Long-term warming restructures Arctic tundra without changing net soil carbon storage.

High latitudes contain nearly half of global soil carbon, prompting interest in understanding how the Arctic terrestrial carbon balance will respond to rising temperatures. Low temperatures suppress the activity of soil biota, retarding decomposition and nitrogen release, which limits plant and microbial growth. Warming initially accelerates decomposition, increasing nitrogen availability, productivity and woody-plant dominance. However, these responses may be transitory, because coupled abiotic-biotic feedback loops that alter soil-temperature dynamics and change the structure and activity of soil communities, can develop. Here we report the results of a two-decade summer warming experiment in an Alaskan tundra ecosystem. Warming increased plant biomass and woody dominance, indirectly increased winter soil temperature, homogenized the soil trophic structure across horizons and suppressed surface-soil-decomposer activity, but did not change total soil carbon or nitrogen stocks, thereby increasing net ecosystem carbon storage. Notably, the strongest effects were in the mineral horizon, where warming increased decomposer activity and carbon stock: a 'biotic awakening' at depth.

Surprisingly complex community discovered in the mid-Devonian fossil forest at Gilboa.

The origin of trees by the mid-Devonian epoch (398-385 million years ago) signals a major change in terrestrial ecosystems with potential long-term consequences including increased weathering, drop in atmospheric CO(2), modified climate, changes in sedimentation patterns and mass extinction. However, little is known about the ecology of early forests or how changes in early terrestrial ecosystems influenced global processes. One of the most famous palaeontological records for this time is the 'oldest fossil forest' at Riverside Quarry, Gilboa, New York, USA, discovered in the 1920s. Hundreds of large Eospermatopteris sandstone casts, now thought to represent the bases of standing cladoxylopsid trees, were recovered from a horizon that was originally interpreted as a muddy swamp. After quarry operations ceased, relatively minor outcrops of similar fossils at nearby localities have provided limited opportunities to evaluate this pervasive view using modern methods. In 2010, removal of the quarry backfill enabled reappraisal of the palaeoecology of this important site. Here we describe a 1,200 m(2) map showing numerous Eospermatopteris root systems in life position within a mixed-age stand of trees. Unexpectedly, large woody rhizomes with adventitious roots and aerial branch systems identified as aneurophytalean progymnosperms run between, and probably climb into, Eospermatopteris trees. We describe the overall habit for these surprisingly large aneurophytaleans, the earliest fossil group having wood produced by a bifacial vascular cambium. The site also provides evidence for arborescence within lycopsids, extending the North American range for trees in this ecologically critical group. The rooting horizon is a dark grey sandy mudstone showing limited root penetration. Although clearly belonging to a wetland coastal plain environment, the forest was probably limited in duration and subject to periodic disturbance. These observations provide fundamental clarification of the palaeoecology of this mixed-group early forest, with important implications for interpreting coeval assemblage data worldwide.

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota.

The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on Earth. Notably, soil bacteria are able to multiply inside roots as benign endophytes and modulate plant growth and development, with implications ranging from enhanced crop productivity to phytoremediation. Endophytic colonization represents an apparent paradox of plant innate immunity because plant cells can detect an array of microbe-associated molecular patterns (also known as MAMPs) to initiate immune responses to terminate microbial multiplication. Several studies attempted to describe the structure of bacterial root endophytes; however, different sampling protocols and low-resolution profiling methods make it difficult to infer general principles. Here we describe methodology to characterize and compare soil- and root-inhabiting bacterial communities, which reveals not only a function for metabolically active plant cells but also for inert cell-wall features in the selection of soil bacteria for host colonization. We show that the roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family. Soil type defines the composition of root-inhabiting bacterial communities and host genotype determines their ribotype profiles to a limited extent. The identification of soil-type-specific members within the root-inhabiting assemblies supports our conclusion that these represent soil-derived root endophytes. Surprisingly, plant cell-wall features of other tested plant species seem to provide a sufficient cue for the assembly of approximately 40% of the Arabidopsis bacterial root-inhabiting microbiota, with a bias for Betaproteobacteria. Thus, this root sub-community may not be Arabidopsis-specific but saprophytic bacteria that would naturally be found on any plant root or plant debris in the tested soils. By contrast, colonization of Arabidopsis roots by members of the Actinobacteria depends on other cues from metabolically active host cells.

Comparing the yields of organic and conventional agriculture.

Numerous reports have emphasized the need for major changes in the global food system: agriculture must meet the twin challenge of feeding a growing population, with rising demand for meat and high-calorie diets, while simultaneously minimizing its global environmental impacts. Organic farming­a system aimed at producing food with minimal harm to ecosystems, animals or humans­is often proposed as a solution. However, critics argue that organic agriculture may have lower yields and would therefore need more land to produce the same amount of food as conventional farms, resulting in more widespread deforestation and biodiversity loss, and thus undermining the environmental benefits of organic practices. Here we use a comprehensive meta-analysis to examine the relative yield performance of organic and conventional farming systems globally. Our analysis of available data shows that, overall, organic yields are typically lower than conventional yields. But these yield differences are highly contextual, depending on system and site characteristics, and range from 5% lower organic yields (rain-fed legumes and perennials on weak-acidic to weak-alkaline soils), 13% lower yields (when best organic practices are used), to 34% lower yields (when the conventional and organic systems are most comparable). Under certain conditions­that is, with good management practices, particular crop types and growing conditions­organic systems can thus nearly match conventional yields, whereas under others it at present cannot. To establish organic agriculture as an important tool in sustainable food production, the factors limiting organic yields need to be more fully understood, alongside assessments of the many social, environmental and economic benefits of organic farming systems.

Lowland-upland migration of sauropod dinosaurs during the Late Jurassic epoch.

Sauropod dinosaurs were the largest vertebrates ever to walk the Earth, and as mega-herbivores they were important parts of terrestrial ecosystems. In the Late Jurassic-aged Morrison depositional basin of western North America, these animals occupied lowland river-floodplain settings characterized by a seasonally dry climate. Massive herbivores with high nutritional and water needs could periodically experience nutritional and water stress under these conditions, and thus the common occurrence of sauropods in this basin has remained a paradox. Energetic arguments and mammalian analogues have been used to suggest that migration allowed sauropods access to food and water resources over a wide region or during times of drought or both, but there has been no direct support for these hypotheses. Here we compare oxygen isotope ratios (δ(18)O) of tooth-enamel carbonate from the sauropod Camarasaurus with those of ancient soil, lake and wetland (that is, 'authigenic') carbonates that formed in lowland settings. We demonstrate that certain populations of these animals did in fact undertake seasonal migrations of several hundred kilometres from lowland to upland environments. This ability to describe patterns of sauropod movement will help to elucidate the role that migration played in the ecology and evolution of gigantism of these and associated dinosaurs.

Increased soil emissions of potent greenhouse gases under increased atmospheric CO2.

Increasing concentrations of atmospheric carbon dioxide (CO(2)) can affect biotic and abiotic conditions in soil, such as microbial activity and water content. In turn, these changes might be expected to alter the production and consumption of the important greenhouse gases nitrous oxide (N(2)O) and methane (CH(4)) (refs 2, 3). However, studies on fluxes of N(2)O and CH(4) from soil under increased atmospheric CO(2) have not been quantitatively synthesized. Here we show, using meta-analysis, that increased CO(2) (ranging from 463 to 780 parts per million by volume) stimulates both N(2)O emissions from upland soils and CH(4) emissions from rice paddies and natural wetlands. Because enhanced greenhouse-gas emissions add to the radiative forcing of terrestrial ecosystems, these emissions are expected to negate at least 16.6 per cent of the climate change mitigation potential previously predicted from an increase in the terrestrial carbon sink under increased atmospheric CO(2) concentrations. Our results therefore suggest that the capacity of land ecosystems to slow climate warming has been overestimated.

Interannual variability in the oxygen isotopes of atmospheric CO2 driven by El Niño.

The stable isotope ratios of atmospheric CO(2) ((18)O/(16)O and (13)C/(12)C) have been monitored since 1977 to improve our understanding of the global carbon cycle, because biosphere-atmosphere exchange fluxes affect the different atomic masses in a measurable way. Interpreting the (18)O/(16)O variability has proved difficult, however, because oxygen isotopes in CO(2) are influenced by both the carbon cycle and the water cycle. Previous attention focused on the decreasing (18)O/(16)O ratio in the 1990s, observed by the global Cooperative Air Sampling Network of the US National Oceanic and Atmospheric Administration Earth System Research Laboratory. This decrease was attributed variously to a number of processes including an increase in Northern Hemisphere soil respiration; a global increase in C(4) crops at the expense of C(3) forests; and environmental conditions, such as atmospheric turbulence and solar radiation, that affect CO(2) exchange between leaves and the atmosphere. Here we present 30 years' worth of data on (18)O/(16)O in CO(2) from the Scripps Institution of Oceanography global flask network and show that the interannual variability is strongly related to the El Niño/Southern Oscillation. We suggest that the redistribution of moisture and rainfall in the tropics during an El Niño increases the (18)O/(16)O ratio of precipitation and plant water, and that this signal is then passed on to atmospheric CO(2) by biosphere-atmosphere gas exchange. We show how the decay time of the El Niño anomaly in this data set can be useful in constraining global gross primary production. Our analysis shows a rapid recovery from El Niño events, implying a shorter cycling time of CO(2) with respect to the terrestrial biosphere and oceans than previously estimated. Our analysis suggests that current estimates of global gross primary production, of 120 petagrams of carbon per year, may be too low, and that a best guess of 150-175 petagrams of carbon per year better reflects the observed rapid cycling of CO(2). Although still tentative, such a revision would present a new benchmark by which to evaluate global biospheric carbon cycling models.

Temperature-associated increases in the global soil respiration record.

Soil respiration, R(S), the flux of microbially and plant-respired carbon dioxide (CO(2)) from the soil surface to the atmosphere, is the second-largest terrestrial carbon flux. However, the dynamics of R(S) are not well understood and the global flux remains poorly constrained. Ecosystem warming experiments, modelling analyses and fundamental biokinetics all suggest that R(S) should change with climate. This has been difficult to confirm observationally because of the high spatial variability of R(S), inaccessibility of the soil medium and the inability of remote-sensing instruments to measure R(S) on large scales. Despite these constraints, it may be possible to discern climate-driven changes in regional or global R(S) values in the extant four-decade record of R(S) chamber measurements. Here we construct a database of worldwide R(S) observations matched with high-resolution historical climate data and find a previously unknown temporal trend in the R(S) record after accounting for mean annual climate, leaf area, nitrogen deposition and changes in CO(2) measurement technique. We find that the air temperature anomaly (the deviation from the 1961-1990 mean) is significantly and positively correlated with changes in R(S). We estimate that the global R(S) in 2008 (that is, the flux integrated over the Earth's land surface over 2008) was 98 +/- 12 Pg C and that it increased by 0.1 Pg C yr(-1) between 1989 and 2008, implying a global R(S) response to air temperature (Q(10)) of 1.5. An increasing global R(S) value does not necessarily constitute a positive feedback to the atmosphere, as it could be driven by higher carbon inputs to soil rather than by mobilization of stored older carbon. The available data are, however, consistent with an acceleration of the terrestrial carbon cycle in response to global climate change.

Recent decline in the global land evapotranspiration trend due to limited moisture supply.

More than half of the solar energy absorbed by land surfaces is currently used to evaporate water. Climate change is expected to intensify the hydrological cycle and to alter evapotranspiration, with implications for ecosystem services and feedback to regional and global climate. Evapotranspiration changes may already be under way, but direct observational constraints are lacking at the global scale. Until such evidence is available, changes in the water cycle on land−a key diagnostic criterion of the effects of climate change and variability−remain uncertain. Here we provide a data-driven estimate of global land evapotranspiration from 1982 to 2008, compiled using a global monitoring network, meteorological and remote-sensing observations, and a machine-learning algorithm. In addition, we have assessed evapotranspiration variations over the same time period using an ensemble of process-based land-surface models. Our results suggest that global annual evapotranspiration increased on average by 7.1 ± 1.0 millimetres per year per decade from 1982 to 1997. After that, coincident with the last major El Niño event in 1998, the global evapotranspiration increase seems to have ceased until 2008. This change was driven primarily by moisture limitation in the Southern Hemisphere, particularly Africa and Australia. In these regions, microwave satellite observations indicate that soil moisture decreased from 1998 to 2008. Hence, increasing soil-moisture limitations on evapotranspiration largely explain the recent decline of the global land-evapotranspiration trend. Whether the changing behaviour of evapotranspiration is representative of natural climate variability or reflects a more permanent reorganization of the land water cycle is a key question for earth system science.

Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest.

The accumulation of species-specific enemies around adults is hypothesized to maintain plant diversity by limiting the recruitment of conspecific seedlings relative to heterospecific seedlings. Although previous studies in forested ecosystems have documented patterns consistent with the process of negative feedback, these studies are unable to address which classes of enemies (for example, pathogens, invertebrates, mammals) exhibit species-specific effects strong enough to generate negative feedback, and whether negative feedback at the level of the individual tree is sufficient to influence community-wide forest composition. Here we use fully reciprocal shade-house and field experiments to test whether the performance of conspecific tree seedlings (relative to heterospecific seedlings) is reduced when grown in the presence of enemies associated with adult trees. Both experiments provide strong evidence for negative plant-soil feedback mediated by soil biota. In contrast, above-ground enemies (mammals, foliar herbivores and foliar pathogens) contributed little to negative feedback observed in the field. In both experiments, we found that tree species that showed stronger negative feedback were less common as adults in the forest community, indicating that susceptibility to soil biota may determine species relative abundance in these tropical forests. Finally, our simulation models confirm that the strength of local negative feedback that we measured is sufficient to produce the observed community-wide patterns in tree-species relative abundance. Our findings indicate that plant-soil feedback is an important mechanism that can maintain species diversity and explain patterns of tree-species relative abundance in tropical forests.

Ecosystem response to elevated CO(2) levels limited by nitrogen-induced plant species shift.

Terrestrial ecosystems gain carbon through photosynthesis and lose it mostly in the form of carbon dioxide (CO(2)). The extent to which the biosphere can act as a buffer against rising atmospheric CO(2) concentration in global climate change projections remains uncertain at the present stage. Biogeochemical theory predicts that soil nitrogen (N) scarcity may limit natural ecosystem response to elevated CO(2) concentration, diminishing the CO(2)-fertilization effect on terrestrial plant productivity in unmanaged ecosystems. Recent models have incorporated such carbon-nitrogen interactions and suggest that anthropogenic N sources could help sustain the future CO(2)-fertilization effect. However, conclusive demonstration that added N enhances plant productivity in response to CO(2)-fertilization in natural ecosystems remains elusive. Here we manipulated atmospheric CO(2) concentration and soil N availability in a herbaceous brackish wetland where plant community composition is dominated by a C(3) sedge and C(4) grasses, and is capable of responding rapidly to environmental change. We found that N addition enhanced the CO(2)-stimulation of plant productivity in the first year of a multi-year experiment, indicating N-limitation of the CO(2) response. But we also found that N addition strongly promotes the encroachment of C(4) plant species that respond less strongly to elevated CO(2) concentrations. Overall, we found that the observed shift in the plant community composition ultimately suppresses the CO(2)-stimulation of plant productivity by the third and fourth years. Although extensive research has shown that global change factors such as elevated CO(2) concentrations and N pollution affect plant species differently and that they may drive plant community changes, we demonstrate that plant community shifts can act as a feedback effect that alters the whole ecosystem response to elevated CO(2) concentrations. Moreover, we suggest that trade-offs between the abilities of plant taxa to respond positively to different perturbations may constrain natural ecosystem response to global change.

Stoichiometric control of organic carbon-nitrate relationships from soils to the sea.

The production of artificial fertilizers, fossil fuel use and leguminous agriculture worldwide has increased the amount of reactive nitrogen in the natural environment by an order of magnitude since the Industrial Revolution. This reorganization of the nitrogen cycle has led to an increase in food production, but increasingly causes a number of environmental problems. One such problem is the accumulation of nitrate in both freshwater and coastal marine ecosystems. Here we establish that ecosystem nitrate accrual exhibits consistent and negative nonlinear correlations with organic carbon availability along a hydrologic continuum from soils, through freshwater systems and coastal margins, to the open ocean. The trend also prevails in ecosystems subject to substantial human alteration. Across this diversity of environments, we find evidence that resource stoichiometry (organic carbon:nitrate) strongly influences nitrate accumulation by regulating a suite of microbial processes that couple dissolved organic carbon and nitrate cycling. With the help of a meta-analysis we show that heterotrophic microbes maintain low nitrate concentrations when organic carbon:nitrate ratios match the stoichiometric demands of microbial anabolism. When resource ratios drop below the minimum carbon:nitrogen ratio of microbial biomass, however, the onset of carbon limitation appears to drive rapid nitrate accrual, which may then be further enhanced by nitrification. At low organic carbon:nitrate ratios, denitrification appears to constrain the extent of nitrate accretion, once organic carbon and nitrate availability approach the 1:1 stoichiometry of this catabolic process. Collectively, these microbial processes express themselves on local to global scales by restricting the threshold ratios underlying nitrate accrual to a constrained stoichiometric window. Our findings indicate that ecological stoichiometry can help explain the fate of nitrate across disparate environments and in the face of human disturbance.

Grazing-induced reduction of natural nitrous oxide release from continental steppe.

Atmospheric concentrations of the greenhouse gas nitrous oxide (N(2)O) have increased significantly since pre-industrial times owing to anthropogenic perturbation of the global nitrogen cycle, with animal production being one of the main contributors. Grasslands cover about 20 per cent of the temperate land surface of the Earth and are widely used as pasture. It has been suggested that high animal stocking rates and the resulting elevated nitrogen input increase N(2)O emissions. Internationally agreed methods to upscale the effect of increased livestock numbers on N(2)O emissions are based directly on per capita nitrogen inputs. However, measurements of grassland N(2)O fluxes are often performed over short time periods, with low time resolution and mostly during the growing season. In consequence, our understanding of the daily and seasonal dynamics of grassland N(2)O fluxes remains limited. Here we report year-round N(2)O flux measurements with high and low temporal resolution at ten steppe grassland sites in Inner Mongolia, China. We show that short-lived pulses of N(2)O emission during spring thaw dominate the annual N(2)O budget at our study sites. The N(2)O emission pulses are highest in ungrazed steppe and decrease with increasing stocking rate, suggesting that grazing decreases rather than increases N(2)O emissions. Our results show that the stimulatory effect of higher stocking rates on nitrogen cycling and, hence, on N(2)O emission is more than offset by the effects of a parallel reduction in microbial biomass, inorganic nitrogen production and wintertime water retention. By neglecting these freeze-thaw interactions, existing approaches may have systematically overestimated N(2)O emissions over the last century for semi-arid, cool temperate grasslands by up to 72 per cent.

Anticipating land surface change.

The interplay of human actions and natural processes over varied spatial and temporal scales can result in abrupt transitions between contrasting land surface states. Understanding these transitions is a key goal of sustainability science because they can represent abrupt losses of natural capital. This paper recognizes flickering between alternate land surface states in advance of threshold change and critical slowing down in advance of both threshold changes and noncritical transformation. The early warning signals we observe are rises in autocorrelation, variance, and skewness within millimeter-resolution thickness measurements of tephra layers deposited in A.D. 2010 and A.D. 2011. These signals reflect changing patterns of surface vegetation, which are known to provide early warning signals of critical transformations. They were observed toward migrating soil erosion fronts, cryoturbation limits, and expanding deflation zones, thus providing potential early warning signals of land surface change. The record of the spatial patterning of vegetation contained in contemporary tephra layers shows how proximity to land surface change could be assessed in the widespread regions affected by shallow layers of volcanic fallout (those that can be subsumed within the existing vegetation cover). This insight shows how we could use tephra layers in the stratigraphic record to identify "near misses," close encounters with thresholds that did not lead to tipping points, and thus provide additional tools for archaeology, sustainability science, and contemporary land management.

Emergent relation between surface vapor conductance and relative humidity profiles yields evaporation rates from weather data.

The ability to predict terrestrial evapotranspiration (E) is limited by the complexity of rate-limiting pathways as water moves through the soil, vegetation (roots, xylem, stomata), canopy air space, and the atmospheric boundary layer. The impossibility of specifying the numerous parameters required to model this process in full spatial detail has necessitated spatially upscaled models that depend on effective parameters such as the surface vapor conductance (C(surf)). C(surf) accounts for the biophysical and hydrological effects on diffusion through the soil and vegetation substrate. This approach, however, requires either site-specific calibration of C(surf) to measured E, or further parameterization based on metrics such as leaf area, senescence state, stomatal conductance, soil texture, soil moisture, and water table depth. Here, we show that this key, rate-limiting, parameter can be estimated from an emergent relationship between the diurnal cycle of the relative humidity profile and E. The relation is that the vertical variance of the relative humidity profile is less than would occur for increased or decreased evaporation rates, suggesting that land-atmosphere feedback processes minimize this variance. It is found to hold over a wide range of climate conditions (arid-humid) and limiting factors (soil moisture, leaf area, energy). With this relation, estimates of E and C(surf) can be obtained globally from widely available meteorological measurements, many of which have been archived since the early 1900s. In conjunction with precipitation and stream flow, long-term E estimates provide insights and empirical constraints on projected accelerations of the hydrologic cycle.

Possible incipient sympatric ecological speciation in blind mole rats (Spalax).

Sympatric speciation has been controversial since it was first proposed as a mode of speciation. Subterranean blind mole rats (Spalacidae) are considered to speciate allopatrically or peripatrically. Here, we report a possible incipient sympatric adaptive ecological speciation in Spalax galili (2n = 52). The study microsite (0.04 km(2)) is sharply subdivided geologically, edaphically, and ecologically into abutting barrier-free ecologies divergent in rock, soil, and vegetation types. The Pleistocene Alma basalt abuts the Cretaceous Senonian Kerem Ben Zimra chalk. Only 28% of 112 plant species were shared between the soils. We examined mitochondrial DNA in the control region and ATP6 in 28 mole rats from basalt and in 14 from chalk habitats. We also sequenced the complete mtDNA (16,423 bp) of four animals, two from each soil type. Remarkably, the frequency of all major haplotype clusters (HC) was highly soil-biased. HCI and HCII are chalk biased. HC-III was abundant in basalt (36%) but absent in chalk; HC-IV was prevalent in basalt (46.5%) but was low (20%) in chalk. Up to 40% of the mtDNA diversity was edaphically dependent, suggesting constrained gene flow. We identified a homologous recombinant mtDNA in the basalt/chalk studied area. Phenotypically significant divergences differentiate the two populations, inhabiting different soils, in adaptive oxygen consumption and in the amount of outside-nest activity. This identification of a possible incipient sympatric adaptive ecological speciation caused by natural selection indirectly refutes the allopatric alternative. Sympatric ecological speciation may be more prevalent in nature because of abundant and sharply abutting divergent ecologies.

High regional climate sensitivity over continental China constrained by glacial-recent changes in temperature and the hydrological cycle.

The East Asian monsoon is one of Earth's most significant climatic phenomena, and numerous paleoclimate archives have revealed that it exhibits variations on orbital and suborbital time scales. Quantitative constraints on the climate changes associated with these past variations are limited, yet are needed to constrain sensitivity of the region to changes in greenhouse gas levels. Here, we show central China is a region that experienced a much larger temperature change since the Last Glacial Maximum than typically simulated by climate models. We applied clumped isotope thermometry to carbonates from the central Chinese Loess Plateau to reconstruct temperature and water isotope shifts from the Last Glacial Maximum to present. We find a summertime temperature change of 6-7 °C that is reproduced by climate model simulations presented here. Proxy data reveal evidence for a shift to lighter isotopic composition of meteoric waters in glacial times, which is also captured by our model. Analysis of model outputs suggests that glacial cooling over continental China is significantly amplified by the influence of stationary waves, which, in turn, are enhanced by continental ice sheets. These results not only support high regional climate sensitivity in Central China but highlight the fundamental role of planetary-scale atmospheric dynamics in the sensitivity of regional climates to continental glaciation, changing greenhouse gas levels, and insolation.

Functional ecology of an Antarctic Dry Valley.

The McMurdo Dry Valleys are the largest ice-free region in Antarctica and are critically at risk from climate change. The terrestrial landscape is dominated by oligotrophic mineral soils and extensive exposed rocky surfaces where biota are largely restricted to microbial communities, although their ability to perform the majority of geobiological processes has remained largely uncharacterized. Here, we identified functional traits that drive microbial survival and community assembly, using a metagenomic approach with GeoChip-based functional gene arrays to establish metabolic capabilities in communities inhabiting soil and rock surface niches in McKelvey Valley. Major pathways in primary metabolism were identified, indicating significant plasticity in autotrophic, heterotrophic, and diazotrophic strategies supporting microbial communities. This represents a major advance beyond biodiversity surveys in that we have now identified how putative functional ecology drives microbial community assembly. Significant differences were apparent between open soil, hypolithic, chasmoendolithic, and cryptoendolithic communities. A suite of previously unappreciated Antarctic microbial stress response pathways, thermal, osmotic, and nutrient limitation responses were identified and related to environmental stressors, offering tangible clues to the mechanisms behind the enduring success of microorganisms in this seemingly inhospitable terrain. Rocky substrates exposed to larger fluctuations in environmental stress supported greater functional diversity in stress-response pathways than soils. Soils comprised a unique reservoir of genes involved in transformation of organic hydrocarbons and lignin-like degradative pathways. This has major implications for the evolutionary origin of the organisms, turnover of recalcitrant substrates in Antarctic soils, and predicting future responses to anthropogenic pollution.

Soil biotic legacy effects of extreme weather events influence plant invasiveness.

Climate change is expected to increase future abiotic stresses on ecosystems through extreme weather events leading to more extreme drought and rainfall incidences [Jentsch A, et al. (2007) Front Ecol Environ 5(7):365-374]. These fluctuations in precipitation may affect soil biota, soil processes [Evans ST, Wallenstein MD (2012) Biogeochemistry 109:101-116], and the proportion of exotics in invaded plant communities [Jiménez MA, et al. (2011) Ecol Lett 14:1277-1235]. However, little is known about legacy effects in soil on the performance of exotics and natives in invaded plant communities. Here we report that drought and rainfall effects on soil processes and biota affect the performance of exotics and natives in plant communities. We performed two mesocosm experiments. In the first experiment, soil without plants was exposed to drought and/or rainfall, which affected soil N availability. Then the initial soil moisture conditions were restored, and a mixed community of co-occurring natives and exotics was planted and exposed to drought during growth. A single stress before or during growth decreased the biomass of natives, but did not affect exotics. A second drought stress during plant growth resetted the exotic advantage, whereas native biomass was not further reduced. In the second experiment, soil inoculation revealed that drought and/or rainfall influenced soil biotic legacies, which promoted exotics but suppressed natives. Our results demonstrate that extreme weather events can cause legacy effects in soil biota, promoting exotics and suppressing natives in invaded plant communities, depending on the type, frequency, and timing of extreme events.

Ammonia oxidation pathways and nitrifier denitrification are significant sources of N2O and NO under low oxygen availability.

The continuous increase of nitrous oxide (N2O) abundance in the atmosphere is a global concern. Multiple pathways of N2O production occur in soil, but their significance and dependence on oxygen (O2) availability and nitrogen (N) fertilizer source are poorly understood. We examined N2O and nitric oxide (NO) production under 21%, 3%, 1%, 0.5%, and 0% (vol/vol) O2 concentrations following urea or ammonium sulfate [(NH4)2SO4] additions in loam, clay loam, and sandy loam soils that also contained ample nitrate. The contribution of the ammonia (NH3) oxidation pathways (nitrifier nitrification, nitrifier denitrification, and nitrification-coupled denitrification) and heterotrophic denitrification (HD) to N2O production was determined in 36-h incubations in microcosms by (15)N-(18)O isotope and NH3 oxidation inhibition (by 0.01% acetylene) methods. Nitrous oxide and NO production via NH3 oxidation pathways increased as O2 concentrations decreased from 21% to 0.5%. At low (0.5% and 3%) O2 concentrations, nitrifier denitrification contributed between 34% and 66%, and HD between 34% and 50% of total N2O production. Heterotrophic denitrification was responsible for all N2O production at 0% O2. Nitrifier denitrification was the main source of N2O production from ammonical fertilizer under low O2 concentrations with urea producing more N2O than (NH4)2SO4 additions. These findings challenge established thought attributing N2O emissions from soils with high water content to HD due to presumably low O2 availability. Our results imply that management practices that increase soil aeration, e.g., reducing compaction and enhancing soil structure, together with careful selection of fertilizer sources and/or nitrification inhibitors, could decrease N2O production in agricultural soils.