Plant-growth-promoting compounds produced by two agronomically important strains of Azospirillum brasilense, and implications for inoculant formulation

Phenogenetic profile and agronomic contribution of Azospirillum argentinense Az39T, a reference strain for the South American inoculant industry

Azospirillum sp. is a plant growth-promoting rhizobacteria largely recognized for its potential to increase the yield of different important crops. In this work, we present a thorough genomic and phenotypic analysis of A. argentinense Az39T to provide new insights into the beneficial mechanisms of this microorganism. Phenotypic analyses revealed the following in vitro abilities: growth at 20-38 °C (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 6.8), and in the presence of 1% (w/v) NaCl; production of variable amounts of PHB as intracellular granules; nitrogen fixation under microaerophilic conditions; IAA synthesis in the presence of L-tryptophan. Through biochemical (API 20NE) and carbon utilization profiling (Biolog) assays, we proved that A. argentinense Az39T is able to use 15 substrates and metabolize 19 different carbon substrates. Lipid composition indicated a predominance of medium and long-chain saturated fatty acids. A total of 6 replicons classified as one main chromosome, three chromids, and two plasmids, according to their tRNA and core essential genes contents, were identified. Az39T genome includes genes associated with multiple plant growth-promoting (PGP) traits such as nitrogen fixation and production of auxins, cytokinin, abscisic acid, ethylene, and polyamines. In addition, Az39T genome harbor genetic elements associated with physiological features that facilitate its survival in the soil and competence for rhizospheric colonization; this includes motility, secretion system, and quorum sensing genetic determinants. A metadata analysis of Az39T agronomic performance in the pampas region, Argentina, demonstrated significant grain yield increases in wheat and maize, proving its potential to provide better growth conditions for dryland cereals. In conclusion, our data provide a detailed insight into the metabolic profile of A. argentinense Az39T, the strain most widely used to formulate non-legume inoculants in Argentina, and allow a better understanding of the mechanisms behind its field performance.

Evaluation of Tunisian wheat endophytes as plant growth promoting bacteria and biological control agents against Fusarium culmorum

Plant growth-promoting rhizobacteria (PGPR) applications have emerged as an ideal substitute for synthetic chemicals by their ability to improve plant nutrition and resistance against pathogens. In this study, we isolated fourteen root endophytes from healthy wheat roots cultivated in Tunisia. The isolates were identified based from their 16S rRNA gene sequences. They belonged to Bacillota and Pseudomonadota taxa. Fourteen strains were tested for their growth-promoting and defense-eliciting potentials on durum wheat under greenhouse conditions, and for their in vitro biocontrol power against Fusarium culmorum, an ascomycete responsible for seedling blight, foot and root rot, and head blight diseases of wheat. We found that all the strains improved shoot and/or root biomass accumulation, with Bacillus mojavensis, Paenibacillus peoriae and Variovorax paradoxus showing the strongest promoting effects. These physiological effects were correlated with the plant growth-promoting traits of the bacterial endophytes, which produced indole-related compounds, ammonia, and hydrogen cyanide (HCN), and solubilized phosphate and zinc. Likewise, plant defense accumulations were modulated lastingly and systematically in roots and leaves by all the strains. Testing in vitro antagonism against F. culmorum revealed an inhibition activity exceeding 40% for five strains: Bacillus cereus, Paenibacillus peoriae, Paenibacillus polymyxa, Pantoae agglomerans, and Pseudomonas aeruginosa. These strains exhibited significant inhibitory effects on F. culmorum mycelia growth, sporulation, and/or macroconidia germination. P. peoriae performed best, with total inhibition of sporulation and macroconidia germination. These finding highlight the effectiveness of root bacterial endophytes in promoting plant growth and resistance, and in controlling phytopathogens such as F. culmorum. This is the first report identifying 14 bacterial candidates as potential agents for the control of F. culmorum, of which Paenibacillus peoriae and/or its intracellular metabolites have potential for development as biopesticides.

Bacterial indole-3-acetic acid: A key regulator for plant growth, plant-microbe interactions, and agricultural adaptive resilience

Indole-3-acetic acid (IAA), a fundamental phytohormone categorized under auxins, not only influences plant growth and development but also plays a critical role in plant-microbe interactions. This study reviews the role of IAA in bacteria-plant communication, with a focus on its biosynthesis, regulation, and the subsequent effects on host plants. Bacteria synthesize IAA through multiple pathways, which include the indole-3-acetamide (IAM), indole-3-pyruvic acid (IPyA), and several other routes, whose full mechanisms remain to be fully elucidated. The production of bacterial IAA affects root architecture, nutrient uptake, and resistance to various abiotic stresses such as drought, salinity, and heavy metal toxicity, enhancing plant resilience and thus offering promising routes to sustainable agriculture. Bacterial IAA synthesis is regulated through complex gene networks responsive to environmental cues, impacting plant hormonal balances and symbiotic relationships. Pathogenic bacteria have adapted mechanisms to manipulate the host's IAA dynamics, influencing disease outcomes. On the other hand, beneficial bacteria utilize IAA to promote plant growth and mitigate abiotic stresses, thereby enhancing nutrient use efficiency and reducing dependency on chemical fertilizers. Advancements in analytical methods, such as liquid chromatography-tandem mass spectrometry, have improved the quantification of bacterial IAA, enabling accurate measurement and analysis. Future research focusing on molecular interactions between IAA-producing bacteria and host plants could facilitate the development of biotechnological applications that integrate beneficial bacteria to improve crop performance, which is essential for addressing the challenges posed by climate change and ensuring global food security. This integration of bacterial IAA producers into agricultural practice promises to revolutionize crop management strategies by enhancing growth, fostering resilience, and reducing environmental impact.

Azospirillum brasilense activates peroxidase-mediated cell wall modification to inhibit root cell elongation

The molecular mechanism of beneficial bacterium Azospirillum brasilense-mediated root developmental remain elusive. A. brasilense elicited extensively transcriptional changes but inhibited primary root elongation in Arabidopsis. By analyzing root cell type-specific developmental markers, we demonstrated that A. brasilense affected neither overall organization nor cell division of primary root meristem. The cessation of primary root resulted from reduction of cell elongation, which is probably because of bacterially activated peroxidase that will lead to cell wall cross-linking at consuming of H2O2. The activated peroxidase combined with downregulated cell wall loosening enzymes consequently led to cell wall thickness, whereas inhibiting peroxidase restored root growth under A. brasilense inoculation. We further showed that peroxidase activity was probably promoted by cadaverine secreted by A. brasilense. These results suggest that A. brasilense inhibits root elongation by activating peroxidase and inducing cell wall modification in Arabidopsis, in which cadaverine released by A. brasilense is a potential signal compound.

The Biosynthesis and Functions of Polyamines in the Interaction of Plant Growth-Promoting Rhizobacteria with Plants

Plant growth-promoting rhizobacteria (PGPR) are members of the plant rhizomicrobiome that enhance plant growth and stress resistance by increasing nutrient availability to the plant, producing phytohormones or other secondary metabolites, stimulating plant defense responses against abiotic stresses and pathogens, or fixing nitrogen. The use of PGPR to increase crop yield with minimal environmental impact is a sustainable and readily applicable replacement for a portion of chemical fertilizer and pesticides required for the growth of high-yielding varieties. Increased plant health and productivity have long been gained by applying PGPR as commercial inoculants to crops, although with uneven results. The establishment of plant-PGPR relationships requires the exchange of chemical signals and nutrients between the partners, and polyamines (PAs) are an important class of compounds that act as physiological effectors and signal molecules in plant-microbe interactions. In this review, we focus on the role of PAs in interactions between PGPR and plants. We describe the basic ecology of PGPR and the production and function of PAs in them and the plants with which they interact. We examine the metabolism and the roles of PAs in PGPR and plants individually and during their interaction with one another. Lastly, we describe some directions for future research.

Assessment of Tunisian Trichoderma Isolates on Wheat Seed Germination, Seedling Growth and Fusarium Seedling Blight Suppression

Beneficial microorganisms, including members of the Trichoderma genus, are known for their ability to promote plant growth and disease resistance, as well as being alternatives to synthetic inputs in agriculture. In this study, 111 Trichoderma strains were isolated from the rhizospheric soil of Florence Aurore, an ancient wheat variety that was cultivated in an organic farming system in Tunisia. A preliminary ITS analysis allowed us to cluster these 111 isolates into three main groups, T. harzianum (74 isolates), T. lixii (16 isolates) and T. sp. (21 isolates), represented by six different species. Their multi-locus analysis (tef1, translation elongation factor 1; rpb2, RNA polymerase B) identified three T. afroharzianum, one T. lixii, one T. atrobrunneum and one T. lentinulae species. These six new strains were selected to determine their suitability as plant growth promoters (PGP) and biocontrol agents (BCA) against Fusarium seedling blight disease (FSB) in wheat caused by Fusarium culmorum. All of the strains exhibited PGP abilities correlated to ammonia and indole-like compound production. In terms of biocontrol activity, all of the strains inhibited the development of F. culmorum in vitro, which is linked to the production of lytic enzymes, as well as diffusible and volatile organic compounds. An in planta assay was carried out on the seeds of a Tunisian modern wheat variety (Khiar) by coating them with Trichoderma. A significant increase in biomass was observed, which is associated with increased chlorophyll and nitrogen. An FSB bioprotective effect was confirmed for all strains (with Th01 being the most effective) by suppressing morbid symptoms in germinated seeds and seedlings, as well as by limiting F. culmorum aggressiveness on overall plant growth. Plant transcriptome analysis revealed that the isolates triggered several SA- and JA-dependent defense-encoding genes involved in F. culmorum resistance in the roots and leaves of three-week-old seedlings. This finding makes these strains very promising in promoting growth and controlling FSB disease in modern wheat varieties.

Role of microbial inoculants as bio fertilizers for improving crop productivity: A review

The world's population is increasing and is anticipated to spread 10 billion by 2050, and the issue of food security is becoming a global concern. To maintain global food security, it is essential to increase crop productivity under changing climatic conditions. Conventional agricultural practices frequently use artificial/chemical fertilizers to enhance crop productivity, but these have numerous negative effects on the environment and people's health. To address these issues, researchers have been concentrating on substitute crop fertilization methods for many years, and biofertilizers as a crucial part of agricultural practices are quickly gaining popularity all over the globe. Biofertilizers are living formulations made of indigenous plant growth-promoting rhizobacteria (PGPR) which are substantial, environment-friendly, and economical biofertilizers for amassing crop productivity by enhancing plant development either directly or indirectly, and are the renewable source of plant nutrients and sustainable agronomy. The review aims to provide a comprehensive overview of the current knowledge on microbial inoculants as biofertilizers, including their types, mechanisms of action, effects on crop productivity, challenges, and limitations associated with the use of microbial inoculants. In this review, we focused on the application of biofertilizers to agricultural fields in plant growth development by performing several activities like nitrogen fixation, siderophore production, phytohormone production, nutrient solubilization, and facilitating easy uptake by crop plants. Further, we discussed the indirect mechanism of PGPRs, in developing induced system resistance against pest and diseases, and as a biocontrol agent for phytopathogens. This review article presents a brief outline of the ideas and uses of microbial inoculants in improving crop productivity as well as a discussion of the challenges and limitations to use microbial inoculants.

Endophytes in Agriculture: Potential to Improve Yields and Tolerances of Agricultural Crops

Endophytic fungi and bacteria live asymptomatically within plant tissues. In recent decades, research on endophytes has revealed that their significant role in promoting plants as endophytes has been shown to enhance nutrient uptake, stress tolerance, and disease resistance in the host plants, resulting in improved crop yields. Evidence shows that endophytes can provide improved tolerances to salinity, moisture, and drought conditions, highlighting the capacity to farm them in marginal land with the use of endophyte-based strategies. Furthermore, endophytes offer a sustainable alternative to traditional agricultural practices, reducing the need for synthetic fertilizers and pesticides, and in turn reducing the risks associated with chemical treatments. In this review, we summarise the current knowledge on endophytes in agriculture, highlighting their potential as a sustainable solution for improving crop productivity and general plant health. This review outlines key nutrient, environmental, and biotic stressors, providing examples of endophytes mitigating the effects of stress. We also discuss the challenges associated with the use of endophytes in agriculture and the need for further research to fully realise their potential.

Synergistic interplay between Azospirillum brasilense and exogenous signaling molecule H2S promotes Cd stress resistance and growth in pak choi (Brassica chinensis L.)

Inoculation with growth-promoting rhizobacteria inoculation and the addition of exogenous signaling molecules are two distinct strategies for improving heavy metal resistance and promoting growth in crops through several mechanisms. However, whether rhizobacteria and phyllosphere signaling molecules can act synergistically alleviate heavy metal stress and promote growth and the mechanisms underlying these effects remain unclear. Here, a novel strategy involving the co-application of growth-promoting rhizobacteria and an exogenous signaling molecule was developed to reduce cadmium (Cd) phytotoxicity and promote pak choi growth in Cd-contaminated soil. We found that the co-application of Azospirillum brasilense and hydrogen sulfide (H₂S) resulted in significant improvements in shoot biomass and antioxidant enzyme content and a decline in the levels of Cd translocation factors. In addition, this co-application significantly improved pak choi Cd resistance. Furthermore, we observed a significant negative correlation between abscisic acid concentration and Cd content of pak choi and a positive correlation between H₂S concentration and biomass. These findings revealed that the co-application of rhizobacteria and exogenous signaling molecules synergistically promoted the growth of vegetable crops subjected to heavy metal stress. Our results may serve as a guide for improving the food safety of crops grown in soil contaminated with heavy metals.

Phosphate-Solubilizing Capacity of Paecilomyces lilacinus PSF7 and Optimization Using Response Surface Methodology

Phosphorus-solubilizing microorganisms release organic acids that can chelate mineral ions or reduce the pH to solubilize insoluble phosphates for use by plants; it is important to study potential phosphorus-solubilizing microorganisms for use in agriculture. In this study, PSF7 was isolated from the soil of the Wengfu Phosphorus Tailings Dump in Fuquan City, Guizhou Province, China. PSF7 was identified as Paecilomyces lilacinus, based on morphological characterization and ITS sequencing analysis. The relationship between the phosphorus-solubilizing capacity and pH variation of PSF7 under liquid fermentation was studied. The results showed that there was a significant negative correlation (-0.784) between the soluble phosphorus content of PSF7 and the pH value. When PSF7 was placed under low phosphorus stress, eight organic acids were determined from fermentation broth using HPLC, of which tartaric acid and formic acid were the main organic acids. Different optimization parameters of medium components were analyzed using response surface methodology. The optimized medium components were 23.50 g/L sucrose, 1.64 g/L ammonium sulfate and soybean residue, 1.07 g/L inorganic salts, and 9.16 g/L tricalcium phosphate, with a predicted soluble phosphorus content of 123.89 mg/L. Under the optimum medium composition, the actual phosphorus-solubilizing content of PSF7 reached 122.17 mg/L. Moreover, scanning electron microscopy analysis of the sample was carried out to characterize the phosphate-solubilizing efficiency of PSF7 on mineral phosphate. The results provide useful information for the future application of PSF7 as a biological fertilizer.

In-depth characterization of phytase-producing plant growth promotion bacteria isolated in alpine grassland of Qinghai-Tibetan Plateau

The use of plant growth promoting bacteria (PGPB) express phytase (myo-inositol hexakisphosphate phosphohydrolase) capable of hydrolyzing inositol phosphate in soil was a sustainable approach to supply available phosphorus (P) to plants. A total of 73 bacterial isolates with extracellular phytase activity were selected from seven dominant grass species rhizosphere in alpine grassland of Qinghai-Tibetan Plateau. Then, the plant growth promoting (PGP) traits of candidate bacteria were screened by qualitative and quantitative methods, including organic/inorganic Phosphorus solubilization (P. solubilization), plant hormones (PHs) production, nitrogen fixation, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity and antimicrobial activity. Further experiment were conducted to test their growth promoting effect on Lolium perenne L. under P-limitation. Our results indicated that these bacteria as members of phyla Proteobacteria (90.41%) and Actinobacteria (9.59%) were related to 16 different genera. The isolates of Pseudomonas species showed the highest isolates number (36) and average values of phytase activity (0.267 ± 0.012 U mL^-1), and showed a multiple of PGP traits, which was a great candidate for PGPBs. In addition, six strains were positive in phytase gene (β-propeller phytase, bpp) amplification, which significantly increased the shoot length, shoot/root fresh weight, root average diameter and root system phytase activity of Lolium perenne L. under P-limitation, and the expression of phytase gene (bppP) in root system were verified by qPCR. Finally, the PHY101 gene encoding phytase from Pseudomonas mandelii GS10-1 was cloned, sequenced, and recombinantly expressed in Escherichia coli. Biochemical characterization demonstrated that the recombinant phytase PHY101 revealed the highest activity at pH 6 and 40°C temperature. In particular, more than 60% of activity was retained at a low temperature of 15°C. This study demonstrates the opportunity for commercialization of the phytase-producing PGPB to developing localized microbial inoculants and engineering rhizobacteria for sustainable use in alpine grasslands.

The Importance of Microorganisms for Sustainable Agriculture-A Review

In the face of climate change, progressive degradation of the environment, including agricultural land negatively affecting plant growth and development, endangers plant productivity. Seeking efficient and sustainable agricultural techniques to replace agricultural chemicals is one of the most important challenges nowadays. The use of plant growth-promoting microorganisms is among the most promising approaches; however, molecular mechanisms underneath plant-microbe interactions are still poorly understood. In this review, we summarized the knowledge on plant-microbe interactions, highlighting the role of microbial and plant proteins and metabolites in the formation of symbiotic relationships. This review covers rhizosphere and phyllosphere microbiomes, the role of root exudates in plant-microorganism interactions, the functioning of the plant's immune system during the plant-microorganism interactions. We also emphasized the possible role of the stringent response and the evolutionarily conserved mechanism during the established interaction between plants and microorganisms. As a case study, we discussed fungi belonging to the genus Trichoderma. Our review aims to summarize the existing knowledge about plant-microorganism interactions and to highlight molecular pathways that need further investigation.

Genetic Circuit Design in Rhizobacteria

Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

Root system architecture in rice: impacts of genes, phytohormones and root microbiota

To feed the continuously expanding world's population, new crop varieties have been generated, which significantly contribute to the world's food security. However, the growth of these improved plant varieties relies primarily on synthetic fertilizers, which negatively affect the environment and human health; therefore, continuous improvement is needed for sustainable agriculture. Several plants, including cereal crops, have the adaptive capability to combat adverse environmental changes by altering physiological and molecular mechanisms and modifying their root system to improve nutrient uptake efficiency. These plants operate distinct pathways at various developmental stages to optimally establish their root system. These processes include changes in the expression profile of genes, changes in phytohormone level, and microbiome-induced root system architecture (RSA) modification. Several studies have been performed to understand microbial colonization and their involvement in RSA improvement through changes in phytohormone and transcriptomic levels. This review highlights the impact of genes, phytohormones, and particularly root microbiota in influencing RSA and provides new insights resulting from recent studies on rice root as a model system and summarizes the current knowledge about biochemical and central molecular mechanisms.

Genome-based reclassification of Azospirillum brasilense Az39 as the type strain of Azospirillum argentinense sp. nov

Strain Az39T of Azospirillum is a diazotrophic plant growth-promoting bacterium isolated in 1982 from the roots of wheat plants growing in Marcos Juárez, Córdoba, Argentina. It produces indole-3-acetic acid in the presence of l-tryptophan as a precursor, grows at 20–38 °C (optimal 38 °C), and the cells are curved or spiral-shaped, with diameters ranging from 0.5–0.9 to 1.8–2.2 µm. They contain C16 : 0, C18 : 0 and C18 : 1  ω7c/ω6c as the main fatty acids. Phylogenetic analysis of its 16S rRNA gene sequence confirmed that this strain belongs to the genus Azospirillum , showing a close relationship with Azospirillum baldaniorum Sp245T, Azospirillum brasilense Sp7T and Azospirillum formosense CC-Nfb-7T. Housekeeping gene analysis revealed that Az39T, together with five strains of the genus (Az19, REC3, BR 11975, MTCC4035 and MTCC4036), form a cluster apart from A. baldaniorum Sp245T, A. brasilense Sp7T and A. formosense CC-Nfb-7T. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) between Az39T and the aforementioned type strains revealed values below 96 %, the circumscription limit for the species delineation (ANI: 95.3, 94.1 and 94.0 %; dDDH: 62.9, 56.3 and 55.6 %). Furthermore, a phylogeny evaluation of the core proteome, including 809 common shared proteins, showed an independent grouping of Az39T, Az19, REC3, BR 11975, MTCC4035 and MTCC4036. The G+C content in the genomic DNA of these six strains varied from 68.3 to 68.5 %. Based on the combined phylogenetic, genomic and phenotypic characterization presented here, we consider that strain Az39T, along with strains Az19, REC3, BR 11975, MTCC4035 and MTCC4036, are members of a new Azospirillum species, for which the name Azospirillum argentinense sp. nov. is proposed. The type strain is Az39T (=LBPCV39T=BR 148428T=CCCT 22.01T).

Phosphate solubilizing bacteria can significantly contribute to enhance P availability from polyphosphates and their use efficiency in wheat

Rhizosphere microbes significantly enhance phosphorus (P) availability from a variety of unavailable P pools in agricultural soils. However, little is known about the contribution of root-associated microorganisms, notably P solubilizing bacteria (PSB), to enhance the use of polyphosphate (PolyP) fertilizers as well as the key mechanisms involved. This study assesses the ability of four PSB (Bacillus siamensis, Rahnella aceris, Pantoea hericii, Bacillus paramycoides) and their consortium (Cs) to enhance the release rate of available P from two types of PolyP ("PolyB" and "PolyC") with a focus on the key role of phosphatase enzyme activities and organic acids production. Wheat growth performance and P acquisition efficiency were evaluated in response to co-application of PSB and PolyP. Results showed that inoculation with PSB, notably Cs, significantly enhanced available P from PolyC, PolyB and tri-calcium P. Increased available P in response to inoculation with PSB significantly correlated with medium acidification, organic acids production (notably glycolic acid) and induced activities of acid phosphatase and pyrophosphatase. In planta, the co-application of PSB-PolyP improved wheat plant biomass, root growth and P acquisition, with best results obtained from Cs-PolyP co-application as compared to uninoculated and unfertilized plants. At seedling stage, the co-application of Cs-PolyP (PolyB and PolyC) enhanced root hairs length (125 % and 131 %), root length (26 % and 37 %) and root inorganic P (Pi) content (160 % and 182 %), respectively compared to uninoculated plants. Similarly, at tillering stage, plant biomass (35 % and 47 %), Pi content (43 % and 253 %), P translocation (215 % and 315 %) and soil phosphatases (213 % and 219 %) significantly improved under PolyB and PolyC application, respectively. Findings from this study demonstrate the key role of PSB to enhance the use of PolyP through production of organic acids and phosphatases, exhibiting differential traits patterns between the two PolyP. Improved wheat growth and root P acquisition in response to PSB-PolyP co-application can be attributed to induced rhizosphere processes leading to enhanced available P taken up by roots.

Validation and Evaluation of Plant Growth Promoting Potential of Rhizobacteria Towards Paddy Plants

This study aimed to characterize, validate, and evaluate the plant growth potential of bacterial isolates (E-2, T-2, and T-1) to determine their suitability for application as biofertilizers and/or plant-biostimulants. The plant growth-promoting potential of bacteria (E-2, T-2, and T-1) has been validated in a hydroponic study on paddy plants by inoculating bacterial isolates and monitoring the phenotypic and plant growth responses. The applicability of bacteria was tested based on their tolerance to salinity, susceptibility to antibiotics, and identification based on 16S rDNA sequencing. The isolates E-2, T-2, and T-1 improved plant growth variably and significantly (P < 0.05 at 95% confidence interval) when inoculated into the plant growth matrix, ensuring nutrient availability to the plants grown under a nutrient (nitrate or phosphate) deprived growth matrix. Isolates E-2, T-2, and T-1 grew at salt (NaCl) concentrations of 7%, 6%, and 6%, respectively, and were tolerant to saline conditions. Although these three isolates exhibited resistance to certain antibiotics, they were susceptible to a large number of readily available antibiotics. Isolates E-2, T-2, and T-1 were identified as Klebsiella sp. strain BAB-6433, Citrobacter freundii strain R2A5, and Citrobacter sp. DY1981 respectively, and all of these may be assigned to Risk-Group-2 and hence are safe in view of their susceptibility to readily available antibiotics. Hence, these isolates are promising for extensive evaluation as bioinoculants to ecologically improve soil quality, fertility, crop growth, and yield.

Metabolomics and microbiome reveal potential root microbiota affecting the alkaloidal metabolome in Aconitum vilmorinianum Kom

Background

The plant microbiome is vital for plant health, fitness, and productivity. Interestingly, plant metabolites and the plant microbiome can influence each other. The combination of metabolomics and microbiome may reveal the critical links between the plant and its microbiome. It is of great significance to agricultural production and human health, especially for Chinese medicine research. Aconitum vilmorinianum Kom. is a herb with alkaloid activities, and its roots are the raw material for some Chinese medicines. Former studies have investigated alkaloidal metabolites and antibacterial activities of endophytes in A. vilmorinianum roots. However, there are limited reports on the root microbiota that can influence the alkaloidal metabolome of A. vilmorinianum.

Results

This research used ultra performance liquid chromatography-tandem mass spectrometry technology and high-throughput sequencing to examine the alkaloidal metabolome, bacterial microbiota, and fungal microbiota in A. vilmorinianum roots at two different sites in China. The results revealed that the samples from the two sites were rich in distinct alkaloidal metabolites and recruited significantly different root microbiota. Based on bioinformatics analysis, we found the potential bacterial and fungal microbiota impacting the alkaloidal metabolome in A. vilmorinianum.

Conclusion

Our findings reveal the composition of the alkaloidal metabolome, bacterial root microbiota, and fungal root microbiota in A. vilmorinianum roots at two different sites. Potential root microbiota that can influence the alkaloidal metabolome of A. vilmorinianum are indicated. This study provides a strategy for the cultivation and research of A. vilmorinianum and other Chinese herbs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02486-1.

Plant Growth Promotion Diversity in Switchgrass-Colonizing, Diazotrophic Endophytes

Endophytic nitrogen-fixing (diazotrophic) bacteria are essential members of the microbiome of switchgrass (Panicum virgatum), considered to be an important commodity crop in bioenergy production. While endophytic diazotrophs are known to provide fixed atmospheric nitrogen to their host plant, there are many other plant growth-promoting (PGP) capabilities of these organisms to be demonstrated. The diversity of PGP traits across different taxa of switchgrass-colonizing endophytes is understudied, yet critical for understanding endophytic function and improving cultivation methods of important commodity crops. Here, we present the isolation and characterization of three diazotrophic endophytes: Azospirillum agricola R1C, Klebsiella variicola F10Cl, and Raoultella terrigena R1Gly. Strains R1C and F10Cl were isolated from switchgrass and strain R1Gly, while isolated from tobacco, is demonstrated herein to colonize switchgrass. Each strain exhibited highly diverse genomic and phenotypic PGP capabilities. Strain F10Cl and R1Gly demonstrated the highest functional similarity, suggesting that, while endophyte community structure may vary widely based on host species, differences in functional diversity are not a clearly delineated. The results of this study advance our understanding of diazotrophic endophyte diversity, which will allow us to design robust strategies to improve cultivation methods of many economically important commodity crops.

Targeting redox metabolism of the maize-Azospirillum brasilense interaction exposed to arsenic-affected groundwater

Arsenic in groundwater constitutes an agronomic problem due to its potential accumulation in the food chain. Among the agro-sustainable tools to reduce metal(oid)s toxicity, the use of plant growth-promoting bacteria (PGPB) becomes important. For that, and based on previous results in which significant differences of As translocation were observed when inoculating maize plants with Az39 or CD Azospirillum strains, we decided to decipher the redox metabolism changes and the antioxidant system response of maize plants inoculated when exposed to a realistic arsenate (As^V ) dose. Results showed that As^V caused morphological changes in the root exodermis. Photosynthetic pigments decreased only in CD inoculated plants, while oxidative stress evidence was detected throughout the plant, regardless of the assayed strain. The antioxidant response was strain-differential since only CD inoculated plants showed an increase in superoxide dismutase, glutathione S-transferase (GST), and glutathione reductase (GR) activities while other enzymes showed the same behavior irrespective of the inoculated strain. Gene expression assays reported that only GST23 transcript level was upregulated by arsenate, regardless of the inoculated strain. As^V diminished the glutathione (GSH) content of roots inoculated with the Az39 strain, and CD inoculated plants showed a decrease of oxidized GSH (GSSG) levels. We suggest a model in which the antioxidant response of the maize-diazotrophs system is modulated by the strain and that GSH plays a central role acting mainly as a substrate for GST. These findings generate knowledge for a suitable PGPB selection, and its scaling to an effective bioinoculant formulation for maize crops exposed to adverse environmental conditions.

Utilization of Microbial Consortia as Biofertilizers and Biopesticides for the Production of Feasible Agricultural Product

Farmers are now facing a reduction in agricultural crop yield, due to the infertility of soils and poor farming. The application of chemical fertilizers distresses soil fertility and also human health. Inappropriate use of chemical fertilizer leads to the rapid decline in production levels in most parts of the world, and hence requires the necessary standards of good cultivation practice. Biofertilizers and biopesticides have been used in recent years by farmers worldwide to preserve natural soil conditions. Biofertilizer, a replacement for chemical fertilizer, is cost-effective and prevents environmental contamination to the atmosphere, and is a source of renewable energy. In contrast to chemical fertilizers, biofertilizers are cost-effective and a source of renewable energy that preserves long-term soil fertility. The use of biofertilizers is, therefore, inevitable to increase the earth's productivity. A low-input scheme is feasible to achieve farm sustainability through the use of biological and organic fertilizers. This study investigates the use of microbial inoculants as biofertilizers to increase crop production.

Diversity and Taxonomic Distribution of Endophytic Bacterial Community in the Rice Plant and Its Prospective

Endophytic bacterial communities are beneficial communities for host plants that exist inside the surfaces of plant tissues, and their application improves plant growth. They benefit directly from the host plant by enhancing the nutrient amount of the plant’s intake and influencing the phytohormones, which are responsible for growth promotion and stress. Endophytic bacteria play an important role in plant-growth promotion (PGP) by regulating the indirect mechanism targeting pest and pathogens through hydrolytic enzymes, antibiotics, biocontrol potential, and nutrient restriction for pathogens. To attain these benefits, firstly bacterial communities must be colonized by plant tissues. The nature of colonization can be achieved by using a set of traits, including attachment behavior and motility speed, degradation of plant polymers, and plant defense evasion. The diversity of bacterial endophytes colonization depends on various factors, such as plants’ relationship with environmental factors. Generally, each endophytic bacteria has a wide host range, and they are used as bio-inoculants in the form of synthetic applications for sustainable agriculture systems and to protect the environment from chemical hazards. This review discusses and explores the taxonomic distribution of endophytic bacteria associated with different genotypes of rice plants and their origin, movement, and mechanism of PGP. In addition, this review accentuates compressive meta data of endophytic bacteria communities associated with different genotypes of rice plants, retrieves their plant-growth-promoting properties and their antagonism against plant pathogens, and discusses the indication of endophytic bacterial flora in rice plant tissues using various methods. The future direction deepens the study of novel endophytic bacterial communities and their identification from rice plants through innovative techniques and their application for sustainable agriculture systems.

Cork Oak Forests Soil Bacteria: Potential for Sustainable Agroforest Production

Plant growth promoting rhizobacteria (PGPR) are in increasing demand due to their role in promoting sustainable practices, not only in agriculture but also in forestry. Keeping in mind the future application of PGPR for increasing cork oak sustainability, the aim of this study was to find cork oak PGPR isolates with increased nutrient solubilisation traits, able to promote root morphological changes and/or antagonize cork oak bark phytopathogens. Soils from three cork oak forests with distinct bioclimates (humid, semi-humid and semi-arid) were used for isolating bacteria. From the 7634 colony-forming units, 323 bacterial isolates were biochemically assayed for PGPR traits (siderophores production, phosphate solubilizing and organic acids production), and 51 were found to display all these traits. These PGPR were able to induce root morphological changes on Arabidopsis thaliana, like suppression of primary root growth, increase of lateral roots or root hairs formation. However, the most proficient PGPR displayed specific ability in changing a single root morphological trait. This ability was related not only to bacterial genotype, but also with the environment where bacteria thrived and isolation temperature. Bacteria from semi-arid environments (mainly Bacillus megaterium isolates) could hold a promising tool to enhance plant development. Other isolates (Serratia quinivorens or B. cereus) could be further explored for biocontrol purposes.

Growth-promoting effects of Bradyrhizobium soybean symbionts in black oats, white oats, and ryegrass

Although inoculating soybean with rhizobia for biological nitrogen fixation is a common practice in agriculture, rhizobia are also known to associate with grasses. In this study, we evaluate the potential utility of the rhizobial strains SEMIA 587 and 5019 (Bradyrhizobium elkanii), 5079 (Bradyrhizobium japonicum), and 5080 (Bradyrhizobium diazoefficiens), recommended for Brazilian soybean inoculation, in colonizing black oat plants and promoting growth in black and white oats, and ryegrass. Inoculation of white oats with SEMIA 587 increase the seed germination (SG) by 32.09%, whereas the SG of black oats inoculated with SEMIA 587 and 5019 increased by 40.38% and 37.85%, respectively. Similarly, inoculation of ryegrass with all strains increased SG values between 24.63 and 27.59%. In addition, white oats with SEMIA 587 and 5080 had root areas significantly superior to those in other treatments, whereas inoculation with SEMIA 5079 and 5080 resulted in the highest volume of roots. Likewise, SEMIA 5079 and 5080 significantly increased the length, volume, and area of black oats roots, whereas SEMIA 587 increased the volume, area, and dry mass of roots and shoot. Inoculation in ryegrass with SEMIA 587 significantly increased the root volume. Moreover, most strains transformed with gfp and gus were observed to colonize the roots of black oats. Collectively, the findings of this study indicate that rhizobial strains recommended for inoculation of soybean can also be used to promote the growth of the three assessed grass species, and are able to colonize the roots of black oats.

Localization and survival of Azospirillum brasilense Az39 in soybean leaves

In recent years, foliar inoculation has gained acceptance among the available methods to deliver plant beneficial micro-organisms to crops under field conditions. Colonization efficiency by such micro-organisms largely depends on their ability to survive when applied on the leaves. In this work, we evaluated the survival and localization of Azospirillum brasilense Az39 (Az39) in excised soybean leaves. Scanning electron microscopy and confocal laser scanning microscopy of a red fluorescent-transformed variant of Az39 were used to determine bacterial localization, while the most probable number and plate count methods were applied for bacterial quantification. Microscopic observations indicated a decrease in the number of Az39 cells on the leaf surface at 24 h after treatment, whereas midribs and cell-cell junctions of the inner leaf epidermis became highly populated zones. The presence of Az39 inside xylem vessels was corroborated at 6 h after bacterization. Az39 population did not significantly decrease throughout 24 h. We could visualize Az39 cells on the surface and in internal tissues of soybean leaves and recover them through culture methodologies. These results evidence the survival capacity of Az39 on and inside leaves and suggest a previously unnoticed endophytic potential for this well-known plant growth-promoting rhizobacteria strain.

Delineation of mechanistic approaches employed by plant growth promoting microorganisms for improving drought stress tolerance in plants

Drought stress is expected to increase in intensity, frequency, and duration in many parts of the world, with potential negative impacts on plant growth and productivity. The plants have evolved complex physiological and biochemical mechanisms to respond and adjust to water-deficient environments. The physiological and biochemical mechanisms associated with water-stress tolerance and water-use efficiency have been extensively studied. Besides these adaptive and mitigating strategies, the plant growth-promoting rhizobacteria (PGPR) play a significant role in alleviating plant drought stress. These beneficial microorganisms colonize the endo-rhizosphere/rhizosphere of plants and enhance drought tolerance. The common mechanism by which these microorganisms improve drought tolerance included the production of volatile compounds, phytohormones, siderophores, exopolysaccharides, 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase), accumulation of antioxidant, stress-induced metabolites such as osmotic solutes proline, alternation in leaf and root morphology and regulation of the stress-responsive genes. The PGPR is an easy and efficient alternative approach to genetic manipulation and crop enhancement practices because plant breeding and genetic modification are time-consuming and expensive processes for obtaining stress-tolerant varieties. In this review, we will elaborate on PGPR's mechanistic approaches in enhancing the plant stress tolerance to cope with the drought stress.

PGPR Mediated Alterations in Root Traits: Way Toward Sustainable Crop Production

The above ground growth of the plant is highly dependent on the belowground root system. Rhizosphere is the zone of continuous interplay between plant roots and soil microbial communities. Plants, through root exudates, attract rhizosphere microorganisms to colonize the root surface and internal tissues. Many of these microorganisms known as plant growth promoting rhizobacteria (PGPR) improve plant growth through several direct and indirect mechanisms including biological nitrogen fixation, nutrient solubilization, and disease-control. Many PGPR, by producing phytohormones, volatile organic compounds, and secondary metabolites play important role in influencing the root architecture and growth, resulting in increased surface area for nutrient exchange and other rhizosphere effects. PGPR also improve resource use efficiency of the root system by improving the root system functioning at physiological levels. PGPR mediated root trait alterations can contribute to agroecosystem through improving crop stand, resource use efficiency, stress tolerance, soil structure etc. Thus, PGPR capable of modulating root traits can play important role in agricultural sustainability and root traits can be used as a primary criterion for the selection of potential PGPR strains. Available PGPR studies emphasize root morphological and physiological traits to assess the effect of PGPR. However, these traits can be influenced by various external factors and may give varying results. Therefore, it is important to understand the pathways and genes involved in plant root traits and the microbial signals/metabolites that can intercept and/or intersect these pathways for modulating root traits. The use of advanced tools and technologies can help to decipher the mechanisms involved in PGPR mediated determinants affecting the root traits. Further identification of PGPR based determinants/signaling molecules capable of regulating root trait genes and pathways can open up new avenues in PGPR research. The present review updates recent knowledge on the PGPR influence on root architecture and root functional traits and its benefits to the agro-ecosystem. Efforts have been made to understand the bacterial signals/determinants that can play regulatory role in the expression of root traits and their prospects in sustainable agriculture. The review will be helpful in providing future directions to the researchers working on PGPR and root system functioning.

Effects of Mineral-Solubilizing Microorganisms on Root Growth, Soil Nutrient Content, and Enzyme Activities in the Rhizosphere Soil of Robinia pseudoacacia

Background: Abandoned mining sites are becoming increasingly common due to anthropogenic activities. Consequently, external-soil spray seeding technology has attracted increasing attention as a strategy to remediate them. However, significant challenges remain that greatly inhibit the efficacy of such technologies, such as insufficient nutrients available for plants. Methods: For this study, we designed an experiment, which involved the addition of mineral-solubilizing microorganisms and R. pseudoacacia seedlings to the external-soil spray seeding (ESSS) substrate, and measured the soil nutrients, enzyme activities, and root growth of R. pseudoacacia. Results: First, the combination of certain mineral-solubilizing microorganisms with ESSS advanced its efficiency by increasing the availability of soil nutrients and soil enzymatic activities in association with R. pseudoacacia. Furthermore, the improvement of root growth of R. pseudoacacia was intimately related to soil nutrients, particularly for soil total nitrogen (TN) and total sulfur (TS). In general, the effects of the J2 (combined Bacillus thuringiensis and Gongronella butleri) treatment for soil nutrients, enzyme activities, and plant growth were the strongest. Conclusion: In summary, the results of our experiment revealed that these mineral-solubilizing microorganisms conveyed a promotional effect on R. pseudoacacia seedlings by increasing the soil nutrient content. These results provide basic data and microbial resources for the development and applications of mineral-solubilizing microorganisms for abandoned mine remediation.

Signs of a phyllospheric lifestyle in the genome of the stress-tolerant strain Azospirillum brasilense Az19

Azospirillum brasilense Az19 is a plant-beneficial bacterium capable of protecting plants from the negative effects of drought. The objective of this study was to determine and analyze the genomic sequence of strain Az19 as a means of identifying putative stress-adaptation mechanisms. A high-quality draft genome of ca. 7 Mb with a predicted coding potential of 6710 genes was obtained. Phylogenomic analyses confirmed that Az19 belongs to the brasilense clade and is closely related to strains Az39 and REC3. Functional genomics revealed that the denitrification pathway of Az19 is incomplete, which was in agreement with a reduced growth on nitrate under low O₂ concentrations. Putative genes of the general stress response and oxidative stress-tolerance, as well as synthesis of exopolysaccharides, carotenoids, polyamines and several osmolytes, were detected. An additional poly-beta-hydroxybutyrate (PHB) synthase coding gene was found in Az19 genome, but the accumulation of PHB did not increase under salinity. The detection of exclusive genes related to DNA repair led to discover that strain Az19 also has improved UV-tolerance, both in vitro and in planta. Finally, the analysis revealed the presence of multiple kaiC-like genes, which could be involved in stress-tolerance and, possibly, light responsiveness. Although A. brasilense has been a model for the study of beneficial plant-associated rhizobacteria, the evidence collected in this current study suggests, for the first time in this bacterial group, an unexpected possibility of adaptation to the phyllosphere.

Plant growth-promoting endophytic bacteria augment growth and salinity tolerance in rice plants

Salt stress negatively affects growth and development of plants. However, it is hypothesized that plant growth-promoting endophytic bacteria can greatly alleviate the adverse effects of salinity and can promote growth and development of plants. In the present research, we aimed to isolate endophytic bacteria from halotolerant plants and evaluate their capacity for promoting crop plant growth. The bacterial endophytes were isolated from selected plants inhabiting sand dunes at Pohang beach, screened for plant growth-promoting traits and applied to rice seedlings under salt stress (NaCl; 150 mm). Out of 59 endophytic bacterial isolates, only six isolates, i.e. Curtobacterium oceanosedimentum SAK1, Curtobacterium luteum SAK2, Enterobacter ludwigii SAK5, Bacillus cereus SA1, Micrococcus yunnanensis SA2, Enterobacter tabaci SA3, resulted in a significant increase in the growth of Waito-C rice. The cultural filtrates of bacterial endophytes were tested for phytohormones, including indole-3-acetic acid, gibberellins and organic acids. Inoculation of the selected strains considerably reduced the amount of endogenous ABA in rice plants under NaCl stress, however, they increased GSH and sugar content. Similarly, these strains augmented the expression of flavin monooxygenase (OsYUCCA1) and auxin efflux carrier (OsPIN1) genes under salt stress. In conclusion, the pragmatic application of the above selected bacterial strains alleviated the adverse effects of NaCl stress and enhanced rice growth attributes by producing various phytohormones.

Characterization of bacterial community structure in the rhizosphere of Triticum aestivum L

The plant microbiome influence plant health, yield and vigor and has attained a considerable attention in the present era. In the current study, native bacterial community composition and diversity colonizing Triticum aestivum L. rhizosphere at two distant geographical locations including Mirpur Azad Kashmir and Islamabad was elucidated. Based on IonS5™XL platform sequencing of respective samples targeting 16S rRNA gene that harbor V3-V4 conserved region revealed 1364 and 1254 microbial operational taxonomic units (OTUs) at ≥97% similarity and were classified into 23, 20 phyla; 70, 65 classes; 101, 87 orders; 189,180 families; 275, 271 genera and 94, 95 species. Respective predominant phyla accounting for 97.90% and 98.60% of bacterial community were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Chloroflexi and Gemmatimonadetes. Diversity indices revealed variations in relative abundance of bacterial taxa owing to distant geographical locations however predominant bacterial taxa at both locations were similar. These findings paved a way to dissect consequence of associated microbiota on future wheat production system.

Plant Growth Enhancement using Rhizospheric Halotolerant Phosphate Solubilizing Bacterium Bacillus licheniformis QA1 and Enterobacter asburiae QF11 Isolated from Chenopodium quinoa Willd

Plant growth-promoting rhizobacteria represent a promising solution to enhancing agricultural productivity. Here, we screened phosphate solubilizing bacteria from the rhizospheric soil of Chenopodium quinoa Willd and assessed their plant-growth promoting rhizobacteria (PGPR) properties including production of indole-3-acetic acid (IAA), siderophores, hydrogen cyanide (HCN), ammonia and extracellular enzymes. We also investigated their tolerance to salt stress and their capacity to form biofilms. Two isolated strains, named QA1 and QF11, solubilized phosphate up to 346 mg/L, produced IAA up to 795.31 µg/mL, and tolerated up to 2 M NaCl in vitro. 16S rRNA and Cpn60 gene sequencing revealed that QA1 and QF11 belong to the genus Bacillus licheniformis and Enterobacter asburiae, respectively. In vivo, early plant growth potential showed that quinoa seeds inoculated either with QA1 or QF11 displayed higher germination rates and increased seedling growth. Under saline irrigation conditions, QA1 enhanced plant development/growth. Inoculation with QA1 increased leaf chlorophyll content index, enhanced P and K+ uptake and decreased plant Na+ uptake. Likewise, plants inoculated with QF11 strain accumulated more K+ and had reduced Na+ content. Collectively, our findings support the use of QA1 and QF11 as potential biofertilizers.

Endophytic microbes: biodiversity, plant growth-promoting mechanisms and potential applications for agricultural sustainability

Endophytic microbes are known to live asymptomatically inside their host throughout different stages of their life cycle and play crucial roles in the growth, development, fitness, and diversification of plants. The plant-endophyte association ranges from mutualism to pathogenicity. These microbes help the host to combat a diverse array of biotic and abiotic stressful conditions. Endophytic microbes play a major role in the growth promotion of their host by solubilizing of macronutrients such as phosphorous, potassium, and zinc; fixing of atmospheric nitrogen, synthesizing of phytohormones, siderophores, hydrogen cyanide, ammonia, and act as a biocontrol agent against wide array of phytopathogens. Endophytic microbes are beneficial to plants by directly promoting their growth or indirectly by inhibiting the growth of phytopathogens. Over a long period of co-evolution, endophytic microbes have attained the mechanism of synthesis of various hydrolytic enzymes such as pectinase, xylanases, cellulase, and proteinase which help in the penetration of endophytic microbes into tissues of plants. The effective usage of endophytic microbes in the form of bioinoculants reduce the usage of chemical fertilizers. Endophytic microbes belong to different phyla such as Actinobacteria, Acidobacteria, Bacteroidetes, Deinococcus-thermus, Firmicutes, Proteobacteria, and Verrucomicrobia. The most predominant and studied endophytic bacteria belonged to Proteobacteria followed by Firmicutes and then by Actinobacteria. The most dominant among reported genera in most of the leguminous and non-leguminous plants are Bacillus, Pseudomonas, Fusarium, Burkholderia, Rhizobium, and Klebsiella. In future, endophytic microbes have a wide range of potential for maintaining health of plant as well as environmental conditions for agricultural sustainability. The present review is focused on endophytic microbes, their diversity in leguminous as well as non-leguminous crops, biotechnological applications, and ability to promote the growth of plant for agro-environmental sustainability.

Biochemical and molecular characterization of arsenic response from Azospirillum brasilense Cd, a bacterial strain used as plant inoculant

Azospirillum brasilense Cd is a bacterial strain widely used as an inoculant of several crops due to its plant growth promoting properties. However, its beneficial effects depend on its viability and functionality under adverse environmental conditions, including the presence of arsenic (As) in agricultural soils. Therefore, the aim of this work was to evaluate the response of A. brasilense Cd to arsenate (AsV) and arsenite (AsIII). This bacterium was tolerant to As concentrations frequently found in soils. Moreover, properties related to roots colonization (motility, biofilm, and exopolymers) and plant growth promotion (auxin, siderophore production, and N₂ fixation) were not significantly affected by the metalloid. In order to deepen the understanding on As responses of A. brasilense Cd, As resistance genes were sequenced and characterized for the first time in this work. These genes could mediate the redox As transformation and its extrusion outside the cell, so they could have direct association with the As tolerance observed. In addition, its As oxidation/reduction capacity could contribute to change the AsV/AsIII ratio in the environment. In conclusion, the results allowed to elucidate the As response of A. brasilense Cd and generate interest for its potential use in polluted environments.

Microbial inoculants: reviewing the past, discussing the present and previewing an outstanding future for the use of beneficial bacteria in agriculture

More than one hundred years have passed since the development of the first microbial inoculant for plants. Nowadays, the use of microbial inoculants in agriculture is spread worldwide for different crops and carrying different microorganisms. In the last decades, impressive progress has been achieved in the production, commercialization and use of inoculants. Nowadays, farmers are more receptive to the use of inoculants mainly because high-quality products and multi-purpose elite strains are available at the market, improving yields at low cost in comparison to chemical fertilizers. In the context of a more sustainable agriculture, microbial inoculants also help to mitigate environmental impacts caused by agrochemicals. Challenges rely on the production of microbial inoculants for a broader range of crops, and the expansion of the inoculated area worldwide, in addition to the search for innovative microbial solutions in areas subjected to increasing episodes of environmental stresses. In this review, we explore the world market for inoculants, showing which bacteria are prominent as inoculants in different countries, and we discuss the main research strategies that might contribute to improve the use of microbial inoculants in agriculture.

Promising bacterial genera for agricultural practices: An insight on plant growth-promoting properties and microbial safety aspects

In order to address the ever-increasing problem of the world's population food needs, the optimization of farming crops yield, the combat of iron deficiency in plants (chlorosis) and the elimination/reduction of crop pathogens are of key challenges to solve. Traditional ways of solving these problems are either unpractical on a large scale (e.g. use of manure) or are not environmental friendly (e.g. application of iron-synthetic fertilizers or indiscriminate use of pesticides). Therefore, the search for greener substitutes, such as the application of siderophores of bacterial source or the use of plant-growth promoting bacteria (PGPB), is presented as a very promising alternative to enhance yield of crops and performance. However, the use of microorganisms is not a risk-free solution and the potential biohazards associated with the utilization of bacteria in agriculture should be considered. The present work gives a current overview of the main mechanisms associated with the use of bacteria in the promotion of plant growth. The potentiality of several bacterial genera (Azotobacter, Azospirillum, Bacillus, Pantoea, Pseudomonas and Rhizobium) regarding to siderophore production capacity and other plant growth-promoting properties are presented. In addition, the field performance of these bacteria genera as well as the biosafety aspects related with their use for agricultural proposes are reviewed and discussed.

Plant Tissue Localization and Morphological Conversion of Azospirillum brasilense upon Initial Interaction with Allium cepa L

The genus Azospirillum is recognized as plant growth-promoting bacteria that exert beneficial effects on the host plant and is morphologically converted into cyst-like cells (i.e., c-form) in association with poly-β-hydroxybutyrate (PHB) accumulation in the cells under stress conditions. We constructed Azospirillum brasilense, labeled with reporter genes (gus/gfp, mCherry) and examined the plant tissue localization along with a morphological conversion into the c-form upon its initial interaction with onion seedlings (Allium cepa L.). The PHB granules in the A. brasilense cells were easily detected under fluorescence as “black holes”, rendering it possible to monitor the morphological conversion from vegetative to the c-form cells. The results showed that the A. brasilense cells on the surface of the roots and bulbs (underground stem) began converting at three days following inoculation and that the cell conversion was significantly advanced with time along with the cell population increase. The endophytic infection of A. brasilense into the bulb tissues was also confirmed, although these likely constituted vegetative cells. Moreover, the morphological conversion into the c-form was induced under nitrogen-restricted conditions. Analysis of the biochemical properties of the A. brasilense cells during cell conversion revealed that the acetylene reduction activity correlated positively with the PHB accumulation in the cells converting into the c-form under nitrogen-restricted conditions.

Analysis of Indole-3-acetic Acid (IAA) Production in Klebsiellaby LC-MS/MS and the Salkowski Method

Many rhizobacteria isolated from plant rhizosphere produce various phytohormones in the form of secondary metabolites, the most common of which is Indole-3-acetic acid (IAA). Here, we detail analytical protocols of IAA detection and quantification, in vitro and in situ, as recently applied to Klebsiella SGM 81, a rhizobacterium isolated from the rhizosphere of Dianthus caryophyllus (a commercially important flower across the globe). Specifically, we describe a detailed protocol for a colorimetric assay using the Salkowski reagent method, which can be used to screen for the presence of Indole compounds. To further detect and quantify IAA, a highly accurate analytical approach of LC-MS/MS is used. To detect the presence of IAA around the root system of Dianthus caryophyllus, in situ staining of plant roots is done using Salkowski reagent.

Azospirillum brasilense Az39, a model rhizobacterium with AHL quorum-quenching capacity

AIMS

The aim of this research was to analyse the quorum-sensing (QS) and quorum-quenching (QQ) mechanisms based on N-acyl-l-homoserine lactones (AHLs) in Azospirillum brasilense Az39, a strain with remarkable capacity to benefit a wide range of crops under agronomic conditions.

METHODS AND RESULTS

We performed an in silico and in vitro analysis of the quorum mechanisms in A. brasilense Az39. The results obtained in vitro using the reporter strains Chromobacterium violaceum and Agrobacterium tumefaciens and liquid chromatography coupled with mass-mass spectrometry analysis showed that although Az39 does not produce AHL molecules, it is capable of degrading them by at least two hypothetical enzymes identified by bioinformatics approach, associated with the bacterial cell. In Az39 cultures supplemented with 500 nmol l^-1 of the C3 unsubstituted AHLs (C4, C6, C8, C10, C12, C14), AHL levels were lower than in noninoculated LB media controls. Similar results were observed upon the addition of AHLs with hydroxy (OH-) and keto (oxo-) substitutions in C3. These results not only demonstrate the ability of Az39 to degrade AHLs. They also show the wide spectrum of molecules that can be degraded by this bacterium.

CONCLUSIONS

Although A. brasilense Az39 is a silent bacterium unable to produce AHL signals, it is able to interrupt the communications between other bacteria and/or plants by a QQ activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report confirming by unequivocal methodology the ability of A. brasilense, one of the most agriculturally used benefic bacteria around the world, to degrade AHLs by a QQ mechanism.

Azospirillum brasilense inoculation counteracts the induction of nitrate uptake in maize plants

Nitrogen (N) represents one of the limiting factors for crop growth and productivity and to date has been widely supplied via external application of fertilizers. However, the use of plant growth-promoting rhizobacteria (PGPR) might represent a valuable tool to further improve plant nutrition. This study examines the influence of Azospirillum brasilense strain Cd on nitrate uptake in maize (Zea mays) plants, focusing on the high-affinity transport system (HATS). Plants were induced with nitrate (500 µM) and either inoculated or not with Azospirillum. Inoculation decreased the nitrate uptake rate in induced plants, suggesting that Azospirillum may negatively affect HATS in the short term. The expression dynamics of ZmNF-YA and ZmLBD37 suggested that Azospirillum affected the N balance in the plants, most probably by supplying them with reduced N, i.e. NH4+. This was further corroborated by measurements of total N and the expression of ammonium transporter genes. Overall, our data demonstrate that Azospirillum can counteract the plant response to nitrate induction, albeit without compromising N nutrition. This suggests that the agricultural application of microbial inoculants requires fine-tuning of external fertilizer inputs.

Diversity analysis of the rhizospheric and endophytic bacterial communities of Senecio vulgaris L. (Asteraceae) in an invasive range

Increasing evidence has confirmed the importance of plant-associated bacteria for plant growth and productivity, and thus it is hypothesized that interactions between bacteria and alien plants might play an important role in plant invasions. However, the diversity of the bacterial communities associated with invasive plants is poorly understood. We therefore investigated the diversity of rhizospheric and endophytic bacteria associated with the invasive annual plant Senecio vulgaris L. (Asteraceae) based on 16S rRNA gene data obtained from 57 samples of four Senecio vulgaris populations in a subtropical mountainous area in central China. Significant differences in diversity were observed between plant compartments. Specifically, the rhizosphere harbored many more bacterial operational taxonomic units and showed higher alpha diversity than the leaf and root endospheres. The relative abundance profiles of the bacterial community composition differed substantially between the compartments and populations, especially at the phylum and family levels. However, the top five phyla (Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Acidobacteria) accounted for more than 90% of all the bacterial communities. Moreover, similar endophytic communities with a shared core set of bacteria were observed from different Senecio vulgaris populations. Heavy-metal-resistant, phosphate-solubilizing bacteria (Brevundimonas diminuta), nitrogen-fixing bacteria (Rhizobium leguminosarum), and cold-resistant bacteria (Exiguobacterium sibiricum) were present in the endosphere at relatively high abundance. This study, which reveals the structure of bacterial communities and their putative function in invasive Senecio vulgaris plants, is the first step in investigating the role of plant-bacteria interactions in the invasion of this species in China.

Modulation of polyamine biosynthesis in Arabidopsis thaliana by a drought mitigating Pseudomonas putida strain

Plant growth promoting rhizobacteria (PGPR) are a diverse group of beneficial soil bacteria that help plants in myriad ways. They are implicated in the processes of general growth and development, as well as stress mitigation. Although the physiology of plant-PGPR interaction for abiotic stress tolerance has been well reported, the underlying molecular mechanisms in this phenomenon are not clearly understood. Among the many endogenous molecules that have been reported to impart abiotic stress tolerance in plants are a group of aliphatic amines called polyamines. Here, we report the impact of a free living, drought-mitigating rhizobacterial strain, Pseudomonas putida GAP-P45 on the expression of key genes in the polyamine metabolic pathway and the accumulation of the three major polyamines, putrescine, spermidine and spermine in water-stressed Arabidopsis thaliana. We observed that, inoculation of A. thaliana with P. putida GAP-P45 with or without water-stress, caused significant fluctuations in the expression of most polyamine biosynthetic genes (ADC, AIH, CPA, SPDS, SPMS and SAMDC) and cellular polyamine levels at different days of analysis post treatments. The enhanced accumulation of free cellular putrescine and spermidine observed in this study correlated positively with the water stress tolerant phenotype of A. thaliana in response to P. putida GAP-P45 inoculation reported in our previous study (Ghosh et al., 2017). Our data point towards (a) transcriptional regulation of polyamine biosynthetic genes and (b) complex post transcriptional regulation and/or interconversion/canalization of polyamines, by P. putida GAP-P45 under normal and water-stressed conditions.

Regulation of IAA Biosynthesis in Azospirillum brasilense Under Environmental Stress Conditions

Indole-3-acetic acid (IAA) is one of the most important molecules produced by Azospirillum sp., given that it affects plant growth and development. Azospirillum brasilense strains Sp245 and Az39 (pFAJ64) were pre-incubated in MMAB medium plus 100 mg/mL L-tryptophan and treated with or exposed to the following (a) abiotic and (b) biotic stress effectors: (a) 100 mM NaCl or Na₂SO_4, 4.0% (w/v) PEG_6000, 0.5 mM H₂O_2, 0.1 mM abscisic acid, 0.1 mM 1-aminocyclopropane 1-carboxylic acid, 45 °C or daylight, and (b) 4.0% (v/v) filtered supernatant of Pseudomonas savastanoi (Ps) or Fusarium oxysporum (Fo), 0.1 mM salicylic acid (SA), 0.1 mM methyl jasmonic acid (MeJA), and 0.01% (w/v) chitosan (CH). After 30 and 120 min of incubation, biomass production, cell viability, IAA concentration (µg/mL), and ipdC gene expression were measured. Our results show that IAA production increases with daylight or in the presence of PEG₆₀₀₀, ABA, SA, CH, and Fo. On the contrary, exposure to 45 °C or treatment with H₂O_2, NaCl, Na₂SO_4, ACC, MeJA, and Ps decrease IAA biosynthesis. In this report, growth and IAA biosynthesis in A. brasilense under biotic and abiotic stress conditions are discussed from the point of view of their role in bacterial lifestyle and their potential application as bioproducts.