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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Tree Canopies Reflect Mycorrhizal Composition

Mycorrhizae alter global patterns of CO 2 fertilization, carbon storage, and elemental cycling, yet knowledge of their global distributions is currently limited by the availability of forest inventory data. Here, we show that maps of tree-mycorrhizal associations (hereafter “mycorrhizal maps”) can be improved by the novel technology of imaging spectroscopy because mycorrhizal signatures propagate up from plant roots to impact forest canopy chemistry. We analyzed measurements from 143 airborne imaging spectroscopy surveys over 112,975 individual trees collected across 13 years. Results show remarkable accuracy in capturing ground truth observations of mycorrhizal associations from canopy signals across disparate landscapes (R 2 = 0.92, p < 0.01). Additionally, upcoming imaging spectroscopy satellite missions can reveal new insights into landscape-scale variations in water, nitrogen, phosphorus, carotenoid/anthocyanin, and cellulose/lignin composition. Applied globally, this approach could improve the spatial precision of mycorrhizal distributions by a factor of roughly 104 and facilitate the incorporation of dynamic shifts in forest composition into Earth system models.

58 GEOSCIENCES↗
DOE OSTI2021

The Switchgrass Microbiome: A Review of Structure, Function, and Taxonomic Distribution

Switchgrass (Panicum virgatum L.) has been championed as a promising bioenergy crop due to its high productivity across a wide environmental range. The switchgrass microbiome—including bacteria, archaea, fungi, and other microbiota inhabiting soil and plant tissues—can influence plant function substantially. We conducted a review of the literature investigating switchgrass microbiome structure, key functional roles, and taxa isolated from field-grown plants. Although site conditions and plant compartment (i.e., location within shoots, roots, or root-influenced soil) appear to be the strongest drivers of switchgrass microbiome structure, the microbiome is also shaped by climate, season, and host genotype. Studies comparing across plant species show that the switchgrass microbiome is more similar to the microbiomes of other perennial plants than to the microbiomes of annual plants. Members of the switchgrass microbiome confer several benefits to their host. Most notably, mycorrhizal fungi can increase plant biomass many-fold, associative nitrogen-fixing bacteria can provide a substantial portion of the plant’s nitrogen demand, and fungal endophytes can improve plant tolerance to drought. Although the fungi and bacteria cultured from switchgrass represent only a portion of the microbiome, these serve as a valuable resource for researchers interested in investigating functional outcomes of the switchgrass microbiome. We highlight areas where additional research is necessary for a more comprehensive understanding of switchgrass microbiome structure, function, and potential to enhance sustainable bioenergy production. Key gaps include the role of understudied organisms (e.g., viruses, microeukaryotes, and nonmycorrhizal fungi), multitrophic relationships, mechanisms underpinning switchgrass–microbiome interactions, and field-scale validation of experimental findings.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Arbuscular Mycorrhizal Tree Communities Have Greater Soil Fungal Diversity and Relative Abundances of Saprotrophs and Pathogens than Ectomycorrhizal Tree Communities

Trees associating with different mycorrhizas often differ in their effects on litter decomposition, nutrient cycling, soil organic matter (SOM) dynamics, and plant-soil interactions. For example, due to differences between arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) tree leaf and root traits, ECM-associated soil has lower rates of C and N cycling and lower N availability than AM-associated soil. These observations suggest that many groups of nonmycorrhizal fungi should be affected by the mycorrhizal associations of dominant trees through controls on nutrient availability. To test this overarching hypothesis, we explored the influence of predominant forest mycorrhizal type and mineral N availability on soil fungal communities using next-generation amplicon sequencing. Soils from four temperate hardwood forests in southern Indiana, United States, were studied; three forests formed a natural gradient of mycorrhizal dominance (100% AM tree basal area to 100% ECM basal area), while the fourth forest contained a factorial experiment testing long-term N addition in both dominant mycorrhizal types. We found that overall fungal diversity, as well as the diversity and relative abundance of plant pathogenic and saprotrophic fungi, increased with greater AM tree dominance. Additionally, tree community mycorrhizal associations explained more variation in fungal community composition than abiotic variables, including soil depth, SOM content, nitrification rate, and mineral N availability. Our findings suggest that tree mycorrhizal associations may be good predictors of the diversity, composition, and functional potential of soil fungal communities in temperate hardwood forests. These observations help explain differing biogeochemistry and community dynamics found in forest stands dominated by differing mycorrhizal types.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mycorrhizal Distributions Impact Global Patterns of Carbon and Nutrient Cycling

Most tree species predominantly associate with a single type of mycorrhizal fungi, which can differentially affect plant nutrient acquisition and biogeochemical cycling. Uncertainties in mycorrhizal distributions are non-trivial, and current estimates disagree in up to 50% over 40% of the land area, including tropical forests. Remote sensing capabilities for mycorrhizal detection show promise for refining these estimates further. Here, we address for the first time the impact of mycorrhizal distributions on global carbon and nutrient cycling. Using the state-of-the-art carbon-nitrogen economics within the Community Land Model version 5, we found Net Primary Productivity (NPP) increased throughout the 21st century by 20%; however, as soil nitrogen has progressively become limiting, the costs to NPP for nitrogen acquisition—that is, to mycorrhizae—have increased at a faster rate by 60%. This suggests that nutrient acquisition will increasingly demand a higher portion of assimilated carbon to support the same productivity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Mycorrhizal effects on crop yield and soil ecosystem functions in a long‐term tillage and fertilization experiment

Summary It is well understood that agricultural management influences arbuscular mycorrhizal (AM) fungi, but there is controversy about whether farmers should manage for AM symbiosis. We assessed AM fungal communities colonizing wheat roots for three consecutive years in a long‐term (> 14 yr) tillage and fertilization experiment. Relationships among mycorrhizas, crop performance, and soil ecosystem functions were quantified. Tillage, fertilizers and continuous monoculture all reduced AM fungal richness and shifted community composition toward dominance of a few ruderal taxa. Rhizophagus and Dominikia were depressed by tillage and/or fertilization, and their abundances as well as AM fungal richness correlated positively with soil aggregate stability and nutrient cycling functions across all or no‐tilled samples. In the field, wheat yield was unrelated to AM fungal abundance and correlated negatively with AM fungal richness. In a complementary glasshouse study, wheat biomass was enhanced by soil inoculum from unfertilized, no‐till plots while neutral to depressed growth was observed in wheat inoculated with soils from fertilized and conventionally tilled plots. This study demonstrates contrasting impacts of low‐input and conventional agricultural practices on AM symbiosis and highlights the importance of considering both crop yield and soil ecosystem functions when managing mycorrhizas for more sustainable agroecosystems.

Peng, Zhenling↗
DOE OSTI2022

Modeling Global Carbon Costs of Plant Nitrogen and Phosphorus Acquisition

Abstract Most Earth system models (ESMs) do not explicitly represent the carbon (C) costs of plant nutrient acquisition, which leads to uncertainty in predictions of the current and future constraints to the land C sink. We integrate a plant productivity‐optimizing nitrogen (N) and phosphorus (P) acquisition model (fixation & uptake of nutrients, FUN) into the energy exascale Earth system (E3SM) land model (ELM). Global plant N and P uptake are dynamically simulated by ELM‐FUN based on the C costs of nutrient acquisition from mycorrhizae, direct root uptake, retranslocation from senescing leaves, and biological N fixation. We benchmarked ELM‐FUN with three classes of products: ILAMB, a remotely sensed nutrient limitation product, and CMIP6 models; we found significant improvements in C cycle variables, although the lack of more observed nutrient data prevents a comprehensive level of benchmarking. Overall, we found N and P co‐limitation for 80% of land area, with the remaining 20% being either predominantly N or P limited. Globally, the new model predicts that plants invested 4.1 Pg C yr −1 to acquire 841.8 Tg N yr −1 and 48.1 Tg P yr −1 (1994–2005), leading to significant downregulation of global net primary production (NPP). Global NPP is reduced by 20% with C costs of N and 50% with C costs of NP. Modeled and observed nutrient limitation agreement increases when N and P are considered together ( r 2 from 0.73 to 0.83).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Modeling Mycorrhizal Carbon Costs in Temperate Forests: The Impacts of Functional Diversity and Global Change Factors

Mycorrhizal fungi form symbiotic relationships with most plant species, facilitating nutrient acquisition while consuming a significant fraction of the plant's photosynthetic carbon (C), which we define as the mycorrhizal C cost. Drivers of the mycorrhizal C cost, which is crucial for predicting environmental impacts on plant productivity, remain under-explored and difficult to quantify. Ecosystem models that incorporate mycorrhizae can offer insights into mycorrhizal C cost dynamics, but their predictions have rarely been validated against empirical data. Here, in this study, we used the Myco-CORPSE model, which explicitly simulates mycorrhizal processes alongside soil carbon and nitrogen cycling, to investigate the drivers of mycorrhizal C cost in temperate forests. Applying this model to over 1,800 forest inventory plots across the eastern United States, we found that the simulations matched published data, showing higher C allocation to ectomycorrhizal (ECM) fungi (16.0% of net primary production (NPP)) compared to arbuscular mycorrhizal (AM) fungi (5.8% of NPP). Further analysis showed that mixed forests, co-dominated by both AM and ECM trees, allocated less C to mycorrhizal fungi compared to forests dominated by either AM or ECM fungi alone, due to complementary nutrient acquisition strategies. Elevated Nitrogen (N) deposition and higher temperatures reduce mycorrhizal C costs, favoring AM strategies. Conversely, elevated CO 2 (eCO 2 ) increased plant N demand and mycorrhizal C costs, favoring ECM strategies that access organic N sources. These findings underscore the critical role of mycorrhizal functional diversity in plant nutrient acquisition and C dynamics, providing new insights into how mycorrhizal symbioses respond to global change.

Shao, Siya [Dartmouth College, Hanover, NH (United↗
DOE OSTI2025

Habitat specialization and edge effects of soil microbial communities in a fragmented landscape

Abstract Soil microorganisms play outsized roles in nutrient cycling, plant health, and climate regulation. Despite their importance, we have a limited understanding of how soil microbes are affected by habitat fragmentation, including their responses to conditions at fragment edges, or “edge effects.” To understand the responses of soil communities to edge effects, we analyzed the distributions of soil bacteria, archaea, and fungi in an experimentally fragmented system of open patches embedded within a forest matrix. In addition, we identified taxa that consistently differed among patch, edge, or matrix habitats (“specialists”) and taxa that showed no habitat preference (“nonspecialists”). We hypothesized that microbial community turnover would be most pronounced at the edge between habitats. We also hypothesized that specialist fungi would be more likely to be mycorrhizal than nonspecialist fungi because mycorrhizae should be affected more by different plant hosts among habitats, whereas specialist prokaryotes would have smaller genomes (indicating reduced metabolic versatility) and be less likely to be able to sporulate than nonspecialist prokaryotes. Across all replicate sites, the matrix and patch soils harbored distinct microbial communities. However, sites where the contrasts in vegetation and pH between the patch and matrix were most pronounced exhibited larger differences between patch and matrix communities and tended to have edge communities that differed from those in the patch and forest. There were similar numbers of patch and matrix specialists, but very few edge specialist taxa. Acidobacteria and ectomycorrhizae were more likely to be forest specialists, while Chloroflexi, Ascomycota, and Glomeromycota (i.e., arbuscular mycorrhizae) were more likely to be patch specialists. Contrary to our hypotheses, nonspecialist bacteria were not more likely than specialist bacteria to have larger genomes or to be spore‐formers. We found partial support for our mycorrhizal hypothesis: arbuscular mycorrhizae, but not ectomycorrhizae, were more likely to be specialists. Overall, our results indicate that soil microbial communities are sensitive to edges, but not all taxa are equally affected, with arbuscular mycorrhizae in particular showing a strong response to habitat edges. In the context of increasing habitat fragmentation worldwide, our results can help inform efforts to maintain the structure and functioning of the soil microbiome.

Winfrey, Claire C. [Department of Ecology and Evol↗
DOE OSTI2022

Grassland ecosystem type drives AM fungal diversity and functional guild distribution in North American grasslands

Nutrient exchange forms the basis of the ancient symbiotic relationship that occurs between most land plants and arbuscular mycorrhizal (AM) fungi. Plants provide carbon (C) to AM fungi and fungi provide the plant with nutrients such as nitrogen (N) and phosphorous (P). Nutrient addition can alter this symbiotic coupling in key ways, such as reducing AM fungal root colonization and changing the AM fungal community composition. However, environmental parameters that differentiate ecosystems and drive plant distribution patterns (e.g., pH, moisture), are also known to impact AM fungal communities. Identifying the relative contribution of environmental factors impacting AM fungal distribution patterns is important for predicting biogeochemical cycling patterns and plant-microbe relationships across ecosystems. Here, to evaluate the relative impacts of local environmental conditions and long-term nutrient addition on AM fungal abundance and composition across grasslands, we studied experimental plots amended for 10 years with N, P, or N and P fertilizer in different grassland ecosystem types, including tallgrass prairie, montane, shortgrass prairie, and desert grasslands. Contrary to our hypothesis, we found ecosystem type, not nutrient treatment, was the main driver of AM fungal root colonization, diversity, and community composition, even when accounting for site-specific nutrient limitations. We identified several important environmental drivers of grassland ecosystem AM fungal distribution patterns, including aridity, mean annual temperature, root moisture, and soil pH. This work provides empirical evidence for niche partitioning strategies of AM fungal functional guilds and emphasizes the importance of long-term, large scale research projects to provide ecologically relevant context to nutrient addition studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Comparative transcriptomics uncovers poplar and fungal genetic determinants of ectomycorrhizal compatibility

Ectomycorrhizal symbiosis supports tree growth and is crucial for nutrient cycling and temperate and boreal ecosystems functioning. The establishment of functional ectomycorrhiza (ECM) first requires the association of compatible partners. However, host and fungal genetic determinants governing mycorrhizal compatibility are unknown. To identify such factors in poplar and its fungal associates, we mined existing and de novo tree and fungal transcriptional datasets. We identified co-expressed genes enabling ECM symbiosis at early and mature stages of the interaction. These sets of genes can be divided into general fungal-sensing and ECM-specific components. We highlight the importance of fungal modulation of plant JA-related defenses and the regulation of secretory pathways for ECM compatibility, including upregulation of key fungal small secreted proteins, the downregulation of plant secreted peroxidases, and the downregulation of plant cell wall remodeling proteins concomitantly with the upregulation of fungal glycosyl hydrolases acting on pectin. Not only gene regulation, but also its temporal scale and dynamics seem to play a crucial role for mycorrhizal compatibility. The expression profile of the host Common Symbiosis Pathway and nutrient transporters was also studied, revealing constitutive levels of expression and moderate upregulation in compatible ECM interactions. Overall, these results underscore the importance of novel biological functions during the establishment of ECM symbiosis, help us gain insights into the molecular events determining mycorrhiza compatibility, and serve as a data-rich transcriptomic resource to open new research questions in the field.

Marqués‐Gálvez, José Eduardo↗
DOE OSTI2023

Shifts in bacterial traits under chronic nitrogen deposition align with soil processes in arbuscular, but not ectomycorrhizal-associated trees

Nitrogen (N) deposition increases soil carbon (C) storage by reducing microbial activity. These effects vary in soil beneath trees that associate with arbuscular (AM) and ectomycorrhizal (ECM) fungi. Variation in carbon C and N uptake traits among microbes may explain differences in soil nutrient cycling between mycorrhizal associations in response to high N loads, a mechanism not previously examined due to methodological limitations. Here, we used quantitative Stable Isotope Probing (qSIP) to measure bacterial C and N assimilation rates from an added organic compound, which we conceptualize as functional traits. As such, we applied a trait-based approach to explore whether variation in assimilation rates of bacterial taxa can inform shifts in soil function under chronic N deposition. We show taxon-specific and community-wide declines of bacterial C and N uptake under chronic N deposition in both AM and ECM soils. N deposition-induced reductions in microbial activity were mirrored by declines in soil organic matter mineralization rates in AM but not ECM soils. Our findings suggest C and N uptake traits of bacterial communities can predict C cycling feedbacks to N deposition in AM soils, but additional data, for instance on the traits of fungi, may be needed to connect microbial traits with soil C and N cycling in ECM systems. In conclusion, our study also highlights the potential of employing qSIP in conjunction with trait-based analytical approaches to inform how ecological processes of microbial communities influence soil functioning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Root biomass and traits across four lowland Panamanian forests from 0 - 1.2 m soil depths

Fine roots are key to ecosystem-scale nutrient, carbon (C), and water cycling, yet our understanding of fine root traits variation within and among tropical forests, one of Earth’s most C-rich ecosystems, is limited. We characterized root biomass, morphology, nutrient content, and arbuscular mycorrhizal fungal (AMF) colonization in 10 cm increments to 1.2 m depth across four distinct lowland Panamanian forests. The datasets provided include a .xlsx file for fine root characteristics across 10 cm increment depths to 1.2 m collected from late 2017 to 2018 across four different forests. Root characteristics include live fine root biomass, dead fine root biomass, coarse root biomass, specific root length, root diameter, root tissue density, specific root area, arbuscular mycorrhizal fungi colonization, root chemistry (e.g., organic chemistry), root %N, root %C, root C/N ratio, and root radiocarbon content. This .xlsx file contain four tabs with 1) Dataset; 2) Metadata with information about each column in the dataset; 3) The sampling methods summarized; 4) Sites information. We also provided csv files for each of these tabs. Additionally, a .kml file is provided with coordinates for all 32 plots included in the study across four forests (n = 8 plots per site/forest). This dataset serves as baseline data before a throughfall exclusion experiment, Panama Rainforest Changes with Experimental Drying (PARCHED), was implemented. No special software is needed to open these files.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Data from a throughfall exclusion experiment: Fine root dynamics, morphology, chemistry, and AMF colonization across four lowland Panamanian forests

Fine roots regulate forest nutrient, carbon, and water cycling, yet their variation within and among tropical forests remains under-characterized. We quantified root productivity, disappearance, and stocks to 1 m using minirhizotron imaging, and we measured morphology, elemental composition [root carbon (C), root nitrogen (N), root phosphorus (P)], and arbuscular mycorrhizal fungi (AMF) colonization to 20 cm using ingrowth cores and sequential coring. Sampling took place in four distinct lowland Panamanian forests (32 plots; 8 per forest) from 2018 through 2022 under control and throughfall-exclusion (drought) treatments in the Panama Rainforest Changes with Experimental Drying (PARCHED) experiment.The dataset is presented as an Excel workbook with six tabs. The first tab is the data dictionary. Tab S1 contains ingrowth-core production and mortality, morphology and soil moisture. Tab S2 contains sequential-coring standing stocks with associated morphology and soil moisture. Tab S3 contains minirhizotron row data records to 1 m depth, including per-frame root length and diameter, normalized length metrics, and session timing. Tab S4 contains AMF colonization. Tab S5 contains fine-root chemistry at 0–10 cm, reporting %P, %C, %N, and C:N for samples collected via ingrowth cores and sequential-coring standing stocks. CSV mirrors for each tab are provided, and a KML file supplies coordinates for all 32 plots.Key variables span live and dead fine-root biomass (and coarse fractions where applicable), specific root length (SRL) and area (SRA), diameter, root tissue density (RTD), soil moisture, AMF colonization, root %N, %C, %P, and C:N, along with minirhizotron root length and diameter. Depth, season, treatment, and plot/site identifiers are included to support cross-tab integration and analysis from 0–100 cm (minirhizotron) and 0–20 cm (cores).Units are reported in-column and missing values are coded as NA. No special software is required to open or use the files (Excel, CSV, and KML compatible).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Testing mechanisms of how mycorrhizal associations affect forest soil carbon and nitrogen cycling (Final Technical Report)

Trees are in a symbiotic partnership with mycorrhizal fungi in which they provide the fungi with carbon from photosynthesis and the fungi provide the trees with nutrients and water. In temperate forests, the vast majority of trees form symbioses with one of two types of mycorrhizal fungi—arbuscular mycorrhizal (AM) fungi or ectomycorrhizal (EcM) fungi. These fungi differ in their morphology, hyphal length, and nutrient acquisition strategies. Many studies have found systematic differences in soil organic matter and nitrogen availability between forest stands dominated by AM-associating trees versus EcM-associating trees. For instance, there is a larger proportion of organic matter that is mineral-associated, more available nitrogen, and lower soil carbon to nitrogen ratios in AM forest stands relative to EcM forests stands. However, the mechanisms driving these patterns are not known, which complicates our ability to model soil organic matter dynamics in forested ecosystems. The main objective of this research was to understand the degree to which the observed differences in soil C and N dynamics between AM and EcM dominated forests are driven by tree traits like litter decomposability and root exudation versus mycorrhizal fungal nutrient acquisition strategies. We investigated these mechanisms using observations and targeted experiments and incorporated this knowledge into a process-based soil organic matter model. The observational studies compared the importance of leaf litter decomposability versus fungal identity on soil organic matter processes. We found that often fungal identity and traits were more important drivers of soil organic matter patterns than leaf litter decomposability. We ran two novel experiments: 1) a growth chamber experiment across four EcM and four AM tree species using a 13 C-labeled atmosphere to trace seedling-derived C into hyphae, the rhizosphere, and soil; and 2) an in situ decomposition experiment of six different 13 C and 15 N labeled litters that ranged in decomposability incubated across a gradient of EcM dominance at three sites that capture important variation in climate, soils, and forest species composition. In the first experiment, we found no significant differences of seedling mycorrhizal association on soil carbon sequestration over a growing season, but we did find that mycorrhizal association affected rhizodeposition with EcM-associating seedlings depositing more carbon in response to increased nitrogen availability. The decomposition experiment is still ongoing, but thus far, we have found slower litter decomposition in only one of three EcM-dominated forests which suggests that differences between AM- and EcM-dominated forests depend on the environmental context and identity of the EcM fungi. Lastly, we explicitly incorporated mycorrhizal processes into the Carbon, Organisms, Rhizosphere, and Protection in the Soil Environment (CORPSE) model creating Myco-CORPSE. By including the different nutrient acquisition strategies of AM and EcM fungi, we explored the conditions under which EcM fungi can slow decomposition rates and lead to greater soil organic carbon accumulation compared to AM fungi. We found that the effect of EcM fungi was highly context dependent and that EcM fungi decreased decomposition in colder forests with recalcitrant litter inputs and when they produced oxidases and necromass-degrading enzymes. Our research highlights the importance of fungal nutrient acquisition in driving soil organic matter patterns and the need to move beyond the AM-EcM dichotomy to consider the identity and traits of the specific fungi participating in the symbiosis. Overall, this research has resulted in six, peer-reviewed published papers in journals such as Global Change Biology, Ecology (2), Soil Biology and Biochemistry, and Ecosystems (2). There are at least two more papers in progress on this research including one that was recently submitted to Global Change Biology.

54 ENVIRONMENTAL SCIENCES↗