Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient

Mondav, Rhiannon; McCalley, Carmody K.; Hodgkins, Suzanne B.; Frolking, Steve; Saleska, Scott R.; Rich, Virginia I.; Chanton, Jeff P.; Crill, Patrick M.

doi:10.1111/1462-2920.13809

Title: Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient

Journal Article · Fri Jun 02 00:00:00 EDT 2017 · Environmental Microbiology

DOI:https://doi.org/10.1111/1462-2920.13809· OSTI ID:1856865

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Uppsala Univ., Uppsala (Sweden); Univ. of Queensland, Brisbane (Australia)
Univ. of Arizona, Tucson, AZ (United States); Univ. of New Hampshire, Durham, NH (United States)
Florida State Univ., Tallahassee, FL (United States)
Univ. of New Hampshire, Durham, NH (United States)
Univ. of Arizona, Tucson, AZ (United States)
Stockholm Univ., Stockholm (Sweden)

Biogenic production and release of methane (CH₄) from thawing permafrost has the potential to be an important source of radiative forcing. We studied changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa site (intact permafrost and low radiative forcing signature) had a phylogenetically clustered community dominated by Acidobacteria and Proteobacteria. The bog (thawing permafrost and low radiative forcing signature) had lower alpha diversity and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering. Hydrogenotrophic methanogens and Acidobacteria dominated the bog shifting from palsa-like to fen-like at the waterline. The fen (no underlying permafrost, high radiative forcing signature) had the highest alpha, beta and phylogenetic diversity, was dominated by Proteobacteria and Euryarchaeota and was significantly enriched in methanogens. The Mire microbial network was modular with module cores consisting of clusters of Acidobacteria, Euryarchaeota or Xanthomonodales. Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta and phylogenetic diversity associated with a higher radiative forcing signature. These results imply the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing.

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Research Organization:: Univ. of Queensland, Brisbane, QLD (Australia); Univ. of Arizona, Tucson, AZ (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0004632; SC0010580

OSTI ID:: 1856865

Alternate ID(s):: OSTI ID: 1506093

Journal Information:: Environmental Microbiology, Vol. 19, Issue 8; ISSN 1462-2912

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Fundamentals of Microbial Community Resistance and Resilience Shade, Ashley; Peter, Hannes; Allison, Steven D. Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00417	journal	January 2012
Unusual Members of the PVC Superphylum: The Methanotrophic Verrucomicrobia Genus “Methylacidiphilum” Sharp, Christine E.; den Camp, Huub J. M. Op; Tamas, Ivica Planctomycetes: Cell Structure, Origins and Biology https://doi.org/10.1007/978-1-62703-502-6_9	book	January 2013
Patterns of permafrost formation and degradation in relation to climate and ecosystems Shur, Y. L.; Jorgenson, M. T. Permafrost and Periglacial Processes, Vol. 18, Issue 1 https://doi.org/10.1002/ppp.582	journal	January 2007
Loss of microbial diversity in soils is coincident with reductions in some specialized functions: Microbial diversity and ecosystem functions Singh, Brajesh K.; Quince, Christopher; Macdonald, Catriona A. Environmental Microbiology, Vol. 16, Issue 8 https://doi.org/10.1111/1462-2920.12353	journal	January 2014
Methanosaeta, the forgotten methanogen? Smith, Kerry S.; Ingram-Smith, Cheryl Trends in Microbiology, Vol. 15, Issue 4 https://doi.org/10.1016/j.tim.2007.02.002	journal	April 2007
Quantifying community assembly processes and identifying features that impose them Stegen, James C.; Lin, Xueju; Fredrickson, Jim K. The ISME Journal, Vol. 7, Issue 11 https://doi.org/10.1038/ismej.2013.93	journal	June 2013
Stochastic and deterministic assembly processes in subsurface microbial communities Stegen, James C.; Lin, Xueju; Konopka, Allan E. The ISME Journal, Vol. 6, Issue 9 https://doi.org/10.1038/ismej.2012.22	journal	March 2012
The disappearance of relict permafrost in boreal north America: Effects on peatland carbon storage and fluxes Turetsky, M. R.; Wieder, R. K.; Vitt, D. H. Global Change Biology, Vol. 13, Issue 9 https://doi.org/10.1111/j.1365-2486.2007.01381.x	journal	September 2007
Organic carbon transformations in high-Arctic peat soils: key functions and microorganisms Tveit, Alexander; Schwacke, Rainer; Svenning, Mette M. The ISME Journal, Vol. 7, Issue 2 https://doi.org/10.1038/ismej.2012.99	journal	September 2012
Phylogenetic distance and species richness interactively affect the productivity of bacterial communities Venail, Patrick A.; Vives, Martha J. Ecology, Vol. 94, Issue 11 https://doi.org/10.1890/12-2002.1	journal	November 2013
Global Warming and Carbon Dynamics in Permafrost Soils: Methane Production and Oxidation Wagner, Dirk; Liebner, Susanne Soil Biology https://doi.org/10.1007/978-3-540-69371-0_15	book
Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes Wang, Jianjun; Shen, Ji; Wu, Yucheng The ISME Journal, Vol. 7, Issue 7 https://doi.org/10.1038/ismej.2013.30	journal	February 2013
Three Genomes from the Phylum Acidobacteria Provide Insight into the Lifestyles of These Microorganisms in Soils Ward, N. L.; Challacombe, J. F.; Janssen, P. H. Applied and Environmental Microbiology, Vol. 75, Issue 7 https://doi.org/10.1128/AEM.02294-08	journal	February 2009
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Correlation detection strategies in microbial data sets vary widely in sensitivity and precision Weiss, Sophie; Van Treuren, Will; Lozupone, Catherine The ISME Journal, Vol. 10, Issue 7 https://doi.org/10.1038/ismej.2015.235	journal	February 2016
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Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host Marasco, Ramona; Mosqueira, María J.; Fusi, Marco Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0597-y	journal	December 2018
Large carbon cycle sensitivities to climate across a permafrost thaw gradient in subarctic Sweden Chang, Kuang-Yu; Riley, William J.; Crill, Patrick M. The Cryosphere, Vol. 13, Issue 2 https://doi.org/10.5194/tc-13-647-2019	journal	January 2019
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils Trubl, Gareth; Roux, Simon; Solonenko, Natalie PeerJ, Vol. 7 https://doi.org/10.7717/peerj.7265	journal	January 2019
Spatiotemporal Distribution and Assemblages of Planktonic Fungi in the Coastal Waters of the Bohai Sea Wang, Yaqiong; Sen, Biswarup; He, Yaodong Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00584	journal	March 2018

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