Shape Analytics for In Situ Fine Root Measurements
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54 ENVIRONMENTAL SCIENCES↗
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Novel Deep Learning Methods for In-Situ Fine Roots Measurements
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09 BIOMASS FUELS↗
SBIR Phase II Final Report for Rhizomatic - Next Generation Image Processing for In Situ Fine Root Measurement
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54 ENVIRONMENTAL SCIENCES↗
Ultra-Wideband Microwave Imaging System for Root Phenotyping
The roots are a vital organ for plant growth and health. The opaque surrounding environment of the roots and the complicated growth process means that in situ and non-destructive root phenotyping face great challenges, which thus spur great research interests. The existing methods for root phenotyping are either unable to provide high-precision and high accuracy in situ detection, or they change the surrounding root environment and are destructive to root growth and health. Thus,we propose and develop an ultra-wideband microwave scanning method that uses time reversal to achieve in situ root phenotyping nondestructively. To verify the method’s feasibility, we studied an electromagnetic numerical model that simulates the transmission signal of two ultra-wideband microwave antennas. The simulated signal of roots with different shapes shows the proposed system’s capability to measure the root size in the soil. Experimental validations were conducted considering three sets of measurements with different sizes, numbers and locations, and the experimental results indicate that the developed imaging system was able to differentiate root sizes and numbers with high contrast. The reconstruction from both simulations and experimental measurements provided accurate size estimation of the carrots in the soil, which indicates the system’s potential for root imaging.
59 BASIC BIOLOGICAL SCIENCES↗
Belowground respiration, root traits, and soil characteristics of an East Tennessee deciduous forest, 2019-2020
This dataset contains empirical physiological, morphological, and chemical data of root systems, and elemental, nutrient content for soils collected on forty individuals of eight temperate tree species, between June 2019 and July 2020 at The University of Tennessee Forest Research Center and Arboretum in Oak Ridge, Tennessee. The project used a novel methodology to empirically derive estimates of the autotrophic and heterotrophic components of soil respiration in-situ. The project consists of two measurement approaches. The first set of measurements uses a standard approach for measuring specific root respiration on excised root systems. The second used “in-situ root trays” This dataset includes 10 data files in comma separate (*.csv) ASCII format. Data include measurements of leaf and root functional traits for excised root systems and for living root systems housed within in-situ root trays, data on soil carbon and nitrogen pools, in-situ measurements of soil moisture and temperature, data on soil respiration rates for in-situ root trays (both as soil mass-based fluxes, and soil-area based fluxes), and data on the geographic coordinates and tree sizes of study trees. Forty study trees of eight temperate tree species were studied (five individuals per species). Two in-situ root trays were installed per species, each housing one entire root system comprising < 3 root orders, and still being attached to the tree via transportive root. All respiration measurements were conducted with the Li-6800 portable photosynthesis system (Li-COR, Lincoln, NE, USA). Root respiration measurements of excised root tissues were made using the Li-6800 and the Walz 3010-GWK1 gas exchange chamber (Heinz Walz GmbH, Effeltrich, Germany). Root scan images were analyzed using WinRHIZO. These images are companion files to this dataset and are contained in two compressed (*.zip) folders. Additional metadata are provided: 10 data dictionaries and a file-level metadata file in comma separate (*.csv) format and a user guide in PDF (*.pdf) format.
EARTH SCIENCE > BIOSPHERE > VEGETATION > LEAF CHAR↗
On Soil Moisture Retrieval and Target Decomposition
In an earlier study, an empirical model was developed to infer soil moisture and surface roughness from radar data. The inversion technique was extensively tested over bare surfaces by comparing the estimated soil moisture to in situ measurements. The overall root mean square (RMS) error in the soil moisture estimate was found to be about 3.5% and the RMS error in the RMS height estimate was less than 0.35 cm absolute for bare or slightly vegetated surfaces. However, inversion results indicate that significant amounts of vegetation cause the algorithm to underestimate soil moisture and overestimate RMS height. Among the areas over which the inversion cannot be applied, the areas with intermediate vegetation cover are of particular interest as both the vegetation and the underlying bare surface affect the backscatter. This paper concentrates mostly on these areas. Using the full polarimetric information and the Cloude target decomposition approach, three different components of the target backscattering can be isolated. One of these three components can be identified as the surface component in the case of intermediate vegetation cover. Once the surface component of the scattering is isolated, the bare surface inversion can then be applied.
Dubois, Pascale C.↗
Post-Test Inspection of NASA's Evolutionary Xenon Thruster Long Duration Test Hardware: Ion Optics
A Long Duration Test (LDT) was initiated in June 2005 as a part of NASA's Evolutionary Xenon Thruster (NEXT) service life validation approach. Testing was voluntarily terminated in February 2014, with the thruster accumulating 51,184 hours of operation, processing 918 kg of xenon propellant, and delivering 35.5 MN-s of total impulse. The post-test inspection objectives for the ion optics were derived from the original NEXT LDT test objectives, such as service life model validation, and expanded to encompass other goals that included verification of in situ measurements, test issue root causes, and past design changes. The ion optics cold grid gap had decreased only by an average of 7% of pretest center grid gap, so efforts to stabilize NEXT grid gap were largely successful. The upstream screen grid surface exhibited a chamfered erosion pattern. Screen grid thicknesses were ≥ 86% of the estimated pretest thickness, indicating that the screen grid has substantial service life remaining. Deposition was found on the screen aperture walls and downstream surfaces that was primarily composed of grid material and back-sputtered carbon, and this deposition likely caused the minor decreases in screen grid ion transparency during the test. Groove depths had eroded through up to 35% of the accelerator grid thickness. Minimum accelerator aperture diameters increased only by about 5-7% of the pretest values and downstream surface diameters increased by about 24-33% of the pretest diameters. These results suggest that increasing the accelerator aperture diameters, improving manufacturing tolerances, and masking down the perforated diameter to 36 cm were successful in reducing the degree of accelerator aperture erosion at larger radii.
Ion Thruster↗
Post-test Inspection of NASA’s Evolutionary Xenon Thruster Long Duration Test Hardware: Ion Optics
A Long Duration Test (LDT) was initiated in June 2005 as a part of NASA’s Evolutionary Xenon Thruster (NEXT) service life validation approach. Testing was voluntarily terminated in February 2014, with the thruster accumulating 51,184 hours of operation, processing 918 kg of xenon propellant, and delivering 35.5 MN-s of total impulse. The post-test inspection objectives for the ion optics were derived from the original NEXT LDT test objectives, such as service life model validation, and expanded to encompass other goals that included verification of in situ measurements, test issue root causes, and past design changes. The ion optics cold grid gap had decreased only by an average of 7% of pretest center grid gap, so efforts to stabilize NEXT grid gap were largely successful. The upstream screen grid surface exhibited a chamfered erosion pattern. Screen grid thicknesses were ≥ 86% of the estimated pretest thickness, indicating that the screen grid has substantial service life remaining. Deposition was found on the screen aperture walls and downstream surfaces that was primarily composed of grid material and back-sputtered carbon, and this deposition likely caused the minor decreases in screen grid ion transparency during the test. Groove depths had eroded through up to 35% of the accelerator grid thickness. Minimum accelerator aperture diameters increased only by about 5-7% of the pretest values and downstream surface diameters increased by about 24-33% of the pretest diameters. These results suggest that increasing the accelerator aperture diameters, improving manufacturing tolerances, and masking down the perforated diameter to 36 cm were successful in reducing the degree of accelerator aperture erosion at larger radii.
George C. Soulas↗
Long-term variability of root production in bioenergy crops from ingrowth core measurements
Long-term determination of root biomass production upon land-use conversion to biofuel crops is rare. To assess land-use legacy influences on belowground biomass accumulation, we converted 22-year-old Conservation Reserve Program (CRP) grasslands and 50+-year-old agricultural (AGR) lands to corn (C), switchgrass (Sw) and restored prairie (Pr) biofuel crops. We maintained one CRP grassland as a reference (Ref). We hypothesized that land-use history and crop type have significant effects on root density, with perennial crops on CRP grasslands having a higher root biomass productivity, while corn grown on former agricultural lands produce the lowest root biomass. Methods The ingrowth core method was used to determine in situ ingrowth root biomass, alongside measurements of aboveground net primary productivity (ANPP). Ancillary measurements, including air temperature, growing season length and precipitation were used to examine their influences on root biomass production. Important Findings Root biomass productivity was the highest in unconverted CRP grassland (1716 g m-2 yr-1) and lowest in corn fields (526 g m-2 yr-1). All perennial sites converted from CRP and AGR lands had lower root biomass and ANPP in the first year of planting but peaked in 2011 for switchgrass and a year later for restored prairies. Ecosystem stability was higher in restored prairies (AGR-Pr: 4.3 ± 0.11; CRP-Pr: 4.1 ± 0.10), with all monocultures exhibiting a lower stability. Root biomass production was positively related to ANPP (R2 = 0.40). Overall, attention should be given to root biomass accumulation in large-scale biofuel production as it is a major source of carbon sequestration.
Environmental Sciences & Ecology↗
Differential Exudation Creates Biogeochemically Distinct Microenvironments during Rhizosphere Evolution
Plant roots and associated microbes release a diverse range of functionally distinct exudates into the surrounding rhizosphere with direct impacts on soil carbon storage, nutrient availability, and contaminant dynamics. Yet mechanistic linkages between root exudation and emergent biogeochemical processes remain challenging to measure nondestructively, in real soil, over time. Here we used a novel combination of in situ microsensors with high-resolution mass spectrometry to measure, nondestructively, changing exudation and associated biogeochemical dynamics along single growing plant roots (Avena sativa). We found that metabolite and dissolved organic carbon (DOC) concentrations as well as microbial growth, redox potential (EH), and pH dynamics vary significantly among bulk soil, root tip, and more mature root zones. Surprisingly, the significant spike of rhizosphere DOC upon root tip emergence did not significantly correlate with any biogeochemical parameters. However, the presence of sugars significantly correlated with declines in EH following the arrival of the root tip, likely due to enhanced microbial oxygen demand. Similarly, the presence of organic acids significantly correlated to declines in pH upon root tip emergence. Altogether, our in situ measurements highlight how different exudates released along growing roots create functionally distinct soil microenvironments that evolve over time.
54 ENVIRONMENTAL SCIENCES↗
Assimilation of SMAP Brightness Temperature Observations in the GEOS Land–Atmosphere Data Assimilation System
Errors in soil moisture adversely impact the modeling of land–atmosphere water and energy fluxes and, consequently, near-surface atmospheric conditions in atmospheric data assimilation systems (ADAS). To mitigate such errors, a land surface analysis is included in many such systems, although not yet in the currently operational NASA Goddard Earth Observing System (GEOS) ADAS. This article investigates the assimilation of L-band brightness temperature (Tb) observations from the Soil Moisture Active Passive (SMAP) mission in the GEOS weakly coupled land–atmosphere data assimilation system (LADAS) during boreal summer 2017. The SMAP Tb analysis improves the correlation of LADAS surface and root-zone soil moisture versus in situ measurements by ∼0.1–0.26 over that of ADAS estimates; the unbiased root-mean-square error of LADAS soil moisture is reduced by 0.002–0.008 m^3 /m^3 from that of ADAS. Furthermore, the global land average RMSE versus in situ measurements of screen-level air specific humidity (q2m) and daily maximum temperature (T2m_max ) is reduced by 0.05 g/kg and 0.04 K, respectively, for LADAS compared to ADAS estimates. Regionally, the RMSE of LADAS q2m and T2m_max is improved by up to 0.4 g/kg and 0.3 K, respectively. Improvement in LADAS specific humidity extends into the lower troposphere (below ∼700 mb), with relative improvements in bias of 15–25%, although LADAS air temperature bias slightly increases relative to that of ADAS. Finally, the root mean square of the LADAS Tb observation-minus-forecast residuals is smaller by up to ∼0.1 K than in a land-only assimilation system, corroborating the positive impact of the Tb analysis on the modeled land–atmosphere coupling.
microwave remote sensing↗
In-vivo Raman microspectroscopy reveals differential nitrate concentration in different developmental zones in Arabidopsis roots
Abstract Background Nitrate (NO 3 − ) is one of the two major forms of inorganic nitrogen absorbed by plant roots, and the tissue nitrate concentration in roots is considered important for optimizing developmental programs. Technologies to quantify the expression levels of nitrate transporters and assimilating enzymes at the cellular level have improved drastically in the past decade. However, a technological gap remains for detecting nitrate at a high spatial resolution. Using extraction-based methods, it is challenging to reliably estimate nitrate concentration from a small volume of cells (i.e., with high spatial resolution), since targeting a small or specific group of cells is physically difficult. Alternatively, nitrate detection with microelectrodes offers subcellular resolution with high cell specificity, but this method has some limitations on cell accessibility and detection speed. Finally, optical nitrate biosensors have very good ( in-vivo ) sensitivity (below 1 mM) and cellular-level spatial resolution, but require plant transformation, limiting their applicability. In this work, we apply Raman microspectroscopy for high-dynamic range in-vivo mapping of nitrate in different developmental zones of Arabidopsis thaliana roots in-situ . Results As a proof of concept, we have used Raman microspectroscopy for in-vivo mapping of nitrate content in roots of Arabidopsis seedlings grown on agar media with different nitrate concentrations. Our results revealed that the root nitrate concentration increases gradually from the meristematic zone (~ 250 µm from the root cap) to the maturation zone (~ 3 mm from the root cap) in roots grown under typical growth conditions used for Arabidopsis, a trend that has not been previously reported. This trend was observed for plants grown in agar media with different nitrate concentrations (0.5–10 mM). These results were validated through destructive measurement of nitrate concentration. Conclusions We present a methodology based on Raman microspectroscopy for in-vivo label-free mapping of nitrate within small root tissue volumes in Arabidopsis. Measurements are done in-situ without additional sample preparation. Our measurements revealed nitrate concentration changes from lower to higher concentration from tip to mature root tissue. Accumulation of nitrate in the maturation zone tissue shows a saturation behavior. The presented Raman-based approach allows for in-situ non-destructive measurements of Raman-active compounds.
Fernández González, Alma↗
Functional variability in specific root respiration translates to autotrophic differences in soil respiration in a temperate deciduous forest
CO 2 release from forest soils (R s ) is a prominent flux in the global carbon cycle. Rs is derived from roots (autotrophic respiration, R a ) and microbial (heterotrophic) respiration and is highly dynamic, as it depends on edaphic and environmental conditions as well as root functional traits and microbial community composition. It is unclear how root functional traits affect root and microbial respiration rates; however, their consideration may help parse out the relative contributions of root and microbial respiration to R s . At a temperate forest site, root systems of 3–4 functional root orders and their surrounding surface soil were carefully excavated and placed into custom trays designed to repeatedly measure R s in situ on eight temperate tree species that varied in their root functional strategies and mycorrhizal affinity. R s was measured bi-weekly to monthly for nearly one year using a custom chamber attached to a gas exchange system. R s varied over time, ranging from 0.3 to 12 µmol m -2 s -1 . Comparable root systems of the same species were excised from the soil and specific root respiration rates (R r ) were measured. Rr ranged from 2.5 to 9.0 nmol g -1 s -1 and was negatively correlated with root tissue density and positively related to root tissue nitrogen concentration. Using R r to estimate R a , we estimate that R a accounts for <10%, on average 2–3%, of R s for individual root systems (averaging 1.2 g dry biomass) housed in surrounding soil (average 1.3 kg dry mass) in situ; thus, Ra was roughly 20 times greater than Rh per unit mass. The contribution of R a peaked in the fall and coincided with leaf senescence of the forest canopy. A soil-sterilizing experimental treatment designed to help isolate R a in situ reduced bacterial biomass and shifted fungal community composition, but there was no reduction in Rs of the in-situ root-soil tray systems. The relative R a to R s ratio increased with root functional strategies characterized by greater specific root length and tip abundance, but also to greater root tissue density. The ratio of R a to R s also increased with warmer soil temperatures and decreased slightly with increasing soil moisture. We discuss how incorporating root functional traits as modulators of the autotrophic contribution to R s could be considered when modeling total soil CO 2 efflux from forests.
54 ENVIRONMENTAL SCIENCES↗
Estimating Surface Soil Moisture from SMAP Observations Using a Neural Network Technique
A Neural Network (NN) algorithm was developed to estimate global surface soil moisture for April 2015 to March 2017 with a 2-3 day repeat frequency using passive microwave observations from the Soil Moisture Active Passive (SMAP) satellite, surface soil temperatures from the NASA Goddard Earth Observing System Model version 5 (GEOS-5) land modeling system, and Moderate Resolution Imaging Spectroradiometer-based vegetation water content. The NN was trained on GEOS-5 soil moisture target data, making the NN estimates consistent with the GEOS-5 climatology, such that they may ultimately be assimilated into this model without further bias correction. Evaluated against in situ soil moisture measurements, the average unbiased root mean square error (ubRMSE), correlation and anomaly correlation of the NN retrievals were 0.037 m(exp. 3)m(exp. -3), 0.70 and 0.66, respectively, against SMAP core validation site measurements and 0.026 m(exp. 3)m(exp. -3), 0.58 and 0.48, respectively, against International Soil Moisture Network (ISMN) measurements. At the core validation sites, the NN retrievals have a significantly higher skill than the GEOS-5 model estimates and a slightly lower correlation skill than the SMAP Level-2 Passive (L2P) product. The feasibility of the NN method was reflected by a lower ubRMSE compared to the L2P retrievals as well as a higher skill when ancillary parameters in physically-based retrievals were uncertain. Against ISMN measurements, the skill of the two retrieval products was more comparable. A triple collocation analysis against Advanced Microwave Scanning Radiometer 2 (AMSR2) and Advanced Scatterometer (ASCAT) soil moisture retrievals showed that the NN and L2P retrieval errors have a similar spatial distribution, but the NN retrieval errors are generally lower in densely vegetated regions and transition zones.
Soil Moisture Remote Sensing↗
Advances in Land Data Assimilation at the NASA Goddard Space Flight Center
Research in land surface data assimilation has grown rapidly over the last decade. In this presentation we provide a brief overview of key research contributions by the NASA Goddard Space Flight Center (GSFC). The GSFC contributions to land assimilation primarily include the continued development and application of the Land Information System (US) and the ensemble Kalman filter (EnKF). In particular, we have developed a method to generate perturbation fields that are correlated in space, time, and across variables and that permit the flexible modeling of errors in land surface models and observations, along with an adaptive filtering approach that estimates observation and model error input parameters. A percentile-based scaling method that addresses soil moisture biases in model and observational estimates opened the path to the successful application of land data assimilation to satellite retrievals of surface soil moisture. Assimilation of AMSR-E surface soil moisture retrievals into the NASA Catchment model provided superior surface and root zone assimilation products (when validated against in situ measurements and compared to the model estimates or satellite observations alone). The multi-model capabilities of US were used to investigate the role of subsurface physics in the assimilation of surface soil moisture observations. Results indicate that the potential of surface soil moisture assimilation to improve root zone information is higher when the surface to root zone coupling is stronger. Building on this experience, GSFC leads the development of the Level 4 Surface and Root-Zone Soil Moisture (L4_SM) product for the planned NASA Soil-Moisture-Active-Passive (SMAP) mission. A key milestone was the design and execution of an Observing System Simulation Experiment that quantified the contribution of soil moisture retrievals to land data assimilation products as a function of retrieval and land model skill and yielded an estimate of the error budget for the SMAP L4_SM product. Terrestrial water storage observations from GRACE satellite system were also successfully assimilated into the NASA Catchment model and provided improved estimates of groundwater variability when compared to the model estimates alone. Moreover, satellite-based land surface temperature (LST) observations from the ISCCP archive were assimilated using a bias estimation module that was specifically designed for LST assimilation. As with soil moisture, LST assimilation provides modest yet statistically significant improvements when compared to the model or satellite observations alone. To achieve the improvement, however, the LST assimilation algorithm must be adapted to the specific formulation of LST in the land model. An improved method for the assimilation of snow cover observations was also developed. Finally, the coupling of LIS to the mesoscale Weather Research and Forecasting (WRF) model enabled investigations into how the sensitivity of land-atmosphere interactions to the specific choice of planetary boundary layer scheme and land surface model varies across surface moisture regimes, and how it can be quantified and evaluated against observations. The on-going development and integration of land assimilation modules into the Land Information System will enable the use of GSFC software with a variety of land models and make it accessible to the research community.
Reichle, Rolf↗
Land Surface Precipitation and Hydrology in MERRA-2
The Modern-Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2), provides global, 1-hourly estimates of land surface conditions for 1980-present at 50-km resolution. Outside of the high latitudes, MERRA-2 uses observations-based precipitation data products to correct the precipitation falling on the land surface. This paper describes the precipitation correction method and evaluates the MERRA-2 land surface precipitation and hydrology. Compared to monthly GPCPv2.2 observations, the corrected MERRA-2 precipitation (M2CORR) is better than the precipitation generated by the atmospheric models within the cyclingMERRA-2 system and the earlier MERRA reanalysis. Compared to 3-hourlyTRMM observations, the M2CORR diurnal cycle has better amplitude but less realistic phasing than MERRA-2 model-generated precipitation. Because correcting the precipitation within the coupled atmosphere-land modeling system allows the MERRA-2 near-surface air temperature and humidity to respond to the improved precipitation forcing, MERRA-2 provides more self-consistent surface meteorological data than were available from the earlier, offline MERRA-Land reanalysis. Overall, MERRA-2 land hydrology estimates are better than those of MERRA-Land and MERRA. A comparison against GRACE satellite observations of terrestrial water storage demonstrates clear improvements in MERRA-2 over MERRA in South America and Africa but also reflects known errors in the observations used to correct the MERRA-2 precipitation. The MERRA-2 and MERRA-Land surface and root zone soil moisture skill vs. in situ measurements is slightly higher than that of ERA-Interim Land and higher than that of MERRA (significantly for surface soil moisture). Snow amounts from MERRA-2 have lower bias and correlate better against reference data than do those of MERRA-Land and MERRA, with MERRA-2 skill roughly matching that of ERA-Interim Land. Seasonal anomaly R values against naturalized stream flow measurements in the United States are, on balance, highest for MERRA-2 and ERA-Interim Land, somewhat lower for MERRA-Land, and lower still for MERRA.
MERRA-↗
In Situ Detection of Amino Acids from Bacterial Biofilms and Plant Root Exudates by Liquid Microjunction Surface-Sampling Probe Mass Spectrometry
The plant rhizosphere is a complex and dynamic chemical environment where the exchange of molecular signals between plants, microbes, and fungi drives the development of the entire biological system. Exogenous compounds in the rhizosphere are known to affect plant-microbe organization, interactions between organisms, and ultimately, growth and survivability. The function of exogenous compounds in the rhizosphere is still under much investigation, specifically with respect to their roles in plant growth and development, the assembly of the associated microbial community, and the spatiotemporal distribution of molecular components. A major challenge for spatiotemporal measurements is developing a nondisruptive and nondestructive technique capable of analyzing the exogenous compounds contained within the environment. A methodology using liquid microjunction-surface sampling probe-mass spectrometry (LMJ-SSP-MS) and microfluidic devices with attached microporous membranes was developed for in situ, spatiotemporal measurement of amino acids (AAs) from bacterial biofilms and plant roots. Exuded arginine was measured from a living Pantoea YR 343 biofilm, which resulted in a chemical image indicative of biofilm growth within the device. Spot sampling along the roots of Populus trichocarpa with the LMJ-SSP-MS resulted in the detection of 15 AAs. Of note, variation in AA concentrations across the root system was observed, indicating that exudation is not homogeneous and may be linked to local rhizosphere architecture and different biological processes along the root.
59 BASIC BIOLOGICAL SCIENCES↗
POLSCAT Ku-Band Radar Remote Sensing of Terrestrial Snow Cover
Characteristics of the POLSCAT data acquired from five sets of aircraft flights in the winter months of 2006-2008 for the second Cold Land Processes Experiment (CLPX-II) in Colorado are described in this paper. The data showed the response of the Ku-band radar echoes to snowpack changes for various types of background vegetation in the study site in north central Colorado. We observed about 0.15 to 0.5 dB increases in backscatter for every 1 cm of snow water equivalent (SWE) accumulation for areas with short vegetation. Based on a simplified radiative transfer model, the change detection technique is used to convert the temporal change of radar backscatter into SWE accumulation for dry snow conditions. The resulting SWE accumulation estimates are consistent with the in-situ SWE measurements, with about 2 to 3 cm Root-Mean-Square (RMS) difference for regions with sagebrush or pasture.
radar↗