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DOE OSTI2021

Identifying dominant environmental predictors of freshwater wetland methane fluxes across diurnal to seasonal time scales

While wetlands are the largest natural source of methane (CH 4 ) to the atmosphere, they represent a large source of uncertainty in the global CH 4 budget due to the complex biogeochemical controls on CH 4 dynamics. Here we present, to our knowledge, the first multi-site synthesis of how predictors of CH 4 fluxes (FCH4) in freshwater wetlands vary across wetland types at diel, multiday (synoptic), and seasonal time scales. In this work we used several statistical approaches (correlation analysis, generalized additive modeling, mutual information, and random forests) in a wavelet-based multi-resolution framework to assess the importance of environmental predictors, nonlinearities and lags on FCH4 across 23 eddy covariance sites. Seasonally, soil and air temperature were dominant predictors of FCH4 at sites with smaller seasonal variation in water table depth (WTD). In contrast, WTD was the dominant predictor for wetlands with smaller variations in temperature (e.g., seasonal tropical/subtropical wetlands). Changes in seasonal FCH4 lagged fluctuations in WTD by ~17 ± 11 days, and lagged air and soil temperature by median values of 8 ± 16 and 5 ± 15 days, respectively. Temperature and WTD were also dominant predictors at the multiday scale. Atmospheric pressure (PA) was another important multiday scale predictor for peat-dominated sites, with drops in PA coinciding with synchronous releases of CH 4 . At the diel scale, synchronous relationships with latent heat flux and vapor pressure deficit suggest that physical processes controlling evaporation and boundary layer mixing exert similar controls on CH 4 volatilization, and suggest the influence of pressurized ventilation in aerenchymatous vegetation. In addition, 1- to 4-h lagged relationships with ecosystem photosynthesis indicate recent carbon substrates, such as root exudates, may also control FCH4. By addressing issues of scale, asynchrony, and nonlinearity, this work improves understanding of the predictors and timing of wetland FCH4 that can inform future studies and models, and help constrain wetland CH 4 emissions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Changing Interactions Between Trace Gas Fluxes, Belowground Chemistry, and Plant Traits Across an Arctic Thermokarst Landscape

Arctic permafrost soils are increasingly subject to thermokarst that is, abrupt ground subsidence caused by thaw. Wetlands can form within these depressions, leading to changes in organic matter decomposition and gas fluxes (CO 2 , CH 4 , N 2 O, NH 3 ). Thermokarst wetlands tend to be dominated by graminoids, while surrounding upland tussock tundra tends to be dominated by mixed communities of shrubs and graminoids. Here, to investigate how thermokarst alters the land-atmosphere exchange of C and N gases in Arctic tundra, we analyzed soil, porewater, above- and belowground biomass, and measured gas fluxes across dominant plant functional types (PFTs) within a lowland thermokarst wetland and adjacent upland tussock tundra. Both locations were overall sinks of CO 2 , sources of CH 4 , and sources of both N 2 O and NH 3 . We found that thermokarst wetlands emitted enough CH 4 to generate a positive radiative forcing in CO 2 equivalents (+1.2 μmol m −2 s −1 CO 2 -eq), counteracting the high CO 2 uptake. In contrast, the upland tussock tundra had a net negative radiative forcing (−1.2 μmol m −2 s −1 CO 2 -eq). Differences in gas flux and soil chemistry between upland and lowland are primarily driven by flooded conditions present in thermokarst wetland. Additionally, root biomass from graminoids across both lowlands and uplands significantly correlated with CH 4 fluxes, supporting previous observations of plant-mediated transport of CH 4 . Graminoid cover was correlated with increases in low molecular weight dissolved organic carbon, possibly associated with root exudates that fuel methanogenesis. Forb cover in the upland tussock tundra was significantly correlated with nine soil chemical variables, indicating that forbs may influence local soil chemistry or conversely, that soil chemistry controls where forbs grow. Overall, our findings indicate the variability in gas fluxes in the upland tussock tundra is partially controlled by PFT cover, while thermokarst wetlands emit enough CH 4 to counteract CO 2 uptake, with implications for carbon budget changes in Arctic systems.

Land-atmosphere feedback↗

DOE OSTI2022

Intra‐ and inter‐annual variability of nitrification in the rhizosphere of field‐grown bioenergy sorghum

Abstract Biological nitrification inhibition (BNI) and plant–microbe competition for ammonium (NH 4 + ) by sorghum ( Sorghum bicolor (L.) Moench) have the potential to suppress nitrification, reducing nitrate (NO 3 − ) and nitrous oxide (N 2 O) production for more sustainable bioenergy feedstock production. However, it is unknown how variability in environmental factors, field management, and plant growth affect the suppression of nitrification. We conducted a field trial with four genotypes of energy sorghum and four fertilization rates in central Illinois, USA, and measured soil N pools, potential nitrification and denitrification rates, and microbial community composition in bulk and rhizosphere soils to assess nitrification suppression throughout the 2018 and 2019 growing seasons. Concentrations of NO 3 − and NH 4 + were very low in rhizosphere soil regardless of fertilization level, suggesting strong N demand by plants and microbes. Potential nitrification was lower in the rhizosphere soil than bulk soil, and this suppression was strongest mid‐season ~2 months after planting in both years (20% suppression in 2018 and 58% in 2019). Since precipitation was lower during the mid‐growing season of 2019 compared to 2018, we speculate that hydrophilic BNI root exudates accumulated in the rhizosphere and suppressed nitrification more than in 2018 when soil moisture was higher. Unfertilized plots had greater nitrification suppression than fertilized plots during the mid‐season in 2018, but otherwise nitrification suppression was insensitive to fertilizer treatment. Potential denitrification was stimulated in the rhizosphere compared to bulk soil in both study years, suggesting that heterotrophic activity was stimulated by plant carbon inputs, possibly further suppressing slower‐growing chemoautotrophic nitrifying microbes. Overall, we found inter‐ and intra‐annual variation in nitrification suppression in the rhizosphere of field‐grown biomass sorghum, suggesting that plant phenology and environmental conditions should be considered when devising strategies to improve the nitrogen sustainability of this annual bioenergy crop.

09 BIOMASS FUELS↗

DOE OSTI2025

Rhizosphere Microbiome Diversity Potentially Supports Robust Nature of Field Pennycress ( Thlaspi arvense L.) in Dryland Cropping Systems of Eastern Washington

ABSTRACT Field pennycress ( Thlaspi arvense L.) is an annual in the Brassicaceae family and is currently being developed as an oilseed intermediate crop suitable for renewable biodiesel and jet fuel. It displays many desirable characteristics for this role including cold tolerance, a rapid life cycle, and a seed fatty acid profile conducive to bioenergy generation. These traits make field pennycress favorable for winter oilseed cultivation in the inland Pacific Northwest (iPNW). Simultaneously, intermediate crops are an increasingly recognized component of both agronomic sustainability and soil health management. Intermediate crops enhance soil microbial diversity, which benefits both soil and plant health. To understand the impact of field pennycress on soil microbial diversity, two natural accessions and seven experimental accessions were grown at three sites in Eastern Washington. Aboveground biomass and rhizosphere soil were then collected. Soil genomic DNA was extracted from rhizosphere samples and used to generate an amplicon library for bacterial (16S) and fungal (ITS) rRNA sequences. The resulting libraries were analyzed in QIIME2, which revealed that not only did the fad2 deficient line from the Spring32‐10 background have significantly increased aboveground biomass production compared to other pennycress genotypes, but also displayed significantly higher β‐diversity in the rhizosphere community specifically at the site experiencing the driest conditions. ANCOM analysis showed that multiple sequences similar to beneficial plant and soil health enhancing organisms such as Trichoderma spirale , Pseudomonas spp., and Methylobacterium goesingense were found to be enriched in the microbiome of the fad2 Spring32‐10 background also at that site. To add additional context to rhizosphere community data, root exudates from two pennycress genotypes were captured in magenta boxes and analyzed using HPLC. Future work will expand our understanding of the mechanisms by which field pennycress creates diversity in the rhizosphere, thus expanding our ability to cultivate this crop in the iPNW.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Virocell Necromass Provides Limited Plant Nitrogen and Elicits Rhizosphere Metabolites That Affect Phage Dynamics

Bacteriophages impact soil bacteria through lysis, altering the availability of organic carbon and plant nutrients. However, the magnitude of nutrient uptake by plants from lysed bacteria remains unknown, partly because this process is challenging to investigate in the field. In this study, we extend ecosystem fabrication (EcoFAB 2.0) approaches to study plant-bacteria-phage interactions by comparing the impact of virocell (phage-lysed) and uninfected 15 N-labelled bacterial necromass on plant nitrogen acquisition and rhizosphere exometabolites composition. We show that grass Brachypodium distachyon derives some nitrogen from amino acids in uninfected Pseudomonas putida necromass lysed by sonication but not from virocell necromass. Additionally, the bacterial necromass elicits the formation of rhizosphere exometabolites, some of which (guanosine), alongside tested aromatic acids ( p -coumaric and benzoic acid), show bacterium-specific effects on bacteriophage-induced lysis when tested in vitro. The study highlights the dynamic feedback between virocell necromass and plants and suggests that root exudate metabolites can impact bacteriophage infection dynamics.

Brachypodium↗

DOE OSTI2026

Lost and found: Rediscovering microbiome-associated phenotypes that reshape agricultural sustainability

Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification—key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and exudate metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. These findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2025

BONCAT-Live for isolation and cultivation of active environmental bacteria

In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including associations with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular, and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating individual microbial cells that respond to specific changes for cultivation has been difficult. To address this, we implemented a novel bacterial isolation approach (BONCAT-Live) by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient-enriched conditions. From the Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in-depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.

Analytical Methods↗

DOE OSTI2021

Visualizing the Hidden Half: Plant-Microbe Interactions in the Rhizosphere

Plant roots and the associated rhizosphere constitute a dynamic environment that fosters numerous intra- and interkingdom interactions, including metabolite exchange between plants and soil mediated by root exudates and the rhizosphere microbiome. These interactions affect plant fitness and performance, soil health, and the belowground carbon budget.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Breaking the reproducibility barrier with standardized protocols for plant–microbiome research

Inter-laboratory replicability is crucial yet challenging in microbiome research. Leveraging microbiomes to promote soil health and plant growth requires understanding underlying molecular mechanisms using reproducible experimental systems. In a global collaborative effort involving five laboratories, we aimed to help advance reproducibility in microbiome studies by testing our ability to replicate synthetic community assembly experiments. Our study compared fabricated ecosystems constructed using two different synthetic bacterial communities, the model grass Brachypodium distachyon, and sterile EcoFAB 2.0 devices. All participating laboratories observed consistent inoculum-dependent changes in plant phenotype, root exudate composition, and final bacterial community structure, where Paraburkholderia sp. OAS925 could dramatically shift microbiome composition. Comparative genomics and exudate utilization linked the pH-dependent colonization ability of Paraburkholderia, which was further confirmed with motility assays. The study provides detailed protocols, benchmarking datasets, and best practices to help advance replicable science and inform future multi-laboratory reproducibility studies.

Novak, Vlastimil↗

DOE OSTI2021

Carbon–Nutrient Economy of the Rhizosphere: Improving Biogeochemical Prediction and Scaling Feedbacks from Ecosystem to Regional Scales

Our project has advanced the science of plant-soil-microbial dynamics across these areas: i) nutrient cycling and plant uptake; ii) root exudation and priming; and, iii) mycorrhizal dynamics. Our project has accomplished 5 main developments: 1) Incorporation of phosphorus cycling into the Fixation & Uptake of Nutrients (FUN 3.0) model. 2) Coupling of FUN 3.0 into the E3SM Land Model (ELM). 3) Data collection across a large mycorrhizal gradient in the US, as well data in the tropics, to parameterize, test, and validate the model. 4)Scaling up mycorrhizal association measurements across landscapes using airborne hyperspectral remote sensing data. 5) Evaluation of global carbon and nutrient cycle impacts in the Community Land Model (CLM5.0) from a suite of new global mycorrhizal association maps. Over 25 publications resulted from this project, with more continuing past the project funded lifetime. Paper highlights from most of these publications have already been submitted to the DOE paper submission online system. These publications include journals such as Science and PNAS, as well as top disciplinary journals from the Nature journals, Global Change Biology, New Phytologist, and Ecology Letters, for example. Our project also contributed to improving the process representation, capabilities, and accuracy of the DOE ELM. Overall, this project significantly advanced the science of belowground plant-soil-microbial interactions as well as technical capabilities from remote sensing to modeling.

59 BASIC BIOLOGICAL 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↗

DOE OSTI2025

RhizoGrid Indexed Sorghum Rhizosphere Multi-Omics

PerCon SFA project data dentification of spatially resolved biomarkers of drought in Sorghum bicolor rhizosphere molecular-microbe interactions using a novel root cartography "RhizoGrid" system for sampling plants under drought and control conditions across 10 equally sized root zone environments (4 quadrants each). Each quadrant was sampled and processed for 16S amplicon, metabolomics, and X-ray computed tomography (XCT). Data download includes experimental metadata and results files for 16S rRNA sequence analysis of microbial community assembly (processed data files), liquid chromatography mass spectrometry (LC-MS) metabolomics analysis of microbial community root exudates (processed data files), X-ray computed tomography (XCT) spatial gradient analysis (raw and processed data files) of microbial community composition, and related computational modeling outputs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture

The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Understanding the dynamic interactions of root-knot nematodes and their host: role of plant growth promoting bacteria and abiotic factors

Root-knot nematodes (Meloidogyne spp., RKN) are among the most destructive endoparasitic nematodes worldwide, often leading to a reduction of crop growth and yield. Insights into the dynamics of host-RKN interactions, especially in varied biotic and abiotic environments, could be pivotal in devising novel RKN mitigation measures. Plant growth-promoting bacteria (PGPB) involves different plant growth-enhancing activities such as biofertilization, pathogen suppression, and induction of systemic resistance. We summarized the up-to-date knowledge on the role of PGPB and abiotic factors such as soil pH, texture, structure, moisture, etc. in modulating RKN-host interactions. RKN are directly or indirectly affected by different PGPB, abiotic factors interplay in the interactions, and host responses to RKN infection. We highlighted the tripartite (host-RKN-PGPB) phenomenon with respect to (i) PGPB direct and indirect effect on RKN-host interactions; (ii) host influence in the selection and enrichment of PGPB in the rhizosphere; (iii) how soil microbes enhance RKN parasitism; (iv) influence of host in RKN-PGPB interactions, and (v) the role of abiotic factors in modulating the tripartite interactions. Furthermore, we discussed how different agricultural practices alter the interactions. Finally, we emphasized the importance of incorporating the knowledge of tripartite interactions in the integrated RKN management strategies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Phyllosphere exudates select for distinct microbiome members in sorghum epicuticular wax and aerial root mucilage

Phyllosphere exudates create specialized microhabitats that shape microbial community diversity. We explored the microbiome associated with two sorghum phyllosphere exudates, the epicuticular wax and aerial root mucilage. We assessed the microbiome associated with the wax from sorghum plants over two growth stages, and the root mucilage additionally from nitrogen-fertilized and non-fertilized plants. In parallel, we isolated and characterized hundreds of bacteria from wax and mucilage, and integrated data from cultivation-independent and cultivation-dependent approaches to gain insights into exudate diversity and bacterial phenotypes. We found that Sphingomonadaceae and Rhizobiaceae families were the major taxa in the wax regardless of water availability and plant developmental stage to plants. The cultivation-independent mucilage-associated bacterial microbiome contained Erwiniaceae, Flavobacteriaceae, Rhizobiaceae, Pseudomonadaceae, Sphingomonadaceae, and its structure was strongly influenced by sorghum development but only modestly influenced by fertilization. In contrast, the fungal community structure of mucilage was strongly affected by the year of sampling but not by fertilization or plant developmental stage, suggesting a decoupling of fungal-bacterial dynamics in the mucilage. Our bacterial isolate collection from wax and mucilage had several isolates that matched 100% to detected amplicon sequence variants, and were enriched on media that selected for phenotypes including phosphate solubilization, putative diazotrophy, resistance to desiccation, capability to grow on methanol as a carbon source, and ability to grow in the presence of linalool and β-caryophyllene (terpenes in sorghum wax). This work expands our understanding of the microbiome of phyllosphere exudates and supports our long-term goal to translate microbiome research to support sorghum cultivation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Prevalent root-derived phenolics drive shifts in microbial community composition and prime decomposition in forest soil

Phenolic compounds perform various functions in soil ranging from microbial substrate to toxin and form the basis of several plant-mediated processes. The aim of this study was to investigate how phenolics commonly exuded by tree roots influence soil organic matter (SOM) decomposition and interact with other labile forms of carbon (C) abundant in root exudates. Therefore, we performed a 38-day incubation experiment and assessed whether phenolic compounds (benzoic acid, caffeic acid and catechin) facilitated or inhibited SOM decomposition in a glucose-amended forest soil. Changes in decomposition, substrate use, fungal and bacterial community composition, and microbial abundance and activity were measured over time using 13 C-stable-isotope tracing, DNA-based molecular methods and enzyme assays. Our findings showed that phenolics inhibited microbial activity and abundance to varying degrees. Yet, benzoic acid was the only compound producing a substantial priming effect leading to a 21% increase in SOM decomposition, which was amplified in glucose-amended soils. This stimulation in microbial activity was associated with an increase in β-1,4-glucosidase activity and the bacterial genera Paraburkholderia and Caballeronia of the Burkholderiaceae family. Phenolics drove microbial community shifts in glucose-amended soils with negligible interactive effects. In conclusion, phenolic priming of SOM decomposition is associated with microbial community shifts and amplified in the presence of glucose. This evidence emphasizes the need for considering phenolics and interactions among root exudates as priming mechanisms in the rhizosphere and other soil environments where aromatics and phenolic compounds are abundant.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Choreographing root architecture and rhizosphere interactions through synthetic biology

Abstract Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Arbuscular mycorrhizal trees cause a higher carbon to nitrogen ratio of soil organic matter decomposition via rhizosphere priming than ectomycorrhizal trees

Tree roots and their associated microbes can significantly influence soil organic matter (SOM) decomposition, i.e., the rhizosphere priming effect. This effect is expected to be greater in trees associated with arbuscular mycorrhizal (AM) fungi, which produce higher extracellular enzymes especially surrounding hyphae, than in trees associated with ectomycorrhizal (ECM) fungi. In this work, we selected five tree species associated with AM (Juglans mandshurica Maxim. and Cunninghamia lanceolata (Lamb.) Hook.) or ECM (Picea koraiensis Nakai, Quercus mongolica Fischer ex Turcz. and Larix kaempferi (Lamb.) Carriere). We grew tree seedlings inside of cores lined with different mesh sizes to investigate how roots, hyphae and exudates influence soil carbon (C) and nitrogen (N) mineralization via the rhizosphere priming effect, using a 13 C natural abundance approach and a 15 N pool dilution method, concurrently. We found that tree seedlings significantly accelerated soil C decomposition by on average 78%, i.e., positive priming, compared to unplanted control pots. AM-associated trees induced 2.1 times greater soil C decomposition than ECM-associated trees across all mesh sizes. In contrast, gross N mineralization did not differ between tree-mycorrhizal associations. Compared to ECM counterparts, AM-associated trees had higher C- and lower N-degrading enzyme activities. Consequently, AM-associated trees induced a significantly higher C:N ratio of SOM decomposition than their ECM counterparts, which could be associated with the differences in soil enzyme activities for C and N degradation. Further, for both AM- and ECM-associated trees, we found no significant influences of mesh size on soil C decomposition, suggesting that the rhizosphere priming effect of mycorrhizal symbiosis was predominantly driven by root exudates. We conclude that SOM decomposition caused by AM-associated trees may have a higher C:N ratio than that by ECM-associated trees mainly due to differences in microbial enzyme investment. Our findings imply that tree-mycorrhizal associations are capable of modulating soil biogeochemical cycling via the rhizosphere priming effect.

54 ENVIRONMENTAL SCIENCES↗