Bacterial Siderophores: Classification, Biosynthesis, Perspectives of Use in Agriculture

Unearthing the soil-bacteria nexus to enhance potassium bioavailability for global sustainable agriculture: A mechanistic preview

Established as a plant macronutrient, potassium (K) substantially bestows plant growth and thus, global food production. It is absorbed by plants as potassium cation (K+) from soil solution, which is enriched through slow-release from soil minerals or addition of soluble fertilizers. Contribution of bioavailable K+ from soil is usually insignificant (< 2 %), although the earth's crust is rich in K-bearing minerals. However, K is fixed largely in interlayer spaces of K-bearing minerals, which can be released by K-solubilizing bacteria (KSB) such as Bacillus, Pseudomonas, Enterobacter, and Acidithiobacillus. The underlying mechanisms of K dissolution by KSB include acidolysis, ion exchange reactions, chelation, complexolysis, and release of various organic and inorganic acids such as citric, oxalic, acetic, gluconic, and tartaric acids. These acids cause disintegration of K-bearing minerals and bring K+ into soil solution that becomes available to the plants. Current literature review updates the scientific information about microbial species, factors, and mechanisms governing the bio-intrusion of K-bearing minerals. Moreover, it explores the potential of KSB not only for K-solubilization but also to enhance bioavailability of phosphorus, nitrogen, and micronutrients, as well as its other beneficial impact on plant growth. Thus, in the context of sustainable agricultural production and global food security, utilization of KSB may facilitate plant nutrient availability, conserve natural resources, and reduce environmental impacts caused by chemical fertilizers.

Assessment of rice rhizosphere-isolated bacteria for their ability to stimulate plant growth and their antagonistic effects against Xanthomonas arboricola pv. juglandis

This study looked at the possibility of using bacteria that were separated from the rhizosphere of rice plants to promote plant development and offer biological control against pests that affect agriculture. A total of 119 bacteria were isolated from rice rhizospheres collected from six different locations. Of these, 15.47% showed phosphate solubilization, 47.05% showed IAA, 89.07% showed siderophore, and 10.08% showed ACC deaminase activity. Generally, high siderophore production was observed in strains showing ACC deaminase activity. The antagonistic behavior of all strains against the walnut pest Xanthomonas arbiricola was also studied, and eight (6.7%) isolates suppressed the growth of this pathogen (7-43 ± 2 mm zone diameter). It was also noted that these eight isolates showed almost exclusively siderophore activity. In contrast to IAA and siderophore synthesis, the study demonstrated reduced activity levels for phosphate solubilization and ACC deaminase. The 16S rRNA sequence results of some of the bacteria selected in this study and AFLP analysis based on some restriction enzymes showed that the diversity was quite high. According to the 16S rRNA analysis, the high antagonistic effect of strain 71, which is one of the members of the Enterobacter genus, shows that it can be used as a biocontrol agent. In this study, it was revealed in detail that bacteria can be preferred as alternative biological agents for plant growth instead of synthetic fertilizers. This is the first study on this subject in this region, which is one of the important points of the country in terms of rice production.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04077-5.

PGPR: Key to Enhancing Crop Productivity and Achieving Sustainable Agriculture

Due to the burgeoning global population and the advancement of economies, coupled with human activities leading to the degradation of soil ecosystems and the depletion of non-renewable resources, concerns have arisen regarding food security and human survival. In order to address these adverse impacts, the spotlight has been cast upon plant growth-promoting rhizobacteria (PGPR), driven by a strong environmental consciousness. PGPR possesses the capability to foster plant growth and amplify crop yield through both direct and indirect mechanisms. By expediting plant growth, augmenting nutrient assimilation, heightening crop yield and caliber, and fortifying stress resilience, the application of PGPR can mitigate reliance on chemical fertilizers and pesticides while diminishing ecological perils. This exposition delves into the function of PGPR in modulating plant hormones, fostering nutrient solubilization, and fortifying plant resistance against biotic and abiotic stressors. This review offers valuable insights into the intricate interplay between PGPR and plants, elucidating uncertainties ripe for further investigation. Profound comprehension and judicious utilization of PGPR are indispensable for attaining sustainable agricultural progression, making substantial contributions to resolving the conundrums of global food security and environmental conservation.

Complete Genome of Achromobacter xylosoxidans, a Nitrogen-Fixing Bacteria from the Rhizosphere of Cowpea (Vigna unguiculata [L.] Walp) Tolerant to Cucumber Mosaic Virus Infection

Achromobacter xylosoxidans is one of the nitrogen-fixing bacteria associated with cowpea rhizosphere across Africa. Although its role in improving soil fertility and inducing systemic resistance in plants against pathogens has been documented, there is limited information on its complete genomic characteristics from cowpea roots. Here, we report the complete genome sequence of A. xylosoxidans strain DDA01 isolated from the topsoil of a field where cowpea plants tolerant to cucumber mosaic virus (CMV) were grown in Ibadan, Nigeria. The genome of DDA01 was sequenced via Illumina MiSeq and contained 6,930,067 nucleotides with 67.55% G + C content, 73 RNAs, 59 tRNAs, and 6421 protein-coding genes, including those associated with nitrogen fixation, phosphate solubilization, Indole3-acetic acid production, and siderophore activity. Eleven genetic clusters for secondary metabolites, including alcaligin, were identified. The potential of DDA01 as a plant growth-promoting bacteria with genetic capabilities to enhance soil fertility for resilience against CMV infection in cowpea is discussed. To our knowledge, this is the first complete genome of diazotrophic bacteria obtained from cowpea rhizosphere in sub-Saharan Africa, with potential implications for improved soil fertility, plant disease resistance, and food security.

BioSolutions for Green Agriculture: Unveiling the Diverse Roles of Plant Growth-Promoting Rhizobacteria

The extensive use of chemical pesticides and fertilizers in conventional agriculture has raised significant environmental and health issues, including the emergence of resistant pests and pathogens. Plant growth-promoting rhizobacteria (PGPR) present a sustainable alternative, offering dual benefits as biofertilizers and biocontrol agents. This review delves into the mechanisms by which PGPR enhance plant growth, including nutrient solubilization, phytohormone production, and pathogen suppression. PGPR's commercial viability and application, particularly under abiotic stress conditions, are also examined. PGPR improves plant growth directly by enhancing nutrient uptake and producing growth-promoting substances and indirectly by inhibiting phytopathogens through mechanisms such as siderophore production and the secretion of lytic enzymes. Despite their potential, the commercialization of PGPR faces challenges, including strain specificity, formulation stability, and regulatory barriers. The review highlights the need for ongoing research to deepen our understanding of plant-microbe interactions and develop more robust PGPR formulations. Addressing these challenges will be crucial for integrating PGPR into mainstream agricultural practices and reducing reliance on synthetic agrochemicals. The successful adoption of PGPR could lead to more sustainable agricultural practices, promoting healthier crops and ecosystems.

Siderophore Biosynthesis and Transport Systems in Model and Pathogenic Fungi

Fungi employ diverse mechanisms for iron uptake to ensure proliferation and survival in iron-limited environments. Siderophores are secondary metabolite small molecules with a high affinity specifically for ferric iron; these molecules play an essential role in iron acquisition in fungi and significantly influence fungal physiology and virulence. Fungal siderophores, which are primarily hydroxamate types, are synthesized via non-ribosomal peptide synthetases (NRPS) or NRPS-independent pathways. Following synthesis, siderophores are excreted, chelate iron, and are transported into the cell by specific cell membrane transporters. In several human pathogenic fungi, siderophores are pivotal for virulence, as inhibition of their synthesis or transport significantly reduces disease in murine models of infection. This review briefly highlights siderophore biosynthesis and transport mechanisms in fungal pathogens as well the model fungi Saccharomyces cerevisiae and Schizosaccharomyces pombe. Understanding siderophore biosynthesis and transport in pathogenic fungi provides valuable insights into fungal biology and illuminates potential therapeutic targets for combating fungal infections.

How Do Plant Growth-Promoting Bacteria Use Plant Hormones to Regulate Stress Reactions?

Phytohormones play a crucial role in regulating growth, productivity, and development while also aiding in the response to diverse environmental changes, encompassing both biotic and abiotic factors. Phytohormone levels in soil and plant tissues are influenced by specific soil bacteria, leading to direct effects on plant growth, development, and stress tolerance. Specific plant growth-promoting bacteria can either synthesize or degrade specific plant phytohormones. Moreover, a wide range of volatile organic compounds synthesized by plant growth-promoting bacteria have been found to influence the expression of phytohormones. Bacteria-plant interactions become more significant under conditions of abiotic stress such as saline soils, drought, and heavy metal pollution. Phytohormones function in a synergistic or antagonistic manner rather than in isolation. The study of plant growth-promoting bacteria involves a range of approaches, such as identifying singular substances or hormones, comparing mutant and non-mutant bacterial strains, screening for individual gene presence, and utilizing omics approaches for analysis. Each approach uncovers the concealed aspects concerning the effects of plant growth-promoting bacteria on plants. Publications that prioritize the comprehensive examination of the private aspects of PGPB and cultivated plant interactions are of utmost significance and crucial for advancing the practical application of microbial biofertilizers. This review explores the potential of PGPB-plant interactions in promoting sustainable agriculture. We summarize the interactions, focusing on the mechanisms through which plant growth-promoting bacteria have a beneficial effect on plant growth and development via phytohormones, with particular emphasis on detecting the synthesis of phytohormones by plant growth-promoting bacteria.

Diversity of endophytic bacteria with antimicrobial potential isolated from marine macroalgae from Yacila and Cangrejos beaches, Piura-Peru

Endophytic bacteria found in marine macroalgae have been studied for their potential antimicrobial activity, consequently, they could serve as a valuable source of bioactive compounds to control pathogenic bacteria, yeasts, and fungi. Algae endophytic bacteria were isolated from Caulerpa sp., Ulva sp., Ahnfeltiopsis sp., and Chondracantus chamissoi from Yacila and Cangrejo Beaches (Piura, Peru). Antimicrobial assays against pathogenic bacteria were evaluated using cross-culture, over-plate, and volatile organic compound tests. Afterward, the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of selected crude extracts were determined, also ITS molecular analysis, antifungal activity, and PCR of iturin, fengycin, and surfactin genes were performed for bacteria strains exhibiting better activity. Forty-six algae endophytic bacteria were isolated from algae. Ten strains inhibited gram-positive pathogenic bacteria (Enterococcus faecalis, Staphylococcus epidermidis, S. aureus, and Listeria monocytogenes), and 12 inhibited gram-negative bacteria (Escherichia coli and Salmonella enteric sv typhimurium). Bacteria with better activity belong to Bacillus sp., Kluyvera ascorbata, Pantoea agglomerans, Leclercia adecarboxylata, and Enterobacter sp., which only four showed antifungal activities against Candida albicans, C. tropicalis, Colletotrichium sp., Fusarium sp., Fusarium oxysporum, and Alternaria sp. Furthermore, K. ascorbata YAFE21 and Bacillus sp. YCFE4 exhibited iturin and fengycin genes. The results indicate that the algae endophytic bacteria found in this study, particularly K. ascorbata YAFE21, Bacillus sp. YCFR6, L. adecarboxylata CUFE2, Bacillus sp. YUFE8, Enterobacter sp. YAFL1, and P. agglomerans YAFL6, could be investigated as potential producers of antimicrobial compounds due to their broad activity against various microorganisms.

Employment of pqqE gene as molecular marker for the traceability of Gram negative phosphate solubilizing bacteria associated to plants

Insoluble phosphorous compounds solubilization by soil bacteria is of great relevance since it puts available the phosphorus to be used by plants. The production of organic acids is the main microbiological mechanism by which insoluble inorganic phosphorus compounds are solubilized. In Gram negative bacteria, gluconic acid is synthesized by the activity of the holoenzyme glucose dehydrogenase-pyrroloquinoline quinine named GDH-PQQ. The use of marker genes is a very useful tool to evaluate the persistence of the introduced bacteria and allow to follow-up the effect of biotic and abiotic factors on these beneficial microorganisms in the soil. In previous studies we detected the presence of the pqqE gene in a great percentage of both non-culturable and culturable native soil bacteria. The objective of this study was to analyze the phylogeny of the sequence of pqqE gene and its potential for the study of phosphate solubilizing bacteria from pure and mixed bacterial cultures and rhizospheric soil samples. For this, the presence of the pqqE gene in the genome of phosphate solubilizing bacteria that belong to several bacteria was determined by PCR. Also, this gene was analyzed from mixed bacterial cultures and rhizospheric soil associated to peanut plants inoculated or not with phosphate solubilizing bacteria. For this, degenerate primers designed from several bacterial genera and specific primers for the genus Pseudomonas spp., designed in this study, were used. DNA template used from simple or mixed bacterial cultures and from rhizospheric soil samples was obtained using two different DNA extraction techniques. Results indicated that pqqE gene amplification product was found in the genome of all Gram negative phosphate solubilizing bacteria analyzed. It was possible to detect this gene in the DNA obtained from mixed cultures where these bacteria grew in interaction with other microorganisms and in that obtained from rhizospheric soil samples inoculated or not with these bacteria. The phylogenetic analysis indicated that pqqE gene is a conserved gene within related genera. In conclusion, pqqE gene could be a potential marker for the study of phosphate solubilizing bacterial populations.

Native metabolomics for mass spectrometry-based siderophore discovery

Microorganisms, plants, and animals alike have specialized acquisition pathways for obtaining metals, with microorganisms and plants biosynthesizing and secreting small molecule natural products called siderophores and metallophores with high affinities and specificities for iron or other non-iron metals, respectively. This chapter details a novel approach to discovering metal-binding molecules, including siderophores and metallophores, from complex samples ranging from microbial supernatants to biological tissue to environmental samples. This approach, called Native Metabolomics, is a mass spectrometry method in which pH adjustment and metal infusion post-liquid chromatography are interfaced with ion identity molecular networking (IIMN). This rule-based data analysis workflow that enables the identification of metal-binding species based on defined mass (m/z) offsets with the same chromatographic profiles and retention times. Ion identity molecular networking connects compounds that are structurally similar by their fragmentation pattern and species that are ion adducts of the same compound by chromatographic shape correlations. This approach has previously revealed new insights into metal binding metabolites, including that yersiniabactin can act as a biological zincophore (in addition to its known role as a siderophore), that the recently elucidated lepotchelin natural products are cyanobacterial metallophores, and that antioxidants in traditional medicine bind iron. Native metabolomics can be conducted on any liquid chromatography-mass spectrometry system to explore the binding of any metal or multiple metals simultaneously, underscoring the potential for this method to become an essential strategy for elucidating biological metal-binding molecules.

Strategies for combating plant salinity stress: the potential of plant growth-promoting microorganisms

Global climate change and the decreasing availability of high-quality water lead to an increase in the salinization of agricultural lands. This rising salinity represents a significant abiotic stressor that detrimentally influences plant physiology and gene expression. Consequently, critical processes such as seed germination, growth, development, and yield are adversely affected. Salinity severely impacts crop yields, given that many crop plants are sensitive to salt stress. Plant growth-promoting microorganisms (PGPMs) in the rhizosphere or the rhizoplane of plants are considered the "second genome" of plants as they contribute significantly to improving the plant growth and fitness of plants under normal conditions and when plants are under stress such as salinity. PGPMs are crucial in assisting plants to navigate the harsh conditions imposed by salt stress. By enhancing water and nutrient absorption, which is often hampered by high salinity, these microorganisms significantly improve plant resilience. They bolster the plant's defenses by increasing the production of osmoprotectants and antioxidants, mitigating salt-induced damage. Furthermore, PGPMs supply growth-promoting hormones like auxins and gibberellins and reduce levels of the stress hormone ethylene, fostering healthier plant growth. Importantly, they activate genes responsible for maintaining ion balance, a vital aspect of plant survival in saline environments. This review underscores the multifaceted roles of PGPMs in supporting plant life under salt stress, highlighting their value for agriculture in salt-affected areas and their potential impact on global food security.

A Comprehensive Approach Combining Short-Chain Polyphosphate and Bacterial Biostimulants for Effective Nutrient Solubilization and Enhanced Wheat Growth

Phosphorus constitutes a crucial macronutrient for crop growth, yet its availability often limits food production. Efficient phosphorus management is crucial for enhancing crop yields and ensuring food security. This study aimed to enhance the efficiency of a short-chain polyphosphate (PolyP) fertilizer by integrating it with plant growth-promoting bacteria (PGPB) to improve nutrient solubilization and wheat growth. Specifically, the study investigated the effects of various bacterial strains on wheat germination and growth when used in conjunction with PolyP. To achieve this, a greenhouse experiment was conducted in which the wheat rhizosphere was amended with a short-chain PolyP fertilizer. Based on the morphological aspect, eight bacteria, designated P1 to P8, were isolated and further characterized. Plant growth-promoting traits were observed in all bacterial strains, as they presented the ability to produce Indole Acetic Acid (IAA) in significant amounts ranging from 7.5 ± 0.3 µg/mL to 44.1 ± 2 µg/mL, expressed by B. tropicus P4 and P. soyae P1, respectively. They also produced ammonia, hydrogen cyanide (HCN), and siderophores. Their effect against the plant pathogen Fusarium culmorum was also assessed, with P. reinekei P2 demonstrating the highest biocontrol activity as it presented a total inhibitory effect. Additionally, some strains exhibited the ability to solubilize/hydrolyze phosphorus, potassium, and zinc. In vivo, the initial growth potential of wheat seeds indicated that those inoculated with the isolated strains exhibited elevated germination rates and enhanced root growth. Based on their plant growth-promoting traits and performance in the germination assay, three strains were selected for producing the best results, specifically phosphorus hydrolyzation/solubilization, zinc solubilization, IAA production, HCN, and siderophores production. Wheat seeds were inoculated by drenching in a bacterial suspension containing 1010 CFU/mL of log phase culture, and an in planta bioassay was conducted in a growth chamber using three selected strains (Pseudomonas soyae P1, Pseudomonas reinekei P2, and Bacillus tropicus P4), applied either individually or with PolyP on a P-deficient soil (28 mg/kg of P Olsen). Our findings demonstrated that the combination of Pseudomonas soyae P1 and PolyP achieved the highest shoot biomass, averaging 41.99 ± 0.87 g. Notably, applying P. soyae P1 or Bacillus tropicus P4 alone yielded similar results to the use of PolyP alone. At the heading growth stage, the combination of Bacillus tropicus P4 and PolyP significantly increased the Chlorophyll Content Index (CCI) to 37.02 µmol/m2, outperforming both PolyP alone (24.07 µmol/m2) and the control (23.06 µmol/m2). This study presents an innovative approach combining short-chain PolyP with bacterial biostimulants to enhance nutrient availability and plant growth. By identifying and characterizing effective bacterial strains, it offers a sustainable alternative to conventional fertilizers.

Endosaccharibacter trunci gen. nov., sp. nov. and Rhizosaccharibacter radicis gen. nov., sp. nov., two novel bacteria of the family Acetobacteraceae isolated from sugarcane

Two novel endophytic bacterial strains, designated KSS8T and KSS12T, were isolated from the stems and roots of sugarcane, respectively, collected in Nakhon Ratchasima, Thailand. They were Gram-stain-negative, aerobic, and rod-shaped. The strain KSS8T was a motile bacterium with a subpolar flagellum, while the strain KSS12T was non-motile. Strains KSS8T and KSS12T were closely related to Lichenicola cladoniae PAMC 26569T (97.3 and 95.6 %, respectively) and Lichenicoccus roseus KEBCLARHB70RT (97.2 and 95.8 %, respectively) based on the similarity on their 16S rRNA gene sequence. This similarity corresponded to their phylogenomic positions within the evolutionary radiation of the family Acetobacteraceae. The average nucleotide identities and digital DNA-DNA hybridization values between the genome sequences of the two strains and other genera were significantly lower than the defined threshold values of 95-96 % and 70 %, respectively, which are used for the delineation of prokaryotic species. Both strains contained summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C16:0, C19:0 cyclo ω8c, C18:0, and C18:1 2OH as the predominant cellular fatty acids, but C18:3 ω6c (6, 9, 12) were found only in strain KSS12T. Based on phenotypic, chemotaxonomic, phylogenetic, and genomic analyses, these strains clearly represented two novel genera within the family Acetobacteraceae, for which the name Endosaccharibacter gen. nov., with the type species Endosaccharibacter trunci sp. nov. (type strain, KSS8T = TBRC 14669T = NBRC 115232T = KCTC 92115T = LMG 32414T) and the name Rhizosacchari bacter gen. nov., with the type species Rhizosaccharibacter radicis sp. nov. (type strain, KSS12T = TBRC 13066T = NBRC 114898T = KCTC 82433T = LMG 32137T) are proposed.

Production of the siderophore lysochelin in rich media through maltose-promoted high-density growth of Lysobacter sp. 3655

Siderophores are produced by bacteria in iron-restricted conditions. However, we found maltose could induce the biosynthesis of the siderophore lysochelin in Lysobacter sp. 3655 in rich media that are not compatible with siderophore production. Maltose markedly promoted cell growth, with over 300% increase in cell density (OD600) when LB medium was added with maltose (LBM). While lysochelin was not detectable when OD600 in LBM was below 5.0, the siderophore was clearly produced when OD600 reached 7.5 and dramatically increased when OD600 was 15.0. Coincidently, the transcription of lysochelin biosynthesis genes was remarkably enhanced following the increase of OD600. Conversely, the iron concentration in the cell culture dropped to 1.2 μM when OD600 reached 15.0, which was 6-fold lower than that in the starting medium. Moreover, mutants of the maltose-utilizing genes (orf2677 and orf2678) or quorum-sensing related gene orf644 significantly lowered the lysochelin yield. Transcriptomics analysis showed that the iron-utilizing/up-taking genes were up-regulated under high cell density. Accordingly, the transcription of lysochelin biosynthetic genes and the yield of lysochelin were stimulated when the iron-utilizing/up-taking genes were deleted. Finally, lysochelin biosynthesis was positively regulated by a TetR regulator (ORF3043). The lysochelin yield in orf3043 mutant decreased to 50% of that in the wild type and then restored in the complementary strain. Together, this study revealed a previously unrecognized mechanism for lysochelin biosynthetic regulation, by which the siderophore could still be massively produced in Lysobacter even grown in a rich culture medium. This finding could find new applications in large-scale production of siderophores in bacteria.

Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum

Bacterial endophytes dwelling in medicinal plants represent an as yet underexplored source of bioactive natural products with the potential to be developed into drugs against various human diseases. For the first time, several Streptomyces spp. were isolated from the rare and endangered traditional medicinal plant Leontopodium nivale ssp. alpinum, also known as Edelweiss. In the search for novel natural products, nine endophytic Streptomyces spp. from Edelweiss were investigated via genome sequencing and analysis, followed by fermentation in different media and investigation of secondary metabolomes. A total of 214 secondary metabolite biosynthetic gene clusters (BGCs), of which 35 are presumably unique, were identified by the bioinformatics tool antiSMASH in the genomes of these isolates. LC-MS analyses of the secondary metabolomes of these isolates revealed their potential to produce both known and presumably novel secondary metabolites, whereby most of the identified molecules could be linked to their cognate BGCs. This work sets the stage for further investigation of endophytic streptomycetes from Edelweiss aimed at the discovery and characterization of novel bioactive natural products.

Exploring the Biological Pathways of Siderophores and Their Multidisciplinary Applications: A Comprehensive Review

Siderophores are a class of small molecules renowned for their high iron binding capacity, essential for all life forms requiring iron. This article provides a detailed review of the diverse classifications, and biosynthetic pathways of siderophores, with a particular emphasis on siderophores synthesized via nonribosomal peptide synthetase (NRPS) and non-NRPS pathways. We further explore the secretion mechanisms of siderophores in microbes and plants, and their role in regulating bioavailable iron levels. Beyond biological functions, the applications of siderophores in medicine, agriculture, and environmental sciences are extensively discussed. These applications include biological pest control, disease treatment, ecological pollution remediation, and heavy metal ion removal. Through a comprehensive analysis of the chemical properties and biological activities of siderophores, this paper demonstrates their wide prospects in scientific research and practical applications, while also highlighting current research gaps and potential future directions.

Plant-Growth-Promoting Bacteria

Global food-production levels may soon be insufficient for feeding the population, and changing climatic conditions could further limit agri-food production [...].

A Siderophore Mimicking Gelation Component for Capturing and Self-Separation of Fe(III) from an Aqueous Solution of Mixture of Metal Ions

The carbohydrazide-based gelation component N2,N4,N6-(1,3,5-triazine-2,4,6-triyl)tris(benzene-1,3,5-tricarbohydrazide) (CBTC) was synthesized and characterized using various spectroscopic tools. CBTC and trimesic acid (TMA) get self-assembled to form metallogel with Fe3+, specifically through various noncovalent interactions in a DMSO and H2O mixture. The self-assembly shows remarkable specificity toward Fe(III) among different transition metal salts. It is pertinent to point out that the binding specificity for Fe3+ can also be found in nature in the form of siderophores, as they are mainly involved in scavenging iron selectively from the surroundings. DFT studies have been used to investigate the possible interaction between the different components of the iron metallogel. To determine the selectivity of CBTC for iron, CBTC, along with trimesic acid, is used to interact with other metal ions, including Fe(III) ions, in a single system. The gelation components CBTC and TMA selectively bind with iron(III), which leads to the formation of metallogel and gets separated as a discrete layer, leaving the other metal ions in the solution. Therefore, CBTC and TMA together show iron-scavenging properties. This selective scavenging property is explored through FE-SEM, XPS, PXRD, IR, and ICP-AES analysis. The FE-SEM analysis shows a flower-petal-like morphology for the Fe(III) metallogel. The resemblance in the CBTC-TMA-Fe metallogel and metallogel obtained from the mixture of different metal salts is established through FE-SEM images and XPS analysis. The release of iron from the metallogel is achieved with the help of ascorbic acid, which converts Fe3+ to Fe2+. In biological systems, iron also gets released similarly from siderophores. This is the first report where the synthesized gelation component CBTC molecule is capable of scavenging out iron in the form of metallogel and self-separating from the aqueous mixture in the presence of various other metal ions.

Analysis of the vibrioferrin biosynthetic pathway of Vibrio parahaemolyticus

Siderophores are small-molecule iron chelators produced by many microorganisms that capture and uptake iron from the natural environment and host. Their biosynthesis in microorganisms is generally performed using non-ribosomal peptide synthetase (NRPS) or NRPS-independent siderophore (NIS) enzymes. Vibrio parahaemolyticus secretes its cognate siderophore vibrioferrin under iron-starvation conditions. Vibrioferrin is a dehydrated condensate composed of α-ketoglutarate, L-alanine, aminoethanol, and citrate, and pvsA (the gene encoding the ATP-grasp enzyme), pvsB (the gene encoding the NIS enzyme), pvsD (the gene encoding the NIS enzyme), and pvsE (the gene encoding decarboxylase) are engaged in its biosynthesis. Here, we elucidated the biosynthetic pathway of vibrioferrin through in vitro enzymatic reactions using recombinant PvsA, PvsB, PvsD, and PvsE proteins. We also found that PvsD condenses L-serine and citrate to generate O-citrylserine, and that PvsE decarboxylates O-citrylserine to form O-citrylaminoethanol. In addition, we showed that O-citrylaminoethanol is converted to alanyl-O-citrylaminoethanol by amidification with L-Ala by PvsA and that alanyl-O-citrylaminoethanol is then converted to vibrioferrin by amidification with α-ketoglutarate by PvsB.

Screening of heavy metal-resistant rhizobial and non-rhizobial microflora isolated from Trifolium sp. growing in mining areas

Plant growth-promoting rhizobacteria (PGPR) can promote plant growth and development with several beneficial effects, especially in challenging environmental conditions, such as the presence of toxic contaminants. In this study, 49 isolates obtained from Trifolium sp. nodules growing on a Pb/Zn mine site were characterized for PGP traits including siderophores production, phosphate solubilization, extracellular enzymes production, and antifungal activity. The isolates were also screened for their ability to grow at increasing concentrations of NaCl and heavy metals, including lead, zinc, cobalt, copper, nickel, cadmium, and chromium. The findings of our study indicated that isolates Cupriavidus paucula RSCup01-RSCup08, Providencia rettgeri RSPro01, Pseudomonas putida RSPs01, Pseudomonas thivervalensis RSPs03-RSPs09, and Acinetobacter beijerinckii RSAci01 showed several key traits crucial for promoting plant growth, thus demonstrating the greatest potential. Most isolates displayed resistance to salt and heavy metals. Notably, Staphylococcus xylosus RSSta01, Pseudomonas sp. RSPs02, Micrococcus yunnanensis RSMicc01, and Kocuria dechangensis RSKoc01 demonstrated a significant capacity to grow at salt concentrations ranging from 10 to 20%, and isolates including Cupravidus paucula RSCup01-RSCup08 exhibited resistance to high levels of heavy metals, up to 1300 mg/L Pb++, 1200 mg/L Zn++, 1000 mg/L Ni++, 1000 mg/L Cd++, 500 mg/L Cu++, 400 mg/L Co++, and 50 mg/L CrVI+. Additionally, the analysis revealed that metal-resistant genes pbrA, czcD, and nccA were exclusively detected in the Cupriavidus paucula RSCup01 strain. The results of this study provide insights into the potential of plant growth-promoting rhizobacteria strains that might be used as inoculants to improve phytoremediation in heavy metal-contaminated soils.

Pantoea trifolii sp. nov., a novel bacterium isolated from Trifolium rubens root nodules

A novel bacterium, designated strain MMK2T, was isolated from a surface-sterilised root nodule of a Trifolium rubens plant growing in south-eastern Poland. Cells were Gram negative, non-spore forming and rod shaped. The strain had the highest 16S rRNA gene sequence similarity with P. endophytica (99.4%), P. leporis (99.4%) P. rwandensis (98.8%) and P. rodasii (98.45%). Phylogenomic analysis clearly showed that strain MMK2T and an additional strain, MMK3, should reside in the genus Pantoea and that they were most closely related to P. endophytica and P. leporis. Genome comparisons showed that the novel strain shared 82.96-93.50% average nucleotide identity and 26.2-53. 2% digital DNA:DNA hybridization with closely related species. Both strains produced siderophores and were able to solubilise phosphates. The MMK2T strain was also able to produce indole-3-acetic acid. The tested strains differed in their antimicrobial activity, but both were able to inhibit the growth of Sclerotinia sclerotiorum 10Ss01. Based on the results of the phenotypic, phylogenomic, genomic and chemotaxonomic analyses, strains MMK2T and MMK3 belong to a novel species in the genus Pantoea for which the name Pantoea trifolii sp. nov. is proposed with the type strain MMK2T (= DSM 115063T = LMG 33049T).

Colonization compatibility with Bacillus altitudinis confers soybean seed rot resistance

The plant microbiome and plant-associated bacteria are known to support plant health, but there are limited studies on seed and seedling microbiome to reveal how seed-associated bacteria may confer disease resistance. In this study, the application of antibiotics on soybean seedlings indicated that seed-associated bacteria were involved in the seed rot resistance against a soil-borne pathogen Calonectria ilicicola, but this resistance cannot be carried to withstand root rot. Using PacBio 16S rRNA gene full-length sequencing and microbiome analyses, 14 amplicon sequence variants (ASVs) including 2 ASVs matching to Bacillus altitudinis were found to be more abundant in the four most resistant varieties versus the four most susceptible varieties. Culture-dependent isolation obtained two B. altitudinis isolates that both exhibit antagonistic capability against six fungal pathogens. Application of B. altitudinis on the most resistant and susceptible soybean varieties revealed different colonization compatibility, and the seed rot resistance was restored in the five varieties showing higher bacterial colonization. Moreover, quantitative PCR confirmed the persistence of B. altitudinis on apical shoots till 21 days post-inoculation (dpi), but 9 dpi on roots of the resistant variety TN5. As for the susceptible variety HC, the persistence of B. altitudinis was only detected before 6 dpi on both shoots and roots. The short-term colonization of B. altitudinis on roots may explain the absence of root rot resistance. Collectively, this study advances the insight of B. altitudinis conferring soybean seed rot resistance and highlights the importance of considering bacterial compatibility with plant varieties and colonization persistence on plant tissues.

Identification of siderophores blocking infection of Pseudomonas aeruginosa from Kitasatospora sp. LS1784

Siderophores are low-molecular-mass, high-affinity chelators of Fe3+ ions that are critical for the survival of bacteria in ferric deficient environment. Exogenous siderophores are potential bacteriostat by disrupting the iron-uptake process of pathogens. In our previous work to discover siderophores, strain LS1784 was previously predicted to produce new catecholate-type siderophores by genome analysis but no compounds were obtained. In this work, we reclassified train LS1784 as Kitasatospora sp. LS1784 according to the genome phylogenetic analysis. Then guided by CAS colorimetric assay and molecular network analysis, four catecholate-type siderophores were isolated from the ethyl acetate extract of LS1784 which were coincident with the initial prediction. Notably, compounds 2 and 3 were reported for the first time. Following activity screening, compound 3 showed sufficient anti-Pseudomonas aeruginosa-infection activity in Caenorhabditis elegans infection models, whereas all compounds exhibited no antimicrobial activity. These results indicated that compound 3 can enhance the survival of P. aeruginosa infecting C. elegans by reducing the virulence of P. aeruginosa rather than killing P. aeruginosa, which aligns with our previous findings. Moreover, these findings highlight the effectiveness of comprehensive approaches, including genome mining, CAS (Chromeazurol S) testing, and molecular network (MN) analysis, in identifying potential siderophores, thereby expanding the siderophores arsenal in bacteria for the development of anti-infective drugs.

A review of chemical signaling pathways in the quorum sensing circuit of Pseudomonas aeruginosa

Pseudomonas aeruginosa, an increasingly common competitive and biofilm organism in healthcare infection with sophisticated, interlinked and hierarchic quorum systems (Las, Rhl, PQS, and IQS), creates the greatest threats to the medical industry and has rendered prevailing chemotherapy medications ineffective. The rise of multidrug resistance has evolved into a concerning and potentially fatal occurrence for human life. P. aeruginosa biofilm development is assisted by exopolysaccharides, extracellular DNA, proteins, macromolecules, cellular signaling and interaction. Quorum sensing is a communication process between cells that involves autonomous inducers and regulators. Quorum-induced infectious agent biofilms and the synthesis of virulence factors have increased disease transmission, medication resistance, infection episodes, hospitalizations and mortality. Hence, quorum sensing may be a potential therapeutical target for bacterial illness, and developing quorum inhibitors as an anti-virulent tool could be a promising treatment strategy for existing antibiotics. Quorum quenching is a prevalent technique for treating infections caused by microbes because it diminishes microbial pathogenesis and increases microbe biofilm sensitivity to antibiotics, making it a potential candidate for drug development. This paper examines P. aeruginosa quorum sensing, the hierarchy of quorum sensing mechanism, quorum sensing inhibition and quorum sensing inhibitory agents as a drug development strategy to supplement traditional antibiotic strategies.

Plant Growth-Promoting Soil Bacteria: Nitrogen Fixation, Phosphate Solubilization, Siderophore Production, and Other Biological Activities

This review covers the literature data on plant growth-promoting bacteria in soil, which can fix atmospheric nitrogen, solubilize phosphates, produce and secrete siderophores, and may exhibit several different behaviors simultaneously. We discuss perspectives for creating bacterial consortia and introducing them into the soil to increase crop productivity in agrosystems. The application of rhizosphere bacteria-which are capable of fixing nitrogen, solubilizing organic and inorganic phosphates, and secreting siderophores, as well as their consortia-has been demonstrated to meet the objectives of sustainable agriculture, such as increasing soil fertility and crop yields. The combining of plant growth-promoting bacteria with mineral fertilizers is a crucial trend that allows for a reduction in fertilizer use and is beneficial for crop production.

Nobachelins, new siderophores from Nocardiopsisbaichengensis protecting Caenorhabditiselegans from Pseudomonasaeruginosa infection

The biosynthetic potential of actinobacteria to produce novel natural products is still regarded as immense. In this paper, we correlated a cryptic biosynthetic gene cluster to chemical molecules by genome mining and chemical analyses, leading to the discovery of a new group of catecholate-hydroxamate siderophores, nobachelins, from Nocardiopsisbaichengensis DSM 44845. Nobachelin biosynthesis genes are conserved in several bacteria from the family Nocardiopsidaceae. Structurally, nobachelins feature fatty-acylated hydroxy-ornithine and a rare chlorinated catecholate group. Intriguingly, nobachelins rescued Caenorhabditiselegans from Pseudomonasaeruginosa-mediated killing.

Optimization of Siderophore Production in Three Marine Bacterial Isolates along with Their Heavy-Metal Chelation and Seed Germination Potential Determination

Siderophores are low-molecular-weight and high-affinity molecules produced by bacteria under iron-limited conditions. Due to the low iron (III) (Fe+3) levels in surface waters in the marine environment, microbes produce a variety of siderophores. In the current study, halophilic bacteria Bacillus taeanensis SMI_1, Enterobacter sp., AABM_9, and Pseudomonas mendocina AMPPS_5 were isolated from marine surface water of Kalinga beach, Bay of Bengal (Visakhapatnam, Andhra Pradesh, India) and were investigated for siderophore production using the Chrome Azurol S (CAS) assay. The effect of various production parameters was also studied. The optimum production of siderophores for SMI_1 was 93.57% siderophore units (SU) (after 48 h of incubation at 30 °C, pH 8, sucrose as carbon source, sodium nitrate as nitrogen source, 0.4% succinic acid), and for AABM_9, it was 87.18 %SU (after 36 h of incubation period at 30 °C, pH 8, in the presence of sucrose, ammonium sulfate, 0.4% succinic acid). The maximum production of siderophores for AMPPS_5 was 91.17 %SU (after 36 h of incubation at 35 °C, pH 8.5, glucose, ammonium sulfate, 0.4% citric acid). The bacterial isolates SMI_1, AABM_9, and AMPPS_5 showed siderophore production at low Fe+3 concentrations of 0.10 µM, 0.01 µM, and 0.01 µM, respectively. The SMI_1 (73.09 %SU) and AMPPS_5 (68.26 %SU) isolates showed siderophore production in the presence of Zn+2 (10 µM), whereas AABM_9 (50.4 %SU) exhibited siderophore production in the presence of Cu+2 (10 µM). Additionally, these bacterial isolates showed better heavy-metal chelation ability and rapid development in seed germination experiments. Based on these results, the isolates of marine-derived bacteria effectively produced the maximum amount of siderophores, which could be employed in a variety of industrial and environmental applications.

Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production

Plant growth-promoting bacteria are commonly used in agriculture, particularly for seed inoculation. Multispecies consortia are believed to be the most promising form of these bacteria. However, designing and modeling bacterial consortia to achieve desired phenotypic outcomes in plants is challenging. This review aims to address this challenge by exploring key antimicrobial interactions. Special attention is given to approaches for developing soil plant growth-promoting bacteria consortia. Additionally, advanced omics-based methods are analyzed that allow soil microbiomes to be characterized, providing an understanding of the molecular and functional aspects of these microbial communities. A comprehensive discussion explores the utilization of bacterial preparations in biofertilizers for agricultural applications, focusing on the intricate design of synthetic bacterial consortia with these preparations. Overall, the review provides valuable insights and strategies for intentionally designing bacterial consortia to enhance plant growth and development.

Hydrophilic Copolymers with Hydroxamic Acid Groups as a Protective Biocompatible Coating of Maghemite Nanoparticles: Synthesis, Physico-Chemical Characterization and MRI Biodistribution Study

Superparamagnetic iron oxide nanoparticles (SPION) with a "non-fouling" surface represent a versatile group of biocompatible nanomaterials valuable for medical diagnostics, including oncology. In our study we present a synthesis of novel maghemite (γ-Fe₂O₃) nanoparticles with positive and negative overall surface charge and their coating by copolymer P(HPMA-co-HAO) prepared by RAFT (reversible addition-fragmentation chain-transfer) copolymerization of N-(2-hydroxypropyl)methacrylamide (HPMA) with N-[2-(hydroxyamino)-2-oxo-ethyl]-2-methyl-prop-2-enamide (HAO). Coating was realized via hydroxamic acid groups of the HAO comonomer units with a strong affinity to maghemite. Dynamic light scattering (DLS) demonstrated high colloidal stability of the coated particles in a wide pH range, high ionic strength, and the presence of phosphate buffer (PBS) and serum albumin (BSE). Transmission electron microscopy (TEM) images show a narrow size distribution and spheroid shape. Alternative coatings were prepared by copolymerization of HPMA with methyl 2-(2-methylprop-2-enoylamino)acetate (MMA) and further post-polymerization modification with hydroxamic acid groups, carboxylic acid and primary-amino functionalities. Nevertheless, their colloidal stability was worse in comparison with P(HPMA-co-HAO). Additionally, P(HPMA-co-HAO)-coated nanoparticles were subjected to a bio-distribution study in mice. They were cleared from the blood stream by the liver relatively slowly, and their half-life in the liver depended on their charge; nevertheless, both cationic and anionic particles revealed a much shorter metabolic clearance rate than that of commercially available ferucarbotran.

The Contribution of PGPR in Salt Stress Tolerance in Crops: Unravelling the Molecular Mechanisms of Cross-Talk between Plant and Bacteria

Soil salinity is a major abiotic stress in global agricultural productivity with an estimated 50% of arable land predicted to become salinized by 2050. Since most domesticated crops are glycophytes, they cannot be cultivated on salt soils. The use of beneficial microorganisms inhabiting the rhizosphere (PGPR) is a promising tool to alleviate salt stress in various crops and represents a strategy to increase agricultural productivity in salt soils. Increasing evidence underlines that PGPR affect plant physiological, biochemical, and molecular responses to salt stress. The mechanisms behind these phenomena include osmotic adjustment, modulation of the plant antioxidant system, ion homeostasis, modulation of the phytohormonal balance, increase in nutrient uptake, and the formation of biofilms. This review focuses on the recent literature regarding the molecular mechanisms that PGPR use to improve plant growth under salinity. In addition, very recent -OMICs approaches were reported, dissecting the role of PGPR in modulating plant genomes and epigenomes, opening up the possibility of combining the high genetic variations of plants with the action of PGPR for the selection of useful plant traits to cope with salt stress conditions.

Promotion of the growth and yield of Zea mays by synthetic microbial communities from Jala maize

Plant growth-promoting bacteria (PGPB) are a source of nutrient supply, stimulate plant growth, and even act in the biocontrol of phytopathogens. However, these phenotypic traits have rarely been explored in culturable bacteria from native maize landraces. In this study, synthetic microbial communities (SynCom) were assembled with a set of PGPB isolated from the Jala maize landrace, some of them with additional abilities for the biocontrol of phytopathogenic fungi and the stimulation of plant-induced systemic resistance (ISR). Three SynCom were designed considering the phenotypic traits of bacterial strains, including Achromobacter xylosoxidans Z2K8, Burkholderia sp. Z1AL11, Klebsiella variicola R3J3HD7, Kosakonia pseudosacchari Z2WD1, Pantoea ananatis E2HD8, Pantoea sp. E2AD2, Phytobacter diazotrophicus Z2WL1, Pseudomonas protegens E1BL2, and P. protegens E2HL9. Plant growth promotion in gnotobiotic and greenhouse seedlings assays was performed with Conejo landrace; meanwhile, open field tests were carried out on hybrid CPL9105W maize. In all experimental models, a significant promotion of plant growth was observed. In gnotobiotic assays, the roots and shoot length of the maize seedlings increased 4.2 and 3.0 times, respectively, compared to the untreated control. Similarly, the sizes and weights of the roots and shoots of the plants increased significantly in the greenhouse assays. In the open field assay performed with hybrid CPL9105W maize, the yield increased from 11 tons/ha for the control to 16 tons/ha inoculated with SynCom 3. In addition, the incidence of rust fungal infections decreased significantly from 12.5% in the control to 8% in the treatment with SynCom 3. All SynCom designs promoted the growth of maize in all assays. However, SynCom 3 formulated with A. xylosoxidans Z2K8, Burkholderia sp. Z1AL11, K. variicola R3J3HD7, P. ananatis E2HD8, P. diazotrophicus Z2WL1, and P. protegens E1BL2 displayed the best results for promoting plant growth, their yield, and the inhibition of fungal rust. This study demonstrated the biotechnological eco-friendly plant growth-promoting potential of SynCom assemblies with culturable bacteria from native maize landraces for more sustainable and economic agriculture.

Metabolically versatile psychrotolerant Antarctic bacterium Pseudomonas sp. ANT_H12B is an efficient producer of siderophores and accompanying metabolites (SAM) useful for agricultural purposes

BACKGROUND

Bacterial siderophores are chelating compounds with the potential of application in agriculture, due to their plant growth-promoting (PGP) properties, however, high production and purification costs are limiting factors for their wider application. Cost-efficiency of the production could be increased by omitting purification processes, especially since siderophores accompanying metabolites (SAM) often also possess PGP traits. In this study, the metabolism versatility of Pseudomonas sp. ANT_H12B was used for the optimization of siderophores production and the potential of these metabolites and SAM was characterized in the context of PGP properties.

RESULTS

The metabolic diversity of ANT_H12B was examined through genomic analysis and phenotype microarrays. The strain was found to be able to use numerous C, N, P, and S sources, which allowed for the design of novel media suitable for efficient production of siderophores in the form of pyoverdine (223.50-512.60 μM). Moreover, depending on the culture medium, the pH of the siderophores and SAM solutions varied from acidic (pH < 5) to alkaline (pH > 8). In a germination test, siderophores and SAM were shown to have a positive effect on plants, with a significant increase in germination percentage observed in beetroot, pea, and tobacco. The PGP potential of SAM was further elucidated through GC/MS analysis, which revealed other compounds with PGP potential, such as indolic acetic acids, organic acids, fatty acids, sugars and alcohols. These compounds not only improved seed germination but could also potentially be beneficial for plant fitness and soil quality.

CONCLUSIONS

Pseudomonas sp. ANT_H12B was presented as an efficient producer of siderophores and SAM which exhibit PGP potential. It was also shown that omitting downstream processes could not only limit the costs of siderophores production but also improve their agricultural potential.

Stimulation of PGP Bacteria on the Development of Seeds, Plants and Cuttings of the Obligate Halophyte Arthrocaulon (Arthrocnemum) macrostachyum (Moric.) Piirainen & G. Kadereit

The Earth is undergoing alterations at a high speed, which causes problems such as environmental pollution and difficulty in food production. This is where halophytes are interesting, due to their high potential in different fields, such as remediation of the environment and agriculture. For this reason, it is necessary to deepen the knowledge of the development of halophytes and how plant growth-promoting bacteria (PGP) can play a fundamental role in this process. Therefore, in this work were tested the effects of five PGP bacteria on its rhizosphere and other endophytic bacteria at different concentrations of NaCl on seed germination, plant growth (0 and 171 mM) and cutting growth (0 mM) of Arthrocaulon macrostachyum. The growth promotion in this strict halophyte is highlighted due to the presence of PGP bacteria and the fact that no salt is needed. Thus, without salt, the bacterial strains Kocuria polaris Hv16, Pseudarthrobacter psychrotolerans C58, and Rahnella aceris RTE9 enhanced the biomass production by more than 60% in both stems and roots. Furthermore, germination was encouraged by more than 30% in the presence of both R. aceris RTE9 and K. polaris Hv16 at 171 mM NaCl; the latter also had a biocontrol effect on the fungi that grew on the seeds. Additionally, for the first time in cuttings of this perennial species, the root biomass was improved thanks to the consortium of K. polaris Hv16 and P. psychrotolerans C58. Finally, this study demonstrates the potential of PGPs for optimising the development of halophytes, either for environmental or agronomic purposes.