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DOE OSTI2026

Deep Convection‐Driven Downward Transport of Trace Gases and Aerosols From the Free Troposphere to the Boundary Layer

Deep convective clouds regulate Earth's energy and moisture budgets, yet their impact on the atmospheric boundary layer (BL) composition remains underexplored. Using long-term observations from three mid-latitude sites, we show that deep convection (DC) consistently enhances nighttime surface ozone and is often accompanied by modest increases in ultrafine particle concentrations. Within the BL, the condensational growth of these transported ultrafine particles may contribute up to 60% of total cloud condensation nuclei (CCN). Mass flux calculations suggest that short-lived convective cores (∼30 min) account for ∼2% of total vertical air mass transport relative to steady entrainment, increasing to ∼13% when the trailing stratiform regions are included. These results show that DC provides an episodic but efficient pathway linking the free troposphere and BL, influencing oxidant budgets, CCN variability, and climate forcing. Accurately representing this process in climate models may help reduce uncertainties in climate projections, under both preindustrial and present-day conditions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Anisotropic magnetism of polymorphic ErAl 3

ErAl 3 can form in either a trigonal (α) or cubic (β) polymorph and this paper investigates the physical properties of these polymorphs through characterizations of single crystals grown in an aluminum flux. Here, we demonstrate that polymorph selection can be achieved based on the nominal composition of the crystal growth. Magnetic measurements confirm that both β-ErAl 3 and α-ErAl 3 order antiferromagnetically at low temperatures. β-ErAl 3 undergoes antiferromagnetic ordering at a Néel temperature T N = 5.1 K, and the transition is suppressed continually with applied field. α-ErAl 3 displays more complex behavior, with successive magnetic transitions at T N = 5.7 K and T 2 = 4.6 K for zero field, where heat capacity and dilatometry measurements evidence that these transitions are second and first order, respectively. Under magnetic field, strong anisotropy is revealed in α-ErAl 3 , with several steplike metamagnetic transitions observed below T 2 for H ∥ c. These transitions produce sequential magnetization plateaus near one-half of the apparent saturation magnetization. The electrical resistivity of α-ErAl 3 is strongly coupled to its magnetism. At T = 2 K, we observe a positive magnetoresistance reaching 60%, with distinct anomalies at the metamagnetic transitions. The results are summarized in H-T phase diagrams that demonstrate complex magnetic behavior for α-ErAl 3 , suggesting an important role of competing interactions in this metallic system that possesses characteristics of Ising physics.

36 MATERIALS SCIENCE↗

DOE OSTI2021

The diurnal cycle of entrainment and detrainment in LES of the Southern Ocean driven by observed surface fluxes and waves

Empirical rules for both entrainment and detrainment are developed from LES of the Southern Ocean boundary layer when the turbulence, stratification, and shear cannot be assumed to be in equilibrium with diurnal variability in surface flux and wave (Stokes drift) forcing. A major consequence is the failure of downgradient eddy viscosity, which becomes more serious with Stokes drift and is overcome by relating the angle between the stress and shear vectors to the orientations of Lagrangian shear to the surface and of local Eulerian shear over 5 m. Thus, the momentum flux can be parameterized as a stress magnitude and this empirical direction. In addition, the response of a deep boundary layer to sufficiently strong diurnal heating includes boundary layer collapse and the subsequent growth of a morning boundary layer, whose depth is empirically related to the time history of the forcing, as are both morning detrainment and afternoon entrainment into weak diurnal stratification. Below the boundary layer, detrainment rules give the maximum buoyancy flux and its depth, as well a specific stress direction. Another rule relates both afternoon and nighttime entrainment depth and buoyancy flux to surface layer turbulent kinetic energy production integrals. These empirical relationships are combined with rules for boundary layer transport to formulate two parameterizations; one based on eddy diffusivity and viscosity profiles and another on flux profiles of buoyancy and of stress magnitude. Evaluations against LES fluxes show the flux profiles to be more representative of the diurnal cycle, especially with Stokes drift.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N . europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N . europaea , i GC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

The effects of photosynthetic rate on respiration in light, starch/sucrose partitioning, and other metabolic fluxes within photosynthesis

In the future, plants may encounter increased light and elevated CO 2 levels. How consequent alterations in photosynthetic rates will impact fluxes in photosynthetic carbon metabolism remains uncertain. Respiration in light ( R L ) is pivotal in plant carbon balance and a key parameter in photosynthesis models. Understanding the dynamics of photosynthetic metabolism and R L under varying environmental conditions is essential for optimizing plant growth and agricultural productivity. However, measuring R L under high light and high CO 2 (HLHC) conditions poses challenges using traditional gas exchange methods. In this study, we employed isotopically nonstationary metabolic flux analysis (INST-MFA) to estimate RL and investigate photosynthetic carbon flux, unveiling nuanced adjustments in Camelina sativa under HLHC. Despite numerous flux alterations in HLHC, RL remained stable. HLHC affects several factors influencing RL, such as starch and sucrose partitioning, v o /v c ratio, triose phosphate partitioning, and hexose kinase activity. Analysis of A/C i curve operational points reveals that HLHC’s major changes primarily stem from CO 2 suppressing photorespiration. Integration of these fluxes into a simplified model predicts changes in CBC labeling under HLHC. This study extends our prior discovery that incomplete CBC labeling is due to unlabeled carbon reimported during R L , offering insights into manipulating labeling through adjustments in photosynthetic rates.

Elevated CO2↗

DOE OSTI2026

Metabolic rewiring and biomass redistribution enable optimized mixotrophic growth in Chlamydomonas

Aquatic photosynthetic systems account for approximately one-half of all global carbon assimilation and could be a significant source of renewable fuels and feedstocks. However, rapid growth and biomass production in algae have not always translated into high product yields, partly because central metabolism is context specific, with metabolic fluxes being influenced by nutrient conditions and other environmental factors. In the green microalga Chlamydomonas reinhardtii (Chlamydomonas), mixotrophic cultures (acetate + light) grow far faster than phototrophic (light only) or heterotrophic (acetate + dark) cultures, even though acetate partially suppresses photosynthesis. Here, an isotopic dilution strategy with unlabeled acetate was combined with 13 CO 2 transient labeling to perform isotopically nonstationary metabolic flux analysis (INST-MFA) and to directly compare autotrophic and mixotrophic metabolism in Chlamydomonas supported by data from transcriptomics, proteomics, and metabolomics. INST-MFA indicated that acetate induces a synergistic rewiring of metabolism, conserving carbon by using the glyoxylate cycle and suppressing gluconeogenesis, the latter of which was discordant with omics results and prior models. Additionally, our data provide a plausible rationale for the well-known suppression of photosynthesis by acetate. We propose that reduced total protein content in mixotrophic versus phototrophic cells, much of which is attributed to reduced levels of photosynthetic proteins, decreases the costly metabolic burden of protein synthesis and represents a growth rate optimization strategy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

How does negative triangularity mitigate ITG turbulence and transport?

Improved confinement in negative triangularity (NT) experiments is attributed to reduced fluxes driven by micro-turbulence. The physical mechanism of why thermal confinement improves in NT relative to PT is unknown. This study employs gyrokinetic flux tube simulations using the GENE code with local Miller equilibrium to elucidate the physical mechanisms behind the beneficial effects of NT flux surface shapes. The focus is on collisionless ion temperature gradient (ITG) driven turbulence with adiabatic electrons. The kinetic profiles are held fixed across a scan of triangularity values, thus enabling comparisons on a level playing field. The reduced linear growth rates for NT is shown to be due to a reduced eigenmode averaged magnetic drift frequency and a wider, stronger negative local magnetic shear region about the outboard mid-plane. The nonlinear heat flux is lower for NT than that for PT, due to reduced radial correlation length and increased correlation time (τ c ) of fluctuations. These, in turn, are due to a comparatively higher level of self-generated zero-frequency E × B zonal shearing rate ω E in NT as compared to PT. Though the linear zonal potential residual is lower for NT, the nonlinearly generated E × B zonal shearing rate is higher for NT than for PT. This outcome is linked to the distinctive features of the radial wavenumber spectra of the zonal potential and the zonal shearing rate. The dimensionless parameter ω E τ c is suggested as a figure of merit. This is higher for NT than for PT. Thus, the reduced heat diffusivity for NT is linked to increased ω E τ c . Self-generated temperature corrugations (i.e. zonal temperature gradients) are much weaker than the background mean temperature gradient. Nevertheless, temperature corrugations are more pronounced in NT than in PT.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Integration of proteomics and metabolomics into the Design, Build, Test, Learn cycle to improve 3-hydroxypropionic acid production in Aspergillus pseudoterreus

Biological engineering of microorganisms to produce value-added chemicals is a promising route to sustainable manufacturing. However, overproduction of metabolic intermediates at high titer, rate, and yield from inexpensive substrates is challenging in non-model systems where limited information is available regarding metabolic flux and its control in production conditions. Integrated multi-omic analyses of engineered strains offers an in-depth look at metabolites and proteins directly involved in growth and production of target and non-target bioproducts. Here we applied multi-omic analyses to overproduction of the polymer precursor 3-hydroxypropionic acid (3HP) in the filamentous fungus Aspergillus pseudoterreus. A synthetic pathway consisting of aspartate decarboxylase, beta-alanine pyruvate transaminase, and 3HP dehydrogenase was designed and built for A. pseudoterreus. Strains with single- and multi-copy integration events were isolated and multi-omics analysis consisting of intracellular and extracellular metabolomics and targeted and global proteomics was used to interrogate the strains in shake-flask and bioreactor conditions. Production of a variety of co-products (organic acids and glycerol) and oxidative degradation of 3HP were identified as metabolic pathways competing with 3HP production. Intracellular accumulation of nitrogen as 2,4-diaminobutanoate was identified as an off-target nitrogen sink that may also limit flux through the engineered 3HP pathway. Elimination of the high-expression oxidative 3HP degradation pathway by deletion of a putative malonate semialdehyde dehydrogenase improved the yield of 3HP by 3.4× after 10 days in shake-flask culture. This is the first report of 3HP production in a filamentous fungus amenable to industrial scale biomanufacturing of organic acids at high titer and low pH.

Pomraning, Kyle R.↗

DOE OSTI2022

Evolution of Droplet Size Distributions During the Transition of an Ultraclean Stratocumulus Cloud System to Open Cell Structure: An LES Investigation Using Lagrangian Microphysics

Here, a state-of-the-art Lagrangian microphysics scheme is used in a large-eddy simulation to investigate the stratocumulus transition from closed to open cell structure. Processes controlling precipitation development, which is a key to the transition, are analyzed by leveraging unique benefits of Lagrangian microphysics, particularly the ability to track computational drops in the flow. Sufficient time is needed for coalescence growth of cloud drops to drizzle within the updraft-downdraft cycle of large eddies. This favors broad drop size distributions (DSDs) and drizzle growth in downdrafts, where drops are typically much older than in updrafts. During the closed cell stage, mean cloud drop radius is too small, and the DSDs are too narrow, so that the timescale for coalescence is much longer than the large eddy turnover time and drizzle growth is limited. The closed-to-open cell transition occurs when these timescales become comparable and the precipitation flux increases sharply.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Quantifying biases in stellar masses of JWST high- z quasar host galaxies caused by quasar subtraction

The James Webb Space Telescope (JWST) has enabled dozens of high-z quasar host galaxy detections. Many of these observations imply galaxies with black holes that are overmassive compared to their low-z counterparts. However, the bright quasar point source removal can cause significant biases in recovered host magnitudes and stellar mass measurements due to the degeneracy in host galaxy and quasar light. We develop a statistical method to disentangle the quasar host galaxy stellar mass measurements from observational biases during the point source removal assuming the PSF is modelled perfectly. We use the BlueTides simulation to generate mock images and perform point source removal on thousands of simulated high-z quasar host galaxies, constructing corrected host magnitude posteriors. We find that removing a bright quasar in JWST photometry tends to either correctly recover or modestly misestimate host magnitudes, with a maximum magnitude underestimate of 0.2 mag. With our corrected magnitude posteriors, we perform SED fitting on each quasar host galaxy and compare the stellar mass measurement before and after the correction. We find that stellar mass estimates are generally robust, or misestimated by $<$ 0.3 dex. We also find that the stellar masses of a subset of hosts (J0844−0132, J0911+0152, and J1146−0005) remain unconstrained, as key photometric bands provide only flux upper limits. Accounting for observational biases does not resolve the apparent mismatch between black hole and host galaxy growth at high-z, where some quasars appear to host overmassive black holes while others reside in relatively massive galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

AmeriFlux CL-ACF Alerce Costero Forest

This is the AmeriFlux version of the carbon flux data for the site CL-ACF Alerce Costero Forest. Site Description - Tower located in an old-growth coniferous rainforest (~300 years) at the Alerce Costero National Park. The forest is locally known as Alerce type. More information at: https://jbarichivich.github.io/page_acos.html

Lara, Antonio [Universidad Austral de Chile]↗

DOE OSTI2023

The circular nutrient economy of terrestrial ecosystems and the consequences for rock weathering

Earth’s biosphere is thought to exert a substantial influence on regolith evolution and chemical weathering rates. However, ecosystems are also highly efficient at retaining and recycling nutrients. Thus, when the ecological demand for rock-derived nutrients (e.g., P, Ca, K) exceeds the rates of regolith supply, ecological retention and recycling strategies can minimize nutrient limitations. To evaluate the balance between nutrient recycling and new nutrient input, we combined a plant model that drives growth according to foliar P levels with a weathering model that includes regolith rejuvenation via erosion and export via chemical weathering according to water flow, regolith thickness, mineral dissolution rates, secondary minerals, and nutrient storage in organic and mineral phases. We find that plant growth is strongly dependent on the total regolith nutrient inventory, resulting in a strong correlation between plant productivity and erosion. Increased water export or decreased regolith thickness diminish the total inventory of nutrient corresponding to lower rates of recycling and lower plant growth. In contrast, purported biogenic drivers of weathering, such as enhanced mineral dissolution, only support higher growth rates at high erosion rates. At erosion rates typical of the global land surface, more rapid mineral dissolution combined with enhanced formation of secondary minerals, depletes the inventory of mineral P, resulting in no benefit for plant growth. We also find that the increased chemical weathering export does not scale directly with plant growth. For example, accelerated mineral weathering does increase chemical weathering export but not potential plant growth. Conversely, thicker regolith is associated with a small increase in weathering export, but a large increase in potential plant growth. Collectively, when plant growth is coupled to regolith weathering our calculations suggest that plant productivity is not directly correlated with silicate weathering fluxes, and that biotic drivers of silicate weathering may only be effective at high erosion rates not typical at the Earth’s surface.

58 GEOSCIENCES↗

DOE OSTI2024

Validating a microphysical prognostic stratospheric aerosol implementation in E3SMv2 using observations after the Mount Pinatubo eruption

Abstract. This paper describes the addition of a stratospheric prognostic aerosol (SPA) capability – developed with the goal of accurately simulating sulfate aerosol formation and evolution in the stratosphere – in the Department of Energy (DOE) Energy Exascale Earth System Model, version 2 (E3SMv2). The implementation includes changes to the four-mode Modal Aerosol Module microphysics in the stratosphere to allow for larger particle growth and more accurate stratospheric aerosol lifetime following the Pinatubo eruption. E3SMv2-SPA reasonably reproduces stratospheric aerosol lifetime, burden, aerosol optical depth, and top-of-atmosphere flux when compared to remote sensing observations. E3SMv2-SPA also has close agreement with the interactive chemistry–climate model CESM2-WACCM (Community Earth System Model version 2–Whole Atmosphere Community Climate Model) – which has a more complete chemical treatment – and the observationally constrained, prescribed volcanic aerosol treatment in E3SMv2. Global stratospheric aerosol size distributions identify the nucleation and growth of sulfate aerosol from volcanically injected SO2 from both major and minor volcanic eruptions from 1991 to 1993. The modeled aerosol effective radius is consistently lower than satellite and in situ measurements (max differences of ∼ 30 %). Comparisons with in situ size distribution samples indicate that this simulated underestimation in both E3SMv2-SPA and CESM2-WACCM is due to overly small accumulation and coarse-mode aerosols 6–18 months post-eruption, with E3SMv2-SPA simulating ∼ 50 % of the coarse-mode geometric mean diameters of observations 11 months post-eruption. Effective radii from the models and observations are used to calculate offline scattering and absorption efficiencies to explore the implications of smaller simulated aerosol size for the Pinatubo climate impacts. Scattering efficiencies at wavelengths of peak solar irradiance (∼ 0.5 µm) are 10 %–80 % higher for daily samples in models relative to observations through 1993, suggesting higher diffuse radiation at the surface and a larger cooling effect in the models due to the smaller simulated aerosol; absorption efficiencies at the peak wavelengths of outgoing terrestrial radiation (∼ 10 µm) are 15 %–40 % lower for daily samples in models relative to observations, suggesting an underestimation in stratospheric heating in the models due to the smaller simulated aerosol. These potential biases are based on aerosol size alone and do not take into account differences in the aerosol number. The overall agreement of E3SMv2-SPA with observations and its similar performance to the well-validated CESM2-WACCM makes E3SMv2-SPA a viable alternative to simulating climate impacts from stratospheric sulfate aerosols.

Brown, Hunter York (ORCID:0000000218147874)↗

DOE OSTI2021

Microbubble dynamics and heat transfer in boiling droplets

Dissipating large heat fluxes from a surface is critically important in numerous industrial and natural applications. Boiling based spray cooling and surface texturing are two of the most promising methods being investigated to address this problem. Although our understanding on these topics has significantly improved over past decades, critical gaps remain in the knowledgebase stymieing the realization of their full potential. As an example, while bubble growth in pool boiling have been investigated in detail, comparatively little is known about how the bubbles evolve inside boiling drops. In the present work, we have investigated for the first time, the microbubble dynamics inside water droplets boiling on superhydrophilic textured substrates using high-speed X-ray phase contrast imaging (XRPCI). Our observations show that the transient bubble density variation follows similar characteristics irrespective of the texture spacing at a given surface temperature. For an example microstructure, we found that the number of discrete bubbles on the surface decreases as temperature is increased although their growth rate increases. Here, we observe that bubble growth is highly non-uniform during the lifetime of a drop on the surface. Initially, bubbles grow under diffusion-limited regime, but at later times they grow as ~t 1.45 due to combined effects of coalescence and evaporation. In some conditions, we found that bubbles shrink dramatically af- ter the initial growth spurt presumably due to severe quenching of the surface, and migration of bubbles on the surface. Using the bubble sizes, for the first time we analyzed the heat flux removed by a single bubble and also by all the bubbles at a given time. We find that the highest dissipation through latent- heat component (~600 W/cm 2 ) occurs just in the beginning and thereafter it decreases. We expect that our findings and the analysis would guide further work on the topic and will aid in the overarching goal of engineering surfaces that are more efficient in boiling heat transfer.

42 ENGINEERING↗

DOE OSTI2021

Wheat respiratory O2 consumption falls with night warming alongside greater respiratory CO2 loss and reduced biomass

Abstract Warming nights are correlated with declining wheat growth and yield. As a key determinant of plant biomass, respiration consumes O2 as it produces ATP and releases CO2 and is typically reduced under warming to maintain metabolic efficiency. We compared the response of respiratory O2 and CO2 flux to multiple night and day warming treatments in wheat leaves and roots, using one commercial (Mace) and one breeding cultivar grown in controlled environments. We also examined the effect of night warming and a day heatwave on the capacity of the ATP-uncoupled alternative oxidase (AOX) pathway. Under warm nights, plant biomass fell, respiratory CO2 release measured at a common temperature was unchanged (indicating higher rates of CO2 release at prevailing growth temperature), respiratory O2 consumption at a common temperature declined, and AOX pathway capacity increased. The uncoupling of CO2 and O2 exchange and enhanced AOX pathway capacity suggest a reduction in plant energy demand under warm nights (lower O2 consumption), alongside higher rates of CO2 release under prevailing growth temperature (due to a lack of down-regulation of respiratory CO2 release). Less efficient ATP synthesis, teamed with sustained CO2 flux, could thus be driving observed biomass declines under warm nights.

Posch, Bradley C. (ORCID:0000000309246608)↗

DOE OSTI2024

A DFT-based kinetic Monte Carlo simulation of multiphase oxide-metal thin film growth

Functional thin films of nanoscale metal pillars in oxide or nitride matrices known as vertically aligned nanocomposite (VAN) have gained much interest owing to their unique strain-coupled and highly anisotropic properties. So far, the deposition of these films has been explored mostly experimentally. In this work, a density functional theory (DFT)-based kinetic Monte Carlo simulation model using Bortz–Kalos–Lebowitz algorithm was developed to understand the growth of VAN films deposited by pulsed laser technique on mismatching substrates. The model has been parameterized and applied to understand the kinetics of growth thin films consisting of Au pillars in CeO2 matrix deposited on SrTiO3 substrates. The effects of pulsed laser deposition (PLD) conditions including the pulse frequency, deposition flux, and substrate temperature were explored. The simulations indicate that the Au pillar size and shape exhibit significant dependence on the PLD conditions. Namely, increasing the temperature increases the average pillar size and lowers the pillar density, and vice versa. In addition, the simulations revealed that increasing the deposition rate results in lowering the average pillar size and increasing the density. Particularly, the DFT results suggest that Au pillar size can be tuned during the initial growth of the first monolayer due to the significantly low activation barrier. Our analysis showed that the relationship between the average pillar size and pillar density is influenced by the kinetics. Furthermore, autocorrelation analysis showed that pillars self-organize in quasi-ordered patterns at certain windows of the deposition conditions, which is attributed to the complex nature of the chemical interactions in the system, the kinetics, and the deposition parameters.

Physics↗

DOE OSTI2022

Twin-free, directly synthesized MFI nanosheets with improved thickness uniformity and their use in membrane fabrication

Zeolite nanosheets can be used for the fabrication of low-defect-density, thin, and oriented zeolite separation membranes. However, methods for manipulating their morphology are limited, hindering progress toward improved performance. We report the direct synthesis (i.e., without using exfoliation, etching, or other top-down processing) of thin, flat MFI nanosheets and demonstrate their use as high-performance membranes for xylene isomer separations. Our MFI nanosheets were synthesized using nanosheet fragments as seeds instead of the previously used MFI nanoparticles. The obtained MFI nanosheets exhibit improved thickness uniformity and are free of rotational and MEL intergrowths as shown by transmission electron microscopy (TEM) imaging. The nanosheets can form well-packed nanosheet coatings. Upon gel-free secondary growth, the obtained zeolite MFI membranes show high separation performance for xylene isomers at elevated temperature (e.g., p-xylene flux up to 1.5 × 10 –3 mol m –2 s –1 and p-/o-xylene separation factor of ~600 at 250°C).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Root system architecture and environmental flux analysis in mature crops using 3D root mesocosms

Current methods of root sampling typically only obtain small or incomplete sections of root systems and do not capture their true complexity. To facilitate the visualization and analysis of full-sized plant root systems in 3-dimensions, we developed customized mesocosm growth containers. While highly scalable, the design presented here uses an internal volume of 45 ft 3 (1.27 m 3 ), suitable for large crop and bioenergy grass root systems to grow largely unconstrained. Furthermore, they allow for the excavation and preservation of 3-dimensional root system architecture (RSA), and facilitate the collection of time-resolved subterranean environmental data. Sensor arrays monitoring matric potential, temperature and CO 2 levels are buried in a grid formation at various depths to assess environmental fluxes at regular intervals. Methods of 3D data visualization of fluxes were developed to allow for comparison with root system architectural traits. Following harvest, the recovered root system can be digitally reconstructed in 3D through photogrammetry, which is an inexpensive method requiring only an appropriate studio space and a digital camera. We developed a pipeline to extract features from the 3D point clouds, or from derived skeletons that include point cloud voxel number as a proxy for biomass, total root system length, volume, depth, convex hull volume and solidity as a function of depth. Ground-truthing these features with biomass measurements from manually dissected root systems showed a high correlation. We evaluated switchgrass, maize, and sorghum root systems to highlight the capability for species wide comparisons. We focused on two switchgrass ecotypes, upland (VS16) and lowland (WBC3), in identical environments to demonstrate widely different root system architectures that may be indicative of core differences in their rhizoeconomic foraging strategies. Finally, we imposed a strong physiological water stress and manipulated the growth medium to demonstrate whole root system plasticity in response to environmental stimuli. Hence, these new “3D Root Mesocosms” and accompanying computational analysis provides a new paradigm for study of mature crop systems and the environmental fluxes that shape them.

59 BASIC BIOLOGICAL SCIENCES↗