Landscape topography structures the soil microbiome in arctic polygonal tundra

Neslihan Taş; Emmanuel Prestat; Shi Wang; Yuxin Wu; Craig Ulrich; Timothy Kneafsey; Susannah G. Tringe; Margaret S. Torn; Susan S. Hubbard; Janet K. Jansson

doi:10.1038/s41467-018-03089-z

Landscape topography structures the soil microbiome in arctic polygonal tundra

Neslihan Taş, Emmanuel Prestat, Shi Wang, Yuxin Wu, Craig Ulrich, Timothy Kneafsey, Susannah G. Tringe, Margaret S. Torn, Susan S. Hubbard, Janet K. Jansson

Research output: Contribution to journal › Article › peer-review

87 Scopus citations

Abstract

In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH₄ oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N₂O, reflecting low N₂O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions.

Original language	English
Article number	777
Journal	Nature Communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-018-03089-z
State	Published - Dec 1 2018
Externally published	Yes

Funding

The Next-Generation Ecosystem Experiments (NGEE Arctic) project is supported by the Office of Biological and Environmental Research in the DOE Office of Science. The Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported through contract number DE-AC0205CH11231 to Lawrence Berkeley National Laboratory. We acknowledge Stan Wullschleger at Oak Ridge National Laboratory as the NGEE Project PI. Additional support was provided by JGI under CSP 2013 1044 “Next Generation Ecosystem Experiment (NGEE) in the Arctic” and the Microbiomes in Transition Initiative LDRD Program at the Pacific Northwest National Laboratory, a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC06-76RL01830.

Funders	Funder number
DOE Office of Science
DOE Office of Science user facility	DE-AC0205CH11231
Department of Energy Joint Genome Institute
JGI	CSP 2013 1044
Next Generation Ecosystem Experiment
Office of Biological and Environmental Research
U.S. Department of Energy	DE-AC06-76RL01830
Lawrence Berkeley National Laboratory
Laboratory Directed Research and Development
Pacific Northwest National Laboratory

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abstract = "In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH4 oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N2O, reflecting low N2O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions.",

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AU - Prestat, Emmanuel

AU - Wang, Shi

AU - Wu, Yuxin

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AU - Kneafsey, Timothy

AU - Tringe, Susannah G.

AU - Torn, Margaret S.

AU - Hubbard, Susan S.

AU - Jansson, Janet K.

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Landscape topography structures the soil microbiome in arctic polygonal tundra

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