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DOE OSTI2023

Integrating fine root diameter and watershed mapping to characterize rhizosphere hydrology

Root morphology and soil hydraulic characteristics were integrated using watershed distance mapping to show water distribution and uptake across the plant-soil interface. Poplar (Populus deltoides, P. trichocarpa), maize (Zea mays), juniper (Juniperus virginiana), grape (Vitis rotundifolia) and maple (Acer saccharum) seedlings were grown in sand, after which root diameter and soil water dynamics were assessed via sequential neutron radiography. Three local soil regions (root-soil interface or edge, rhizosphere, bulk soil) were classified based on both radial distance from the root surface and diameter of the nearest root, from which changes in water content and distribution were characterized using digital image processing. Water content dynamics across the rhizosphere showed two different species-independent processes: a consistently elevated water content at the root-soil edge interface which increased with root diameter, and hysteresis as the rhizosphere transitioned to bulk soil (~0.5 cm from the root), independent of root diameter. Water uptake per unit root surface area declined exponentially with root diameter, independent of species. Results highlight the species-independent hydrologic characteristics of the rhizosphere and the potential for evaluating them in a local spatially connected soil context. Avenues for improved integration of soil and root characteristics are discussed.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

From pixels to patterns: Coupling Optical Coherence Tomography and machine learning for monitoring coastal wetland root systems

Coastal wetlands are crucial in shoreline stabilization, carbon sequestration, and storm protection. Yet, due to limitations in traditional destructive sampling techniques, the belowground biomass (live root mass) and necromass (dead and decaying roots) remain difficult to assess in coastal wetlands, limiting our understanding on coastal resilience, nutrient cycling, and soil structure. This study employs Optical Coherence Tomography (OCT) as a high-resolution imaging technique to analyze root biomass and necromass in the Terrebonne Basin, Louisiana. A Random Forest (RF) model was developed to classify root health states based on OCT-derived features, achieving an accuracy of 70% in distinguishing live from dead root segments. The results demonstrate that OCT, combined with ML, offers a promising novel approach to root analysis, providing fine-scale insights into root morphology and decay patterns that are not easily captured by conventional methods. This research lays the foundation for future integration of OCT with complementary imaging modalities such as X-ray Computed Tomography (XCT) and advanced ML algorithms to enhance classification accuracy and scalability. Future work aims to expand the dataset diversity across different wetland types and apply the methodology for large-scale, repeatable assessments of root biomass turnover and accumulation, with important implications for wetland monitoring, conservation, and restoration under changing environmental conditions.

AI/ML↗

DOE OSTI2026

Fine-Root Ecology Database (FRED): A Global Collection of Root Trait Data with Coincident Site, Vegetation, Edaphic, and Climatic Data, Version 4.

To address the need for a centralized root trait database, we compiled the Fine-Root Ecology Database (FRED) from published and unpublished data sources. We have continued to add to the FRED database since the release of FRED 1.0 in 2017, followed by 2.0 in 2018, and 3.0 in 2021. This new release of FRED 4.0 now has 213,941 observations of 238 root traits, for a combined total of roughly 3.4 million data fields for root traits and ancillary data together. FRED 4.0 has 39.8% more root trait observations than FRED 3.0 and a 34.4% increase in unique data sources. This release of FRED 4.0 also includes significant increases in geographic regions that have long been underrepresented in global datasets, notably in the tropical low latitudes. Ancillary data on associated site, vegetation, edaphic, and climatic conditions from across the globe have also increased concurrently with root trait observations. FRED is focused on fine roots (traditionally defined as roots less than 2 mm in diameter), as coarse roots are studied using different methodology, often at very different scales, and have different traits and trait interpretations. Despite this fine-root focus, FRED accepts data collected from roots of all sizes and contains observations of many root classes including coarse roots. Data collection will continue for the foreseeable future. The FRED4_Entire_Database_2026.csv file is the flat csv data file for FRED 4.0, and the FRED4_dd.csv file is the data dictionary of all columns available in FRED, including column IDs, column names, definitions, and unit (where applicable).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

The State of the Art in Root System Architecture Image Analysis Using Artificial Intelligence: A Review

Roots are essential for acquiring water and nutrients to sustain and support plant growth and anchorage. However, they have been studied less than the aboveground traits in phenotyping and plant breeding until recent decades. In modern times, root properties such as morphology and root system architecture (RSA) have been recognized as increasingly important traits for creating more and higher quality food in the “Second Green Revolution”. To address the paucity in RSA and other root research, new technologies are being investigated to fill the increasing demand to improve plants via root traits and overcome currently stagnated genetic progress in stable yields. Artificial intelligence (AI) is now a cutting-edge technology proving to be highly successful in many applications, such as crop science and genetic research to improve crop traits. A burgeoning field in crop science is the application of AI to high-resolution imagery in analyses that aim to answer questions related to crops and to better and more speedily breed desired plant traits such as RSA into new cultivars. This review is a synopsis concerning the origins, applications, challenges, and future directions of RSA research regarding image analyses using AI.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Weak phylogenetic and habitat effects on root trait variation of 218 Neotropical tree species

Tropical forests harbor a large diversity of closely related tree species that can thrive across habitats. This biodiversity has been found to correspond to large functional diversity in aboveground traits, and likely also relates to belowground trait variation. Globally, root trait (co-)variation is driven by different belowground resource strategies of species, environmental variation, and phylogeny; however, these patterns mostly reflect observations from temperate biomes and remain unconfirmed in tropical trees. We examine phylogenetic and environmental effects on root trait (co-)variation of trees across habitats in an Amazonian rainforest. Roots of 218 tree species from ten dominant families were sampled across three major habitats near Manaus, Brazil. We quantified five morphological and architectural root traits to (i) investigate how they reflected different resource strategies across species, (ii) compare them between families and superorders to test phylogenetic effects, and (iii) compare them between habitats to determine environmental effects on root trait expressions and variability. Root traits discriminated species along a tradeoff between root diameter and root branching and, secondly, due to variation in root tissue density. Our results further show weak phylogenetic effects on tropical tree root variation, for example, families from the same superorder showed large divergence in their root traits, while those from different superorders often overlapped in their root morphology and architecture. Root traits differed significantly between habitats but habitat type had only little effect on overall root trait variation. Our work suggests that the dimensions and drivers that underlie (co-)variation in tropical root traits may differ from global patterns defined by mostly temperate datasets. Due to (a)biotic environmental differences, different root trait dimensions may underlie the belowground functional diversity in (Neo)tropical forests, and we found little evidence for the strong phylogenetic conservatism observed in root traits in temperate biomes. We highlight important avenues for future research on tropical roots in order to determine the degree of, and shifts in functional diversity belowground as communities and environments change in tropical forests.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Fine-Root Ecology Database (FRED): A Global Collection of Root Trait Data with Coincident Site, Vegetation, Edaphic, and Climatic Data, Version 3.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Root Characteristics Vary with Depth Across Four Lowland Seasonal Tropical Forests

Fine roots are key to ecosystem-scale nutrient, carbon (C), and water cycling, yet our understanding of fine root trait variation within and among tropical forests, one of Earth’s most C-rich ecosystems, is limited. We characterized root biomass, morphology, nutrient content, and arbuscular mycorrhizal fungal (AMF) colonization to 1.2 m depths across four distinct lowland Panamanian forests, and related root characteristics to soil C stocks. We hypothesized that: (H1) Fine root characteristics vary consistently with depth across seasonal tropical forests, with deeper roots exhibiting more exploratory traits, such as for deep water acquisition; (H2) fine root characteristics vary among tropical forests mainly in surface soils, where resource availability also varies. Here we found consistent variation with depth across the four forests, including decreased root biomass, root tissue density, and AMF, and increased specific root length. Among the forests, there was variation in some fine root characteristics, including greater surface root biomass and lower SRL in the wettest forest, and smaller fine root diameter in the driest forest. We also found that root characteristics were related to total soil C stocks, which were positively related to root biomass and negatively related to specific root length. These results indicate emergent properties of root variation with depth across tropical forests, and show site-scale variation in surface root characteristics. Future work could explore the flexibility in root characteristics under changing conditions such as drought.

13C NMR↗

DOE OSTI2021

Fine-root functional trait responses to experimental warming: a global meta-analysis

Whether and how warming alters functional traits of absorptive plant roots remains to be answered across the globe. Tackling this question is crucial to better understanding terrestrial responses to climate change as fine-root traits drive many ecosystem processes. In this work, we carried out a detailed synthesis of fine-root trait responses to experimental warming by performing a meta-analysis of 964 paired observations from 177 publications. Warming increased fine-root biomass, production, respiration and nitrogen concentration as well as decreased root carbon : nitrogen ratio and nonstructural carbohydrates. Warming effects on fine-root biomass decreased with greater warming magnitude, especially in short-term experiments. Furthermore, the positive effect of warming on fine-root biomass was strongest in deeper soil horizons and in colder and drier regions. Total fine-root length, morphology, mortality, life span and turnover were unresponsive to warming. Our results highlight the significant changes in fine-root traits in response to warming as well as the importance of warming magnitude and duration in understanding fine-root responses. These changes have strong implications for global soil carbon stocks in a warmer world associated with increased root-derived carbon inputs into deeper soil horizons and increases in fine-root respiration.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Acquisitive root exploration strategies help maintain higher peak sap flux rates during summer drought, but more root biomass does not

Roots are responsible for soil water uptake, yet little is known about how variation in fine-root traits relates to whole-tree water movement, particularly during periods of drought. By combining a 3-yr dataset monitoring sap flow rates with measures of fine-root biomass, length, and morphology across 10 tree species, we addressed hypotheses concerning the role of fine-root system size and morphology in determining tree responses to summer drought as well as potential changes in their relative importance under more severe droughts. Greater fine-root biomass and length did not enable trees to maintain high rates of sap flow during drought, whereas the morphological traits, specific root length and specific root area, were linked to sustained sap flow rates during drought. We found that all species, irrespective of root traits, progressively reduced their sap flow under more extreme drought conditions, although more acquisitive root morphology was still associated with smaller reductions. Our results run counter to long-standing assumptions that larger root systems are better able to access soil water and maintain photosynthetic activity during drought. Instead, we find evidence that root morphology at least partially determines the capacity for water uptake and movement as soil moisture declines.

drought↗

DOE OSTI2024

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

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

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites

Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome-focused studies and may result in confounding microbial signals and host-filtering across different root microbiome compartments. Using a 26-year-old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root-microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Root traits of perennial C 4 grasses contribute to cultivar variations in soil chemistry and species patterns in particulate and mineral‐associated carbon pool formation

Abstract Recent studies have indicated that the C 4 perennial bioenergy crops switchgrass ( Panicum virgatum ) and big bluestem ( Andropogon gerardii ) accumulate significant amounts of soil carbon (C) owing to their extensive root systems. Soil C accumulation is likely driven by inter‐ and intraspecific variability in plant traits, but the mechanisms that underpin this variability remain unresolved. In this study we evaluated how inter‐ and intraspecific variation in root traits of cultivars from switchgrass (Cave‐in‐Rock, Kanlow, Southlow) and big bluestem (Bonanza, Southlow, Suther) affected the associations of soil C accumulation across soil fractions using stable isotope techniques. Our experimental field site was established in June 2008 at Fermilab in Batavia, IL. In 2018, soil cores were collected (30 cm depth) from all cultivars. We measured root biomass, root diameter, specific root length, bulk soil C, C associated with coarse particulate organic matter (CPOM) and fine particulate organic matter plus silt‐ and clay‐sized fractions, and characterized organic matter chemical class composition in soil using high‐resolution Fourier‐transform ion cyclotron resonance mass spectrometry. C 4 species were established on soils that supported C 3 grassland for 36 years before planting, which allowed us to use differences in the natural abundance of stable C isotopes to quantify C 4 plant‐derived C. We found that big bluestem had 36.9% higher C 4 plant‐derived C compared to switchgrass in the CPOM fraction in the 0–10 cm depth, while switchgrass had 60.7% higher C 4 plant‐derived C compared to big bluestem in the clay fraction in the 10–20 cm depth. Our findings suggest that the large root system in big bluestem helps increase POM‐C formation quickly, while switchgrass root structure and chemistry build a mineral‐bound clay C pool through time. Thus, both species and cultivar selection can help improve bioenergy management to maximize soil carbon gains and lower CO 2 emissions.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Root hairs vs. trichomes: Not everyone is straight!

Trichomes show 47 morphological phenotypes, while literature reports only two root hair phenotypes in all plants. However, could hair-like structures exist below-ground in a similar wide range of morphologies like trichomes? Genetic mutants and root hair stress phenotypes point to the possibility of uncharacterized morphological variation existing belowground. For example, such root hairs in Arabidopsis (Arabidopsis thaliana) can be wavy, curled, or branched. We found hints in the literature about hair-like structures that emerge before root hairs belowground. As such, these early emerging hair structures can be potential exceptions to the contrasting morphological variation between trichomes and root hairs. Here, in this work, we show a previously unreported ‘hooked’ hair structure growing below-ground in common bean. The unique ‘hooking’ shape distinguishes the ‘hooked hair’ morphologically from root hairs. Currently, we cannot fully characterize the phenotype of our observation due to the lack of automated methods for phenotyping root hairs. This phenotyping bottleneck also handicaps the discovery of more morphology types that might exist below-ground as manual screening across species is slower than computer-assisted high-throughput screening.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Annual Herbaceous Plants Exhibit Altered Morphological Traits in Response to Altered Precipitation and Drought Patterns in Semiarid Sandy Grassland, Northern China

The frequency and intensity of extreme precipitation events and severe drought are predicted to increase in semiarid areas due to global climate change. Plant morphological traits can reflect plant responses to a changing environment, such as altered precipitation or drought patterns. In this study, we examined the response of morphological traits of root, stem, leaf and reproduction meristems of annual herbaceous species to altered precipitation and drought patterns in a semiarid sandy grassland. The study involved a control treatment (100% of background precipitation) and the following six altered precipitation treatments: (1) P(+): precipitation increased by 30%, (2) P(++): precipitation increased by 60%, (3) P(-): precipitation decreased by 30%, (4) P(--): precipitation decreased by 60%, (5) drought 1 (D1): 46-day drought from May 1st to June 15th, and (6) drought 2 (D2): 46-day drought from July 1st to August 15th. P(++) significantly increased root length, flower length-to-width ratio, both P(+) and P(++) significantly increased stem length and flower number in the plant growing seasons, while all of them decreased under P(-) and P(--). The annual herbaceous plants marginally increased the number of second-level stem branches and stem diameter in order to better resist the severe drought stress under P(--). P(+) and P(++) increased the root, stem, leaf, and flower dry weight, with the flower dry weight accounting for a larger proportion than the other aboveground parts. Under D2, the plants used the limited water resources more efficiently by increasing the root-to-shoot ratio compared with P(-), P(--) and D1, which reflects biomass allocation to belowground increased. The linear mixed-effects models and redundancy analysis showed that the root-to-shoot ratio and the dry weight of various plant components were significantly affected by morphological traits and altered precipitation magnitude. Our results showed that the herbaceous species have evolved morphological trait responses that allow them to adapt to climate change. Such differences in morphological traits may ultimately affect the growing patterns of annual herbaceous species, enhancing their drought-tolerant capacity in semiarid sandy grassland during the ongoing climate change.

Sun, Shan-Shan↗

DOE OSTI2023

Effects of root litter traits on soil organic matter dynamics depend on decay stage and root branching order

Decaying roots contribute disproportionately to soil organic carbon (SOC) stocks in many ecosystems, yet few studies have examined the afterlife effects of root trait variability on the formation, stability and mineralization of SOC. In order to assess how root functional class (absorptive vs. transport) and mycorrhizal association (ectomycorrhizal vs. arbuscular mycorrhizal fungi) affect both formation and loss of SOC, we decayed lower-order absorptive (orders 1–2) and higher-order transport (orders 3–4) roots from six arbuscular mycorrhizal (AM) and six ectomycorrhizal (EcM) associated hardwood tree species in an isotopically distinct soil under laboratory conditions. We found that root litter effects on SOC differed significantly among root functional classes and mycorrhizal types. AM absorptive and transport roots (high in nitrogen and soluble compounds) contributed more to the formation of new mineral-associated organic carbon (MAOC), but also contributed to higher mineralization of native SOC (via priming effects). Moreover, absorptive AM roots formed MAOC gradually and rates saturated, whereas ECM roots formed MAOC more quickly, despite slower decay (via greater formation efficiency). Altogether, these findings demonstrate how different combinations of root traits might contribute to soil C balance, and that failure to account for the chemical and morphological heterogeneity of roots, as well their interactions with microbes over time, may lead to incorrect projections of SOC stocks and turnover.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Molecular remodeling in Populus PdKOR RNAi roots profiled using LC-MS/MS proteomics

Plant endo-β-1,4-glucanases belonging to the Glycoside Hydrolase Family 9 have functional roles in cell wall biosynthesis and remodeling via endohydrolysis of (1→4)-β-D-glucosidic linkages. Modification of cell wall chemistry via RNAi-mediated downregulation of Populus deltoides KOR1 (PdKOR), a endo-β-1,4-glucanase gene, in Populus deltoides has been shown to have functional consequences for the composition of secondary metabolome and the ability of modified roots to interact with beneficial microbes. The molecular remodeling that underlies the observed differences at metabolic, physiological, and morphological levels in roots is not well understood. Here we used a LC-MS/MS-based proteome profiling approach to survey the molecular remodeling in root tissues of PdKOR and control plants. A total of 14316 peptides were identified and these mapped to 7139 P. deltoides proteins. Based on 90% sequence identity, the measured protein accessions represent 1187 functional protein groups. Analysis of GO categories and specific individual proteins showed differential expression of proteins relevant to plant-microbe interactions, cell wall chemistry, and metabolism. The new proteome dataset serves as a useful resource for deriving new hypotheses and empirical testing pertaining to functional roles of proteins and pathways in differential priming of plant roots to interactions with microbes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Fine-root traits from common tree species in Puerto Rico before and after Hurricane María (2017-2018)

This dataset is a compilation of root trait measurements from common tree species in the Luquillo Experimental Forest in Puerto Rico taken in February 2017 (before Hurricane María), and in February 2018 (after the hurricane). This dataset is being used on a publication called "Tradeoffs in phosphorus acquisition strategies of five tree species in a tropical forest of Puerto Rico", where we describe belowground P-acquisition strategies of five common tree species (two pioneers and three non-pioneers) growing in the lowland tropical wet forests of Puerto Rico. Additionally, we used the unique opportunity of two consecutive hurricanes that passed over the island (Irma and Maria) to compare root traits before and after the hurricanes to determine which traits were the most responsive and whether such disturbance affected root trait relationships and trade-offs. For this, we sampled trees from EV1, SB2, and NGEE Tropics' plots EVV and EVR in 2017 (before hurricanes) and 2018 (after hurricanes). Morphological fine-root traits include root length, diameter, and SRL. Root architectural traits includes root branching ratio and intensity. Root physiological trait measured includes phosphatase activity, and root microbial association trait measured includes percentage mycorrhizal colonization. Chemistry data includes root phosphorus concentration, soil available, and organic phosphorus.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

High-throughput screening of Protein-DNA interactions in Sorghum

Drought is the primary abiotic factors negatively affecting agriculture, causing tremendous reductions in yield world-wide. Drought responsive adaptation strategies require complex molecular responses to including hormone signaling and production of osmo-protectants, as well as developmental responses including stomatal closure, changes to leaf morphology, and altered root system architecture. A common strategy to better understand these adaptation mechanisms is to compare plants with differing drought tolerances and has been successful in multiple crop plants including wheat, rice, and maize. To better understand drought adaptation strategies, we compared the cytosolic- and organelle-enriched protein profiles of leaves from two Sorghum bicolor genotypes with differing pre-flowering drought tolerances after 8-weeks of growth under water limitation. In agreement with previous literature findings, we observed significant drought-induced changes in the abundance of multiple heat shock proteins and dehydrins in both genotypes. We also identified unique proteins that might play a role in genotype dependent drought adaptation.

60 APPLIED LIFE SCIENCES↗