Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes.
Over 20% of Earth's terrestrial surface is underlain by permafrost with vast stores of carbon that, once thawed, may represent the largest future transfer of carbon from the biosphere to the atmosphere. This process is largely dependent on microbial responses, but we know little about microbial activity in intact, let alone in thawing, permafrost. Molecular approaches have recently revealed the identities and functional gene composition of microorganisms in some permafrost soils and a rapid shift in functional gene composition during short-term thaw experiments. However, the fate of permafrost carbon depends on climatic, hydrological and microbial responses to thaw at decadal scales. Here we use the combination of several molecular 'omics' approaches to determine the phylogenetic composition of the microbial communities, including several draft genomes of novel species, their functional potential and activity in soils representing different states of thaw: intact permafrost, seasonally thawed active layer and thermokarst bog. The multi-omics strategy reveals a good correlation of process rates to omics data for dominant processes, such as methanogenesis in the bog, as well as novel survival strategies for potentially active microbes in permafrost.
Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, 94720, USA.
Jenni
J
Hultman
US Geological Survey, 345 Middlefield Road, Menlo Park, California 94025, USA.
Mark P
MP
Waldrop
1] Biology Department, 18111 Nordhoff Street, California State University Northridge, Northridge, California 91330, USA [2] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
Rachel
R
Mackelprang
Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, 94720, USA.
Maude M
MM
David
US Geological Survey, 345 Middlefield Road, Menlo Park, California 94025, USA.
Jack
J
McFarland
US Geological Survey, 345 Middlefield Road, Menlo Park, California 94025, USA.
Steven J
SJ
Blazewicz
US Geological Survey, 345 Middlefield Road, Menlo Park, California 94025, USA.
Jennifer
J
Harden
Department of Integrative Biology, 50 Stone Road East, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
Merritt R
MR
Turetsky
US Geological Survey, Alaska Cooperative Fish and Wildlife Research Unit, 211A Irving I Building, University of Alaska Fairbanks, Fairbanks, Alaska 99775, USA.
A David
AD
McGuire
Chemical Sciences Division, One Bethel Valley Road, Building 1059, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6420, USA.
Manesh B
MB
Shah
Chemical Sciences Division, One Bethel Valley Road, Building 1059, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6420, USA.
Nathan C
NC
VerBerkmoes
Graduate School of Genome Science and Technology, University of Tennessee and Oak Ridge National Laboratory, 2510 River Drive, Knoxville, Tennessee 37996, USA.
Lang Ho
LH
Lee
US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA.
Kostas
K
Mavrommatis
1] Earth Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California, 94720, USA [2] US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA [3] Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, Berkeley, California 94720, USA [4] Center for Permafrost Research (CENPERM), Department of Biology, Universitetsparken 15, University of Copenhagen, Copenhagen, DK-2100 Copenhagen, Denmark.
Janet K
JK
Jansson
D000413:Alaska; D001272:Atmosphere / Q000737:chemistry; D057486:Carbon Cycle; D002980:Climate; D058440:Denitrification; D005615:Freezing; D016680:Genome, Bacterial / Q000235:genetics*; D007501:Iron / Q000378:metabolism; D054892:Metagenome / Q000235:genetics*; D008697:Methane / Q000378:metabolism; D064307:Microbiota / Q000235:genetics / Q000502:physiology*; D009566:Nitrates / Q000378:metabolism; D009584:Nitrogen / Q000378:metabolism; D010084:Oxidation-Reduction; D065946:Permafrost / Q000382:microbiology*; D010802:Phylogeny; D012621:Seasons; D012988:Soil Microbiology; D013455:Sulfur / Q000378:metabolism; D013997:Time Factors; D053833:Wetlands
D009566:Nitrates; D013455:Sulfur; D007501:Iron; D009584:Nitrogen; D008697:Methane