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Abstract Cold‐air pooling is an important topoclimatic process that creates temperature inversions with the coldest air at the lowest elevations. Incomplete understanding of sub‐canopy spatiotemporal cold‐air pooling dynamics and associated ecological impacts hinders predictions and conservation actions related to climate change and cold‐dependent species and functions. To determine if and how cold‐air pooling influences forest composition, we characterized the frequency, strength, and temporal dynamics of cold‐air pooling in the sub‐canopy at local to regional scales in New England, USA. We established a network of 48 plots along elevational transects and continuously measured sub‐canopy air temperatures for 6–10 months (depending on site). We then estimated overstory and understory community temperature preferences by surveying tree composition in each plot and combining these data with known species temperature preferences. We found that cold‐air pooling was frequent (19–43% seasonal occurrences) and that sites with the most frequent inversions displayed inverted forest composition patterns across slopes with more cold‐adapted species, namely conifers, at low instead of high elevations. We also observed both local and regional variability in cold‐air pooling dynamics, revealing that while cold‐air pooling is common, it is also spatially complex. Our study, which uniquely focused on broad spatial and temporal scales, has revealed some rarely reported cold‐air pooling dynamics. For instance, we discovered frequent and strong temperature inversions that occurred across seasons and in some locations were most frequent during the daytime, likely affecting forest composition. Together, our results show that cold‐air pooling is a fundamental ecological process that requires integration into modeling efforts predicting future forest vegetation patterns under climate change, as well as greater consideration for conservation strategies identifying potential climate refugia for cold‐adapted species.

Abstract Background In light of the biodiversity crisis and our limited ability to explain variation in biodiversity, tools to quantify spatial and temporal variation in biodiversity and its underlying drivers are critically needed. Inspired by the recently published ecospace framework, we developed and tested a sampling design for environmental and biotic mapping. We selected 130 study sites (40 × 40 m) across Denmark using stratified random sampling along the major environmental gradients underlying biotic variation. Using standardized methods, we collected site species data on vascular plants, bryophytes, macrofungi, lichens, gastropods and arthropods. To evaluate sampling efficiency, we calculated regional coverage (relative to the known species number per taxonomic group), and site scale coverage (i.e., sample completeness per taxonomic group at each site). To extend taxonomic coverage to organisms that are difficult to sample by classical inventories (e.g., nematodes and non-fruiting fungi), we collected soil for metabarcoding. Finally, to assess site conditions, we mapped abiotic conditions, biotic resources and habitat continuity. Results Despite the 130 study sites only covering a minute fraction (0.0005%) of the total Danish terrestrial area, we found 1774 species of macrofungi (54% of the Danish fungal species pool), 663 vascular plant species (42%), 254 bryophyte species (41%) and 200 lichen species (19%). For arthropods, we observed 330 spider species (58%), 123 carabid beetle species (37%) and 99 hoverfly species (33%). Overall, sample coverage was remarkably high across taxonomic groups and sufficient to capture substantial spatial variation in biodiversity across Denmark. This inventory is nationally unprecedented in detail and resulted in the discovery of 143 species with no previous record for Denmark. Comparison between plant OTUs detected in soil DNA and observed plant species confirmed the usefulness of carefully curated environmental DNA-data. Correlations among species richness for taxonomic groups were predominantly positive, but did not correlate well among all taxa suggesting differential and complex biotic responses to environmental variation. Conclusions We successfully and adequately sampled a wide range of diverse taxa along key environmental gradients across Denmark using an approach that includes multi-taxon biodiversity assessment and ecospace mapping. Our approach is applicable to assessments of biodiversity in other regions and biomes where species are structured along environmental gradient.

Abstract Biodiversity—both above‐ and belowground—influences multiple functions in terrestrial ecosystems. Yet, it is unclear whether differences in above‐ and belowground species composition (β‐diversity) are associated with differences in multiple ecosystem functions (e.g., spatial turnover in ecosystem function). Here, we partitioned the contributions of above‐ and belowground β‐diversity and abiotic factors (geographic distance, differences in environments) on the spatial turnover of multiple grassland ecosystem functions. We compiled a dataset of plant and soil microbial communities and six indicators of grassland ecosystem functions (i.e., plant aboveground live biomass, plant nitrogen [N], plant phosphorus [P], root biomass, soil total N, and soil extractable P) from 18 grassland sites on four continents contributing to the Nutrient Network experiment. We used Mantel tests and structural equation models to disentangle the relationship between above‐ and belowground β‐diversity and spatial turnover in grassland ecosystem functions. We found that the effects of abiotic factors on the spatial turnover of ecosystem functions were largely indirect through their influences on above‐ and belowground β‐diversity, and that spatial turnover of ecosystem function was more strongly associated with plant β‐diversity than with soil microbial β‐diversity. These results indicate that changes in above‐ and belowground species composition are one mechanism that interacts with environmental change to determine variability in multiple ecosystem functions across spatial scales. As grasslands face global threats from shrub encroachment, conversion to agriculture, or are lost to development, the functions and services they provide will more strongly converge with increased aboveground community homogenization than with soil microbial community homogenization.

Abstract Understanding soil systems is critical because they form the structural and nutritional foundation for plants and thus every terrestrial habitat and agricultural system. In this paper, we encourage increased use of mathematical models to drive forward understanding of interactions in soil ecological systems. We discuss several distinctive features of soil ecosystems and empirical studies of them. We explore some perceptions that have previously deterred more extensive use of models in soil ecology and some advances that have already been made using models to elucidate soil ecological interactions. We provide examples where mathematical models have been used to test the plausibility of hypothesized mechanisms, to explore systems where experimental manipulations are currently impossible, or to determine the most important variables to measure in experimental and natural systems. To aid in the development of theory in this field, we present a table describing major soil ecology topics, the theory previously used, and providing key terms for theoretical approaches that could potentially address them. We then provide examples from the table that may either contribute to important incremental developments in soil science or potentially revolutionize our understanding of plant–soil systems. We challenge scientists and mathematicians to push theoretical explorations in soil systems further and highlight three major areas for the development of mathematical models in soil ecology: theory spanning scales and ecological hierarchies, processes, and evolution.

Abstract Warming is altering the way soils function in ecosystems both directly by changing microbial physiology and indirectly by causing shifts in microbial community composition. Some of these warming‐driven changes are short term, but others may persist over time. Here, we took advantage of a long‐term (14 yr) warming experiment in a tallgrass prairie to tease apart the influence of short‐ and long‐term warming on litter decomposition. We collected soils originating from warmed and control plots and incubated them with a common litter substrate in a reciprocal design under elevated and ambient growth chamber temperatures. Litter decomposition was 40% higher in soils that were warmed in the field for 14 yr (long‐term warming) relative to soils derived from ambient plots. Short‐term warming in the laboratory had less of an impact on decomposition—decomposition increased by 12% under laboratory warming. Using a two‐pool soil carbon model to explore how different carbon pools may be responding, we found that long‐term warming accelerated the turnover of labile, not recalcitrant, carbon in these prairie soils—a result that is likely due to shifts in soil community activity/composition. Taken together, our results offer experimental evidence that warming‐induced changes in the soil community that occur over 14 yr of warming have long‐lasting effects on carbon turnover.

Abstract Global warming and changes in precipitation are altering the phenology of plants that significantly impact the functioning and services of ecosystems. Although a number of studies have addressed responses of plant phenology to warming and altered precipitation individually, their interactions can alter plant phenology differently than either does independently. To explore how the interactions between global change drivers alter alpine ecosystems, we conducted a factorial experiment manipulating warming (ambient and +2°C) and altered precipitation (50% decrease, control, and 50% increase) simultaneously in an alpine meadow on the Tibetan Plateau. Over two years, we monitored plant phenological events, leaf‐out day and first flowering day, for 11 common plant species that account for 74.4% of the total above biomass. Surprisingly, there was no interaction between warming and changes in precipitation on community plant phenology, but warming advanced leaf‐out and first flowering day by 7.10 and 9.79 d, respectively. Unlike the community response, plant functional groups had a variety of direct and interactive responses to the experimental climate drivers. While the phenology of legumes was most influenced by temperature, temperature and precipitation interacted to alter the phenology of grasses and forbs. To explore how plant phenological sensitivity on the Tibetan Plateau is compared with other meadow ecosystems, we combined our dataset with a global plant phenology dataset. Interestingly, the phenological sensitivity of leaf‐out day and first flowering day on the Tibetan Plateau is 7.3 and 37.8 times greater than global phenological sensitivity, respectively. This result highlights that a meta‐analysis of global phenological sensitivity may significantly underestimate change in some regions—even regions as large as the Tibetan Plateau. Together, our results suggest that the Tibetan Plateau may experience rapid change as temperatures warm and that these changes will likely be more rapid than in other regions of the world. Further, our study highlights that if we are to make accurate predictions of how plant phenology may change with warming, we need to understand the specific environmental cues that drive phenological responses across different areas.

Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant phenotype. We chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, net photosynthesis, net photosynthesis at saturating light–Asat, and saturating CO2–Amax). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respond to bacteria by modifying morphology. However, endophyte inoculation had no influence on total plant biomass and photosynthetic traits (net photosynthesis, chlorophyll content). In sum, bacterial inoculation did not significantly increase plant carbon fixation and biomass, but their presence altered where and how carbon was being allocated in the plant host.

Because microorganisms are sensitive to temperature, ongoing global warming is predicted to influence microbial community structure and function. We used large-scale warming experiments established at two sites near the northern and southern boundaries of US eastern deciduous forests to explore how microbial communities and their function respond to warming at sites with differing climatic regimes. Soil microbial community structure and function responded to warming at the southern but not the northern site. However, changes in microbial community structure and function at the southern site did not result in changes in cellulose decomposition rates. While most global change models rest on the assumption that taxa will respond similarly to warming across sites and their ranges, these results suggest that the responses of microorganisms to warming may be mediated by differences across the geographic boundaries of ecosystems.

Abstract Springtails (Collembola) inhabit soils from the Arctic to the Antarctic and comprise an estimated ~32% of all terrestrial arthropods on Earth. Here, we present a global, spatially-explicit database on springtail communities that includes 249,912 occurrences from 44,999 samples and 2,990 sites. These data are mainly raw sample-level records at the species level collected predominantly from private archives of the authors that were quality-controlled and taxonomically-standardised. Despite covering all continents, most of the sample-level data come from the European continent (82.5% of all samples) and represent four habitats: woodlands (57.4%), grasslands (14.0%), agrosystems (13.7%) and scrublands (9.0%). We included sampling by soil layers, and across seasons and years, representing temporal and spatial within-site variation in springtail communities. We also provided data use and sharing guidelines and R code to facilitate the use of the database by other researchers. This data paper describes a static version of the database at the publication date, but the database will be further expanded to include underrepresented regions and linked with trait data.

Springtails are omnipresent soil arthropods, vital for ecosystems. In the first global assessment of springtails, this study shows a 20-fold biomass difference between the tundra and the tropics, with distinct temperature-related patterns for diversity and metabolism that suggest climate change may restructure the functioning of soil biodiversity.

Abstract A growing body of work examines the direct and indirect effects of climate change on ecosystems, typically by using manipulative experiments at a single site or performing meta‐analyses across many independent experiments. However, results from single‐site studies tend to have limited generality. Although meta‐analytic approaches can help overcome this by exploring trends across sites, the inherent limitations in combining disparate datasets from independent approaches remain a major challenge. In this paper, we present a globally distributed experimental network that can be used to disentangle the direct and indirect effects of climate change. We discuss how natural gradients, experimental approaches, and statistical techniques can be combined to best inform predictions about responses to climate change, and we present a globally distributed experiment that utilizes natural environmental gradients to better understand long‐term community and ecosystem responses to environmental change. The warming and (species) removal in mountains (WaRM) network employs experimental warming and plant species removals at high‐ and low‐elevation sites in a factorial design to examine the combined and relative effects of climatic warming and the loss of dominant species on community structure and ecosystem function, both above‐ and belowground. The experimental design of the network allows for increasingly common statistical approaches to further elucidate the direct and indirect effects of warming. We argue that combining ecological observations and experiments along gradients is a powerful approach to make stronger predictions of how ecosystems will function in a warming world as species are lost, or gained, in local communities.

Abstract The impacts of warming on communities and ecosystems are predicted to be significant in mountain ecosystems because physiological processes, including rates of carbon (C) cycling, are often more temperature‐sensitive in colder environments. Plant biodiversity can also influence C exchange, yet few studies integrate how biotic and abiotic factors may directly or interactively impact ecosystem C flux. Here, we examine the link between simultaneous changes in multiple dimensions of plant diversity and peak growing season ecosystem C uptake across a climatic gradient in the Rocky Mountains, Colorado, USA. We found that taxonomic diversity (species richness), functional diversity (functional evenness), and phylogenetic diversity (mean pairwise distance) were significantly and positively related to peak growing season ecosystem C uptake (i.e., net ecosystem exchange) when considered independently. However, when abiotic and biotic factors were integrated in a structural equation model, only plant phylogenetic diversity was significantly related to C uptake. In addition, we found that actual evapotranspiration (AET—a measure that integrates precipitation and temperature) affected ecosystem C exchange indirectly via its impact on the three dimensions of plant diversity that we examined. These findings highlight complex relationships among key measures of biodiversity and ecosystem C uptake in a rapidly warming ecosystem, and the possible mechanisms that underlie relationships between biodiversity and ecosystem functioning. They also point to the need for integrating multiple dimensions of biodiversity into studies of community and ecosystem ecology.

Although herbivores are well known to alter litter inputs and soil nutrient fluxes, their long‐term influences on soil development are largely unknown because of the difficulty of detecting and attributing changes in carbon and nutrient pools against large background levels. The early phase of primary succession reduces this signal‐to‐noise problem, particularly in arid systems where individual plants can form islands of fertility. We used natural variation in tree‐resistance to herbivory, and a 15 year herbivore‐removal experiment in an Arizona piñon‐juniper woodland that was established on cinder soils following a volcanic eruption, to quantify how herbivory shapes the development of soil carbon (C) and nitrogen (N) over 36–54 years (i.e., the ages of the trees used in our study). In this semi‐arid ecosystem, trees are widely spaced on the landscape, which allows direct examination of herbivore impacts on the nutrient‐poor cinder soils. Although chronic insect herbivory increased annual litterfall N per unit area by 50% in this woodland, it slowed annual tree‐level soil C and N accumulation by 111% and 96%, respectively. Despite the reduction in soil C accumulation, short‐term litterfall‐C inputs and soil C‐efflux rates per unit soil surface were not impacted by herbivory. Our results demonstrate that the effects of herbivores on soil C and N fluxes and soil C and N accumulation are not necessarily congruent: herbivores can increase N in litterfall, but over time their impact on plant growth and development can slow soil development. In sum, because herbivores slow tree growth, they slow soil development on the landscape.

Ecological succession drives large-scale changes in ecosystem composition over time, but the mechanisms whereby climatic change might alter succession remain unresolved. Here, we asked if the effects of atmospheric and climatic change would alter tree seedling emergence and establishment in an old-field ecosystem, recognizing that small shifts in rates of seedling emergence and establishment of different species may have long-term repercussions on the transition of fields to forests in the future.We introduced seeds from three early successional tree species into constructed old-field plant communities that had been subjected for 4 years to altered temperature, precipitation, and atmospheric CO(2) regimes in an experimental facility. Our experiment revealed that different combinations of atmospheric CO(2) concentration, air temperature, and soil moisture altered seedling emergence and establishment. Treatments directly and indirectly affected soil moisture, which was the best predictor of seedling establishment, though treatment effects differed among species.The observed impacts, coupled with variations in the timing of seed arrival, are demonstrated as predictors of seedling emergence and establishment in ecosystems under global change.