Studies on the factors modulating indole-3-acetic acid production in endophytic bacterial isolates from Piper nigrum and molecular analysis of ipdc gene

Enhancing rice growth and yield with weed endophytic bacteria Alcaligenes faecalis and Metabacillus indicus under reduced chemical fertilization

Endophytic bacteria, recognized as eco-friendly biofertilizers, have demonstrated the potential to enhance crop growth and yield. While the plant growth-promoting effects of endophytic bacteria have been extensively studied, the impact of weed endophytes remains less explored. In this study, we aimed to isolate endophytic bacteria from native weeds and assess their plant growth-promoting abilities in rice under varying chemical fertilization. The evaluation encompassed measurements of mineral phosphate and potash solubilization, as well as indole-3-acetic acid (IAA) production activity by the selected isolates. Two promising strains, tentatively identified as Alcaligenes faecalis (BTCP01) from Eleusine indica (Goose grass) and Metabacillus indicus (BTDR03) from Cynodon dactylon (Bermuda grass) based on 16S rRNA gene phylogeny, exhibited noteworthy phosphate and potassium solubilization activity, respectively. BTCP01 demonstrated superior phosphate solubilizing activity, while BTDR03 exhibited the highest potassium (K) solubilizing activity. Both isolates synthesized IAA in the presence of L-tryptophan, with the detection of nifH and ipdC genes in their genomes. Application of isolates BTCP01 and BTDR03 through root dipping and spraying at the flowering stage significantly enhanced the agronomic performance of rice variety CV. BRRI dhan29. Notably, combining both strains with 50% of recommended N, P, and K fertilizer doses led to a substantial increase in rice grain yields compared to control plants receiving 100% of recommended doses. Taken together, our results indicate that weed endophytic bacterial strains BTCP01 and BTDR03 hold promise as biofertilizers, potentially reducing the dependency on chemical fertilizers by up to 50%, thereby fostering sustainable rice production.

Effects of Environmental Stresses on Synthesis of 2-Phenylethanol and IAA by Enterobacter sp. CGMCC 5087

2-Phenylethanol (2-PE) and indole-3-acetic acid (IAA) are important secondary metabolites produced by microorganisms, and their production are closely linked to the growth state of microorganisms and environmental factors. Enterobacter CGMCC 5087 can produce both 2-PE and IAA depending on α-ketoacid decarboxylase KDC4427. This study aimed to investigate the effects of different environment factors including osmotic pressure, temperature, and pH on the synthesis of 2-PE and IAA in Enterobacter sp. CGMCC 5087. The bacteria exhibited an enhanced capacity for 2-PE synthesis while not affecting IAA synthesis under 5% NaCl and pH 4.5 stress conditions. In an environment with pH 9.5, the synthesis capacity of 2-PE remained unchanged while the synthesis capacity of IAA decreased. The synthesis ability of 2-PE was enhanced with an increase in temperature within the range of 25 °C to 37 °C, while the synthesis capacity of IAA was not affected significantly. Additionally, the expression of KDC4427 varied under stress conditions. Under 5% NaCl stress and decreased temperature, expression of the KDC4427 gene was increased. However, altering pH did not result in significant differences in gene expression levels, while elevated temperature caused a decrease in gene expression. Furthermore, molecular docking and molecular dynamics simulations suggested that these conditions may induce fluctuation in the geometry shape of binding cavity, binding energy, and especially the dαC-C- value, which played key roles in affecting the enzyme activity. These results provide insights and strategies for the synthesis of metabolic products 2-PE and IAA in bacterial fermentation, even under unfavorable conditions.

Heavy metals mitigation and growth promoting effect of endophytic Agrococcus terreus (MW 979614) in maize plants under zinc and nickel contaminated soil

Introduction

Heavy metals such as iron, copper, manganese, cobalt, silver, zinc, nickel, and arsenic have accumulated in soils for a long time due to the dumping of industrial waste and sewage. Various techniques have been adapted to overcome metal toxicity in agricultural land but utilizing a biological application using potential microorganisms in heavy metals contaminated soil may be a successful approach to decontaminate heavy metals soil. Therefore, the current study aimed to isolate endophytic bacteria from a medicinal plant (Viburnum grandiflorum) and to investigate the growth-promoting and heavy metal detoxification potential of the isolated endophytic bacteria Agrococus tereus (GenBank accession number MW 979614) under nickel and zinc contamination.

Methods

Zinc sulfate and nickel sulfate solutions were prepared at the rate of 100 mg/kg and 50 mg/kg in sterilized distilled water. The experiment was conducted using a completely random design (CRD) with three replicates for each treatment.

Results and Discussion

Inoculation of seeds with A. tereus significantly increased the plant growth, nutrient uptake, and defense system. Treatment T4 (inoculated seeds), T5 (inoculated seeds + Zn100 mg/kg), and T6 (inoculated seeds + Ni 100 mg/kg) were effective, but T5 (inoculated seeds + Zn100 mg/kg) was the most pronounced and increased shoot length, root length, leaf width, plant height, fresh weight, moisture content, and proline by 49%, 38%, 89%, 31%, 113%, and 146%, respectively. Moreover the antioxidant enzymes peroxidase and super oxidase dismutase were accelerated by 211 and 68% in contaminated soil when plants were inoculated by A. tereus respectively. Similarly the inoculation of A. tereus also enhanced maize plants' absorption of Cu, Mn, Ni, Na, Cr, Fe, Ca, Mg, and K significantly. Results of the findings concluded that 100 mg/kg of Zn and Ni were toxic to maize growth, but seed inoculation with A. tereus helped the plants significantly in reducing zinc and nickel stress. The A. tereus strain may be employed as a potential strain for the detoxification of heavy metals.

Whole genome analysis for plant growth promotion profiling of Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte

Reduced agricultural production as well as issues like nutrient-depleted soils, eutrophication, and groundwater contamination have drawn attention to the use of endophyte-based bioformulations to restore soil fertility. Pantoea agglomerans CPHN2, a non-rhizobial nodule endophyte isolated from Cicer arietinum, exhibited a variety of plant growth-promoting traits. In this study, we used NextSeq500 technology to analyze whole-genome sequence information of this plant growth-promoting endophytic bacteria. The genome of P. agglomerans CPHN2 has a length of 4,839,532 bp and a G + C content of 55.2%. The whole genome comprises three different genomic fractions, comprising one circular chromosome and two circular plasmids. A comparative analysis between P. agglomerans CPHN2 and 10 genetically similar strains was performed using a bacterial pan-genome pipeline. All the predicted and annotated gene sequences for plant growth promotions (PGPs), such as phosphate solubilization, siderophore synthesis, nitrogen metabolism, and indole-3-acetic acid (IAA) of P. agglomerans CPHN2, were identified. The whole-genome analysis of P. agglomerans CPHN2 provides an insight into the mechanisms underlying PGP by endophytes and its potential applications as a biofertilizer.

Indole pyruvate decarboxylase gene regulates the auxin synthesis pathway in rice by interacting with the indole-3-acetic acid-amido synthetase gene, promoting root hair development under cadmium stress

This research focused on cadmium (Cd), which negatively affects plant growth and auxin hemostasis. In plants, many processes are indirectly controlled through the expression of certain genes due to the secretion of bacterial auxin, as indole-3-acetic acid (IAA) acts as a reciprocal signaling molecule in plant-microbe interaction. The aim of current studies was to investigate responsible genes in rice for plant-microbe interaction and lateral root development due to the involvement of several metabolic pathways. Studies revealed that GH3-2 interacts with endogenous IAA in a homeostasis manner without directly providing IAA. In rice, indole-3-pyruvate decarboxylase (IPDC) transgenic lines showed a 40% increase in lateral roots. Auxin levels and YUCCA (auxin biosynthesis gene) expression were monitored in osaux1 mutant lines inoculated with Bacillus cereus exposed to Cd. The results showed an increase in root hairs (RHs) and lateral root density, changes in auxin levels, and expression of the YUCCA gene. B. cereus normalizes the oxidative stress caused by Cd due to the accumulation of O 2 - and H₂O₂ in osaux1 mutant lines. Furthermore, the inoculation of B. cereus increases DR5:GUS expression, indicating that bacterial species have a positive role in auxin regulation. Thus, the current study suggests that B. cereus and IPDC transgenic lines increase the RH development in rice by interacting with IAA synthetase genes in the host plant, alleviating Cd toxicity and enhancing plant defense mechanisms.

Evaluating extremophilic microorganisms in industrial regions

Abiotic and biotic stresses have a major impact on crop growth. Stress affects the root system and decreases the amount of nutrients in fruits. Modern agricultural technologies help replace mineral fertilizers with new generation biopreparation. Unlike chemical fertilizers, biofertilizers reduce the risk of adverse environmental impacts. Of special interest are extremophilic microorganisms able to survive in extreme conditions. We aimed to study the phytostimulating ability of extremophilic bacteria isolated from disturbed lands in the coal-mining region. We isolated microorganisms from disturbed lands and studied their cultural, morphological, and biochemical properties. Then, we determined their ability to synthesize indole-3-acetic acids. The extremophilic bacteria were identified and subjected to biocompatibility testing by co-cultivation. Next, we created consortia of pure cultures and analyzed biomass growth. Finally, the biopreparation was experimentally tested on Trifolium prantense L. seeds. We isolated 10 strains of microorganisms that synthesized 4.39 to 16.32 mg/mL of indole-3-acetic acid. The largest amounts of the acid were produced by Pantoea spp., Enterococcus faecium, Leclercia spp., Rothia endophytica, and Klebsiella oxytoca. A consortium of Pantoea spp., E. faecium, and R. endophytica at a ratio of 1:1:1 produced the largest amount of indole-3-acetic acid (15.59 mg/mL) and accumulated maximum biomass. The addition of 0.2% L-tryptophan to the nutrient medium increased the amount of indole-3-acetic acid to 18.45 mg/mL. When the T. prantense L. seeds were soaked in the biopreparation (consortium’s culture fluid) at a concentration of 2.5, the sprouts were 1.4 times longer on the 10th day of growth, compared to the control. The consortium of Pantoea spp., E. faecium, and R. endophytica (1:1:1) stimulated the growth of T. prantense L. seeds. Our findings can be further used to develop biofertilizers for agriculture.

l-Tryptophan-starved cultivation enhances S-allyl-l-cysteine synthesis in various food-related microorganisms

S-Allyl-l-cysteine (SAC) has received much interest due to its beneficial effects on human health. To satisfy the increasing demand for SAC, this study aims to develop a valuable culturing method for microbial screening synthesizing SAC from readily available materials. Although tryptophan synthase is a promising enzyme for SAC synthesis, its expression in microorganisms is strictly regulated by environmental l-tryptophan. Thus, we constructed a semisynthetic medium lacking l-tryptophan using casamino acids. This medium successfully enhanced the SAC-synthesizing activity of Lactococcus lactis ssp. cremoris NBRC 100676. In addition, microorganisms with high SAC-synthesizing activity were screened by the same medium. Food-related Klebsiella pneumoniae K-15 and Pantoea agglomerans P-3 were found to have a significantly increased SAC-synthesizing activity. The SAC-producing process established in this study is shorter in duration than the conventional garlic aging method. Furthermore, this study proposes a promising alternative strategy for producing food-grade SAC by microorganisms.

Chitosan and Gold Nanoparticles Supplementation for Augmentation of Indole-3-Acetic Acid Production by Rhizospheric Pseudomonas aeruginosa and Plant Growth Enhancement

The present study has been focused to evaluate the effect of chitosan nanoparticles (CNPs) and gold nanoparticles (AuNPs) on the phytohormone production by rhizospheric Pseudomonas aeruginosa. The gold nanoparticles were synthesized biologically and characterized by UV-Visible spectrophotometry, transmission electron microscopy, and X-ray diffraction analysis. The indole-3-acetic acid (IAA) production by P. aeruginosa supplemented with CNPs and AuNPs was quantified by using Salkowski's method and confirmed by high-performance liquid chromatography (HPLC) analysis. This revealed the effect of 5 mg/mL CNPs and 100 µg/mL AuNPs to enhance the IAA production by P. aeruginosa. By Salkowski's method, 07.16 ± 0.28 and 09.56 ± 0.28 µg/mL of IAA could be detected in the samples prepared from P. aeruginosa supplemented with 5 mg/mL CNPs and 100 µg/mL AuNPs, respectively. HPLC analysis also confirmed the production of IAA by P. aeruginosa. The CNPs and AuNPs-supplemented P. aeruginosa was also found to have enhancement effect on the shoot length (25.25 ± 0.85 cm and 26.57 ± 0.73 cm) and fresh weight (0.94 ± 0.09 g and 0.96 ± 0.09 g) of Vigna unguiculata plants, which highlight the significance of the study and the agricultural promises of nanomaterials-supplemented rhizobacteria.

Chitosan nanoparticles augmented indole-3-acetic acid production by rhizospheric Pseudomonas monteilii

Rhizospheric Pseudomonas spp. are widely used for upgrading sustainable agriculture because of their ability to execute multifaceted plant beneficial functions. In the current study, chitosan nanoparticles (CNPs) were used to analyze their effect on plant beneficial properties of rhizospheric Pseudomonas monteilii. The CNPs were characterized by transmission electron microscopy (TEM) and dynamic light scattering (DLS) analysis. The impact of CNPs on indole-3-acetic acid (IAA) production of P. monteilii was analyzed and quantified by spectrophotometric and confirmed high-performance liquid chromatography analysis. This revealed the beneficial effect of CNPs (1 mg/ml) by enhancing the IAA production of P. monteilii. In planta effect of varied bacterial IAA production was further demonstrated in Vigna unguiculata. Here, enhancement in shoot length (35.79 ± 0.37 cm), leaf number (7 ± 0.54), and fresh weight (3.07 ± 0.11 g) were observed in the plants treated with the culture filtrate collected from P. monteilii cultivated with 1 mg/ml CNPs. The results of the study highlight the beneficial effect of the CNPs to augment the rhizobacterial functioning by inducing the expression of plant beneficial properties.

Caenorhabditis elegans Extracts Stimulate IAA Biosynthesis in Arthrobacter pascens ZZ21 via the Indole-3-pyruvic Acid Pathway

Inter-organismal metabolites play important roles in regulating organism behavior and the communication between organisms. Nematodes, the most abundant animals on earth, are crucial participants in soil ecosystems through their interactions with microbes. For example, bacterial-feeding nematodes increase the activity of indole-3-acetic acid (IAA)-producing bacteria and the IAA content in soil. However, the way in which these nematodes interact with bacteria and affect IAA biosynthesis is not well understood. Here, using the model nematode Caenorhabditis elegans and the plant-beneficial bacterium Arthrobacter pascens ZZ21, we examined the effects of nematode excretions or extracts on bacterial IAA biosynthesis. To explore the underlying regulatory mechanism in more detail, we performed transcriptome sequencing and metabolomic analysis. Our findings suggest that C. elegans extracts promote IAA biosynthesis in A. pascens ZZ21 by increasing the expression of genes and the abundance of intermediates involved in the indole-3-pyruvic acid (IPyA) pathway. C. elegans extracts also significantly influenced biosynthetic and metabolic activity in A. pascens ZZ21. Treatment with C. elegans extracts promoted pyruvate metabolism, the citrate cycle (TCA) cycle and the production of some TCA-cycle-related amino acids and inhibited oxidative phosphorylation, which induced the accumulation of reduced nicotinamide adenine dinucleotide (NADH). We propose that the extracts altered the metabolism of A. pascens ZZ21 to help the bacteria resist stress caused by their predator. Our findings indicate that bacterial-feeding nematodes mediate the interaction between nematodes and bacteria via their extracts, providing insights into the ecological function of C. elegans in soil.

Optimization of Fermentation Medium for Indole Acetic Acid Production by Pseudarthrobacter sp. NIBRBAC000502770

Indole acetic acid (IAA) has been an important compound for plant growth and is widely known to be produced by plant growth-promoting rhizobacteria (PGPR). The isolate producing the maximum amount of IAA from the Korea shooting range soil was identified as Pseudarthrobacter sp. NIBRBAC000502770, using 16S rRNA gene sequencing. IAA production was determined in Luria-Bertani (LB) broth and optimized using different temperatures, agitation rates, L-tryptophan concentrations, carbon and nitrogen sources, and inorganic salts. The strain NIBRBAC000502770 showed better production of IAA at temperature 30 °C (29.47 mg·L^-1) and at an agitation rate of 200 rpm (32.65 mg·L^-1). Maltose (0.5%) was found to be the best carbon source for the strain (yielding 36.48 mg·L^-1 IAA). IAA yield was 19.17 mg·L^-1 and 24.73 mg·L^-1 at 1% yeast extract and 1% tryptone as nitrogen sources, respectively. qRT-PCR showed the transcript levels of amiE and aldH genes, which had been predicted to encode indole-3-acetamide hydrolase and indole-3-acetaldehyde dehydrogenase, to be significantly upregulated in response to tryptophan. This study has examined that NIBRBAC000502770 has significant effects as a biological agent such as plant growth promotion, and development of optimal medium could significantly reduce the cost of mass production of microorganisms.

Indole Derivatives Obtained from Egyptian Enterobacter sp. Soil Isolates Exhibit Antivirulence Activities against Uropathogenic Proteus mirabilis

Proteus mirabilis is a frequent cause of catheter associated urinary tract infections (CAUTIs). Several virulence factors contribute to its pathogenesis, but swarming motility, biofilm formation, and urease activity are considered the hallmarks. The increased prevalence in antibiotic resistance among uropathogens is alarming and requires searching for new treatment alternatives. With this in mind, our study aims to investigate antivirulence activity of indole derivatives against multidrug resistant P. mirabilis isolates. Ethyl acetate (EtOAc) extracts from Enterobacter sp. (rhizobacterium), isolated from Egyptian soil samples were tested for their ability to antagonize the virulence capacity and biofilm activity of P. mirabilis uropathogens. Extracts of two Enterobacter sp. isolates (coded Zch127 and Cbg70) showed the highest antivirulence activities against P. mirabilis. The two promising rhizobacteria Zch127 and Cbg70 were isolated from soil surrounding: Cucurbita pepo (Zucchini) and Brassica oleracea var. capitata L. (Cabbage), respectively. Sub-minimum inhibitory concentrations (Sub-MICs) of the two extracts showed potent antibiofilm activity with significant biofilm reduction of ten P. mirabilis clinical isolates (p-value < 0.05) in a dose-dependent manner. Interestingly, the Zch127 extract showed anti-urease, anti-swarming and anti-swimming activity against the tested strains. Indole derivatives identified represented key components of indole pyruvate, indole acetamide pathways; involved in the synthesis of indole acetic acid. Additional compounds for indole acetonitrile pathway were detected in the Zch127 extract which showed higher antivirulence activity. Accordingly, the findings of the current study model the feasibility of using these extracts as promising antivirulence agent against the P. mirabilis uropathogens and as potential therapy for treatment of urinary tract infections (UTIs).

The Endophytic Microbiome as a Hotspot of Synergistic Interactions, with Prospects of Plant Growth Promotion

The plant root is the primary site of interaction between plants and associated microorganisms and constitutes the main components of plant microbiomes that impact crop production. The endophytic bacteria in the root zone have an important role in plant growth promotion. Diverse microbial communities inhabit plant root tissues, and they directly or indirectly promote plant growth by inhibiting the growth of plant pathogens, producing various secondary metabolites. Mechanisms of plant growth promotion and response of root endophytic microorganisms for their survival and colonization in the host plants are the result of complex plant-microbe interactions. Endophytic microorganisms also assist the host to sustain different biotic and abiotic stresses. Better insights are emerging for the endophyte, such as host plant interactions due to advancements in 'omic' technologies, which facilitate the exploration of genes that are responsible for plant tissue colonization. Consequently, this is informative to envisage putative functions and metabolic processes crucial for endophytic adaptations. Detection of cell signaling molecules between host plants and identification of compounds synthesized by root endophytes are effective means for their utilization in the agriculture sector as biofertilizers. In addition, it is interesting that the endophytic microorganism colonization impacts the relative abundance of indigenous microbial communities and suppresses the deleterious microorganisms in plant tissues. Natural products released by endophytes act as biocontrol agents and inhibit pathogen growth. The symbiosis of endophytic bacteria and arbuscular mycorrhizal fungi (AMF) affects plant symbiotic signaling pathways and root colonization patterns and phytohormone synthesis. In this review, the potential of the root endophytic community, colonization, and role in the improvement of plant growth has been explained in the light of intricate plant-microbe interactions.

Screening and optimization of indole-3-acetic acid production and phosphate solubilization by rhizobacterial strains isolated from Acacia cyanophylla root nodules and their effects on its plant growth

Background

Plant growth-promoting rhizobacteria (PGPR) are known to improve plant growth and are used as biofertilizers, thanks to their numerous benefits to agriculture such as phosphorus solubilization and phytohormone production. In this paper, four rhizospheric bacteria (Phyllobacterium sp., Bacillus sp., Agrobacterium sp., and Rhizobium sp.) isolated from surface-sterilized root nodules of Acacia cyanophylla were tested for their ability to solubilize inorganic phosphate and to produce indole-3-acetic acid (IAA) under laboratory conditions. Then, the best IAA producer (Rhizobium sp.) was selected to test optimized conditions for IAA production. Finally, the effect of the four strains on plant growth for A. cyanophylla was evaluated in vivo.

Results

The results showed that the totality of the tested isolates had solubilized inorganic phosphate (P) in both NBRIP (National Botanical Research Institute Phosphate) and PVK (Pikovskaya) media. Bacillus sp. was a high P-solubilizer and showed maximum solubilization in PVK (519 μg ml^-1) and NBRIP (782 μg ml^-1). The optimization of maximum phosphate solubilization was done using different sources of carbon (1%) and nitrogen (0.1%). Glucose and ammonium sulfate were selected to be the best carbon and nitrogen source for phosphate solubilization by all tested strains, except for Phyllobacterium sp., which recorded the highest phosphate solubilization with ammonium nitrate. The IAA production by the tested strains indicated that Rhizobium sp. produced the highest amount of IAA (90.21 μg ml^-1) in culture media supplemented with L-tryptophan. The best production was observed with L-Trp concentration of 0.2% (116.42 μg ml^-1) and at an initial pH of 9 (116.07 μg ml^-1). The effect of NaCl on IAA production was tested at concentrations of 0 to 5% and the maximum production of  89.43 μg ml^-1 was found at 2% NaCl. The extraction of crude IAA from this strain was done and purity was confirmed with Thin Layer Chromatography (TLC) analysis. A specific spot from the extracted IAA production was found to correspond with a standard spot of IAA with the same Rf value. Finally, the tested PGPR demonstrated growth stimulatory effects on Acacia cyanophylla seedlings in vivo, with a great increase of shoots’ and roots’ dry weights, and shoot length compared to control.

The rhizobacterial isolates were identified by 16S rDNA sequence analysis as Agrobacterium sp. NA11001, Phyllobacterium sp. C65, Bacillus sp. CS14, and Rhizobium sp. V3E1.

Conclusion

This study highlights the importance of the use of phosphate solubilizing and IAA producer microorganisms as biofertilizers to increase crop yields. The studied strains showed a significant phosphate solubilization potential and IAA production. The use of selected strains as inoculants would be interesting, in particular with a view of promoting sustainable agriculture. However, further studies to verify the efficacy of the best isolates in situ is certainly required.

Evaluation of plant probiotic performance of Pseudomonas sp. encapsulated in alginate supplemented with salicylic acid and zinc oxide nanoparticles

Plant growth promoting rhizobacteria (PGPR) are efficient candidates for the application in agricultural field to enhance the crop yield and to suppress the plant diseases. As the changes in agro-climatic conditions negatively affect the soil fertility and functioning of soil microbial community, there are significant demand for the innovative delivery methods for the PGPR to ensure its optimal performance. In the present study, Pseudomonas sp. DN18 has been entrapped in the alginate beads along with the supplemented salicylic acid (SA) and zinc oxide nanoparticles (ZnONPs). This modified formulation was further demonstrated for the IAA production and also antifungal activity against the Sclerotium rolfsii. In addition, superior plant growth promoting and biocontrol properties of the encapsulated Pseudomonas sp. DN18 supplemented with SA and ZnONPs have also been demonstrated on Oryza sativa seedlings by comparing with the free living Pseudomonas sp. DN18. This revealed the agricultural promises of Pseudomonas sp. DN18 encapsulated in a modified delivery system due to its functional superiority and stability over the free living bacteria based formulation.

Rhizobacterial biofilm and plant growth promoting trait enhancement by organic acids and sugars

In the study,Pseudomonas sp. K6 and Pseudomonas monteilii were found to form an enhanced biofilm when cultured in the presence of organic acids and sugars. Here, the highest biofilm could be observed for Pseudomonas sp. K6 (3.08 ± 0.13) and P. monteilii (1.99 ± 0.12) when cultured in presence of 10 µM malic acid. However, maximum production of indole 3 acetic acid (IAA) was observed with 25 µM succinic acid treatment for Pseudomonas sp. K6 (24.33 ± 0.57 µg ml^-1) and with 25 µM galactose for P. monteilii (20 ± 0.0 µg ml^-1). At the same time, Pseudomonas sp. K6 solubilized the highest quantity of phosphate in the presence of 50 µM citric acid (21.33 ± 0.0 µM) and P. monteilii was observed to produce 32.66 ± 1.25 µM soluble phosphate in the presence of 10 µM galactose. The results of the study demonstrate the role of organic acids and sugars in the enhancement of biofilm formation, IAA production and phosphate solubilization in selected Pseudomonas spp. and highlight the potential use of rhizobacteria in conjugation with supplement for the agricultural applications.

Role of Microorganisms in the Remediation of Wastewater in Floating Treatment Wetlands: A Review

This article provides useful information for understanding the specific role of microbes in the pollutant removal process in floating treatment wetlands (FTWs). The current literature is collected and organized to provide an insight into the specific role of microbes toward plants and pollutants. Several aspects are discussed, such as important components of FTWs, common bacterial species, rhizospheric and endophytes bacteria, and their specific role in the pollutant removal process. The roots of plants release oxygen and exudates, which act as a substrate for microbial growth. The bacteria attach themselves to the roots and form biofilms to get nutrients from the plants. Along the plants, the microbial community also influences the performance of FTWs. The bacterial community contributes to the removal of nitrogen, phosphorus, toxic metals, hydrocarbon, and organic compounds. Plant–microbe interaction breaks down complex compounds into simple nutrients, mobilizes metal ions, and increases the uptake of pollutants by plants. The inoculation of the roots of plants with acclimatized microbes may improve the phytoremediation potential of FTWs. The bacteria also encourage plant growth and the bioavailability of toxic pollutants and can alleviate metal toxicity.

Fungal pretreatment of lignocellulosic biomass for the production of plant hormone by Pichia fermentans under submerged conditions

The study was designed to evaluate the production of auxin by eukaryotic unicellular organism Pichia fermentans. Different media formulations were used for the production of indole-3-acetic acid (IAA) under broth and submerged conditions. Wheat straw-based production medium was formulated and optimized using statistical approach. The IAA production was significantly enhanced by nine folds, when the wheat straw was pretreated with Phanerochaete chrysosporium (150 µg/ml) as compared to untreated wheat straw (16.44 µg/ml). Partial purification of IAA was carried out by silica gel column chromatography and further confirmed by high-performance liquid chromatography. Exogenous application of crude and partially purified IAA positively influenced the Vigna radiata seedling growth. The number of lateral roots in the growing seedlings was significantly higher as compared to the control seeds. Thus, the present findings point towards an efficient production of plant hormone by yeast and white rot fungus using abundantly available wheat straw, which may lead to the development of cost-effective production of such metabolites and their further use in agricultural field to reduce the negative impact of chemical fertilizers.

Plant Growth Enhancement, Disease Resistance, and Elemental Modulatory Effects of Plant Probiotic Endophytic Bacillus sp. Fcl1

Endophytic bacteria have already been studied for their beneficial support to plants to manage both biotic and abiotic stress through an array of well-established mechanisms. They have either direct or indirect impact on mobilizing diverse nutrients and elements from soil to plants. However, detailed insight into the fine-tuning of plant elemental composition by associated microorganism is very limited. In this study, endophytic Bacillus Fcl1 characterized from the rhizome of Curcuma longa was found to have broad range of plant growth-promoting and biocontrol mechanisms. The organism was found to have indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase production properties along with nitrogen fixation. The Bacillus Fcl1 could also inhibit diverse phytopathogens as confirmed by dual culture and well diffusion. By LC-MS/MS analysis, chemical basis of its antifungal activity has been proved to be due to the production of iturin A and a blend of surfactin compounds. Moreover, the organism was found to induce both plant growth and disease resistance in vivo in model plant system. Because of these experimentally demonstrated multiple plant probiotic features, Bacillus Fcl1 was selected as a candidate organism to study its role in modulation of plant elemental composition. ICP-MS analysis of Bacillus Fcl1-treated plants provided insight into relation of bacterial interaction with elemental composition of plants.

Biogenic Gold Nanoparticle Supplementation to Plant Beneficial Pseudomonas monteilii was Found to Enhance its Plant Probiotic Effect

Rhizosphere provides unique space for intensive chemical conversation between plant and microorganisms. The common rhizobacterial mechanisms which have been demonstrated to promote plant growth include production of phytohormones, nitrogen fixation, synthesis of 1-aminocyclopropane-1-carboxylate deaminase (ACC deaminase) and phosphate solubilization. The microbially produced phytohormone indole-3-acetic acid (IAA) is considered to have significant role in interaction between plant and bacteria. Hence any substance with modulatory effect on rhizobacterial IAA production can expect to have its impact on plant-microbe interaction. With the advent of nanotechnology, nanoparticles are being used for diverse applications. However, applications of nanotechnology in agriculture have not been studied in detail. In the study, rhizospheric Pseudomonas monteilii was selected to investigate the concentration-dependent effect of biogenic gold nanoparticles (AuNPs) on its IAA production. For this, AuNPs synthesized by Bacillus subtilis SJ15 were characterized by UV-Vis spectroscopy, FT-IR, TEM and EDS. The results showed AuNPs to have spherical, hexagonal and triangular shapes with a size range of 12-32 nm and absorption peak at 545 nm. Further, various concentrations of AuNPs were used to identify its impact on IAA production by P. monteilii. From this, enhanced production of IAA by P. monteilii was found to take place in the presence of 50 µg/mL AuNPs. When Vigna unguiculata seedlings were grown in presence of 50 µg/mL of AuNPs, increased growth was observed. The results of the study thus showed the ability of AuNPs to augment the IAA-producing potential of P. monteilii.

A resourceful methodology to profile indolic auxins produced by rhizo-fungi using spectrophotometry and HPTLC

Plant growth-promoting fungi play an important role in development of sustainable agriculture. In the current study, 13 fungal strains were isolated from the rhizosphere of healthy Triticum aestivum (wheat) plant and screened for their indolic auxin production potential. Aspergillus flavus strain PGFW, Aspergillus niger strain BFW and Aspergillus caespitosus strain DGFW were amongst the most efficient indolic auxin-producing strains. Indolic auxins such as indole 3 acetate (IAA), indole 3 butyrate (IBA) and indole 3 propionate (IPA) are produced by fungi. The conventional method to assess the IAA production is through a spectrophotometric assay using Salkowski's reagent, which quantifies all indolic auxins and not individual auxins. Moreover, it was also observed that the absorption maxima (λ_max) of the samples, when compared to that of standard indole-3-acetic acid, showed deviation from the latter, indicative of production of a mixture of indolic derivatives by the fungi. Hence, for further profiling of these indolic compounds, high-performance thin layer chromatography (HPTLC) based protocol was standardized to precisely detect and quantify individual indolic auxins like IAA, IBA and IPA in the range of 100-1000 ng per spot. HPTLC analysis also showed that the fungal strains produce different indolic auxins in media with and without fortification of tryptophan, with the production of indolic auxins being enhanced in presence of tryptophan. Thus, this standardized HPTLC protocol is an efficient and sensitive methodology to separate and quantify the indolic derivatives.

The Effects of the Endophytic Bacterium Pseudomonas fluorescens Sasm05 and IAA on the Plant Growth and Cadmium Uptake of Sedum alfredii Hance

Endophytic bacteria have received attention for their ability to promote plant growth and enhance phytoremediation, which may be attributed to their ability to produce indole-3-acetic acid (IAA). As a signal molecular, IAA plays a key role on the interaction of plant and its endomicrobes. However, the different effects that endophytic bacteria and IAA may have on plant growth and heavy metal uptake is not clear. In this study, the endophytic bacterium Pseudomonas fluorescens Sasm05 was isolated from the stem of the zinc (Zn)/cadmium (Cd) hyperaccumulator Sedum alfredii Hance. The effects of Sasm05 and exogenous IAA on plant growth, leaf chlorophyll concentration, leaf Mg²⁺-ATPase and Ca²⁺-ATPase activity, cadmium (Cd) uptake and accumulation as well as the expression of metal transporter genes were compared in a hydroponic experiment with 10 μM Cd. The results showed that after treatment with 1 μM IAA, the shoot biomass and chlorophyll concentration increased significantly, but the Cd uptake and accumulation by the plant was not obviously affected. Sasm05 inoculation dramatically increased plant biomass, Cd concentration, shoot chlorophyll concentration and enzyme activities, largely improved the relative expression of the three metal transporter families ZRT/IRT-like protein (ZIP), natural resistance associated macrophage protein (NRAMP) and heavy metal ATPase (HMA). Sasm05 stimulated the expression of the SaHMAs (SaHMA2, SaHMA3, and SaHMA4), which enhanced Cd root to shoot translocation, and upregulated SaZIP, especially SaIRT1, expression to increase Cd uptake. These results showed that although both exogenous IAA and Sasm05 inoculation can improve plant growth and photosynthesis, Sasm05 inoculation has a greater effect on Cd uptake and translocation, indicating that this endophytic bacterium might not only produce IAA to promote plant growth under Cd stress but also directly regulate the expression of putative key Cd uptake and transport genes to enhance Cd accumulation of plant.

High-yield production of indole-3-acetic acid by Enterobacter sp. DMKU-RP206, a rice phyllosphere bacterium that possesses plant growth-promoting traits

Enterobacter sp. DMKU-RP206 was isolated from rice leaves in Thailand and identified by the 16S rRNA gene and multilocus sequence (gyrB, rpoB, atpD, and infB genes) analysis. The bacterium was assessed on plant growth-promoting traits including indole-3-acetic acid (IAA) production. Phosphate solubilization, ammonia production, and antagonism to fungal plant pathogens, as well as siderophore production, were shown by this bacterium. However, only IAA production was focused on. The production of IAA by Enterobacter sp. DMKU-RP206 was optimized by statistical methods. A Box-Behnken design was used for the investigation of interactions among the basic influencing factors and for the optimization of IAA production. The results showed that l-tryptophan had a significant importance in terms of IAA production. Enterobacter sp. DMKU-RP206 produced a higher amount of IAA than previously reported for the genus Enterobacter. 0.85% of lactose as a carbon source, 1.3% of yeast extract as a nitrogen source, 1.1% of l-tryptophan as a precursor, 0.4% of NaCl, an initial pH of 5.8, an incubation temperature at 30 °C, and a shaking speed of 200 rpm were found to be the optimum conditions for IAA production. In addition, IAA production was performed to scale up IAA production, and the highest amount, 5561.7 mg l^-1, was obtained. This study reported a 13.4-fold improvement in IAA production by Enterobacter sp. DMKU-RP206.

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates

Plant root secreted compounds alter the gene expression of associated microorganisms by acting as signal molecules that either stimulate or repel the interaction with beneficial or harmful species, respectively. However, it is still unclear whether two distinct groups of beneficial bacteria, non-plant-associated (soil) strains and plant-associated (endophytic) strains, respond uniformly or variably to the exposure with root exudates. Therefore, Bacillus mycoides, a potential biocontrol agent and plant growth-promoting bacterium, was isolated from the endosphere of potatoes and from soil of the same geographical region. Confocal fluorescence microscopy of plants inoculated with GFP-tagged B. mycoides strains showed that the endosphere isolate EC18 had a stronger plant colonization ability and competed more successfully for the colonization sites than the soil isolate SB8. To dissect these phenotypic differences, the genomes of the two strains were sequenced and the transcriptome response to potato root exudates was compared. The global transcriptome profiles evidenced that the endophytic isolate responded more pronounced than the soil-derived isolate and a higher number of significant differentially expressed genes were detected. Both isolates responded with the alteration of expression of an overlapping set of genes, which had previously been reported to be involved in plant–microbe interactions; including organic substance metabolism, oxidative reduction, and transmembrane transport. Notably, several genes were specifically upregulated in the endosphere isolate EC18, while being oppositely downregulated in the soil isolate SB8. These genes mainly encoded membrane proteins, transcriptional regulators or were involved in amino acid metabolism and biosynthesis. By contrast, several genes upregulated in the soil isolate SB8 and downregulated in the endosphere isolate EC18 were related to sugar transport, which might coincide with the different nutrient availability in the two environments. Altogether, the presented transcriptome profiles provide highly improved insights into the life strategies of plant-associated endophytes and soil isolates of B. mycoides.

Endophytic Phomopsis sp. colonization in Oryza sativa was found to result in plant growth promotion and piperine production

Endophytic fungi have been reported to have the acquired ability to synthesize host plant specific medicinal natural products. Many fungi with such properties have been characterized and optimized for the conditions which favor maximal production of desired products. However, the inherent plant colonization property of promising endophytic fungi is least studied. Exploiting the transgenome functioning of these fungi have immense applications to add beneficial features to nonhost plants. In the present study, the endophytic fungus Phomopsis sp. isolated from Piper nigrum was confirmed for piperine production by HPLC and LCMS/MS. Further, the fungal isolate was studied for its colonization ability in Oryza sativa. Interestingly, the fungi treated plants were found to have significant plant growth enhancement when compared to the control. Further screening of extract from treated plants by HPLC and LCMS/MS resulted in the confirmation of presence of piperine. The observed result is extremely significant as it opens up novel applications of endophytic fungal colonization in taxonomically diverse plants.

Bioengineering of Dioscorea nipponica with rhizospheric Proteus spp. for enhanced tuber size and diosgenin content

Rhizobacterial production of plant hormones, ACC deaminase, fixation of nitrogen, solubilization of phosphate and antimicrobial metabolites play very important role in the health and growth of plants. Hence exploration of plant probiotic prospectives of promising rhizobacterial isolates from biodiversity rich areas can have enormous applications to engineer both the biomass and active ingredients of plants. In the present study, rhizospheric Proteus spp. R6 and R60 isolated from Pseudarthria viscida and Glycosmis arborea were analyzed for tuber and diosgenin enhancement effects in Dioscorea nipponica under field conditions for 1 year. Among the two Proteus spp. selected, both were positive for ACC deaminase, siderophore, nitrogen fixation, IAA and ammonia production. However, the isolate R6 was found to have additional phosphate solubilizing activity. Quantitative analysis of IAA by HPTLC showed its maximum production by Proteus sp. R60 (714.47 ± 8.7 µg/mL) followed by Proteus sp. R6 (588.06 ± 7.0 µg/mL). The tubers formed from the Proteus sp. R6 treated samples were identified to have significant enhancement in size, root number and diosgenin content when compared to control. Interestingly, HPLC analysis has confirmed twofold higher diosgenin content in Proteus sp. R6 treated samples than control during 1 year period of its field growth. The obtained results are of great importance as it involved the utilization of rhizospheric bacteria to improve tuber size which suggests its potential use in developing cost-effective, eco-friendly and multifunctional biofertilizer.

Characterization of plant growth promoting traits of bacterial isolates from the rhizosphere of barley (Hordeum vulgare L.) and tomato (Solanum lycopersicon L.) grown under Fe sufficiency and deficiency

Plant Growth Promoting Bacteria (PGPB) are considered a promising approach to replace the conventional agricultural practices, since they have been shown to affect plant nutrient-acquisition processes by influencing nutrient availability in the rhizosphere and/or those biochemical processes determining the uptake at root level of nitrogen (N), phosphorus (P), and iron (Fe), that represent the major constraints for crop productivity worldwide. We have isolated novel bacterial strains from the rhizosphere of barley (Hordeum vulgare L.) and tomato (Solanum lycopersicon L.) plants, previously grown in hydroponic solution (either Fe deficient or Fe sufficient) and subsequently transferred onto an agricultural calcareous soil. PGPB have been identified by molecular tools and characterized for their capacity to produce siderophores and indole-3-acetic acid (IAA), and to solubilize phosphate. Selected bacterial isolates, showing contemporarily high levels of the three activities investigated, were finally tested for their capacity to induce Fe reduction in cucumber roots two isolates, from barley and tomato plants under Fe deficiency, significantly increased the root Fe-chelate reductase activity; interestingly, another isolate enhanced the reduction of Fe-chelate reductase activity in cucumber plant roots, although grown under Fe sufficiency.

Surfactin, Iturin, and Fengycin Biosynthesis by Endophytic Bacillus sp. from Bacopa monnieri

Endophytic microorganisms which are ubiquitously present in plants may colonize intracellularly or intercellularly without causing any diseases. By living within the unique chemical environment of a host plant, they produce a vast array of compounds with a wide range of biological activities. Because of this, natural products of endophytic origin have been exploited for antimicrobial, antiviral, anticancer, and antioxidant properties. Also, they can be considered to function as an efficient microbial barrier to protect plants from various pathogens. In the present study, endophytic bacterium BmB 9 with antifungal and antibacterial activity isolated from the stem tissue of Bacopa monnieri was studied for the molecular and chemical basis of its activity. PCR-based genome mining for various biosynthetic gene clusters proved the presence of surfactin, iturin, and type I polyketide synthase (PKS) genes in the isolate. The LC-MS/MS based analysis of the extract further confirmed the production of surfactin derivatives (M + H(+)-1008.6602, 1022.6755), iturin (M + H(+)-1043.5697), and fengycin (M + H(+)-1491.8195, 1477.8055) by the selected bacterial isolate. The 16S rDNA sequence similarity based analysis identified the isolate BmB 9 as Bacillus sp. with 100 % identity to Bacillus sp. LCF1 (KP257289).

Studies on Plant Growth Promoting Properties of Fruit-Associated Bacteria from Elettaria cardamomum and Molecular Analysis of ACC Deaminase Gene

Endophytic microorganisms have been reported to have diverse plant growth promoting mechanisms including phosphate solubilization, N2 fixation, production of phyto-hormones and ACC (1-aminocyclopropane-1-carboxylate) deaminase and antiphyto-pathogenic properties. Among these, ACC deaminase production is very important because of its regulatory effect on ethylene which is a stress hormone with precise role in the control of fruit development and ripening. However, distribution of these properties among various endophytic bacteria associated with fruit tissue and its genetic basis is least investigated. In the current study, 11 endophytic bacteria were isolated and identified from the fruit tissue of Elettaria cardamomum and were studied in detail for various plant growth promoting properties especially ACC deaminase activity using both culture-based and PCR-based methods. PCR-based screening identified the isolates EcB 2 (Pantoea sp.), EcB 7 (Polaromonas sp.), EcB 9 (Pseudomonas sp.), EcB 10 (Pseudomonas sp.) and EcB 11 (Ralstonia sp.) as positive for ACC deaminase. The PCR products were further subjected to sequence analysis which proved the similarity of the sequences identified in the study with ACC deaminase sequences reported from other sources. The detailed bioinformatic analysis of the sequence including homology-based modelling and molecular docking confirmed the sequences to have ACC deaminase activity. The docking of the modelled proteins was done using patch dock, and the detailed scrutiny of the protein ligand interaction revealed conservation of key amino acids like Lys51, Ser78, Tyr268 and Tyr294 which play important role in the enzyme activity. These suggest the possible regulatory effect of these isolates on fruit physiology.