Bacteroidetes dominated community in the TZ and throughout the PL, a community strongly dominated by a single Actinobacteria family (Intrasporangiaceae). The contrasting abundances of these two taxa caused a community difference of about 60%, just within 3 cm from TZ to PL. We incubated subsamples at about 5°C and measured highest CO2 production rates under aerobic incubations, yet contrasting for five different layers and correlating to the microbial community composition. This high resolution strategy provides new insights on how microbial communities are structured in permafrost and a better understanding of how they respond to thaw.},
doi = {10.1111/1462-2920.14348},
journal = {Environmental Microbiology},
issn = {1462-2912},
number = 12,
volume = 20,
place = {United States},
year = {2018},
month = {7}
}

Journal Article:

Figures / Tables:

Figure 1 Figure 1: Permafrost soil profile illustrating: A. The soil structure in Adventdalen. Photograph shows the sedimentation process with periods of low sedimentation rates (small darker organic rich layers, marked with white triangles) and periods with higher sedimentation rates (thicker more pale layers). B. Relative abundance of the 20 most abundantmore » taxa at different taxonomical levels based on 16S rRNA gene sequence data showing the taxonomic prokaryotic community composition of the permafrost core profile. When taxonomical classes within a phylum showed very contrasting trends, the most abundant classes were illustrated instead of the entire phyla. Taxonomical levels are indicated by a one-letter code (p = phylum; c = class; f = family). Taxa comprising <1% of the total number of sequences within a sample were summarized as ‘Other’. Relative abundances for each sampling point are average values calculated from 2 to 6 replicates (Supporting Information Table S1). C. Bray–Curtis dissimilarity values calculated for 16S rRNA gene sequence data at OTU level. Black triangles mark the transition from AL to TZ and from TZ to PL. D. Alpha diversity indices (Chao1, Shannon and Simpson). E. Bulk density measurement using X-ray CT scanning with measuring points for every centimetre (11 example images illustrated on the left). F. Soil chemistry (n = 1) showing in blue the water content, in grey the carbon content and in red the pH throughout the core. Note that data was not available between 30 and 80 cm.« less

Save / Share:

Works referenced in this record:

A Mathematical Theory of Communication
journal, July 1948


Impact of fire on active layer and permafrost microbial communities and metagenomes in an upland Alaskan boreal forest
journal, April 2014

  • Taş, Neslihan; Prestat, Emmanuel; McFarland, Jack W.
  • The ISME Journal, Vol. 8, Issue 9
  • DOI: 10.1038/ismej.2014.36

Respiration of 13C-Labeled Substrates Added to Soil in the Field and Subsequent 16S rRNA Gene Analysis of 13C-Labeled Soil DNA
journal, March 2003


Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming
journal, February 2016

  • Xue, Kai; M. Yuan, Mengting; J. Shi, Zhou
  • Nature Climate Change, Vol. 6, Issue 6
  • DOI: 10.1038/nclimate2940

Distinct microbial communities associated with buried soils in the Siberian tundra
journal, December 2013

  • Gittel, Antje; Bárta, Jiří; Kohoutová, Iva
  • The ISME Journal, Vol. 8, Issue 4
  • DOI: 10.1038/ismej.2013.219

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw
journal, November 2011

  • Mackelprang, Rachel; Waldrop, Mark P.; DeAngelis, Kristen M.
  • Nature, Vol. 480, Issue 7377
  • DOI: 10.1038/nature10576

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006

  • DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
  • Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
  • DOI: 10.1128/AEM.03006-05

Microbial diversity of active layer and permafrost in an acidic wetland from the Canadian High Arctic
journal, April 2011

  • Wilhelm, Roland C.; Niederberger, Thomas D.; Greer, Charles
  • Canadian Journal of Microbiology, Vol. 57, Issue 4
  • DOI: 10.1139/w11-004

Microbial activity of tundra and taiga soils at sub-zero temperatures
journal, September 1995


Trimmomatic: a flexible trimmer for Illumina sequence data
journal, April 2014


Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils
journal, October 2014

  • Koyama, Akihiro; Wallenstein, Matthew D.; Simpson, Rodney T.
  • Frontiers in Microbiology, Vol. 5
  • DOI: 10.3389/fmicb.2014.00516

The functional potential of high Arctic permafrost revealed by metagenomic sequencing, qPCR and microarray analyses
journal, April 2010

  • Yergeau, Etienne; Hogues, Hervé; Whyte, Lyle G.
  • The ISME Journal, Vol. 4, Issue 9
  • DOI: 10.1038/ismej.2010.41

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
journal, January 2015


An overview of soil heterogeneity: quantification and implications on geotechnical field problems
journal, February 2003

  • Elkateb, Tamer; Chalaturnyk, Rick; Robertson, Peter K.
  • Canadian Geotechnical Journal, Vol. 40, Issue 1
  • DOI: 10.1139/t02-090

Microbial Iron Oxidation in the Arctic Tundra and Its Implications for Biogeochemical Cycling
journal, September 2015

  • Emerson, David; Scott, Jarrod J.; Benes, Joshua
  • Applied and Environmental Microbiology, Vol. 81, Issue 23
  • DOI: 10.1128/AEM.02832-15

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
journal, November 2013


A model-data intercomparison of CO 2 exchange across North America: Results from the North American Carbon Program site synthesis
journal, January 2010

  • Schwalm, Christopher R.; Williams, Christopher A.; Schaefer, Kevin
  • Journal of Geophysical Research, Vol. 115
  • DOI: 10.1029/2009JG001229

The ImageJ ecosystem: An open platform for biomedical image analysis: T
journal, July 2015

  • Schindelin, Johannes; Rueden, Curtis T.; Hiner, Mark C.
  • Molecular Reproduction and Development, Vol. 82, Issue 7-8
  • DOI: 10.1002/mrd.22489

Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010


Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores
journal, January 2018


Effects of water regime on archaeal community composition in Arctic soils
journal, June 2006


Viability, diversity and composition of the bacterial community in a high Arctic permafrost soil from Spitsbergen, Northern Norway
journal, November 2007


FLASH: fast length adjustment of short reads to improve genome assemblies
journal, September 2011


Uncoupling of microbial CO2 production and release in frozen soil and its implications for field studies of arctic C cycling
journal, February 2003


The effect of permafrost thaw on old carbon release and net carbon exchange from tundra
journal, May 2009

  • Schuur, Edward A. G.; Vogel, Jason G.; Crummer, Kathryn G.
  • Nature, Vol. 459, Issue 7246
  • DOI: 10.1038/nature08031

Fast and sensitive protein alignment using DIAMOND
journal, November 2014

  • Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
  • Nature Methods, Vol. 12, Issue 1
  • DOI: 10.1038/nmeth.3176

Influence of Vegetation, Temperature, and Water Content on Soil Carbon Distribution and Mineralization in Four High Arctic Soils
journal, November 2004


Site- and horizon-specific patterns of microbial community structure and enzyme activities in permafrost-affected soils of Greenland
journal, October 2014

  • Gittel, Antje; Bárta, Jiří; Kohoutová, Iva
  • Frontiers in Microbiology, Vol. 5
  • DOI: 10.3389/fmicb.2014.00541

KEGG: Kyoto Encyclopedia of Genes and Genomes
journal, January 1999

  • Ogata, H.; Goto, S.; Sato, K.
  • Nucleic Acids Research, Vol. 27, Issue 1
  • DOI: 10.1093/nar/27.1.29

Search and clustering orders of magnitude faster than BLAST
journal, August 2010


Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska
journal, December 2014

  • Deng, Jie; Gu, Yunfu; Zhang, Jin
  • Molecular Ecology, Vol. 24, Issue 1
  • DOI: 10.1111/mec.13015

Permafrost thermal state in the polar Northern Hemisphere during the international polar year 2007-2009: a synthesis
journal, April 2010

  • Romanovsky, Vladimir E.; Smith, Sharon L.; Christiansen, Hanne H.
  • Permafrost and Periglacial Processes, Vol. 21, Issue 2
  • DOI: 10.1002/ppp.689

Long-term CO2 production following permafrost thaw
journal, July 2013

  • Elberling, Bo; Michelsen, Anders; Schädel, Christina
  • Nature Climate Change, Vol. 3, Issue 10
  • DOI: 10.1038/nclimate1955

Microbial Functional Potential and Community Composition in Permafrost-Affected Soils of the NW Canadian Arctic
journal, January 2014


The transient layer: implications for geocryology and climate-change science
journal, January 2005

  • Shur, Yuri; Hinkel, Kenneth M.; Nelson, Frederick E.
  • Permafrost and Periglacial Processes, Vol. 16, Issue 1
  • DOI: 10.1002/ppp.518

The rate of permafrost carbon release under aerobic and anaerobic conditions and its potential effects on climate
journal, September 2011


Estimated stocks of circumpolar permafrost carbon with quantified uncertainty ranges and identified data gaps
journal, January 2014


Metagenomic analyses of the late Pleistocene permafrost – additional tools for reconstruction of environmental conditions
journal, January 2016

  • Rivkina, Elizaveta; Petrovskaya, Lada; Vishnivetskaya, Tatiana
  • Biogeosciences, Vol. 13, Issue 7
  • DOI: 10.5194/bg-13-2207-2016

Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil
journal, April 2011


The microbial ecology of permafrost
journal, May 2014

  • Jansson, Janet K.; Taş, Neslihan
  • Nature Reviews Microbiology, Vol. 12, Issue 6
  • DOI: 10.1038/nrmicro3262

Repeated freeze–thaw cycles and their effects on biological processes in two arctic ecosystem types
journal, October 2002


Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
journal, November 2015

  • O'Leary, Nuala A.; Wright, Mathew W.; Brister, J. Rodney
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1189

Fast gapped-read alignment with Bowtie 2
journal, March 2012

  • Langmead, Ben; Salzberg, Steven L.
  • Nature Methods, Vol. 9, Issue 4
  • DOI: 10.1038/nmeth.1923

Kinetics of iron(II) oxygenation at low partial pressure of oxygen in the presence of natural organic matter
journal, September 1993

  • Liang, Liyuan; McNabb, J. Andrew; Paulk, John M.
  • Environmental Science & Technology, Vol. 27, Issue 9
  • DOI: 10.1021/es00046a014

Microbial hitchhikers on intercontinental dust: high-throughput sequencing to catalogue microbes in small sand samples
journal, June 2012


The subzero microbiome: microbial activity in frozen and thawing soils
journal, April 2016

  • Nikrad, Mrinalini P.; Kerkhof, Lee J.; Häggblom, Max M.
  • FEMS Microbiology Ecology, Vol. 92, Issue 6
  • DOI: 10.1093/femsec/fiw081

Vulnerability and Feedbacks of Permafrost to Climate Change
journal, March 2011

  • Grosse, Guido; Romanovsky, Vladimir; Jorgenson, Torre
  • Eos, Transactions American Geophysical Union, Vol. 92, Issue 9
  • DOI: 10.1029/2011EO090001

QIIME allows analysis of high-throughput community sequencing data
journal, April 2010

  • Caporaso, J. Gregory; Kuczynski, Justin; Stombaugh, Jesse
  • Nature Methods, Vol. 7, Issue 5
  • DOI: 10.1038/nmeth.f.303

Thawing permafrost and thicker active layers in sub-arctic Sweden
journal, July 2008

  • Åkerman, H. Jonas; Johansson, Margareta
  • Permafrost and Periglacial Processes, Vol. 19, Issue 3
  • DOI: 10.1002/ppp.626

Potential microbial contamination during sampling of permafrost soil assessed by tracers
journal, February 2017

  • Bang-Andreasen, Toke; Schostag, Morten; Priemé, Anders
  • Scientific Reports, Vol. 7, Issue 1
  • DOI: 10.1038/srep43338

Global Biogeography and Quantitative Seasonal Dynamics of Gemmatimonadetes in Soil
journal, July 2011

  • DeBruyn, Jennifer M.; Nixon, Lauren T.; Fawaz, Mariam N.
  • Applied and Environmental Microbiology, Vol. 77, Issue 17
  • DOI: 10.1128/AEM.05005-11

The impacts of recent permafrost thaw on land–atmosphere greenhouse gas exchange
journal, April 2014

  • Hayes, Daniel J.; Kicklighter, David W.; McGuire, A. David
  • Environmental Research Letters, Vol. 9, Issue 4
  • DOI: 10.1088/1748-9326/9/4/045005

Changes in Marine Prokaryote Composition with Season and Depth Over an Arctic Polar Year
journal, April 2017


Methane dynamics regulated by microbial community response to permafrost thaw
journal, October 2014

  • McCalley, Carmody K.; Woodcroft, Ben J.; Hodgkins, Suzanne B.
  • Nature, Vol. 514, Issue 7523
  • DOI: 10.1038/nature13798

Holocene permafrost history and cryostratigraphy in the High-Arctic Adventdalen Valley, central Svalbard
journal, October 2017

  • Cable, Stefanie; Elberling, Bo; Kroon, Aart
  • Boreas, Vol. 47, Issue 2
  • DOI: 10.1111/bor.12286

Sequential Reduction and Oxidation of Inorganic Nitrogen, Manganese, and Iron in Flooded Soil
journal, January 1992


Distinct summer and winter bacterial communities in the active layer of Svalbard permafrost revealed by DNA- and RNA-based analyses
journal, April 2015


Measurement of Diversity
journal, April 1949


Toward an Ecological Classification of soil Bacteria
journal, June 2007

  • Fierer, Noah; Bradford, Mark A.; Jackson, Robert B.
  • Ecology, Vol. 88, Issue 6
  • DOI: 10.1890/05-1839

    Works referencing / citing this record:

    Bacterial and Archaeal Metagenome-Assembled Genome Sequences from Svalbard Permafrost
    journal, July 2019

    • Xue, Yaxin; Jonassen, Inge; Øvreås, Lise
    • Microbiology Resource Announcements, Vol. 8, Issue 27
    • DOI: 10.1128/mra.00516-19

    Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska
    journal, June 2019


      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.