Search

Despite gaining significant attention in recent years, it remains unclear whether mycorrhizal fungi distribute meaningful amounts of resources among trees in ways that increase the fitness of the receiving trees. To investigate this, we used pairs of shaded and unshaded Pinus halepensis or Quercus calliprinos saplings, growing in both inter‐ and intra‐specific combinations outdoors in forest soil. We examined the combined effects of indirect and direct below‐ground connections on tree performance and Non‐Structural Carbohydrate (NSC) pools. Although we did not observe any growth benefits, shaded recipient oaks exhibited higher levels of root and branch NSC compared to their control counterparts, which were not connected below‐ground. This finding suggests a potential benefit of establishing below‐ground connections. However, no such benefits were observed among the unshaded pairs or in the other inter‐ and intra‐specific pairs of pines and oaks. We monitored the carbon (C) flow from a 13CO2‐labelled donor pine tree to a below‐ground connected oak tree and demonstrated C transfer from pines to shaded oaks. We also identified the main fungal symbionts interacting with pines and oaks. Our findings indicate that the effects of below‐ground C transfer are context‐dependent, manifesting in nuanced alterations in plant NSC that are not readily apparent through conventional growth metrics. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Tree lines in high latitudes and high altitudes are considered sentinels of global change. This manifests in accelerated encroachment of trees and shrubs and enhanced plant productivity, with currently unknown implications for the carbon balance of these biomes. Given the large soil organic carbon stocks in many tree line soils, we here wondered whether introducing highly productive plants would accelerate carbon cycling through rhizosphere priming effects and if certain soils would be more vulnerable to carbon loss from positive priming than others. To test this, organic and mineral soils were sampled above and below tree lines in the Swedish sub‐arctic and the Peruvian Andes. A greenhouse experiment was then performed to quantify plant‐induced changes in soil mineralisation rates (rhizosphere priming effect) and new C formation using natural abundance labelling and the C4‐species Cynodon dactylon. Several environmental, plant, soil and microbial parameter were monitored during the experiment to complement the observations on soil C cycling. Priming was predominantly positive at the beginning of the experiment, then systematically decreased in all soils during the plant growth season to be mostly negative at the end of the experiment at plant senescence. Independent of direction of priming, the magnitude of priming was always greater in organic than in corresponding mineral soils, which was best explained by the higher C contents of these soils. Integrated over the entire study period, the overall impact of priming (positive and negative) on the soil C balance was mostly negligible. Though net soil C loss was observed in organic soils from the sub‐arctic tundra in Sweden. Most notably, positive and negative priming effects were not mutually exclusive, rather omnipresent across ecosystems, depending on sampling time. The direction of priming seems to be fluctuating with plant productivity, rhizosphere carbon inputs and nutrient uptake. This highlights the need for integrative long‐term studies if we aim to understand priming effects at ecosystem scale and greenhouse and laboratory studies must be validated in situ to enable reliable ecological upscaling. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Drought is one of the major yield‐limiting factors under climatic adversaries. The positive role of silicon (Si) in drought tolerance of plants has unfolded a new avenue for enhancing crop productivity through better Si use efficiency. It is hence interesting to understand the mechanistic insights pertaining to its beneficial roles under drought stress conditions. Higher plants sense drought stress via roots which, regulate aboveground plant growth under stress. Cellular and molecular modulations occurring at the root and soil interphases influence the survival and growth of plants under drought stress; therefore, it is intriguing to know how Si influences the soil–root interphase and how this interaction augments overall plant growth under drought. In this review, we summarised the roles of Si in the root systems, rhizosphere and their interactions that could improve plant's growth and development under drought conditions. We have discussed the direct and indirect effects of Si‐induced belowground changes on plant roots, soil physical, chemical and biological properties, and their mutual interactions in eliciting defence signalling, including hormone signalling pathways. A mechanistic model of Si‐induced beneficial effects in water‐limited environments is suggested, which could help improve the management of rainfed croplands through Si fertilisation. [ABSTRACT FROM AUTHOR]

Background: Peanut (Arachis hypogaea L.) is regarded as a crop with high nutrient use efficiency, but there may be differences between cultivars. Furthermore, there is little information on the strategy of peanut cultivars to adapt to soil P availability and to what extent they explore non‐labile P pools. Aims: Our objective was to evaluate growth, root morphology, enzymatic activity in the rhizosphere, and P uptake of peanut cultivars grown under different soil P status. Methods: The study was conducted in a greenhouse in 6‐L pots. Soils with low P (without fertilization) and high P content (with fertilization) and seven peanut cultivars of different origins, different maturation groups, and release years were investigated. Peanut shoot yield, phosphorus uptake, root growth, soil P fractions as well as phosphatase activity in the rhizosphere soil were determined. Results: In P‐deficient soil, a higher dry matter yield was associated with longer root hairs and root length, which resulted in decreased soil non‐labile P was observed mainly with cultivars developed in Argentina (ARG‐medium‐old and ARG‐medium‐new) and the late maturity Brazilian cultivar (BR I‐late new). These cultivars adapted well to P deficiency and were less dependent on labile P. New Brazilian early and medium maturity cultivars developed less, shorter root hairs, and showed low acid phosphatase activity in the rhizosphere under P deficiency, resulting in lower P uptake and dry matter yield. Under high P availability, new Brazilian cultivars of medium and late maturity showed the highest dry matter yield (9.0 and 9.8 g plant−1, respectively) and longest roots, around 120 m plant−1. High P availability decreased root hairs in all cultivars. Conclusion: Overall, the adaptation of peanut cultivars to P‐deficient soils was lower for the new mid‐ and early‐maturing Brazilian cultivars compared with the Argentinian and old or late‐maturing Brazilian cultivars. The main strategies of P‐efficient cultivars under low P availability are to increase root length, root hair length, and root hair density. [ABSTRACT FROM AUTHOR]

Tree‐mycorrhizal associations are associated with patterns in nitrogen (N) availability and soil organic matter storage; however, we still lack a mechanistic understanding of what tree and fungal traits drive these patterns and how they will respond to global changes in soil N availability. To address this knowledge gap, we investigated how arbuscular mycorrhizal (AM)‐ and ectomycorrhizal (EcM)‐associated seedlings alter rhizodeposition in response to increased seedling inorganic N acquisition. We grew four species each of EcM and AM seedlings from forests of the eastern United States in a continuously 13C‐labeled atmosphere within an environmentally controlled chamber and subjected to three levels of 15N‐labeled fertilizer. We traced seedling 15N uptake from, and 13C‐labeled inputs (net rhizodeposition) into, root‐excluded or ‐included soil over a 5‐month growing season. N uptake by seedlings was positively related to rhizodeposition for EcM‐ but not AM‐associated seedlings in root‐included soils. Despite this contrast in rhizodeposition, there was no difference in soil C storage between mycorrhizal types over the course of the experiment. Instead root‐inclusive soils lost C, while root‐exclusive soils gained C. Our findings suggest that mycorrhizal associations mediate tree belowground C investment in response to inorganic N availability, but these differences do not affect C storage. Continued soil warming and N deposition under global change will increase soil inorganic N availability and our seedling results indicate this could lead to greater belowground C investment by EcM‐associated trees. This potential for less efficient N uptake by EcM‐trees could contribute to AM‐tree success and a shift toward more AM‐dominated temperate forests. [ABSTRACT FROM AUTHOR]

Plant–microbe interactions are essential in shaping plant performance and overall ecosystem functioning. However, the regulatory mechanisms underlying plant–microbe interactions mediated by mycorrhizal symbiosis in saline–alkaline soils are still not fully understood. Here, we aimed to clarify the synergistic regulatory mechanism through which arbuscular mycorrhizal fungi (AMF) symbiosis drives the rhizosphere microbiome to improve perennial herbage growth in saline–alkaline soils and evaluate phytoremediation efficiency. This study revealed that Funneliformis mosseae inoculation (i) strongly promoted the growth of all three herbage species (with values ranging from 21.62% to 233.33%), Na+ accumulation in plants (with values ranging from 24.63% to 188.89%), and decreased soil electrical conductivity (with values ranging from 7.68% to 12.87%), potentially suggesting improved phytoremediation efficiency with AMF symbiosis; (ii) increased nutritional content and decreased C:P and N:P ratios (with values ranging from 27.20% to 92.87%) and improved K+/Na+ and P/Na+ ratios (with values ranging from 2.60% to 302.96%); (iii) increased the abundance of some beneficial bacterial taxa and strengthened the significant strong relationships among most of these bacteria and plant biomass, ion homeostasis as well as stoichiometric ratio constants, and AMF inoculation treatments also consisted the higher proportion of differential genera significantly correlated with these plant factors as well as plant nutrient contents, potentially reflecting that AMF mediated the enrichment process of beneficial bacterial taxa and may strength functional interaction between plant and bacterial taxa, which may be importance for the enhancement of saline–alkaline tolerance of plants; and (iv) enhanced stability of the rhizosphere bacterial community and complexity of interaction networks, and the related indictors also established significant correlations with plant/soil factors, suggesting that the improvement of stability and functional complexity driven by AMF may also be beneficial for enhancing phytoremediation efficiency. These findings indicate that AMF inoculation plays its own beneficial role by simultaneously activating the potential of beneficial rhizosphere bacterial taxa and that their synergistic interaction is more beneficial for enhancing plant growth in salt‐affected soils and enhancing phytoremediation efficiency. This study helps to elucidate the underlying mechanisms through which AMF‐mediated rhizosphere bacterial community improve plant growth and tolerance to saline–alkaline stresses, and provides evidence that effective ecological restoration of saline–alkaline degraded grasslands can be achieved via the use of mycorrhizal symbiosis herbage. [ABSTRACT FROM AUTHOR]

The abiotic environment exerts strong effects on plant‐associated microbes, shaping their interactions with plants and resulting ecosystem processes. However, these abiotic effects on plant–microbe interactions are often highly specific and contingent on the abiotic driver or microbial group, requiring synthesis work describing general patterns and from this generate hypotheses and guide mechanistic work. To address this, we conducted a meta‐analysis of the effects of climate change‐related abiotic factors, namely warming, drought, and eCO2, on plant‐associated microbes distinguishing by microbial taxonomic or biological group (bacteria, fungi or virus) and the plant part where microbes are found or associated with (phyllosphere or rhizosphere). We found abiotic driver‐specific patterns, whereby drought significantly reduced microbial abundance, whereas warming and eCO2 had no significant effects. In addition, these abiotic effects were contingent on the microbial taxonomic group, with fungi being negatively affected by drought but positively affected by warming (eCO2 enrichment had no effect), whereas bacteria and viruses were not significantly affected by any factor. Likewise, rhizospheric microbes were negatively affected by drought but positively affected by warming (eCO2 enrichment had no effect), whereas phyllospheric microbes were not significantly affected by any factor. Collectively, these findings point to important implications for global change research by highlighting contrasting effects of climate change‐related abiotic drivers on plant‐associated microbes and the contingency of such effects on microbe life histories and the nature of their interactions with plants. [ABSTRACT FROM AUTHOR]

Rhizodeposition fuels carbon (C) and nutrient cycling in soil. However, changes in the dynamics of microbial growth on rhizodeposits with increasing distance from the root is not well studied. This study investigates microbial growth on individual organic components of rhizodeposits and maize root‐derived exudates and mucilage from agricultural soil. By creating a gradient of substrate concentrations, we simulated reduced microbial access to rhizosphere C with increasing distance to the root surface. We identified distinct C‐thresholds for the activation of microbial growth, and these were significantly higher for rhizodeposits than singular, simple sugars. In addition, testing for stoichiometric constraints of microbial growth by supplementing nitrogen (N) and phosphorus (P) showed accelerated and increased microbial growth by activating a larger proportion of the microbial biomass. Early and late season exudates triggered significantly different microbial growth responses. The mineralization of early‐season exudates was induced at a high C‐threshold. In contrast, the mineralization of late‐season exudates showed 'sugar‐like' properties, with a low C‐threshold, high substrate affinity, and a reduced maximum respiration rate of microorganisms growing on the added substrate. Mucilage exhibited the highest C‐threshold for the activation of microbial growth, although with a short lag‐period and with an efficient mucilage degradation comparable to that of sugars. By determining kinetic parameters and turnover times for different root‐derived substrates, our data enable the upscaling of micro‐scale processes to the whole root system, allowing more accurate predictions of how rhizodeposition drives microbial C and nutrient dynamics in the soil. [ABSTRACT FROM AUTHOR]

The dynamics of the physiological adaptability of plants and the rhizosphere soil environment after waterlogging remain unclear. Here we investigated the mechanisms regulating plant condition and shaping of the rhizosphere microbiome in a pot experiment. In the experiment, we added melatonin to waterlogged plants, which promoted waterlogging relief. The treatment significantly enhanced photosynthesis and the antioxidant capacity of apple plants, and significantly promoted nitrogen (N) utilization efficiency by upregulating genes related to N transport and metabolism. Multiperiod soil microbiome analysis showed the dynamic effects of melatonin on the diversity of the microbial community during waterlogging recovery. Random forest and linear regression analyses were used to screen for potential beneficial bacteria (e.g., Azoarcus, Pseudomonas and Nocardioides) specifically regulated by melatonin and revealed a positive correlation with soil nutrient levels and plant growth. Furthermore, metagenomic analyses revealed the regulatory effects of melatonin on genes involved in N cycling in soil. Melatonin positively contributed to the accumulation of plant dry weight by upregulating the expression of nifD and nifK (N fixation). In summary, melatonin positively regulates physiological functions in plants and the structure and function of the microbial community; it promoted the recovery of apple plants after waterlogging stress. Summary Statement: The application of melatonin to waterlogged plants significantly enhanced photosynthesis and antioxidant capacity, promoted nitrogen utilization efficiency and regulated the diversity and function of the rhizosphere microbial community, ultimately facilitating the recovery of apple plants after waterlogging stress. [ABSTRACT FROM AUTHOR]

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. Summary statement: This study provides novel insights into the diversity of soil resource acquisition strategies within a single plant species. By comparing landraces and modern cultivars of maize and considering plant‐soil‐microbe interactions, we reveal functional differences in root and rhizosphere economics and trait plasticity that shed light on their ecological role and breeding relevance. [ABSTRACT FROM AUTHOR]

Methanogenic and methanotrophic microbes together determine the net methane flux from rice fields. Despite much research on them as separate communities, there has been little study of combined community patterns, and how these vary between the rhizoplane (root surface), rhizosphere (soil surrounding the root) and bulk soil around rice plants, especially at larger spatial scale. We collected samples from 32 geographically scattered rice fields in east central China, amplicon targeting the mcrA gene for methanogenesis and pmoA gene for methanotrophy by using high‐throughput sequencing. Distinct communities of both methanogens and methanotrophs occurred in each of the three compartments, and predominantly positive links were found between methanogens and methanotrophs in all compartments indicating cross‐feeding or consortia relationships. Methanogens were acting as the network hub in the bulk soil, and methanotrophs in rhizoplane. Network complexity and stability was greater in the rhizosphere than rhizoplane and bulk soil, with no network hubs detected, suggesting the strongest effect of homeostatic influence by plant occurred in the rhizosphere. The proportion of determinism (homogeneous selection) and distance–decay relation (DDR) in rhizoplane was consistently lower than that in the rhizosphere for both communities, indicating weaker phylogenetic clustering in rice root surface. Our results have provided a better understanding of CH4 oxidation and emission in rice paddy fields and future agriculture management could take into consideration of the subtle variation among different soil compartments and interactions within methanogenic and methanotrophic communities. [ABSTRACT FROM AUTHOR]

Drought is a major factor limiting plant growth. Plants cope with stress via morphophysiological responses. Rhizosphere‐related bacteria, fungi and other microorganisms can help plants cope with drought via various mechanisms. We conducted a pot experiment on Cyperus esculentus wherein we subjected it to various drought levels and analyzed the functional traits of its aboveground and belowground organs. High‐throughput sequencing was used to study the structure and diversity of the microbial community in the rhizosphere. Drought stress substantially lowered the densities of the leaves, stems, roots and seeds relative to the untreated control. Drought stress inhibited the growth and reduced the yield of C. esculentus. The leaves and seeds have higher water content and are more sensitive to drought stress than the roots. With the aggravation of drought stress, the plant height of C. esculentus decreased significantly, the root:shoot ratio increased and the specific leaf weight had no significant difference. Change in shoot height was the most evident response of C. esculentus to drought stress. Plants under drought stress reduced their leaf area and assumed a specific leaf weight to maintain photosynthetic performance. Rhizosphere fungi were more sensitive to drought stress than rhizosphere bacteria. Drought stress increased the relative abundances of Bacteroidetes, Verrucomicrobia, Patescibacteria, Actinobacteria and Nitrospirae. Drought‐stressed C. esculentus maintained their photosynthetic performance by reducing shoot height and leaf area while assuming a stable specific leaf weight. Drought stress exerted a significantly stronger negative impact on rhizosphere fungi than rhizosphere bacteria. The results clarified the response strategies of functional traits and rhizosphere microorganisms of C. esculentus to drought stress. [ABSTRACT FROM AUTHOR]

Summary: The onset of stomatal closure reduces transpiration during drought. In seed plants, drought causes declines in plant water status which increases leaf endogenous abscisic acid (ABA) levels required for stomatal closure. There are multiple possible points of increased belowground resistance in the soil–plant atmospheric continuum that could decrease leaf water potential enough to trigger ABA production and the subsequent decreases in transpiration.We investigate the dynamic patterns of leaf ABA levels, plant hydraulic conductance and the point of failure in the soil–plant conductance in the highly embolism‐resistant species Callitris tuberculata using continuous dendrometer measurements of leaf water potential during drought.We show that decreases in transpiration and ABA biosynthesis begin before any permanent decreases in predawn water potential, collapse in soil–plant hydraulic pathway and xylem embolism spread.We find that a dynamic but recoverable increases in hydraulic resistance in the soil in close proximity to the roots is the most likely driver of declines in midday leaf water potential needed for ABA biosynthesis and the onset of decreases in transpiration. [ABSTRACT FROM AUTHOR]

Summary: The rhizosphere microbiome plays critical roles in plant growth and provides promising solutions for sustainable agriculture. While the rhizosphere microbiome frequently fluctuates with the soil environment, recent studies have demonstrated that a small proportion of the microbiome is consistently assembled in the rhizosphere of a specific plant genotype regardless of the soil condition, which is determined by host genetics. Based on these breakthroughs, which involved exploiting the plant‐beneficial function of the rhizosphere microbiome, we propose to divide the rhizosphere microbiome into environment‐dominated and plant genetic‐dominated components based on their different assembly mechanisms. Subsequently, two strategies to explore the different rhizosphere microbiome components for agricultural production are suggested, that is, the precise management of the environment‐dominated rhizosphere microbiome by agronomic practices, and the elucidation of the plant genetic basis of the plant genetic‐dominated rhizosphere microbiome for breeding microbiome‐assisted crop varieties. We finally present the major challenges that need to be overcome to implement strategies for modulating these two components of the rhizosphere microbiome. [ABSTRACT FROM AUTHOR]

Summary: Microbial communities can rapidly respond to stress, meaning plants may encounter altered soil microbial communities in stressful environments. These altered microbial communities may then affect natural selection on plants. Because stress can cause lasting changes to microbial communities, microbes may also cause legacy effects on plant selection that persist even after the stress ceases.To explore how microbial responses to stress and persistent microbial legacy effects of stress affect natural selection, we grew Chamaecrista fasciculata plants in stressful (salt, herbicide, or herbivory) or nonstressful conditions with microbes that had experienced each of these environments in the previous generation.Microbial community responses to stress generally counteracted the effects of stress itself on plant selection, thereby weakening the strength of stress as a selective agent. Microbial legacy effects of stress altered plant selection in nonstressful environments, suggesting that stress‐induced changes to microbes may continue to affect selection after stress is lifted.These results suggest that soil microbes may play a cryptic role in plant adaptation to stress, potentially reducing the strength of stress as a selective agent and altering the evolutionary trajectory of plant populations. [ABSTRACT FROM AUTHOR]

Summary: Legume nodulation requires the detection of flavonoids in the rhizosphere by rhizobia to activate their production of Nod factor countersignals. Here we investigated the flavonoids involved in nodulation of Medicago truncatula.We biochemically characterized five flavonoid‐O‐methyltransferases (OMTs) and a lux‐based nod gene reporter was used to investigate the response of Sinorhizobium medicae NodD1 to various flavonoids.We found that chalcone‐OMT 1 (ChOMT1) and ChOMT3, but not OMT2, 4, and 5, were able to produce 4,4′‐dihydroxy‐2′‐methoxychalcone (DHMC). The bioreporter responded most strongly to DHMC, while isoflavones important for nodulation of soybean (Glycine max) showed no activity. Mutant analysis revealed that loss of ChOMT1 strongly reduced DHMC levels. Furthermore, chomt1 and omt2 showed strongly reduced bioreporter luminescence in their rhizospheres. In addition, loss of both ChOMT1 and ChOMT3 reduced nodulation, and this phenotype was strengthened by the further loss of OMT2.We conclude that: the loss of ChOMT1 greatly reduces root DHMC levels; ChOMT1 or OMT2 are important for nod gene activation in the rhizosphere; and ChOMT1/3 and OMT2 promote nodulation. Our findings suggest a degree of exclusivity in the flavonoids used for nodulation in M. truncatula compared to soybean, supporting a role for flavonoids in rhizobial host range. [ABSTRACT FROM AUTHOR]

Rhizosphere microbes play important roles in plant performance and ecosystem functioning. It is becoming increasingly clear that rhizosphere communities vary with soil properties and variation in root traits among plant species. However, less is known about whether and how variation in root traits within plant species influences the rhizosphere microbial communities.We evaluated the intraspecific root traits variation and explored their associations with bacterial and fungal communities in rhizosphere by focusing on an ectomycorrhizal tree species, that is Pinus massoniana, in 22 sites in subtropical China.The first dimension of the principal component analysis on root traits revealed evidence for the 'conservation' gradient of the root economics space. Overall, root traits explained more variation in fungal communities than in bacterial communities in the rhizosphere. Functional composition of rhizosphere microbial communities changed significantly along the 'conservation' gradient, with fast‐growing copiotrophic bacteria and symbiotic ectomycorrhizal fungi were significantly enriched on the 'acquisition' side, while slow‐growing oligotrophic bacteria were significantly enriched on the 'conservation' side of the gradient.Synthesis: Our study demonstrates that intraspecific variation in plant roots significantly influence rhizosphere microbial communities, which in turn can influence plant nutrition and therefore plant performance within the community. [ABSTRACT FROM AUTHOR]

Rhizosphere microbial community assembly results from microbe‐microbe‐plant interactions mediated by small molecules of plant and microbial origin. Studies with Arabidopsis thaliana have indicated a critical role of glucosinolates in shaping the root and/or rhizosphere microbial community, likely through breakdown products produced by plant or microbial myrosinases inside or outside of the root. Plant nitrile‐specifier proteins (NSPs) promote the formation of nitriles at the expense of isothiocyanates upon glucosinolate hydrolysis with unknown consequences for microbial colonisation of roots and rhizosphere. Here, we generated the A. thaliana triple mutant nsp134 devoid of nitrile formation in root homogenates. Using this line and mutants lacking aliphatic or indole glucosinolate biosynthesis pathways or both, we found bacterial/archaeal alpha‐diversity of the rhizosphere to be affected only by the ability to produce aliphatic glucosinolates. In contrast, bacterial/archaeal community composition depended on functional root NSPs as well as on pathways of aliphatic and indole glucosinolate biosynthesis. Effects of NSP deficiency were strikingly distinct from those of impaired glucosinolate biosynthesis. Our results demonstrate that rhizosphere microbial community assembly depends on functional pathways of both glucosinolate biosynthesis and breakdown in support of the hypothesis that glucosinolate hydrolysis by myrosinases and NSPs happens before secretion of products to the rhizosphere. Summary statement: This research demonstrates differential effects of lacking root nitrile‐specifier proteins and glucosinolate biosynthesis pathways on Arabidopsis rhizosphere microbiota. The results strengthen the hypothesis that glucosinolate hydrolysis in planta precedes secretion of products to the rhizosphere. [ABSTRACT FROM AUTHOR]

Nitrogen availability in the rhizosphere relies on root‐microorganism interactions, where root exudates trigger soil organic matter (SOM) decomposition through the rhizosphere priming effect (RPE). Though microbial necromass contribute significantly to organically bound soil nitrogen (N), the role of RPEs in regulating necromass recycling and plant nitrogen acquisition has received limited attention. We used 15N natural abundance as a proxy for necromass‐N since necromass is enriched in 15N compared to other soil‐N forms. We combined studies using the same experimental design for continuous 13CO2 labelling of various plant species and the same soil type, but considering top‐ and subsoil. RPE were quantified as difference in SOM‐decomposition between planted and unplanted soils. Results showed higher plant N uptake as RPEs increased. The positive relationship between 15N‐enrichment of shoots and roots and RPEs indicated an enhanced necromass‐N turnover by RPE. Moreover, our data revealed that RPEs were saturated with increasing carbon (C) input via rhizodeposition in topsoil. In subsoil, RPEs increased linearly within a small range of C input indicating a strong effect of root‐released C on decomposition rates in deeper soil horizons. Overall, this study confirmed the functional importance of rhizosphere C input for plant N acquisition through enhanced necromass turnover by RPEs. Summary statement: Interactions between roots and microorganisms in the rhizosphere enhance nitrogen availability through the rhizosphere priming effect (RPE). Our study confirmed that increasing RPEs promote higher plant nitrogen uptake and indicate enhanced turnover of necromass‐nitrogen through rhizosphere priming. [ABSTRACT FROM AUTHOR]

Summary: In plants under drought stress, sugar content in roots increases, which is important for drought resistance. However, the molecular mechanisms for controlling the sugar content in roots during response to drought remain elusive. Here, we found that the MdDOF3‐MdHT1.2 module‐mediated glucose influx into the root is essential for drought resistance in apple (Malus × domestica). Drought induced glucose uptake from the rhizosphere and up‐regulated the transcription of hexose transporter MdHT1.2. Compared with the wild‐type plants, overexpression of MdHT1.2 promoted glucose uptake from the rhizosphere, thereby facilitating sugar accumulation in root and enhancing drought resistance, whereas silenced plants showed the opposite phenotype. Furthermore, ATAC‐seq, RNA‐seq and biochemical analysis demonstrated that MdDOF3 directly bound to the promoter of MdHT1.2 and was strongly up‐regulated under drought. Overexpression of MdDOF3 in roots improved MdHT1.2‐mediated glucose transport capacity and enhanced plant resistance to drought, but MdDOF3‐RNAihr apple plants showed the opposite phenotype. Moreover, overexpression of MdDOF3 in roots did not attenuate drought sensitivity in MdHT1.2‐RNAi plants, which was correlated with a lower glucose uptake capacity and glucose content in root. Collectively, our findings deciphered the molecular mechanism through which glucose uptake from the rhizosphere is mediated by MdDOF3‐MdHT1.2, which acts to modulate sugar content in root and promote drought resistance. [ABSTRACT FROM AUTHOR]

Microorganisms in the rhizosphere, particularly arbuscular mycorrhiza, have a broad symbiotic relationship with their host plants. One of the major fungi isolated from the rhizosphere of Peucedanum praeruptorum is Penicillium restrictum. The relationship between the metabolites of P. restrictum and the root exudates of P. praeruptorum is being investigated. The accumulation of metabolites in the mycelium and fermentation broth of P. restrictum was analysed over different fermentation periods. Non‐targeted metabolomics was used to compare the differences in intracellular and extracellular metabolites over six periods. There were significant differences in the content and types of mycelial metabolites during the incubation. Marmesin, an important intermediate in the biosynthesis of coumarins, was found in the highest amount on the fourth day of incubation. The differential metabolites were screened to obtain 799 intracellular and 468 extracellular differential metabolites. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed that the highly enriched extracellular metabolic pathways were alanine, aspartate and glutamate metabolism, glyoxylate and dicarboxylate metabolism, and terpenoid backbone biosynthesis. In addition, the enrichment analysis associated with intracellular and extracellular ATP‐binding cassette transporter proteins revealed that some ATP‐binding cassette transporters may be involved in the transportation of certain amino acids and carbohydrates. Our results provide some theoretical basis for the regulatory mechanisms between the rhizosphere and the host plant and pave the way for the heterologous production of furanocoumarin. [ABSTRACT FROM AUTHOR]

Arid and semi‐arid areas are facing increasingly severe water deficits that are being intensified by global climate changes. Microbes associated with plants native to arid regions provide valuable benefits to plants, especially in water‐stressed environments. In this study, we used 16S rDNA metabarcoding analysis to examine the bacterial communities in the bulk soil, rhizosphere and root endosphere of the plant Malva sylvestris L. in Morocco, along a gradient of precipitation. We found that the rhizosphere of M. sylvestris did not show significant differences in beta‐diversity compared to bulk soil, although, it did display an increased degree of alpha‐diversity. The endosphere was largely dominated by the genus Rhizobium and displayed remarkable variation between plants, which could not be attributed to any of the variables observed in this study. Overall, the effects of precipitation level were relatively weak, which may be related to the intense drought in Morocco at the time of sampling. The dominance of Rhizobium in a non‐leguminous plant is particularly noteworthy and may permit the utilization of this bacterial taxon to augment drought tolerance; additionally, the absence of any notable selection of the rhizosphere of M. sylvestris suggests that it is not significatively affecting its soil environment. [ABSTRACT FROM AUTHOR]

The rhizosphere influence on the soil microbiome and function of crop wild progenitors (CWPs) remains virtually unknown, despite its relevance to develop microbiome‐oriented tools in sustainable agriculture. Here, we quantified the rhizosphere influence—a comparison between rhizosphere and bulk soil samples—on bacterial, fungal, protists and invertebrate communities and on soil multifunctionality across nine CWPs at their sites of origin. Overall, rhizosphere influence was higher for abundant taxa across the four microbial groups and had a positive influence on rhizosphere soil organic C and nutrient contents compared to bulk soils. The rhizosphere influence on abundant soil microbiomes was more important for soil multifunctionality than rare taxa and environmental conditions. Our results are a starting point towards the use of CWPs for rhizosphere engineering in modern crops. [ABSTRACT FROM AUTHOR]

Altering plant carbon allocation from leaves to stems is key to improve biomass for forage, fuel, and renewable chemicals. The sorghum dry stalk (D) locus controls a quantitative trait for sugar accumulation, with enhanced carbon allocation in the stems of juicy green (dd) sorghum but reduced carbon allocation in that of dry white (DD) sorghum. However, it remains unclear whether altering sorghum sugar accumulation in stem affects below‐ground microbiome. Here we investigated sorghum rhizosphere soil microbiome in near isogenic lines with different magnitude of carbon allocations and accumulation in the stems. Results showed that enhanced carbon accumulation in stems of juicy green sorghum results in stronger selection in rhizosphere microbiome assembly. The rhizosphere soil microbial communities selected in juicy green sorghum tended to be fast‐growing microbial taxa which possessed potential functions that would promote higher potential capacity to use chemically labile carbon sources and potentially result in higher potential decomposition rates. We found the rhizosphere microbes selected by juicy green sorghum form weaker interactions than dry white sorghum. This is the first comprehensive study revealing how the different magnitude of carbon allocations to stems regulates microbial community assembly, microbial interaction, and microbial functions. This study indicates that future plant modification for bioenergy crops should also consider the impacts on belowground microbial community without compromising the sustainability. [ABSTRACT FROM AUTHOR]

Background: Cotton productivity is commonly limited by the imbalanced nutritional status of phosphorus (P) and zinc (Zn) in Brazil. Evaluating the effect of the P–Zn interaction on nutrient availability in soil is crucial, as this interaction promotes plant adaptations that modify the availability of these nutrients in the rhizosphere. However, the influence of root growth on the P–Zn interaction and its adsorption in rhizosphere soil remains poorly understood. Aim: We tested the interaction of P and Zn rates in two classes of soil cultivated with cotton. The aim of this investigation was to evaluate the P and Zn availability and adsorption capacity by rhizosphere soils cultivated with cotton plants subjected to P and Zn rates. Methods: Cotton plants were grown under greenhouse conditions in two different soils (Entisol and Oxisol), with different P and Zn rates. Phosphorus fractionation and Zn sequential extraction were assessed in rhizosphere soil, while total P and Zn concentrations were measured in the shoot and roots. Results: Soil type significantly affected the P–Zn availabilities on rhizosphere soils. Although increased P‐rates raised P‐soil availability on bulk and rhizosphere soils, cotton growth was not increased under low soil‐Zn availability. The labile inorganic P content was influenced by P and Zn rates just in Oxisol. In both soils, the Zn‐ Zn‐exchangeable content was decreased by P rates, while Zn bound to oxides increased. Conclusions: Soil‐type effects on P–Zn interaction could have important implications for increasing cotton productivity. Increased cotton productivity by P application was only achieved with an adequate supply of Zn. [ABSTRACT FROM AUTHOR]

Vascular plants develop diverse root system architectures and exudates to facilitate acquisition of soil nutrients (nitrogen and phosphorus). Plant species have inherently specific properties of root system architectures and exudates, but some plants exhibit high plasticity to respond to spatiotemporal variations in soil nutrient forms and availability. This paper synthesizes evidence on how plant species diversity and root plasticity contribute to soil nutrient mobilization and uptake in plants from the tropics to the Arctic with varying plant species diversity. The development of finer roots in the surface soil is a well‐known strategy for the acquisition of limited nutrients (especially phosphorus), but the allocation of roots foraging “nutrient hotspots” in deeper soil (podzolic soil or permafrost‐affected soils) is an alternative strategy for coniferous trees tested in the Arctic and boreal forests. This contrasts with findings in tropical forests, where diverse plant species with different capacities of organic acid exudation coexist and species composition shifts in response to phosphorus deficiency. In particular, high malate exudation from roots and rhizosphere microbes stimulates phosphorus solubilization, aluminum detoxification, and lignin degradation in acidic soils. The diversity and plasticity of the root system architecture, root exudation, and the flexibility of nutrient sources mitigate nutrient limitation in soil. Root plasticity facilitating soil nutrient acquisition has a large impact on biogeochemistry and soil formation, such as podzolization, in the long term. [ABSTRACT FROM AUTHOR]

Cover crops improve soil fertility in orchard ecosystems, however, the response of soil microbial metabolism to fruit tree interactions with cover legumes at different stages of the life cycle remains uncertain, thereby limiting our understanding of the mechanisms that regulate nutrient cycling in orchards with cover crop management. Here, the characteristics of microbial energy (carbon, C) and nutrient (nitrogen, N or phosphorus, P) metabolism in the citrus rhizosphere and bulk soil in orchards were analyzed with two managements, that is, smooth vetch (Vicia villosa Roth var. glabresens Koch) cover and clean tillage, using an extracellular enzymatic stoichiometry model. Microbial C limitation was significantly reduced by cover during the vetch growing season owing to the resulting higher plant root C and soil organic C content. Competition for N between plants and microbes in the bulk soil might lead to significant microbial N limitation in covered orchards during the vetch-decomposition season, presumably owing to a significant increase in citrus root N and a concomitant decrease in bulk soil total N. Partial least squares path modeling showed that citrus root nutrient contents negatively affected microbial C limitation, while soil nutrients negatively affected microbial relative nutrient limitation in covered orchards. Conversely, both effects were reversed by tillage. Smooth vetch cover mitigated microbial C limitation, and the microbial relative N/P limitation was also influenced by the life state of smooth vetch. Our study highlights the importance of changes in microbial metabolism driven by seasonal nutrient dynamics for understanding soil nutrient cycling and optimizing cover-legumes management in orchards. [ABSTRACT FROM AUTHOR]

Polyploidy – whole genome duplication – is common in plants. Studies over the last several decades have documented numerous mixed‐ploidy populations. Whether arising via recurrent whole genome duplication events within a population, or from secondary contact, the persistence of mixed populations is possible by niche differentiation. Specifically, one mechanism facilitating ploidy co‐occurrence is microbially‐mediated niche differentiation (MMND), wherein cytotypes occupy different niches via interactions with different sets of microbes. Inherently cryptic, MMND is underexplored in polyploid plant populations. Here, we search for evidence of MMND in creosotebush Larrea tridentata, a dominant desert shrub of the southwestern US and northern Mexico. We sequenced root‐associated fungal taxa in soils of diploid, autotetraploid, and autohexaploid plants growing in two naturally‐occurring mixed‐cytotype populations. Within populations, we found substantial fungal assemblage overlap across host plant cytotypes. However, using indicator species analysis, we identified some fungi that are differentiated by host plant cytotype, satisfying a necessarycondition for MMND. Future study is needed to determine the degree of niche differentiation conferred, if any, and whether the identified fungi play a role in the long‐term persistence of multiple cytotypes within populations. [ABSTRACT FROM AUTHOR]

Summary: Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root–soil interactions across soils with different nutrient statuses remain elusive.We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long‐term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones.The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient‐deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input.In conclusion, our results show that maize selects microbes at the root–soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species. [ABSTRACT FROM AUTHOR]

Summary: The link between above‐ and belowground communities is a key uncertainty in drought and rewetting effects on forest carbon (C) cycle.In young beech model ecosystems and mature naturally dry pine forest exposed to 15‐yr‐long irrigation, we performed 13C pulse labeling experiments, one during drought and one 2 wk after rewetting, tracing tree assimilates into rhizosphere communities.The 13C pulses applied in tree crowns reached soil microbial communities of the young and mature forests one and 4 d later, respectively. Drought decreased the transfer of labeled assimilates relative to the irrigation treatment. The 13C label in phospholipid fatty acids (PLFAs) indicated greater drought reduction of assimilate incorporation by fungi (−85%) than by gram‐positive (−43%) and gram‐negative bacteria (−58%).13C label incorporation was more strongly reduced for PLFAs (cell membrane) than for microbial cytoplasm extracted by chloroform. This suggests that fresh rhizodeposits are predominantly used for osmoregulation or storage under drought, at the expense of new cell formation. Two weeks after rewetting, 13C enrichment in PLFAs was greater in previously dry than in continuously moist soils. Drought and rewetting effects were greater in beech systems than in pine forest.Belowground C allocation and rhizosphere communities are highly resilient to drought. [ABSTRACT FROM AUTHOR]

Summary: 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. [ABSTRACT FROM AUTHOR]

The rhizosphere and phyllosphere of plants are home to a diverse range of microorganisms that play pivotal roles in ecosystem services. Consequently, plant growth‐promoting bacteria (PGPB) are extensively utilized as inoculants to enhance plant growth and boost productivity. Despite this, the interactions between the rhizosphere and phyllosphere, which are influenced by PGPB inoculation, have not been thoroughly studied to date. In this study, we inoculated Bacillus velezensis SQR9, a PGPB, into the bulk soil, rhizosphere or phyllosphere, and subsequently examined the bacterial communities in the rhizosphere and phyllosphere using amplicon sequencing. Our results revealed that PGPB inoculation increased its abundance in the corresponding compartment, and all treatments demonstrated plant growth promotion effects. Further analysis of the sequencing data indicated that the presence of PGPB exerted a more significant impact on bacterial communities in both the rhizosphere and phyllosphere than in the inoculation compartment. Notably, the PGPB stimulated similar rhizosphere‐beneficial microbes regardless of the inoculation site. We, therefore, conclude that PGPB can promote plant growth both directly and indirectly through the interaction between the rhizosphere and phyllosphere, leading to the enrichment of beneficial microorganisms. [ABSTRACT FROM AUTHOR]

The present study focuses on the 1‐aminocyclopropane‐1‐carboxylic acid (ACC) deaminase assay and the rhizospheric interactions affecting enzyme activity. We investigate the efficacy of ACC deaminase‐producing rhizobacterial activity in alleviating salt stress in rice. Among the five selected isolates, only two strains, KFSC2 and PK7, possessed the enzyme activity. The amplification of the acdS gene resulted in gene identification in all five isolates. The newly designed primer in this study was suitable for both Pseudomonas and Enterobacter species. The gene products of KFSC1 and KFSC2 were amplified, sequenced and subsequently submitted to GenBank with accession numbers OQ703930 and OQ798805, respectively. This marks the first‐ever submission of the acdS gene sequence from Pseudomonas aeruginosa to GenBank. The interactive effect of root exudates on ACC deaminase activity was assessed using amino acids, organic acids and sugars. The highest enzyme activity was obtained with aspartic acid and fructose, while organic acids and varying pH levels had negative influences on enzyme activity. Additionally, salt and proline had positive effects. These results indicate that there is a positive interaction occurring among these compounds from plants and root‐colonizing bacteria. The selected strain PK7 had a significant impact on growth parameters. Moreover, yield resulted in 252 kg/hec over the control suggests its future possibility of promising bioformulations. [ABSTRACT FROM AUTHOR]

Beneficial microorganisms play essential roles in soil fertility, plant nutrition, and health. In this study, we examined the potential of a collection of 138 bacterial strains to promote plant growth. The strains were isolated from the rhizosphere of two monocotyledonous and two dicotyledonous plant species and from bare fallow soil, all from the same site. Our interest in this study was to investigate the diversity and the potential for growth promotion in this collection of culturable bacteria. The most common trait was phosphorus (P) solubilization from aluminium phosphate (in 66.7% of the strains), whereas solubilization of P from phytic acid (6.5%) and from iron phosphate (5.8%) was the least common and they were only detected in bacterial strains from faba bean and oilseed rape. All bacterial strains inhibited the growth of Fusarium graminearum (from 5.4% to 87.2%). In total, 10 genera were identified among the strains by 16S rRNA sequencing and Pseudomonas was the most common in monocotyledonous plants and in bulk soil, while Stenotrophomonas was dominant in the rhizosphere of the dicotyledonous plants. Combinations of bacterial strains improved the spectrum of in vitro activity in most cases, however, wheat growth was generally lower. These strains have potential to be used as biofertilizers and/or biocontrol agents and further studies should be pursued to develop them into practical solutions for a more sustainable agricultural production. [ABSTRACT FROM AUTHOR]

High soil pH can lead to Mn2+ and P deficiency and yield losses. In addition, it is unclear which process, nitrification‐induced acidification of bulk soil or nitrification inhibitor‐driven rhizosphere acidification, is more effective in increasing Mn2+ availability and shoot concentration. Thus, this topic was investigated in this study. Moreover, we also evaluated if applying NIs can avoid P deficiency in soil with high pH and high buffering capacity. Two greenhouse experiments were carried out to investigate the impact of applying 3,4‐Dimethylpyrazole phosphate (DMPP) in sandy soil subjected to the application of different lime rates, simulating several soil pH and buffering capacity conditions. The utilized lime rates were 0, 0.5, 1, 2 and 4 g CaCO3 kg−1. The measured variables were bulk and rhizosphere soil pH, Mn2+ and P availability, maize biomass production, as well as Mn and P shoot concentrations. DMPP significantly reduced shoot biomass by 10% in unlimed soil; however, it promoted the overall shoot biomass by 30% in limed soil in both experiments. In addition, DMPP decreased the overall Mn shoot concentration by 24 and 21% in experiments I and II, respectively. In contrast, DMPP increased the overall P shoot concentration due to rhizosphere acidification by 24 and 17% in experiments I and II, respectively. The DMPP application did not avoid P deficiency under the highest lime rate (4 g CaCO3 kg−1) despite alleviating it. In conclusion, the application of NIs is not beneficial for increasing Mn2+ shoot concentration and, when performed to increase P availability in high pH soils, should consider the likelihood of causing Mn deficiency. [ABSTRACT FROM AUTHOR]

The article titled "Corrigendum to Conservation of beneficial microbes between the rhizosphere and the cyanosphere" in the journal New Phytologist acknowledges errors in several figures in a previously published article by Zheng et al. The errors were due to a discrepancy in the R-script used during the revision process, resulting in large error bars in the figures. The corrected figures and their associated legends are provided in the article. The authors apologize for the errors. [Extracted from the article]

The use of microbial inoculant is a promising strategy to improve plant health, but their efficiency often faces challenges due to difficulties in successful microbial colonization in soil environments. To this end, the application of biostimulation products derived from microbes is expected to resolve these barriers via direct interactions with plants or soil pathogens. However, their effectiveness and mechanisms for promoting plant growth and disease resistance remain elusive. In this study, we showed that root irrigation with the extracts of Streptomyces ahygroscopicus strain 769 (S769) solid fermentation products significantly reduced watermelon Fusarium wilt disease incidence by 30% and increased the plant biomass by 150% at a fruiting stage in a continuous cropping field. S769 treatment led to substantial changes in both bacterial and fungal community compositions, and induced a highly interconnected microbial association network in the rhizosphere. The root transcriptome analysis further suggested that S769 treatment significantly improved the expression of the MAPK signalling pathway, plant hormone signal transduction and plant–pathogen interactions, particular those genes related to PR‐1 and ethylene, as well as genes associated with auxin production and reception. Together, our study provides mechanistic and empirical evidences for the biostimulation products benefiting plant health through coordinating plant and rhizosphere microbiome interaction. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Plants and bacteria interact in complex ways that are crucial to the health and productivity of native vegetation and croplands. While the range of characterised plant‐beneficial bacterial traits continues to grow, key questions remain regarding the distribution and mobility of genes associated with these traits. This work explores the diversity of mobile genetic elements carried by bacteria associated with plant root surfaces, assessing their capacity to help shape plant–bacterial interactions. The significance of this work lies in the potential to contribute to new strategies for enhancing plant health, promoting sustainable agriculture and managing plant diseases in an era when we must respond to environmental change. Summary: Integrons are gene capture and expression systems that contribute to bacterial adaptation. Integron research has mainly focused on the role that these elements play in spreading antimicrobial resistance. However, their contribution to niche adaptation is potentially much broader because integrons can sample the vast repertoire of diverse functions encoded by integron gene cassettes. Integrons and gene cassettes have been identified in many bacterial lineages residing in soil and water across varied ecosystems, but there has been little investigation of integrons in plant‐associated bacteria.Bacteria and plants have complex, dynamic relationships that influence plant health and productivity. To investigate whether integrons contribute to adaptative processes in plant microbiomes, we examined gene cassette and microbial taxonomic profiles in rhizoplanes of four important crop species grown under controlled glasshouse conditions. We identified 38,546 unique gene cassettes, including elements carrying genes associated with antibiotic resistance, type II toxin–antitoxin systems and genes with putative functions associated with plant growth promotion, along with a larger set encoding genes of unknown functions.Rhizoplane microbiomes of different plant species showed more similarity in their community composition profiles than in their gene cassette profiles, with complex and distinct suites of gene cassettes associated with each plant species, suggesting that gene cassettes might have a role in specific plant–bacterial interactions.We show that rhizoplane microbiomes carry diverse integron gene cassettes that could play a role in establishing and maintaining rhizoplane communities. [ABSTRACT FROM AUTHOR]

General plant diseases as well as soil‐borne pathogens severely reduce agricultural yield. The rhizosphere (the region of the soil that includes and surrounds the roots) is an important niche for microbial diversity in particular phytobeneficial bacteria including plant growth‐promoting rhizobacteria (PGPR) which have been used for a very long time to combat plant diseases. Pathogen control and crop productivity can both be improved through the use of PGPR several mechanisms, including iron‐based nutrition, antibiotics, volatile substances, enzymes, biofilm, allelochemicals, and so on. Their modes of action and molecular mechanisms have improved our comprehension of how they are used to control crop disease. Therefore, there is a lot of literal information available regarding PGPR, but this review stands out since it starts with the fundamentals: the concept of the rhizosphere and the colonization process of the latter, particularly because it covers the most mechanisms. A broad figure is used to present the study's findings. The advantages of using PGPR as bioinoculants in sustainable agriculture are also mentioned. [ABSTRACT FROM AUTHOR]

Keystone species are more important than others for community dynamics and stability. Keystone species can be identified and evaluated by their centrality (i.e., a relative ranking of the topological positional importance of a species) in ecological networks. Studies of node centrality of plant–fungus bipartite networks, for example, have identified the keystone species that are important for maintaining network structure and stability. However, the underlying drivers of the importance of species in a network have rarely been examined. We assessed the centrality (degree, closeness, and betweenness) of plant and fungal species in a plant–ectomycorrhizal fungus network in a subtropical forest in southern China. Based on the phylogenies of plants and fungi and plant traits, we explored ecological factors that led to a species taking a central position or not. We found one plant species (Ternstroemia gymnanthera) and four species of ectomycorrhizal fungi (Russula citrina, Scleroderma sp., and two Cenococcum sp.) were characterized by the highest centrality of degree, closeness, and betweenness among the bipartite network nodes and thus played key roles in maintaining network structure. Centrality for fungi (not for plants) was phylogenetically constrained. Plant traits and abundance together explained 46.36%, 46.0%, and 43.7% of variation in the centrality of degree, closeness, and betweenness of plant species in the bipartite network, respectively. When plant or fungal species were sequentially removed on the order of higher to lower centrality, network was less stable than randomly removed. We suggest that abundance and traits determine the positional importance of plant species in a network. This work helps understand how plant–fungus association networks will respond to species extinction and changes in species abundance and functional traits due to habitat fragmentation and human activities. [ABSTRACT FROM AUTHOR]

The optimization of phosphate (P) fertilizer application strategies to improve the utilization of P fertilizer in farmlands is urgently required. The objective of this study is to evaluate the effect of P fertilizer application rate and position on maize (Zea mays L.) P utilization. A 2‐year field experiment was conducted with P fertilizer application rate (0, 40, 80, and 120 kg ha−1) and position (5 and 10 cm). Compared with the 5‐cm P position, the 10‐cm P position significantly increased the available phosphorus (AP) content in rhizosphere soil. Surprisingly, the rhizosphere AP content increased or remained the same when the amount of P fertilizer was reduced to 80 kg ha−1 at a distance of 5 cm, compared with that when the amount of P fertilizer was 120 kg ha−1 at a distance of 10 cm. Additionally, there was also an improvement in the root weight, root number, biomass, and maize yield in the 5‐cm position compared to the 10‐cm position. The P fertilizer use efficiency was significantly increased at the 5‐cm position compared to the 10‐cm P position, with increases of 8.93% and 4.11% (P40), 6.38% and 5.10% (P80), and 4.72% and 2.36% (P120) in 2021 and 2022, respectively. Our results showed that a closer position increased the available P content in rhizosphere soil, promoted maize growth, and improved P fertilizer utilization and maize yield, suggesting that the agronomy method with proper location of P increases the soil P availability in rhizosphere soil and P utilization in maize. Core Ideas: P fertilizer application strategies can be improved by altering the phosphate position.Rhizosphere phosphorus content of P80 + 5 cmis greater or equal to P120 + 10 cm.Phosphate fertilizer use efficiency can be improved by 2.3%–8.9% at the 5‐cm position compared to the 10‐cm phosphate position. [ABSTRACT FROM AUTHOR]

Noninvasive phenotyping can quantify dynamic plant growth processes at higher temporal resolution than destructive phenotyping and can reveal phenomena that would be missed by end‐point analysis alone. Additionally, whole‐plant phenotyping can identify growth conditions that are optimal for both above‐ and below‐ground tissues. However, noninvasive, whole‐plant phenotyping approaches available today are generally expensive, complex, and non‐modular. We developed a low‐cost and versatile approach to noninvasively measure whole‐plant physiology over time by growing plants in isolated hydroponic chambers. We demonstrate the versatility of our approach by measuring whole‐plant biomass accumulation, water use, and water use efficiency every two days on unstressed and osmotically stressed sorghum accessions. We identified relationships between root zone acidification and photosynthesis on whole‐plant water use efficiency over time. Our system can be implemented using cheap, basic components, requires no specific technical expertise, and should be suitable for any non‐aquatic vascular plant species. [ABSTRACT FROM AUTHOR]

Root hairs are considered important for rhizosphere formation, which affects root system functioning. Through interactions with soil microorganisms mediated by root exudation, root hairs may affect the phenotypes and growth of young plants. We tested this hypothesis by integrating results from two experiments: (1) a factorial greenhouse seedling experiment with Zea mays B73‐wt and its root‐hairless mutant, B73‐rth3, grown in live and autoclaved soil, quantifying 15 phenotypic traits, seven growth rates, and soil microbiomes and (2) a semi‐hydroponic system quantifying root exudation of maize genotypes. Possibly as compensation for lacking root hairs, B73‐rth3 seedlings allocated more biomass to roots and grew slower than B73‐wt seedlings in live soil, whereas B73‐wt seedlings grew slowest in autoclaved soil, suggesting root hairs can be costly and their benefits were realized with more complete soil microbial assemblages. There were substantial differences in root exudation between genotypes and in rhizosphere versus non‐rhizosphere microbiomes. The microbial taxa enriched in the presence of root hairs generally enhanced growth compared to taxa enriched in their absence. Our findings suggest the root hairs' adaptive value extends to plant‐microbe interactions mediated by root exudates, affecting plant phenotypes, and ultimately, growth. Summary Statement: An experiment with seedlings of Zea mays B73 and its root‐hairless mutant (Z. mays B73‐rth3) with contrasting soil microbiomes showed that root hairs are beneficial towards plant growth but can be costly. Root hairs' adaptive value was partly mediated by plant‐microbe interactions involving exudates, which feedback to plant phenotypes and growth. [ABSTRACT FROM AUTHOR]

SUMMARY: In natural and agricultural situations, ammonium (NH4+) is a preferred nitrogen (N) source for plants, but excessive amounts can be hazardous to them, known as NH4+ toxicity. Nitrate (NO3−) has long been recognized to reduce NH4+ toxicity. However, little is known about Brassica napus, a major oil crop that is sensitive to high NH4+. Here, we found that NO3− can mitigate NH4+ toxicity by balancing rhizosphere and intracellular pH and accelerating ammonium assimilation in B. napus. NO3− increased the uptake of NO3− and NH4+ under high NH4+ circumstances by triggering the expression of NO3− and NH4+ transporters, while NO3− and H+ efflux from the cytoplasm to the apoplast was enhanced by promoting the expression of NO3− efflux transporters and genes encoding plasma membrane H+‐ATPase. In addition, NO3− increased pH in the cytosol, vacuole, and rhizosphere, and down‐regulated genes induced by acid stress. Root glutamine synthetase (GS) activity was elevated by NO3− under high NH4+ conditions to enhance the assimilation of NH4+ into amino acids, thereby reducing NH4+ accumulation and translocation to shoot in rapeseed. In addition, root GS activity was highly dependent on the environmental pH. NO3− might induce metabolites involved in amino acid biosynthesis and malate metabolism in the tricarboxylic acid cycle, and inhibit phenylpropanoid metabolism to mitigate NH4+ toxicity. Collectively, our results indicate that NO3− balances both rhizosphere and intracellular pH via effective NO3− transmembrane cycling, accelerates NH4+ assimilation, and up‐regulates malate metabolism to mitigate NH4+ toxicity in oilseed rape. [ABSTRACT FROM AUTHOR]

Host–microbe interactions are increasingly recognized as important drivers of organismal health, growth, longevity and community‐scale ecological processes. However, less is known about how genetic variation affects hosts' associated microbiomes and downstream phenotypes. We demonstrate that sunflower (Helianthus annuus) harbours substantial, heritable variation in microbial communities under field conditions. We show that microbial communities co‐vary with heritable variation in resistance to root infection caused by the necrotrophic pathogen Sclerotinia sclerotiorum and that plants grown in autoclaved soil showed almost complete elimination of pathogen resistance. Association mapping suggests at least 59 genetic locations with effects on both microbial relative abundance and Sclerotinia resistance. Although the genetic architecture appears quantitative, we have elucidated previously unexplained genetic variation for resistance to this pathogen. We identify new targets for plant breeding and demonstrate the potential for heritable microbial associations to play important roles in defence in natural and human‐altered environments. [ABSTRACT FROM AUTHOR]

Putative allelochemicals released by tillering onion promote cucumber growth in intercropping systems. However, the underlying molecular mechanisms remain unclear. This study focused on PHENYLALANINE AMMONIA‐LYASE (PAL) and ALLIINASE (ALL), which play crucial roles in phenylpropanoid biosynthesis and organic sulfur metabolism, respectively. The expression levels of AcPAL and AcALL, their enzyme activities, and trans‐cinnamic acid (t‐CA) and allicin content were analyzed in the donor tillering onions. Exogenous application of t‐CA and allicin was conducted on target cucumbers to investigate seedling growth, and differentially expressed genes (DEGs) were screened using transcriptome analysis to determine the response metabolic pathways. The results showed that intercropping with cucumber up‐regulated the expression of AcPAL and AcALL and increased the enzymatic activities of AcPAL and AcALL, resulting in increased accumulation of t‐CA and allicin in the tillering onion and rhizosphere soil, particularly in the roots of accession L‐hh, with strong allelopathic potential, compared to monocropping. Application of t‐CA at 25 μg mL−1 and allicin at 50 μg mL−1 significantly enhanced root fresh weight, shoot length, and shoot fresh weight in cucumber seedlings, whereas transcriptome analysis revealed that the DEGs were significantly enriched in plant hormone signal transduction, phenylpropanoid biosynthesis, MAPK signaling pathway, phenylalanine pathway, and starch and sucrose metabolism. In conclusion, AcPAL and AcALL of tillering onions participate in the accumulation of t‐CA and allicin, inducing the expression of genes involved in phenylpropanoid biosynthesis and MAPK signaling pathways to enhance environmental adaptability as well as auxin‐related genes to promote cucumber seedling growth. [ABSTRACT FROM AUTHOR]

While there is an extensive body of research on the influence of climate warming on total soil microbial communities, our understanding of how rhizosphere and non‐rhizosphere soil microorganisms respond to warming remains limited. To address this knowledge gap, we investigated the impact of 4 years of soil warming on the diversity and composition of microbial communities in the rhizosphere and non‐rhizosphere soil of a temperate steppe, focusing on changes in root exudation rates and exudate compositions. We used open top chambers to simulate warming conditions, resulting in an average soil temperature increase of 1.1°C over a span of 4 years. Our results showed that, in the non‐rhizosphere soil, warming had no significant impact on dissolved organic carbon concentrations, compositions, or the abundance of soil microbial functional genes related to carbon and nitrogen cycling. Moreover, soil microbial diversity and community composition remained largely unaffected, although warming resulted in increased complexity of soil bacteria and fungi in the non‐rhizosphere soil. In contrast, warming resulted in a substantial decrease in root exudate carbon (by 19%) and nitrogen (by 12%) concentrations and induced changes in root exudate compositions, primarily characterized by a reduction in the abundance in alcohols, coenzymes and vitamins, and phenylpropanoids and polyketides. These changes in root exudation rates and exudate compositions resulted in significant shifts in rhizosphere soil microbial diversity and community composition, ultimately leading to a reduction in the complexity of rhizosphere bacterial and fungal community networks. Altered root exudation and rhizosphere microbial community composition therefore decreased the expression of functional genes related to soil carbon and nitrogen cycling. Interestingly, we found that changes in soil carbon‐related genes were primarily driven by the fungal communities and their responses to warming, both in the rhizosphere and non‐rhizosphere soil. The study of soil microbial structure and function in rhizosphere and non‐rhizosphere soil provides an ideal setting for understanding mechanisms for governing rhizosphere and non‐rhizosphere soil carbon and nitrogen cycles. Our results highlight the distinctly varied responses of soil microorganisms in the rhizosphere and non‐rhizosphere soil to climate warming. This suggests the need for models to address these processes individually, enabling more accurate predictions of the impacts of climate change on terrestrial carbon cycling. [ABSTRACT FROM AUTHOR]

There may be trade‐offs in the allocation patterns of recent photosynthetic carbon (RPC) allocation in response to environmental changes, with a greater proportion of RPC being directed towards compartments experiencing limited resource availability. Alternatively, the allocation of RPC could shift from sources to sinks as plants processing excess photosynthates. It prompts the question: Does the pattern of RPC allocation vary under global changes? If so, is this variation driven by optimal or by residual C allocation strategies? We conducted a meta‐analysis by complicating 273 pairwise observations from 55 articles with 13C or 14C pulse or continuous labeling to assess the partitioning of RPC in biomass (leaf, stem, shoot, and root), soil pools (soil organic C, rhizosphere, and microbial biomass C) and CO2 fluxes under elevated CO2 (eCO2), warming, drought and nitrogen (N) addition. We propose that the increased allocation of RPC to belowground under sufficient CO2 results from the excretion of excess photosynthates. Warming led to a significant reduction in the percentage of RPC allocated to shoots, alongside an increase in roots allocation, although this was not statistically significant. This pattern is due to the reduced water availability resulting from warming. In conditions of drought, there was a notable increase in the partitioning of RPC to stems (+7.25%) and roots (+36.38%), indicative of a greater investment of RPC in roots for accessing water from deeper soil. Additionally, N addition led to a heightened allocation of RPC in leaves (+10.18%) and shoots (+5.78%), while reducing its partitioning in soil organic C (−8.92%). Contrary to the residual C partitioning observed under eCO2, the alterations in RPC partitioning in response to warming, drought, and N supplementation are more comprehensively explained through the lens of optimal partitioning theory, showing a trade‐off in the partitioning of RPC under global change. [ABSTRACT FROM AUTHOR]

Redesigning agrosystems to include more ecological regulations can help feed a growing human population, preserve soils for future productivity, limit dependency on synthetic fertilizers, and reduce agriculture contribution to global changes such as eutrophication and warming. However, guidelines for redesigning cropping systems from natural systems to make them more sustainable remain limited. Synthetizing the knowledge on biogeochemical cycles in natural ecosystems, we outline four ecological systems that synchronize the supply of soluble nutrients by soil biota with the fluctuating nutrient demand of plants. This synchrony limits deficiencies and excesses of soluble nutrients, which usually penalize both production and regulating services of agrosystems such as nutrient retention and soil carbon storage. In the ecological systems outlined, synchrony emerges from plant–soil and plant–plant interactions, eco‐physiological processes, soil physicochemical processes, and the dynamics of various nutrient reservoirs, including soil organic matter, soil minerals, atmosphere, and a common market. We discuss the relative importance of these ecological systems in regulating nutrient cycles depending on the pedoclimatic context and on the functional diversity of plants and microbes. We offer ideas about how these systems could be stimulated within agrosystems to improve their sustainability. A review of the latest advances in agronomy shows that some of the practices suggested to promote synchrony (e.g., reduced tillage, rotation with perennial plant cover, crop diversification) have already been tested and shown to be effective in reducing nutrient losses, fertilizer use, and N2O emissions and/or improving biomass production and soil carbon storage. Our framework also highlights new management strategies and defines the conditions for the success of these nature‐based practices allowing for site‐specific modifications. This new synthetized knowledge should help practitioners to improve the long‐term productivity of agrosystems while reducing the negative impact of agriculture on the environment and the climate. [ABSTRACT FROM AUTHOR]

Land degradation reduces productivity and biodiversity, and requires restoration of both soil condition and vegetation to re‐establish ecosystem services. Organic amendments can improve soil biological and chemical properties, thereby enhancing revegetation success in severely degraded soil. This study investigated the use of compost and biochar to support revegetation and soil restoration. Soil was collected from a severely degraded creek bed in an agricultural farm in south‐western Australia (UWA Farm Ridgefield) and amended with compost (2.5% and 5%) and biochar (5% and 10%), both alone and in all pairwise combinations. Saltbush (Atriplex nummularia) seedlings were grown for 10 weeks in glasshouse conditions. Following harvest, plant growth and soil chemical properties were analysed. DNA was extracted from rhizosphere soil for bacterial diversity profiling with subsequent putative functional genes relating to carbon, nitrogen and phosphorus cycling using an in‐silico approach. Compost improved growth of root and shoot biomass. Both compost and biochar improved the alkaline soil by reducing pH and increasing nitrate, phosphorus and potassium levels. Compost addition also had a significant effect on rhizosphere bacterial community structure, decreasing alpha diversity and altering beta diversity indices. Amendment of soil also changed the relative abundance of putative nutrient cycling genes, with an increase in the potential for denitrification, carbon and phosphorus cycling and a decrease in ammonification potential. Application of this compost‐biochar combination improved plant growth and soil condition by altering both chemical and biological characteristics of the soil, and therefore may provide an effective management strategy for supporting restoration in a degraded landscape. [ABSTRACT FROM AUTHOR]