Root-soil Interface Research Articles

Changes in rhizosphere-specific enzyme activity during secondary grassland succession in the Loess Plateau, China

ABSTRACT Dynamics of soil enzyme activity during plant restoration processes have been studied extensively; however, a general understanding of the rhizosphere-specific enzyme activity during plant secondary succession is limited. Rhizosphere samples were collected from the dominant and main companion species in farmlands abandoned for up to 32 years in the Loess Plateau. We determined soil chemical properties, phospholipid fatty acid (PLFA) profiles and activities of four enzymes (β-1,4-glucosidase, BG; β-1,4-N-acetylglucosaminidase, NAG; L-leucine aminopeptidase, LAP and alkaline phosphatase, AP), specific enzyme activity per soil organic carbon (SOC) and per PLFA unit. Specific BG, NAG, LAP and AP activities per SOC unit significantly decreased 77.1%, 53.2%, 83.0% and 49.2% with plant succession. Specific BG, NAG and LAP activities per PLFA unit significantly decreased 59.6%, 18.9% and 70.9% with plant succession. Furthermore, specific BG and LAP activities in the dominant species were lower than those in the companion species. Redundancy analysis revealed that variations in specific enzyme activities per SOC and per PLFA unit were explained 76.6% and 68.6% by soil chemical properties. SOC, total nitrogen (TN) and available phosphorus (aP) significantly influenced the rhizosphere-specific enzyme activities. This study improved the understanding of the element cycle at the root–soil interface under secondary succession ecosystems.

Soil oxidoreductase zymography: Visualizing spatial distributions of peroxidase and phenol oxidase activities at the root-soil interface

Decomposition of organic material in the rhizosphere – the most dynamic microbial habitat in soil – involves arrays of oxidoreductase and hydrolytic enzymes. Spatial distributions of various hydrolytic activities in soil have already been explored by zymographic techniques. However, the distribution of oxidative activity in the rhizosphere remains to be studied. Thus, we extended a Time-Lapse Zymography technique, using Amplex Red® reagent, to visualize and quantify distributions of phenol oxidase and peroxidase activities in the rhizosphere of Zea mays L. growing in a Haplic Phaeozem and the non-rhizospheric soil. The gross oxidative activity was greatest at the root surfaces, and fell to background soil levels 1.26 and 0.73 mm from seminal (>1 mm diameter) and lateral (<0.5 mm diameter) roots, respectively. The rhizosphere extent relative to the root radius was 59% broader around lateral than around seminal roots. The greatest activities, up to 30 nmol cm−2 min−1, were peroxidase-dominated and closely associated with roots. The results confirm the utility of the approach for studying spatio-temporal distributions of oxidative activities in soil. However, actual activity of oxidoreductases in the field will be strongly controlled by fluctuating environmental conditions such as soil aeration and the gradient of reactive oxygen species, which need to be considered especially in anoxic soils.

Root hydraulic phenotypes impacting water uptake in drying soils.

Soil drying is a limiting factor for crop production worldwide. Yet, it is not clear how soil drying impacts water uptake across different soils, species, and root phenotypes. Here we ask (1) what root phenotypes improve the water use from drying soils? and (2) what root hydraulic properties impact water flow across the soil–plant continuum? The main objective is to propose a hydraulic framework to investigate the interplay between soil and root hydraulic properties on water uptake. We collected highly resolved data on transpiration, leaf and soil water potential across 11 crops and 10 contrasting soil textures. In drying soils, the drop in water potential at the soil–root interface resulted in a rapid decrease in soil hydraulic conductance, especially at higher transpiration rates. The analysis reveals that water uptake was limited by soil within a wide range of soil water potential (−6 to −1000 kPa), depending on both soil textures and root hydraulic phenotypes. We propose that a root phenotype with low root hydraulic conductance, long roots and/or long and dense root hairs postpones soil limitation in drying soils. The consequence of these root phenotypes on crop water use is discussed.

Elevated atmospheric CO2 alters the microbial community composition and metabolic potential to mineralize organic phosphorus in the rhizosphere of wheat

BackgroundUnderstanding how elevated atmospheric CO2 (eCO2) impacts on phosphorus (P) transformation in plant rhizosphere is critical for maintaining ecological sustainability in response to climate change, especially in agricultural systems where soil P availability is low.MethodsThis study used rhizoboxes to physically separate rhizosphere regions (plant root-soil interface) into 1.5-mm segments. Wheat plants were grown in rhizoboxes under eCO2 (800 ppm) and ambient CO2 (400 ppm) in two farming soils, Chromosol and Vertosol, supplemented with phytate (organic P). Photosynthetic carbon flow in the plant-soil continuum was traced with 13CO2 labeling. Amplicon sequencing was performed on the rhizosphere-associated microbial community in the root-growth zone, and 1.5 mm and 3 mm away from the root.ResultsElevated CO2 accelerated the mineralization of phytate in the rhizosphere zones, which corresponded with increases in plant-derived 13C enrichment and the relative abundances of discreet phylogenetic clades containing Bacteroidetes and Gemmatimonadetes in the bacterial community, and Funneliformis affiliated to arbuscular mycorrhizas in the fungal community. Although the amplicon sequence variants (ASVs) associated the stimulation of phytate mineralization under eCO2 differed between the two soils, these ASVs belonged to the same phyla associated with phytase and phosphatase production. The symbiotic mycorrhizas in the rhizosphere of wheat under eCO2 benefited from increased plant C supply and increased P access from soil. Further supportive evidence was the eCO2-induced increase in the genetic pool expressing the pentose phosphate pathway, which is the central pathway for biosynthesis of RNA/DNA precursors.ConclusionsThe results suggested that an increased belowground carbon flow under eCO2 stimulated bacterial growth, changing community composition in favor of phylotypes capable of degrading aromatic P compounds. It is proposed that energy investments by bacteria into anabolic processes increase under eCO2 to level microbial P-use efficiencies and that synergies with symbiotic mycorrhizas further enhance the competition for and mineralization of organic P.33SwUUA3eFb3g78WvKtJiVVideo

Label-Free Multiphoton Imaging of Microbes in Root, Mineral, and Soil Matrices with Time-Gated Coherent Raman and Fluorescence Lifetime Imaging.

Imaging biogeochemical interactions in complex microbial systems─such as those at the soil-root interface─is crucial to studies of climate, agriculture, and environmental health but complicated by the three-dimensional (3D) juxtaposition of materials with a wide range of optical properties. We developed a label-free multiphoton nonlinear imaging approach to provide contrast and chemical information for soil microorganisms in roots and minerals with epi-illumination by simultaneously imaging two-photon excitation fluorescence (TPEF), coherent anti-Stokes Raman scattering (CARS), second-harmonic generation (SHG), and sum-frequency mixing (SFM). We used fluorescence lifetime imaging (FLIM) and time gating to correct CARS for the autofluorescence background native to soil particles and fungal hyphae (TG-CARS) using time-correlated single-photon counting (TCSPC). We combined TPEF, TG-CARS, and FLIM to maximize image contrast for live fungi and bacteria in roots and soil matrices without fluorescence labeling. Using this instrument, we imaged symbiotic arbuscular mycorrhizal fungi (AMF) structures within unstained plant roots in 3D to 60 μm depth. High-quality imaging was possible at up to 30 μm depth in a clay particle matrix and at 15 μm in complex soil preparation. TG-CARS allowed us to identify previously unknown lipid droplets in the symbiotic fungus, Serendipita bescii. We also visualized unstained putative bacteria associated with the roots of Brachypodium distachyon in a soil microcosm. Our results show that this multimodal approach holds significant promise for rhizosphere and soil science research.

Impacts of Shade Trees on the Adjacent Cacao Rhizosphere in a Young Diversified Agroforestry System

Cacao agroforestry systems offer the potential to diversify farmer income sources, enhance biodiversity, sequester carbon, and deliver other important ecosystem services. To date, however, studies have emphasized field- and system-scale outcomes of shade tree integration, and potential impacts on the rhizosphere of adjacent cacao trees have not been fully characterized. Interactions at the root–soil interface are closely linked to plant health and productivity, making it important to understand how diverse shade tree species may affect soil fertility and microbial communities in the cacao rhizosphere. We assessed the impacts of neighboring shade tree presence and identity on cacao yields and physical, chemical, and biological components of the cacao rhizosphere in a recently established diversified agroforestry system in South Sulawesi, Indonesia. Stepwise regression revealed surprising and strong impacts of microbial diversity and community composition on cacao yields and pod infection rates. The presence of neighboring shade trees increased nitrogen, phosphorus, and pH in the rhizosphere of nearby cacao trees without yield losses. Over a longer time horizon, these increases in rhizosphere soil fertility will likely increase cacao productivity and shape microbial communities, as regression models showed nitrogen and phosphorus in particular to be important predictors of cacao yields and microbiome diversity and composition. However, neither presence nor identity of shade trees directly affected microbial diversity, community composition, or field-scale distance-decay relationships at this early stage of establishment. These results highlight locally specific benefits of shade trees in this agroecological context and emphasize the rhizosphere as a key link in indirect impacts of shade trees on cacao health and productivity in diversified systems.

Modelling of stress transfer in root-reinforced soils informed by four-dimensional X-ray computed tomography and digital volume correlation data.

Vegetation enhances soil shearing resistance through water uptake and root reinforcement. Analytical models for soils reinforced with roots rely on input parameters that are difficult to measure, leading to widely varying predictions of behaviour. The opaque heterogeneous nature of rooted soils results in complex soil–root interaction mechanisms that cannot easily be quantified. The authors measured, for the first time, the shear resistance and deformations of fallow, willow-rooted and gorse-rooted soils during direct shear using X-ray computed tomography and digital volume correlation. Both species caused an increase in shear zone thickness, both initially and as shear progressed. Shear zone thickness peaked at up to 35 mm, often close to the thickest roots and towards the centre of the column. Root extension during shear was 10–30% less than the tri-linear root profile assumed in a Waldron-type model, owing to root curvature. Root analogues used to explore the root–soil interface behaviour suggested that root lateral branches play an important role in anchoring the roots. The Waldron-type model was modified to incorporate non-uniform shear zone thickness and growth, and accurately predicted the observed, up to sevenfold, increase in shear resistance of root-reinforced soil.

Tensile strength of a compacted vegetated soil: Laboratory results and reinforcement interpretation

So far, root reinforcement on soil has been primarily evaluated through direct shear and roots pull-out tests, while the effect of other stress paths and the behaviour at the soil–root​ interface are still poorly investigated. In this regard, an apparatus with the facility to test soil and roots jointly under uniaxial extension is presented in the paper, together with its first results.Vegetated samples with Cynodon dactilon were tested after one and three months of growth. Soil exhibited a ductile response when close to saturation and a brittle one at drier states within the field capacity domain. The presence of roots increased the material’s tensile strength and enhanced its post-peak ductility. Measurements of matric suction and degree of saturation allowed interpreting the results in terms of constitutive stresses within a shear strength failure criterion for partially saturated soils. Even if plant roots critically impacted soil hydraulics, a positive strengthening effect was noticed on its mechanical behaviour.Roots mechanical and morphological features were characterised after tests. Two well-established root reinforcement models in the literature were used to interpret the results at the phenomenological scale while considering the hydro-mechanical behaviour at the soil–root interface, different root’s reinforcement mechanisms and the effect of soil’s hydro-mechanical states.

The wheat secreted root proteome: Implications for phosphorus mobilisation and biotic interactions

Root secreted acid phosphatases and organic anions are widely perceived as major players of plant phosphorus (P) mobilisation from the rhizosphere under P limiting growth conditions. Previous research indicated that other mechanisms play a role, especially in species with fine roots, such as wheat. In this study we characterised the plant-derived extracellular proteome of wheat roots by profiling root tip mucilage, soluble root secreted and root tip proteomes. Extracellular acid phosphatases and enzymes of the central carbon metabolism were targeted using selected reaction monitoring. More than 140 proteins with extracellular localisation prediction were identified in mucilage. P starvation induced proteins predicted to be localised to the apoplast which are related to cell wall modification and defence in both, root tip and soluble root-secreted proteomes. Glycolytic enzymes were strongly increased in abundance by P limitation in root tips, as were PEPC and plastidial MDH. Soluble acid phosphatases were not identified in extracellular protein samples. Our results indicate that root tip mucilage contains proteins with the functional potential to actively shape their immediate environment by modification of plant structural components and biotic interactions. Wheat acid phosphatases appear to play a minor role in P mobilisation beyond the immediate root surface. SignificancePhosphorus (P) is a plant growth limiting nutrient in many agricultural situations and the development of phosphorus efficient crops is of paramount importance for future agricultural management practices. As P is relatively immobile in soils, processes occurring at the root-soil interface, the rhizosphere, are suspected to play a key role in plant-induced P mobilisation. According to the current view, the secretion of extracellular acid phosphatases and organic anions enhances P mobilisation within several millimetres beyond the root surface, either directly or indirectly through the selection and appropriate soil microbes. However, the mechanisms of P mobilisation in species with fine roots, such as wheat, and the role of other secreted root proteins are poorly understood. Here, we carried out the profiling of wheat root tip mucilage, soluble root secreted and root tip proteomes. We analysed proteome changes in response to P starvation. We found that proteins with a predicted localisation to the apoplast made up a major proportion of stress-responsive proteins. Acid phosphatases were not identified within extracellular protein samples, which were enriched in proteins with predicted extracellular localisation. The absence of extracellular APases was further validated by multiple reaction monitoring. Our data indicates that wheat acid phosphatases play a minor role in P mobilisation beyond the immediate root surface and provides a resource for breeding strategies and further investigations of the functional roles of root tip-released proteins in the rhizosphere under P limitation.

Soil-root interaction in the rhizosheath regulates the water uptake of wheat

The development of crops better adapted to endure weather extremes requires knowledge of the belowground traits that have potential to improve plant water uptake. Recent evidence has indicated that root induced modification of soil pore geometry of the rhizosheath is linked with drought tolerance of crops. Here we sought to understand whether the regulation of plant water uptake by rhizosheath is mediated through the rhizodeposits present at the soil-root interface. We compared eight wheat cultivars and demonstrated that cultivars with longer root hairs and greater rhizosheath mass and cover transpired more water. The wheat cultivars with less rhizosheath had the highest concentration of trehalose in the rhizosheath. Trehalose may increase the surface tension of soil water, which could further modify the transpiration of cultivars with less rhizosheath. Moreover, rhizosheath mass and cover had significant negative association with the bacterial abundance, indicating a link between metabolite concentration and bacterial abundance in the rhizosheath. We propose that the complex interactions of root, microbes and rhizodeposits in the rhizosheath have the potential to regulate water uptake by crops. The root and rhizosheath traits highlighted here can be targeted to develop crops with better ability to uptake water.

Effect of Pseudomonas putida-producing pyoverdine on copper uptake by Helianthus annuus cultivated on vineyard soils

Bioaugmentation-assisted phytoextraction was used to reduce the Cu load in vineyard soils. While performance is usually the endpoint of such studies, here we identified some mechanisms underlying Cu soil to plant transfer, particularly the role of siderophores in the extraction of Cu from the soil-bearing phases and its phytoavailability.Carbonated vs. non‑carbonated vineyard soils were cultivated with sunflower in rhizoboxes bioaugmented with Pseudomonas putida. gfp-Tagged P. putida was monitored in the soil and pyoverdine (Pvd), Cu, Fe, Mn, and Zn were measured in the soil solution. Trace elements (TE) were analysed in the roots and shoots. Plant growth and nutritional status were also measured.With bioaugmentation, the concentration of total Cu (vs. Cu2+) in the soil solution increased (decreased) by a factor of 1.6 to 2.6 (7 to 13) depending on the soil. The almost 1:1 relationship between the excess of Fe + Cu mobilized from the solid phase and the amount of Pvd in the soil solution in bioaugmented treatments suggests that Pvd mobilized Fe and Cu mainly by ligand-controlled dissolution via a 1:1 metal-Pvd complex. Bioaugmentation increased the Cu concentration by 17% in the shoots and by 93% in the roots, and by 30% to 60% the sunflower shoot biomass leading to an increase in the amount of Cu phytoextracted by up to 87%. The amount of Fe, Mn, Zn, and P also increased in the roots and shoots. Contrary to what was expected, carbonated soil did not increase the mobilization of TE.Our results showed that bioaugmentation increased phytoextraction, and its performance can be further improved by promoting the dissociation of Pvd-Cu complex in the solution at the soil-root interface.

Biochar and Trichoderma aureoviride URM 5158 as alternatives for the management of cassava root rot

The root soil interface harbors complex microbial interactions that influence plant and soil health. A better understanding of using of biochar derived from different waste sources with Trichoderma spp. (TRI), and the relationship between plant disease and environmental parameters would assist setting priorities. Here, we hypothesized that biochar and TRI could be useful in managing cassava root rot, by mainly altering soil properties and their interactions. This hypothesis was tested by assessing the severity of plant disease and soil parameters using biochar derived from four sources (coffee grounds-CG, coffee husks-CH, bean husks-BH, and soursop residue-SW). Our analysis revealed that all TRI-inoculated biochar applied to the soil decreased cassava root rot severity, which was attributed to changes in soil parameters such as pH, P, K, and total organic carbon. Additionally, SW + TRI reduced the severity in shoots by 75% and increased beta-glucosidase (109%) and urease (200%) enzyme activities, thereby reducing cassava root rot severity, which contributed to plant growth and improved soil; hence, this biochar can be recommended in controlling this disease. Overall, our findings expand our knowledge about the reuse of wastes transformed into biochar, which could serve as an alternative tool for plant disease management and provide important information to develop strategies that can be incorporated in the global health concept.

Soil-root interface influences the assembly of the endophytic bacterial community in rice plants

Soil-root interface influences the assembly of the endophytic bacterial community in rice plants

Applications of the indole-alkaloid gramine modulate the assembly of individual members of the barley rhizosphere microbiota.

Microbial communities proliferating at the root-soil interface, collectively referred to as the rhizosphere microbiota, represent an untapped beneficial resource for plant growth, development and health. Integral to a rational manipulation of the microbiota for sustainable agriculture is the identification of the molecular determinants of these communities. In plants, biosynthesis of allelochemicals is centre stage in defining inter-organismal relationships in the environment. Intriguingly, this process has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but has been counter selected in several modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how exogenous applications of gramine impacted on the rhizosphere microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. High throughput 16S rRNA gene amplicon sequencing revealed that applications of gramine interfere with the proliferation of a subset of soil microbes with a relatively broad phylogenetic assignment. Strikingly, growth of these bacteria appeared to be rescued by barley plants in a genotype- and dosage-independent manner. In parallel, we discovered that host recruitment cues can interfere with the impact of gramine application in a host genotype-dependent manner. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the prokaryotic communities inhabiting the root-soil interface.

Novel indicator for assessing wetland degradation based on the index of hydrological connectivity and its correlation with the root-soil interface

In this study, an innovative method was used to assess the spatial and temporal patterns of the hydrological connectivity in soil profiles in the Yellow River Delta wetland. In this method, field dye-tracing experiments conducted in the study area (i.e., large [LWa] and small communities [LWb] of Phragmites australis and Suaeda glauca [JP]) were considered, and the root-soil interface in the region and the status of the wetland degradation were analyzed. The results revealed that the index of hydrological connectivity (IHC) significantly changed both spatially and temporally. The high IHC values reaching a 0.392 ± 0.209 gradient were concentrated in the middle and western parts of the study areas. The spatial distribution of the high hydrological connectivity has been extremely fragmented since 2010. The LWb (severely degraded wetland) and JP (extremely degraded wetland) were found to be more seriously degraded than the LWa (moderately degraded wetland) in the study area. The changes in the IHC were positively correlated with the principal component (PC) values of the wetland degradation. The IHC is a novel indicator of the status of wetland degradation. Furthermore, the soil holding capacity, soil non-capacity porosity, and soil ventilation were relatively important for the changes in the IHC. Compared with the soil properties, the hydrological responses of the roots systems can be neglected at the root-soil interface. Based on our results, we propose an alternative wetland restoration solution for the Yellow River Delta wetland: 1) a seepage layer in the surface soils (0–10 cm), shallow ploughing treatment, and litter or straw return to the soil surface should be conducted to increase the hydrological connectivity of the soil surface; 2) reeds should not be reaped every year to remove the nutrients from this area; and 3) appropriate freshwater inputs should be strengthened.

Niche Differentiation of Arsenic-Transforming Microbial Groups in the Rice Rhizosphere Compartments as Impacted by Water Management and Soil-Arsenic Concentrations.

Arsenic (As) bioavailability in the rice rhizosphere is influenced by many microbial interactions, particularly by metal-transforming functional groups at the root-soil interface. This study was conducted to examine As-transforming microbes and As-speciation in the rice rhizosphere compartments, in response to two different water management practices (continuous and intermittently flooded), established on fields with high to low soil-As concentration. Microbial functional gene composition in the rhizosphere and root-plaque compartments were characterized using the GeoChip 4.0 microarray. Arsenic speciation and concentrations were analyzed in the rhizosphere soil, root-plaque, pore water, and grain samples. Results confirmed several As-biotransformation processes in the rice rhizosphere compartments, and distinct assemblage of As-reducing and methylating bacteria was observed between the root-plaque and rhizosphere. Results confirmed higher potential for microbial As-reduction and As-methylation in continuously flooded, long term As-contaminated fields, which accumulated highest concentrations of AsIII and methyl-As concentrations in pore water and rice grains. Water management treatment significantly altered As-speciation in the rhizosphere, and intermittent flooding reduced methyl-As and AsIII concentrations in the pore water, root-plaque and rice grain. Ordination and taxonomic analysis of detected gene-probes indicated that root-plaque and rhizosphere assembled significantly different microbial functional groups demonstrating niche separation. Taxonomic non-redundancy was evident, suggesting that As-reduction, -oxidation and -methylation processes were performed by different microbial functional groups. It was also evident that As transformation was coupled to different biogeochemical cycling processes (nutrient assimilation, carbon metabolism etc.) in the compartments and between treatments, revealing functional non-redundancy of rice-rhizosphere microbiome in response to local biogeochemical conditions and As contamination. This study provided novel insights on As-biotransformation processes and their implications on As-chemistry at the root-soil interface and their responses to water management, which could be applied for mitigating As-bioavailability and accumulation in rice grains.

On pedagogy of a Soil Science Centre for Doctoral Training

AbstractHere we describe and evaluate the success of a multi‐institutional Centre for Doctoral Training (CDT), which was established to address a UK skills shortage in Soil Science. The government‐funded ‘STARS’ (Soils Training And Research Studentships) CDT was established in 2015 across a range of universities and research institutes in the UK. It recruited 41 PhD students equitably split across the institutions under four core research themes identified as being central to the national need, namely, (1) Understanding the soil–root interface, (2) Soils and the delivery of ecosystem services, (3) Resilience and response of functions in soil systems and (4) Modelling the soil ecosystem at different spatial and temporal scales. In addition, the STARS CDT provided a diverse skills programme, including: Holistic training in soils, the promotion of collegiality and joint working, strategies to promote science and generate impact, internships with end users (e.g., policymakers, industry), personal wellbeing, and ways to generate a lasting soils training legacy. Overall, both supervisors and students have reported a positive experience of the CDT in comparison to the conventional doctoral training programmes, which have less discipline focus and little chance for students to scientifically interact with their cohorts or to undertake joint training activities. The STARS CDT also allowed students to freely access research infrastructure across the partner institutions (e.g., long‐term field trials, specialised analytical facilities, high‐performance computing), breaking down traditional institutional barriers and thus maximising the students' potential to undertake high‐quality research. The success and legacy of the STARS CDT can be evidenced in many ways; however, it is exemplified by the large number and diversity of journal papers produced, the lasting collaborations, final career destinations, and creation of a web‐based legacy portal including new and reflective video material.Highlights Soil science was identified as having a scientific skills shortage in the UK. A dedicated soil science Centre for Doctoral Training (CDT) was established to address this skills gap. The multi‐institutional, discipline‐focused CDT proved more successful than conventional generic PhD training programmes. The CDT model provides critical mass to provide more effective training of soil scientists.

2D distribution of Pseudomonas fluorescens activities at the soil-root interface of sunflower grown on vineyard soils: Effects on copper uptake

Pseudomonas fluorescens is a siderophore producing bacteria that is expected to alter the mobility and bioavailability of Cu in vineyard soils due to its ability to produce pyoverdine under iron deficiency. In this study, we monitored the effect of this bacterial species, particularly the production of siderophore, on the mobility and bioavailability of copper (Cu) and other elements using a spatialized approach. Two vineyard soils cultivated with sunflower, one non-carbonated (N-Carb) and one carbonated (Carb), were bioaugmented with P. fluorescens or not. 2D mapping using diffusive equilibration in thin films (DET) and diffusive gradient in thin films (DGT) was performed on day 15 after germination. At the end of the experiment, elements concentrations were measured in the plants and in the soil extracts (CaCl2 0.01 M). The results showed that the mobility of Cu and other elements (Fe, Al, Mn, Zn, N and P) was enhanced in both soils when bioaugmented. The chemistry of DET and DGT provided insights into the processes behind mobility, such as the presence and distribution of free metallophore spots (2–3.5 μM), interpreted as pyoverdine, which played a non-negligible role in Cu, Fe, Al mobilization and to a lesser extent in that of Mn, whereas pH played a limited role. DGT imaging showed that, depending on the speciation of metals in the soil solution, the increase in mobility measured by DET did not always increase bioavailability. Nevertheless, the concentration of copper in the aerial part of sunflower cultivated on the bioaugmented carbonated soil increased by 30% and copper content by 200%. These results identify bioaugmentation with P. fluorescens as a potential way to increase Cu phytoextraction, especially in carbonated soil, mainly because of its effect on plant growth but also on Cu bioavailability at the soil-plant interface.

Arbuscular Mycorrhiza Symbiosis Enhances Water Status and Soil-Plant Hydraulic Conductance Under Drought.

Recent studies have identified soil drying as a dominant driver of transpiration reduction at the global scale. Although Arbuscular Mycorrhiza Fungi (AMF) are assumed to play a pivotal role in plant response to soil drying, studies investigating the impact of AMF on plant water status and soil-plant hydraulic conductance are lacking. Thus, the main objective of this study was to investigate the influence of AMF on soil-plant conductance and plant water status of tomato under drought. We hypothesized that AMF limit the drop in matric potential across the rhizosphere, especially in drying soil. The underlying mechanism is that AMF extend the effective root radius and hence reduce the water fluxes at the root-soil interface. The follow-up hypothesis is that AMF enhance soil-plant hydraulic conductance and plant water status during soil drying. To test these hypotheses, we measured the relation between transpiration rate, soil and leaf water potential of tomato with reduced mycorrhiza colonization (RMC) and the corresponding wild type (WT). We inoculated the soil of the WT with Rhizophagus irregularis spores to potentially upsurge symbiosis initiation. During soil drying, leaf water potential of the WT did not drop below −0.8MPa during the first 6days after withholding irrigation, while leaf water potential of RMC dropped below −1MPa already after 4days. Furthermore, AMF enhanced the soil-plant hydraulic conductance of the WT during soil drying. In contrast, soil-plant hydraulic conductance of the RMC declined more abruptly as soil dried. We conclude that AMF maintained the hydraulic continuity between root and soil in drying soils, hereby reducing the drop in matric potential at the root-soil interface and enhancing soil-plant hydraulic conductance of tomato under edaphic stress. Future studies will investigate the role of AMF on soil-plant hydraulic conductance and plant water status among diverse plant species growing in contrasting soil textures.

Genetic Elucidation of Quorum Sensing and Cobamide Biosynthesis in Divergent Bacterial-Fungal Associations Across the Soil-Mangrove Root Interface.

Plant roots in soil host a repertoire of bacteria and fungi, whose ecological interactions could improve their functions and plant performance. However, the potential microbial interactions and underlying mechanisms remain largely unknown across the soil-mangrove root interface. We herein analyzed microbial intra- and inter-domain network topologies, keystone taxa, and interaction-related genes across four compartments (non-rhizosphere, rhizosphere, episphere, and endosphere) from a soil-mangrove root continuum, using amplicon and metagenome sequencing technologies. We found that both intra- and inter-domain networks displayed notable differences in the structure and topology across four compartments. Compared to three peripheral compartments, the endosphere was a distinctive compartment harboring more dense co-occurrences with a higher average connectivity in bacterial-fungal network (2.986) than in bacterial (2.628) or fungal network (2.419), which could be related to three bacterial keystone taxa (Vibrio, Anaerolineae, and Desulfarculaceae) detected in the endosphere as they are known to intensify inter-domain associations with fungi and stimulate biofilm formation. In support of this finding, we also found that the genes involved in cell-cell communications by quorum sensing (rhlI, lasI, pqsH, and lasR) and aerobic cobamide biosynthesis (cobG, cobF, and cobA) were highly enriched in the endosphere, whereas anaerobic cobamide biosynthesis (encoded by cbiT and cbiE) was dominant in three peripheral compartments. Our results provide genetic evidence for the intensified bacterial-fungal associations of root endophytes, highlighting the critical role of the soil-root interface in structuring the microbial inter-domain associations.