Rhizosphere engineering for soil carbon sequestration

The rhizosphere is the central hotspot of water and nutrient uptake by plants, rhizodeposition, microbial activities, and plant-soil-microbial interactions. The plasticity of plants offers possibilities to engineer the rhizosphere to mitigate climate change. We define rhizosphere engineering as targeted manipulation of plants, soil, microorganisms, and management to shift rhizosphere processes for specific aims [e.g., carbon (C) sequestration]. The rhizosphere components can be engineered by agronomic, physical, chemical, biological, and genomic approaches. These approaches increase plant productivity with a special focus on C inputs belowground, increase microbial necromass production, protect organic compounds and necromass by aggregation, and decrease C losses. Finally, we outline multifunctional options for rhizosphere engineering: how to boost C sequestration, increase soil health, and mitigate global change effects.

Rhizosheath drought responsiveness is variety-specific and a key component of belowground plant adaptation

Biophysicochemical rhizosheath properties play a vital role in plant drought adaptation. However, their integration into the framework of plant drought response is hampered by incomplete mechanistic understanding of their drought responsiveness and unknown linkage to intraspecific plant-soil drought reactions. Thirty-eight Zea mays varieties were grown under well-watered and drought conditions to assess the drought responsiveness of rhizosheath properties, such as soil aggregation, rhizosheath mass, net-rhizodeposition, and soil organic carbon distribution. Additionally, explanatory traits, including functional plant trait adaptations and changes in soil enzyme activities, were measured. Drought restricted soil structure formation in the rhizosheath and shifted plant-carbon from litter-derived organic matter in macroaggregates to microbially processed compounds in microaggregates. Variety-specific functional trait modifications determined variations in rhizosheath drought responsiveness. Drought responses of the plant-soil system ranged among varieties from maintaining plant-microbial interactions in the rhizosheath through accumulation of rhizodeposits, to preserving rhizosheath soil structure while increasing soil exploration through enhanced root elongation. Drought-induced alterations at the root-soil interface may hold crucial implications for ecosystem resilience in a changing climate. Our findings highlight that rhizosheath soil properties are an intrinsic component of plant drought response, emphasizing the need for a holistic concept of plant-soil systems in future research on plant drought adaptation.

Keep in touch: the soil-root hydraulic continuum and its role in drought resistance in crops

Drought is a major threat to food security worldwide. Recently, the root-soil interface has emerged as a major site of hydraulic resistance during water stress. Here, we review the impact of soil drying on whole-plant hydraulics and discuss mechanisms by which plants can adapt by modifying the properties of the rhizosphere either directly or through interactions with the soil microbiome.

Identification of sugars as root exudates of the macrophyte species Juncus effusus and Philodendron cordatum in constructed wetland-microbial fuel cells during bioelectricity production

Constructed wetland-microbial fuel cells (CW-MFCs) systems are a sustainable technology capable of producing bioelectricity and treating wastewater simultaneously. It is also possible to obtain bioelectricity from the photosynthetic substrates obtained by the rhizodeposition of macrophytes, where the electroactive microorganisms present in the rhizosphere use these compounds as biofuel. In the present study, the bioelectricity production capacity of Juncus effusus and Philodendron cordatum species was evaluated in a CW-MFC without an external carbon source. The Juncus effusus species showed a higher bioelectrochemical performance, as they recorded a maximum voltage of 399 mV, a power density of 63.7 mW/m2, a volumetric power density of 15.9 W/m3, an internal resistance of 200 Ω, an anodic potential of -368 mV, and a cathodic potential of 229 mV. In addition, different types of carbohydrates in the form of sugars (sucrose, fructose, galactose, and glucose) were quantified by liquid chromatography, with concentrations of 100-450 μg/L. Chromatographic analysis were performed from the root exudates released in the effluent of both species of macrophyte. Sucrose and glucose were the types of sugars that produced the largest amount with portions of up to 35% and 24%, respectively. Sugars are compounds that worked as electron donors for the production of bioelectricity by using endogenous substrates that fed the anodic biofilm. Consumption was 45-55% for sucrose and 40-65% for glucose. Of the different macrophytes evaluated in the CW-MFCs, it was observed that the production of bioelectricity differs mainly due to the quantity of the root exudates released in the rhizosphere.

Characterisation of Soil Bacterial Communities That Exhibit Chemotaxis to Root Exudates from Phosphorus-Limited Plants

The ability to sense and direct movement along chemical gradients is known as 'chemotaxis' and is a common trait among rhizosphere microorganisms, which are attracted to organic compounds released from plant roots. In response to stress, the compounds released from roots can change and may recruit symbionts that enhance host stress tolerance. Decoding this language of attraction could support the development of microbiome management strategies that would enhance agricultural production and sustainability. In this study, we employ a culture-independent bait-trap chemotaxis assay to capture microbial communities attracted to root exudates from phosphorus (P)-sufficient and P-deficient Arabidopsis thaliana Col-0 plants. The captured populations were then enumerated and characterised using flow cytometry and phylogenetic marker gene sequencing, respectively. Exudates attracted significantly more cells than the control but did not differ between P treatments. Relative to exudates from P-sufficient plants, those collected from P-deficient plants attracted a significantly less diverse bacterial community that was dominated by members of the Paenibacillus, which is a genus known to include powerful phosphate solubilisers and plant growth promoters. These results suggest that in response to P deficiency, Arabidopsis exudates attract organisms that could help to alleviate nutrient stress.

Cover crop root morphology rather than quality controls the fate of root and rhizodeposition C into distinct soil C pools

Cover crops increase carbon (C) inputs to agricultural soils, and thus have the potential to mitigate climate change through enhanced soil organic carbon (SOC) storage. However, few studies have explored the fate of belowground C inputs associated with varying root traits into the distinct SOC pools of mineral-associated organic carbon (MAOC) particulate organic carbon (POC). Therefore, a packed 0.5 m column trial was established with 0.25 m topsoil and 0.25 m subsoil with four cover crops species (winter rye, oilseed radish, chicory, and hairy vetch) known to differ in C:N ratio and root morphology. Cover crops were 14 CO2 -labeled for 3 months, and then, half of the columns were sampled to quantify root and rhizodeposition C. In the remaining columns, plant shoots were harvested and the undisturbed soil and roots were left for incubation. Bulk soil from both sampling times was subjected to a simple fractionation scheme, where 14 C in the <50 and >50 μm fraction was assumed to represent MAOC and POC, respectively. The fast-growing rye and radish produced the highest root C. The percentage loss of C via rhizodeposition (%ClvR) showed a distinct pattern, with 22% for the more branched roots (rye and vetch) and 6%-8% for the less branched roots (radish and chicory). This suggests that root morphology plays a key role in determining rhizodeposition C. After 1 year of incubation at room temperature, the remaining MAOC and POC were positively correlated with belowground inputs in absolute terms. However, topsoil MAOC formation efficiencies (cover crop-derived MAOC remaining as a share of belowground inputs) were higher for vetch and rye (21% and 15%, respectively) than for chicory and radish (9% and 10%, respectively), suggesting a greater importance of rhizodeposition (or indirectly, root morphology) than solely substrate C:N ratio for longer term C stabilization.

Root exudation of carbon and nitrogen compounds varies over the day-night cycle in pea: The role of diurnal changes in internal pools

Rhizodeposition is the export of organic compounds from plant roots to the soil. Carbon allocation towards rhizodeposition has to be balanced with allocation for other physiological functions, which depend on both newly assimilated and stored nonstructural carbohydrate (NSC). To test whether the exudation of primary metabolites scales with plant NSC status, we studied diurnal dynamics of NSC and amino acid (AA) pools and fluxes within the plant and the rhizosphere. These diurnal dynamics were measured in the field and under hydroponic-controlled conditions. Further, C-limiting treatments offered further insight into the regulation of rhizodeposition. The exudation of primary metabolites fluctuated diurnally. The diurnal dynamics of soluble sugars (SS) and AA concentrations in tissues coincided with exudate pool fluctuations in the rhizosphere. SS and AA pools in the rhizosphere increased with NSC and AA pools in the roots. C starvation treatments offset the balance of exudates: AA exudate content in the rhizosphere significantly decreased while SS exudate content remained stable. Our results suggest that rhizodeposition is to some extent controlled by plant C:N status. We propose that SS exudation is less controlled than AA exudation because N assimilation depends on controlled C supply while SS exudation relies to a greater extent on passive diffusion mechanisms.

The spatial distribution of rhizosphere microbial activities under drought: water availability is more important than root-hair-controlled exudation

Root hairs and soil water content are crucial in controlling the release and diffusion of root exudates and shaping profiles of biochemical properties in the rhizosphere. But whether root hairs can offset the negative impacts of drought on microbial activity remains unknown. Soil zymography, ¹⁴ C imaging and neutron radiography were combined to identify how root hairs and soil moisture affect rhizosphere biochemical properties. To achieve this, we cultivated two maize genotypes (wild-type and root-hair-defective rth3 mutant) under ambient and drought conditions. Root hairs and optimal soil moisture increased hotspot area, rhizosphere extent and kinetic parameters (V_max and K_m ) of β-glucosidase activities. Drought enlarged the rhizosphere extent of root exudates and water content. Colocalization analysis showed that enzymatic hotspots were more colocalized with root exudate hotspots under optimal moisture, whereas they showed higher dependency on water hotspots when soil water and carbon were scarce. We conclude that root hairs are essential in adapting rhizosphere properties under drought to maintain plant nutrition when a continuous mass flow of water transporting nutrients to the root is interrupted. In the rhizosphere, soil water was more important than root exudates for hydrolytic enzyme activities under water and carbon colimitation.

Functional Diversity of Microbial Communities in the Soybean (Glycine max L.) Rhizosphere from Free State, South Africa

The plant microbiome is involved in enhancing nutrient acquisition, plant growth, stress tolerance, and reducing chemical inputs. The identification of microbial functional diversity offers the chance to evaluate and engineer them for various agricultural processes. Using a shotgun metagenomics technique, this study examined the functional diversity and metabolic potentials of microbial communities in the rhizosphere of soybean genotype link 678. The dominant genera are Geobacter, Nitrobacter, Burkholderia, Candidatus, Bradyrhizobium and Streptomyces. Twenty-one functional categories were present, with fourteen of the functions being dominant in all samples. The dominant functions include carbohydrates, fatty acids, lipids and isoprenoids, amino acids and derivatives, sulfur metabolism, and nitrogen metabolism. A Kruskal–Wallis test was used to test samples’ diversity differences. There was a significant difference in the alpha diversity. ANOSIM was used to analyze the similarities of the samples and there were significant differences between the samples. Phosphorus had the highest contribution of 64.3% and was more prominent among the soil properties that influence the functional diversity of the samples. Given the functional groups reported in this study, soil characteristics impact the functional role of the rhizospheric microbiome of soybean.

Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. IMPORTANCE Decrypting the chemical interactions between plant roots and the soil microbiome is a gateway for future manipulation and management of the rhizosphere, a soil compartment critical to promoting plant fitness and yields. Our experimental results demonstrate how soil microbial community and genomic diversity is influenced by root exudates of differing chemical compositions and how changes in this microbiome result in altered production of plant-relevant metabolites. Together, these findings demonstrate the tractability of high-resolution multiomics tools to investigate soil microbiomes and provide new information on plant-soil environments useful for the development of efficient and precise microbiota management strategies in agricultural systems.

Functional diversity and identity of plant genotypes regulate rhizodeposition and soil microbial activity

Our understanding of the linkages between plant diversity and soil carbon and nutrient cycling is primarily derived from studies at the species level, while the importance and mechanisms of diversity effects at the genotype level are poorly understood. Here we examine how genotypic diversity and identity, and associated variation in functional traits, within a common grass species, Anthoxanthum odoratum, modified rhizodeposition, soil microbial activity and litter decomposition. Root litter quality was not significantly affected by plant genotypic diversity, but decomposition was enhanced in soils with the legacy of higher genotypic diversity. Plant genotypic diversity and identity modified rhizodeposition and associated microbial activity via two independent pathways. Plant genotypic diversity enhanced soil functioning via positive effects on variation in specific leaf area and total rhizodeposition. Genotype identity affected both rhizodeposit quantity and quality, and these effects were mediated by differences in mean specific leaf area, shoot mass and plant height. Rhizodeposition was more strongly predicted by aboveground than belowground traits, suggesting strong linkages between photosynthesis and root exudation. Our study demonstrates that functional diversity and identity of plant genotypes modulates belowground carbon supply and quality, representing an important but overlooked pathway by which biodiversity affects ecosystem functioning.

Root effects on soil organic carbon: a double-edged sword

From recent developments on how roots affect soil organic carbon (SOC) an apparent paradox has emerged where roots drive SOC stabilization causing SOC accrual, but also SOC destabilization causing SOC loss. We synthesize current results and propose the new Rhizo-Engine framework consisting of two linked components: microbial turnover and the soil physicochemical matrix. The Rhizo-Engine is driven by rhizodeposition, root turnover, and plant uptake of nutrients and water, thereby accelerating SOC turnover through both stabilization and destabilization mechanisms. This Rhizo-Engine framework emphasizes the need for a more holistic approach to study root-driven SOC dynamics. This framework would provide better understanding of plant root effects on soil carbon sequestration and the sensitivity of SOC stocks to climate and land-use changes.

Rhizosphere control of soil nitrogen cycling: a key component of plant economic strategies

Understanding how plant species influence soil nutrient cycling is a major theme in terrestrial ecosystem ecology. However, the prevailing paradigm has mostly focused on litter decomposition, while rhizosphere effects on soil organic matter (SOM) decomposition have attracted little attention. Using a dual ¹³ C/¹⁵ N labeling approach in a 'common garden' glasshouse experiment, we investigated how the economic strategies of 12 grassland plant species (graminoids, forbs and legumes) drive soil nitrogen (N) cycling via rhizosphere processes, and how this in turn affects plant N acquisition and growth. Acquisitive species with higher photosynthesis, carbon rhizodeposition and N uptake than conservative species induced a stronger acceleration of soil N cycling through rhizosphere priming of SOM decomposition. This allowed them to take up larger amounts of N and allocate it above ground to promote photosynthesis, thereby sustaining their faster growth. The N₂ -fixation ability of legumes enhanced rhizosphere priming by promoting photosynthesis and rhizodeposition. Our study demonstrates that the economic strategies of plant species regulate a plant-soil carbon-nitrogen feedback operating through the rhizosphere. These findings provide novel mechanistic insights into how plant species with contrasting economic strategies sustain their nutrition and growth through regulating the cycling of nutrients by soil microbes in their rhizosphere.

Root exudation of mature beech forests across a nutrient availability gradient: the role of root morphology and fungal activity

Root exudation is a key plant function with a large influence on soil organic matter dynamics and plant-soil feedbacks in forest ecosystems. Yet despite its importance, the main ecological drivers of root exudation in mature forest trees remain to be identified. During two growing seasons, we analyzed the dependence of in situ collected root exudates on root morphology, soil chemistry and nutrient availability in six mature European beech (Fagus sylvatica L.) forests on a broad range of bedrock types. Root morphology was a major driver of root exudation across the nutrient availability gradient. A doubling of specific root length exponentially increased exudation rates of mature trees by c. 5-fold. Root exudation was also closely negatively related to soil pH and nitrogen (N) availability. At acidic and N-poor sites, where fungal biomass was reduced, exudation rates were c. 3-fold higher than at N- and base-richer sites and correlated negatively with the activity of enzymes degrading less bioavailable carbon (C) and N in the bulk soil. We conclude that root exudation increases on highly acidic, N-poor soils, in which fungal activity is reduced and a greater portion of the assimilated plant C is shifted to the external ecosystem C cycle.

A Return to the Wild: Root Exudates and Food Security

Challenges to food security under conditions of global change are forcing us to increase global crop production. Focussing on belowground plant traits, especially root exudation, has great promise to meet this challenge. Root exudation is the release of a vast array of compounds into the soil. These exudates are involved in many biotic and abiotic interactions. Wild relatives of crops provide a large potential source of information and genetic material and have desirable traits that could be incorporated into modern breeding programs. However, root exudates are currently underexploited. Here, we highlight how the traits of root exudates of crop wild relatives could be used to improve agricultural output and reduce environmental impacts, particularly by decreasing our dependence on pesticides and fertilisers.

Metabolic niches in the rhizosphere microbiome: new tools and approaches to analyse metabolic mechanisms of plant-microbe nutrient exchange

Plants nourish rhizospheric microbes via provision of carbon substrates, and the composition of the microbiome is strongly influenced by metabolic phenomena such as niche differentiation, competitive exclusion, and cross-feeding. Despite intensive investigations of the taxonomic structure in root microbiomes, there is relatively little biochemical knowledge of the metabolic niches occupied by microbial strains in the rhizosphere. Here, we review new tools and approaches that are boosting our knowledge of the metabolic mechanisms that shape the composition of the root microbiome. New studies have elucidated biochemical pathways that mediate root colonisation and pathogen suppression, and synthetic communities are emerging as a powerful tool to understand microbe-microbe interactions. Knowledge of root exudate composition is being advanced by new metabolomics methodologies, which have highlighted that specific exudate components can inhibit pathogen growth, and that certain metabolites can recruit mutualistic strains according to substrate uptake preferences. Microbial genomics is rapidly advancing, with large collections of isolated rhizosphere strains and mutant libraries giving new insights into the metabolic mechanisms of root colonisation. Exometabolomics is emerging as a powerful methodology for directly observing microbial uptake of root metabolites, and also for profiling microbial cross-feeding. Integrative studies using these resources should enable rapid advances, particularly when applied to standardised experimental set-ups and model synthetic communities.

Pathways of mineral-associated soil organic matter formation: Integrating the role of plant carbon source, chemistry, and point of entry

To predict the behavior of the terrestrial carbon cycle, it is critical to understand the source, formation pathway, and chemical composition of soil organic matter (SOM). There is emerging consensus that slow-cycling SOM generally consists of relatively low molecular weight organic carbon substrates that enter the mineral soil as dissolved organic matter and associate with mineral surfaces (referred to as "mineral-associated OM," or MAOM). However, much debate and contradictory evidence persist around: (a) whether the organic C substrates within the MAOM pool primarily originate from aboveground vs. belowground plant sources and (b) whether C substrates directly sorb to mineral surfaces or undergo microbial transformation prior to their incorporation into MAOM. Here, we attempt to reconcile disparate views on the formation of MAOM by proposing a spatially explicit set of processes that link plant C source with MAOM formation pathway. Specifically, because belowground vs. aboveground sources of plant C enter spatially distinct regions of the mineral soil, we propose that fine-scale differences in microbial abundance should determine the probability of substrate-microbe vs. substrate-mineral interaction. Thus, formation of MAOM in areas of high microbial density (e.g., the rhizosphere and other microbial hotspots) should primarily occur through an in vivo microbial turnover pathway and favor C substrates that are first biosynthesized with high microbial carbon-use efficiency prior to incorporation in the MAOM pool. In contrast, in areas of low microbial density (e.g., certain regions of the bulk soil), MAOM formation should primarily occur through the direct sorption of intact or partially oxidized plant compounds to uncolonized mineral surfaces, minimizing the importance of carbon-use efficiency, and favoring C substrates with strong "sorptive affinity." Through this framework, we thus describe how the primacy of biotic vs. abiotic controls on MAOM dynamics is not mutually exclusive, but rather spatially dictated. Such an understanding may be integral to more accurately modeling soil organic matter dynamics across different spatial scales.

Evidence for the primacy of living root inputs, not root or shoot litter, in forming soil organic carbon

Soil organic carbon (SOC) is primarily formed from plant inputs, but the relative carbon (C) contributions from living root inputs (i.e. rhizodeposits) vs litter inputs (i.e. root + shoot litter) are poorly understood. Recent theory suggests that living root inputs exert a disproportionate influence on SOC formation, but few field studies have explicitly tested this by separately tracking living root vs litter inputs as they move through the soil food web and into distinct SOC pools. We used a manipulative field experiment with an annual C₄ grass in a forest understory to differentially track its living root vs litter inputs into the soil and to assess net SOC formation over multiple years. We show that living root inputs are 2-13 times more efficient than litter inputs in forming both slow-cycling, mineral-associated SOC as well as fast-cycling, particulate organic C. Furthermore, we demonstrate that living root inputs are more efficiently anabolized by the soil microbial community en route to the mineral-associated SOC pool (dubbed 'the in vivo microbial turnover pathway'). Overall, our findings provide support for the primacy of living root inputs in forming SOC. However, we also highlight the possibility of nonadditive effects of living root and litter inputs, which may deplete SOC pools despite greater SOC formation rates.

Processes that determine the interplay of root exudation, methane emission and yield in rice agriculture

Rice is the most important staple food for half of the world's population, but also accounts for about 10% of all anthropogenic CH₄ emissions. In spite of a wealth of information on the mechanistic basis and the importance of the rice plant in mediating these emissions, the significance of root exudation for CH₄ emissions and the processes that determine root exudation are not well understood. Root exudates derive from photosynthate allocated to the root and subjected to root anabolic and catabolic processes. Key processes in roots that determine the extent of root exudation and, hence, CH₄ emission from rice agriculture, include (i) deviation of metabolites from root anabolic and catabolic pathways facilitating root exudation, but also (ii) xylem loading and transport of potential root exudates for reallocation to the leaves, and (iii) xylem loading of sucrose in roots for its transport into reproductive organs, both suppressing root exudation. These processes are modulated by plant development and metabolic requirements resulting from different functions of root exudation. In the present report the interplay of root exudation, CH₄ emission and yield are discussed.

[Estimation of Winter Wheat Photosynthesized Carbon Distribution and Allocation Belowground via 13C Pulse-labeling]

Evaluating the allocation of carbon (C) photosynthesized by winter wheat belowground is essential for C sequestration in soil and crop production. During the four growth stages of winter wheat, i. e., tillering, elongation, anthesis, and grain-filling, the method of ¹³CO₂ pulse-labeling for the wheat was adopted. Destructive samplings were undertaken at 28 d after each labeling and the total C and ¹³C contents of shoots, roots, soil, and rhizosphere respiration were determined. Results showed that the majority of the fixed ¹³C was recovered in the aboveground (straw and grain), ranging from 51.6% to 90.8% in all growth stages. The allocation of ¹³C photosynthesized belowground (roots, soil, and rhizosphere respiration) decreased as the wheat growth advanced, while the ¹³C transferred to the aboveground increased. Of the total ¹³C input belowground, 22.9%-65.3% was respired by the rhizosphere, 24.3%-59.3% remained in the roots, and 10.4%-17.8% was incorporated into the soil organic carbon by rhizodeposition. Respired ¹³C within the last 2 d of the whole chase period (28 d) only accounted for 0.7%-2.7% of the total respired ¹³C, indicating that 28 days were long enough to ensure a complete distribution of photosynthesized C within all the wheat and soil pools. For the whole growth season of winter wheat, the photosynthesized C allocated aboveground, to roots, soil organic carbon, and rhizosphere respiration was 78.5%, 6.0%, 3.1%, and 12.4% of the net assimilated C, respectively. Based on local wheat production, the total C transferred belowground was quantified as 1.72 t·hm^-2, with 0.99 t·hm^-2 respired as rhizosphere respiration, 0.48 t·hm^-2 retained in roots, and 0.25 t·hm^-2 incorporated into soil organic carbon.

Split-root labelling to investigate 15N rhizodeposition by Pinus sylvestris and Picea abies

We investigated the transfer of ¹⁵N into the soil via ¹⁵N uptake and release by tree roots, which involves the principles of the split-root technique. One half of the root system received an injection of (¹⁵NH₄)₂SO₄ and the other half equivalent amounts of (NH₄)₂SO₄ at ¹⁵N natural abundance level. ¹⁵N was transferred from one side of the root system (¹⁵N side) to the other side (¹⁴N side) and released into the soil. The method was conducted with Scots pine (Pinus sylvestris L.) and Norway spruce (Picea abies [L.] Karst). Two concentration levels of (NH₄)₂SO₄ were used, corresponding with annual N deposition in the Netherlands (30 kg N ha^-1) and a twelfth of that (2.5 kg N ha^-1). Samples were taken 3 and 6 weeks after labelling and divided into needles + stem, roots, rhizosphere and bulk soil. Already 3 weeks after labelling, Scots pine took up 23.7 % of the low and 9.1 % of the high amounts of ¹⁵N, while Norway spruce took up 21.5 and 32.1 %, respectively. Both species transported proportions of ¹⁵N to the rhizosphere (0.1-0.2 %) and bulk soil (0.3-0.9 %). The method is a useful tool to investigate the fate of root-derived N in soils, for example, for the formation of stable forms of soil organic matter.

The mycorrhizal type governs root exudation and nitrogen uptake of temperate tree species

Even though the two dominant mycorrhizal associations of temperate tree species differentially couple carbon (C) and nitrogen (N) cycles in temperate forests, systematic differences between the biogeochemical cycles of arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) tree species remain poorly described. A classification according to the mycorrhizal type offers the chance, though, to develop a global frame concept for the prediction of temperate ecosystem responses to environmental change. Focusing on the influence of mycorrhizal types on two key plant processes of biogeochemical cycling (root exudation and N acquisition), we investigated four temperate deciduous tree species per mycorrhizal type in a drought experiment in large mesocosms. We hypothesized that (H1) C loss by root exudation is higher in ECM than in AM trees, (H2) drought leads to higher reductions in root exudation of drought-sensitive ECM trees and (H3) inorganic N uptake is higher in AM than in ECM trees. In contradiction to H2, we found no systematic difference in root exudation between the mycorrhizal types at ample soil moisture, but almost twofold higher exudation in ECM trees when exposed to soil drought. In addition, photosynthetic C cost of root exudation strongly increased by ~10-fold in drought-treated ECM trees, while it only doubled in AM trees, which confirms H1. With respect to H3, we corroborated that AM trees had higher absolute and relative inorganic N acquisition rates than ECM trees, while the organic N uptake did not differ between mycorrhizal types. We conclude that ECM trees are less efficient in inorganic N uptake than AM trees, but ECM trees increase root C release as an adaptive response to dry soil to maintain hydraulic conductivity and/or nutrient availability. These systematic differences in key biogeochemical processes support hints on the key role of the mycorrhizal types in coupling C and N cycles in temperate forests.

The Automated Root Exudate System (ARES): a method to apply solutes at regular intervals to soils in the field

Root exudation is a key component of nutrient and carbon dynamics in terrestrial ecosystems. Exudation rates vary widely by plant species and environmental conditions, but our understanding of how root exudates affect soil functioning is incomplete, in part because there are few viable methods to manipulate root exudates in situ. To address this, we devised the Automated Root Exudate System (ARES), which simulates increased root exudation by applying small amounts of labile solutes at regular intervals in the field.The ARES is a gravity-fed drip irrigation system comprising a reservoir bottle connected via a timer to a micro-hose irrigation grid covering c. 1 m2; 24 drip-tips are inserted into the soil to 4-cm depth to apply solutions into the rooting zone. We installed two ARES subplots within existing litter removal and control plots in a temperate deciduous woodland. We applied either an artificial root exudate solution (RE) or a procedural control solution (CP) to each subplot for 1 min day-1 during two growing seasons. To investigate the influence of root exudation on soil carbon dynamics, we measured soil respiration monthly and soil microbial biomass at the end of each growing season.The ARES applied the solutions at a rate of c. 2 L m-2 week-1 without significantly increasing soil water content. The application of RE solution had a clear effect on soil carbon dynamics, but the response varied by litter treatment. Across two growing seasons, soil respiration was 25% higher in RE compared to CP subplots in the litter removal treatment, but not in the control plots. By contrast, we observed a significant increase in microbial biomass carbon (33%) and nitrogen (26%) in RE subplots in the control litter treatment.The ARES is an effective, low-cost method to apply experimental solutions directly into the rooting zone in the field. The installation of the systems entails minimal disturbance to the soil and little maintenance is required. Although we used ARES to apply root exudate solution, the method can be used to apply many other treatments involving solute inputs at regular intervals in a wide range of ecosystems.

[Input and Distribution of Photosynthesized Carbon in Soil-Rice System Affected by Water Management and Nitrogen Fertilization]

Fertilizer and water management are two key factors for rice growth. A better understanding of the carbon (C) cycling in paddy soil requires investigation into the input characteristics and distribution dynamics of photosynthesized carbon in rice-soil system. We grew rice (Zhongzao 39) in PVC pots and used the ¹³ C-CO₂ continuous labeling method to quantify the allocation of photosynthesized carbon in rice-soil system under two regimes(Drying-rewetting vs. continuous watering) and N fertilization (250 mg·kg^-1vs. no addition). The results showed that nitrogen fertilizer application increased rice shoot biomass and the amount of C and N, but had no significant influence on rice root biomass. Thus, nitrogen fertilizer application decreased rice biomass root/shoot ratio significantly. Drying-rewetting with N fertilizer treatment resulted in higher total C and N amount by 22% and 33%, respectively, in the shoot, and by 36% and 44%, respectively in the root than continuous watering with nitrogen fertilizer treatment. These results indicated that nitrogen fertilizer application promoted the growth of rice shoot. Nitrogen fertilizer application significantly increased the ¹³ C content in rice shoot by 32%-83% over the control without N addition. Nitrogen fertilizer application also increased the ¹³ C recovery in rice shoot by 6%-32%, but decreased that in the root by 18%-59%. Pertaining to water effect, drying-rewetting with N application increased the amount of ¹³ C in rice shoot and root. However, without N addition, the amount and the recovery of ¹³ C in shoot dropped by 10.3 mg·pot^-1 and 12%, respectively, compared with the continuous watering treatment. The root, on the other hand, recorded increases in both the amount and the recovery of ¹³ C by 1.9 mg·pot^-1 and 57%, respectively. Furthermore, the deposition of assimilated C into rhizosphere-soil increased by both the individual and the interactive effects of N fertilizer application and drying-rewetting treatment. Thus, combining N fertilizer and drying-rewetting water management led to more increased allocation and deposition of photosynthesized carbon in soil-rice system compared with combined continuous flooding and N application. This study was able to quantify the partitioning and allocation of rice photosynthesized carbon into different plant and soil pools under different water and N fertilizer treatments, and can serve as a useful guide for better water and nutrient management practices in paddy-rice production that can achieve both sustainable high yield and sequestration of more C within the paddy soil system.

Stress differentially causes roots of tree seedlings to exude carbon

How carbon (C) flows through plants into soils is poorly understood. Carbon exuded comes from a pool of non-structural carbohydrates (NSC) in roots. Simple models of diffusion across concentration gradients indicate that the more C in roots, the more C should be exuded from roots. However, the mechanisms underlying the accumulation and loss of C from roots may differ depending on the stress experienced by plants. Thus, stress type may influence exudation independent of NSC. We tested this hypothesis by examining the relationship between NSC in fine roots and exudation of organic C in aspen (Populus tremuloides Michx.) seedlings after exposure to shade, cold soils and drought in a controlled environment. Fine root concentrations of NSC varied by treatment. Mass-specific C exudation increased with increasing fine root sugar concentration in all treatments, but stress type affected exudation independently of sugar concentration. Seedlings exposed to cold soils exuded the most C on a per mass basis. Through 13C labeling, we also found that stressed seedlings allocated relatively more new C to exudates than roots compared with unstressed seedlings. Stress affects exudation of C via mechanisms other than changes in root carbohydrate availability.

Root exudate cocktails: the link between plant diversity and soil microorganisms?

Higher plant diversity is often associated with higher soil microbial biomass and diversity, which is assumed to be partly due to elevated root exudate diversity. However, there is little experimental evidence that diversity of root exudates shapes soil microbial communities. We tested whether higher root exudate diversity enhances soil microbial biomass and diversity in a plant diversity gradient, thereby negating significant plant diversity effects on soil microbial properties. We set up plant monocultures and two- and three-species mixtures in microcosms using functionally dissimilar plants and soil of a grassland biodiversity experiment in Germany. Artificial exudate cocktails were added by combining the most common sugars, organic acids, and amino acids found in root exudates. We applied four different exudate cocktails: two exudate diversity levels (low- and high-diversity) and two nutrient-enriched levels (carbon- and nitrogen-enriched), and a control with water only. Soil microorganisms were more carbon- than nitrogen-limited. Cultivation-independent fingerprinting analysis revealed significantly different soil microbial communities among exudate diversity treatments. Most notably and according to our hypothesis, adding diverse exudate cocktails negated the significant plant diversity effect on soil microbial properties. Our findings provide the first experimental evidence that root exudate diversity is a crucial link between plant diversity and soil microorganisms.

The holistic rhizosphere: integrating zones, processes, and semantics in the soil influenced by roots

Despite often being conceptualized as a thin layer of soil around roots, the rhizosphere is actually a dynamic system of interacting processes. Hiltner originally defined the rhizosphere as the soil influenced by plant roots. However, soil physicists, chemists, microbiologists, and plant physiologists have studied the rhizosphere independently, and therefore conceptualized the rhizosphere in different ways and using contrasting terminology. Rather than research-specific conceptions of the rhizosphere, the authors propose a holistic rhizosphere encapsulating the following components: microbial community gradients, macroorganisms, mucigel, volumes of soil structure modification, and depletion or accumulation zones of nutrients, water, root exudates, volatiles, and gases. These rhizosphere components are the result of dynamic processes and understanding the integration of these processes will be necessary for future contributions to rhizosphere science based upon interdisciplinary collaborations. In this review, current knowledge of the rhizosphere is synthesized using this holistic perspective with a focus on integrating traditionally separated rhizosphere studies. The temporal dynamics of rhizosphere activities will also be considered, from annual fine root turnover to diurnal fluctuations of water and nutrient uptake. The latest empirical and computational methods are discussed in the context of rhizosphere integration. Clarification of rhizosphere semantics, a holistic model of the rhizosphere, examples of integration of rhizosphere studies across disciplines, and review of the latest rhizosphere methods will empower rhizosphere scientists from different disciplines to engage in the interdisciplinary collaborations needed to break new ground in truly understanding the rhizosphere and to apply this knowledge for practical guidance.

Defoliation reduces soil biota - and modifies stimulating effects of elevated CO2

To understand the responses to external disturbance such as defoliation and possible feedback mechanisms at global change in terrestrial ecosystems, it is necessary to examine the extent and nature of effects on aboveground-belowground interactions. We studied a temperate heathland system subjected to experimental climate and atmospheric factors based on prognoses for year 2075 and further exposed to defoliation. By defoliating plants, we were able to study how global change modifies the interactions of the plant-soil system. Shoot production, root biomass, microbial biomass, and nematode abundance were assessed in the rhizosphere of manually defoliated patches of Deschampsia flexuosa in June in a full-factorial FACE experiment with the treatments: increased atmospheric CO 2, increased nighttime temperatures, summer droughts, and all of their combinations. We found a negative effect of defoliation on microbial biomass that was not apparently affected by global change. The negative effect of defoliation cascades through to soil nematodes as dependent on CO 2 and drought. At ambient CO 2, drought and defoliation each reduced nematodes. In contrast, at elevated CO 2, a combination of drought and defoliation was needed to reduce nematodes. We found positive effects of CO 2 on root density and microbial biomass. Defoliation affected soil biota negatively, whereas elevated CO 2 stimulated the plant-soil system. This effect seen in June is contrasted by the effects seen in September at the same site. Late season defoliation increased activity and biomass of soil biota and more so at elevated CO 2. Based on soil biota responses, plants defoliated in active growth therefore conserve resources, whereas defoliation after termination of growth results in release of resources. This result challenges the idea that plants via exudation of organic carbon stimulate their rhizosphere biota when in apparent need of nutrients for growth.

Root traits and microbial community interactions in relation to phosphorus availability and acquisition, with particular reference to Brassica

Brassicas are among the most widely grown and important crops worldwide. Phosphorus (P) is a key mineral element in the growth of all plants and is largely supplied as inorganic rock-phosphate, a dwindling resource, which is likely to be an increasingly significant factor in global agriculture. In order to develop crops which can abstract P from the soil, utilize it more efficiently, require less of it or obtain more from other sources such as soil organic P reservoirs, a detailed understanding the factors that influence P metabolism and cycling in plants and associated soil is required. This review focuses on the current state of understanding of root traits, rhizodeposition and rhizosphere community interaction as it applies to P solubilization and acquisition, with particular reference to Brassica species. Physical root characteristics, exudation of organic acids (particularly malate and citrate) and phosphatase enzymes are considered and the potential mechanisms of control of these responses to P deficiency examined. The influence of rhizodeposits on the development of the rhizosphere microbial community is discussed and the specific features of this community in response to P deficiency are considered; specifically production of phosphatases, phytases and phosphonate hydrolases. Finally various potential approaches for improving overall P use efficiency in Brassica production are discussed.

Influence of light, temperature and salinity on dissolved organic carbon exudation rates in Zostera marina L

BACKGROUND

Marine angiosperms, seagrasses, are sentinel species of marine ecosystem health and function. Seagrass carbon budgets provide insight on the minimum requirements needed to maintain this valuable resource. Carbon budgets are a balance between C fixation, growth, storage and loss rates, most of which are well characterized. However, relatively few measurements of dissolved organic carbon (DOC) leaf exudation or rhizodeposition rates exist for most seagrass species. Here I evaluate how eelgrass (Zostera marina L.) DOC exudation is affected by a single factor manipulation (light, temperature or salinity). Eelgrass plants were hydroponically exposed to treatments in experimental chambers (separate leaf and rhizome/root compartments) with artificial seawater medium. Regression analysis of changes in the DOC concentration through time was used to calculate DOC exudation rates.

RESULTS

Exudation rates were similar across all treatments in all experiments. For all experiments, pooled leaf DOC exudation ranged between 0.032 and 0.069 mg C gdw-1 h-1, while rhizodeposition ranged between 0.024 and 0.045 mg C gdw-1 h-1. These rates are consistent with previously published values and provide first-order estimates for mechanistic models.

CONCLUSIONS

Zostera marina carbon losses from either leaf exudation or rhizodeposition account for a small proportion of gross primary production (1.2-4.6%) and appear to be insensitive to short-term (e.g., hours to days) environmental variations in chamber experiments. Based on these preliminary experiments, I suggest that Z. marina DOC exudation may be a passive process and not an active transport process.

Source-sink balance and carbon allocation below ground in plants exposed to ozone

The role of tropospheric ozone in altering plant growth and development has been the subject of thousands of publications over the last several decades. Still, there is limited understanding regarding the possible effects of ozone on soil processes. In this review, the effects of ozone are discussed using the flow of carbon from the atmosphere, through the plant to soils, and back to the atmosphere as a framework. A conceptual model based on carbohydrate signaling is used to illustrate physiological changes in response to ozone, and to discuss possible feedbacks that may occur. Despite past emphasis on above-ground effects, ozone has the potential to alter below-ground processes and hence ecosystem characteristics in ways that are not currently being considered. Contents Summary 213 I. Introduction 213 II. Source-sink model: carbohydrate signaling 214 III. Effect of ozone on above-ground sources and sinks 216 IV. Decreased allocation below ground 218 V. Carbon flux to soils 220 VI. Soil food web 223 VII. Summary, conclusions and future research 223 Acknowledgements 223 References 223.

Sloughing of cap cells and carbon exudation from maize seedling roots in compacted sand

Sloughing of root cap cells and exudation of mucilage plays an important role in the penetration of compacted soils by roots. For the first time we have quantified the rate of sloughing of root cap cells in an abrasive growth medium that was compacted to create mechanical impedance to root growth. The number of maize (Zea mays) root cap cells sloughed into sand increased as a result of compaction, from 1930 to 3220 d^-1 per primary root. This represented a 12-fold increase in the number of cells sloughed per mm root extension (from 60 to >700). We estimated that the whole of the cap surface area was covered with detached cells in compacted sand, compared with c. 7% of the surface area in loose sand. This lubricating layer of sloughed cells and mucilage probably decreases frictional resistance to soil penetration. The total carbon deposited by the root was estimated at c. 110 μg g^-1 sand d^-1 . Sloughed cells accounted for <10% of the total carbon, the vast majority of carbon being contained in mucilage exudates.