Rhizosphere Effect Research Articles

Impact of Combining Bio-Inoculants along with Inorganic Fertilizers on Soil Biological Characteristics in Transplanted Rice (Oryza sativa L.) Crop

A field experiment was carried out during the Kharif season in the year 2022 to assess the impact of inorganic fertilizers along with Bio-inoculants on soil biological properties in rice (Oryza sativa L.). The experiment consists of seven treatments viz., T1 Control, T2 100% RDF (150, 60, 40 N2, P2O5, K2O kg ha-1), T3 80% RDF + 10 kg BGA ha-1 Soil application + PSB (Phosphate solubilizing bacteria) 3kg/ha, T4 60% RDF + 10kg BGA ha-1 Soil application + PSB, T5 80% RDF + 500kg Azolla ha-1 Soil application +PSB, T6 60% RDF + 500kg Azolla ha-1 Soil application +PSB and T7 10kg BGA ha-1 Soil application + 500kg Azolla ha-1 Soil application + PSB were comprised in Randomized Block Design with three replication. The incorporation of inorganics, Azolla PSB, and BGA (bio-inoculants) actively activated microbial activities, resulting in a greater increase in the populations of total bacteria, actinomycetes, and fungi was observed throughout all growth stages, regardless of the treatments applied, when compared to their initial densities. This phenomenon supports the notion of a stronger rhizosphere effect. This trend aligns with the rise in organic carbon content. Moreover, soil dehydrogenase, alkaline phosphatase activities, along with microbial biomass carbon, displayed an upward trend in tandem with the progressive growth phases of the rice plant.

Determinants of rhizospheric organic carbon fractions and accumulation in four different vegetations of coastal saline-alkali soils

Rhizosphere processes are key pathways through which plants influence the carbon cycling of diverse ecosystems and are closely associated with vegetation types. However, the environmental responses of rhizospheric soil organic carbon (SOC) mediated by the interaction between rhizospheric effect and vegetation type remain uncertain, severely limiting our assessment of the carbon sequestration potential of different coastal vegetation. Here, we identified the core factors driving changes in various soil carbon fractions in the rhizosphere of four coastal vegetation types by testing the contents of the reactive, dissolved, particulate, mineral-associated, heavy and light fractions of SOC and their relationships with physicochemical properties and enzyme activities. It was found that the rhizosphere effect significantly influenced SOC, with rhizospheric SOC contents varying significantly among vegetation types, ranging from 2.12 to 9.04 g/kg. Besides, rhizospheric soil pH was found to contribute significantly to SOC fractions (except for light organic carbon) and exert significant inhibitory effects on SOC, reactive organic carbon, mineral-associated organic carbon and heavy organic carbon. Despite the different responses of various SOC fractions to physicochemical properties and enzyme activities, soil available phosphorus and alkaline phosphatase activity emerged as core environmental factors influencing rhizospheric SOC accumulation across different coastal vegetation types. This study presents a promising framework for understanding the determinants of SOC fractions in rhizospheric soil, and their accumulation in the vegetation of coastal saline-alkali soils. In addition to alkalinity, phosphorus acquisition capacity can be a key predictor of coastal SOC fractions and their accumulation.

Rhizosphere effect: microbial and enzymatic dynamics in the rhizosphere of various shrub species

Abstract Aims The aim of our research was to compare the properties of the rhizosphere soil of different shrub species. We assumed that the physicochemical properties and microbiome of the rhizosphere differ from bulk soil and the species of shrub is important in their formation. Methods The study involved determining the abundance and diversity of microorganisms in the rhizosphere, along with assessing the basic chemical properties and enzymatic activity. Samples were collected from both rhizosphere and bulk soil in pine stands with an understory of shrubs forming biogroups. Results The enzymatic activity in the rhizosphere was significantly higher than in bulk soil. At the same time enzymatic activity in the rhizosphere differed between the shrub species tested. Both intracellular and extracellular enzymes exhibited a positive correlation with basic biochemical parameters. The number of bacteria and fungi correlated with physicochemical and biochemical properties. The number of bacteria and fungi was notably higher in the rhizosphere of the examined shrub species compared to bulk soil, at the same time, we noted a significant influence of the shrub species on microorganisms in the rhizosphere zone. Among the bacteria in the rhizosphere of shrubs, genera Edaphobaculum, Gemmatimonas, Bdellovibrio, Jorgensenbacteria, Rhodoplanes, and Acidocella were more abundant. Regarding fungi, Mortierella longigemmata, Didymella viburnicola, Trichoderma stellatum, and Phacidium pseudophacidioides were found to be more abundant in the rhizosphere. Conclusions The findings from our research may have practical applications in shaping the species composition of tree stands, with potential implications for future soil health condition.

Key Chemical Soil Parameters for the Assembly of Rhizosphere Bacteria Associated with Avocado Cv Hass Grafted on Landrace Rootstocks

Avocado cultivation holds significant economic importance in many countries, ranking Colombia as the fifth largest global producer. Particularly, the Hass cultivar plays a pivotal role in Colombia’s avocado industry, especially in the Department of Antioquia, the primary export region. This cultivar is grown under diverse soil and climate conditions and exhibits considerable genetic polymorphism due to the hybridization of varieties of agronomic significance, leading to a diverse array of landrace rootstocks. However, the role of soil conditions and rootstock genotype in structuring rhizosphere bacterial communities is still lacking. In addressing this knowledge gap, we investigated the influence of two soil conditions on the structure of rhizosphere bacterial communities associated with two landrace genotypes of Persea americana cv. Hass, utilizing 16S rRNA sequencing. Notably, no significant differences related to genotypes were observed. This study reports that the rhizosphere bacterial microbiome remains consistent across avocado landrace rootstocks, while variations in key parameters such as phosphorus, pH, Mg, and Ca drive distinct rhizosphere effects. Our results reveal that despite the soils having similar management, increases in these crucial parameters can lead to bacterial communities with lower alpha diversity and a more complex co-occurrence network. In addition, we found substantial variations in beta diversity, bacterial composition, and metagenome predictions between the two farms, underscoring the role of soil variables in shaping the bacterial microbiome. These findings provide valuable insights into the factors influencing the bacterial communities that may play a role in the health and productivity of crops with agro-industrial potential, such as Hass avocado.

Rhizosphere Effect Enhanced the Immobilization Efficiency of Mercapto-Palygorskite for Cd in Alkaline Soil: Mechanism from the Perspective of Microorganism

Rhizosphere Effect Enhanced the Immobilization Efficiency of Mercapto-Palygorskite for Cd in Alkaline Soil: Mechanism from the Perspective of Microorganism

Intercropping of tobacco and maize at seedling stage promotes crop growth through manipulating rhizosphere microenvironment.

Changes in the rhizosphere microbiome and metabolites resulting from crop intercropping can significantly enhance crop growth. While there has been an increasing number of studies on various crop combinations, research on the intercropping of tobacco and maize at seedling stage remains limited. This study is the first to explore rhizosphere effects of intercropping between tobacco and maize seedling stages, we analyzed the nitrogen, phosphorus and potassium nutrients in the soil, and revealed the important effects on soil microbial community composition and metabolite profiles, thereby regulating crop growth and improving soil balance. Compared with mono-cropping, intercropping increased the biomass of the two crops and promoted the nutrient absorption of nitrogen, phosphorus and potassium. Under intercropping conditions, the activities of sucrase, catalase and nitrate reductase in tobacco rhizosphere soil and the content of available potassium, the activities of nitrate reductase and acid phosphatase in maize rhizosphere soil were significantly increasing. Rhizosphere soil bacterial and fungal communities such as Sphingomonas, Massilia, Humicola and Penicillium respond differently to crop planting patterns, and soil dominant microbial communities are regulated by environmental factors such as pH, Organic Matter, Available Potassium, Nitrate Reductase, and Urease Enzyme. Network analysis showed that soil microbial communities were more complex after intercropping, and the reciprocal relationship between bacteria and fungi was enhanced. The difference of metabolites in soil between intercropping and monocropping system was mainly concentrated in galactose metabolism, starch and sucrose metabolism pathway, and the content of carbohydrate metabolites was significantly higher than that of monocropping soil. Key metabolites such as D-Sucrose, D-Fructose-6-Phosphate, D-Glucose-1-Phosphatel significantly influence the composition of dominant microbial communities such as Sphingomonas and Penicillium. This study explained the effects of intercropping between flue-cured tobacco and maize on the content of soil metabolites and soil microbial composition in rhizosphere soil, and deepened the understanding that intercropping system can improve the growth of flue-cured crops seedlings through rhizosphere effects.

Rhizosphere priming and effects on mobilization and immobilization of multiple soil nutrients

Living roots and their rhizodeposition play a vital role in mediating soil organic carbon (SOC) decomposition and nutrient mobilization. It is virtually unknown how the rhizosphere effects on soil nutrient mobilization are connected with the rhizosphere priming on SOC decomposition. Here we investigated the rhizosphere effects of six grassland species (four grasses and two legumes) on soil nutrient mobilization and SOC decomposition with and without nitrogen (N) fertilization in a 95-day pot experiment. Plant nutrient acquisition, soil extractable nutrients, and net nutrient mobilization or immobilization were determined to evaluate the rhizosphere effect on soil nutrient dynamics. Primed SOC decomposition was measured as the difference in soil-derived CO2–C between planted and unplanted treatments. Without N fertilization, all species consistently increased net phosphorus (P), sodium (Na), iron (Fe), and copper (Cu) mobilization and most species increased net N, sulfur (S), calcium (Ca), and zinc (Zn) mobilization and net potassium (K), magnesium (Mg), and manganese (Mn) immobilization compared to the unplanted soil. These results suggest that grassland species could induce both positive and negative rhizosphere effects on soil nutrient mobilization with different magnitude. With N fertilization, plant-induced net N mobilization increased, while plant-induced net P and S mobilization decreased. Further, plant biomass, plant N, P, and S acquisition, and plant-induced net N, P, and S mobilization (i.e., net nutrient mobilization in excess of the unplanted control), were positively correlated with primed SOC decomposition across six species, indicating that the mobilization of organically bound nutrients (N, P, and S) was connected with the rhizosphere priming on SOC decomposition. In contrast, plant-induced net nutrient mobilization of base cations and micronutrients was not related to primed SOC decomposition. Overall, our results demonstrate that a substantial portion of nutrient availability stems from rhizosphere processes and is plant species-specific, and that nutrient release of N, P and S are closely connected with rhizosphere priming on SOC decomposition.

Evaluation of functional plant growth-promoting activities of culturable rhizobacteria associated to tunicate maize (Zea mays var. tunicata A. St. Hil), a Mexican exotic landrace grown in traditional agroecosystems.

Tunicate maize (Zea mays var. tunicata A. St. Hil) is a landrace that constitutes a fundamental aspect of the socio-cultural identity of Ixtenco, Tlaxcala (Mexico) and represents an exotic phenotype whose kernels are enclosed in leaflike glumes. Despite multiple studies conducted worldwide on plant growth-promoting-rhizobacteria (PGPR) in commercial maize varieties grown under monoculture systems, very little is known about bacteria inhabiting native maize landraces in agroecosystems, but for tunicate maize such knowledge is non-existent. This research described and profiled functional groups of culturable rhizobacteria from tunicate maize at two phenological stages (tasseling and maturity/senescence) in a polyculture system, highlighting potential PGPR for biotechnological purposes. Ninety-five rhizobacteria were isolated and molecularly identified, and their physiological activities such as plant growth promotion, production of exogenous lytic enzymes, and antagonism against fungal pathogens were determined. The culturable rhizobacterial community associated to tunicate maize comprised 42 genera, dominated by Bacillaceae, Comamonadaceae, Microbacteriaceae, Micrococcaceae, Oxalobacteraceae, Pseudomonadaceae, and Rhizobaceae families. At tasseling stage, the identified bacteria corresponded to Arthrobacter, Priestia, Herbaspirillum, Pseudomonas, and Rhizobium, and exhibited redundant capabilities for stimulating plant growth and nutrition, and inhibiting fungal phytopathogens. At maturity/senescence stage, the main genera Arthrobacter and Microbacterium displayed lytic capabilities to support mineralization process. We recorded potential novel rhizosphere functional bacteria such as Rhizobium, Sphingobium, and Arthrobacter which are not previously described associated to maize landraces, as well as their bioprospection as PGPR detected at plant phenological stages poorly explored (like maturity/senescence). This taxonomic and functional diversity was attributed to the application of agricultural practices as well as the rhizosphere effect during specific phenological stages. Results described the diversity and functionality of culturable rhizosphere bacteria from tunicate maize in polyculture systems that allowed us the detection of potential rhizobacteria for further developing of biofertilizers and biocontrollers directed as biotechnology for sustainable agriculture, and for generating strategies for conservation of native plants and their microbial genetic resources.

A rhizosphere effect promotes the persistence of gas oxidization activity in soil

Labile carbon and nutrients of the rhizosphere promote the activity of trace gas oxidizing bacteria (TGOB), but the capacity of the rhizosphere effect to support their persistence upon activation has received less attention. Here, we hypothesized that the activation response of TGOB in soil before planting is proportional to the persistence of their activity after wheat growth. The TGOB were activated in sandy-loam and peat soils under a static atmosphere containing elevated concentration of hydrogen (H2), carbon monoxide (CO) or methane (CH4). Our hypothesis was proven to hold true in sandy-loam soil, whereas higher organic matter in peat soil was less favourable for the persistence of TGOB activity. We conclude that the energy potential of the trace gas oxidation reaction and soil nutrients both intervein in the persistence of TGOB activity.

Exploring microbial diversity and function in companion planting systems of white clover and orchard grass

Companion planting of white clover (Trifolium repens L.) with orchard grass (Dactylis glomerata L.), a famous hay grass, improves the forage quality of orchard grass. Microbiome profiling techniques can reveal the specific role of white clover companion planting with orchard grass. This study aimed to explore the microbiome distribution and gene functions of rhizosphere and non-rhizosphere soil via companion planting systems of white clover and orchard grass. From metagenomics sequencing analysis, we confirmed the significant role of white clover on soil environment modeling during companion planting with orchard grass. Twenty-eight biomarkers of rhizosphere soil organisms were identified during companion planting, including Proteobacteria, Betaproteobacteria, Flavobacteriia, and Caulobacterales. The number of gene functions of nitrogen and carbon fixation in companion planting was higher than that in single plants, indicating new functional flora for companion planting. We characterized specific rhizosphere effects, typical biomarker flora, and potential regulatory mechanisms for white clover-related companion planting by metagenomics analyses.

Opposite Effects of Planting on Antibiotic Resistomes in Rhizosphere Soil with Different Sulfamethoxazole Levels.

Achieving consensus about the rhizosphere effect on soil antibiotic resistomes is challenging due to the variability in antibiotic concentrations, sources, and the elusory underlying mechanisms. Here, we characterized the antibiotic resistomes in both the rhizosphere and bulk soils of soybean plants grown in environments with varying levels of antibiotic contamination, using sulfamethoxazole (SMX) as a model compound. We also investigated the factors influencing resistome profiles. Soybean cultivation altered the structure of antibiotic-resistant genes (ARGs) and increased their absolute abundance. However, the rhizosphere effect on the relative abundance of ARGs was dependent on SMX concentrations. At low SMX levels, the rhizosphere effect was characterized by the inhibition of antibiotic-resistant bacteria (ARBs) and the promotion of sensitive bacteria. In contrast, at high SMX levels, the rhizosphere promoted the growth of ARBs and facilitated horizontal gene transfer of ARGs. This novel mechanism provides new insights into accurately assessing the rhizosphere effect on soil antibiotic resistomes.

Regulation of drought stress on nutrient cycle and metabolism of rhizosphere microorganisms in desert riparian forest

Microbial communities in desert riparian forest ecosystems have developed unique adaptive strategies to thrive in harsh habitats shaped by prolonged exposure to abiotic stressors. However, the influence of drought stress on the functional and metabolic characteristics of soil rhizosphere microorganisms remains unknown. Therefore, this study aimed to investigate the effects of drought stress on soil biogeochemistry and metabolism and analyze the relationship between the biogeochemical cycle processes and network of differentially-expressed metabolites. Using metagenomics and metabolomics, this study explored the microbial functional cycle and differential metabolic pathways within desert riparian forests. The predominant biogeochemical cycles in the study area were the Carbon and Nitrogen cycles, comprising 78.90 % of C, N, Phosphorus, Sulfur and Iron cycles. Drought led to increased soil C fixation, reduced C degradation and methane metabolism, weakened denitrification, and decreased N fixation. Furthermore, drought can disrupt iron homeostasis and reduce its absorption. The differential metabolic pathways of drought stress include flavonoid biosynthesis, arachidonic acid metabolism, steroid hormone biosynthesis, and starch and sucrose degradation. Network analysis of functional genes and metabolism revealed a pronounced competitive relationship between the C cycle and metabolic network, whereas the Fe cycle and metabolic network promoted each other, optimizing resource utilization. Partial least squares analysis revealed that drought hindered the expression and metabolic processes and functional genes, whereas the rhizosphere environment facilitated metabolic expression and the functional genes. The rhizosphere effect primarily promoted metabolic processes indirectly through soil enzyme activities. The integrated multi-omics analysis further revealed that the effects of drought and the rhizosphere play a predominant role in shaping soil functional potential and the accumulation of metabolites. These insights deepen our comprehension of desert riparian forest ecosystems and offer strong support for the functionality of nutrient cycling and metabolite dynamics.

Root-associated bacterial communities of vegetable Brassica parachinensis enrich pollutant-degrading taxa and functions for enhancing phthalate dissipation

Soil pollution by organic contaminants like phthalates (PAEs) significantly impacts root-associated microbial community and soil health. However, the rhizosphere effects of different vegetable cultivars on root-associated bacterial communities and their effects on PAE degradation in rhizosphere are not well uncovered. Here, two cultivars (i.e., Huaguan and Lvbao) of vegetable Brassica parachinensis significantly enhanced the dissipation of di-(2-ethylhexyl) phthalate (DEHP) in rhizosphere (higher by 23.9 % - 86.8 % compared with bulk soil). PERMANOVA tests demonstrated that the bacterial community structure was significantly impacted by niche variation and DEHP pollution, but not by vegetable genotypes, with significant gradient divergences along bulk soil to (far-) rhizosphere to rhizoplane. Niche variation and DEHP pollution also remarkably influenced the ecological networks of bacterial communities in soil-root continuum with high proportions of positive microbial interaction. Furthermore, rhizosphere and DEHP pollution significantly enriched PAE-degrading functions and bacteria (e.g., Aeromicrobium and TM7a, as keystone taxa), which is beneficial for enhancing DEHP degradation. Meanwhile, metagenomic binning identified various bacterial families such as Chitinophagaceae and Nocardioidaceae capable of degrading PAEs in rhizosphere, which may play important roles in PAE biodegradation through cooperation and co-metabolism. This study advances our understandings on the promotion of vegetables for PAE removal in rhizosphere and its related mechanisms.

Comparative genomics of Metarhizium brunneum strains V275 and ARSEF 4556: unraveling intraspecies diversity.

Entomopathogenic fungi belonging to the Order Hypocreales are renowned for their ability to infect and kill insect hosts, while their endophytic mode of life and the beneficial rhizosphere effects on plant hosts have only been recently recognized. Understanding the molecular mechanisms underlying their different lifestyles could optimize their potential as both biocontrol and biofertilizer agents, as well as the wider appreciation of niche plasticity in fungal ecology. This study describes the comprehensive whole genome sequencing and analysis of one of the most effective entomopathogenic and endophytic EPF strains, Metarhizium brunneum V275 (commercially known as Lalguard Met52), achieved through Nanopore and Illumina reads. Comparative genomics for exploring intraspecies variability and analyses of key gene sets were conducted with a second effective EPF strain, M. brunneum ARSEF 4556. The search for strain- or species-specific genes was extended to M. brunneum strain ARSEF 3297 and other species of genus Metarhizium, to identify molecular mechanisms and putative key genome adaptations associated with mode of life differences. Genome size differed significantly, with M. brunneum V275 having the largest genome amongst M. brunneum strains sequenced to date. Genome analyses revealed an abundance of plant-degrading enzymes, plant colonization-associated genes, and intriguing intraspecies variations regarding their predicted secondary metabolic compounds and the number and localization of Transposable Elements. The potential significance of the differences found between closely related endophytic and entomopathogenic fungi, regarding plant growth-promoting and entomopathogenic abilities, are discussed, enhancing our understanding of their diverse functionalities and putative applications in agriculture and ecology.

Synergism of endophytic microbiota and plants promotes the removal of polycyclic aromatic hydrocarbons from the Alfalfa rhizosphere

Endophytic bacteria can promote plant growth and accelerate pollutant degradation. However, it is unclear whether endophytic consortia (Consortium_E) can stabilize colonisation and degradation. We inoculated Consortium_E into the rhizosphere to enhance endophytic bacteria survival and promote pollutant degradation. Rhizosphere-inoculated Consortium_E enhanced polycyclic aromatic hydrocarbon (PAH) degradation rates by 11.5–13.1 % compared with sole bioaugmentation and plant treatments. Stable-isotope-probing (SIP) showed that the rhizosphere-inoculated Consortium_E had the largest number of degraders (8 amplicon sequence variants). Furthermore, only microbes from Consortium_E were identified among the degraders in bioaugmentation treatments, indicating that directly participated in phenanthrene metabolism. Interestingly, Consortium_E reshaped the community structure of degraders without significantly altering the rhizosphere community structure, and strengthened the core position of degraders in the network, facilitating close interactions between degraders and non-degraders in the rhizosphere, which were crucial for ensuring stable functionality. The synergistic effect between plants and Consortium_E significantly enhanced the upregulation of aromatic hydrocarbon degradation and auxiliary degradation pathways in the rhizosphere. These pathways showed a non-significant increasing trend in the uninoculated rhizosphere compared with the control, indicating that Consortium_E primarily promotes rhizosphere effects. Our results explore the Consortium_E bioaugmentation mechanism, providing a theoretical basis for the ecological restoration of contaminated soils.

Specific root length regulated the rhizosphere effect on denitrification across distinct macrophytes

Macrophytes influence nitrogen (N) removal from wetlands. However, the specific plant traits responsible for this effect and the related microbial mechanisms remain largely unknown, especially root traits. In a mesocosm experiment, we determined the rhizosphere effect (RE) on microbial N removal processes by incubating rhizosphere and bulk soils collected from 11 macrophyte species. In addition, we examined root traits (involved in chemistry and morphology), along with examining the diversity, compositions, and abundance of bacterial communities involved in denitrification (nirS and nirK) and anammox (hzsB). Across the 11 macrophyte species, the positive RE on denitrification ranged from 66% to 412%, with an average of 194.72%. RE on denitrification was significantly and positively correlated with the recruitment of nir-type denitrifiers in the rhizosphere. We found that higher specific root length (SRL) root promoted the stronger RE, by increasing the abundance of nir-type denitrifiers and further enhancing N removal. Net N removal from water in the wetlands increased with a higher positive RE on nir-type denitrifiers. In addition, SRL significantly influenced the compositions of denitrifiers in the rhizosphere soil. We further found that the enrichment of Azospira, Bradyrhizobium, Sinorhizobium, Rhodopseudomonas, Alcaligenaceae, Bradyrhizobiaceae, and Pleomorphomonas improved the denitrification rate. These findings highlight the potential of root morphology in regulating plant–microbe interactions, thereby improving water purification.

Coupled effects of redox-active substances and microbial communities on reactive oxygen species in rhizosphere sediments of submerged macrophytes

Reactive oxygen species (ROS) play crucial roles in element cycling and pollutant dynamics, but their variations and mechanisms in the rhizosphere of submerged macrophytes are poorly investigated. This study investigated the light-dark cycle fluctuations and periodic variations in ROS, redox-active substances, and microbial communities in the rhizosphere of Vallisneria natans. The results showed sustained production and significant diurnal fluctuations in the O2•− and •OH from 27.6 ± 3.7 to 61.7 ± 3.0 μmol/kg FW and 131.0 ± 6.8 to 195.4 ± 8.7 μmol/kg FW, respectively, which simultaneously fluctuated with the redox-active substances. The ROS contents in the rhizosphere were higher than those observed in non-rhizosphere sediments over the V. natans growth period, exhibiting increasing-decreasing trends. According to the redundancy analysis results, water-soluble phenols, fungi, and bacteria were the main factors influencing ROS production in the rhizosphere, showing contribution rates of 74.0, 17.3, and 4.4 %, respectively. The results of partial least squares path modeling highlighted the coupled effects of redox-active substances and microbial metabolism. Our findings also demonstrated the degradation effect of ROS in rhizosphere sediments of submerged macrophytes. This study provides experimental evidence of ROS-related rhizosphere effects and further insights into submerged macrophytes-based ecological restoration.

Rhizosphere effects and microbial N limitations drive the root N limitations in the rhizosphere during secondary succession in a Pinus tabuliformis forest in North China.

Rhizosphere effects (REs) have recently been identified as important regulators of root and microbial nutrient acquisition and are positively involved in nutrient cycling of belowground carbon (C), nitrogen (N), and phosphorus (P). Nutrient conditions of the fine roots and soil N are likely to influence REs. Still, it is unclear how REs of soil nutrients themselves variably impact the supply of nutrients to plants in terms of the responses to soil N due to succession. In this study, we applied both fine roots and extracellular enzymes for vector analysis and stoichiometry of N:P to explore the metabolic limitations of roots and rhizospheric soil microbes and their relationships with REs across five levels of soil N (0, 5, 10, 15, and 20kg N m-2 year-1) along successional age classes of 42, 55, and 65 years in a Pinus tabuliformis forest. Overall, the metabolism of root and rhizospheric soil microbes was mediated by soil N. N limitation of roots initially decreased before increasing, whereas that of microbes demonstrated opposite trends to the N levels owing to competition for inorganic N between them by REs of NO3 --N. However, N limitations of both roots and microbes were alleviated in young stands and increased with succession after the application of N. In addition, root N limitations were manipulated by REs of three different soil N-related indicators, i.e., total N, NH4 +-N, and NO3 --N. Rhizospheric soil microbial N limitation was almost unaffected by REs due to their strong homeostasis but was an important driver in the regulation of root N limitation. Our results indicated that successional age was the most critical driver that directly and indirectly affected root N metabolism. However, the level of N application had a slight effect on root N limitation. Microbial N limitation and variations in the REs of N indicators regulated root N limitation in the rhizosphere. As a result, roots utilized REs to sequester N to alleviate N limitations. Thesefindings contribute to novel mechanistic perspectives on the sustainability of N nutrition by regulating N cycling in a system of plant-soil-microbes in the rhizosphere to adapt to global N deposition or the heterogeneous distribution of bioavailable soil N with succession.

Response of comammox Nitrospira clades A and B communities to long-term fertilization and rhizosphere effects and their relative contribution to nitrification in a subtropical paddy field of China

The recently discovered complete ammonia oxidation (comammox Nitrospira) containing clade A and clade B has further complemented our understanding of nitrification process. Nevertheless, understanding the community feature of comammox Nitrospira clades A and B and their relative contribution to nitrification in paddy rhizosphere are still in its infancy. In this study, we assessed the community diversity and structure of comammox Nitrospira clades A and B in paddy rhizosphere and bulk soils under thirty years of different fertilization strategies, i.e., non-fertilization control (CK), chemical fertilizers application (NPK), and NPK plus swine manure (NPKM), respectively. NPKM significantly increased the a-diversity (Chao1 and Shannon indices) of comammox Nitrospira clade A and altered the community structure (P < 0.05) but had little effect on clade B. A two-way analysis of variance (ANOVA) showed that the effect of long-term fertilization on soil comammox Nitrospira community and nitrification potential rate (PNR) was much greater than that of rhizosphere. Compared with NPK, soil PNR was greatly increased by 51.0% under the NPKM treatment in the rhizosphere (P < 0.05). Phylogenetic analysis showed that NPKM improved the relative abundances of sub-clade A.2.1 and sub-clade A.3.2 of the comammox clade A community, with an average increase of 212.2 and 210.4% in both rhizosphere and bulk soils relative to the NPK treatment. Soil organic matter, NH4+-N, and pH were significant soil drivers of comammox Nitrospira clades A and B community. Furthermore, linear regression and structural equation modeling clearly showed that comammox Nitrospira clade A a-diversity were significantly associated with soil PNR (P < 0.05). Our results suggest (i) that comammox Nitrospira clade A are sensitive to the organic fertilization; and (ii) that comammox Nitrospira clade A contribute more to nitrification than clade B under the long-term organic fertilized paddy soil.

Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions

Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.