A stoichiometric approach to estimate sources of mineral-associated soil organic matter.

Mineral-associated soil organic matter (MAOM) is the largest, slowest cycling pool of carbon (C) in the terrestrial biosphere. MAOM is primarily derived from plant and microbial sources, yet the relative contributions of these two sources to MAOM remain unresolved. Resolving this issue is essential for managing and modeling soil carbon responses to environmental change. Microbial biomarkers, particularly amino sugars, are the primary method used to estimate microbial versus plant contributions to MAOM, despite systematic biases associated with these estimates. There is a clear need for independent lines of evidence to help determine the relative importance of plant versus microbial contributions to MAOM. Here, we synthesized 288 datasets of C/N ratios for MAOM, particulate organic matter (POM), and microbial biomass across the soils of forests, grasslands, and croplands. Microbial biomass is the source of microbial residues that form MAOM, whereas the POM pool is the direct precursor of plant residues that form MAOM. We then used a stoichiometric approach-based on two-pool, isotope-mixing models-to estimate the proportional contribution of plant residue (POM) versus microbial sources to the MAOM pool. Depending on the assumptions underlying our approach, microbial inputs accounted for between 34% and 47% of the MAOM pool, whereas plant residues contributed 53%-66%. Our results therefore challenge the existing hypothesis that microbial contributions are the dominant constituents of MAOM. We conclude that biogeochemical theory and models should account for multiple pathways of MAOM formation, and that multiple independent lines of evidence are required to resolve where and when plant versus microbial contributions are dominant in MAOM formation.

The importance of accounting method and sampling depth to estimate changes in soil carbon stocks.

BACKGROUND: As interest in the voluntary soil carbon market surges, carbon registries have been developing new soil carbon measurement, reporting, and verification (MRV) protocols. These protocols are inconsistent in their approaches to measuring soil organic carbon (SOC). Two areas of concern include the type of SOC stock accounting method (fixed-depth (FD) vs. equivalent soil mass (ESM)) and sampling depth requirement. Despite evidence that fixed-depth measurements can result in error because of changes in soil bulk density and that sampling to 30 cm neglects a significant portion of the soil profile's SOC stock, most MRV protocols do not specify which sampling method to use and only require sampling to 30 cm. Using data from UC Davis's Century Experiment ("Century") and UW Madison's Wisconsin Integrated Cropping Systems Trial (WICST), we quantify differences in SOC stock changes estimated by FD and ESM over 20 years, investigate how sampling at-depth (> 30 cm) affects SOC stock change estimates, and estimate how crediting outcomes taking an empirical sampling-only crediting approach differ when stocks are calculated using ESM or FD at different depths. RESULTS: We find that FD and ESM estimates of stock change can differ by over 100 percent and that, as expected, much of this difference is associated with changes in bulk density in surface soils (e.g., r = 0.90 for Century maize treatments). This led to substantial differences in crediting outcomes between ESM and FD-based stocks, although many treatments did not receive credits due to declines in SOC stocks over time. While increased variability of soils at depth makes it challenging to accurately quantify stocks across the profile, sampling to 60 cm can capture changes in bulk density, potential SOC redistribution, and a larger proportion of the overall SOC stock. CONCLUSIONS: ESM accounting and sampling to 60 cm (using multiple depth increments) should be considered best practice when quantifying change in SOC stocks in annual, row crop agroecosystems. For carbon markets, the cost of achieving an accurate estimate of SOC stocks that reflect management impacts on soils at-depth should be reflected in the price of carbon credits.

Plant mycorrhizal associations mediate the zoogeochemical effects of calving subsidies by a forest ungulate.

Animals interact with and impact ecosystem biogeochemical cycling-processes known as zoogeochemistry. While the deposition of various animal materials (e.g. carcasses and faeces) has been shown to create nutrient hotspots and alter nutrient cycling and storage, the inputs from parturition (i.e. calving) have yet to be explored. We examine the effects of ungulate parturition, which often occurs synchronously during spring green-up and therefore aligns with increased plant nitrogen demand in temperate biomes. Impacts of zoogeochemical inputs are likely context-dependent, where differences in material quality, quantity and the system of deposition modulate their impacts. Plant mycorrhizal associations, especially, create different nutrient-availability contexts, which can modify the effects of nutrient inputs. We, therefore, hypothesize that mycorrhizal associations modulate the consequences of parturition on soil nutrient dynamics and nitrogen pools. We established experimental plots that explore the potential of two kinds of zoogeochemical inputs deposited at ungulate parturition (placenta and natal fluid) in forest microsites dominated by either ericoid mycorrhizal (ErM) or ectomycorrhizal (EcM) plants. We assess how these inputs affect rates of nutrient cycling and nitrogen content in various ecosystem pools, using isotope tracers to track the fate of nitrogen inputs into plant and soil pools. Parturition treatments accelerate nutrient cycling processes and increase nitrogen contents in the plant leaf, stem and fine root pools. The ecosystem context strongly modulates these effects. Microsites dominated by ErM plants mute parturition treatment impacts on most nutrient cycling processes and plant pools. Both plant-fungal associations are, however, equally efficient at retaining nitrogen, although retention of nitrogen in the parturition treatment plots was more than two times lower than in control plots. Our results highlight the potential importance of previously unexamined nitrogen inputs from animal inputs, such as those from parturition, in contributing to fine-scale heterogeneity in nutrient cycling and availability. Animal inputs should therefore be considered, along with their interactions with plant mycorrhizal associations, in terms of how zoogeochemical dynamics collectively affect nutrient heterogeneity in ecosystems.

Depth-dependent effects of ericoid mycorrhizal shrubs on soil carbon and nitrogen pools are accentuated under arbuscular mycorrhizal trees.

Plant mycorrhizal associations influence the accumulation and persistence of soil organic matter and could therefore shape ecosystem biogeochemical responses to global changes that are altering forest composition. For instance, arbuscular mycorrhizal (AM) tree dominance is increasing in temperate forests, and ericoid mycorrhizal (ErM) shrubs can respond positively to canopy disturbances. Yet how shifts in the co-occurrence of trees and shrubs with different mycorrhizal associations will affect soil organic matter pools remains largely unknown. We examine the effects of ErM shrubs on soil carbon and nitrogen stocks and indicators of microbial activity at different depths across gradients of AM versus ectomycorrhizal (EcM) tree dominance in three temperate forest sites. We find that ErM shrubs strongly modulate tree mycorrhizal dominance effects. In surface soils, ErM shrubs increase particulate organic matter accumulation and weaken the positive relationship between soil organic matter stocks and indicators of microbial activity. These effects are strongest under AM trees that lack fungal symbionts that can degrade organic matter. In subsurface soil organic matter pools, by contrast, tree mycorrhizal dominance effects are stronger than those of ErM shrubs. Ectomycorrhizal tree dominance has a negative influence on particulate and mineral-associated soil organic matter pools, and these effects are stronger for nitrogen than for carbon stocks. Our findings suggest that increasing co-occurrence of ErM shrubs and AM trees will enhance particulate organic matter accumulation in surface soils by suppressing microbial activity while having little influence on mineral-associated organic matter in subsurface soils. Our study highlights the importance of considering interactions between co-occurring plant mycorrhizal types, as well as their depth-dependent effects, for projecting changes in soil carbon and nitrogen stocks in response to compositional shifts in temperate forests driven by disturbances and global change.

The functional role of ericoid mycorrhizal plants and fungi on carbon and nitrogen dynamics in forests.

Ericoid mycorrhizal (ErM) shrubs commonly occur in forest understories and could therefore alter arbuscular (AM) and/or ectomycorrhizal (EcM) tree effects on soil carbon and nitrogen dynamics. Specifically, ErM fungi have extensive organic matter decay capabilities, and ErM plant and fungal tissues have high concentrations of secondary compounds that can form persistent complexes in the soil. Together, these traits could contribute to organic matter accumulation and inorganic nutrient limitation. These effects could also differ in AM- vs EcM-dominated stands at multiple scales within and among forest biomes by, for instance, altering fungal guild interactions. Most work on ErM effects in forests has been conducted in boreal forests dominated by EcM trees. However, ErM plants occur in c. 96, 69 and 29% of boreal, temperate and tropical forests, respectively. Within tropical montane forests, the effects of ErM plants could be particularly pronounced because their traits are more distinct from AM than EcM trees. Because ErM fungi can function as free-living saprotrophs, they could also be more resilient to forest disturbances than obligate symbionts. Further consideration of ErM effects within and among forest biomes could improve our understanding of how cooccurring mycorrhizal types interact to collectively affect soil carbon and nitrogen dynamics under changing conditions.

Belowground community turnover accelerates the decomposition of standing dead wood.

Standing dead trees (snags) decompose more slowly than downed dead wood and provide critical habitat for many species. The rate at which snags fall therefore influences forest carbon dynamics and biodiversity. Fall rates correlate strongly with mean annual temperature, presumably because warmer climates facilitate faster wood decomposition and hence degradation of the structural stability of standing wood. These faster decomposition rates coincide with turnover from fungal-dominated wood decomposer communities in cooler forests to codomination by fungi and termites in warmer regions. A key question for projecting forest dynamics is therefore whether temperature effects on wood decomposition arise primarily because warmer conditions facilitate faster decomposer metabolism, or are also influenced indirectly by belowground community turnover (e.g., termites exert additional influence beyond fungal-plus-bacterial mediated decomposition). To test between these possibilities, we simulate standing dead trees with untreated wooden posts and follow them in the field across 5 yr at 12 sites, before measuring buried, soil-air interface and aerial post sections to quantify wood decomposition and organism activities. High termite activities at the warmer sites are associated with rates of postfall that are three times higher than at the cooler sites. Termites primarily consume buried wood, with decomposition rates greatest where termite activities are highest. However, where higher microbial and termite activities co-occur, they appear to compensate for one another first, and then to slow decomposition rates at their highest activities, suggestive of interference competition. If the range of microbial and termite codomination of wood decomposer communities expands under climate warming, our data suggest that expansion will accelerate snag fall with consequent effects on forest carbon cycling and biodiversity in forests previously dominated by microbial decomposers.

Positive long-term impacts of restoration on soils in an experimental urban forest.

As urbanization increases worldwide, investments in nature-based solutions that aim to mitigate urban stressors and counter the impacts of global climate change are also on the rise. Tree planting on degraded urban lands-or afforestation-is one form of nature-based solution that has been increasingly implemented in cities around the world. The benefits of afforestation are, however, contingent on the capacity of soils to support the growth of planted trees, which poses a challenge in some urban settings where unfavorable soil conditions limit tree performance. Soil-focused site treatments could help urban areas overcome impediments to afforestation, yet few studies have examined the long-term (>5 yr) effects of site treatments on soils and other management objectives. We analyzed the impacts of compost amendments, interplanting with shrubs, and tree species composition (six species vs. two species) on soil conditions and associated tree growth in 54 experimental afforestation plots in New York City, USA. We compared baseline soil conditions to conditions after 6 yr and examined changes in the treatment effects from 1 to 6 yr. Site treatments and tree planting increased soil microbial biomass, water holding capacity, and total carbon and nitrogen, and reduced soil pH and bulk density relative to baseline conditions. These changes were most pronounced in compost-amended plots, and the effects of the shrub and species composition treatments were minimal. In fact, compost was key to sustaining long-term changes in soil carbon stocks, which increased by 17% in compost-amended plots but declined in unamended plots. Plots amended with compost also had 59% more nitrogen than unamended plots, which was associated with a 20% increase in the basal area of planted trees. Improvements in soil conditions after 6 yr departed from the initial trends observed after 1 yr, highlighting the importance of longer-term studies to quantify restoration success. Altogether, our results show that site treatments and tree planting can have long-lasting impacts on soil conditions and that these changes can support multiple urban land management objectives.

A trait-based understanding of wood decomposition by fungi.

As the primary decomposers of organic material in terrestrial ecosystems, fungi are critical agents of the global carbon cycle. Yet our ability to link fungal community composition to ecosystem functioning is constrained by a limited understanding of the factors accounting for different wood decomposition rates among fungi. Here we examine which traits best explain fungal decomposition ability by combining detailed trait-based assays on 34 saprotrophic fungi from across North America in the laboratory with a 5-y field study comprising 1,582 fungi isolated from 74 decomposing logs. Fungal growth rate (hyphal extension rate) was the strongest single predictor of fungal-mediated wood decomposition rate under laboratory conditions, and accounted for up to 27% of the in situ variation in decomposition in the field. At the individual level, decomposition rate was negatively correlated with moisture niche width (an indicator of drought stress tolerance) and with the production of nutrient-mineralizing extracellular enzymes. Together, these results suggest that decomposition rates strongly align with a dominance-tolerance life-history trade-off that was previously identified in these isolates, forming a spectrum from slow-growing, stress-tolerant fungi that are poor decomposers to fast-growing, highly competitive fungi with fast decomposition rates. Our study illustrates how an understanding of fungal trait variation could improve our predictive ability of the early and midstages of wood decay, to which our findings are most applicable. By mapping our results onto the biogeographic distribution of the dominance-tolerance trade-off across North America, we approximate broad-scale patterns in intrinsic fungal-mediated wood decomposition rates.

Refining national greenhouse gas inventories.

The importance of greenhouse gas inventories cannot be overstated: the process of producing inventories informs strategies that governments will use to meet emissions reduction targets. The Intergovernmental Panel on Climate Change (IPCC) leads an effort to develop and refine internationally agreed upon methodologies for calculating and reporting greenhouse gas emissions and removals. We argue that these guidelines are not equipped to handle the task of developing national greenhouse gas inventories for most countries. Inventory guidelines are vital to implementing climate action, and we highlight opportunities to improve their timeliness and accuracy. Such reforms should provide the means to better understand and advance the progress countries are making toward their Paris commitments. Now is the time to consider challenges posed by the current process to develop the guidelines, and to avail the policy community of recent major advances in quantitative and expert synthesis to overhaul the process and thereby better equip multi-national efforts to limit climate change.

Direct evidence using a controlled greenhouse study for threshold effects of soil organic matter on crop growth.

Soil organic matter (SOM) is a key indicator of soil fertility, and building SOM is assumed to decrease reliance on external inputs and ensure stable crop production. Recent syntheses of field data support this assumption with positive SOM-productivity relationships that asymptote at ~4% SOM. Teasing out the directionality of this relationship-the extent to which SOM increases crop growth vs. greater growth leading to higher SOM concentrations-requires controlled experimentation. To disentangle this causative pathway, we conducted a greenhouse experiment whereby we manipulated SOM concentrations from 1% to 9% and evaluated whether the SOM-productivity relationship differed for spring wheat (Triticum aestivum, L.) under nitrogen fertilization crossed with irrigation due to the expectation that SOM buffers the effects of reduced fertilization and/or irrigation. We found that higher concentrations of SOM led to greater productivity (measured as aboveground biomass) up to a threshold of 5% SOM, after which productivity declined across all treatments. These declines occurred despite the fact that indicators of soil health (water-holding capacity, microbial biomass, and bulk density) improved linearly with increasing SOM concentrations. That is, improvements in soil properties did not translate to gains in productivity at the highest SOM levels. Nitrogen fertilization led to greater productivity across all treatments, but to a greater relative extent at lower SOM levels, where we found that productivity on unfertilized soils with 4% SOM matched that of fertilized soils with 2% SOM. Differences in productivity on unfertilized soils due to irrigation emerged at higher SOM levels (>5%), highlighting SOM's role in water retention. Our results demonstrate that building SOM leads to improved growth of a globally important crop; however, our results also indicated a pronounced SOM threshold, after which crop growth declined. This underscores the need to develop optimal SOM targets for desired agricultural and environmental outcomes.

Increasing microbial carbon use efficiency with warming predicts soil heterotrophic respiration globally.

The degree to which climate warming will stimulate soil organic carbon (SOC) losses via heterotrophic respiration remains uncertain, in part because different or even opposite microbial physiology and temperature relationships have been proposed in SOC models. We incorporated competing microbial carbon use efficiency (CUE)-mean annual temperature (MAT) and enzyme kinetic-MAT relationships into SOC models, and compared the simulated mass-specific soil heterotrophic respiration rates with multiple published datasets of measured respiration. The measured data included 110 dryland soils globally distributed and two continental to global-scale cross-biome datasets. Model-data comparisons suggested that a positive CUE-MAT relationship best predicts the measured mass-specific soil heterotrophic respiration rates in soils distributed globally. These results are robust when considering models of increasing complexity and competing mechanisms driving soil heterotrophic respiration-MAT relationships (e.g., carbon substrate availability). Our findings suggest that a warmer climate selects for microbial communities with higher CUE, as opposed to the often hypothesized reductions in CUE by warming based on soil laboratory assays. Our results help to build the impetus for, and confidence in, including microbial mechanisms in soil biogeochemical models used to forecast changes in global soil carbon stocks in response to warming.

Consistent trade-offs in fungal trait expression across broad spatial scales.

Fungi are the primary agents of terrestrial decomposition, yet our understanding of fungal biogeography lags far behind that of plants, animals and bacteria. Here, we use a trait-based approach to quantify the niches of 23 species of basidiomycete wood decay fungi from across North America, and explore the linkages among functional trait expression, climate and phylogeny. Our analysis reveals a fundamental trade-off between abiotic stress tolerance and competitive ability, whereby fungi with wide thermal and moisture niches exhibit lower displacement ability. The magnitude of this dominance-tolerance trade-off is partially related to the environmental conditions under which the fungi were collected, with thermal niche traits exhibiting the strongest climate relationships. Nevertheless, moisture and thermal dominance-tolerance patterns exhibited contrasting phylogenetic signals, suggesting that these trends are influenced by a combination of niche sorting along taxonomic lines in tandem with acclimation and adaptation at the level of the individual. Collectively, our work reveals key insight into the life history strategies of saprotrophic fungi, demonstrating consistent trait trade-offs across broad spatial scales.

Soil microbial respiration adapts to ambient temperature in global drylands.

Heterotrophic soil microbial respiration-one of the main processes of carbon loss from the soil to the atmosphere-is sensitive to temperature in the short term. However, how this sensitivity is affected by long-term thermal regimes is uncertain. There is an expectation that soil microbial respiration rates adapt to the ambient thermal regime, but whether this adaptation magnifies or reduces respiration sensitivities to temperature fluctuations remains unresolved. This gap in understanding is particularly pronounced for drylands because most studies conducted so far have focused on mesic systems. Here, we conduct an incubation study using soil samples from 110 global drylands encompassing a wide gradient in mean annual temperature. We test how mean annual temperature affects soil respiration rates at three assay temperatures while controlling for substrate depletion and microbial biomass. Estimated soil respiration rates at the mean microbial biomass were lower in sites with higher mean annual temperatures across the three assayed temperatures. The patterns observed are consistent with expected evolutionary trade-offs in the structure and function of enzymes under different thermal regimes. Therefore, our results suggest that soil microbial respiration adapts to the ambient thermal regime in global drylands.

Cross-biome patterns in soil microbial respiration predictable from evolutionary theory on thermal adaptation.

Climate warming may stimulate microbial metabolism of soil carbon, causing a carbon-cycle-climate feedback whereby carbon is redistributed from the soil to atmospheric CO2. The magnitude of this feedback is uncertain, in part because warming-induced shifts in microbial physiology and/or community composition could retard or accelerate soil carbon losses. Here, we measure microbial respiration rates for soils collected from 22 sites in each of 3 years, at locations spanning boreal to tropical climates. Respiration was measured in the laboratory with standard temperatures, moisture and excess carbon substrate, to allow physiological and community effects to be detected independent of the influence of these abiotic controls. Patterns in respiration for soils collected across the climate gradient are consistent with evolutionary theory on physiological responses that compensate for positive effects of temperature on metabolism. Respiration rates per unit microbial biomass were as much as 2.6 times higher for soils sampled from sites with a mean annual temperature of -2.0 versus 21.7 °C. Subsequent 100-d incubations suggested differences in the plasticity of the thermal response among microbial communities, with communities sampled from sites with higher mean annual temperature having a more plastic response. Our findings are consistent with adaptive metabolic responses to contrasting thermal regimes that are also observed in plants and animals. These results may help build confidence in soil-carbon-climate feedback projections by improving understanding of microbial processes represented in biogeochemical models.

Evidence for the primacy of living root inputs, not root or shoot litter, in forming soil organic carbon.

Soil organic carbon (SOC) is primarily formed from plant inputs, but the relative carbon (C) contributions from living root inputs (i.e. rhizodeposits) vs litter inputs (i.e. root + shoot litter) are poorly understood. Recent theory suggests that living root inputs exert a disproportionate influence on SOC formation, but few field studies have explicitly tested this by separately tracking living root vs litter inputs as they move through the soil food web and into distinct SOC pools. We used a manipulative field experiment with an annual C4 grass in a forest understory to differentially track its living root vs litter inputs into the soil and to assess net SOC formation over multiple years. We show that living root inputs are 2-13 times more efficient than litter inputs in forming both slow-cycling, mineral-associated SOC as well as fast-cycling, particulate organic C. Furthermore, we demonstrate that living root inputs are more efficiently anabolized by the soil microbial community en route to the mineral-associated SOC pool (dubbed 'the in vivo microbial turnover pathway'). Overall, our findings provide support for the primacy of living root inputs in forming SOC. However, we also highlight the possibility of nonadditive effects of living root and litter inputs, which may deplete SOC pools despite greater SOC formation rates.

Pathways of mineral-associated soil organic matter formation: Integrating the role of plant carbon source, chemistry, and point of entry.

To predict the behavior of the terrestrial carbon cycle, it is critical to understand the source, formation pathway, and chemical composition of soil organic matter (SOM). There is emerging consensus that slow-cycling SOM generally consists of relatively low molecular weight organic carbon substrates that enter the mineral soil as dissolved organic matter and associate with mineral surfaces (referred to as "mineral-associated OM," or MAOM). However, much debate and contradictory evidence persist around: (a) whether the organic C substrates within the MAOM pool primarily originate from aboveground vs. belowground plant sources and (b) whether C substrates directly sorb to mineral surfaces or undergo microbial transformation prior to their incorporation into MAOM. Here, we attempt to reconcile disparate views on the formation of MAOM by proposing a spatially explicit set of processes that link plant C source with MAOM formation pathway. Specifically, because belowground vs. aboveground sources of plant C enter spatially distinct regions of the mineral soil, we propose that fine-scale differences in microbial abundance should determine the probability of substrate-microbe vs. substrate-mineral interaction. Thus, formation of MAOM in areas of high microbial density (e.g., the rhizosphere and other microbial hotspots) should primarily occur through an in vivo microbial turnover pathway and favor C substrates that are first biosynthesized with high microbial carbon-use efficiency prior to incorporation in the MAOM pool. In contrast, in areas of low microbial density (e.g., certain regions of the bulk soil), MAOM formation should primarily occur through the direct sorption of intact or partially oxidized plant compounds to uncolonized mineral surfaces, minimizing the importance of carbon-use efficiency, and favoring C substrates with strong "sorptive affinity." Through this framework, we thus describe how the primacy of biotic vs. abiotic controls on MAOM dynamics is not mutually exclusive, but rather spatially dictated. Such an understanding may be integral to more accurately modeling soil organic matter dynamics across different spatial scales.

Methane emissions from tree stems: a new frontier in the global carbon cycle.

Tree stems from wetland, floodplain and upland forests can produce and emit methane (CH4 ). Tree CH4 stem emissions have high spatial and temporal variability, but there is no consensus on the biophysical mechanisms that drive stem CH4 production and emissions. Here, we summarize up to 30 opportunities and challenges for stem CH4 emissions research, which, when addressed, will improve estimates of the magnitudes, patterns and drivers of CH4 emissions and trace their potential origin. We identified the need: (1) for both long-term, high-frequency measurements of stem CH4 emissions to understand the fine-scale processes, alongside rapid large-scale measurements designed to understand the variability across individuals, species and ecosystems; (2) to identify microorganisms and biogeochemical pathways associated with CH4 production; and (3) to develop a mechanistic model including passive and active transport of CH4 from the soil-tree-atmosphere continuum. Addressing these challenges will help to constrain the magnitudes and patterns of CH4 emissions, and allow for the integration of pathways and mechanisms of CH4 production and emissions into process-based models. These advances will facilitate the upscaling of stem CH4 emissions to the ecosystem level and quantify the role of stem CH4 emissions for the local to global CH4 budget.

A city-scale assessment reveals that native forest types and overstory species dominate New York City forests.

Cities are increasingly focused on expanding tree canopy cover as a means to improve the urban environment by, for example, reducing heat island effects, promoting better air quality, and protecting local habitat. The majority of efforts to expand canopy cover focus on planting street trees or on planting native tree species and removing nonnatives in natural areas through reforestation. Yet many urban canopy assessments conducted at the city-scale reveal co-dominance by nonnative trees, fueling debates about the value of urban forests and native-specific management targets. In contrast, assessments within cities at site or park scales find that some urban forest stands harbor predominantly native biodiversity. To resolve this apparent dichotomy in findings, about the extent to which urban forests are native dominated, between the city-scale canopy and site-level assessments, we measure forest structure and composition in 1,124 plots across 53 parks in New York City's 2,497 ha of natural area forest. That is, we assess urban forests at the city-scale and deliberately omit sampling trees existing outside of forest stands but which are enumerated in citywide canopy assessments. We find that on average forest stand canopy is comprised of 82% native species in New York City forests, suggesting that conclusions that the urban canopy is co-dominated by nonnatives likely results from predominantly sampling street trees in prior city-scale assessments. However, native tree species' proportion declines to 75% and 53% in the midstory and understory, respectively, suggesting potential threats to the future native dominance of urban forest canopies. Furthermore, we find that out of 57 unique forest types in New York City, the majority of stands (81%) are a native type. We find that stand structure in urban forest stands is more similar to rural forests in New York State than to stand structure reported for prior assessments of the urban canopy at the city scale. Our results suggest the need to measure urban forest stands apart from the entire urban canopy. Doing so will ensure that city-scale assessments return data that align with conservation policy and management strategies that focus on maintaining and growing native urban forests rather than individual trees.

Understanding how microbiomes influence the systems they inhabit.

Translating the ever-increasing wealth of information on microbiomes (environment, host or built environment) to advance our understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here, we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system-level processes that they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted using constituent taxa (community-aggregated traits) from those properties that cannot currently be predicted using constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these three categories of microbial characteristics and connect them with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

Species associations overwhelm abiotic conditions to dictate the structure and function of wood-decay fungal communities.

Environmental conditions exert strong controls on the activity of saprotrophic microbes, yet abiotic factors often fail to adequately predict wood decomposition rates across broad spatial scales. Given that species interactions can have significant positive and negative effects on wood-decay fungal activity, one possibility is that biotic processes serve as the primary controls on community function, with abiotic controls emerging only after species associations are accounted for. Here we explore this hypothesis in a factorial field warming- and nitrogen-addition experiment by examining relationships among wood decomposition rates, fungal activity, and fungal community structure. We show that functional outcomes and community structure are largely unrelated to abiotic conditions, with microsite and plot-level abiotic variables explaining at most 19% of the total variability in decomposition and fungal activity, and 2% of the variability in richness and evenness. In contrast, taxonomic richness, evenness, and species associations (i.e., co-occurrence patterns) exhibited strong relationships with community function, accounting for 52% of the variation in decomposition rates and 73% in fungal activity. A greater proportion of positive vs. negative species associations in a community was linked to strong declines in decomposition rates and richness. Evenness emerged as a key mediator between richness and function, with highly even communities exhibiting a positive richness-function relationship and uneven communities exhibiting a negative or null response. These results suggest that community-assembly processes and species interactions are important controls on the function of wood-decay fungal communities, ultimately overwhelming substantial differences in abiotic conditions.