Microbes in thawing permafrost: The unknown variable in the climate change equation

Abstract

Considering that 25% of Earth s terrestrial surface is underlain by permafrost (ground that has been continuously frozen for at least 2 years), our understanding of the diversity of microbial life in this extreme habitat is surprisingly limited. Taking into account the total mass of perennially frozen sediment (up to several hundred meters deep), permafrost contains a huge amount of buried, ancient organic carbon (Tarnocai et al., 2009). In addition, permafrost is warming rapidly in response to global climate change (Romanovsky et al., 2010), potentially leading to widespread thaw and a larger, seasonally thawed soil active layer. This concern has prompted the question: will permafrost thawing lead to the release of massive amounts of carbon dioxide (CO2) and methane (CH4) into the atmosphere? This question can only be answered by understanding how the microbes residing in permafrost will respond to thaw, through processes such as respiration, fermentation, methanogenesis and CH4 oxidation (Schuur et al., 2009). Predicting future carbon fluxes is complicated by the diversity of permafrost environments, ranging from high mountains, southern boreal forests, frozen peatlands and Pleistocene ice complexes (yedoma) up to several hundred meters deep, which vary widely in soil composition, soil organic matter (SOM) quality, hydrology and thermal regimes (Figure 1). Permafrost degradation can occur in many forms: thaw can progress downward from seasonally-thawed active layer soils in warming climates or laterally because of changes in surface or groundwater flow paths (Grosse et al., 2011). Permafrost degradation can sometimes lead to dramatic changes in ecosystem structure and function

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COMMENTARY
Microbes in thawing permafrost: the unknown
variable in the climate change equation
David E Graham, Matthew D Wallenstein, Tatiana A Vishnivetskaya, Mark P Waldrop,
Tommy J Phelps, Susan M Pfiffner, Tullis C Onstott, Lyle G Whyte, Elizaveta M Rivkina,
David A Gilichinsky, Dwayne A Elias, Rachel Mackelprang, Nathan C VerBerkmoes,
Robert L Hettich, Dirk Wagner, Stan D Wullschleger and Janet K Jansson
The ISME Journal (2012) 6, 709–712; doi:10.1038/
ismej.2011.163; published online 17 November 2011
Considering that 25% of Earth’s terrestrial surface
is underlain by permafrost (ground that has
been continuously frozen for at least 2 years), our
understanding of the diversity of microbial life in
this extreme habitat is surprisingly limited. Taking
into account the total mass of perennially frozen
sediment (up to several hundred meters deep),
permafrost contains a huge amount of buried,
ancient organic carbon (Tarnocai et al., 2009). In
addition, permafrost is warming rapidly in response
to global climate change (Romanovsky et al., 2010),
potentially leading to widespread thaw and a larger,
seasonally thawed soil active layer. This concern
has prompted the question: will permafrost thawing
lead to the release of massive amounts of carbon
dioxide (CO
2
) and methane (CH
4
) into the atmo-
sphere? This question can only be answered by
understanding how the microbes residing in perma-
frost will respond to thaw, through processes
such as respiration, fermentation, methanogenesis
and CH
4
oxidation (Schuur et al., 2009).
Predicting future carbon fluxes is complicated by
the diversity of permafrost environments, ranging
from high mountains, southern boreal forests, frozen
peatlands and Pleistocene ice complexes (yedoma)
up to several hundred meters deep, which vary
widely in soil composition, soil organic matter
(SOM) quality, hydrology and thermal regimes
(Figure 1). Permafrost degradation can occur in
many forms: thaw can progress downward from
seasonally-thawed ‘active layer’ soils in warming
climates or laterally because of changes in surface
or groundwater flow paths (Grosse et al., 2011).
Permafrost degradation can sometimes lead to
dramatic changes in ecosystem structure and func-
tion, such as the formation of thermokarst bogs.
Wildfires and other disturbances that remove
vegetation and organic matter warm the ground,
hastening permafrost degradation. The complexity
of the Northern Arctic and Subarctic environments
in terms of geology, vegetation, paleohistory and
climate, suggests that understanding the microbial
ecology in permafrost regions will require numerous
studies throughout the Pan-Arctic.
Frozen conditions in permafrost efficiently
preserve biological material from DNA to wooly
mammoths. Low water potential, reduced protein
flexibility and enzyme activity, limited membrane
fluidity, and ice nucleation and melting are all
potentially lethal, so it was long assumed that
microbes were either dead or dormant when frozen.
However, high ionic strength within pore water
can depress the freezing point and preserve cell
viability. Recent experiments demonstrated that
permafrost microorganisms remain active at extre-
mely low temperatures (Vishnivetskaya et al., 2006;
Gilichinsky and Rivkina, 2011): indigenous bacteria
incorporated
14
C-labeled acetate into lipids down to
20 1C, many isolates showed psychroactive growth
at 2.5 1C and acetotrophic methanogenesis contin-
ued between 5 1C and 17 1C. Thus, warming could
induce SOM decomposition even before permafrost
thaws completely. Microbial activity at low tem-
peratures could transform complex organic com-
pounds to soluble metabolites and gases, including
the greenhouse gases (GHG): CO
2
,CH
4
and N
2
O
(Figure 2). Microbial transformations of carbon and
nitrogen compounds in the soil active layer can in
turn affect plant productivity and community
composition, changing animal habitats and affecting
human land use. Although these gas fluxes and
landscape changes can be directly measured, we
need more detailed, mechanistic models that
integrate geochemical and structural parameters
with microbial processes to explain and predict
future changes in permafrost regions. In order to
accurately predict the vulnerability of permafrost
carbon to decomposition and the resulting fluxes of
GHG products, we should understand how Arctic
microbial communities respond to permafrost
thawing. In addition to an increase in the rate of organic
matter decomposition because of warming, there
will most likely be shifts in the microbial commu-
nity composition and in the relative consumption
of different organic constituents.
Here we address how combining information
about microbial identity (from phylotyping) and
The ISME Journal (2012) 6, 709 –712
&
2012 International Society for Microbial Ecology All rights reserved 1751-7362/12
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metabolic potential (from metagenomes) with
information on what genes are expressed and
functioning (from metatranscriptomes and metapro-
teomes) (VerBerkmoes et al., 2009; Jansson, 2011)
has begun to open a new window of opportunity to
map and predict biochemical processes in soils.
They provide the tools to distinguish among
different mechanisms for increased organic matter
decomposition caused by increasing temperature
(Conant et al., 2011). Two potential applications of
this systems biology framework, discussed below,
illustrate how these molecular techniques could be
used to improve our ability to model SOM degrada-
tion rates and mechanisms, and to predict changes
in CH
4
and CO
2
emissions from thawing permafrost.
Currently, we cannot predict how microbes will
use SOM released by permafrost thawing, or reliably
estimate the temperature-dependent activities of the
enzymes they produce to degrade this material.
Current biogeochemical models segregate SOM into
conceptual pools with different mean residence
times (Smith et al., 1997). If most organic matter
trapped in permafrost is difficult to degrade because
of its chemical structure (for example, lignin) or its
physical structure (for example, particulates or
mineral complexes), then this humus comprises a
recalcitrant pool that will slowly stimulate micro-
bial growth and GHG production. Alternatively, if
plant litter was rapidly frozen in permafrost, then
microbes could quickly metabolize thawed poly-
mers like cellulose or protein. Although chemical
methods can be used to characterize this SOM, a
complementary approach could use transcriptional
and proteomic measurements of enzyme expression
to analyze the microbial response to this SOM and
infer its properties. Increased temperature may also
cause changes in protein structure and conforma-
tion, protein adsorption, altered protein expression
and shifts in microbial populations, which are not
currently modeled (Waldrop et al., 2010; Wallen-
stein et al., 2011). We might expect soil warming to
select for microbes producing enzymes that degrade
SOM more efficiently at higher temperatures. If
transcriptomic, proteomic and enzymatic analyses
confirm this hypothesis through experiments repli-
cating in situ conditions, then thermal acclimation
of enzymes would need to be incorporated into
models to accurately predict long-term C dynamics
in response to permafrost thaw (Allison et al., 2010).
Predictions of soil GHG flux include increasingly
sophisticated representations of processes in the
subsurface carbon cycle (Figure 2), but these models
are poorly parameterized for permafrost regions
(Riley et al., 2011). 16S rRNA gene sequence data
have identified both hydrogenotrophic and aceto-
trophic (methylotrophic) methanogen phylotypes in
Arctic tundra samples, at substantial abundance
(Wagner and Liebner, 2010). The two groups of
methanogens differ in their substrates, syntrophic
associations and isotopic fractionation of carbon:
it is important to distinguish between the methano-
genic pathways to predict the proportions of
CH
4
and CO
2
, as well as fluxes (Walter et al.,
2008). Changes in methanogen abundance could
also confuse estimates of the temperature and pH
response factors. Comparative metagenomics can
identify changes in the abundance of characteristic
methanogen genes required for coenzyme biosynth-
esis and methyl-coenzyme M reductase production,
as well as methanotrophic genes from CH
4
-oxidizing
bacteria. Metaproteomics can measure peptides
from highly abundant signature enzymes in soil
(Chourey et al., 2010), such as methyl-coenzyme M
reductase and CH
4
monooxygenase. This high-
Figure 1 Several Alaskan permafrost features that affect carbon cycling in northern circumpolar soils. (a) Low-centered polygonal
ground and thaw lakes from the North Slope; (b,c) polygonal tundra in Barrow; (d) thermokarst terrain in tussock tundra near
Council; (e) subsurface core section containing organic matter in permafrost from Fairbanks.
Commentary
710
The ISME Journal

resolution portrait will help determine how the CH
4
flux changes in response to permafrost thawing, new
SOM inputs and increased fermentation by other
community members.
Until recently, the high microbial diversity of
Arctic soils (Bartram et al., 2011) has hindered
metagenomic studies. New technologies produce
sequences on an unprecedented scale, at a fraction
of the traditional cost. Accordingly, the first meta-
genomic analyses of permafrost are now becoming
available. An analysis of one active layer soil
and two-meter deep permafrost sample from the
Canadian high Arctic identified signature genes for
hydrogenotrophic methanogenesis, CH
4
oxidation
by type I methanotrophs, nitrification and carbohy-
drate degradation (Yergeau et al., 2010). Microbial
abundances were 10–100 times lower in the perma-
frost than in the active layer sample, resulting in low
DNA yields and complicating the downstream
analysis. This report illustrates the feasibility and
challenges of large-scale comparative analyses
of metabolic potential in a complex permafrost
microbiome. To improve the analysis of permafrost
metagenomic data, more reference genome seque-
nces should be produced through parallel techniques,
such as genome sequencing of isolated or enriched
microbes and single-cell genome sequencing.
Eventually, microbial activities will dictate
whether permafrost environments will be a net
source or sink of GHG in the coming decades and
whether large-scale feedbacks to regional and global
climate will develop because of increased CO
2
,N
2
O
and CH
4
emissions and vegetation changes in
the Arctic. The new ‘omics’ techniques of metage-
nomics, metatranscriptomics, metaproteomics and
metabolomics are developing at an opportune time
to provide process-level insights to microbial com-
munities’ responses to rapidly changing environ-
ments. We need this mechanistic understanding to
extrapolate beyond observed events and conse-
quently improve our ability to predict and quantify
GHG flux from different permafrost ecosystems as a
result of global warming. Biomolecular evidence of
key processes in nitrogen and carbon cycling is
essential for prioritizing and interpreting geochem-
ical measurements and representing them in high-
resolution ecosystem models. These detailed mod-
els could in turn help parameterize global climate
models. As a scientific community, we advocate
coordination and integration of our microbiological
data with geochemical measurements to determine
the magnitude and impacts of warming in high
latitude, circumpolar permafrost systems.
Acknowledgements
We thank Diana Swantek for assistance preparing Figure 2
and Peter Thornton for helpful discussions. This work is
funded in part by the US Department of Energy, Office of
Science, Biological and Environmental Research (BER)
Program. Oak Ridge National Laboratory is managed by
UT Battelle, LLC under Contract No. DE-AC05-00OR22725
for the US Department of Energy. Additional support was
provided by the US Department of Energy under Contract
No. DE-AC02-05CH11231 with the Lawrence Berkeley
National Laboratory.
DE Graham, TA Vishnivetskaya, TJ Phelps and
DA Elias are at Biosciences Division, Oak Ridge
National Laboratory, Oak Ridge, TN, USA;
MD Wallenstein is at Natural Resource Ecology
Laboratory, Colorado State University,
Fort Collins, CO, USA;
TA Vishnivetskaya and SM Pfiffner are at Center for
Figure 2 Key biological processes in the carbon cycle of permafrost environments. Permafrost thawing at the transition zone introduces
previously unavailable organic matter into the expanded active layer of soil. Enzymatic hydrolysis decomposes complex organic matter
into soluble substrates for microbial fermentation, producing a mixture of organic acids, alcohols and microbial biomass. Methanogenic
archaea convert acetate, methylated compounds or H
2
and CO
2
into CH
4
that can be released to the atmosphere through ebullition,
diffusion or aerenchyma. Methanotrophs oxidize some of this CH
4
, converting it to CO
2
.
Commentary
711
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Environmental Biotechnology, The University of
Tennessee, Knoxville, TN, USA;
MP Waldrop is at United States Geological Survey,
Geologic Discipline, Menlo Park, CA, USA;
TC Onstott is at Department of Geosciences,
Princeton University, Princeton, NJ, USA;
LG Whyte is at Department of Natural Resource
Sciences, McGill University, Montre
´al,
Quebec, Canada;
EM Rivkina and DA Gilichinsky are at
Soil Cryology Laboratory,
Institute of Physicochemical and Biological
Problems in Soil Science, Russian Academy of
Sciences, Pushchino, Russia;
R Mackelprang and JK Jansson are at Department of
Energy, Joint Genome Institute,
Walnut Creek, CA, USA;
R Mackelprang is also at Department of
Biology, California State University Northridge,
Northridge, CA, USA;
NC VerBerkmoes and RL Hettich are at Chemical
Sciences Division, Oak Ridge National Laboratory,
Oak Ridge, TN, USA;
D Wagner is at Alfred Wegener Institute for Polar
and Marine Research, Research Unit Potsdam,
Potsdam, Germany;
SD Wullschleger is at Environmental Sciences
Division, Oak Ridge National Laboratory, Oak Ridge,
TN, USA and
JK Jansson is at Earth Sciences Division, Lawrence
Berkeley National Laboratory, Berkeley, CA, USA and
DoE Joint Bioenergy Institute, Emeryville,
CA, USA
E-mail: grahamde@ornl.gov
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