Institute of Physical-Chemical and Biological Problems in Soil Science

Permafrost warming has the potential to amplify global climate change, because when frozen sediments thaw it unlocks soil organic carbon. Yet to date, no globally consistent assessment of permafrost temperature change has been compiled. Here we use a global data set of permafrost temperature time series from the Global Terrestrial Network for Permafrost to evaluate temperature change across permafrost regions for the period since the International Polar Year (2007-2009). During the reference decade between 2007 and 2016, ground temperature near the depth of zero annual amplitude in the continuous permafrost zone increased by 0.39 ± 0.15 °C. Over the same period, discontinuous permafrost warmed by 0.20 ± 0.10 °C. Permafrost in mountains warmed by 0.19 ± 0.05 °C and in Antarctica by 0.37 ± 0.10 °C. Globally, permafrost temperature increased by 0.29 ± 0.12 °C. The observed trend follows the Arctic amplification of air temperature increase in the Northern Hemisphere. In the discontinuous zone, however, ground warming occurred due to increased snow thickness while air temperature remained statistically unchanged.

The increasing input of anthropogenically derived nitrogen (N) to ecosystems raises a crucial question: how does available N modify the decomposer community and thus affects the mineralization of soil organic matter (SOM). Moreover, N input modifies the priming effect (PE), that is, the effect of fresh organics on the microbial decomposition of SOM. We studied the interactive effects of C and N on SOM mineralization (by natural (13) C labelling adding C4 -sucrose or C4 -maize straw to C3 -soil) in relation to microbial growth kinetics and to the activities of five hydrolytic enzymes. This encompasses the groups of parameters governing two mechanisms of priming effects - microbial N mining and stoichiometric decomposition theories. In sole C treatments, positive PE was accompanied by a decrease in specific microbial growth rates, confirming a greater contribution of K-strategists to the decomposition of native SOM. Sucrose addition with N significantly accelerated mineralization of native SOM, whereas mineral N added with plant residues accelerated decomposition of plant residues. This supports the microbial mining theory in terms of N limitation. Sucrose addition with N was accompanied by accelerated microbial growth, increased activities of β-glucosidase and cellobiohydrolase, and decreased activities of xylanase and leucine amino peptidase. This indicated an increased contribution of r-strategists to the PE and to decomposition of cellulose but the decreased hemicellulolytic and proteolytic activities. Thus, the acceleration of the C cycle was primed by exogenous organic C and was controlled by N. This confirms the stoichiometric decomposition theory. Both K- and r-strategists were beneficial for priming effects, with an increasing contribution of K-selected species under N limitation. Thus, the priming phenomenon described in 'microbial N mining' theory can be ascribed to K-strategists. In contrast, 'stoichiometric decomposition' theory, that is, accelerated OM mineralization due to balanced microbial growth, is explained by domination of r-strategists.

Genetic analyses of permafrost and temperate sediments reveal that plant and animal DNA may be preserved for long periods, even in the absence of obvious macrofossils. In Siberia, five permafrost cores ranging from 400,000 to 10,000 years old contained at least 19 different plant taxa, including the oldest authenticated ancient DNA sequences known, and megafaunal sequences including mammoth, bison, and horse. The genetic data record a number of dramatic changes in the taxonomic diversity and composition of Beringian vegetation and fauna. Temperate cave sediments in New Zealand also yielded DNA sequences of extinct biota, including two species of ratite moa, and 29 plant taxa characteristic of the prehuman environment. Therefore, many sedimentary deposits may contain unique, and widespread, genetic records of paleoenvironments.

Abstract The results of the International Permafrost Association's International Polar Year Thermal State of Permafrost (TSP) project are presented based on field measurements from Russia during the IPY years (2007–09) and collected historical data. Most ground temperatures measured in existing and new boreholes show a substantial warming during the last 20 to 30 years. The magnitude of the warming varied with location, but was typically from 0.5°C to 2°C at the depth of zero annual amplitude. Thawing of Little Ice Age permafrost is ongoing at many locations. There are some indications that the late Holocene permafrost has begun to thaw at some undisturbed locations in northeastern Europe and northwest Siberia. Thawing of permafrost is most noticeable within the discontinuous permafrost domain. However, permafrost in Russia is also starting to thaw at some limited locations in the continuous permafrost zone. As a result, a northward displacement of the boundary between continuous and discontinuous permafrost zones was observed. This data set will serve as a baseline against which to measure changes of near‐surface permafrost temperatures and permafrost boundaries, to validate climate model scenarios, and for temperature reanalysis. Copyright © 2010 John Wiley & Sons, Ltd.

Significance Giant DNA viruses are visible under a light microscope and their genomes encode more proteins than some bacteria or intracellular parasitic eukaryotes. There are two very distinct types and infect unicellular protists such as Acanthamoeba . On one hand, Megaviridae possess large pseudoicosahedral capsids enclosing a megabase-sized adenine–thymine-rich genome, and on the other, the recently discovered Pandoraviruses exhibit micron-sized amphora-shaped particles and guanine–cytosine-rich genomes of up to 2.8 Mb. While initiating a survey of the Siberian permafrost, we isolated a third type of giant virus combining the Pandoravirus morphology with a gene content more similar to that of icosahedral DNA viruses. This suggests that pandoravirus-like particles may correspond to an unexplored diversity of unconventional DNA virus families.

Abstract Temperature sensitivity (Q 10 ) of soil organic matter (SOM) decomposition is a crucial parameter to predict the fate of soil carbon (C) under global warming. Nonetheless, the response pattern of Q 10 to continuous warming and the underlying mechanisms are still under debate, especially considering the complex interactions between Q 10 , SOM quality, and soil microorganisms. We examined the Q 10 of SOM decomposition across a mean annual temperature (MAT) gradient from −1.9 to 5.1°C in temperate mixed forest ecosystems in parallel with SOM quality and bioavailability, microbial taxonomic composition, and functional genes responsible for organic carbon decomposition. Within this temperature gradient of 7.0°C, the Q 10 values increased with MAT, but decreased with SOM bioavailability. The Q 10 values increased with the prevalence of K‐strategy of soil microbial community, which was characterized by: (i) high ratios of oligotrophic to copiotrophic taxa, (ii) ectomycorrhizal to saprotrophic fungi, (iii) functional genes responsible for degradation of recalcitrant to that of labile C, and (iv) low average 16S rRNA operon copy number. Because the recalcitrant organic matter was mainly utilized by the K‐strategists, these findings independently support the carbon quality‐temperature theory from the perspective of microbial taxonomic composition and functions. A year‐long incubation experiment was performed to determine the response of labile and recalcitrant C pools to warming based on the two‐pool model. The decomposition of recalcitrant SOM was more sensitive to increased temperature in southern warm regions, which might attribute to the dominance of K‐selected microbial communities. It implies that climate warming would mobilize the larger recalcitrant pools in warm regions, exacerbating the positive feedback between increased MAT and CO 2 efflux. This is the first attempt to link temperature sensitivity of SOM decomposition with microbial eco‐strategies by incorporating the genetic information and disentangling the complex relationship between Q 10 and soil microorganisms.

Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.

Large stocks of soil organic carbon (SOC) have accumulated in the Northern Hemisphere permafrost region, but their current amounts and future fate remain uncertain. By analyzing dataset combining >2700 soil profiles with environmental variables in a geospatial framework, we generated spatially explicit estimates of permafrost-region SOC stocks, quantified spatial heterogeneity, and identified key environmental predictors. We estimated that Pg C are stored in the top 3 m of permafrost region soils. The greatest uncertainties occurred in circumpolar toe-slope positions and in flat areas of the Tibetan region. We found that soil wetness index and elevation are the dominant topographic controllers and surface air temperature (circumpolar region) and precipitation (Tibetan region) are significant climatic controllers of SOC stocks. Our results provide first high-resolution geospatial assessment of permafrost region SOC stocks and their relationships with environmental factors, which are crucial for modeling the response of permafrost affected soils to changing climate.

Changes in active layer thickness (ALT) over northern high‐latitude permafrost regions have important impacts on the surface energy balance, hydrologic cycle, carbon exchange between the atmosphere and the land surface, plant growth, and ecosystems as a whole. This study examines the 20th century variations of ALT for the Ob, Yenisey, and Lena River basins. ALT is estimated from historical soil temperature measurements from 17 stations (1956–1990, Lena basin only), an annual thawing index based on both surface air temperature data (1901–2002) and numerical modeling (1980–2002). The latter two provide spatial fields. Based on the thawing index, the long‐term average (1961–1990) ALT is about 1.87 m in the Ob, 1.67 in the Yenisey, and 1.69 m in the Lena basin. Over the past several decades, ALT over the three basins shows positive trends, but with different magnitudes. Based on the 17 stations, ALT increased about 0.32 m between 1956 and 1990 in the Lena. To the extent that results based on the soil temperatures represent ground “truth,” ALT obtained from both the thawing index and numerical modeling is underestimated. It is widely believed that ALT will increase with global warming. However, this hypothesis needs further refinement since ALT responds primarily to summer air temperature while observed warming has occurred mainly in winter and spring. It is also shown that ALT exhibits complex and inconsistent responses to variations in snow cover.

Permafrost is a distinct feature of the terrestrial Arctic and is vulnerable to climate warming. Permafrost degrades in different ways, including deepening of a seasonally unfrozen surface and localized but rapid development of deep thaw features. Pleistocene ice-rich permafrost with syngenetic ice-wedges, termed Yedoma deposits, are widespread in Siberia, Alaska, and Yukon, Canada and may be especially prone to rapid-thaw processes. Freeze-locked organic matter in such deposits can be re-mobilized on short time-scales and contribute to a carbon-cycle climate feedback. Here we synthesize the characteristics and vulnerability of Yedoma deposits by synthesizing studies on the Yedoma origin and the associated organic carbon pool. We suggest that Yedoma deposits accumulated under periglacial weathering, transport, and deposition dynamics in non-glaciated regions during the late Pleistocene until the beginning of late glacial warming. The deposits formed due to a combination of aeolian, colluvial, nival, and alluvial deposition and simultaneous ground ice accumulation. We found up to 130gigatons organic carbon in Yedoma, parts of which are well-preserved and available for fast decomposition after thaw. Based on incubation experiments, up to 10 of the Yedoma carbon is considered especially decomposable and may be released upon thaw. The substantial amount of ground ice in Yedoma makes it highly vulnerable to disturbances such as thermokarst and thermo-erosion processes. Mobilization of permafrost carbon is expected to increase under future climate warming. Our synthesis results underline the need of accounting for Yedoma carbon stocks in next generation Earth-System-Models for a more complete representation of the permafrost-carbon feedback.

. Well-recognized approaches for soil C accretion include reducing soil disturbance, increasing plant biomass inputs, and enhancing plant diversity. Yet experimental evidence often fails to support anticipated C gains, suggesting that our integrated understanding of soil C accretion remains insufficient. Here we use a unique combination of X-ray micro-tomography and micro-scale enzyme mapping to demonstrate for the first time that plant-stimulated soil pore formation appears to be a major, hitherto unrecognized, determinant of whether new C inputs are stored or lost to the atmosphere. Unlike monocultures, diverse plant communities favor the development of 30-150 µm pores. Such pores are the micro-environments associated with higher enzyme activities, and greater abundance of such pores translates into a greater spatial footprint that microorganisms make on the soil and consequently soil C storage capacity.

The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling.

Seasonal freezing and thawing processes in cold regions play a major role in ecosystem diversity, productivity, and the Arctic hydrological system. Long‐term changes in seasonal freeze and thaw depths are also important indicators of climate change. Only sparse historical measurements of seasonal freeze and thaw depths are available for permafrost and seasonally frozen ground regions. Using mean monthly soil temperature data for 1930–1990 for 242 stations located throughout Russia, we employed a linear interpolation method to determine the depth of the 0°C isotherm based on soil temperature data measured between 0.2 m and 3.2 m depth. The relationship between available observed annual maximum freeze and thaw depths and our interpolated values indicates a perfect correlation. A comprehensive evaluation of long‐term trends in these new interpolated data for Russia indicates that in permafrost regions, active layer depths have been steadily increasing. In the period 1956–1990 the active layer exhibited a statistically significant deepening by approximately 20 cm. The changes in the seasonally frozen ground areas are even greater: The depth of the freezing layer decreased 34 cm between 1956 and 1990. Potential forcings of the observed changes include air temperature, freezing and thawing index, and snow depth. Correlation and multiple regression reveal that active layer depth is most strongly related to snow depth. Air temperature, both mean annual and thawing index, is also significantly related to changes in the active layer. Freeze depth is influenced most strongly by the freezing index and mean annual air temperature, although snow depth is also a significant contributor. Air temperature and snow depth have been changing less in the seasonally frozen ground regions of Russia compared to permafrost regions, although observed changes in freeze depth are greater than changes in active layer depth for 1930–1990. This indicates that the seasonally frozen ground regions of the Russian high latitudes are more susceptible to climate change than the Russian permafrost. However, as temperatures have been rising, especially in the high‐latitude continental regions, both permafrost and seasonally frozen ground regions are being greatly impacted. These changes can potentially result in increased river runoff and changes in discharge throughout the Russian Arctic drainage basin, as well as changes in high‐latitude ecosystems.

Recent claims of cultivable ancient bacteria within sealed environments highlight our limited understanding of the mechanisms behind long-term cell survival. It remains unclear how dormancy, a favored explanation for extended cellular persistence, can cope with spontaneous genomic decay over geological timescales. There has been no direct evidence in ancient microbes for the most likely mechanism, active DNA repair, or for the metabolic activity necessary to sustain it. In this paper, we couple PCR and enzymatic treatment of DNA with direct respiration measurements to investigate long-term survival of bacteria sealed in frozen conditions for up to one million years. Our results show evidence of bacterial survival in samples up to half a million years in age, making this the oldest independently authenticated DNA to date obtained from viable cells. Additionally, we find strong evidence that this long-term survival is closely tied to cellular metabolic activity and DNA repair that over time proves to be superior to dormancy as a mechanism in sustaining bacteria viability.

Input of labile carbon may accelerate the decomposition of existing soil organic matter (priming effect), with the priming intensity depending on changes in soil nitrogen availability after permafrost thaw. However, experimental evidence for the linkage between the priming effect and post-thaw nitrogen availability is unavailable. Here we test the hypothesis that elevated nitrogen availability after permafrost collapse inhibits the priming effect by increasing microbial metabolic efficiency based on a combination of thermokarst-induced natural nitrogen gradient and nitrogen addition experiment. We find a negative correlation between the priming intensity and soil total dissolved nitrogen concentration along the thaw sequence. The negative effect is confirmed by the reduced priming effect after nitrogen addition. In contrast to the prevailing view, this nitrogen-regulated priming intensity is independent of extracellular enzyme activities but associated with microbial metabolic efficiency. These findings demonstrate that post-thaw nitrogen availability regulates topsoil carbon dynamics through its modification of microbial metabolic efficiency.

Acanthamoeba species are infected by the largest known DNA viruses. These include icosahedral Mimiviruses, amphora-shaped Pandoraviruses, and Pithovirus sibericum, the latter one isolated from 30,000-y-old permafrost. Mollivirus sibericum, a fourth type of giant virus, was isolated from the same permafrost sample. Its approximately spherical virion (0.6-µm diameter) encloses a 651-kb GC-rich genome encoding 523 proteins of which 64% are ORFans; 16% have their closest homolog in Pandoraviruses and 10% in Acanthamoeba castellanii probably through horizontal gene transfer. The Mollivirus nucleocytoplasmic replication cycle was analyzed using a combination of "omic" approaches that revealed how the virus highjacks its host machinery to actively replicate. Surprisingly, the host's ribosomal proteins are packaged in the virion. Metagenomic analysis of the permafrost sample uncovered the presence of both viruses, yet in very low amount. The fact that two different viruses retain their infectivity in prehistorical permafrost layers should be of concern in a context of global warming. Giant viruses' diversity remains to be fully explored.

Antarctic permafrost soils have not received as much geocryological and biological study as has been devoted to the ice sheet, though the permafrost is more stable and older and inhabited by more microbes. This makes these soils potentially more informative and a more significant microbial repository than ice sheets. Due to the stability of the subsurface physicochemical regime, Antarctic permafrost is not an extreme environment but a balanced natural one. Up to 10(4) viable cells/g, whose age presumably corresponds to the longevity of the permanently frozen state of the sediments, have been isolated from Antarctic permafrost. Along with the microbes, metabolic by-products are preserved. This presumed natural cryopreservation makes it possible to observe what may be the oldest microbial communities on Earth. Here, we describe the Antarctic permafrost habitat and biodiversity and provide a model for martian ecosystems.

Deep subterranean layers may be regarded as the most stable environment for microorganisms where possible fluctuations should be explained by geological events only. The analysis of the total amount of microorganisms has revealed that in sedimentary deposits their number is only one order of magnitude lower than the same parameter in soil. Taking into account the depth of sediments the microbial biomass in subterranean rocks has to be considerably larger than that in soils. Permafrost is the most constant and stable environment among deep habitats. Microbial communities survive in permafrost for at least some millions of years. The diversity of organisms and of microbial activities after permafrost thawing displays distinct differences to those in soils. The abundance of the bacterial biomass assumed is comparable in frozen and unfrozen sediments. Therefore, the permanently low temperature in permafrost is a stabilizing factor that sustains life in deep cold biotopes. Studies of microbial communities in permafrost sediments of different lithology and age suggest that the level of subzero temperature and the duration of its influence define the ratio between the hypometabolic cells, readily reversible to proliferation, and the so-called viable but non-culturable cells (deep resting cells). To a certain extent, cell aggregates in the extracellular matrix may be regarded as an additional survival mechanism supporting the hypometabolic state of cells. There is indirect evidence for adaptive physiological and biochemical processes in microorganisms during the long-term impact of cold.

Abstract Partitioning the root‐derived CO 2 efflux from soil (frequently termed rhizosphere respiration) into actual root respiration (RR, respiration by autotrophs) and rhizomicrobial respiration (RMR, respiration by heterotrophs) is crucial in determining the carbon (C) and energy balance of plants and soils. It is also essential in quantifying C sources for rhizosphere microorganisms and in estimation of the C contributing to turnover of soil organic matter (SOM), as well as in linking net ecosystem production (NEP) and net ecosystem exchange (NEE). Artificial‐environment studies such as hydroponics or sterile soils yield unrealistic C‐partitioning values and are unsuitable for predicting C flows under natural conditions. To date, several methods have been suggested to separate RR and RMR in nonsterile soils: 1) component integration, 2) substrate‐induced respiration, 3) respiration by excised roots, 4) comparison of root‐derived 14 CO 2 with rhizomicrobial 14 CO 2 after continuous labeling, 5) isotope dilution, 6) model‐rhizodeposition technique, 7) modeling of 14 CO 2 efflux dynamics, 8) exudate elution, and 9) δ 13 C of CO 2 and microbial biomass. This review describes the basic principles and assumptions of these methods and compares the results obtained in the original papers and in studies designed to compare the methods. The component‐integration method leads to strong disturbance and non‐proportional increase of CO 2 efflux from different sources. Four of the methods (5 to 8) are based on the pulse labeling of shoots in a 14 CO 2 atmosphere and subsequent monitoring of 14 CO 2 efflux from the soil. The model‐rhizodeposition technique and exudate‐elution procedure strongly overestimate RR and underestimate RMR. Despite alternative assumptions, isotope dilution and modeling of 14 CO 2 ‐efflux dynamics yield similar results. In crops and grasses (wheat, ryegrass, barley, buckwheat, maize, meadow fescue, prairie grasses), RR amounts on average to 48±5% and RMR to 52±5% of root‐derived CO 2 . The method based on the 13 C isotopic signature of CO 2 and microbial biomass is the most promising approach, especially when the plants are continuously labeled in 13 CO 2 or 14 CO 2 atmosphere. The “difference” methods, i.e. , trenching, tree girdling, root‐exclusion techniques, etc., are not suitable for separating the respiration by autotrophic and heterotrophic organisms because the difference methods neglect the importance of microbial respiration of rhizodeposits.

Plant-microbial interactions alter C and N balance in the rhizosphere and affect the microbial carbon use efficiency (CUE)-the fundamental characteristic of microbial metabolism. Estimation of CUE in microbial hotspots with high dynamics of activity and changes of microbial physiological state from dormancy to activity is a challenge in soil microbiology. We analyzed respiratory activity, microbial DNA content and CUE by manipulation the C and nutrients availability in the soil under Beta vulgaris. All measurements were done in root-free and rhizosphere soil under steady-state conditions and during microbial growth induced by addition of glucose. Microorganisms in the rhizosphere and root-free soil differed in their CUE dynamics due to varying time delays between respiration burst and DNA increase. Constant CUE in an exponentially-growing microbial community in rhizosphere demonstrated the balanced growth. In contrast, the CUE in the root-free soil increased more than three times at the end of exponential growth and was 1.5 times higher than in the rhizosphere. Plants alter the dynamics of microbial CUE by balancing the catabolic and anabolic processes, which were decoupled in the root-free soil. The effects of N and C availability on CUE in rhizosphere and root-free soil are discussed.