Siderophore-Mediated Aluminum Uptake by Bacillus megaterium ATCC 19213

Comparative genomics of plant growth promoting phosphobacteria isolated from acidic soils

Despite being one of the most abundant elements in soil, phosphorus (P) often becomes a limiting macronutrient for plants due to its low bioavailability, primarily locked away in insoluble organic and inorganic forms. Phosphate solubilizing and mineralizing bacteria, also called phosphobacteria, isolated from P-deficient soils have emerged as a promising biofertilizer alternative, capable of converting these recalcitrant P forms into plant-available phosphates. Three such phosphobacteria strains-Serratia sp. RJAL6, Klebsiella sp. RCJ4, and Enterobacter sp. 198-previously demonstrated their particular strength as plant growth promoters for wheat, ryegrass, or avocado under abiotic stresses and P deficiency. Comparative genomic analysis of their draft genomes revealed several genes encoding key functionalities, including alkaline phosphatases, isonitrile secondary metabolites, enterobactin biosynthesis and genes associated to the production of indole-3-acetic acid (IAA) and gluconic acid. Moreover, overall genome relatedness indexes (OGRIs) revealed substantial divergence between Serratia sp. RJAL6 and its closest phylogenetic neighbours, Serratia nematodiphila and Serratia bockelmanii. This compelling evidence suggests that RJAL6 merits classification as a novel species. This in silico genomic analysis provides vital insights into the plant growth-promoting capabilities and provenance of these promising PSRB strains. Notably, it paves the way for further characterization and potential application of the newly identified Serratia species as a powerful bioinoculant in future agricultural settings.

Proteomic response to phosphorus deficiency and aluminum stress of three aluminum-tolerant phosphobacteria isolated from acidic soils

Aluminum (Al)-tolerant phosphobacteria enhance plant growth in acidic soils by improving Al complexing and phosphorus (P) availability. However, the impact of Al stress and P deficiency on bacterial biochemistry and physiology remains unclear. We investigated the single and mutual effects of Al stress (10 mM) and P deficiency (0.05 mM) on the proteome of three aluminum-tolerant phosphobacteria: Enterobacter sp. 198, Enterobacter sp. RJAL6, and Klebsiella sp. RCJ4. Cultivated under varying conditions, P deficiency upregulated P metabolism proteins while Al exposure downregulated iron-sulfur and heme-containing proteins and upregulated iron acquisition proteins. This demonstrated that Al influence on iron homeostasis and bacterial central metabolism. This study offers crucial insights into bacterial behavior in acidic soils, benefiting the development of bioinoculants for crops facing Al toxicity and P deficiency. This investigation marks the first proteomic study on the interaction between high Al and P deficiency in acid soils-adapted bacteria.

Proteomic analysis to unravel the biochemical mechanisms triggered by Bacillus toyonensis SFC 500-1E under chromium(VI) and phenol stress

Bacillus toyonensis SFC 500-1E is a member of the consortium SFC 500-1 able to remove Cr(VI) and simultaneously tolerate high phenol concentrations. In order to elucidate mechanisms utilized by this strain during the bioremediation process, the differential expression pattern of proteins was analyzed when it grew with or without Cr(VI) (10 mg/L) and Cr(VI) + phenol (10 and 300 mg/L), through two complementary proteomic approaches: gel-based (Gel-LC) and gel-free (shotgun) nanoUHPLC-ESI-MS/MS. A total of 400 differentially expressed proteins were identified, out of which 152 proteins were down-regulated under Cr(VI) and 205 up-regulated in the presence of Cr(VI) + phenol, suggesting the extra effort made by the strain to adapt itself and keep growing when phenol was also added. The major metabolic pathways affected include carbohydrate and energetic metabolism, followed by lipid and amino acid metabolism. Particularly interesting were also ABC transporters and the iron-siderophore transporter as well as transcriptional regulators that can bind metals. Stress-associated global response involving the expression of thioredoxins, SOS response, and chaperones appears to be crucial for the survival of this strain under treatment with both contaminants. This research not only provided a deeper understanding of B. toyonensis SFC 500-1E metabolic role in Cr(VI) and phenol bioremediation process but also allowed us to complete an overview of the consortium SFC 500-1 behavior. This may contribute to an improvement in its use as a bioremediation strategy and also provides a baseline for further research.

Genomic insights into Bacillus subtilis MBB3B9 mediated aluminium stress mitigation for enhanced rice growth

Aluminium (Al) toxicity in acid soil ecosystems is a major impediment to crop production as it drastically affects plant root growth, thereby acquisition of nutrients from the soil. Plant growth-promoting bacteria offers an interesting avenue for promoting plant growth under an Al-phytotoxic environment. Here, we report the plant growth-promoting activities of an acid-tolerant isolate of Bacillus subtilis that could ameliorate acid-induced Al-stress in rice (Oryza sativa L.). The whole genome sequence data identified the major genes and genetic pathways in B. subtilis MBB3B9, which contribute to the plant growth promotion in acidic pH. Genetic pathways for organic acid production, denitrification, urea metabolism, indole-3-acetic acid (IAA) production, and cytokinin biosynthesis were identified as major genetic machinery for plant growth promotion and mitigation of Al-stress in plants. The in-vitro analyses revealed the production of siderophores and organic acid production as primary mechanisms for mitigation of Al-toxicity. Other plant growth-promoting properties such as phosphate solubilization, zinc solubilization, and IAA production were also detected in significant levels. Pot experiments involving rice under acidic pH and elevated concentrations of aluminium chloride (AlCl3) suggested that soil treatment with bacterial isolate MBB3B9 could enhance plant growth and productivity compared to untreated plants. A significant increase in plant growth and productivity was recorded in terms of plant height, chlorophyll content, tiller number, panicle number, grain yield, root growth, and root biomass production.

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

Siderophores are synthesized and secreted by many bacteria, yeasts, fungi, and plants for Fe (III) chelation. A variety of plant-growth-promoting bacteria (PGPB) colonize the rhizosphere and contribute to iron assimilation by plants. These microorganisms possess mechanisms to produce Fe ions under iron-deficient conditions. Under appropriate conditions, they synthesize and release siderophores, thereby increasing and regulating iron bioavailability. This review focuses on various bacterial strains that positively affect plant growth and development through synthesizing siderophores. Here we discuss the diverse chemical nature of siderophores produced by plant root bacteria; the life cycle of siderophores, from their biosynthesis to the Fe-siderophore complex degradation; three mechanisms of siderophore biosynthesis in bacteria; the methods for analyzing siderophores and the siderophore-producing activity of bacteria and the methods for screening the siderophore-producing activity of bacterial colonies. Further analysis of biochemical, molecular-biological, and physiological features of siderophore synthesis by bacteria and their use by plants will allow one to create effective microbiological preparations for improving soil fertility and increasing plant biomass, which is highly relevant for sustainable agriculture.

Perspective on the biotechnological production of bacterial siderophores and their use

Iron (Fe) is an essential element in several fundamental cellular processes. Although present in high amounts in the Earth's crust, Fe can be a scarce element due to its low bioavailability. To mitigate Fe limitation, microorganism (bacteria and fungi) and grass plant biosynthesis and secret secondary metabolites, called siderophores, with capacity to chelate Fe(III) with high affinity and selectivity. This review focuses on the current state of knowledge concerning the production of siderophores by bacteria. The main siderophore types and corresponding siderophore-producing bacteria are summarized. A concise outline of siderophore biosynthesis, secretion and regulation is given. Important aspects to be taken into account in the selection of a siderophore-producing bacterium, such as biological safety, complexing properties of the siderophores and amount of siderophores produced are summarized and discussed. An overview containing recent scientific advances on culture medium formulation and cultural conditions that influence the production of siderophores by bacteria is critically presented. The recovery, purification and processing of siderophores are outlined. Potential applications of siderophores in different sectors including agriculture, environment, biosensors and the medical field are sketched. Finally, future trends regarding the production and use of siderophores are discussed. KEY POINTS : • An overview of siderophore production by bacteria is critically presented • Scientific advances on factors that influence siderophores production are discussed • Potential applications of siderophores, in different fields, are outlined.

Perspective on the biotechnological production of bacterial siderophores and their use

Iron (Fe) is an essential element in several fundamental cellular processes. Although present in high amounts in the Earth's crust, Fe can be a scarce element due to its low bioavailability. To mitigate Fe limitation, microorganism (bacteria and fungi) and grass plant biosynthesis and secret secondary metabolites, called siderophores, with capacity to chelate Fe(III) with high affinity and selectivity. This review focuses on the current state of knowledge concerning the production of siderophores by bacteria. The main siderophore types and corresponding siderophore-producing bacteria are summarized. A concise outline of siderophore biosynthesis, secretion and regulation is given. Important aspects to be taken into account in the selection of a siderophore-producing bacterium, such as biological safety, complexing properties of the siderophores and amount of siderophores produced are summarized and discussed. An overview containing recent scientific advances on culture medium formulation and cultural conditions that influence the production of siderophores by bacteria is critically presented. The recovery, purification and processing of siderophores are outlined. Potential applications of siderophores in different sectors including agriculture, environment, biosensors and the medical field are sketched. Finally, future trends regarding the production and use of siderophores are discussed. KEY POINTS : • An overview of siderophore production by bacteria is critically presented • Scientific advances on factors that influence siderophores production are discussed • Potential applications of siderophores, in different fields, are outlined.

Siderophores: an alternative bioremediation strategy?

Siderophores are small molecular weight iron scavengers that are mainly produced by bacteria, fungi, and plants. Recently, they have attracted increasing attention because of their potential role in environmental bioremediation. Although siderophores are generally considered to exhibit high specificity for iron, they have also been reported to bind to various metal and metalloid ions. This unique ability allows siderophores to solubilise and mobilise heavy metals and metalloids from soil, thereby facilitating their bioremediation. In addition, because of their redox nature, they can mediate the production of reactive oxygen species (ROS), and thus promote the biodegradation of organic contaminants. The aim of this review is to summarise the existing knowledge on the developed strategies of siderophore-assisted bioremediation of metals, metalloids, and organic contaminants. Additionally, this review also includes the biosynthesis and classification of microbial and plant siderophores.

The Cell Membrane of a Novel Rhizobium phaseoli Strain Is the Crucial Target for Aluminium Toxicity and Tolerance

Soils with low pH and high aluminium (Al) contamination restrict common bean production, mainly due to adverse effects on rhizobia. We isolated a novel rhizobium strain, B3, from Kenyan soil which is more tolerant to Al stress than the widely used commercial strain CIAT899. B3 was resistant to 50 µM Al and recovered from 100 µM Al stress, while CIAT899 did not. Calcein labeling showed that less Al binds to the B3 membranes and less ATP and mScarlet-1 protein, a cytoplasmic marker, leaked out of B3 than CIAT899 cells in Al-containing media. Expression profiles showed that the primary targets of Al are genes involved in membrane biogenesis, metal ions binding and transport, carbohydrate, and amino acid metabolism and transport. The identified differentially expressed genes suggested that the intracellular γ-aminobutyric acid (GABA), glutathione (GSH), and amino acid levels, as well as the amount of the extracellular exopolysaccharide (EPS), might change during Al stress. Altered EPS levels could also influence biofilm formation. Therefore, these parameters were investigated in more detail. The GABA levels, extracellular EPS production, and biofilm formation increased, while GSH and amino acid level decreased. In conclusion, our comparative analysis identified genes that respond to Al stress in R. phaseoli. It appears that a large portion of the identified genes code for proteins stabilizing the plasma membrane. These genes might be helpful for future studies investigating the molecular basis of Al tolerance and the characterization of candidate rhizobial isolates that perform better in Al-contaminated soils than commercial strains.

Antimicrobial Bacillus: Metabolites and Their Mode of Action

The agricultural industry utilizes antibiotic growth promoters to promote livestock growth and health. However, the World Health Organization has raised concerns over the ongoing spread of antibiotic resistance transmission in the populace, leading to its subsequent ban in several countries, especially in the European Union. These restrictions have translated into an increase in pathogenic outbreaks in the agricultural industry, highlighting the need for an economically viable, non-toxic, and renewable alternative to antibiotics in livestock. Probiotics inhibit pathogen growth, promote a beneficial microbiota, regulate the immune response of its host, enhance feed conversion to nutrients, and form biofilms that block further infection. Commonly used lactic acid bacteria probiotics are vulnerable to the harsh conditions of the upper gastrointestinal system, leading to novel research using spore-forming bacteria from the genus Bacillus. However, the exact mechanisms behind Bacillus probiotics remain unexplored. This review tackles this issue, by reporting antimicrobial compounds produced from Bacillus strains, their proposed mechanisms of action, and any gaps in the mechanism studies of these compounds. Lastly, this paper explores omics approaches to clarify the mechanisms behind Bacillus probiotics.

Potential Plant Growth-Promoting Bacteria with Heavy Metal Resistance

Plant growth-promoting (PGP) bacteria commonly have many strategies to cope with heavy metal toxicity. Heavy metal-resistant PGP bacteria can be used to improve the growth of plants in heavy metal contaminated soils. In this study, the soil samples were collected from the lead-zinc mineral deposits in Gümüşhane Province, Turkey. Nine bacterial isolates were obtained on the nutrient agar medium supplemented with 100 mg/mL zinc and lead. All of the isolates were screened in terms of plant growth-promoting characteristics including production of indole-3-acetic acid and siderophore, nitrogen fixation and phosphate solubilisation. Nine bacteria were identified as Bacillus cereus, Bacillus atrophaeus, Bacillus pumilus, Bacillus amyloliquefaciens, Bacillus tropicus, Bacillus subtilis, Bacillus halotolerans, Bacillus vallismortis, and Enterococcus mundtii by classical and 16S rDNA-PCR assays. In addition, these isolates were evaluated for their response to three heavy metals (lead, zinc, copper) dominant in the soil samples and minimal inhibitory concentration (MIC) of the heavy metals was determined with plate dilution method. Consequently, the bacterial isolates in this study possess plant growth-promoting traits and can ameliorate heavy metal contaminated soil. E. mundtii was reported to be found in heavy metal contaminated soil for the first time. This study is the first report about PGP characteristics (IAA production and phosphate solubilisation) of B. vallismortis.

Isolation of Efficient Metal-Binding Bacteria from Boreal Peat Soils and Development of Microbial Biosorbents for Improved Nickel Scavenging

Boreal peatlands with low iron availability are a potential, but rarely studied, source for the isolation of bacteria for applications in metal sorption. The present research focused on the isolation and identification of Actinobacteria from northern Finland, which can produce siderophores for metal capture. The 16S rDNA analysis showed that isolated strains belonged to Firmicutes (Bacillus sp.) and Actinobacteria (Microbacterium sp.). The culture most efficiently producing siderophores in the widest array of the media was identified as Microbacterium sp. The most appropriate media for siderophore production by the Microbacterium strain were those prepared with glucose supplemented with asparagine or glutamic acid, and those prepared with glycerol or fructose supplemented with glutamic acid. The microorganism obtained and its siderophores were used to develop Sphagnum moss-based hybrid biosorbents. It was showed that the hybrid sorbent could bind nickel ions and that the nickel removal was enhanced by the presence of siderophores. Bacterial cells did not have a significant effect on sorption efficiency compared to the use of siderophores alone. The microbial biosorbent could be applied in the final effluent treatment stage for wastewater with low metal concentrations.

An overview of siderophore biosynthesis among fluorescent Pseudomonads and new insights into their complex cellular organization

Siderophores are iron-chelating molecules produced by bacteria to access iron, a key nutrient. These compounds have highly diverse chemical structures, with various chelating groups. They are released by bacteria into their environment to scavenge iron and bring it back into the cells. The biosynthesis of siderophores requires complex enzymatic processes and expression of the enzymes involved is very finely regulated by iron availability and diverse transcriptional regulators. Recent data have also highlighted the organization of the enzymes involved in siderophore biosynthesis into siderosomes, multi-enzymatic complexes involved in siderophore synthesis. An understanding of siderophore biosynthesis is of great importance, as these compounds have many potential biotechnological applications because of their metal-chelating properties and their key role in bacterial growth and virulence. This review focuses on the biosynthesis of siderophores produced by fluorescent Pseudomonads, bacteria capable of colonizing a large variety of ecological niches. They are characterized by the production of chromopeptide siderophores, called pyoverdines, which give the typical green colour characteristic of fluorescent pseudomonad cultures. Secondary siderophores are also produced by these strains and can have highly diverse structures (such as pyochelins, pseudomonine, yersiniabactin, corrugatin, achromobactin and quinolobactin).

Metal binding ability of microbial natural metal chelators and potential applications

Metallophores can chelate many different metal and metalloid ions next to iron, make them valuable for many applications.

Non-specific interference of cobalt with siderophore-dependent iron uptake pathways

Presence of Co²⁺affects the production of the siderophore Pyochelin inPseudomonas aeruginosa. This repression is not Fur-dependent but due to competition of Pyochelin–Co²⁺with Pyochein–Fe³⁺for PchR (transcriptional activator).

Nickel exposure reduces enterobactin production in Escherichia coli

Escherichia coli is a well‐studied bacterium that can be found in many niches, such as industrial wastewater, where the concentration of nickel can rise to low‐millimolar levels. Recent studies show that nickel exposure can repress pyochelin or induce pyoverdine siderophore production in Pseudomonas aueroginosa. Understanding the molecular cross‐talk between siderophore production, metal homeostasis, and metal toxicity in microorganisms is critical for designing bioremediation strategies for metal‐contaminated sites. Here, we show that high‐nickel exposure prolongs lag phase duration as a result of low‐intracellular iron levels in E. coli. Although E. coli cells respond to low‐intracellular iron during nickel stress by maintaining high expression of iron uptake systems such as fepA, the demand for iron is not met due to a lack of siderophores in the extracellular medium during nickel stress. Taken together, these results indicate that nickel inhibits iron accumulation in E. coli by reducing the presence of enterobactin in the extracellular medium.

Cadmium-induced changes in the production of siderophores by a plant growth promoting strain of Pseudomonas fulva

The impact of increasing Cd²⁺ exposure on the quality and quantity of siderophores produced by a plant growth promoting Pseudomonas fulva strain was tested to gain insight into the degree of change. P. fulva was cultured in the increasing concentrations of Cd²⁺ (0, 0.5, 1.0, 2.0 mM). The secreted siderophores were separated by HPLC and characterized by UHPLC-QTOF/MS. In the presence of 2 mM Cd²⁺ synthesis of siderophores (hydroxamates, catecholates, phenolates) was mitigated compared to the treatments with lower concentrations of Cd²⁺ (0.5 and 1 mM). Increased synthesis of catecholates in 0.5 and 1 mM Cd²⁺ and of phenolates in 0.5-2 mM Cd²⁺ was revealed compared to the variant without Cd²⁺ . Out of seven different hydroxamates, the secretion of ferrioxamine E was significantly decreased in the highest Cd²⁺ concentration. Two additional ferrioxamines, X2 and D2, were secreted independent of the presence or absence of Cd²⁺ . Exposure to Cd²⁺ change the composition of siderophores secreted by P. fulva with selective promotion of catecholates and phenolates at the expense of hydroxamates. Successful adaptation in a Cd-contaminated soil in the frame of practical applications to promote phytoremediation can be assumed.

Dual action of chromium-reducing and nitrogen-fixing Bacillus megaterium-ASNF3 for improved agro-rehabilitation of chromium-stressed soils

We conducted a study for enhanced biological rehabilitation of chromium-contaminated soils using a chromium-reducing and nitrogen-fixing bacterial species (Bacillus megaterium-ASNF3). The bacterial species was isolated from a chromium-rich land area, characterized, and employed under optimum conditions for the treatment of artificially prepared chromium-rich soil. The bacterium reduced Cr(VI) up to 86 % in a 60-day trial of incubation in the soil bioreactor. The nitrogenase activity of the bacterium yielded up to 486 nmol of ethylene/mL/h after an incubation period of 40 days when it was optimally cultured in growth medium at neutral pH and 30 °C. Although the nitrogen-fixing ability of the bacterium reduced significantly in the presence of 1000 ppm of Cr(VI), yet, the bacterium was proved to be a potential bio-fertilizer for enhancing nitrogen contents of the contaminated soil even under the higher chromium stress, together with the metal reduction. In the biologically treated soil, higher values of wheat growth variables were achieved. Application of metal-resistant B. megaterium-ASNF3 in selected situations rendered chromium-laden soils arable with significant increment in crop-yield parameters.

Beyond iron: non-classical biological functions of bacterial siderophores

Bacteria secrete small molecules known as siderophores to acquire iron from their surroundings. For over 60 years, investigations into the bioinorganic chemistry of these molecules, including fundamental coordination chemistry studies, have provided insight into the crucial role that siderophores play in bacterial iron homeostasis. The importance of understanding the fundamental chemistry underlying bacterial life has been highlighted evermore in recent years because of the emergence of antibiotic-resistant bacteria and the need to prevent the global rise of these superbugs. Increasing reports of siderophores functioning in capacities other than iron transport have appeared recently, but reports of "non-classical" siderophore functions have long paralleled those of iron transport. One particular non-classical function of these iron chelators, namely antibiotic activity, was documented before the role of siderophores in iron transport was established. In this Perspective, we present an exposition of past and current work into non-classical functions of siderophores and highlight the directions in which we anticipate that this research is headed. Examples include the ability of siderophores to function as zincophores, chalkophores, and metallophores for a variety of other metals, sequester heavy metal toxins, transport boron, act as signalling molecules, regulate oxidative stress, and provide antibacterial activity.

The binding, transport and fate of aluminium in biological cells

Aluminium is the most abundant metal in the Earth's crust and yet, paradoxically, it has no known biological function. Aluminium is biochemically reactive, it is simply that it is not required for any essential process in extant biota. There is evidence neither of element-specific nor evolutionarily conserved aluminium biochemistry. This means that there are no ligands or chaperones which are specific to its transport, there are no transporters or channels to selectively facilitate its passage across membranes, there are no intracellular storage proteins to aid its cellular homeostasis and there are no pathways which evolved to enable the metabolism and excretion of aluminium. Of course, aluminium is found in every compartment of every cell of every organism, from virus through to Man. Herein we have investigated each of the 'silent' pathways and metabolic events which together constitute a form of aluminium homeostasis in biota, identifying and evaluating as far as is possible what is known and, equally importantly, what is unknown about its uptake, transport, storage and excretion.

Draft Genome Sequence of Bacillus megaterium Type Strain ATCC 14581

Bacillus megaterium is a Gram-positive, rod-shaped, spore-forming bacterium of biotechnological importance. Here, we report a 5.7-Mbp draft genome sequence of B. megaterium ATCC 14581, which is the type strain of the species.

Effect of metals on a siderophore producing bacterial isolate and its implications on microbial assisted bioremediation of metal contaminated soils

A bacterial isolate producing siderophore under iron limiting conditions, was isolated from mangroves of Goa. Based on morphological, biochemical, chemotaxonomical and 16S rDNA studies, the isolate was identified as Bacillus amyloliquefaciens NAR38.1. Preliminary characterization of the siderophore indicated it to be catecholate type with dihydroxy benzoate as the core component. Optimum siderophore production was observed at pH 7 in mineral salts medium (MSM) without any added iron with glucose as the carbon source. Addition of NaCl in the growth medium showed considerable decrease in siderophore production above 2% NaCl. Fe(+2) and Fe(+3) below 2 μM and 40 μM concentrations respectively, induced siderophore production, above which the production was repressed. Binding studies of the siderophore with Fe(+2) and Fe(+3) indicated its high affinity towards Fe(+3). The siderophore concentration in the extracellular medium was enhanced when MSM was amended with essential metals Zn, Co, Mo and Mn, however, decreased with Cu, while the concentration was reduced with abiotic metals As, Pb, Al and Cd. Significant increase in extracellular siderophore production was observed with Pb and Al at concentrations of 50 μM and above. The effect of metals on siderophore production was completely mitigated in presence of Fe. The results implicate effect of metals on the efficiency of siderophore production by bacteria for potential application in bioremediation of metal contaminated iron deficient soils especially in the microbial assisted phytoremediation processes.

The role of plant-associated bacteria in the mobilization and phytoextraction of trace elements in contaminated soils

Phytoextraction makes use of trace element-accumulating plants that concentrate the pollutants in their tissues. Pollutants can be then removed by harvesting plants. The success of phytoextraction depends on trace element availability to the roots and the ability of the plant to intercept, take up, and accumulate trace elements in shoots. Current phytoextraction practises either employ hyperaccumulators or fast-growing high biomass plants; the phytoextraction process may be enhanced by soil amendments that increase trace element availability in the soil. This review will focus on the role of plant-associated bacteria to enhance trace element availability in the rhizosphere. We report on the kind of bacteria typically found in association with trace element - tolerating or - accumulating plants and discuss how they can contribute to improve trace element uptake by plants and thus the efficiency and rate of phytoextraction. This enhanced trace element uptake can be attributed to a microbial modification of the absorptive properties of the roots such as increasing the root length and surface area and numbers of root hairs, or by increasing the plant availability of trace elements in the rhizosphere and the subsequent translocation to shoots via beneficial effects on plant growth, trace element complexation and alleviation of phytotoxicity. An analysis of data from literature shows that effects of bacterial inoculation on phytoextraction efficiency are currently inconsistent. Some key processes in plant-bacteria interactions and colonization by inoculated strains still need to be unravelled more in detail to allow full-scale application of bacteria assisted phytoremediation of trace element contaminated soils.

Interkingdom metabolic transformations captured by microbial imaging mass spectrometry

In polymicrobial infections, microbes can interact with both the host immune system and one another through direct contact or the secretion of metabolites, affecting disease progression and treatment options. The thick mucus in the lungs of patients with cystic fibrosis is highly susceptible to polymicrobial infections by opportunistic pathogens, including the bacterium Pseudomonas aeruginosa and the fungus Aspergillus fumigatus. Unravelling the hidden molecular interactions within such polymicrobial communities and their metabolic exchange processes will require effective enabling technologies applied to model systems. In the present study, MALDI-TOF and MALDI-FT-ICR imaging mass spectrometry (MALDI-IMS) combined with MS/MS networking were used to provide insight into the interkingdom interaction between P. aeruginosa and A. fumigatus at the molecular level. The combination of these technologies enabled the visualization and identification of metabolites secreted by these microorganisms grown on agar. A complex molecular interplay was revealed involving suppression, increased production, and biotransformation of a range of metabolites. Of particular interest is the observation that P. aeruginosa phenazine metabolites were converted by A. fumigatus into other chemical entities with alternative properties, including enhanced toxicities and the ability to induce fungal siderophores. This work highlights the capabilities of MALDI-IMS and MS/MS network analysis to study interkingdom interactions and provides insight into the complex nature of polymicrobial metabolic exchange and biotransformations.

Microbial siderophores: a mini review

Iron is one of the major limiting factors and essential nutrients of microbial life. Since in nature it is not readily available in the preferred form, microorganisms produce small high affinity chelating molecules called siderophores for its acquisition. Microorganisms produce a wide variety of siderophores controlled at the molecular level by different genes to accumulate, mobilize and transport iron for metabolism. Siderophores also play a critical role in the expression of virulence and development of biofilms by different microbes. Apart from maintaining microbial life, siderophores can be harnessed for the sustainability of human, animals and plants. With the advent of modern molecular tools, a major breakthrough is taking place in the understanding of the multifaceted role of siderophores in nature. This mini review is intended to provide a general overview on siderophore along with its role and applications.

Interactive and Single Effects of Ectomycorrhiza Formation and Bacillus cereus on Metallothionein MT1 Expression and Phytoextraction of Cd and Zn by Willows

Single and joint ectomycorrhizal (+ Hebeloma mesophaeum) and bacterial (+ Bacillus cereus) inoculations of willows (Salix viminalis) were investigated for their potential and mode of action in the promotion of cadmium (Cd) and zinc (Zn) phytoextraction. Dual fungal and bacterial inoculations promoted the biomass production of willows in contaminated soil. Single inoculations either had no effect on the plant growth or inhibited it. All inoculated willows showed increased concentrations of nutritional elements (N, P, K and Zn) and decreased concentrations of Cd in the shoots. The lowest biomass production and concentration of Cd in the willows (+ B. cereus) were combined with the strongest expression of metallothioneins. It seems that biotic stress from bacterial invasion increased the synthesis of these stress proteins, which responded in decreased Cd concentrations. Contents of Cd and Zn in the stems of willows were combination-specific, but were always increased in dual inoculated plants. In conclusion, single inoculations with former mycorrhiza-associated B. cereus strains decreased the phytoextraction efficiency of willows by causing biotic stress. However, their joint inoculation with an ectomycorrhizal fungus is a very promising method for promoting the phytoextraction of Cd and Zn through combined physiological effects on the plant.

New roles for bacterial siderophores in metal transport and tolerance

Siderophores are chelators with extremely strong affinity for ferric iron and are best known for their capacity to feed microorganisms with this metal. Despite their preference for iron, they can also chelate numerous other metals with variable affinities. There is also increasing evidence that metals other than iron can activate the production of siderophores by bacteria, thereby implicating siderophores in the homeostasis of metals other than iron and especially heavy metal tolerance. This article considers this new concept that siderophores play a role in protecting bacteria against metal toxicity and discusses the possible contribution of these chelators to the transport of biological relevant metals in addition to iron.

Presence of the siderophores pyoverdine and pyochelin in the extracellular medium reduces toxic metal accumulation in Pseudomonas aeruginosa and increases bacterial metal tolerance

In order to get access to iron, Pseudomonas aeruginosa strain PAO1 produces two major siderophores pyoverdine (PVD) and pyochelin (PCH). Both siderophores are able to chelate many other metals in addition to iron. However, despite this property, only iron is transported efficiently into the bacteria by the PVD and PCH uptake pathways. Growth studies with P. aeruginosa strains showed a lower sensitivity to toxic metals for the siderophore-producing strain than for the mutants unable to produce siderophores. Moreover, addition of PVD or PCH to the growth medium of a siderophore-deficient strain considerably reduced the toxicity of toxic metals present at concentrations of 100 µM in iron-limited and iron-supplemented growth conditions. Measurement by Inductively Coupled Plasma-Atomic Emission Spectrometry of the concentration of metals present in bacteria incubated with metals in the presence or absence of PVD or PCH indicated that both siderophores were able to sequester metals from the extracellular medium of the bacteria, decreasing metal diffusion into the bacteria. Pyoverdine was able to sequester Al(3+) , Co(2+) , Cu(2+) , Eu(3+) , Ni(2+) , Pb(2+) , Tb(3+) and Zn(2+) from the extracellular medium, and PCH, Al(3+) , Co(2+) , Cu(2+) , Ni(2+) , Pb(2+) and Zn(2+) . Moreover, the presence of 100 µM Cu(2+) and Ni(2+) increased PVD production by 290% and 380%, respectively, in a medium supplemented with iron. All these data suggest that PVD and PCH may contribute to P. aeruginosa resistance to heavy metals.

Arsenic-resistant bacteria associated with roots of the wild Cirsium arvense (L.) plant from an arsenic polluted soil, and screening of potential plant growth-promoting characteristics

A rhizobacterial community, associated with the roots of wild thistle Cirsium arvense (L.) growing in an arsenic polluted soil, was studied by fluorescence in situ hybridization (FISH) analysis in conjunction with cultivation-based methods. In the bulk, rhizosphere, and rhizoplane fractions of the soil, the qualitative picture obtained by FISH analysis of the main phylogenetic bacterial groups was similar and was predominantly comprised of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. The arsenic-resistant isolates belonged to 13 genera, the most abundant being those of Bacillus, Achromobacter, Brevundimonas, Microbacterium, and Ochrobactrum. Most bacteria grew in the presence of high arsenic concentrations (over 100mM arsenate and 10mM arsenite). Most strains possessed the ArsC, ArsB and ACR3 genes homologous to arsenate reductase and to the two classes of arsenite efflux pumps, respectively, peculiar to the ars operon of the arsenic detoxification system. ArsB and ACR3 were present simultaneously in highly resistant strains. An inconsistency between 16S rRNA phylogenetic affiliations and the arsenate reductase sequences of the strains was observed, indicating possible horizontal transfer of arsenic resistance genes in the soil bacterial community. Several isolates were able to reduce arsenate and to oxidise arsenite. In particular, Ancylobacter dichloromethanicum strain As3-1b possessed both characteristics, and arsenite oxidation occurred in the strain also under chemoautotrophic conditions. Some rhizobacteria produced siderophores, indole acetic acid and 1-amino-cyclopropane-1-carboxylic acid deaminase, thus possessing potential plant growth-promoting traits.

Siderophores mediate reduced and increased uptake of cadmium by Streptomyces tendae F4 and sunflower (Helianthus annuus), respectively

AIMS

As a toxic metal, cadmium (Cd) affects microbial and plant metabolic processes, thereby potentially reducing the efficiency of microbe or plant-mediated remediation of Cd-polluted soil. The role of siderophores produced by Streptomyces tendae F4 in the uptake of Cd by bacteria and plant was investigated to gain insight into the influence of siderophores on Cd availability to micro-organisms and plants.

METHODS AND RESULTS

The bacterium was cultured under siderophore-inducing conditions in the presence of Cd. The kinetics of siderophore production and identification of the siderophores and their metal-bound forms were performed using electrospray ionization mass spectrometry. Inductively coupled plasma spectroscopy was used to measure iron (Fe) and Cd contents in the bacterium and in sunflower plant grown in Cd-amended soil. Siderophores significantly reduced the Cd uptake by the bacterium, while supplying it with iron. Bacterial culture filtrates containing three hydroxamate siderophores secreted by S. tendae F4 significantly promoted plant growth and enhanced uptake of Cd and Fe by the plant, relative to the control. Furthermore, application of siderophores caused slightly more Cd, but similar Fe uptake, compared with EDTA. Bioinoculation with Streptomyces caused a dramatic increase in plant Fe content, but resulted only in slight increase in plant Cd content.

CONCLUSION

It is concluded that siderophores can help reduce toxic metal uptake in bacteria, while simultaneously facilitating the uptake of such metals by plants. Also, EDTA is not superior to hydroxamate siderophores in terms of metal solubilization for plant uptake.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study showed that microbial processes could indirectly influence the availability and amount of toxic metals taken up from the rhizosphere of plants. Furthermore, although EDTA is used for chelator-enhanced phytoremediation, microbial siderophores would be ideal for this purpose.

New insights into the metal specificity of the Pseudomonas aeruginosa pyoverdine-iron uptake pathway

Pyoverdine (PvdI) is the major siderophore secreted by Pseudomonas aeruginosa PAOI in order to get access to iron. After being loaded with iron in the extracellular medium, PvdI is transported across the bacterial outer membrane by the transporter, FpvAI. We used the spectral properties of PvdI to show that in addition to Fe(3+), this siderophore also chelates, but with lower efficiencies, all the 16 metals used in our screening. Afterwards, FpvAI at the cell surface binds Ag(+), Al(3+), Cd(2+), Co(2+), Cu(2+), Fe(3+), Ga(3+), Hg(2+), Mn(2+), Ni(2+) or Zn(2+) in complex with PvdI. We used Inductively Coupled Plasma-Atomic Emission Spectrometry to monitor metal uptake in P. aeruginosa: TonB-dependent uptake, in the presence of PvdI, was only efficient for Fe(3+). Cu(2+), Ga(3+), Mn(2+) and Ni(2+) were also transported into the cell but with lower uptake rates. The presence of Al(3+), Cu(2+), Ga(3+), Mn(2+), Ni(2+) and Zn(2+) in the extracellular medium induced PvdI production in P. aeruginosa. All these data allow a better understanding of the behaviour of the PvdI uptake pathway in the presence of metals other than iron: FpvAI at the cell surface has broad metal specificity at the binding stage and it is highly selective for Fe(3+) only during the uptake process.

Involvement of siderophores in the reduction of metal-induced inhibition of auxin synthesis in Streptomyces spp

Unlike synthetic metal chelators, microbe-assisted phytoremediation provides plants with natural metal-solubilizing chelators which do not constitute a potential source of environmental pollution. Concurrently with microbial chelators, plant growth promotion can be enhanced through bacterially-produced phytohormones. In this work, the simultaneous production of siderophores and auxins by Streptomyces was studied to gain insight for future application in plant growth and phytoremediation in a metal-contaminated soil. Standard auxin and siderophore detection assays indicated that all of the investigated Streptomyces strains can produce these metabolites simultaneously. However, Al(3+), Cd(2+), Cu(2+), Fe(3+) and Ni(2+), or a combination of Fe(3+) and Cd(2+), and Fe(3+) and Ni(2+) affected auxin production negatively, as revealed by spectrophotometry and gas chromatography-mass spectrometry. This effect was more dramatic in a siderophore-deficient mutant. In contrast, except for Fe, all the metals stimulated siderophore production. Mass spectrometry showed that siderophore and auxin-containing supernatants from a representative Streptomyces species contain three different hydroxamate siderophores, revealing the individual binding responses of these siderophores to Cd(2+) and Ni(2+), and thus, showing their auxin-stimulating effects. We conclude that siderophores promote auxin synthesis in the presence of Al(3+), Cd(2+), Cu(2+) and Ni(2+) by chelating these metals. Chelation makes the metals less able to inhibit the synthesis of auxins, and potentially increases the plant growth-promoting effects of auxins, which in turn enhances the phytoremediation potential of plants.

Effects of inoculation of plant-growth promoting bacteria on Ni uptake by Indian mustard

In this study, among a collection of Ni resistant bacterial strains isolated from serpentine soil, two plant growth promoting bacteria (PGPB), Ps29C and Bm4C were selected based on their ability to utilize ACC as the sole N source and promote seedling growth in roll towel assay. The Ni resistant PGPB, Ps29C and Bm4C were characterized as Pseudomonas sp. and Bacillus megaterium, respectively, on the basis of their 16s rDNA sequences. Assessment of the parameters of plant growth promotion revealed the intrinsic ability of the strains for the production of IAA, siderophore and solubilization of insoluble phosphate. Further, the plant growth promoting activity of Ps29C and Bm4C on the Indian mustard (Brassica juncea) were assessed with different concentrations of Ni in soil. Inoculation of Ps29C or Bm4C promoted plant growth and protected the plant from Ni toxicity. However, the maximum growth was observed in the plants inoculated with strain Bm4C. Inoculation with Ps29C or Bm4C had little influence on the accumulation of Ni in root and shoot system, but produced a much larger aboveground biomass. The present observations showed that the strains Ps29C and Bm4C protect the plants against the inhibitory effects of nickel, probably due to the production of IAA, siderophore and solubilization of phosphate. The above results provided a new insight into the phytoremediation of Ni contaminated soil.

Hydroxamate siderophores produced by Streptomyces acidiscabies E13 bind nickel and promote growth in cowpea (Vigna unguiculata L.) under nickel stress

The siderophore-producing ability of nickel-resistant Streptomyces acidiscabies E13 and the role of the elicited siderophores in promoting plant growth under iron and nickel stress are described. Siderophore assays indicated that S. acidiscabies E13 can produce siderophores. Electrospray ionization mass spectrometry (ESI-MS) revealed that the bacterium simultaneously produces 3 different hydroxamate siderophores. ESI-MS showed that in addition to iron, all 3 siderophores can bind nickel. In vitro plant growth tests were conducted with cowpea (Vigna unguiculata) in the presence and absence of the elicited siderophores. Culture filtrates containing hydroxamate siderophores significantly increased cowpea height and biomass, irrespective of the iron status of the plants, under nickel stress. The presence of reduced iron was found to be high in siderophore-containing treatments in the presence of nickel. Measurements of iron and nickel contents of cowpea roots and shoots indicated that the siderophore-mediated plant growth promotion reported here involves the simultaneous inhibition of nickel uptake and solubilization and supply of iron to plants. We conclude that hydroxamate siderophores contained in culture filtrates of S. acidiscabies E13 promoted cowpea growth under nickel contamination by binding iron and nickel, thus playing a dual role of sourcing iron for plant use and protecting against nickel toxicity.

Pyridine-2,6-bis(thiocarboxylic acid) Produced by Pseudomonas stutzeri KC Reduces Chromium(VI) and Precipitates Mercury, Cadmium, Lead and Arsenic

Interactions of the Pseudomonas stutzeri KC siderophore pyridine-2,6-bis(thiocarboxylic acid) (pdtc) with chromium(VI), mercury(II), cadmium(II), lead(II), and arsenic(III) are described. Pdtc was found to reduce Cr(VI) to Cr(III) in both bacterial cultures and in abiotic reactions with chemically synthesized pdtc. Cr(III) subsequently formed complexes with pdtc and pdtc hydrolysis products, and their presence was confirmed using electrospray ionization-mass spectrometry (ESI-MS). Cr(III):pdtc complexes were found to slowly release Cr(III) as chromium sulfide and possibly Cr(III) oxides. Pdtc also formed poorly soluble complexes with Hg, Cd, Pb, and As(III). Hydrolysis of those complexes led to the formation of their respective metal sulfides as confirmed by energy dispersive X-ray spectroscopy (EDS) elemental analysis. The pdtc-producing strain P. stutzeri KC showed higher tolerance to most of these metals as compared to a pdtc-negative mutant. A novel role of pdtc is postulated as its involvement in providing an extracellular pool of thiols that are used for redox processes in detoxification of the bacterial extracellular environment. These redox processes can be mediated by transition metal:pdtc complexes.

Interactions between iron availability, aluminium toxicity and fungal siderophores

The influence of iron, aluminium and of the combined application of both metals on microbial biomass and production of siderophores by three fungi (Aspergillus nidulans, Neurospora crassa and Hymenoscyphus ericae) were investigated. All three species showed a strong iron regulation and Al-sensitivity of siderophore biosynthesis although several differences remained species dependent. Inhibitory effects of Fe and Al on siderophore-production were additive and the higher binding capacity of siderophores towards iron could be compensated by a higher Al-availability. Although pH itself is also important for regulation of siderophore biosynthesis, an indirect effect of Al on siderophore production via an Al-induced pH decrease could be outlined. The toxic effects of Al resulting in a reduced biomass production were compensated by high Fe-availability, whereas the addition of DFAM, a bacterial siderophore, enhanced Al-toxicity.

Pyridine-2,6-bis(thiocarboxylic acid) produced by Pseudomonas stutzeri KC reduces and precipitates selenium and tellurium oxyanions

The siderophore of Pseudomonas stutzeri KC, pyridine-2,6-bis(thiocarboxylic acid) (pdtc), is shown to detoxify selenium and tellurium oxyanions in bacterial cultures. A mechanism for pdtc's detoxification of tellurite and selenite is proposed. The mechanism is based upon determination using mass spectrometry and energy-dispersive X-ray spectrometry of the chemical structures of compounds formed during initial reactions of tellurite and selenite with pdtc. Selenite and tellurite are reduced by pdtc or its hydrolysis product H(2)S, forming zero-valent pdtc selenides and pdtc tellurides that precipitate from solution. These insoluble compounds then hydrolyze, releasing nanometer-sized particles of elemental selenium or tellurium. Electron microscopy studies showed both extracellular precipitation and internal deposition of these metalloids by bacterial cells. The precipitates formed with synthetic pdtc were similar to those formed in pdtc-producing cultures of P. stutzeri KC. Culture filtrates of P. stutzeri KC containing pdtc were also active in removing selenite and precipitating elemental selenium and tellurium. The pdtc-producing wild-type strain KC conferred higher tolerance against selenite and tellurite toxicity than a pdtc-negative mutant strain, CTN1. These observations support the hypothesis that pdtc not only functions as a siderophore but also is involved in an initial line of defense against toxicity from various metals and metalloids.

A role for cyclic hydroxamates in aluminium resistance in maize?

Hydroxamate siderophores have been found to alleviate Al toxicity in bacteria. In Poaceae plants cyclic hydroxamates, like DIMBOA (2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one) and its derivatives have mostly been studied in relation to either defence against insects or allelopathy. In this study the influence of Al on concentrations of these benzoxazinoids (Bx) in root tips, whole roots and root xylem exudates of Zea mays L. varieties differing in Al resistance was analyzed by HPLC-MS. Aluminium resistant maize variety Sikuani maintained considerably higher Bx levels in root tips than the Al sensitive variety Bakero. In vitro binding of Al to DIMBOA was shown by fluorescence quenching. Addition of DIMBOA to Al-containing nutrient solution protected the sensitive maize against Al toxicity as shown by bioassays using callose and haematoxylin staining of root tips as stress indicators. This is the first study showing that Bx can detoxify Al in solution. Tissue analysis data provide first, circumstantial, support for a role of Bx in defence against Al toxicity also in planta.

Isolation and Functional Characterization of Siderophore-Producing Lead- and Cadmium-Resistant Pseudomonas putida KNP9

Heavy metals, being phytotoxic, cause growth inhibition and even plant death. Siderophore-producing bacterial strain KNP9 is growth promoting and has been isolated from Panki Power Plant, Kanpur, India. It simulated significant (p > 5%) root and shoot growth of mung bean to the extent of 16.48% and 28.80%, respectively in the presence of CdCl(2) (110 microM: ). However, the increase in root and shoot growth was 20% and 19.5%, respectively, in the presence of (CH(3)COO)(2)Pb (660 microM: ). Moreover, concentration of accumulated lead and cadmium in root and shoot was also reduced in the presence of this isolate ranging from 37.5 to 93.19%. A moderate reduction in chlorophyll content (39.14%) in the presence of 110 microM: CdCl(2) was rescued by bioinoculant KNP9. However, the 19.58% decrease in chlorophyll content in the case of lead acetate remained unchanged even in the presence of KNP9. Nevertheless, 16S ribosomal DNA (rDNA) sequencing identified KNP9 as a strain of Pseudomonas putida.

Analysis of rhizobacterial communities in perennial Graminaceae from polluted water meadow soil, and screening of metal-resistant, potentially plant growth-promoting bacteria

This study investigates the impact of long-term heavy metal contamination on the culturable, heterotrophic, functional and genetic diversity of rhizobacterial communities of perennial grasses in water meadow soil. The culturable heterotrophic diversity was investigated by colony appearance on solid LB medium. Genetic diversity was measured as bands in denaturing gradient gel electrophoresis (DGGE) obtained directly from rhizosphere soil and rhizoplane DNA extracts, and from the corresponding culturable communities. In the two rhizospheric fractions the DGGE profiles of the direct DNA extracts were similar and stable among replicates, whereas in the enriched cultures the profiles of the fractions differed, but among the replicates they were similar. One hundred isolates were collected into 33 different operational taxonomic units by use of amplified internal transcribed spacers and into 19 heavy metal-resistant phenotypes. The phylogenetic position of strains belonging to 18 operational taxonomic units, representing more than 80% of the isolates, was determined by 16S rRNA gene sequencing. Several heavy metal-resistant strains were isolated from rhizoplane. Finally, metal-resistant rhizobacteria were tested for plant growth-promoting characteristics; some were found to contain 1-aminocyclopropane-1-carboxylic acid deaminase and/or to produce indole acetic acid and siderophores. Two strains resistant to cadmium and zinc, Pseudomonas tolaasii RP23 and Pseudomonas fluorescens RS9, had all three plant growth-promoting characteristics. Our findings suggest that bacteria can respond to soil metal contamination, and the described methodological approach appears promising for targeting potential plant growth-promoting rhizobacteria.