Ensifer adhaerens strain OV14 seed application enhances Triticum aestivum L. and Brassica napus L. development

Given the challenges imposed by climate change and societal challenges, the European Union established ambitious goals as part of its Farm to Fork (F2F) strategy. Focussed on accelerating the transition to systems of sustainable food production, processing and consumption, a key element of F2F is to reduce the use of fertilisers by at least 20% and plant protection products by up to 50% by 2030. In recent years, a substantial body of research has highlighted the potential impact of microbial-based applications to support crop production practices through both biotic/abiotic stresses via maintaining or even improving yields and reducing reliance on intensive chemical inputs. Here, we have characterised the ability of a new soil-borne free-living bacterium strain Ensifer adhaerens OV14 (EaOV14) to significantly enhance crop vigour index by up to 50% for monocot (wheat, Triticum aestivum L., p < 0.0001) and by up to 40% for dicot (oilseed rape, Brassica napus L., p < 0.0001) species under in-vitro conditions (n = 360 seedlings/treatment). The beneficial effect was further studied under controlled glasshouse growing conditions (n = 60 plants/treatment) where EaOV14 induced significantly increased seed yield of spring oilseed rape compared to the controls (p < 0.0001). Moreover, using bespoke rhizoboxes, enhanced root architecture (density, roots orientation, roots thickness etc.) was observed for spring oilseed rape and winter wheat, with the median number of roots 55% and 33% higher for oilseed rape and wheat respectively, following EaOV14 seed treatment compared to the control. In addition, EaOV14 treatment increased root tip formation and root volume, suggesting the formation of a more robust root system architecture post-seed treatment. However, like other microbial formulations, the trade-offs associated with field translation, such as loss or limited functionality due to inoculum formulation or environmental distress, need further investigation. Moreover, the delivery method requires further optimisation to identify the optimal inoculum formulation that will maximise the expected beneficial impact on yield under field growing conditions.

The alleviation of salt stress on rice through increasing photosynthetic capacity, maintaining redox homeostasis and regulating soil enzyme activities by Enterobacter sp. JIV1 assisted with putrescine

The detrimental impact of soil salinization on crop productivity and agricultural economy has garnered significant attention. A rhizosphere bacterium with favorable salt tolerance and plant growth-promoting (PGP) functions was isolated in this work. The bacterium was identified as Enterobacter through 16 S rDNA sequencing analysis and designated as Enterobacter sp. JIV1. Interestingly, the presence of putrescine (Put), which had been shown to contribute in reducing abiotic stress damage to plants, significantly promoted strain JIV1 to generate 1-aminocyclopropane-1-carboxylic (ACC) deaminase, dissolve phosphorus and secrete indole-3-acetic acid (IAA). However, the synergy of plant growth promoting rhizobacteria (PGPR) and Put in improving plant salt resistance has not been extensively studied. In this study, strain JIV1 and exogenous Put effectively mitigated the inhibitory impact of salt stress simulated by 200 mM NaCl on rice (Oryza sativa L.) growth. The chlorophyll accumulation, photosynthetic efficiency and antioxidant capacity of rice were also significantly strengthened. Notably, the combined application of strain JIV1 and Put outperformed individual treatments. Moreover, the co-addition of strain JIV1 and Put increased soil protease and urease activities by 451.97% and 51.70% compared to that of salt treatment group. In general, Put-assisted PGPR JIV1 provides a new perspective on alleviating the salt-induced negative impacts on plants.

Erythrobacter oryzae sp. nov., isolated from rice paddy soil

Two novel bacterial strains, designated as COR-2T and CR-8, were isolated from paddy soil. These isolates were aerobic, Gram-stain-negative, non-spore-forming, non-motile, rod-shaped, and formed orange-coloured colonies. Phylogenetic analysis based on 16S rRNA gene sequences showed that two strains formed a clear phylogenetic lineage with the genus Erythrobacter. Strains COR-2T and CR-8 showed 99.9 % 16S rRNA gene sequence similarity. Both strains had the highest 16S rRNA gene similarity of 99.1-99.7 % to Erythrobacter colymbi TPW-24T, Erythrobacter donghaensis SW-132T and Erythrobacter tepidarius DSM 10594T, respectively. The genome of strain COR-2T comprised 3 559 918 bp and the genomic DNA G + C content was 67.7 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain COR-2T and its closely related species of the genus Erythrobacter were 79.3-85.5% and 24.1-29.1 %, respectively. The major respiratory quinone was Q-10, while the major fatty acids were C18 : 1  ω7c and C17 : 1  ω6c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids and eight unidentified lipids. Based on phylogenetic and phenotypic considerations, the two strains [COR-2T (type strain; = KACC 22941T=JCM 35529T) and CR-8 (= KACC 22945=JCM 35530)] are considered to represent novel species of the genus Erythrobacter, for which the name Erythrobacter oryzae sp. nov. is proposed.

The impact of various forms of silver nanoparticles on the rhizosphere of wheat (Triticum aestivum L.) - Shifts in microbiome structure and predicted microbial metabolic functions

The study investigated the effects of different silver nanoparticles (AgNPs) on the soil microbiome and wheat growth. For comparison purposes, a commercial fungicide and silver nitrate (AgNO3) were used. The results revealed three distinct groups of nanoparticles based on their impacts. Small-size AgNPs (10 nm) with a negative charge, as well as fungicide had limited effects on the microbiome, similar to the no-treatment control. Bigger in size (30-60 nm) and a negative charge AgNPs showed the most beneficial effects on soil microbiota shifts. These AgNPs increased the abundance of bacteria with beneficial traits such as nitrogen-fixing, urease, protease, and lignin degradation bacteria. The third type of AgNPs had a positive charge of nanostructure and influenced specific microbial populations, increasing the abundance of anaerobic and autotrophic groups of microorganisms, which could be assessed as a harmful shift for plants growth promotions and was similar to the AgNO3 treatment. Overall, the study emphasized the potential of AgNPs in agriculture not only as biocidal. The conducted study proved that AgNPs with bigger size/negative charge, used in low concentration can have a surprisingly stimulating effect on the positive characteristics of the rhizosphere microbiome. Moreover, the surface charge of AgNPs is a significant factor affecting microbial activity of wheat rhizosphere soil, which in this treatment is significantly similar to the AgNO3 treatment.

Secretory molecules from secretion systems fine-tune the host-beneficial bacteria (PGPRs) interaction

Numerous bacterial species associate with plants through commensal, mutualistic, or parasitic association, affecting host physiology and health. The mechanism for such association is intricate and involves the secretion of multiple biochemical substances through dedicated protein systems called secretion systems SS. Eleven SS pathways deliver protein factors and enzymes in their immediate environment or host cells, as well as in competing microbial cells in a contact-dependent or independent fashion. These SS are instrumental in competition, initiation of infection, colonization, and establishment of association (positive or negative) with host organisms. The role of SS in infection and pathogenesis has been demonstrated for several phytopathogens, including Agrobacterium, Xanthomonas, Ralstonia, and Pseudomonas. Since there is overlap in mechanisms of establishing association with host plants, several studies have investigated the role of SSs in the interaction of plant and beneficial bacteria, including symbiotic rhizobia and plant growth bacteria (PGPB). Therefore, the present review updates the role of different SSs required for the colonization of beneficial bacteria such as rhizobia, Burkholderia, Pseudomonas, Herbaspirillum, etc., on or inside plants, which can lead to a long-term association. Most SS like T3SS, T4SS, T5SS, and T6SS are required for the antagonistic activity needed to prevent competing microbes, including phytopathogens, ameliorate biotic stress in plants, and produce substances for successful colonization. Others are required for chemotaxis, adherence, niche formation, and suppression of immune response to establish mutualistic association with host plants.

Survival of a microbial inoculant in soil after recurrent inoculations

Microbial inoculants are attracting growing interest in agriculture, but their efficacy remains unreliable in relation to their poor survival, partly due to the competition with the soil resident community. We hypothesised that recurrent inoculation could gradually alleviate this competition and improve the survival of the inoculant while increasing its impact on the resident bacterial community. We tested the effectiveness of such strategy with four inoculation sequences of Pseudomonas fluorescens strain B177 in soil microcosms with increasing number and frequency of inoculation, compared to a non-inoculated control. Each sequence was carried out at two inoculation densities (106 and 108 cfu.g soil-1). The four-inoculation sequence induced a higher abundance of P. fluorescens, 2 weeks after the last inoculation. No impact of inoculation sequences was observed on the resident community diversity and composition. Differential abundance analysis identified only 28 out of 576 dominants OTUs affected by the high-density inoculum, whatever the inoculation sequence. Recurrent inoculations induced a strong accumulation of nitrate, not explained by the abundance of nitrifying or nitrate-reducing microorganisms. In summary, inoculant density rather than inoculation pattern matters for inoculation effect on the resident bacterial communities, while recurrent inoculation allowed to slightly enhance the survival of the inoculant and strongly increased soil nitrate content.

The Microbial Community Structure in the Rhizosphere of Theobroma cacao L. and Euterpe oleracea Mart. Is Influenced by Agriculture System in the Brazilian Amazon

This study tested the hypothesis that cocoa monoculture (MS) and cocoa-açai agroforestry systems (AFS) may influence the microbial community structure and populations of plant growth-promoting bacteria (PGPR). Accordingly, the aim was to analyze the microbial community structure and PGPR populations in different agroecosystems in the Brazilian Amazon. To achieve this, the rhizosphere microbial community of cocoa and açai plants in both Amazonian seasons (dry and rainy) was analyzed using culture-dependent (PGPR screening) and -independent methods [PCR-DGGE based on rrs, alp, nifH gene, and intergenic region (ITS) of fungi]. Concerning PGPR screening, out of 48 isolated bacterial strains, 25% were capable of siderophore production, 29% of mineralized organic phosphate, 8% of inorganic phosphate solubilization, and 4% of indole acetic acid production. Moreover, 17% of isolates could inhibit the growth of various phytopathogenic fungi. Statistical analyses of DGGE fingerprints (p < 0.05) showed that bacterial and fungal community structures in the rhizosphere were influenced by the seasons, supporting the results of the physicochemical analysis of the environment. Furthermore, as hypothesized, microbial communities differed statistically when comparing the MS and AFS. These findings provide important insights into the influence of climate and cultivation systems on soil microbial communities to guide the development of sustainable agricultural practices.

Long-term detection of Hartmannibacter diazotrophicus on winter wheat and spring barley roots under field conditions revealed positive correlations on yield parameters with the bacterium abundance

Monitoring of bioinoculants once released into the field remains largely unexplored; thus, more information is required about their survival and interactions after root colonization. Therefore, specific primers were used to perform a long-term tracking to elucidate the effect of Hartmannibacter diazotrophicus on wheat and barley production at two experimental organic agriculture field stations. Three factors were evaluated: organic fertilizer application (with and without), row spacing (15 and 50 cm), and bacterial inoculation (H. diazotrophicus and control without bacteria). Hartmannibacter diazotrophicus was detected by quantitative polymerase chain reaction on the roots (up to 5 × 105 copies g-1 dry weight) until advanced developmental stages under field conditions during two seasons, and mostly in one farm. Correlation analysis showed a significant effect of H. diazotrophicus copy numbers on the yield parameters straw yield (increase of 453 kg ha-1 in wheat compared to the mean) and crude grain protein concentration (increase of 0.30% in wheat and 0.80% in barley compared to the mean). Our findings showed an apparently constant presence of H. diazotrophicus on both wheat and barley roots until 273 and 119 days after seeding, respectively, and its addition and concentration in the roots are associated with higher yields in one crop.

Paenibacillus lentimorbus alleviates nutrient deficiency-induced stress in Zea mays by modulating root system architecture, auxin signaling, and metabolic pathways

KEY MESSAGE

Paenibacillus lentimorbus reprograms auxin signaling and metabolic pathways for modulating root system architecture to mitigate nutrient deficiency in maize crops. The arable land across the world is having deficiency and disproportionate nutrients, limiting crop productivity. In this study, the potential of plant growth-promoting rhizobacteria (PGPR) viz., Pseudomonas putida, Paenibacillus lentimorbus, and their consortium was explored for growth promotion in maize (Zea mays) under nutrient-deficient conditions. PGPR inoculation improved the overall health of plants under nutrient-deficient conditions. The PGPR inoculation significantly improved the root system architecture and also induced changes in root cortical aerenchyma. Based on plant growth and physiological parameters inoculation with P. lentimorbus performed better as compared to P. putida, consortium, and uninoculated control. Furthermore, expression of auxin signaling (rum1, rul1, lrp1, rtcs, rtcl) and root hair development (rth)-related genes modulated the root development process to improve nutrient acquisition and tolerance to nutrient-deficient conditions in P. lentimorbus inoculated maize plants. Further, GC-MS analysis indicated the involvement of metabolites including carbohydrates and organic acids due to the interaction between maize roots and P. lentimorbus under nutrient-deficient conditions. These findings affirm that P. lentimorbus enhance overall plant growth by modulating the root system of maize to provide better tolerance to nutrient-deficient condition.

Fostering plant growth performance under drought stress using rhizospheric microbes, their gene editing, and biochar

Stress due to drought lowers crop yield and frequently leads to a rise in food scarcity. Plants' intricate metabolic systems enable them to tolerate drought stress, but they are unable to handle it well. Adding some external, environmentally friendly supplements can boost plant growth and productivity when it comes to drought-stressed plants. In order to prevent the detrimental effects of drought in agricultural regions, environmentally friendly practices must be upheld. Plant growth-promoting rhizobacteria (PGPR) can exhibit beneficial phytostimulation, mineralization, and biocontrol activities under drought stress. The significant impact of the PGPR previously reported has not been accepted as an effective treatment to lessen drought stress. Recent studies have successfully shown that manipulating microbes can be a better option to reduce the severity of drought in plants. In this review, we demonstrate how modifying agents such as biochar, PGPR consortia, PGPR, and mycorrhizal fungi can help overcome drought stress responses in crop plants. This article also discusses CRISPR/Cas9-modifiable genes, increase plant's effectiveness in drought conditions, and increase plant resistance to drought stress. With an eco-friendly approach in mind, there is a need for practical management techniques having potential prospects based on an integrated strategy mediated by CRISPR-Cas9 editing, PGPR, which may alleviate the effects of drought stress in crops and aid in achieving the United Nation Sustainable Development Goals (UN-SDGs-2030).

Meta-analysis of plant growth-promoting rhizobacteria interaction with host plants: implications for drought stress response gene expression

Introduction

The molecular and physiological mechanisms activated in plants during drought stress tolerance are regulated by several key genes with both metabolic and regulatory roles. Studies focusing on crop gene expression following plant growth-promoting rhizobacteria (PGPR) inoculation may help understand which bioinoculant is closely related to the induction of abiotic stress responses.

Methods

Here, we performed a meta-analysis following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to summarise information regarding plant-PGPR interactions, focusing on the regulation of nine genes involved in plant drought stress response. The literature research yielded 3,338 reports, of which only 41 were included in the meta-analysis based on the chosen inclusion criteria. The meta-analysis was performed on four genes (ACO, APX, ACS and DREB2); the other five genes (ERD15, MYB, MYC, acdS, WRKY) had an insufficient number of eligible articles.

Results

Forest plots obtained through each meta-analysis showed that the overexpression of ACO, APX, ACS and DREB2 genes was not statistically significant. Unlike the other genes, DREB2 showed statistically significant results in both the presence and absence of PGPR. Considering I2>75 %, the results showed a high heterogeneity among the studies included, and the cause for this was examined using subgroup analysis. Moreover, the funnel plot and Egger's test showed that the analyses were affected by strong publication bias.

Discussion

This study argues that the presence of PGPR may not significantly influence the expression of drought stress response-related crop genes. This finding may be due to high heterogeneity, lack of data on the genes examined, and significant publication bias.

Plant growth-promoting rhizobacteria: Peribacillus frigoritolerans 2RO30 and Pseudomonas sivasensis 2RO45 for their effect on canola growth under controlled as well as natural conditions

Even though canola is one of the most important industrial crops worldwide, it has high nutrient requirements and is susceptible to pests and diseases. Therefore, natural methods are sought to support the development of these plants. One of those methods could be a plant growth-promoting rhizobacteria (PGPR) that have a beneficial effect on plant development. The aim of this study was a genomic comparison of two PGPR strains chosen based on their effect on canola growth: Peribacillus frigoritolerans 2RO30, which stimulated canola growth only in sterile conditions, and Pseudomonas sivasensis 2RO45, which promoted canola growth in both sterile and non-sterile conditions. First of all, six bacterial strains: RO33 (Pseudomonas sp.), RO37 (Pseudomonas poae), RO45 (Pseudomonas kairouanensis), 2RO30 (Peribacillus frigoritolerans), 2RO45 (Pseudomonas sivasensis), and 3RO30 (Pseudomonas migulae), demonstrating best PGP traits in vitro, were studied for their stimulating effect on canola growth under sterile conditions. P. frigoritolerans 2RO30 and P. sivasensis 2RO45 showed the best promoting effect, significantly improving chlorophyll content index (CCI) and roots length compared to the non-inoculated control and to other inoculated seedlings. Under non-sterile conditions, only P. sivasensis 2RO45 promoted the canola growth, significantly increasing CCI compared to the untreated control and to other inoculants. Genome comparison revealed that the genome of P. sivasensis 2RO45 was enriched with additional genes responsible for ACC deaminase (acdA), IAA (trpF, trpG), and siderophores production (fbpA, mbtH, and acrB) compared to 2RO30. Moreover, P. sivasensis 2RO45 showed antifungal effect against all the tested phytopathogens and harbored six more biosynthetic gene clusters (BGC), namely, syringomycin, pyoverdin, viscosin, arylpolyene, lankacidin C, and enterobactin, than P. frigoritolerans 2RO30. These BGCs are well known as antifungal agents; therefore, it can be assumed that these BGCs were responsible for the antifungal activity of P. sivasensis 2RO45 against all plant pathogens. This study is the first report describing P. sivasensis 2RO45 as a canola growth promoter, both under controlled and natural conditions, thus suggesting its application in improving canola yield, by improving nutrient availability, enhancing stress tolerance, and reducing environmental impact of farming practices.

Tomato seed bio-priming with Pseudomonas aeruginosa strain PAR: a study on plant growth parameters under sodium fluoride stress

The primary goal of this experiment is to examine the effectiveness of Pseudomonas aeruginosa strain PAR as a rhizobacterium that promotes plant growth in mitigating the negative effects of fluoride-induced stress in tomato (Lycopersicon esculentum Mill.) plants. A total of 16 rhizobacterial strains were tested for plant growth-promoting (PGP) attributes, with isolates S1, S2, and S3 exhibiting different characteristics. Furthermore, growth kinetics studies revealed that these isolates were resilient to fluoride stress (10, 20, 40, and 80 ppm), with isolate S2 exhibiting notable resilience compared to the other two strains. Phylogenetic analysis revealed isolate S2 as P. aeruginosa strain PAR. Physiological analyses demonstrated that P. aeruginosa strain PAR had a beneficial impact on plant properties under fluoride stress, comprising seed germination, root length, shoot height, relative water content, and leaf area, the strain also impacted the buildup of glycine betaine, soluble sugar, and proline, demonstrating its significance in enhancing plant stress tolerance. In P. aeruginosa strain PAR-treated plants, chlorophyll content increased while malondialdehyde (MDA) levels decreased, indicating enhanced photosynthetic efficiency and less oxidative stress. The strain modified antioxidant enzyme action (catalase, ascorbate, glutathione reductase, peroxidase, and superoxide dismutase), which contributed to improved stress resilience. Mineral analysis revealed a decrease in sodium and fluoride concentrations while increasing magnesium, potassium, phosphorus, and iron levels, emphasizing the strain's significance in nutrient management. Correlation and principal component analysis revealed extensive correlations between physiological and biochemical parameters, underscoring P. aeruginosa strain PAR's multifaceted impact on plant growth and stress response. This study offers valuable information on effectively utilizing PGPR, particularly P. aeruginosa strain PAR, in fluoride-contaminated soils for sustainable agriculture. It presents a promising biological strategy to enhance crop resilience and productivity.

Polysaccharides Produced by Plant Growth-Promoting Rhizobacteria Strain Burkholderia sp. BK01 Enhance Salt Stress Tolerance to Arabidopsis thaliana

Salt stress is one of the most serious abiotic stresses leading to reduced agricultural productivity. Polysaccharides from seaweed have been used as biostimulants to promote crop growth and improve plant resistance to abiotic stress. In this study, PGPR strain Burkholderia sp. BK01 was isolated from the rhizosphere of wheat, and it was characterized for phosphorus (Pi) dissolution, indole-3-acetic acid (IAA) production, ammonia (NH3) and exopolysaccharides (EPS). In particular, strain BK01 can efficiently produce extracellular polysaccharide with a yield of 12.86 g/L, using sorbitol as carbon source. BK01 EPS was identified as an heteropolysaccharide with Mw 3.559 × 106 Da, composed of (D)-galactose (75.3%), (D)-glucose (5.5%), (L)-rhamnose (5.5%), (D)-galactouronic acid (4.9%) and (D)-glucuronic acid (8.8%). The present work aims to highlight the effect of the BK01 EPS on growth and biochemical changes in Arabidopsis thaliana under salt stress (100 mM). The purified BK01 EPS at a concentration of 100 mg/L efficiently promoted the growth of plants in pot assays, improved the chlorophyll content, enhanced the activities of SOD, POD and CAT, and decreased the content of MDA. This results suggested that the polysaccharides produced by PGPR strain Burkholderia sp. BK01 can be used as biostimulants to promote plant growth and improve plant resistance to salt stress.

Growth and protein response of rice plant with plant growth-promoting rhizobacteria inoculations under salt stress conditions

Soil salinity has been one of the significant barriers to improving rice production and quality. According to reports, Bacillus spp. can be utilized to boost plant development in saline soil, although the molecular mechanisms behind the interaction of microbes towards salt stress are not fully known. Variations in rice plant protein expression in response to salt stress and plant growth-promoting rhizobacteria (PGPR) inoculations were investigated using a proteomic method and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Findings revealed that 54 salt-responsive proteins were identified by mass spectrometry analysis (LC-MS/MS) with the Bacillus spp. interaction, and the proteins were functionally classified as gene ontology. The initial study showed that all proteins were labeled by mass spectrometry analysis (LC-MS/MS) with Bacillus spp. interaction; the proteins were functionally classified into six groups. Approximately 18 identified proteins (up-regulated, 13; down-regulated, 5) were involved in the photosynthetic process. An increase in the expression of eight up-regulated and two down-regulated proteins in protein synthesis known as chaperones, such as the 60 kDa chaperonin, the 70 kDa heat shock protein BIP, and calreticulin, was involved in rice plant stress tolerance. Several proteins involved in protein metabolism and signaling pathways also experienced significant changes in their expression. The results revealed that phytohormones regulated the manifestation of various chaperones and protein abundance and that protein synthesis played a significant role in regulating salt stress. This study also described how chaperones regulate rice salt stress, their different subcellular localizations, and the activity of chaperones.

A novel PGPR strain homologous to Beijerinckia fluminensis induces biochemical and molecular changes involved in Arabidopsis thaliana salt tolerance

The use of PGPR is widely accepted as a promising tool for a more sustainable agricultural production and improved plant abiotic stress resistance. This study tested the ability of PVr_9, a novel bacterial strain, homologous to Beijerinckia fluminensis, to increase salt stress tolerance in A. thaliana. In vitro plantlets inoculated with PVr_9 and treated with 150 mM NaCl showed a reduction in primary root growth inhibition compared to uninoculated ones, and a leaf area significantly less affected by salt. Furthermore, salt-stressed PVr_9-inoculated plants had low ROS and 8-oxo-dG, osmolytes, and ABA content along with a modulation in antioxidant enzymatic activities. A significant decrease in Na+ in the leaves and a corresponding increase in the roots were also observed in salt-stressed inoculated plants. SOS1, NHX1 genes involved in plant salt tolerance, were up-regulated in PVr_9-inoculated plants, while different MYB genes involved in salt stress signal response were down-regulated in both roots and shoots. Thus, PVr_9 was able to increase salt tolerance in A. thaliana, thereby suggesting a role in ion homeostasis by reducing salt stress rather than inhibiting total Na+ uptake. These results showed a possible molecular mechanism of crosstalk between PVr_9 and plant roots to enhance salt tolerance, and highlighted this bacterium as a promising PGPR for field applications on agronomical crops.

Long-Term Field Application of a Plant Growth-Promoting Rhizobacterial Consortium Suppressed Root-Knot Disease by Shaping the Rhizosphere Microbiota

Root-knot nematodes (Meloidogyne spp.) are one of the most economically important plant parasitic nematodes, infecting almost all cultivated plants and resulting in severe yield losses every year. Plant growth-promoting rhizobacteria (PGPR) have been extensively used to prevent and control root-knot diseases and increase yield. In this study, the effect of a consortium of three PGPR strains (Bacillus cereus AR156, B. subtilis SM21, and Serratia sp. XY21; hereafter "BBS") on root-knot disease of cucumber was evaluated. The application of BBS significantly reduced the severity of root-knot disease by 56 to 72%, increased yield by 36 to 55%, and improved fruit quality by 14 to 90% and soil properties by 1 to 90% relative to the control in the cucumber fields of the Nanjing suburb, Jiangsu Province, from 2015 to 2018. BBS altered the rhizosphere bacterial community. Compared with the control group, it significantly (false discovery rate, P < 0.05) increased the abundance of 14 bacterial genera that were negatively correlated with disease severity. Additionally, the redundancy analysis suggested that BBS-treated rhizosphere soil samples were dominated by disease-suppressive bacteria, including the genera Iamia, Kutzneria, Salinibacterium, Mycobacterium, Kribbella, Pseudonocardia, Sporichthya, Sphaerisporangium, Actinomadura, Flavisolibacter, Phenylobacterium, Bosea, Hyphomicrobium, Agrobacterium, Sphingomonas, and Nannocystis, which were positively related to total organic carbon, total nitrogen, total organic matter, dissolved organic carbon, [Formula: see text]-N, and available phosphorus contents. This suggests that BBS suppresses root-knot nematodes and improves the soil chemical properties of cucumber by altering the rhizosphere microbial community.

B. subtilis CNBG-PGPR-1 induces methionine to regulate ethylene pathway and ROS scavenging for improving salt tolerance of tomato

Soil salinity severely threatens plant growth and crop yields. The utilization of PGPR is an effective strategy for enhancing plant salt tolerance, but the mechanisms involved in this process have rarely been reported. In this study, we investigated the effects of Bacillus subtilis CNBG-PGPR-1 on improving plant salt tolerance and elucidated the molecular pathways involved. The results showed that CNBG-PGPR-1 significantly improved the cellular homeostasis and photosynthetic efficiency of leaves and reduced ion toxicity and osmotic stress caused by salt in tomato. Transcriptome analysis uncovered that CNBG-PGPR-1 enhanced plant salt tolerance through the activation of complex molecular pathways, with plant hormone signal transduction playing an important role. Comparative analysis and pharmacological experiments confirmed that the ethylene pathway was closely related to the beneficial effect of CNBG-PGPR-1 on improving plant salt tolerance. Furthermore, we found that methionine, a precursor of ethylene synthesis, significantly accumulated in response to CNBG-PGPR-1 in tomato. Exogenous L-methionine largely mimicked the beneficial effects of CNBG-PGPR-1 and activated the expression of ethylene pathway-related genes, indicating CNBG-PGPR-1 induces methionine accumulation to regulate the ethylene pathway in tomato. Finally, CNBG-PGPR-1 reduced salt-induced ROS by activating ROS scavenger-encoding genes, mainly involved in GSH metabolism and POD-related genes, which were also closely linked to methionine metabolism. Overall, our studies demonstrate that CNBG-PGPR-1-induced methionine is a key regulator in enhancing plant salt tolerance through the ethylene pathway and ROS scavenging, providing a novel understanding of the mechanism by which beneficial microbes improve plant salt tolerance.

The hidden harmony: Exploring ROS-phytohormone nexus for shaping plant root architecture in response to environmental cues

Root system architecture, encompassing lateral roots and root hairs, plays a vital in overall plant growth and stress tolerance. Reactive oxygen species (ROS) and plant hormones intricately regulate root growth and development, serving as signaling molecules that govern processes such as cell proliferation and differentiation. Manipulating the interplay between ROS and hormones has the potential to enhance nutrient absorption, stress tolerance, and agricultural productivity. In this review, we delve into how studying these processes provides insights into how plants respond to environmental changes and optimize growth patterns to better control cellular processes and stress responses in crops. We discuss various factors and complex signaling networks that may exist among ROS and phytohormones during root development. Additionally, the review highlights possible role of reactive nitrogen species (RNS) in ROS-phytohormone interactions and in shaping root system architecture according to environmental cues.

Comprehensive analysis of OsJAZ gene family deciphers rhizobacteria-mediated nutrient stress modulation in rice

The JASMONATE-ZIM DOMAIN (JAZ) repressors are crucial proteins in jasmonic acid signaling pathway that are critical for plant growth. Therefore, the present study aimed to identify and characterize OsJAZs in the rice genome, revealing their structural attributes, regulatory elements, miRNA interactions, and subcellular localization. 23 JAZ transcripts across the 6 chromosomes of rice genome were identified having conserved domains and different physiochemical characteristics. Phylogenetically classified into five clades, they showed highest syntenic relationship with P. virgatum. The non-synonymous/synonymous values ranged from 0.44 to 1.21 suggesting purifying/stabilizing selection in OsJAZs. The study examined the 1.5 kb promoter region for cis-regulatory elements, and also identified 92 miRNAs targets. Furthermore, homology modeling provided insights into the 3D-structures of JAZ proteins while in-silico gene expression analysis revealed their functional diversity in various tissues and developmental stages. Additionally, qRT-PCR analysis highlighted their involvement in stress adaptation to sub-optimum nutrient conditions induced by plant-beneficial rhizobacteria Bacillus amyloliquefaciens (SN13) in two rice varieties. Distinct OsJAZ expression patterns in the two varieties correlated with altered root architecture, xylem structure, and lignification. These findings affirmed that specific up-or down-regulation of OsJAZs might play critical role in SN13 induced changes in the two varieties that enabled them to survive under stress.

Study on the mechanism of salt relief and growth promotion of Enterobacter cloacae on cotton

AIMS

In-depth studies on plant ion uptake and plant growth-promoting rhizobacteria (PGPR) at the molecular level will help to further reveal the effects of PGPR on plants and their interaction mechanisms under salt stress.

METHODS

Cotton was inoculated with a PGPR-Enterobacter cloacae Rs-35, and the ion uptake capacity, membrane transporter protein activity, and expression of key genes were determined under salt stress. Changes in the endogenous hormone content of cotton were also determined. Further, the genome-wide metabolic pathway annotation of E. cloacae Rs-35 and its differential enrichment pathway analysis of multi-omics under salinity environments were performed.

RESULTS

In a pot experiment of saline-alkali soil, E. cloacae Rs-35-treated cotton significantly increased its uptake of K+ and Ca2+ and decreased uptake of Na+, elevated the activity of the H+-ATPase, and increased the sensitivity of the Na+/H+ reverse transporter protein on the vesicle membrane. Meanwhile, inoculation with E. cloacae Rs-35 could promote cotton to maintain the indole-3-acetic acid (IAA) content under salt stress. Genome-wide annotation showed that E. cloacae Rs-35 was respectively annotated to 31, 38, and 130 related genes in osmotic stress, phytohormone and organic acid metabolism, and ion uptake metabolic pathway. Multi-omics differences analysis showed that E. cloacae Rs-35 were enriched to tryptophan metabolism, multiple amino acid biosynthesis, carbon and glucose synthesis, and oxidative phosphorylation metabolic pathways at the transcriptome, proteome, and metabolome.

CONCLUSION

E. cloacae Rs-35 can promote cotton balance cell ion concentration, stabilize intracellular IAA changes, stimulate induction of systemic tolerance, and promote the growth of cotton plants under salt stress.

Endosphere microbial communities and plant nutrient acquisition toward sustainable agriculture

Endophytic microbial communities have essential information for scientists based on their biological contribution to agricultural practices. In the external plant environment, biotic and abiotic factors affect microbial populations before getting into plant tissues. Endophytes are involved in mutualistic and antagonistic activities with the host plant. Microbial communities inhabiting the internal tissues of plant roots depend on their ability to live and contend with other plant microflora. The advantageous ones contribute to soil health and plant growth either directly or indirectly. The microbial communities move via soil-root environment into the endosphere of plants promoting plant growth features like antibiosis, induced systemic resistance, phytohormone synthesis, and bioremediation. Therefore, the existence of these microorganisms contributes to plant genomes, nutrient availability in the soil, the presence of pathogens, and abiotic factors. This review aims at how endophytic microorganisms have displayed great interest in contributing to abundant crop production and phytopathogen inhibition.

Competition and co-association, but not phosphorous availability, shape the benefits of phosphate-solubilizing root bacteria for maize (Zea mays)

Predicting the conditions under which rhizobacteria benefit plant growth remains challenging. Here we tested the hypothesis that benefits from inoculation with phosphate-solubilizing rhizobacteria will depend upon two environmental conditions: phosphate availability and competition between bacteria. We used maize-associated rhizobacteria with varying phosphate solubilization ability in experiments in soil, sterilized soil and gnotobiotic microcosms under conditions of varying orthophosphate availability, while we manipulated the intensity of competition by varying the number of isolates in plant inocula. Growth promotion by microbes did not depend on phosphate availability but was affected by interactions between inoculants: the beneficial effects of one Serratia isolate were only detectable when plants were inoculated with a single strain and the beneficial effects of a competition-sensitive Rhizobium was only detectable in sterilized soil or in microcosms inoculated with single strains. Moreover, microcosm experiments suggested that facilitation of a parasitic isolate, not competitive interactions between bacteria, prevented plants from gaining benefits from a potential mutualist. Competition and facilitation affected colonization of plants in microcosms but growth promotion by Serratia was more affected by inoculation treatment than culturable densities on roots. Experimental manipulation of seed inocula can reveal whether plant growth stimulation is robust with respect to competition, as well as the ecological strategies of different rhizobacteria. From an applied perspective, phosphate solubilization may not provide the mechanism for bacterial growth promotion but may indicate mutualistic potential due to phylogenetic associations. Importantly, benefits to plants are vulnerable to interactions between rhizobacteria and may not persist in mixed inoculations.

Promoting plant resilience against stress by engineering root microenvironment with Streptomyces inoculants

Plant growth is directly influenced by biotic and abiotic stress factors resulting from environmental changes. Plant growth-promoting rhizobacteria (PGPR) have become a crucial area of research aimed at addressing these challenges. However, a knowledge gap exists regarding how PGPR impacts the microenvironments surrounding plant roots. The purpose of this study is to elucidate the effects of two distinct PGPR strains, Streptomyces griseorubiginosus BTU6 (known for its resistance to smut disease) and S. chartreusis WZS021, on sugarcane roots. Additionally, we compare the resultant modifications in the physicochemical characteristics of the rhizospheric soil and root architecture. The results reveal that following the inoculation of S. chartreusis WZS021, there was a significant increase in the active chemicals associated with nitrogen metabolism in sugarcane roots. This enhancement led to a substantial enrichment of nitrogen-cycling microbes like Pseudomonas and Gemmatimona. This finding supports earlier research indicating that S. chartreusis WZS021 enhances sugarcane's capacity to utilize nitrogen effectively. Furthermore, after treatment with S. chartreusis, Aspergillus became the predominant strain among endophytic fungi, resulting in alterations to their community structure that conferred drought resistance. In contrast, the relative abundance of Xanthomonas in the root environment decreased following inoculation with S. griseorubiginosus. Instead, Gemmatimona became more prevalent, creating a favorable environment for plants to bolster their resistance against disease. Notably, inoculations with S. chartreusis WZS021 and S. griseorubiginosus BTU6 led to substantial changes in the chemical composition, enzymatic activity, and microbial community composition in the soil surrounding sugarcane roots. However, there were distinct differences in the specific alterations induced by each strain. These findings enhance plant resilience to stress by shedding light on PGPR-mediated modifications in root microenvironments.

Synergistic benefits of Funneliformis mosseae and Bacillus paramycoides: Enhancing soil health and soybean tolerance to root rot disease

To explore the response of soil metabolite composition to soybean disease, the effect of the combined inoculation of arbuscular mycorrhizal fungi (AMF) and plant growth-promoting bacteria on soybean root rot caused by Fusarium oxysporum was studied. A factorial completely randomized design with three factors (AMF, Bacillus. paramycoides, and rot disease stress) was conducted, and eight treatments, including normal groups and stress groups, were performed using pot experiments. GC‒MS and enzymatic assays were used to evaluate the soil factors and soybean growth indicators. The results showed that there were significant differences in the composition of metabolites among the different treatment groups, and 23 metabolites were significantly related to soybean biomass. The combined inoculation of Funneliformis mosseae and Bacillus paramycoides resulted in a significant reduction in harmful soil metabolites associated with root rot disease, such as ethylbenzene and styrene. This reduction in metabolites contributed to improving soil health, as evidenced by enhanced soybean defence enzyme activities and microbial activity, and β-1,3-glucanase, chitinase and phenylalanine ammonia-lyase activities were improved to alleviate plant rhizosphere stress. Furthermore, soybean plants inoculated with the synergistic treatments exhibited reduced root rot disease severity and improved growth indicators compared to control plants. Plant height, root dry weight (RDW), and shoot and root fresh weight (SRFW) were improved by 4.18-53.79%, and the AM fungal colonization rate was also improved under stress. The synergistic application of Funneliformis mosseae and Bacillus paramycoides can effectively enhance soil health by inhibiting the production of harmful soil metabolites and improving soybean tolerance to root rot disease. This approach holds promise for the sustainable management of soil-borne diseases in soybean cultivation.