Metabolites in the root exudates of groundnut change during interaction with plant growth promoting rhizobacteria in a strain-specific manner

Plant growth-promoting bacteria improve the Cd phytoremediation efficiency of soils contaminated with PE-Cd complex pollution by influencing the rhizosphere microbiome of sorghum

Composite pollution by microplastics and heavy metals poses a potential threat to the soilplant system and has received increasing attention. Plant growth-promoting bacteria (PGPB) have good application potential for the remediation of combined microplastic and heavy metal pollution, but few related studies exist. The present study employed a pot experiment to investigate the effects of inoculation with the PGPB Bacillus sp. SL-413 and Enterobacter sp. VY-1 on sorghum growth and Cd accumulation under conditions of combined cadmium (Cd) and polyethylene (PE) pollution. Cd+PE composite contamination led to a significant reduction in sorghum length and biomass due to increased toxicity. Inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 alleviated the stress caused by Cd+PE complex pollution, and the dry weight of sorghum increased by 25.7% to 46.1% aboveground and by 12.3% to 45.3% belowground. Bacillus sp. SL-413 and Enterobacter sp. VY-1 inoculation increased the Cd content and accumulation in sorghum and improved the phytoremediation efficiency of Cd. The inoculation treatment effectively alleviated the nutrient stress caused by the reduction in soil mineral nutrients due to Cd+PE composite pollution. The composition of the soil bacterial communities was also affected by the Cd, Cd+PE and bacterial inoculation treatments, which affected the diversity of the soil bacterial communities. Network analyses indicated that bacterial inoculation regulated the interaction of rhizospheric microorganisms and increased the stability of soil bacterial communities. The Mantel test showed that the changes in the soil bacterial community and function due to inoculation with Bacillus sp. SL-413 and Enterobacter sp. VY-1 were important factors influencing sorghum growth and Cd remediation efficiency. The results of this study will provide new evidence for the research on joint plantmicrobe remediation of heavy metal and microplastic composite pollution.

The Function of Root Exudates in the Root Colonization by Beneficial Soil Rhizobacteria

Soil-beneficial microbes in the rhizosphere play important roles in improving plant growth and health. Root exudates play key roles in plant-microbe interactions and rhizobacterial colonization. This review describes the factors influencing the dynamic interactions between root exudates and the soil microbiome in the rhizosphere, including plant genotype, plant development, and environmental abiotic and biotic factors. We also discuss the roles of specific metabolic mechanisms, regulators, and signals of beneficial soil bacteria in terms of colonization ability. We highlight the latest research progress on the roles of root exudates in regulating beneficial rhizobacterial colonization. Organic acids, amino acids, sugars, sugar alcohols, flavonoids, phenolic compounds, volatiles, and other secondary metabolites are discussed in detail. Finally, we propose future research objectives that will help us better understand the role of root exudates in root colonization by rhizobacteria and promote the sustainable development of agriculture and forestry.

Bioinoculants as a means of increasing crop tolerance to drought and phosphorus deficiency in legume-cereal intercropping systems

Ensuring plant resilience to drought and phosphorus (P) stresses is crucial to support global food security. The phytobiome, shaped by selective pressures, harbors stress-adapted microorganisms that confer host benefits like enhanced growth and stress tolerance. Intercropping systems also offer benefits through facilitative interactions, improving plant growth in water- and P-deficient soils. Application of microbial consortia can boost the benefits of intercropping, although questions remain about the establishment, persistence, and legacy effects within resident soil microbiomes. Understanding microbe- and plant-microbe dynamics in drought-prone soils is key. This review highlights the beneficial effects of rhizobacterial consortia-based inoculants in legume-cereal intercropping systems, discusses challenges, proposes a roadmap for development of P-solubilizing drought-adapted consortia, and identifies research gaps in crop-microbe interactions.

Comparative Functional Genome Analysis Reveals the Habitat Adaptation and Biocontrol Characteristics of Plant Growth-Promoting Bacteria in NCBI Databases

Plant growth-promoting bacteria (PGPB) are a group of beneficial microorganisms that include 60 bacterial genera, such as Bacillus, Pseudomonas, and Burkholderia, which widely colonize plant leaves and soil, promote plant growth, and/or inhibit pathogen infection. However, the genetic factors underpinning adaptation of PGPB to plant leaves and soil remain poorly understood. In this study, we performed a comparative functional genome analysis approach to investigate the functional genes of 195 leaf-associated (LA) and 283 soil-associated (SA) PGPB strains and their roles in adapting to their environment, using 95 strains from other-associated (OA) environmental habitats with growth-promoting or antimicrobial functions as negative controls. Comparison analysis of the enrichment of nonredundant (NR) protein sequence databases showed that cytochrome P450, DNA repair, and motor chemotaxis genes were significantly enriched in LA PGPB strains related to environmental adaptation, while cell wall-degrading enzymes, TetR transcriptional regulatory factors, and sporulation-related genes were highly enriched in SA PGPB strains. Additionally, analysis of carbohydrate-active enzymes demonstrated that glycosyltransferases (GTs) and glycoside hydrolases (GHs) were abundant families in all PGPB strains, which is in favor of plant growth, and enriched in SA PGPB strains. Except for most Bacillus strains, SA PGPB genomes contained significantly more secondary metabolism clusters than LA PGPB. Most LA PGPB contained hormone biosynthesis genes, which may contribute to plant growth promotion, while SA PGPB harbored numerous carbohydrate and antibiotic metabolism genes. In summary, this study further deepens our understanding of the habitat adaptation and biocontrol characteristics of LA and SA PGPB strains. IMPORTANCE Plant growth-promoting bacteria (PGPB) are essential for the effectiveness of biocontrol agents in plant phyllosphere and rhizosphere. However, little is known about the ecological adaptation of PGPB to different habitats. In this study, comparative functional genome analysis of leaf-associated (LA), soil-associated (SA), and other-associated (OA) PGPB strains was performed. We found that genes related to the metabolism of hormones were enriched in LA PGPB. Carbohydrate and antibiotic metabolism genes were enriched in SA PGPB, which likely facilitated their adaptation to the plant growth environment. Our findings provide genetic insights on LA and SA PGPB strains' ecological adaptation and biocontrol characteristics.

Encapsulated plant growth regulators and associative microorganisms: Nature-based solutions to mitigate the effects of climate change on plants

Over the past decades, the atmospheric CO₂ concentration and global average temperature have been increasing, and this trend is projected to soon become more severe. This scenario of climate change intensifies abiotic stress factors (such as drought, flooding, salinity, and ultraviolet radiation) that threaten forest and associated ecosystems as well as crop production. These factors can negatively affect plant growth and development with a consequent reduction in plant biomass accumulation and yield, in addition to increasing plant susceptibility to biotic stresses. Recently, biostimulants have become a hotspot as an effective and sustainable alternative to alleviate the negative effects of stresses on plants. However, the majority of biostimulants have poor stability under environmental conditions, which leads to premature degradation, shortening their biological activity. To solve these bottlenecks, micro- and nano-based formulations containing biostimulant molecules and/or microorganisms are gaining attention, as they demonstrate several advantages over their conventional formulations. In this review, we focus on the encapsulation of plant growth regulators and plant associative microorganisms as a strategy to boost their application for plant protection against abiotic stresses. We also address the potential limitations and challenges faced for the implementation of this technology, as well as possibilities regarding future research.

Certain Tomato Root Exudates Induced by Pseudomonas stutzeri NRCB010 Enhance Its Rhizosphere Colonization Capability

Plant growth-promoting rhizobacteria (PGPR) can colonize plant root surfaces or form biofilms to promote plant growth and enhance plant resistance to harsh external environments. However, plant-PGPR interactions, especially chemical signaling molecules, are poorly understood. This study aimed to gain an in-depth understanding of the rhizosphere interaction mechanisms between PGPR and tomato plants. This study found that inoculation with a certain concentration of Pseudomonas stutzeri significantly promoted tomato growth and induced significant changes in tomato root exudates. Furthermore, the root exudates significantly induced NRCB010 growth, swarming motility, and biofilm formation. In addition, the composition of the root exudates was analyzed, and four metabolites (methyl hexadecanoate, methyl stearate, 2,4-di-tert-butylphenol, and n-hexadecanoic acid) significantly related to the chemotaxis and biofilm formation of NRCB010 were screened. Further assessment showed that these metabolites positively affected the growth, swarming motility, chemotaxis, or biofilm formation of strain NRCB010. Among these, n-hexadecanoic acid induced the most remarkable growth, chemotactic response, biofilm formation, and rhizosphere colonization. This study will help develop effective PGPR-based bioformulations to improve PGPR colonization and crop yields.

The peanut root exudate increases the transport and metabolism of nutrients and enhances the plant growth-promoting effects of burkholderia pyrrocinia strain P10

BACKGROUND

Burkholderia pyrrocinia strain P10 is a plant growth-promoting rhizobacterium (PGPR) that can substantially increase peanut growth. However, the mechanisms and pathways involved in the interaction between B. pyrrocinia P10 and peanut remain unclear. To clarify complex plant-PGPR interactions and the growth-promoting effects of PGPR strains, the B. pyrrocinia P10 transcriptome changes in response to the peanut root exudate (RE) were elucidated and the effects of RE components on biofilm formation and indole-3-acetic acid (IAA) secretion were analyzed.

RESULTS

During the early interaction phase, the peanut RE enhanced the transport and metabolism of nutrients, including carbohydrates, amino acids, nitrogen, and sulfur. Although the expression of flagellar assembly-related genes was down-regulated, the expression levels of other genes involved in biofilm formation, quorum sensing, and Type II, III, and VI secretion systems were up-regulated, thereby enabling strain P10 to outcompete other microbes to colonize the peanut rhizosphere. The peanut RE also improved the plant growth-promoting effects of strain P10 by activating the expression of genes associated with siderophore biosynthesis, IAA production, and phosphorus solubilization. Additionally, organic acids and amino acids were identified as the dominant components in the peanut RE. Furthermore, strain P10 biofilm formation was induced by malic acid, oxalic acid, and citric acid, whereas IAA secretion was promoted by the alanine, glycine, and proline in the peanut RE.

CONCLUSION

The peanut RE positively affects B. pyrrocinia P10 growth, while also enhancing colonization and growth-promoting effects during the early interaction period. These findings may help to elucidate the mechanisms underlying complex plant-PGPR interactions, with potential implications for improving the applicability of PGPR strains.

Dynamic variation of Paris polyphylla root-associated microbiome assembly with planting years

P. polyphylla selectively enriches beneficial microorganisms to help their growth. Paris polyphylla (P. polyphylla) is an important perennial plant for Chinese traditional medicine. Uncovering the interaction between P. polyphylla and the related microorganisms would help to utilize and cultivate P. polyphylla. However, studies focusing on P. polyphylla and related microbes are scarce, especially on the assembly mechanisms and dynamics of the P. polyphylla microbiome. High-throughput sequencing of the 16S rRNA genes was implemented to investigate the diversity, community assembly process and molecular ecological network of the bacterial communities in three root compartments (bulk soil, rhizosphere, and root endosphere) across three years. Our results demonstrated that the composition and assembly process of the microbial community in different compartments varied greatly and were strongly affected by planting years. Bacterial diversity was reduced from bulk soils to rhizosphere soils to root endosphere and varied over time. Microorganisms benefit to plants was selectively enriched in P. polyphylla roots as was its core microbiome, including Pseudomonas, Rhizobium, Steroidobacter, Sphingobium and Agrobacterium. The network's complexity and the proportion of stochasticity in the community assembly process increased. Besides, nitrogen metabolism, carbon metabolism, phosphonate and phosphinate metabolism genes in bulk soils increased over time. These findings suggest that P. polyphylla exerts a selective effect to enrich the beneficial microorganisms and proves the sequential increasing selection pressure with P. polyphylla growth. Our work adds to the understanding of the dynamic processes of plant-associated microbial community assembly, guides the selection and application timing of P. polyphylla-associated microbial inoculants and is vital for sustainable agriculture.

Utilization of isolated microbe and treated wastewater for enhanced growth of Jatropha curcas for bioremediation of fly ash amended soil

The generation of Fly Ash (FA) waste is continuously piling up with the increasing energy demand. Recent research is focused towards reutilizing this fly ash waste through bioremediation practices. But fly ash retards the growth of plants and holds back to support the bioremediation process due to a deficiency of essential main nutrients. The present research envisages overcoming this problem by providing a novel concept of inducing isolated microbes and treated wastewater which provides necessary nutrients and promotes better plant growth and metal extraction. A pot experimental study was executed with treatments T₁ (FA amended soil), T₂ (FA with isolated microbe), and T₃ (FA with microbes and treated wastewater). As an outcome of the present research, T₃ gained relatively higher morphological characteristics viz. Leaf area (29.8%), absolute growth rate (61.7%), plastochron index (18.6%), biomass yield (47.3%) and enhanced metal extraction for Fe (34.4%), Al (27.1%), Mn (72.0%), Zn (17.5%) in comparison to the control. Treatment T₃ also gained higher Remediation Efficiency (RE) and Bio-Concentration Factor (BCF) values for Al, Fe, and Mn. The involvement of nutrients via treated wastewater energizes the process mechanism and increases the working zone for the microbes thereby, enhancing the bioremediation.

The effects of allelochemicals from root exudates of Flaveria bidentis on two Bacillus species

To determine the allelopathic effects of root exudates from Flaveria bidentis on function of Bacillus, pot experiment was used to collect root exudates from living plants and test its allelopathic effects on function of Bacillus frigoritolerans and Bacillus megaterium, which were two dominant bacteria in the rhizosphere soil of F. bidentis. To obtain the allelopathic substances, the root exudates were successively extracted by N-hexane, dichloromethane, ethyl acetate, and N-butanol, and their allelopathic effects were tested. The results showed that B. frigoritolerans and B. megaterium considerably increased the concentration of available phosphorus and nitrogen, respectively, when the soil was treated with different concentrations of root exudates. Among the four organic solvent extracts, dichloromethane extracts significantly increased the abundances of B. frigoritolerans and B. megaterium and promoted their nitrogen-fixing and phosphate-solubilizing abilities. Phenol was detected in dichloromethane extracts by gas chromatograph-mass spectrometer (GC-MS). Meanwhile, phenol promoted the ability to fix nitrogen of B. megaterium and its growth by increasing the soil available nitrogen concentration, but phenol promoted the ability to solubilize phosphate of B. frigoritolerans only in 0.1mg/mL concentration. Therefore, phenol was an allelochemicals in the root exudates of F. bidentis that affects the growth and activities of B. megaterium.

Bacillus for Plant Growth Promotion and Stress Resilience: What Have We Learned?

The rhizosphere is a thin film of soil that surrounds plant roots and the primary location of nutrient uptake, and is where important physiological, chemical, and biological activities are occurring. Many microbes invade the rhizosphere and have the capacity to promote plant growth and health. Bacillus spp. is the most prominent plant growth promoting rhizobacteria due to its ability to form long-lived, stress-tolerant spores. Bacillus-plant interactions are driven by chemical languages constructed by a wide spectrum of metabolites and lead to enhanced plant growth and defenses. Thus, this review is a synthesis and a critical assessment of the current literature on the application of Bacillus spp. in agriculture, highlighting gaps that remain to be explored to improve and expand on the Bacillus-based biostimulants. Furthermore, we suggest that omics sciences, with a focus on metabolomics, offer unique opportunities to illuminate the chemical intercommunications between Bacillus and plants, to elucidate biochemical and molecular details on modes of action of Bacillus-based formulations, to generate more actionable insights on cellular and molecular events that explain the Bacillus-induced growth promotion and stress resilience in plants.

A dynamic rhizosphere interplay between tree roots and soil bacteria under drought stress

Root exudates are thought to play an important role in plant-microbial interactions. In return for nutrition, soil bacteria can increase the bioavailability of soil nutrients. However, root exudates typically decrease in situations such as drought, calling into question the efficacy of solvation and bacteria-dependent mineral uptake in such stress. Here, we tested the hypothesis of exudate-driven microbial priming on Cupressus saplings grown in forest soil in custom-made rhizotron boxes. A 1-month imposed drought and concomitant inoculations with a mix of Bacillus subtilis and Pseudomonas stutzeri, bacteria species isolated from the forest soil, were applied using factorial design. Direct bacteria counts and visualization by confocal microscopy showed that both bacteria associated with Cupressus roots. Interestingly, root exudation rates increased 2.3-fold with bacteria under drought, as well as irrigation. Forty-four metabolites in exudates were significantly different in concentration between irrigated and drought trees, including phenolic acid compounds and quinate. When adding these metabolites as carbon and nitrogen sources to bacterial cultures of both bacterial species, eight of nine metabolites stimulated bacterial growth. Importantly, soil phosphorous bioavailability was maintained only in inoculated trees, mitigating drought-induced decrease in leaf phosphorus and iron. Our observations of increased root exudation rate when drought and inoculation regimes were combined support the idea of root recruitment of beneficial bacteria, especially under water stress.

The soil surrounding the roots of trees, termed the rhizosphere, is full of bacteria and other communities of microorganisms. Trees secrete organic compounds in to the soil which are thought to influence the behavior of bacteria in the rhizosphere. Specifically, these root secretions, or ‘exudates’, attract and feed soil bacteria, which, in return, release nutrients that benefit the tree.

In 2020, a group of researchers found that some trees in the Mediterranean forest produce more exudates during the long dry season. This suggests that the compounds secreted by roots may help trees to tolerate stress conditions, such as drought. To test this hypothesis, Oppenheimer-Shaanan et al. – including some of the researchers involved in the 2020 study – grew young Cupressus sempervirens conifer trees in drought conditions that starved them of the nutrients phosphorous and iron.

Each tree was planted in a custom-built box which allowed easy access to roots growing in the soil. Two species of bacteria from the forest soil C. sempervirens trees naturally live in were then added to the soil in each box. Microscopy revealed that both species of bacteria, which had been tagged with fluorescent markers, were attracted to the roots of the trees, boosting the bacterial community in the rhizosphere.

Oppenheimer-Shaanan et al. found that the recruitment of the two bacterial species caused the rate at which exudates were secreted from the roots to increase. Compounds in the exudate stimulated the bacteria to grow. Ultimately, levels of phosphorous and iron in the leaves of the starved trees increased when in the presence of these soil bacteria. This suggests that bacteria in the rhizosphere helps trees to survive when they are under stress and have low levels of water.

These findings provide further evidence that plants and bacteria can live together in symbiosis and benefit one another. This could have important implications for forest ecology and potentially how trees are grown in orchards and gardens. For example, specific bacteria and organic compounds in the rhizosphere may be able to improve tree health. However, further work is needed to investigate whether the exudate compounds identified in this study are found more widely in nature.

Root Exudates: Mechanistic Insight of Plant Growth Promoting Rhizobacteria for Sustainable Crop Production

The breaking silence between the plant roots and microorganisms in the rhizosphere affects plant growth and physiology by impacting biochemical, molecular, nutritional, and edaphic factors. The components of the root exudates are associated with the microbial population, notably, plant growth-promoting rhizobacteria (PGPR). The information accessible to date demonstrates that PGPR is specific to the plant's roots. However, inadequate information is accessible for developing bio-inoculation/bio-fertilizers for the crop in concern, with satisfactory results at the field level. There is a need to explore the perfect candidate PGPR to meet the need for plant growth and yield. The functions of PGPR and their chemotaxis mobility toward the plant root are triggered by the cluster of genes induced by the components of root exudates. Some reports have indicated the benefit of root exudates in plant growth and productivity, yet a methodical examination of rhizosecretion and its consequences in phytoremediation have not been made. In the light of the afore-mentioned facts, in the present review, the mechanistic insight and recent updates on the specific PGPR recruitment to improve crop production at the field level are methodically addressed.

Alterations of Primary Metabolites in Root Exudates of Intercropped Cajanus cajan-Zea mays Modulate the Adaptation and Proteome of Ensifer (Sinorhizobium) fredii NGR234

Legume-cereal intercropping systems, in the context of diversity, ecological function, and better yield have been widely studied. Such systems enhance nutrient phytoavailability by balancing root-rhizosphere interactions. Root exudates (RE) play an important role in the rhizospheric interactions of plant-plant and/or plant-microbiome interaction. However, the influence of the primary metabolites of RE on plant-rhizobia interactions in a legume-cereal intercrop system is not known. To understand the plant communication with rhizobia, Cajanus cajan-Zea mays intercropped plants and the broad host range legume nodulating Ensifer fredii NGR234 as the model plants and rhizobium used respectively. A metabolomics-based approach revealed a clear separation between intercropped and monocropped RE of the two plants. Intercropped C. cajan showed an increase in the myo-inositol, and proline, while intercropped Z. mays showed enhanced galactose, D-glucopyranoside, and arginine in the RE. Physiological assays of NGR234 with the RE of intercropped C. cajan exhibited a significant enhancement in biofilm formation, while intercropped Z. mays RE accelerated the bacterial growth in the late log phase. Further, using label-free proteomics, we identified a total of 2570 proteins of NGR234 covering 50% annotated protein sequences upon exposure to Z. mays RE. Furthermore, intercropped Z. mays RE upregulated bacterioferritin comigratory protein (BCP), putative nitroreductase, IlvD, LeuC, D (branched-chain amino acid proteins), and chaperonin proteins GroEL2. Identification offered new insights into the metabolome of the legume-cereal intercrop and proteome of NGR234-Z. mays interactions that underline the new molecular candidates likely to be involved in the fitness of rhizobium in the intercropping system.

The genus Caulobacter and its role in plant microbiomes

Recent omics approaches have revealed the prevalent microbial taxa that constitute the microbiome of various plant species. Across global scales and environmental conditions, strains belonging to the bacterial genus Caulobacter have consistently been found in association with various plant species. Aligned with agroecological relevance and biotechnological advances, many scientific communications have demonstrated that several Caulobacter strains (spanning several Caulobacter species) harbor the potential to enhance plant biomass for various plant species ranging from Arabidopsis to Citrullus and Zea mays. In the past several years, co-occurrence data have driven mechanistically resolved communications about select Caulobacter-plant interactions. Given the long-standing history of Caulobacter as a model organism for cell cycle regulation, genetic studies, and the prevalence of Caulobacter species in various plant microbiomes, the genus Caulobacter offers researchers a unique opportunity to leverage for investigating plant-microbe interactions and realizing targeted biotechnological applications. In this review, recent developments regarding Caulobacter-plant interactions are presented in terms of model utility for future biotechnological investigations.

Effects of ectomycorrhizal fungus bolete identity on the community assemblages of endofungal bacteria

Ectomycorrhiza-associated bacteria, especially endofungal bacterial microbiota (EBM) in the fruiting body, play important roles in driving the establishment and function of ectomycorrhizae. However, the influence of ectomycorrhizal fungus bolete identity on their EBM is still unclear. We analysed the EBM of three different bolete fruiting body species on Thousand Island Lake, including Tylopilus felleus, Tylopilus areolatus and Boletus queletii, and compared them with their corresponding mycosphere soil bacterial microbiota by high-throughput sequencing. The EBM was classified into Bacillus, Pseudomonas, Burkholderia and Stenotrophomonas genera. Proteobacteria, Bacteroidetes and Acidobacteria were predominant in the EBM of bolete fruiting bodies as well as their mycosphere soil, while Firmicutes was significantly higher in the EBM. Moreover, the core microbiome (342 operational taxonomic units) of the EBM was shared among the three bolete fungal species. The relative abundances of gene families related to cell cycle control and nucleotide, coenzyme and lipid metabolism were significantly higher in the EBM than in the corresponding mycosphere soil bacterial microbiota, but there was no difference among the three different boletes. The results suggested that the host identity of ectomycorrhizal fungus boletes could affect the EBM, which might be mainly due to the selection of host fungi for the different functional EBM needed.

Multiple analysis of root exudates and microbiome in rice (Oryza sativa) under low P conditions

Plants release various metabolites from roots and root exudates contribute to differences in stress tolerance among plant species. Plant and soil microbes have complex interactions that are affected by biotic and abiotic factors. The purpose of this study was to examine the differences in metabolites in root exudates of rice (Oryza sativa) cultivars and their correlation with bacterial populations in the rhizosphere. Two rice cultivars (O. sativa cv. Akamai and O. sativa cv. Koshihikari) were grown in soils fertilized with 0 g P kg^-1 (- P) or 4.8 g P kg^-1 (+ P). Root exudates and root-attached soil were collected at 13 and 20 days after transplanting (DAT) and their metabolites and bacterial community structure were determined. The exudation of proline, serine, threonine, valine and 4-coumarate were increased under low P conditions in both cultivars. There was a positive correlation between the concentration of pantothenate in root exudates and the representation of members of the genera Clostridium and Sporosarcina, which were negatively correlated with root dry weight. Gracilibacter, Opitutus, Pelotomaculum, Phenylobacterium and Oxobacter were positively correlated with root dry weight and presence of allantoin, 2-aminobtyrate and GlcNac. This study provides new information about the response of plants and rhizosphere soil bacteria to low P conditions.

Multiple strategies of plant colonization by beneficial endophytic Enterobacter sp. SA187

Although many endophytic plant growth-promoting rhizobacteria have been identified, relatively little is still known about the mechanisms by which they enter plants and promote plant growth. The beneficial endophyte Enterobacter sp. SA187 was shown to maintain the productivity of crops in extreme agricultural conditions. Here we present that roots of its natural host (Indigofera argentea), alfalfa, tomato, wheat, barley and Arabidopsis are all efficiently colonized by SA187. Detailed analysis of the colonization process in Arabidopsis showed that colonization already starts during seed germination, where seed-coat mucilage supports SA187 proliferation. The meristematic zone of growing roots attracts SA187, allowing epiphytic colonization in the elongation zone. Unlike primary roots, lateral roots are significantly less epiphytically colonized by SA187. Root endophytic colonization was found to occur by passive entry of SA187 at lateral-root bases. However, SA187 also actively penetrates the root epidermis by enzymatic disruption of plant cell wall material. In contrast to roots, endophytic colonization of shoots occurs via stomata, whereby SA187 can actively re-open stomata similarly to pathogenic bacteria. In summary, several entry strategies were identified that allow SA187 to establish itself as a beneficial endophyte in several plant species, supporting its use as a plant growth-promoting bacterium in agriculture systems.

Plant-Microbiome Crosstalk: Dawning from Composition and Assembly of Microbial Community to Improvement of Disease Resilience in Plants

Plants host diverse but taxonomically structured communities of microorganisms, called microbiome, which colonize various parts of host plants. Plant-associated microbial communities have been shown to confer multiple beneficial advantages to their host plants, such as nutrient acquisition, growth promotion, pathogen resistance, and environmental stress tolerance. Systematic studies have provided new insights into the economically and ecologically important microbial communities as hubs of core microbiota and revealed their beneficial impacts on the host plants. Microbiome engineering, which can improve the functional capabilities of native microbial species under challenging agricultural ambiance, is an emerging biotechnological strategy to improve crop yield and resilience against variety of environmental constraints of both biotic and abiotic nature. This review highlights the importance of indigenous microbial communities in improving plant health under pathogen-induced stress. Moreover, the potential solutions leading towards commercialization of proficient bioformulations for sustainable and improved crop production are also described.

Biochemical characteristics and inoculation effects of multi-trait plant growth-promoting rhizobacteria on upland rice (Oryza sativa L. cv PSB Rc23) seedling growth

Plant growth-promoting rhizobacteria (PGPR) are known to stimulate plant growth because of their versatility in nutrient transformation. However, the success of PGPR inoculation depends not only on their ability to promote plant growth but also on their capacity to metabolize substrates that can be used as energy for the development and survival of the crops. Given the important influence of seed germination and vigor on crop yield, this study investigated the biochemical characteristics and effectiveness of multi-trait PGPR isolates in enhancing upland rice seedling growth and vigor. Biochemical identification was done using Biolog GEN III Microbial Identification System. Isolates were characterized based on their ability to metabolize all major classes of biochemicals in the carbon source utilization and chemical sensitivity assays. Identified rhizobacterial isolates were tested in vitro to evaluate their inoculation effects on the growth of PSB Rc23 upland rice seedlings. Biochemical identification results showed that rhizobacterial isolates have extensive metabolic activities in a wide range of carbon sources. Inoculation effects revealed that isolate IBBw_1a was the most effective in enhancing root length and vigor index of rice seedlings in vitro, yielding a significant increase of 60% and 53%, respectively, over the uninoculated control. This study suggests that rhizobacterial isolates from upland rice may have commercial significance to improve seedling growth and vigor. These isolates will undergo a further assessment of their effectiveness in actual upland rice field conditions as they were already proven effective growth promoters in laboratory and screenhouse conditions. Such future activity can uncover their efficacy as potential biofertilizers in the actual soil environment.

Biological characteristics and salt-tolerant plant growth-promoting effects of an ACC deaminase-producing Burkholderia pyrrocinia strain isolated from the tea rhizosphere

Plant growth-promoting rhizobacteria that produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase can promote plant growth and enhance abiotic stress tolerance. In this study, Burkholderia pyrrocinia strain P10, with an ACC deaminase activity of 33.01-µmol/h/mg protein, was isolated from the tea rhizosphere and identified based on morphological, biochemical, and molecular characteristics. In addition to its ACC deaminase activity at pH 5.0-9.0 and in response to 5% NaCl and 20% polyethylene glycol, strain P10 can also solubilize phosphorus compounds, produce indole-3-acetic acid, and secrete siderophores. Pot experiments revealed that strain P10 can significantly enhance peanut seedling growth under saline conditions (100- and 170-mmol/L NaCl). Specifically, it increased the fresh weight and root length of plants by 90.12% and 79.22%, respectively, compared with high-salt stress. These results provide new insights into the biological characteristics of Burkholderia pyrrocinia, which may be useful as a bio-fertilizer.

Cadmium Immobilization in the Rhizosphere and Plant Cellular Detoxification: Role of Plant-Growth-Promoting Rhizobacteria as a Sustainable Solution

Food is the major cadmium (Cd)-exposure pathway from agricultural soils to humans and other living entities and must be reduced in an effective way. A plant can select beneficial microbes, like plant-growth-promoting rhizobacteria (PGPR), depending upon the nature of root exudates in the rhizosphere, for its own benefits, such as plant growth promotion as well as protection from metal toxicity. This review intends to seek out information on the rhizo-immobilization of Cd in polluted soils using the PGPR along with plant nutrient fertilizers. This review suggests that the rhizo-immobilization of Cd by a combination of PGPR and nanohybrid-based plant nutrient fertilizers would be a potential and sustainable technology for phytoavailable Cd immobilization in the rhizosphere and plant cellular detoxification, by keeping the plant nutrition flow and green dynamics of plant nutrition and boosting the plant growth and development under Cd stress.

Bacillus subtilis biofertilizer mitigating agricultural ammonia emission and shifting soil nitrogen cycling microbiomes

Excessive ammonia (NH₃) emitted from nitrogen fertilizer application in farmland have caused serious disturbance to global environment, including reduction of visibility, formation of regional haze, and increase of nitrogen deposition. Application of biofertilizer has been considered as an effective approach for soil improvement and agriculture sustainability. In this study, a field experiment was conducted to evaluate the potential of B. subtilis biofertilizer on mitigating NH₃ volatilization and to investigate the underlying mechanisms. Compared with organic fertilizer, the incorporation of B. subtilis biofertilizer reduced NH₃ volatilization by up to 44%. Moreover, the application of B. subtilis biofertilizer reduced the abundance of ureC gene, and increased the abundance of functional genes (bacterial amoA and comammox amoA) and ammonia-oxidizing bacteria (AOB). This indicated that the conversion of fertilizer nitrogen to NH₄⁺-N was decreased and the nitrification process was increased. In brief, the application of B. subtilis biofertilizer reduced the "source" and increased the "sink" of NH₄⁺-N, thus reducing the retention of NH₄⁺-N in alkaline soil, and mitigating NH₃ volatilization. These results indicated that B. subtilis biofertilizer is an effective control strategy for agricultural NH₃ emission, maintaining high crop yield and mitigating environmental disturbance.

Rhizosphere engineering through exogenous growth-regulating small molecules improves the colonizing efficiency of a plant growth-promoting rhizobacterium in rice

Enhancing the rhizosphere colonization and persistence of plant growth-promoting rhizobacteria (PGPR) is necessary for maximizing PGPR-mediated benefits for crop growth and fitness in environmentally friendly agriculture. In the present investigation, we attempted manipulation of the rice rhizosphere by spraying of low molecular weight plant-regulating metabolites on the foliage of rice plants to in turn enhance the colonizing efficiency of soil-inoculated PGPR strain. The green fluorescent protein gene-tagged rhizobacterial strain, Pseudomonas chlororaphis ZSB15-M2, was inoculated in sterile plant growth medium (vermiculite coco peat mixture) and non-autoclaved agricultural soil. We sprayed different plant growth-regulating small molecules on the foliage of rice seedlings and monitored the colonizing efficiency of ZSB15-M2 in the rice rhizosphere. Among the chemicals assessed, salicylic acid (SA) at 1 mM or Corynebacterium glutamicum cell extract (CGCE, 0.2% w/v) or Saccharomyces cerevisiae cell extract (SCCE, 0.2% w/v) showed a tenfold increase in rhizosphere colony-forming units of ZSB15-M2 compared to control with a significant decline in non-rhizosphere bulk soil population. Foliar spray of CGCE enhanced soil organic carbon, microbial biomass carbon and soil protein by 21.86%, 9.68% and 11.57% respectively in the rice rhizosphere as compared to mock control. Additionally, CGCE spray enhanced the key soil enzymes, viz., dehydrogenase and acid- and alkaline phosphatase in the rhizosphere ranging 15-36%. The cumulative effect of this engineered rhizosphere resulted in the elevation of nitrogen, phosphorus, potassium and zinc availability by 21.83%, 28.83%, 23.95% and 61.94%, respectively, in rice rhizosphere as compared to control. On the other hand, SCCE and SA spray had an equal influence on the rhizosphere's biological attributes, which is lower than that of GCGE and higher than that of mock control. From the study, we propose that the aboveground management of rice with microbial-based small molecules will modulate the rice rhizosphere to attract more beneficial PGPR-based inoculants, thus improving the crop and soil health.