A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements

Unraveling root and rhizosphere traits in temperate maize landraces and modern cultivars: Implications for soil resource acquisition and drought adaptation

A holistic understanding of plant strategies to acquire soil resources is pivotal in achieving sustainable food security. However, we lack knowledge about variety-specific root and rhizosphere traits for resource acquisition, their plasticity and adaptation to drought. We conducted a greenhouse experiment to phenotype root and rhizosphere traits (mean root diameter [Root D], specific root length [SRL], root tissue density, root nitrogen content, specific rhizosheath mass [SRM], arbuscular mycorrhizal fungi [AMF] colonization) of 16 landraces and 22 modern cultivars of temperate maize (Zea mays L.). Our results demonstrate that landraces and modern cultivars diverge in their root and rhizosphere traits. Although landraces follow a 'do-it-yourself' strategy with high SRLs, modern cultivars exhibit an 'outsourcing' strategy with increased mean Root Ds and a tendency towards increased root colonization by AMF. We further identified that SRM indicates an 'outsourcing' strategy. Additionally, landraces were more drought-responsive compared to modern cultivars based on multitrait response indices. We suggest that breeding leads to distinct resource acquisition strategies between temperate maize varieties. Future breeding efforts should increasingly target root and rhizosphere economics, with SRM serving as a valuable proxy for identifying varieties employing an outsourcing resource acquisition strategy.

Nanoparticles and root traits: mineral nutrition, stress tolerance and interaction with rhizosphere microbiota

MAIN CONCLUSION

This review article highlights a broader perspective of NPs and plant-root interaction by focusing on their beneficial and deleterious impacts on root system architecture (RSA). The root performs a vital function by securing itself in the soil, absorbing and transporting water and nutrients to facilitate plant growth and productivity. In dicots, the architecture of the root system (RSA) is markedly shaped by the development of the primary root and its branches, showcasing considerable adaptability in response to changes in the environment. For promoting agriculture and combating global food hunger, the use of nanoparticles (NPs) may be an exciting option, for which it is essential to understand the behaviour of plants under NPs exposure. The nature of NPs and their physicochemical characteristics play a significant role in the positive/negative response of roots and shoots. Root morphological features, such as root length, root mass and root development features, may regulated positively/negatively by different types of NPs. In addition, application of NPs may also enhance nutrient transport and soil fertility by the promotion of soil microorganisms including plant growth-promoting rhizobacteria (PGPRs) and also soil enzymes. Interestingly the interaction of nanomaterials (NMs) with rhizospheric bacteria can enhance plant development and soil health. However, some studies also suggested that the increased use of several types of engineered nanoparticles (ENPs) may disrupt the equilibrium of the soil-root interface and unsafe morphogenesis by causing the browning of roots and suppressing the growth of root and soil microbes. Thus, this review article has sought to compile a broader perspective of NPs and plant-root interaction by focusing on their beneficial or deleterious impacts on RSA.

Belowground plant allocation regulates rice methane emissions from degraded peat soils

Carbon-rich peat soils have been drained and used extensively for agriculture throughout human history, leading to significant losses of their soil carbon. One solution for rewetting degraded peat is wet crop cultivation. Crops such as rice, which can grow in water-saturated conditions, could enable agricultural production to be maintained whilst reducing CO2 and N2O emissions from peat. However, wet rice cultivation can release considerable methane (CH4). Water table and soil management strategies may enhance rice yield and minimize CH4 emissions, but they also influence plant biomass allocation strategies. It remains unclear how water and soil management influences rice allocation strategies and how changing plant allocation and associated traits, particularly belowground, influence CH4-related processes. We examined belowground biomass (BGB), aboveground biomass (AGB), belowground:aboveground ratio (BGB:ABG), and a range of root traits (root length, root diameter, root volume, root area, and specific root length) under different soil and water treatments; and evaluated plant trait linkages to CH4. Rice (Oryza sativa L.) was grown for six months in field mesocosms under high (saturated) or low water table treatments, and in either degraded peat soil or degraded peat covered with mineral soil. We found that BGB and BGB:AGB were lowest in water saturated conditions where mineral soil had been added to the peat, and highest in low-water table peat soils. Furthermore, CH4 and BGB were positively related, with BGB explaining 60% of the variation in CH4 but only under low water table conditions. Our results suggest that a mix of low water table and mineral soil addition could minimize belowground plant allocation in rice, which could further lower CH4 likely because root-derived carbon is a key substrate for methanogenesis. Minimizing root allocation, in conjunction with water and soil management, could be explored as a strategy for lowering CH4 emissions from wet rice cultivation in degraded peatlands.

A trait-based root acquisition-defence-decomposition framework in angiosperm tree species

To adapt to the complex belowground environment, plants make trade-offs between root resource acquisition and defence ability. This includes forming partnerships with different types of root associating microorganisms, such as arbuscular mycorrhizal and ectomycorrhizal fungi. These trade-offs, by mediating root chemistry, exert legacy effects on nutrient release during decomposition, which may, in turn, affect the ability of new roots to re-acquire resources, thereby generating a feedback loop. However, the linkages at the basis of this potential feedback loop remain largely unquantified. Here, we propose a trait-based root 'acquisition-defence-decomposition' conceptual framework and test the strength of relevant linkages across 90 angiosperm tree species. We show that, at the plant species level, the root-fungal symbiosis gradient within the root economics space, root chemical defence (condensed tannins), and root decomposition rate are closely linked, providing support to this framework. Beyond the dichotomy between arbuscular mycorrhizal-dominated versus ectomycorrhizal-dominated systems, we suggest a continuous shift in feedback loops, from 'high arbuscular mycorrhizal symbiosis-low defence-fast decomposition-inorganic nutrition' by evolutionarily ancient taxa to 'high ectomycorrhizal symbiosis-high defence-slow decomposition-organic nutrition' by more modern taxa. This 'acquisition-defence-decomposition' framework provides a foundation for testable hypotheses on multidimensional linkages between species' belowground strategies and ecosystem nutrient cycling in an evolutionary context.

Tradeoffs among root functional traits for phosphorus acquisition in 13 soybean genotypes contrasting in mycorrhizal colonization

BACKGROUND AND AIMS

Plants have adapted to acquire phosphorus (P) primarily through advantageous root morphologies, responsive physiological pathways and associations with mycorrhizal fungi. Yet, to date, little information exists on how variation in arbuscular mycorrhizal (AM) colonization is coordinated with root morphological and physiological traits to enhance P acquisition.

METHODS

Thirteen root functional traits associated with P acquisition were characterized at full bloom stage in pot cultures under low soil P availability conditions for 13 soybean genotypes contrasting in AM colonization.

KEY RESULTS

Significant variation in root functional traits was observed in response to low P stress among the 13 tested soybean genotypes contrasting in AM colonization. Genotypes with low AM colonization exhibited greater root proliferation but with less advantageous root physiological characteristics for P acquisition. In contrast, genotypes with high AM colonization exhibited less root growth but higher phosphatase activities and carboxylate content in the rhizosheath. Root dry weights, and contents of carbon and P were positively correlated with root morphological traits of different root orders and whole root systems, and were negatively correlated with AM colonization of fine roots and whole root systems, as well as rhizosheath phosphatase activities and carboxylate contents. These results taken in combination with a significant positive correlation between plant P content and root morphological traits indicate that root morphological traits play a primary role in soybean P acquisition.

CONCLUSIONS

The results suggest that efficient P acquisition involves tradeoffs among carbon allocation to root proliferation, mycorrhizal symbiosis or P-mobilizing exudation. Complementarity and complexity in the selection of P acquisition strategies was notable among soybean genotypes contrasting in AM colonization, which is closely related to plant C budgeting.

Phytochemical diversity and their adaptations to abiotic and biotic pressures in fine roots across a climatic gradient

Phytochemicals and their ecological significance are long ignored in trait-based ecology. Moreover, the adaptations of phytochemicals produced by fine roots to abiotic and biotic pressures are less understood. Here, we explored the fine roots metabolomes of 315 tree species and their rhizosphere microbiome in southwestern China spanning tropical, subtropical, and subalpine forest ecosystems, to explore phytochemical diversity and endemism patterns of various metabolic pathways and phytochemical-microorganism interactions. We found that subalpine species showed higher phytochemical diversity but lower interspecific variation than tropical species, which favors coping with high abiotic pressures. Tropical species harbored higher interspecific phytochemical variation and phytochemical endemism, which favors greater species coexistence and adaptation to complex biotic pressures. Moreover, there was evidence of widespread chemical niche partitioning of closely related species in all regions, and phytochemicals showed a weak phylogenetic signal, but were regulated by abiotic and biotic pressures. Our findings support the Latitudinal Biotic Interaction Hypothesis, i.e., the intensity of phytochemical-microorganism interactions decreases from tropical to subalpine regions, which promotes greater microbial community turnover and phytochemical niche partitioning of host plants in the tropics than in higher latitude forests. Our study reveals the convergent phytochemical diversity patterns of various pathways and their interactions with microorganism, thus promoting species coexistence.

The AusTraits plant dictionary

Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. The lack of unified, comprehensive, and machine-readable plant trait definitions limits the utility of trait databases, including reanalysis of data from a single database, or analyses that integrate data across multiple databases. Both can only occur if researchers are confident the trait concepts are consistent within and across sources. Here we describe the AusTraits Plant Dictionary (APD), a new data source of terms that extends the trait definitions included in a recent trait database, AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description; addition of trait metadata; and publication in both human and machine-readable forms. Trait definitions include keywords, references, and links to related trait concepts in other databases, enabling integration of AusTraits with other sources. The APD will both improve the usability of AusTraits and foster the integration of trait data across global and regional plant trait databases.

Root topological order drives variation of fine root vessel traits and hydraulic strategies in tropical trees

Vessel traits contribute to plant water transport from roots to leaves and thereby influence how plants respond to soil water availability, but the sources of variation in fine root anatomical traits remain poorly understood. Here, we explore the variations of fine root vessel traits along topological orders within and across tropical tree species. Anatomical traits were measured along five root topological orders in 80 individual trees of 20 species from a tropical forest in southwestern China. We found large variations for most root anatomical traits across topological orders, and strong co-variations between vessel traits. Within species, theoretical specific xylem hydraulic conductivity (Kth) increased with topological order due to increased mean vessel diameter, size heterogeneity, and decreased vessel density. Across species, Kth was associated with vessel fraction in low-order roots and correlated with mean vessel diameter and vessel density in high-order roots, suggesting a shift in relative anatomical contributors to Kth from the second- to fifth-order roots. We found no clear relationship between Kth and stele: root diameter ratios. Our study shows strong variations in root vessel traits across topological orders and species, and highlights shifts in the anatomical underpinnings by varying vessel-related anatomical structures for an optimized water supply.

Intraspecific alternative phenotypes contribute to variation in species' strategies for growth

Ecologists have historically sought to identify the mechanisms underlying the maintenance of local species diversity. High-dimensional trait-based relationships, such as alternative phenotypes, have been hypothesized as important for maintaining species diversity such that phenotypically dissimilar individuals compete less for resources but have similar performance in a given environment. The presence of alternative phenotypes has primarily been investigated at the community level, despite the importance of intraspecific variation to diversity maintenance. The aims of this research are to (1) determine the presence or absence of intraspecific alternative phenotypes in three species of tropical tree seedlings, (2) investigate if these different species use the same alternative phenotypes for growth success, and (3) evaluate how findings align with species co-occurrence patterns. We model species-specific relative growth rate with individual-level measurements of leaf mass per area (LMA) and root mass fraction (RMF), environmental data, and their interactions. We find that two of the three species have intraspecific alternative phenotypes, with individuals within species having different functional forms leading to similar growth. Interestingly, individuals within these species use the same trait combinations, high LMA × low RMF and low LMA × high RMF, in high soil nutrient environments to acquire resources for higher growth. This similarity among species in intraspecific alternative phenotypes and variables that contribute most to growth may lead to their negative spatial co-occurrence. Overall, we find that multiple traits or interactions between traits and the environment drive species-specific strategies for growth, but that individuals within species leverage this multi-dimensionality in different ways for growth success.

Not so hidden anymore: Advances and challenges in understanding root growth under water deficits

Limited water availability is a major environmental factor constraining plant development and crop yields. One of the prominent adaptations of plants to water deficits is the maintenance of root growth that enables sustained access to soil water. Despite early recognition of the adaptive significance of root growth maintenance under water deficits, progress in understanding has been hampered by the inherent complexity of root systems and their interactions with the soil environment. We highlight selected milestones in the understanding of root growth responses to water deficits, with emphasis on founding studies that have shaped current knowledge and set the stage for further investigation. We revisit the concept of integrated biophysical and metabolic regulation of plant growth and use this framework to review central growth-regulatory processes occurring within root growth zones under water stress at subcellular to organ scales. Key topics include the primary processes of modifications of cell wall-yielding properties and osmotic adjustment, as well as regulatory roles of abscisic acid and its interactions with other hormones. We include consideration of long-recognized responses for which detailed mechanistic understanding has been elusive until recently, for example hydrotropism, and identify gaps in knowledge, ongoing challenges, and opportunities for future research.

Long-term nitrogen addition modifies fine root growth and vertical distribution by affecting soil nutrient availability in a Mongolian pine plantation

Fine roots are the primary organ of tree species in water and nutrient acquisition, and are the major contributor of forest soil organic carbon (C). However, it remains largely unknown how fine root growth dynamics and vertical distribution respond to long-term nitrogen (N) enrichment, which prevents us from accurately evaluating forest C sequestration potential under N deposition. Here, we investigated the effects of nine-year N addition (0 and 10 g N m-2 year-1) on fine root nutrients, biomass, production, turnover rate and vertical distribution in three soil layers (0-10, 10-20 and 20-40 cm) of a Mongolian pine (Pinus sylvestris var. mongolica) plantation in the Keerqin Sandy Lands, Northeast China. We found that soil inorganic N was increased and Olsen-P was decreased by N addition. N addition increased fine root N, C:P and N:P ratios, but reduced fine root P and C:N ratio across all soil layers. N addition reduced fine root biomass in 0-10 cm soil layer but increased it in 20-40 cm soil layer. N addition accelerated fine root turnover rate in 0-10 cm soil layer, and increased fine root necromass across all soil layers. Moreover, N addition significantly enhanced biomass of ectomycorrhizal extraradical hyphae in the 0-10 cm soil layer. Redundancy analysis showed that variations of fine root traits were well explained by soil NO3--N in 0-10 and 10-20 cm soil layers, and by soil NH4+-N and Olsen-P in 20-40 cm soil layer. Collectively, our results highlight the shift from N limitation to P limitation of Mongolian pine plantations under long-term N addition, and suggest that changes in fine root growth and vertical distribution induced by N addition could accelerate belowground C allocation in Mongolian pine plantations.

Root and shoot phenology, architecture, and organ properties: an integrated trait network among 44 herbaceous wetland species

Integrating traits across above- and belowground organs offers comprehensive insights into plant ecology, but their various functions also increase model complexity. This study aimed to illuminate the interspecific pattern of whole-plant trait correlations through a network lens, including a detailed analysis of the root system. Using a network algorithm that allows individual traits to belong to multiple modules, we characterize interrelations among 19 traits, spanning both shoot and root phenology, architecture, morphology, and tissue properties of 44 species, mostly herbaceous monocots from Northern Ontario wetlands, grown in a common garden. The resulting trait network shows three distinct yet partially overlapping modules. Two major trait modules indicate constraints of plant size and form, and resource economics, respectively. These modules highlight the interdependence between shoot size, root architecture and porosity, and a shoot-root coordination in phenology and dry-matter content. A third module depicts leaf biomechanical adaptations specific to wetland graminoids. All three modules overlap on shoot height, suggesting multifaceted constraints of plant stature. In the network, individual-level traits showed significantly higher centrality than tissue-level traits do, demonstrating a hierarchical trait integration. The presented whole-plant, integrated network suggests that trait covariation is essentially function-driven rather than organ-specific.

The effect of ectomycorrhizal fungal exposure on nursery-raised Pinus sylvestris seedlings: plant transpiration under short-term drought, root morphology and plant biomass

Drought is a major environmental stressor that limits seedling growth. Several studies have found that some ectomycorrhizal fungi may increase the drought tolerance of nursery-raised seedlings. However, the precise role that different ectomycorrhizal fungi species play in drought tolerance remains unclear. We evaluated the transpiration rate of Pinus sylvestris seedlings under drought stress in greenhouse conditions by exposing seedlings to 10 ectomycorrhizal fungi species, with different functional traits (exploration type and hydrophobicity), and to 3 natural soil inoculums. We measured the transpiration and water potential of the seedlings during a 10-day drought period and a 14-day recovery period. We then analyzed their root morphology, stem, needle, root biomass and needle chlorophyll fluorescence. We showed that exposing seedlings to ectomycorrhizal fungi or soil inoculum had a positive effect on their transpiration rate during the driest period and through the recovery phase, leading to 2- to 3-fold higher transpiration rates compared with the nonexposed control seedlings. Seedlings exposed to medium-distance ectomycorrhizal fungi performed better than other exploration types under drought conditions, but ectomycorrhizal fungi hydrophobicity did not seem to affect the seedlings response to drought. No significant differences were observed in biomass accumulation and root morphology between the seedlings exposed to different ectomycorrhizal fungi species and the control. Our results highlight the positive and species-specific effect of ectomycorrhizal fungi exposure on drought tolerance in nursery-raised Scots pine seedlings. The studied ectomycorrhizal fungi functional traits may not be sufficient to predict the seedling response to drought stress, thus physiological studies across multiple species are needed to draw the correct conclusion. Our findings have potential practical implications for enhancing seedling drought tolerance in nursery plant production.

Toward a coordinated understanding of hydro-biogeochemical root functions in tropical forests for application in vegetation models

Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest-climate feedbacks for these carbon-rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics that represent important functional processes in tropical forests. We focus on: (1) fine-root strategies for soil resource exploration, (2) coupling and trade-offs in fine-root water vs nutrient acquisition, and (3) aboveground-belowground linkages in plant resource acquisition and use. We suggest avenues for representing these extremely diverse plant communities in computationally manageable and ecologically meaningful groups in models for linked aboveground-belowground hydro-nutrient functions. Tropical forests are undergoing warming, shifting rainfall regimes, and exacerbation of soil nutrient scarcity caused by elevated atmospheric CO2. The accurate model representation of tropical forest functions is crucial for understanding the interactions of this biome with the climate.

A simple method for estimating the coarse lateral root biomass of shrubs using ground-penetrating radar: Validation by Caragana microphylla Lam. in Inner Mongolia

The potential increases in carbon stocks in arid regions due to recent shrub encroachment have attracted extensive interest among both ecologists and carbon policy analysts. Quantifying the shrub root biomass amount in these ecosystems is essential to understanding the ecological changes occurring. In this paper, we proposed a simple nondestructive method for estimating the coarse lateral root biomass of shrubs based on the root counts obtained from ground-penetrating radar (GPR) radargrams. Root data were gathered via field experiments using GPR with antenna center frequencies of 900 MHz and 400 MHz. Five Caragana microphylla Lam. shrubs of different sizes were selected for measuring objects, and a total of 40 GPR survey lines were established for GPR data acquisition. The soil profile wall excavation method was used to obtain the total root biomass from each radargram. A model for estimating the root biomass was built by establishing the relationship between the root biomass in each profile and the root counts interpreted from the radargrams. According to the mathematical relationship between the root diameter and root biomass, the proxy root radius was derived, which could explain the rationality of the proposed model from the biological mechanism. The established model provided high confidence in estimating the root dry biomass using the GPR data obtained at the two antenna frequencies (R2= 0.73 for 900 MHz and R2= 0.71 for 400 MHz). The leave-one-out cross-validation results showed that the model exhibits satisfactory performance. This study expands the application of geophysical methods in root research and offers a new simplified method for estimating the root biomass from GPR data under field conditions.

Understanding role of roots in plant response to drought: Way forward to climate-resilient crops

Drought stress leads to a significant amount of agricultural crop loss. Thus, with changing climatic conditions, it is important to develop resilience measures in agricultural systems against drought stress. Roots play a crucial role in regulating plant development under drought stress. In this review, we have summarized the studies on the role of roots and root-mediated plant responses. We have also discussed the importance of root system architecture (RSA) and the various structural and anatomical changes that it undergoes to increase survival and productivity under drought. Various genes, transcription factors, and quantitative trait loci involved in regulating root growth and development are also discussed. A summarization of various instruments and software that can be used for high-throughput phenotyping in the field is also provided in this review. More comprehensive studies are required to help build a detailed understanding of RSA and associated traits for breeding drought-resilient cultivars.

Identification of genetics and hormonal factors involved in Quercus robur root growth regulation in different cultivation system

Understanding the molecular processes and hormonal signals that govern root growth is of paramount importance for effective forest management. While Arabidopsis studies have shed light on the role of the primary root in root system development, the structure of root systems in trees is considerably more intricate, posing challenges to comprehend taproot growth in acorn-sown and nursery-cultivated seedlings. In this study, we investigated Quercus robur seedlings using rhizotrons, containers, and transplanted containers to rhizotrons, aiming to unravel the impact of forest nursery practices on processes governing taproot growth and root system development. Root samples were subjected to RNA-seq analysis to identify gene expression patterns and perform differential gene expression and phytohormone analysis. Among studied cultivation systems, differentially expressed genes (DEGs) exhibited significant diversity, where the number of co-occurring DEGs among cultivation systems was significantly smaller than the number of unique DEGs in different cultivation systems. Moreover, the results imply that container cultivation triggers the activation of several genes associated with linolenic acid and peptide synthesis in root growth. Upon transplantation from containers to rhizotrons, rapid enhancement in gene expression occurs, followed by gradual reduction as root growth progresses, ultimately reaching a similar expression pattern as observed in the taproot of rhizotron-cultivated seedlings. Phytohormone analysis revealed that taproot growth patterns under different cultivation systems are regulated by the interplay between auxin and cytokinin concentrations. Moreover, the diversification of hormone levels within the root zone and cultivation systems allows for taproot growth inhibition and prompt recovery in transplanted seedlings. Our study highlights the crucial role of hormone interactions during the early stages of taproot elongation, influencing root system formation across.

Lanthanum Significantly Contributes to the Growth of the Fine Roots' Morphology and Phosphorus Uptake Efficiency by Increasing the Yield and Quality of Glycyrrhiza uralensis Taproots

The occurrence of different degrees of phosphorus deficiency in the vast majority of G. uralensis cultivation regions worldwide is common. There is a pressing need within the cultivated G. uralensis industry to identify appropriate exogenous substances that can enhance the uptake of phosphorus and improve both the yield and quality of the taproots of G. uralensis. This study was conducted to investigate the fine root and taproot morphology, physiological characteristics, and secondary metabolite accumulation in response to the supply of varying concentrations of LaCl3 to G. uralensis, to determine the optimal concentration of LaCl3 that can effectively enhance the yield and quality of G. uralensis's taproots, while also alleviating its reliance on soil phosphate fertilizer. The findings indicate that the foliar application of lanthanum enhanced root activity and increased APase activity, eliciting alterations in the fine root morphology, leading to promoting the accumulation of biomass in grown G. uralensis when subjected to P-deficient conditions. Furthermore, it was observed that the nutrient uptake of G. uralensis was significantly improved when subjected to P-deficient conditions but treated with LaCl3. Additionally, the yield and quality of the medicinal organs of G. uralensis were significantly enhanced.

The hidden roots of wetland methane emissions

Wetlands are the largest natural source of methane (CH4 ) globally. Climate and land use change are expected to alter CH4 emissions but current and future wetland CH4 budgets remain uncertain. One important predictor of wetland CH4 flux, plants, play an important role in providing substrates for CH4 -producing microbes, increasing CH4 consumption by oxygenating the rhizosphere, and transporting CH4 from soils to the atmosphere. Yet, there remain various mechanistic knowledge gaps regarding the extent to which plant root systems and their traits influence wetland CH4 emissions. Here, we present a novel conceptual framework of the relationships between a range of root traits and CH4 processes in wetlands. Based on a literature review, we propose four main CH4 -relevant categories of root function: gas transport, carbon substrate provision, physicochemical influences and root system architecture. Within these categories, we discuss how individual root traits influence CH4 production, consumption, and transport (PCT). Our findings reveal knowledge gaps concerning trait functions in physicochemical influences, and the role of mycorrhizae and temporal root dynamics in PCT. We also identify priority research needs such as integrating trait measurements from different root function categories, measuring root-CH4 linkages along environmental gradients, and following standardized root ecology protocols and vocabularies. Thus, our conceptual framework identifies relevant belowground plant traits that will help improve wetland CH4 predictions and reduce uncertainties in current and future wetland CH4 budgets.

Shifting patterns in fine root distribution of four xerophytic species across soil structural gradients and years of growth

Fine root (diameter < 2 mm) distribution influences the potential for resource acquisition in soil profiles, which defines how plants interact with local soil environments; however, a deep understanding of how fine root vertical distribution varies with soil structural variations and across growth years is lacking. We subjected four xerophytic species native to an arid valley of China, Artemisia vestita, Bauhinia brachycarpa, Sophora davidii, and Cotinus szechuanensis, to increasing rock fragment content (RFC) treatments (0%, 25%, 50%, and 75%, v v-1) in an arid environment and measured fine root vertical profiles over 4 years of growth. Fine root depth and biomass of woody species increased with increasing RFC, but the extent of increase declined with growth years. Increasing RFC also increased the degree of interannual decreases in fine root diameter. The limited supply of soil resources in coarse soils explained the increases in rooting depth and variations in the pattern of fine root profiles across RFC. Fine root depth and biomass of the non-woody species (A. vestita) in soil profiles decreased with the increase in RFC and growth years, showing an opposite pattern from the other three woody species. Within woody species, the annual increase in fine root biomass varied with RFC, which led to large interannual differences in the patterns of fine root profiles. Younger or non-woody plants were more susceptible to soil environmental changes than the older or woody plants. These results reveal the limitations of dry and rocky environments on the growth of different plants, with woody and non-woody plants adjusting their root vertical distribution through opposite pathways to cope with resource constraints, which has management implications for degraded agroforest ecosystems.

Improper data practices erode the quality of global ecological databases and impede the progress of ecological research

The scientific community has entered an era of big data. However, with big data comes big responsibilities, and best practices for how data are contributed to databases have not kept pace with the collection, aggregation, and analysis of big data. Here, we rigorously assess the quantity of data for specific leaf area (SLA) available within the largest and most frequently used global plant trait database, the TRY Plant Trait Database, exploring how much of the data were applicable (i.e., original, representative, logical, and comparable) and traceable (i.e., published, cited, and consistent). Over three-quarters of the SLA data in TRY either lacked applicability or traceability, leaving only 22.9% of the original data usable compared with the 64.9% typically deemed usable by standard data cleaning protocols. The remaining usable data differed markedly from the original for many species, which led to altered interpretation of ecological analyses. Though the data we consider here make up only 4.5% of SLA data within TRY, similar issues of applicability and traceability likely apply to SLA data for other species as well as other commonly measured, uploaded, and downloaded plant traits. We end with suggested steps forward for global ecological databases, including suggestions for both uploaders to and curators of databases with the hope that, through addressing the issues raised here, we can increase data quality and integrity within the ecological community.

The origin of bi-dimensionality in plant root traits

Plant roots show extraordinary diversity in form and function in heterogeneous environments. Mounting evidence has shown global bi-dimensionality in root traits, the root economics spectrum (RES), and an orthogonal dimension describing mycorrhizal collaboration; however, the origin of the bi-dimensionality remains unresolved. Here, we propose that bi-dimensionality arises from the cylindrical geometry of roots, allometry between root cortex and stele, and independence between root cell wall thickness and cell number. Root geometry and mycorrhizal collaboration may both underlie the bi-dimensionality. Further, we emphasize why plant roots should be cylindrical rather than flat. Finally, we highlight the need to integrate organ-, cellular-, and molecular-level processes driving the bi-dimensionality in plant roots to fully understand plant diversity and functions.

Bridging Time-series Image Phenotyping and Functional-Structural Plant Modeling to Predict Adventitious Root System Architecture

Root system architecture (RSA) is an important measure of how plants navigate and interact with the soil environment. However, current methods in studying RSA must make tradeoffs between precision of data and proximity to natural conditions, with root growth in germination papers providing accessibility and high data resolution. Functional-structural plant models (FSPMs) can overcome this tradeoff, though parameterization and evaluation of FSPMs are traditionally based in manual measurements and visual comparison. Here, we applied a germination paper system to study the adventitious RSA and root phenology of Populus trichocarpa stem cuttings using time-series image-based phenotyping augmented by FSPM. We found a significant correlation between timing of root initiation and thermal time at cutting collection (P value = 0.0061, R2 = 0.875), but little correlation with RSA. We also present a use of RhizoVision [1] for automatically extracting FSPM parameters from time series images and evaluating FSPM simulations. A high accuracy of the parameterization was achieved in predicting 2D growth with a sensitivity rate of 83.5%. This accuracy was lost when predicting 3D growth with sensitivity rates of 38.5% to 48.7%, while overall accuracy varied with phenotyping methods. Despite this loss in accuracy, the new method is amenable to high throughput FSPM parameterization and bridges the gap between advances in time-series phenotyping and FSPMs.

Experimental warming altered plant functional traits and their coordination in a permafrost ecosystem

Knowledge about changes in plant functional traits is valuable for the mechanistic understanding of warming effects on ecosystem functions. However, observations have tended to focus on aboveground plant traits, and there is little information about changes in belowground plant traits or the coordination of above- and belowground traits under climate warming, particularly in permafrost ecosystems. Based on a 7-yr field warming experiment, we measured 26 above- and belowground plant traits of four dominant species, and explored community functional composition and trait networks in response to experimental warming in a permafrost ecosystem on the Tibetan Plateau. Experimental warming shifted community-level functional traits toward more acquisitive values, with earlier green-up, greater plant height, larger leaves, higher photosynthetic resource-use efficiency, thinner roots, and greater specific root length and root nutrient concentrations. However, warming had a negligible effect in terms of functional diversity. In addition, warming shifted hub traits which have the highest centrality in the network from specific root area to leaf area. These results demonstrate that above- and belowground traits exhibit consistent adaptive strategies, with more acquisitive traits in warmer environments. Such changes could provide an adaptive advantage for plants in response to environmental change.

Defoliation and fertilisation differentially moderate root trait effects on soil abiotic and biotic properties

Root functional traits are known to influence soil properties that underpin ecosystem functioning. Yet few studies have explored how root traits simultaneously influence physical, chemical, and biological properties of soil, or how these responses are modified by common grassland perturbations that shape roots, such as defoliation and fertilisation.Here, we explored how root traits of a wide range of grassland plant species with contrasting resource acquisition strategies (i.e. conservative vs. exploitative strategy plant species) respond to defoliation and fertilisation individually and in combination, and examined cascading impacts on a range of soil abiotic and biotic properties that underpin ecosystem functioning.We found that the amplitude of the response of root traits to defoliation and fertilisation varied among plant species, in most cases independently of plant resource acquisition strategies. However, the direction of the root trait responses (increase or decrease) to perturbations was consistent across all plant species, with defoliation and fertilisation exerting opposing effects on root traits. Specific root length increased relative to non-perturbed control in response to defoliation, while root biomass, root mass density, and root length density decreased. Fertilisation induced the opposite responses. We also found that both defoliation and fertilisation individually enhanced the role of root traits in regulating soil biotic and abiotic properties, especially soil aggregate stability. Synthesis: Our results indicate that defoliation and fertilisation, two common grassland perturbations, have contrasting impacts on root traits of grassland plant species, with direct and indirect short-term consequences for a wide range of soil abiotic and biotic properties that underpin ecosystem functioning.

Semantic segmentation of plant roots from RGB (mini-) rhizotron images-generalisation potential and false positives of established methods and advanced deep-learning models

BACKGROUND

Manual analysis of (mini-)rhizotron (MR) images is tedious. Several methods have been proposed for semantic root segmentation based on homogeneous, single-source MR datasets. Recent advances in deep learning (DL) have enabled automated feature extraction, but comparisons of segmentation accuracy, false positives and transferability are virtually lacking. Here we compare six state-of-the-art methods and propose two improved DL models for semantic root segmentation using a large MR dataset with and without augmented data. We determine the performance of the methods on a homogeneous maize dataset, and a mixed dataset of > 8 species (mixtures), 6 soil types and 4 imaging systems. The generalisation potential of the derived DL models is determined on a distinct, unseen dataset.

RESULTS

The best performance was achieved by the U-Net models; the more complex the encoder the better the accuracy and generalisation of the model. The heterogeneous mixed MR dataset was a particularly challenging for the non-U-Net techniques. Data augmentation enhanced model performance. We demonstrated the improved performance of deep meta-architectures and feature extractors, and a reduction in the number of false positives.

CONCLUSIONS

Although correction factors are still required to match human labelled root lengths, neural network architectures greatly reduce the time required to compute the root length. The more complex architectures illustrate how future improvements in root segmentation within MR images can be achieved, particularly reaching higher segmentation accuracies and model generalisation when analysing real-world datasets with artefacts-limiting the need for model retraining.

Impact of PGPR inoculation on root morphological traits and root exudation in rapeseed and camelina: interactions with heat stress

Root exudation is involved in the recruitment of beneficial microorganisms by trophic relationships and/or signalling pathways. Among beneficial microorganisms, Plant Growth-Promoting Rhizobacteria (PGPR) are known to improve plant growth and stress resistance. These interactions are of particular importance for species that do not interact with mycorrhizal fungi, such as rapeseed (Brassica napus L.) and camelina (Camelina sativa (L.) Crantz). However, heat stress is known to have a quantitative and qualitative impact on root exudation and could affect the interactions between plants and PGPR. We aimed to analyse the effects of PGPR inoculation on root morphology and exudation in rapeseed and camelina at the reproductive stage. The modulation of the effects of these interactions under heat stress was also investigated. The plants were inoculated twice at the reproductive stage with two different Pseudomonas species and were exposed to heat stress after the second inoculation. In non-stressing conditions, after bacterial inoculation, rapeseed and camelina exhibited two contrasting behaviours in C root allocation. While rapeseed plants seemed to suffer from the interactions with the bacteria, camelina plants appeared to control the relationship with the PGPR by modifying the composition of their root exudates. Under heat stress, the plant-PGPR interaction was unbalanced for rapeseed, for which the C allocation strategy is mainly driven by the C cost from the bacteria. Alternatively, camelina plants prioritized C allocation for their own above-ground development. This work opens up new perspectives for understanding plant-PGPR interactions, especially in an abiotic stress context.

Fine root decomposition in forest ecosystems: an ecological perspective

Fine root decomposition is a physio-biochemical activity that is critical to the global carbon cycle (C) in forest ecosystems. It is crucial to investigate the mechanisms and factors that control fine root decomposition in forest ecosystems to understand their system-level carbon balance. This process can be influenced by several abiotic (e.g., mean annual temperature, mean annual precipitation, site elevation, stand age, salinity, soil pH) and biotic (e.g., microorganism, substrate quality) variables. Comparing decomposition rates within sites reveals positive impacts of nitrogen and phosphorus concentrations and negative effects of lignin concentration. Nevertheless, estimating the actual fine root breakdown is difficult due to inadequate methods, anthropogenic activities, and the impact of climate change. Herein, we propose that how fine root substrate and soil physiochemical characteristics interact with soil microorganisms to influence fine root decomposition. This review summarized the elements that influence this process, as well as the research methods used to investigate it. There is also need to study the influence of annual and seasonal changes affecting fine root decomposition. This cumulative evidence will provide information on temporal and spatial dynamics of forest ecosystems, and will determine how logging and reforestation affect fine root decomposition.

Functional and ecological diversification of underground organs in Solanum

The evolution of geophytes in response to different environmental stressors is poorly understood largely due to the great morphological variation in underground plant organs, which includes species with rhizomatous structures or underground storage organs (USOs). Here we compare the evolution and ecological niche patterns of different geophytic organs in Solanum L., classified based on a functional definition and using a clade-based approach with an expert-verified specimen occurrence dataset. Results from PERMANOVA and Phylogenetic ANOVAs indicate that geophytic species occupy drier areas, with rhizomatous species found in the hottest areas whereas species with USOs are restricted to cooler areas in the montane tropics. In addition, rhizomatous species appear to be adapted to fire-driven disturbance, in contrast to species with USOs that appear to be adapted to prolonged climatic disturbance such as unfavorable growing conditions due to drought and cold. We also show that the evolution of rhizome-like structures leads to changes in the relationship between range size and niche breadth. Ancestral state reconstruction shows that in Solanum rhizomatous species are evolutionarily more labile compared to species with USOs. Our results suggest that underground organs enable plants to shift their niches towards distinct extreme environmental conditions and have different evolutionary constraints.

Coordination between leaf and root traits in Mediterranean coastal dune plants

Plant trait-based functional spectra are crucial to assess ecosystem functions and services. Whilst most research has focused on aboveground vegetative traits (leaf economic spectrum, LES), contrasting evidence on any coordination between the LES and root economic spectrum (RES) has been reported. Studying spectra variation along environmental gradients and accounting for species' phylogenetic relatedness may help to elucidate the strength of coordination between above- and belowground trait variation. We focused on leaf and root traits of 39 species sampled in three distinct habitats (front, back and slack) along a shoreline-inland gradient on coastal dunes. We tested, within a phylogenetic comparative framework, for the presence of the LES and RES, for any coordination between these spectra, and explored their relation to variation in ecological strategies along this gradient. In each habitat, three-quarters of trait variation is captured in two-dimensional spectra, with species' phylogenetic relatedness moderately influencing coordination and trade-off between traits. Along the shoreline-inland gradient, aboveground traits support the LES in all habitats. Belowground traits are consistent with the RES in the back-habitat only, where the environmental constraints are weaker, and a coordination between leaf and root traits was also found, supporting the whole-plant spectrum (PES). This study confirms the complexity when seeking any correlation between the LES and RES in ecosystems characterized by multiple environmental pressures, such as those investigated here. Changes in traits adopted to resist environmental constraints are similar among species, independent of their evolutionary relatedness, thus explaining the low phylogenetic contribution in support of our results.

Soil phosphorus availability alters the correlations between root phosphorus-uptake rates and net photosynthesis of dominant C3 and C4 species in a typical temperate grassland of Northern China

Phosphorus (P) fertilization can alleviate a soil P deficiency in grassland ecosystems. Understanding plant functional traits that enhance P uptake can improve grassland management. We measured impacts of P addition on soil chemical and microbial properties, net photosynthetic rate (Pn ) and nonstructural carbohydrate concentrations ([NSC]), and root P-uptake rate (PUR), morphology, anatomy, and exudation of two dominant grass species: Leymus chinensis (C3 ) and Cleistogenes squarrosa (C4 ). For L. chinensis, PUR and Pn showed a nonlinear correlation. Growing more adventitious roots compensated for the decrease in P transport per unit root length, so that it maintained a high PUR. For C. squarrosa, PUR and Pn presented a linear correlation. Increased Pn was associated with modifications in root morphology, which further enhanced its PUR and a greater surplus of photosynthate and significantly stimulated root exudation (proxied by leaf [Mn]), which had a greater impact on rhizosheath micro-environment and microbial PLFAs. Our results present correlations between the PUR and the Pn of L. chinensis and C. squarrosa and reveal that NSC appeared to drive the modifications of root morphology and exudation; they provide more objective basis for more efficient P-input in grasslands to address the urgent problem of P deficiency.

Shift of root nitrogen-acquisition strategy with tree age is mediated by root functional traits along the collaboration gradient of the root economics space

Root nitrogen (N)-uptake rate and uptake preference, and their association with root morphological and chemical traits are important to characterize root N-acquisition strategies of trees. However, how the root N-acquisition strategy varies with tree age, especially for those species that coexist at a common site, remains unknown. In this study, a field isotopic hydroponic method was used to determine the uptake rate and contribution of NH4+, NO3- and glycine, for three coexisting ectomycorrhizal coniferous species [Pinus koraiensis (Korean pine), Picea koraiensis (Korean spruce) and Abies nephrolepis (smelly fir)] at three age classes (young, middle-aged and mature) in a temperate forest. Concurrently, root morphological and chemical traits, as well as mycorrhizal colonization rate were determined. Our results show that the root uptake rate of total N and NH4+ gradually decreased across all three species with increasing tree age. The three species at all age classes preferred NH4+, except for middle-aged Korean spruce and mature smelly fir, which preferred glycine. In contrast, all three species showed the lowest acquisition of NO3-. According to the conceptual framework of 'root economics space', only a 'collaboration' gradient (i.e. dimension of root diameter vs specific root length or area) was identified for each species, in which root N-uptake rate loaded heavily on the side of 'do-it-yourself' (i.e. foraging N more by roots). Young trees of all species tended to exhibit the 'do-it-yourself' strategy for N uptake, and mature trees had an 'outsourcing' strategy (i.e. foraging N by a mycorrhizal partner), whereas middle-aged trees showed a balanced strategy. These findings suggest that shifts of root N-acquisition strategy with tree age in these species are mainly mediated by root traits along the 'collaboration' gradient, which advances our understanding of belowground competition, species coexistence and N cycling in temperate forests.

The allocation of anatomical traits determines the trade-off between fine root resource acquisition-transport function

Cortex radius (CR) and stele radius (SR) are important functional traits associated with the nutrient acquisition and transport functions of fine roots, respectively. However, for developmental and anatomical reasons, the resource acquisition-transport relationship of fine roots is expected to be different for different root orders. To address this issue, critical fine root anatomical traits were examined for the first three orders of roots of 59 subtropical woody plants. Designating the most distal fine roots as order one, SR scaled isometrically with respect to root radius (RR) (i.e., SR ∝ RR1.0) in the three root orders, whereas CR scaled allometrically with respect to RR (i.e., CR ∝ RR>1.0) with the numerical values of scaling exponents increasing significantly with increasing root orders thereby indicating a disproportional increase in CR with increasing root orders. There were also differences between normalized root tissue (CR/RR and SR/RR) and RR in different root orders. A negative isometric relationship (i.e., SR/RR ∝ RR-1.0) existed between SR/RR and RR in three order roots, whereas the allometric exponent between CR/RR and RR increased with root order (from 0.88 to 1.55). Collectively, the data indicate that root anatomical and functional traits change as a function of RR and that these changes need to be considered when modeling fine root resource acquisition-transport functions.

Are absorptive root traits good predictors of ecosystem functioning? A test in a natural temperate forest

Trait-based approaches provide a useful framework to predict ecosystem functions under intensifying global change. However, our current understanding of trait-functioning relationships mainly relies on aboveground traits. Belowground traits (e.g. absorptive root traits) are rarely studied although these traits are related to important plant functions. We analyzed four pairs of analogous leaf and absorptive root traits of woody plants in a temperate forest and examined how these traits are coordinated at the community-level, and to what extent the trait covariation depends on local-scale environmental conditions. We then quantified the contributions of leaf and absorptive root traits and the environmental conditions in determining two important forest ecosystem functions, aboveground carbon storage, and woody biomass productivity. The results showed that both morphological trait pairs and chemical trait pairs exhibited positive correlations at the community level. Absorptive root traits show a strong response to environmental conditions compared to leaf traits. We also found that absorptive root traits were better predictors of the two forest ecosystem functions than leaf traits and environmental conditions. Our study confirms the important role of belowground traits in modulating ecosystem functions and deepens our understanding of belowground responses to changing environmental conditions.

A temporal analysis and response to nitrate availability of 3D root system architecture in diverse pennycress (Thlaspi arvense L.) accessions

Introduction

Roots have a central role in plant resource capture and are the interface between the plant and the soil that affect multiple ecosystem processes. Field pennycress (Thlaspi arvense L.) is a diploid annual cover crop species that has potential utility for reducing soil erosion and nutrient losses; and has rich seeds (30-35% oil) amenable to biofuel production and as a protein animal feed. The objective of this research was to (1) precisely characterize root system architecture and development, (2) understand plastic responses of pennycress roots to nitrate nutrition, (3) and determine genotypic variance available in root development and nitrate plasticity.

Methods

Using a root imaging and analysis pipeline, the 4D architecture of the pennycress root system was characterized under four nitrate regimes, ranging from zero to high nitrate concentrations. These measurements were taken at four time points (days 5, 9, 13, and 17 after sowing).

Results

Significant nitrate condition response and genotype interactions were identified for many root traits, with the greatest impact observed on lateral root traits. In trace nitrate conditions, a greater lateral root count, length, density, and a steeper lateral root angle was observed compared to high nitrate conditions. Additionally, genotype-by-nitrate condition interaction was observed for root width, width:depth ratio, mean lateral root length, and lateral root density.

Discussion

These findings illustrate root trait variance among pennycress accessions. These traits could serve as targets for breeding programs aimed at developing improved cover crops that are responsive to nitrate, leading to enhanced productivity, resilience, and ecosystem service.

Root and branch hydraulic functioning and trait coordination across organs in drought-deciduous and evergreen tree species of a subtropical highland forest

Vessel traits are key in understanding trees' hydraulic efficiency, and related characteristics like growth performance and drought tolerance. While most plant hydraulic studies have focused on aboveground organs, our understanding of root hydraulic functioning and trait coordination across organs remains limited. Furthermore, studies from seasonally dry (sub-)tropical ecosystems and mountain forests are virtually lacking and uncertainties remain regarding potentially different hydraulic strategies of plants differing in leaf habit. Here, we compared wood anatomical traits and specific hydraulic conductivities between coarse roots and small branches of five drought-deciduous and eight evergreen angiosperm tree species in a seasonally dry subtropical Afromontane forest in Ethiopia. We hypothesized that largest vessels and highest hydraulic conductivities are found in roots, with greater vessel tapering between roots and equally-sized branches in evergreen angiosperms due to their drought-tolerating strategy. We further hypothesized that the hydraulic efficiencies of root and branches cannot be predicted from wood density, but that wood densities across organs are generally related. Root-to-branch ratios of conduit diameters varied between 0.8 and 2.8, indicating considerable differences in tapering from coarse roots to small branches. While deciduous trees showed larger branch xylem vessels compared to evergreen angiosperms, root-to-branch ratios were highly variable within both leaf habit types, and evergreen species did not show a more pronounced degree of tapering. Empirically determined hydraulic conductivity and corresponding root-to-branch ratios were similar between both leaf habit types. Wood density of angiosperm roots was negatively related to hydraulic efficiency and vessel dimensions; weaker relationships were found in branches. Wood density of small branches was neither related to stem nor coarse root wood densities. We conclude that in seasonally dry subtropical forests, similar-sized coarse roots hold larger xylem vessels than small branches, but the degree of tapering from roots to branches is highly variable. Our results indicate that leaf habit does not necessarily influence the relationship between coarse root and branch hydraulic traits. However, larger conduits in branches and a low carbon investment in less dense wood may be a prerequisite for high growth rates of drought-deciduous trees during their shortened growing season. The correlation of stem and root wood densities with root hydraulic traits but not branch wood points toward large trade-offs in branch xylem towards mechanical properties.

Embracing fine-root system complexity in terrestrial ecosystem modeling

Projecting the dynamics and functioning of the biosphere requires a holistic consideration of whole-ecosystem processes. However, biases toward leaf, canopy, and soil modeling since the 1970s have constantly left fine-root systems being rudimentarily treated. As accelerated empirical advances in the last two decades establish clearly functional differentiation conferred by the hierarchical structure of fine-root orders and associations with mycorrhizal fungi, a need emerges to embrace this complexity to bridge the data-model gap in still extremely uncertain models. Here, we propose a three-pool structure comprising transport and absorptive fine roots with mycorrhizal fungi (TAM) to model vertically resolved fine-root systems across organizational and spatial-temporal scales. Emerging from a conceptual shift away from arbitrary homogenization, TAM builds upon theoretical and empirical foundations as an effective and efficient approximation that balances realism and simplicity. A proof-of-concept demonstration of TAM in a big-leaf model both conservatively and radically shows robust impacts of differentiation within fine-root systems on simulating carbon cycling in temperate forests. Theoretical and quantitative support warrants exploiting its rich potentials across ecosystems and models to confront uncertainties and challenges for a predictive understanding of the biosphere. Echoing a broad trend of embracing ecological complexity in integrative ecosystem modeling, TAM may offer a consistent framework where modelers and empiricists can work together toward this grand goal.

Response mechanism of growth and gypenosides content for Gynostemma longipes cultivated at two altitude habitats to fine root morphological characteristics

Introduction

Fine roots are the critical functional organs of plants to absorb water and nutrients from the soil environment, while the relation between fine root morphological characteristics and yield & quality has received less attention for medicinal plants.

Methods

Therefore, we investigated the relationship between fine root morphological characteristics and biomass & gypenosides content. We explored the primary environmental drivers of fine root indicators for Gynostemma longipes from three provenances cultivated at two altitude habitats.

Results

At the end of the growing season, compared with the low-altitude habitat, the underground biomass of G. longipes in the high-altitude habitat increased significantly by 200%~290% for all three provenances. The response of gypenosides content to different altitude habitats varied with provenance and plant organs. The biomass of G. longipes strongly depended on the fine root characteristic indicators (P < 0.001), fine root length density, and fine root surface area. Our results also showed that the harvest yield of G. longipes could be effectively increased by promoting the growth of fine roots per unit leaf weight (P < 0.001, R² = 0.63). Both fine root length density and fine root surface area had strong positive correlations with soil nutrient factors (R² > 0.55) and a strong negative correlation with soil pH (R² > 0.48). In a word, the growth of G. longipes is strongly controlled by the fine root morphological characteristics through the response of fine roots to soil nutrient factors and pH.

Discussion

Our findings will help to deepen the understanding of the root ecophysiological basis driven by soil factors for the growth and secondary metabolites formation of G. longipes and other medicinal plants under changing habitat conditions. In future research, we should investigate how environmental factors drive plant morphological characteristics (e.g., fine roots) to affect the growth & quality of medicinal plants over a longer time scale.

Mitigation of Greenhouse Gas Emissions from Rice via Manipulation of Key Root Traits

Rice production worldwide represents a major anthropogenic source of greenhouse gas emissions. Nitrogen fertilization and irrigation practices have been fundamental to achieve optimal rice yields, but these agricultural practices together with by-products from plants and microorganisms, facilitate the production, accumulation and venting of vast amounts of CO₂, CH₄ and N₂O. We propose that the development of elite rice varieties should target root traits enabling an effective internal O₂ diffusion, via enlarged aerenchyma channels. Moreover, gas tight barriers impeding radial O₂ loss in basal parts of the roots will increase O₂ diffusion to the root apex where molecular O₂ diffuses into the rhizosphere. These developments result in plants with roots penetrating deeper into the flooded anoxic soils, producing higher volumes of oxic conditions in the interface between roots and rhizosphere. Molecular O₂ in these zones promotes CH₄ oxidation into CO₂ by methanotrophs and nitrification (conversion of NH₄⁺ into NO₃^-), reducing greenhouse gas production and at the same time improving plant nutrition. Moreover, roots with tight barriers to radial O₂ loss will have restricted diffusional entry of CH₄ produced in the anoxic parts of the rhizosphere and therefore plant-mediated diffusion will be reduced. In this review, we describe how the exploitation of these key root traits in rice can potentially reduce greenhouse gas emissions from paddy fields.

High-throughput, dynamic, multi-dimensional: an expanding repertoire of plant respiration measurements

A recent burst of technological innovation and adaptation has greatly improved our ability to capture respiration rate data from plant sources. At the tissue level, several independent respiration measurement options are now available, each with distinct advantages and suitability, including high-throughput sampling capacity. These advancements facilitate the inclusion of respiration rate data into large-scale biological studies such as genetic screens, ecological surveys, crop breeding trials, and multi-omics molecular studies. As a result, our understanding of the correlations of respiration with other biological and biochemical measurements is rapidly increasing. Difficult questions persist concerning the interpretation and utilization of respiration data; concepts such as allocation of respiration to growth versus maintenance, the unnecessary or inefficient use of carbon and energy by respiration, and predictions of future respiration rates in response to environmental change are all insufficiently grounded in empirical data. However, we emphasize that new experimental designs involving novel combinations of respiration rate data with other measurements will flesh-out our current theories of respiration. Furthermore, dynamic recordings of respiration rate, which have long been used at the scale of mitochondria, are increasingly being used at larger scales of size and time to reflect processes of cellular signal transduction and physiological response to the environment. We also highlight how respiratory methods are being better adapted to different plant tissues including roots and seeds, which have been somewhat neglected historically.

Recent insights into metabolic and signalling events of directional root growth regulation and its implications for sustainable crop production systems

Roots are sensors evolved to simultaneously respond to manifold signals, which allow the plant to survive. Root growth responses, including the modulation of directional root growth, were shown to be differently regulated when the root is exposed to a combination of exogenous stimuli compared to an individual stress trigger. Several studies pointed especially to the impact of the negative phototropic response of roots, which interferes with the adaptation of directional root growth upon additional gravitropic, halotropic or mechanical triggers. This review will provide a general overview of known cellular, molecular and signalling mechanisms involved in directional root growth regulation upon exogenous stimuli. Furthermore, we summarise recent experimental approaches to dissect which root growth responses are regulated upon which individual trigger. Finally, we provide a general overview of how to implement the knowledge gained to improve plant breeding.

Effects of fertilization on soil nematode communities in an alpine meadow of Qinghai-Tibet plateau

Nitrogen and phosphorus are important nutrient elements for plants and underground organisms. The nematode is an important part of the soil food web. Although many studies have explored the effects of fertilization on soil nematode community structure, little is known about the response mechanism of the nematode community to fertilization. In this study, we investigated the diversity and functional diversity of soil nematode communities, as well as soil physicochemical properties, root functional traits, and plant richness. We explored the response mechanism of soil nematode communities to nitrogen and phosphorus fertilizer. Nitrogen fertilizer increased the abundance and richness of bacterivorous nematodes, while phosphorus fertilizer decreased the total abundance of bacterivorous nematodes. Meanwhile, the diversity of the nematode community was significantly affected by soil physicochemical properties and plant root functional traits. Therefore, our study revealed the effects of nitrogen and phosphorus fertilizer on soil nematode community diversity and functional diversity. Exploring the response mechanism of soil nematode communities to fertilization interference provides further evidence for the role of nematodes in maintaining the function of subsurface ecosystems.

Effects of multiwalled carbon nanotube and Bacillus atrophaeus application on crop root zone thermal characteristics of saline farmland

Presently, the effects of crop roots on crop root zone thermal characteristics are poorly understood, and new fertilizers are rarely considered from the perspective of changing crop root zone thermal characteristics. This study explored the effect of applying two new fertilizers, multiwalled carbon nanotubes (MWCNTs) and Bacillus atrophaeus (B. atrophaeus), on the crop root zone thermal characteristics of saline farmland soils through in situ measurements. The results showed that MWCNTs and B. atrophaeus could indirectly affect crop root zone thermal characteristics by changing the crop root growth. Combined application of MWCNTs and B. atrophaeus could promote both to induce positive effects, promote crop root growth, and significantly alleviate the adverse effects of soil salinization. The thermal conductivity and heat capacity of the shallow root zone were reduced due to the presence of crop roots, while the opposite was true in the deep root zone. For example, the thermal conductivity of the 0-5 cm rich root zone in the MWCNT treatment was 0.8174 W m^-1 ·K^-1, and the thermal conductivity of the poor root zone was 13.42% higher than that of the rich root zone. MWCNTs and B. atrophaeus can also change the spatial distribution of soil moisture, soil salt, and soil particle size characteristics by influencing the root-soil interactions and indirectly affecting crop root zone thermal characteristics. In addition, MWCNTs and B. atrophaeus could directly affect the root zone thermal characteristics by changing the soil properties. The higher the soil salt content was, the more obvious the effect of the MWCNTs and B. atrophaeus on the crop root zone thermal characteristics. The thermal conductivity and heat capacity of the crop root zone were positively correlated with the soil moisture content, soil salt content and soil particle specific surface area and negatively correlated with the soil particle size and the fresh and dry root weights. In summary, MWCNTs and B. atrophaeus significantly affected crop root zone thermal characteristics directly and indirectly and could adjust the temperature of the crop root zone.

High frequency root dynamics: sampling and interpretation using replicated robotic minirhizotrons

Automating dynamic fine root data collection in the field is a longstanding challenge with multiple applications for co-interpretation and synthesis for ecosystem understanding. High frequency root data are only achievable with paired automated sampling and processing. However, automatic minirhizotron (root camera) instruments are still rare and data are often not collected in natural soils or analysed at high temporal resolution. Instruments must also be affordable for replication and robust under variable natural conditions. Here, we show a system built with off-the-shelf parts which samples at sub-daily resolution. We paired this with a neural network to analyse all images collected. We performed two mesocosm studies and two field trials alongside ancillary data collection (soil CO2 efflux, temperature, and moisture content, and 'PhenoCam'-derived above-ground dynamics). We produce robust and replicated daily time series of root dynamics under all conditions. Temporal root changes were a stronger driver than absolute biomass on soil CO2 efflux in the mesocosm. Proximal sensed above-ground dynamics and below-ground dynamics from minirhizotron data were not synchronized. Root properties extracted were sensitive to soil moisture and occasionally to time of day (potentially relating to soil moisture). This may only affect high frequency imagery and should be considered in interpreting such data.

The Course of Mechanical Stress: Types, Perception, and Plant Response

Mechanical stimuli, together with the corresponding plant perception mechanisms and the finely tuned thigmomorphogenetic response, has been of scientific and practical interest since the mid-17th century. As an emerging field, there are many challenges in the research of mechanical stress. Indeed, studies on different plant species (annual/perennial) and plant organs (stem/root) using different approaches (field, wet lab, and in silico/computational) have delivered insufficient findings that frequently impede the practical application of the acquired knowledge. Accordingly, the current work distils existing mechanical stress knowledge by bringing in side-by-side the research conducted on both stem and roots. First, the various types of mechanical stress encountered by plants are defined. Second, plant perception mechanisms are outlined. Finally, the different strategies employed by the plant stem and roots to counteract the perceived mechanical stresses are summarized, depicting the corresponding morphological, phytohormonal, and molecular characteristics. The comprehensive literature on both perennial (woody) and annual plants was reviewed, considering the potential benefits and drawbacks of the two plant types, which allowed us to highlight current gaps in knowledge as areas of interest for future research.

As good as human experts in detecting plant roots in minirhizotron images but efficient and reproducible: the convolutional neural network "RootDetector"

Plant roots influence many ecological and biogeochemical processes, such as carbon, water and nutrient cycling. Because of difficult accessibility, knowledge on plant root growth dynamics in field conditions, however, is fragmentary at best. Minirhizotrons, i.e. transparent tubes placed in the substrate into which specialized cameras or circular scanners are inserted, facilitate the capture of high-resolution images of root dynamics at the soil-tube interface with little to no disturbance after the initial installation. Their use, especially in field studies with multiple species and heterogeneous substrates, though, is limited by the amount of work that subsequent manual tracing of roots in the images requires. Furthermore, the reproducibility and objectivity of manual root detection is questionable. Here, we use a Convolutional Neural Network (CNN) for the automatic detection of roots in minirhizotron images and compare the performance of our RootDetector with human analysts with different levels of expertise. Our minirhizotron data come from various wetlands on organic soils, i.e. highly heterogeneous substrates consisting of dead plant material, often times mainly roots, in various degrees of decomposition. This may be seen as one of the most challenging soil types for root segmentation in minirhizotron images. RootDetector showed a high capability to correctly segment root pixels in minirhizotron images from field observations (F1 = 0.6044; r² compared to a human expert = 0.99). Reproducibility among humans, however, depended strongly on expertise level, with novices showing drastic variation among individual analysts and annotating on average more than 13-times higher root length/cm² per image compared to expert analysts. CNNs such as RootDetector provide a reliable and efficient method for the detection of roots and root length in minirhizotron images even from challenging field conditions. Analyses with RootDetector thus save resources, are reproducible and objective, and are as accurate as manual analyses performed by human experts.