New roles for bacterial siderophores in metal transport and tolerance

In vitro exploration of Acinetobacter strain (SG-5) for antioxidative potential and phytohormone biosynthesis in maize (Zea mays L.) cultivars differing in cadmium tolerance

Cadmium (Cd) poses serious threats to plant growth and development, whereas the use of plant growth-promoting rhizobacteria (PGPR) has emerged a promising approach to diminish Cd retention in crops. A pot experiment was conducted to evaluate the effect of Cd tolerant strain Acinetobacter sp. SG-5 on growth, phytohormonal response, and Cd uptake of two maize cultivars (3062 and 31P41) under various Cd stress levels (0, 5, 12, 18, 26, and 30 μM CdCl2). The results revealed that CdCl2 treatment significantly suppressed the seed germination and growth together with higher Cd retention in maize cultivars in a dose-dependent and cultivar-specific manner with pronounced negative effect in 31P41. However, SG-5 strain exerted positive impact by up-regulating seed germination traits, plant biomass, photosynthetic pigments, enzymatic and non-enzymatic antioxidants, endogenous hormone level indole-3-acetic acid (IAA), abscisic acid (ABA), and sustained optimal nutrient's levels in both cultivars but predominantly in Cd-sensitive one (31P41). Further, Cd-resistant PGPR decreased the formation of reactive oxygen species in terms of malondialdehyde (MDA) and hydrogen peroxide (H2O2) verified through 3, 3'-diaminobenzidine (DAB) and nitroblue tetrazolium (NBT) analysis in conjunction with reduced Cd uptake and translocation in maize root and shoots in comparison to controls, advocating its sufficiency for bacterial-assisted Cd bioremediation. In conclusion, both SG-5 inoculated cultivars exhibited maximum Cd tolerance but substantial Cd tolerance was acquired by Cd susceptible cultivar-31P41 than Cd-tolerant one (3062). Current work recommended SG-5 strain as a promising candidate for plant growth promotion and bacterial-assisted phytomanagement of metal-polluted agricultural soils.

Seasonal variation in metabolic profiles and microbial communities in a subarctic ore processing plant

The mining industry strives to reduce its water footprint by recycling water in ore processing. This leads to build-up of ions, flotation chemicals and microbial biomass, which may affect the process. The Boliden Kevitsa mine in Northern Finland is exposed to seasonal change and recycles up to 90% of the process water. We studied the variation in size, composition and putative functions of microbial communities in summer and winter in the ore processing plant. The raw water, Cu and Ni thickener overflow waters had statistically significantly higher bacterial numbers in winter compared to summer, and specific summer and winter communities were identified. Metagenomic analysis indicated that Cu and Hg resistance genes, sulphate/thiosulphate, molybdate, iron(III) and zinc ABC transporters, nitrate reduction, denitrification, thiosulphate oxidation and methylotrophy were more common in winter than in summer. Raw water drawn from the nearby river did not affect the microbial communities in the process samples, indicating that the microbial communities and metabolic capacities develop within the process over time in response to the conditions in the processing plant, water chemistry, used chemicals, ore properties and seasonal variation. We propose that the microbial community structures are unique to the Boliden Kevitsa mine and processing plant.

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.

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.

The highly effective cadmium-resistant mechanism of Pseudomonas aeruginosa and the function of pyoverdine induced by cadmium

Pyoverdine (PVD) plays an important role in reducing cadmium (Cd) accumulation in plants. Some Pseudomonas aeruginosa (P. aeruginosa) species can produce PVD under Cd(Π) stress. However, the function of Cd(Π)-induced PVD remains unclear. In this study, we isolated a highly effective Cd(Π)-resistant P. aeruginosa which can secrete PVD under Cd(Π) stress and found that PVD secretion has a dose-dependent relationship with Cd(Π) concentration. PVD can form a PVD-Cd complex with Cd(Π), though the PVD-Cd complex is unable to be adsorbed by the cell or enter the cell, so the complexation of PVD and Cd(Π) impedes Cd(Π) adsorption on the cell surface and alleviates the oxidative stress, lipid peroxidation, and morphological destruction of the cell caused by Cd(Π) and effectively improves the resistance of P. aeruginosa to Cd(Π). In summary, our research results indicate that the Cd(Π) resistance mechanism of P. aeruginosa screened is the complexation of PVD for Cd(Π) and the adsorption of bacteria for Cd(Π); furthermore, PVD plays an important role in improving the Cd(Π)-resistant ability of bacteria. This study provides a deeper understanding of the highly effective Cd(Π) resistance mechanism of P. aeruginosa and the function of Cd(Π)-induced PVD in bacteria.

Plant Growth-Promoting Rhizobacteria (PGPR) Assisted Bioremediation of Heavy Metal Toxicity

Due to a variety of natural and anthropogenic processes, heavy metal toxicity of soil constitutes a substantial hazard to all living beings in the environment. The heavy metals alter the soil properties, which directly or indirectly influence the agriculture systems. Thus, plant growth-promoting rhizobacteria (PGPR)-assisted bioremediation is a promising, eco-friendly, and sustainable method for eradicating heavy metals. PGPR cleans up the heavy metal-contaminated environment using various approaches including efflux systems, siderophores and chelation, biotransformation, biosorption, bioaccumulation, precipitation, ACC deaminase activity, biodegradation, and biomineralization methods. These PGPRs have been found effective to bioremediate the heavy metal-contaminated soil through increased plant tolerance to metal stress, improved nutrient availability in soil, alteration of heavy metal pathways, and by producing some chemical compounds like siderophores and chelating ions. Many heavy metals are non-degradable; hence, another remediation approach with a broader scope of contamination removal is needed. This article also briefly emphasized the role of genetically modified PGPR strains which improve the soil's degradation rate of heavy metals. In this regard, genetic engineering, a molecular approach, could improve bioremediation efficiency and be helpful. Thus, the ability of PGPRs can aid in heavy metal bioremediation and promote a sustainable agricultural soil system.

Siderophore-producing bacteria from Spitsbergen soils-novel agents assisted in bioremediation of the metal-polluted soils

Siderophores are molecules that exhibit a high specificity for iron (Fe), and their synthesis is induced by a deficiency of bioavailable Fe. Complexes of Fe-siderophore are formed extracellularly and diffuse through porins across membranes into bacterial cells. Siderophores can bind heavy metals facilitating their influx into cells via the same mechanism. The aim of the studies was to determine the ability of siderophore-producing bacteria isolated from soils in the north-west part of Wedel Jarlsberg Land (Spitsbergen) to chelate non-Fe metals (Al, Cd, Co, Cu, Hg, Mn, Sn, and Zn). Specially modified blue agar plates were used, where Fe was substituted by Al, Cd, Co, Cu, Hg, Mn, Sn, or Zn in metal-chrome azurol S (CAS) complex, which retained the blue color. It has been proven that 31 out of 33 strains were capable of producing siderophores that bind to Fe, as well as other metals. Siderophores from Pantoea sp. 24 bound only Fe and Zn, and O. anthropi 55 did not produce any siderophores in pure culture. The average efficiency of Cd, Co, Cu, Mn, Sn, and Zn chelation was either comparable or higher than that of Fe, while Al and Hg showed significantly lower efficiency. Siderophores produced by S. maltophilia 54, P. luteola 27, P. luteola 46, and P. putida 49 exhibited the highest non-Fe metal chelation activity. It can be concluded that the siderophores of these bacteria may constitute an integral part of the metal bioleaching preparation, and this fact will be the subject of further research.

Discovery of YFJ-36: Design, Synthesis, and Antibacterial Activities of Catechol-Conjugated β-Lactams against Gram-Negative Bacteria

Cefiderocol is the first approved catechol-conjugated cephalosporin against multidrug-resistant Gram-negative bacteria, while its application was limited by poor chemical stability associated with the pyrrolidinium linker, moderate potency against Klebsiella pneumoniae and Acinetobacter baumannii, intricate procedures for salt preparation, and potential hypersensitivity. To address these issues, a series of novel catechol-conjugated derivatives were designed, synthesized, and evaluated. Extensive structure-activity relationships and structure-metabolism relationships (SMR) were conducted, leading to the discovery of a promising compound 86b (Code no. YFJ-36) with a new thioether linker. 86b exhibited superior and broad-spectrum in vitro antibacterial activity, especially against A. baumannii and K. pneumoniae, compared with cefiderocol. Potent in vivo efficacy was observed in a murine systemic infection model. Furthermore, the physicochemical stability of 86b in fluid medium at pH 6-8 was enhanced. 86b also reduced potential the risk of allergy owing to the quaternary ammonium linker. The improved properties of 86b supported its further research and development.

The interplay between microbial communities and soil properties

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism-soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.

Global stress response in Pseudomonas aeruginosa upon malonate utilization

Versatility in carbon source utilization assists Pseudomonas aeruginosa in its adaptation to various niches. Recently, we characterized the role of malonate, an understudied carbon source, in quorum sensing regulation, antibiotic resistance, and virulence factor production in P. aeruginosa . These results indicate that global responses to malonate metabolism remain to be uncovered. We leveraged a publicly available metabolomic dataset on human airway and found malonate to be as abundant as glycerol, a common airway metabolite and carbon source for P. aeruginosa . Here, we explored and compared adaptations of P. aeruginosa UCBPP-PA14 (PA14) in response to malonate or glycerol as a sole carbon source using transcriptomics and phenotypic assays. Malonate utilization activated glyoxylate and methylcitrate cycles and induced several stress responses, including oxidative, anaerobic, and metal stress responses associated with increases in intracellular aluminum and strontium. Some induced genes were required for optimal growth of P. aeruginosa in malonate. To assess the conservation of malonate-associated responses among P. aeruginosa strains, we compared our findings in strain PA14 with other lab strains and cystic fibrosis isolates of P. aeruginosa . Most strains grew on malonate as a sole carbon source as efficiently as or better than glycerol. While not all responses to malonate were conserved among strains, formation of biomineralized biofilm-like aggregates, increased tolerance to kanamycin, and increased susceptibility to norfloxacin were the most frequently observed phenotypes. Our findings reveal global remodeling of P. aeruginosa gene expression during its growth on malonate as a sole carbon source that is accompanied by several important phenotypic changes. These findings add to accumulating literature highlighting the role of different carbon sources in the physiology of P. aeruginosa and its niche adaptation.

Importance

Pseudomonas aeruginosa is a notorious pathogen that causes local and systemic infections in immunocompromised individuals. Different carbon sources can uniquely modulate metabolic and virulence pathways in P. aeruginosa , highlighting the importance of the environment that the pathogen occupies. In this work, we used a combination of transcriptomic analysis and phenotypic assays to determine how malonate utilization impacts P. aeruginosa, as recent evidence indicates this carbon source may be relevant to certain niches associated within the human host. We found that malonate utilization can induce global stress responses, alter metabolic circuits, and influence various phenotypes of P. aeruginosa that could influence host colonization. Investigating the metabolism of malonate provides insight into P. aeruginosa adaptations to specific niches where this substrate is abundant, and how it can be leveraged in the development of much-needed antimicrobial agents or identification of new therapeutic targets of this difficult-to-eradicate pathogen.

A novel plant growth-promoting rhizobacterium, Rhizosphaericola mali gen. nov., sp. nov., isolated from healthy apple tree soil

The rhizosphere microbial community is closely associated with plant disease by regulating plant growth, agricultural production, nutrient availability, plant hormone and adaptation to environmental changes. Therefore, it is very important to identify the rhizosphere microbes around plant roots and understand their functions. While studying the differences between the rhizosphere microbiota of healthy and diseased apple trees to find the cause of apple tree disease, we isolated a novel strain, designated as B3-10T, from the rhizosphere soil of a healthy apple tree. The genome relatedness indices between strain B3-10T and other type species of family Chitinophagaceae were in the ranges of 62.4-67.0% for ANI, 18.6-32.1% for dDDH, and 39.0-56.6% for AAI, which were significantly below the cut‑off values for the species delineation, indicating that strain B3-10T could be considered to represent a novel genus in family Chitinophagaceae. Interestingly, the complete genome of strain B3-10T contained a number of genes encoding ACC-deaminase, siderophore production, and acetoin production contributing to plant-beneficial functions. Furthermore, strain B3-10T was found to significantly promote the growth of shoots and roots of the Nicotiana benthamiana, which is widely used as a good model for plant biology, demonstrating that strain B3-10T, a rhizosphere microbe of healthy apple trees, has the potential to promote growth and reduce disease. The phenotypic, chemotaxonomic, phylogenetic, genomic, and physiological properties of this plant growth-promoting (rhizo)bacterium, strain B3-10T supported the proposal of a novel genus in the family Chitinophagaceae, for which the name Rhizosphaericola mali gen. nov., sp. nov. (= KCTC 72123T = NBRC 114178T).

The Mechanisms of Molybdate Distribution and Homeostasis with Special Focus on the Model Plant Arabidopsis thaliana

This review article deals with the pathways of cellular and global molybdate distribution in plants, especially with a full overview for the model plant Arabidopsis thaliana. In its oxidized state as bioavailable molybdate, molybdenum can be absorbed from the environment. Especially in higher plants, molybdenum is indispensable as part of the molybdenum cofactor (Moco), which is responsible for functionality as a prosthetic group in a variety of essential enzymes like nitrate reductase and sulfite oxidase. Therefore, plants need mechanisms for molybdate import and transport within the organism, which are accomplished via high-affinity molybdate transporter (MOT) localized in different cells and membranes. Two different MOT families were identified. Legumes like Glycine max or Medicago truncatula have an especially increased number of MOT1 family members for supplying their symbionts with molybdate for nitrogenase activity. In Arabidopsis thaliana especially, the complete pathway followed by molybdate through the plant is traceable. Not only the uptake from soil by MOT1.1 and its distribution to leaves, flowers, and seeds by MOT2-family members was identified, but also that inside the cell. the transport trough the cytoplasm and the vacuolar storage mechanisms depending on glutathione were described. Finally, supplying the Moco biosynthesis complex by MOT1.2 and MOT2.1 was demonstrated.

Influence of heavy metal exposure on gut microbiota: Recent advances

Gut microbiota plays a functionally important part in retaining the homeostasis of host physiology, however, under exposure of various heavy metals, the composition of gut biota is disturbed in relation to species diversity and richness. Ever since the increase of microbiome-related studies during the last decade, many research studies have delivered an understanding of the reasons and concerns of gut microbiota-related modifications. During the past decade, it's been confirmed from various studies that heavy metals poisoning alters the microbial composition, which results in changes in gene expression, alteration in metabolism, immunity, neurological dysfunction, and causes various other disorders. The present comprehensive review is summarizing an attempt to enumerate the key findings from recent clinical or preclinical studies related to the influence of heavy metals on gut microbiota published recently. Google, PubMed, Science Direct, Scopus, and Google Scholar were employed as primary search engines using the keywords such as "heavy metals, gut microbiota, dysbiosis, and intestinal microbiota" for finding relevant research articles from the past 10 years and some old important articles. Here, we tried to provide insight into some of the key timelines and scientific findings from reported literature, like the effects of heavy metals such as arsenic, cadmium, lead, and mercury on the general body and specifically on the gut microbiota of different model organisms. So, it is important to increase awareness against heavy metal-induced toxicity and formulate guidelines for the benefit of the environment.

Cadmium-chelating ability of the siderophore DHBS secreted by Leclercia adecarboxylata FCH-CR2 and its action mechanism

As one of the most accumulative toxic heavy metals, cadmium (Cd) poses a major threat to human health. Bacterial siderophores, as small molecules with metal-absorbing ability, have great potential activity for Cd-reduction. In this study, the siderophore-producing bacterialstrain FCH-CR2 was isolated from a high-Cd contaminated soil using the CAS method. Leclercia adecarboxylata was identified through 16S rRNA sequence, homology analysis, colony morphology, physiological and biochemical tests. A siderophore, catechol type 2,3-dihydroxy-N-benzoyl-l-serine (DHBS) secreted by FCH-CR2, was purified using RP-HPLC and identified by LC-MS/MS. Intraperitoneal injection of DHBS significantly increased fecal Cd levels, and reduced Cd accumulation in organs. In density flooding theory (DFT) analysis, DHBS may bind to Cd via the hydroxyl site on the benzene ring. Besides, the isothermal titration calorimetry (ITC) assay revealed that the formation of Cd-DHBS is a spontaneous and endothermic reaction with ΔG = -21.4 kJ/mol and ΔH = 1.51 ± 0.142 kJ/mol.

Metabolic Profiling of Endophytic Bacteria in Relation to Their Potential Application as Components of Multi-Task Biopreparations

Agricultural crops are exposed to various abiotic and biotic stresses that can constrain crop productivity. Focusing on a limited subset of key groups of organisms has the potential to facilitate the monitoring of the functions of human-managed ecosystems. Endophytic bacteria can enhance plant stress resistance and can help plants to cope with the negative impacts of stress factors through the induction of different mechanisms, influencing plant biochemistry and physiology. In this study, we characterise endophytic bacteria isolated from different plants based on their metabolic activity and ability to synthesise 1-aminocyclopropane-1-carboxylic acid deaminase (ACCD), the activity of hydrolytic exoenzymes, the total phenolic compounds (TPC) and iron-complexing compounds (ICC). Test GEN III MicroPlate indicated that the evaluated endophytes are highly metabolically active, and the best used substrates were amino acids, which may be important in selecting potential carrier components for bacteria in biopreparations. The ACCD activity of strain ES2 (Stenotrophomonas maltophilia) was the highest, whereas that of strain ZR5 (Delftia acidovorans) was the lowest. Overall, the obtained results indicated that ∼91.3% of the isolates were capable of producing at least one of the four hydrolytic enzymes. In addition, most of the tested strains produced ICC and TPC, which play a significant role in reducing stress in plants. The results of this study suggest that the tested endophytic bacterial strains can potentially be used to mitigate climate change-associated stresses in plants and to inhibit plant pathogens.

Quantitative proteomic analysis of the mechanism of Cd toxicity in Enterobacter sp. FM-1: Comparison of different growth stages

Enterobacter sp. are widely used in bioremediation, but the mechanism of Cadmium (Cd) toxicity in Enterobacter sp. has been poorly studied. In the present study, we determined the tolerance of Enterobacter sp. FM-1 to Cd by analyzing the physiological and biochemical responses of FM-1 induced under Cd stress. Differentially expressed proteins (DEPs) under exposure to different Cd environments were analyzed by 4D-label-free proteomics to provide a comprehensive understanding of Cd toxicity in FM-1. The greatest total number of DEPs, 1148, was found in the High concentration vs. Control comparison group at 10 h. When protein expression was compared after different incubation times, FM-1 showed the highest Cd tolerance at 48 h. Additionally, with an increasing incubation time, different comparison groups gradually began to show similar growth patterns, which was reflected in the GO enrichment analysis. Notably, only 815 proteins were identified in the High concentration vs. Control group, and KEGG enrichment analysis revealed that these proteins were significantly enriched in the pyruvate metabolism, oxidative phosphorylation, peroxisome, glyoxylate and dicarboxylate metabolism, and citrate cycle pathways. These results suggested that an increased incubation time allows FM-1 adapt and survive in an environment with Cd toxicity, and protein expression significantly increased in response to oxidative stress in a Cd-contaminated environment during the pre-growth period. This study provides new perspectives on bacterial participation in bioremediation and expands our understanding of the mechanism of bacterial resistance under Cd exposure.

Host subversion of bacterial metallophore usage drives copper intoxication

IMPORTANCE

During infection, bacteria must overcome the dual threats of metal starvation and intoxication. This work reveals that the zinc-withholding response of the host sensitizes S. aureus to copper intoxication. In response to zinc starvation, S. aureus utilizes the metallophore staphylopine. The current work revealed that the host can leverage the promiscuity of staphylopine to intoxicate S. aureus during infection. Significantly, staphylopine-like metallophores are produced by a wide range of pathogens, suggesting that this is a conserved weakness that the host can leverage to toxify invaders with copper. Moreover, it challenges the assumption that the broad-spectrum metal binding of metallophores is inherently beneficial to bacteria.

Bioremediation of industrial wastewater heavy metals using solo and consortium Enterobacter spp

Heavy metals are considered the most common pollutants in industrial wastewater areas. Out of thirty bacterial isolates, only 3 isolates sighted the highest metal resistance activity for Zn+2, Fe+2, Pb+2, Co+2, Mn+2, Ni+2, and Cd+2. The biochemical and DNA homology identification with similarities 99.58%, 99.79%, and 99.86% of those isolates was identified and deposited in WDCM, respectively, as Enterobacter kobei OM144907 SCUF0000311, Enterobacter cloacae OM180597 SCUF0000312, and Enterobacter hormaechei OM181067 SCUF0000313. The minimum tolerance activity (MIC) of heavy metal concentrations against E. kobei and E. cloacae was 25, 15, and 15 mmol/l for Ni+2, Fe+2, and Mn+2, respectively, and 10 mmol/l for Zn+2, Pb+2, Co+2, and Cd+2, while against E. hormaechei, it is 15 mmol/l for Ni+2, Fe+2, and Mn+2 and 10 mmol/l for Zn+2, Pb+2, Co+2, and Cd+2. The consortium and solitary application of bacterial isolates towards heavy metal removal at 100%, 200%, and 300% industrial wastewater concentrations were conducted and showed that more than 90% removal of Zn+2, Fe+2, Pb+2, Mn+2, Ni+2, and Cd+2 from a non-concentrated polluted sample (100%) was reported by the three strains. With doubling the polluted sample concentration (200%), the highest removal efficiency for Zn+2, Pb+2, Mn+2, Ni+2, and Cd+2 was reported by E. cloacae as 70. 75, 66, 65, and 57%, respectively. Removal efficiency after increasing the polluted sample concentration to 300% showed that E. cloacae removed above 45% of all tested heavy metals except Pb+2. Ultimately, E. cloacae exposed the highest efficiency with recommendations for heavy metals removal under higher concentrations.

Microbial Exudates as Biostimulants: Role in Plant Growth Promotion and Stress Mitigation

Microbes hold immense potential, based on the fact that they are widely acknowledged for their role in mitigating the detrimental impacts of chemical fertilizers and pesticides, which were extensively employed during the Green Revolution era. The consequence of this extensive use has been the degradation of agricultural land, soil health and fertility deterioration, and a decline in crop quality. Despite the existence of environmentally friendly and sustainable alternatives, microbial bioinoculants encounter numerous challenges in real-world agricultural settings. These challenges include harsh environmental conditions like unfavorable soil pH, temperature extremes, and nutrient imbalances, as well as stiff competition with native microbial species and host plant specificity. Moreover, obstacles spanning from large-scale production to commercialization persist. Therefore, substantial efforts are underway to identify superior solutions that can foster a sustainable and eco-conscious agricultural system. In this context, attention has shifted towards the utilization of cell-free microbial exudates as opposed to traditional microbial inoculants. Microbial exudates refer to the diverse array of cellular metabolites secreted by microbial cells. These metabolites enclose a wide range of chemical compounds, including sugars, organic acids, amino acids, peptides, siderophores, volatiles, and more. The composition and function of these compounds in exudates can vary considerably, depending on the specific microbial strains and prevailing environmental conditions. Remarkably, they possess the capability to modulate and influence various plant physiological processes, thereby inducing tolerance to both biotic and abiotic stresses. Furthermore, these exudates facilitate plant growth and aid in the remediation of environmental pollutants such as chemicals and heavy metals in agroecosystems. Much like live microbes, when applied, these exudates actively participate in the phyllosphere and rhizosphere, engaging in continuous interactions with plants and plant-associated microbes. Consequently, they play a pivotal role in reshaping the microbiome. The biostimulant properties exhibited by these exudates position them as promising biological components for fostering cleaner and more sustainable agricultural systems.

Mining-related multi-resistance genes in sulfate-reducing bacteria treatment of typical karst nonferrous metal(loid) mine tailings in China

Management of tailings at metal mine smelter sites can reduce the potential hazards associated with exposure to toxic metal(loid)s and residual organic flotation reagents. In addition, microbes in the tailings harboring multi-resistance genes (e.g., tolerance to multiple antimicrobial agents) can cause high rates of morbidity and global economic problems. The potential co-selection mechanisms of antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) during tailings sulfate-reducing bacteria (SRB) treatment have been poorly investigated. Samples were collected from a nonferrous metal mine tailing site treated with an established SRB protocol and were analyzed for selected geochemical properties and high throughput sequencing of 16S rRNA gene barcoding. Based on the shotgun metagenomic analysis, the bacterial domain was dominant in nonferrous metal(loid)-rich tailings treated with SRB for 12 months. KEGGs related to ARGs and MRGs were detected. Thiobacillus and Sphingomonas were the main genera carrying the bacA and mexEF resistance operons, along with Sulfuricella which were also found as the main genera carrying MRGs. The SRB treatment may mediate the distribution of numerous resistance genes. KOs based on the metagenomic database indicated that ARGs (mexNW, merD, sul, and bla) and MRGs (czcABCR and copRS genes) were found on the same contig. The SRB strains (Desulfosporosinus and Desulfotomaculum), and the acidophilic strain Acidiphilium significantly contributed to the distribution of sul genes. The functional metabolic pathways related to siderophores metabolism were largely from anaerobic genera of Streptomyces and Microbacterium. The presence of arsenate reductase, metal efflux pump, and Fe transport genes indicated that SRB treatment plays a key role in the metal(loid)s transformation. Overall, our findings show that bio-treatment is an effective tool for managing ARGs/MRGs and metals in tailings that contain numerous metal(loid) contaminants.

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.

Dps Functions as a Key Player in Bacterial Iron Homeostasis

Iron plays a vital role in the maintenance of life, being central to various cellular processes, from respiration to gene regulation. It is essential for iron to be stored in a nontoxic and readily available form. DNA binding proteins under starvation (Dps) belong to the ferritin family of iron storage proteins and are adept at storing iron in their hollow protein shells. Existing solely in prokaryotes, these proteins have the additional functions of DNA binding and protection from oxidative stress. Iron storage proteins play a functional role in storage, release, and transfer of iron and therefore are central to the optimal functioning of iron homeostasis. Here we review the multifarious properties of Dps through relevant biochemical and structural studies with a focus on iron storage and ferroxidation. We also examine the role of Dps as a possible candidate as an iron donor to iron-sulfur (Fe-S) clusters, which are ubiquitous to many biological processes.

Synthetic Biology Toolkit for a New Species of Pseudomonas Promissory for Electricity Generation in Microbial Fuel Cells

Microbial fuel cells (MFCs) offer sustainable solutions for various biotechnological applications and are a crucial area of research in biotechnology. MFCs can effectively treat various refuse, such as wastewater and biodiesel waste by decomposing organic matter and generating electricity. Certain Pseudomonas species possess extracellular electron transfer (EET) pathways, enabling them to transfer electrons from organic compounds to the MFC's anode. Moreover, Pseudomonas species can grow under low-oxygen conditions, which is advantageous considering that the electron transfer process in an MFC typically leads to reduced oxygen levels at the anode. This study focuses on evaluating MFCs inoculated with a new Pseudomonas species grown with 1 g.L-1 glycerol, a common byproduct of biodiesel production. Pseudomonas sp. BJa5 exhibited a maximum power density of 39 mW.m-2. Also, the observed voltammograms and genome analysis indicate the potential production of novel redox mediators by BJa5. Additionally, we investigated the bacterium's potential as a synthetic biology non-model chassis. Through testing various genetic parts, including constitutive promoters, replication origins and cargos using pSEVA vectors as a scaffold, we assessed the bacterium's suitability. Overall, our findings offer valuable insights into utilizing Pseudomonas spp. BJa5 as a novel chassis for MFCs. Synthetic biology approaches can further enhance the performance of this bacterium in MFCs, providing avenues for improvement.

Cultivating antimicrobial resistance: how intensive agriculture ploughs the way for antibiotic resistance

Antimicrobial resistance (AMR) is a growing threat to public health, global food security and animal welfare. Despite efforts in antibiotic stewardship, AMR continues to rise worldwide. Anthropogenic activities, particularly intensive agriculture, play an integral role in the dissemination of AMR genes within natural microbial communities - which current antibiotic stewardship typically overlooks. In this review, we examine the impact of anthropogenically induced temperature fluctuations, increased soil salinity, soil fertility loss, and contaminants such as metals and pesticides on the de novo evolution and dissemination of AMR in the environment. These stressors can select for AMR - even in the absence of antibiotics - via mechanisms such as cross-resistance, co-resistance and co-regulation. Moreover, anthropogenic stressors can prime bacterial physiology against stress, potentially widening the window of opportunity for the de novo evolution of AMR. However, research to date is typically limited to the study of single isolated bacterial species - we lack data on how intensive agricultural practices drive AMR over evolutionary timescales in more complex microbial communities. Furthermore, a multidisciplinary approach to fighting AMR is urgently needed, as it is clear that the drivers of AMR extend far beyond the clinical environment.

Isolation of cadmium-resistance and siderophore-producing endophytic bacteria and their potential use for soil cadmium remediation

Endophyte-assisted phytoremediation is an emerging technique for soil heavy metals (HMs) remediation and has become a research focus in the world because of the benefits of endophytes on plant growth and uptake of HMs. In this study, multifunctional endophytic bacteria strains were isolated and screened, and the feasibility of these strains for soil cadmium (Cd) remediation was investigated by soil incubation experiments and pot experiments. All endophytic bacteria were isolated from the roots of woody plants grown on Cd-contaminated soil. Seven endophytic bacteria strains had capacities to tolerate Cd toxicity and produce siderophores, and sequence analysis of the 16S rRNA gene classified these strains as belonging to the genera Burkholderia, Pseudomonas, Pantoea, and Herbaspirillum. All strains were able to produce hydroxamate siderophores (32.40%-91.49%) and had three or more plant growth promoting properties such as phosphorus solubilization, nitrogen fixation, indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase production. They were all strongly resistant to Cd2+ toxicity, with the minimum inhibitory concentration in LB medium ranging from 1.5 mM to 9.0 mM. Except for strain Burkholderia contaminans JLS17, other strains showed decreasing removal rates within continuously elevated Cd2+ concentration of 10-100 mg L-1. Compared with the uninoculated treatment, the inoculation of strains B.contaminans JLS17, Pseudomonas lurida JLS32, and Pantoea endophytica JLS50 effectively increased the concentration of acid-soluble Cd and decreased the concentration of reducible, oxidizable, and residual Cd in the soils of different Cd contamination levels. In pot experiments, inoculation of strains JLS17 and YTG72 significantly (p < 0.05) promoted the growth of above-ground parts and root system of slash pine (Pinus elliottii) under Cd stress. This study provides a valuable biological resource for endophyte-assisted phytoremediation and a theoretical basis for the application of endophytic bacteria for remediation of Cd-contaminated soil.

Functional response of Acinetobacter guillouiae SFC 500-1A to tannery wastewater as revealed by a complementary proteomic approach

Acinetobacter guillouiae SFC 500-1 A is a promising candidate for the bioremediation of tannery wastewater. In this study, we applied shotgun proteomic technology in conjunction with a gel-based assay (Gel-LC) to explore the strain's intracellular protein profile when grown in tannery wastewater as opposed to normal culture conditions. A total of 1775 proteins were identified, 52 of which were unique to the tannery wastewater treatment. Many of them were connected to the degradation of aromatic compounds and siderophore biosynthesis. On the other hand, 1598 proteins overlapped both conditions but were differentially expressed in each. Those that were upregulated in wastewater (109) were involved in the processes mentioned above, as well as in oxidative stress mitigation and intracellular redox state regulation. Particularly interesting were the downregulated proteins under the same treatment (318), which were diverse but mainly linked to the regulation of basic cellular functions (replication, transcription, translation, cell cycle, and wall biogenesis); metabolism (amino acids, lipids, sulphate, energetic processes); and other more complex responses (cell motility, exopolysaccharide production, biofilm formation, and quorum sensing). The findings suggest that SFC 500-1 A engages in survival and stress management strategies to cope with the toxic effects of tannery wastewater, and that such strategies may be mostly oriented at keeping metabolic processes to a minimum. Altogether, the results might be useful in the near future to improve the strain's effectiveness if it will be applied for bioremediation.

Engineering Siderophore Biosynthesis and Regulation Pathways to Increase Diversity and Availability

Siderophores are small metal chelators synthesized by numerous organisms to access iron. These secondary metabolites are ubiquitously present on Earth, and because their production represents the main strategy to assimilate iron, they play an important role in both positive and negative interactions between organisms. In addition, siderophores are used in biotechnology for diverse applications in medicine, agriculture and the environment. The generation of non-natural siderophore analogs provides a new opportunity to create new-to-nature chelating biomolecules that can offer new properties to expand applications. This review summarizes the main strategies of combinatorial biosynthesis that have been used to generate siderophore analogs. We first provide a brief overview of siderophore biosynthesis, followed by a description of the strategies, namely, precursor-directed biosynthesis, the design of synthetic or heterologous pathways and enzyme engineering, used in siderophore biosynthetic pathways to create diversity. In addition, this review highlights the engineering strategies that have been used to improve the production of siderophores by cells to facilitate their downstream utilization.

Host subversion of bacterial metallophore usage drives copper intoxication

Microorganisms can acquire metal ions in metal-limited environments using small molecules called metallophores. While metals and their importers are essential, metals can also be toxic, and metallophores have limited ability to discriminate metals. The impact of the metallophore-mediated non-cognate metal uptake on bacterial metal homeostasis and pathogenesis remains to be defined. The globally significant pathogen Staphylococcus aureus uses the Cnt system to secrete the metallophore staphylopine in zinc-limited host niches. Here, we show that staphylopine and the Cnt system facilitate bacterial copper uptake, potentiating the need for copper detoxification. During in vivo infection, staphylopine usage increased S. aureus susceptibility to host-mediated copper stress, indicating that the innate immune response can harness the antimicrobial potential of altered elemental abundances in host niches. Collectively, these observations show that while the broad-spectrum metal-chelating properties of metallophores can be advantageous, the host can exploit these properties to drive metal intoxication and mediate antibacterial control.

IMPORTANCE

During infection bacteria must overcome the dual threats of metal starvation and intoxication. This work reveals that the zinc-withholding response of the host sensitizes Staphylococcus aureus to copper intoxication. In response to zinc starvation S. aureus utilizes the metallophore staphylopine. The current work revealed that the host can leverage the promiscuity of staphylopine to intoxicate S. aureus during infection. Significantly, staphylopine-like metallophores are produced by a wide range of pathogens, suggesting that this is a conserved weakness that the host can leverage to toxify invaders with copper. Moreover, it challenges the assumption that the broad-spectrum metal binding of metallophores is inherently beneficial to bacteria.

Siderophore conjugates to combat antibiotic-resistant bacteria

Antimicrobial resistance (AMR) is a global threat to society due to the increasing emergence of multi-drug resistant bacteria that are not susceptible to our last line of defence antibiotics. Exacerbating this issue is a severe gap in antibiotic development, with no new clinically relevant classes of antibiotics developed in the last two decades. The combination of the rapidly increasing emergence of resistance and scarcity of new antibiotics in the clinical pipeline means there is an urgent need for new efficacious treatment strategies. One promising solution, known as the 'Trojan horse' approach, hijacks the iron transport system of bacteria to deliver antibiotics directly into cells - effectively tricking bacteria into killing themselves. This transport system uses natively produced siderophores, which are small molecules with a high affinity for iron. By linking antibiotics to siderophores, to make siderophore antibiotic conjugates, the activity of existing antibiotics can potentially be reinvigorated. The success of this strategy was recently exemplified with the clinical release of cefiderocol, a cephalosporin-siderophore conjugate with potent antibacterial activity against carbapenem-resistant and multi-drug resistant Gram-negative bacilli. This review discusses the recent advancements in siderophore antibiotic conjugates and the challenges associated with the design of these compounds that need to be overcome to deliver more efficacious therapeutics. Potential strategies have also been suggested for new generations of siderophore-antibiotics with enhanced activity.

Understanding the Mechanisms of Fe Deficiency in the Rhizosphere to Promote Plant Resilience

One of the most significant constraints on agricultural productivity is the low availability of iron (Fe) in soil, which is directly related to biological, physical, and chemical activities in the rhizosphere. The rhizosphere has a high iron requirement due to plant absorption and microorganism density. Plant roots and microbes in the rhizosphere play a significant role in promoting plant iron (Fe) uptake, which impacts plant development and physiology by influencing nutritional, biochemical, and soil components. The concentration of iron accessible to these live organisms in most cultivated soil is quite low due to its solubility being limited by stable oxyhydroxide, hydroxide, and oxides. The dissolution and solubility rates of iron are also significantly affected by soil pH, microbial population, organic matter content, redox processes, and particle size of the soil. In Fe-limiting situations, plants and soil microbes have used active strategies such as acidification, chelation, and reduction, which have an important role to play in enhancing soil iron availability to plants. In response to iron deficiency, plant and soil organisms produce organic (carbohydrates, amino acids, organic acids, phytosiderophores, microbial siderophores, and phenolics) and inorganic (protons) chemicals in the rhizosphere to improve the solubility of poorly accessible Fe pools. The investigation of iron-mediated associations among plants and microorganisms influences plant development and health, providing a distinctive prospect to further our understanding of rhizosphere ecology and iron dynamics. This review clarifies current knowledge of the intricate dynamics of iron with the end goal of presenting an overview of the rhizosphere mechanisms that are involved in the uptake of iron by plants and microorganisms.

Mineral-Bound Trace Metals as Cofactors for Anaerobic Biological Nitrogen Fixation

Nitrogenase is the only known biological enzyme capable of reducing N₂ to bioavailable NH₃. Most nitrogenases use Mo as a metallocofactor, while alternative cofactors V and Fe are also viable. Both geological and bioinformatic evidence suggest an ancient origin of Mo-based nitrogenase in the Archean, despite the low concentration of dissolved Mo in the Archean oceans. This apparent paradox would be resolvable if mineral-bound Mo were bioavailable for nitrogen fixation by ancient diazotrophs. In this study, the bioavailability of mineral-bound Mo, V, and Fe was determined by incubating an obligately anaerobic diazotroph Clostridium kluyveri with Mo-, V-, and Fe-bearing minerals (molybdenite, cavansite, and ferrihydrite, respectively) and basalt under diazotrophic conditions. The results showed that C. kluyveri utilized mineral-associated metals to express nitrogenase genes and fix nitrogen, as measured by the reverse transcription quantitative polymerase chain reaction and acetylene reduction assay, respectively. C. kluyveri secreted chelating molecules to extract metals from the minerals. As a result of microbial weathering, mineral surface chemistry significantly changed, likely due to surface coating by microbial exudates for metal extraction. These results provide important support for the ancient origin of Mo-based nitrogenase, with profound implications for coevolution of the biosphere and geosphere.

Potential and prospects of Actinobacteria in the bioremediation of environmental pollutants: Cellular mechanisms and genetic regulations

Increasing industrialization and anthropogenic activities have resulted in the release of a wide variety of pollutants into the environment including pesticides, polycyclic aromatic hydrocarbons (PAHs), and heavy metals. These pollutants pose a serious threat to human health as well as to the ecosystem. Thus, the removal of these compounds from the environment is highly important. Mitigation of the environmental pollution caused by these pollutants via bioremediation has become a promising approach nowadays. Actinobacteria are a group of eubacteria mostly known for their ability to produce secondary metabolites. The morphological features such as spore formation, filamentous growth, higher surface area to volume ratio, and cellular mechanisms like EPS secretion, and siderophore production in Actinobacteria render higher resistance and biodegradation ability. In addition, these bacteria possess several oxidoreductase systems (oxyR, catR, furA, etc.) which help in bioremediation. Actinobacteria genera including Arthrobacter, Rhodococcus, Streptomyces, Nocardia, Microbacterium, etc. have shown great potential for the bioremediation of various pollutants. In this review, the bioremediation ability of these bacteria has been discussed in detail. The utilization of various genera of Actinobacteria for the biodegradation of organic pollutants, including pesticides and PAHs, and inorganic pollutants like heavy metals has been described. In addition, the cellular mechanisms in these microbes which help to withstand oxidative stress have been discussed. Finally, this review explores the Actinobacteria mediated strategies and recent technologies such as the utilization of mixed cultures, cell immobilization, plant-microbe interaction, utilization of biosurfactants and nanoparticles, etc., to enhance the bioremediation of various environmental pollutants.

Overview of Yersinia pestis Metallophores: Yersiniabactin and Yersinopine

The pathogenic anaerobic bacteria Yersinia pestis (Y. pestis), which is well known as the plague causative agent, has the ability to escape or inhibit innate immune system responses, which can result in host death even before the activation of adaptive responses. Bites from infected fleas in nature transmit Y. pestis between mammalian hosts causing bubonic plague. It was recognized that a host's ability to retain iron is essential in fighting invading pathogens. To proliferate during infection, Y. pestis, like most bacteria, has various iron transporters that enable it to acquire iron from its hosts. The siderophore-dependent iron transport system was found to be crucial for the pathogenesis of this bacterium. Siderophores are low-molecular-weight metabolites with a high affinity for Fe³⁺. These compounds are produced in the surrounding environment to chelate iron. The siderophore secreted by Y. pestis is yersiniabactin (Ybt). Another metallophore produced by this bacterium, yersinopine, is of the opine type and shows similarities with both staphylopine and pseudopaline produced by Staphylococcus aureus and Pseudomonas aeruginosa, respectively. This paper sheds light on the most important aspects of the two Y. pestis metallophores as well as aerobactin a siderophore no longer secreted by this bacterium due to frameshift mutation in its genome.

Undesirable consequences of the metallic nanoparticles action on the properties and functioning of Escherichia coli, Bacillus cereus and Staphylococcus epidermidis membranes

Controversial and inconsistent findings on the toxicity of metallic nanoparticles (NPs) against many bacteria are common in recorded studies; therefore, further advanced experimental work is needed to elucidate the mechanisms underlying nanotoxicity. This study deciphered the direct effects of Ag-NPs, Cu-NPs, ZnO-NPs and TiO₂-NPs on membrane permeability, cytoplasmic leakage, ATP level, ATPase activity and fatty acid profiling of Escherichia coli, Bacillus cereus and Staphylococcus epidermidis as model microorganisms. A multifaceted analysis of all collected results indicated the different influences of individual NPs on the measured parameters depending on their type and concentration. Predominantly, membrane permeability was correlated with increased cytoplasmic leakage, reduced total ATP levels and ATPase activity. The established fatty acid profiles were unique and concerned various changes in the percentages of hydroxyl, cyclopropane, branched and unsaturated fatty acids. Decisively, E. coli was more susceptible to changes in measured parameters than B. cereus and S. epidermidis. Also, it was established that ZnO-NPs and Cu-NPs had a major differentiating impact on studied parameters. Additionally, bacterial cell imaging using scanning electron microscopy elucidated different NPs distributions on the cell surface. The presented results are believed to provide novel, valuable and accumulated knowledge in the understanding of NPs action on bacterial membranes.

Bioremediation of Heavy Metals by the Genus Bacillus

Environmental contamination with heavy metals is one of the major problems caused by human activity. Bioremediation is an effective and eco-friendly approach that can reduce heavy metal contamination in the environment. Bioremediation agents include bacteria of the genus Bacillus, among others. The best-described species in terms of the bioremediation potential of Bacillus spp. Are B. subtilis, B. cereus, or B. thuringiensis. This bacterial genus has several bioremediation strategies, including biosorption, extracellular polymeric substance (EPS)-mediated biosorption, bioaccumulation, or bioprecipitation. Due to the above-mentioned strategies, Bacillus spp. strains can reduce the amounts of metals such as lead, cadmium, mercury, chromium, arsenic or nickel in the environment. Moreover, strains of the genus Bacillus can also assist phytoremediation by stimulating plant growth and bioaccumulation of heavy metals in the soil. Therefore, Bacillus spp. is one of the best sustainable solutions for reducing heavy metals from various environments, especially soil.

Study of Cadmium Metal Resistance in Stenotrophomonas maltophilia

Metal-resistant bacteria are recommended for metal removal applications due to their rapid multiplication and growth rates. To ensure safety replenishment in contaminated areas frequently hampered by heavy metal toxicity, it is crucial to comprehend their coping mechanisms under heavy metal stress. This study primarily examines the role of EPS (exopolysaccharide) in Stenotrophomonas maltophilia, a Gram-negative, aerobic, and rod-shaped bacteria, in response to Cd, as well as the binding behavior and biosorption mechanism between EPS and Cd, using SEM and FTIR. The studies showed that Stenotrophomonas maltophilia, can resist up to 150 μM of Cd due to the binding of Cd to EPS. SEM analysis showed significant morphological changes and FTIR was to identify main structural groups like carboxyl and hydroxyl which confirms the presence of EPS. The study will also describe the mechanism of cross-reactivity between exopolysaccharide and siderophore production in metal-tolerant Stenotrophomonas maltophilia. This study proved that siderophore-mediated metal detoxification and effective absorption have been linked to metal chelation.

Synthesis of temporin L hydroxamate-based peptides and evaluation of their coordination properties with iron(III )

Ferric iron is an essential nutrient for bacterial growth. Pathogenic bacteria synthesize iron-chelating entities known as siderophores to sequestrate ferric iron from host organisms in order to colonize and replicate. The development of antimicrobial peptides (AMPs) conjugated to iron chelators represents a promising strategy for reducing the iron availability, inducing bacterial death, and enhancing simultaneously the efficacy of AMPs. Here we designed, synthesized, and characterized three hydroxamate-based peptides Pep-cyc1, Pep-cyc2, and Pep-cyc3, derived from a cyclic temporin L peptide (Pep-cyc) developed previously by some of us. The Fe³⁺ complex formation of each ligand was characterized by UV-visible spectroscopy, mass spectrometry, and IR and NMR spectroscopies. In addition, the effect of Fe³⁺ on the stabilization of the α-helix conformation of hydroxamate-based peptides and the cotton effect were examined by CD spectroscopy. Moreover, the antimicrobial results obtained in vitro on some Gram-negative strains (K. pneumoniae and E. coli) showed the ability of each peptide to chelate efficaciously Fe³⁺ obtaining a reduction of MIC values in comparison to their parent peptide Pep-cyc. Our results demonstrated that siderophore conjugation could increase the efficacy and selectivity of AMPs used for the treatment of infectious diseases caused by Gram-negative pathogens.

Pseudomonas aeruginosa virulence attenuation by inhibiting siderophore functions

Pseudmonas aeruginosa is a Gram-negative bacterium known to be ubiquitous and recognized as one of the leading causes of infections such as respiratory, urinary tract, burns, cystic fibrosis, and in immunocompromised individuals. Failure of antimicrobial therapy has been documented to be attributable due to the development of various resistance mechanisms, with a proclivity to develop additional resistance mechanisms rapidly. P. aeruginosa virulence attenuation is an alternate technique for disrupting pathogenesis without impacting growth. The iron-scavenging siderophores (pyoverdine and pyochelin) generated by P. aeruginosa have various properties like scavenging iron, biofilm formation, quorum sensing, increasing virulence, and toxicity to the host. As a result, developing an antivirulence strategy, specifically inhibiting the P. aeruginosa siderophore, has been a promising therapeutic option to limit their infection. Several natural, synthetic compounds and nanoparticles have been identified as potent inhibitors of siderophore production/biosynthesis, function, and transport system. The current review discussed pyoverdine and pyochelin's synthesis and transport system in P. aeruginosa. Furthermore, it is also focused on the role of several natural and synthetic compounds in reducing P. aeruginosa virulence by inhibiting siderophore synthesis, function, and transport. The underlying mechanism involved in inhibiting the siderophore by natural and synthetic compounds has also been explained. KEY POINTS: • Pseudomonas aeruginosa is an opportunistic pathogen linked to chronic respiratory, urinary tract, and burns infections, as well as cystic fibrosis and immunocompromised patients. • P. aeruginosa produces two virulent siderophores forms: pyoverdine and pyochelin, which help it to survive in iron-deficient environments. • The inhibition of siderophore production, transport, and activity using natural and synthesized drugs has been described as a potential strategy for controlling P. aeruginosa infection.

Multi-omics eco-surveillance of bacterial community function in legacy contaminated estuary sediments

Complex legacy contamination is a major issue for many estuaries, with toxicity affecting change in bacterial communities, and their provision of associated goods and services. Sequencing surveys of bacterial community composition provide inferred function; however, additional insights may be generated by measurement of realised metabolic phenotypes. We apply multi-omics (genomics, lipidomics, and metabolomics), with traditional sediment quality analyses, to characterise sediment-associated bacterial communities in an estuary subject to legacy metal contamination (Zn, Hg, As, Cd, Cu and Pb). Analyses of bacterial composition and inferred function (genomics) are coupled with measurements of realised bacterial phenotype (metabolomics and lipidomics) at multiple industrialised and reference sites. At sites with the highest sediment metal concentrations (NTB), we also observed increased abundances of hydrocarbon and sulphuric acid metabolites, indicating additional sediment contamination. Bacterial phyla across sampled sites were dominated by Proteobacteria and Desulfobacteria. NTB sites were enriched with metabolically versatile, cooperative and biofilm forming phyla including, Zixibacteria, Spirochaetota, SAR324 clade, Proteobacteria, Latescibacterota, Desulfobacterota, Deferrisomtota and Acidobateriota; with inferred functions characterised by sulphur metabolism, pathways associated with the degradation of complex organic molecules, and fermentation. Reference sites were characterised by enhanced vitamin biosynthesis, cell wall, cofactor and carbohydrate biosynthesis, and CO₂ fixation. Measured metabolic phenotypes at NTB sites supported predicted functions, with most consistent change observed to naphthalene and aminobenzoate degradation pathways and carbohydrate metabolism (galactose, amino and nucleotide sugar). Change in NTB metabolite profiles was most highly correlated with sediment Hg concentrations, indicative of toxic exposure and potential for Hg methylation. Lipid profiles generated further insight into potential functional (hydroxy fatty acids) and community level change (ceramide phosphoethanolamines, unsaturated glycerides). Multi-omics outputs provided insights into bacterial community functions, modes of contaminant toxicity and expressed mechanisms of adaptation, necessary to better inform management decisions and predictive models in increasingly human-influenced environments.

Chemolithotrophic Biological Nitrogen Fixation Fueled by Antimonite Oxidation May Be Widespread in Sb-Contaminated Habitats

Nitrogen (N) deficiency in mining-contaminated habitats usually hinders plant growth and thus hampers tailing revegetation. Biological N fixation (BNF) is an essential biogeochemical process that contributes to the initial accumulation of N in oligotrophic mining-contaminated regions. Previous studies reported that chemolithotrophic rather than heterotrophic diazotrophs frequently dominated in the mining-contaminated regions. Chemolithotrophic diazotrophs may utilize elements abundant in such habitats (e.g., sulfur (S), arsenic (As), and antimony (Sb)) as electron donors to fix N₂. BNF fueled by the oxidation of S and As has been detected in previous studies. However, BNF fueled by Sb(III) oxidation (Sb-dependent BNF) has never been reported. The current study observed the presence of Sb-dependent BNF in slurries inoculated from Sb-contaminated habitats across the South China Sb belt, suggesting that Sb-dependent BNF may be widespread in this region. DNA-stable isotope probing identified bacteria associated with Rhodocyclaceae and Rhizobiaceae as putative microorganisms responsible for Sb-dependent BNF. Furthermore, metagenomic-binning demonstrated that Rhodocyclaceae and Rhizobiaceae contained essential genes involved in Sb(III) oxidation, N₂ fixation, and carbon fixation, suggesting their genetic potential for Sb-dependent BNF. In addition, meta-analysis indicated that these bacteria are widespread among Sb-contaminated habitats with different niche preferences: Rhodocyclaceae was enriched in river sediments and tailings, while Rhizobiaceae was enriched only in soils. This study may broaden our fundamental understanding of N fixation in Sb-mining regions.

Bacteria isolated from e-waste soil enhance plant growth and mobilize trace metals in e-waste-amended soils

Worldwide accumulation of e-waste poses a major threat to environmental health. However, printed circuit boards contain precious metals, such as gold, and silver, and also contain micronutrient metal elements, such as Fe, Cu, Zn, etc. Therefore, the present study investigated the effects of e-waste-tolerant bacteria (ETB) on promoting plant growth in e-waste-amended soils and mobilizing trace metals into the plants. For this, a total of 18 bacteria were isolated and screened for e-waste tolerance. Screening for plant growth-promoting properties revealed the production of indole-3-acetic acid-like compounds, siderophore production, and phosphate solubilization. Identification based on 16S rRNA gene sequencing revealed that all isolates belonged to the genus Bacillus. Pot experiment revealed that the treated seeds showed the enhancement of chili plants root growth ranging from 106.55 to 208.07% compared to control plants (e-waste) and 0.0 to 47.90% (without e-waste). A similar enhancement was also observed in the shoot length, and size of the leaf compared to e-waste amended control plants. Inoculation of ETB significantly (p < 0.05) mobilized Fe, Zn, Cu, and Ni into chili plants. The identified ETB could be used to mitigate the toxicity posed by the e-waste, enhancing plant growth and mobilization of micronutrients into plants from e-waste.

Ability of aerated compost tea to increase the mobility and phytoextraction of copper in vineyard soil

Aerated compost tea (ACT) contains soluble humic substances (SHS) that are expected to alter the dynamics and ecotoxicity of Cu in soil. This study investigated the efficiency of ACT in enhancing the mobility and phytoextraction of Cu in vineyard soil. Crimson clover (Trifolium incarnatum L.) was grown on a vineyard soil at three concentrations of Cu (90, 261 and 432 mg kg^-1), and supplied (or not) with ACT, then sampled after 56 days to determine the amount of Cu phytoextracted. Soil was extracted with 0.01 M KCl and potentiometric analyses were performed to measure the impact of ACT on the speciation of Cu in the extraction solution. ACT was found to increase the mobility of Cu in the soil by a factor of 3-14 depending on the soil Cu content and on the soil extraction date. The increase in Cu mobility was associated with an increase in absorbance at 254 nm and with a decrease in the free ionic fraction of Cu in the KCl extract, suggesting that Cu was mainly mobilized by the SHS present in the compost tea, and through a ligand-controlled dissolution process. ACT increased Cu phytoextraction at Cu90 and Cu261 by on average 80% thanks to its positive impact on plant growth, and on Cu accumulation in plant shoots, whereas it reduced Cu phytoextraction at Cu432 due to its deleterious effect on plant growth at this soil Cu content. ACT is thus an efficient way to increase the phytoavailability of Cu in soil, but probably should not be used in vineyard soils that are highly contaminated by Cu. To obtain Cu phytoextraction yields in line with the needs of the wine sector, the use of ACT needs to be associated with the cultivation of a Cu-accumulating plant.

Copper selects for siderophore-mediated virulence in Pseudomonas aeruginosa

BACKGROUND

Iron is essential for almost all bacterial pathogens and consequently it is actively withheld by their hosts. However, the production of extracellular siderophores enables iron sequestration by pathogens, increasing their virulence. Another function of siderophores is extracellular detoxification of non-ferrous metals. Here, we experimentally link the detoxification and virulence roles of siderophores by testing whether the opportunistic pathogen Pseudomonas aeruginosa displays greater virulence after exposure to copper. To do this, we incubated P. aeruginosa under different environmentally relevant copper regimes for either two or twelve days. Subsequent growth in a copper-free environment removed phenotypic effects, before we quantified pyoverdine production (the primary siderophore produced by P. aeruginosa), and virulence using the Galleria mellonella infection model.

RESULTS

Copper selected for increased pyoverdine production, which was positively correlated with virulence. This effect increased with time, such that populations incubated with high copper for twelve days were the most virulent. Replication of the experiment with a non-pyoverdine producing strain of P. aeruginosa demonstrated that pyoverdine production was largely responsible for the change in virulence.

CONCLUSIONS

We here show a direct link between metal stress and bacterial virulence, highlighting another dimension of the detrimental effects of metal pollution on human health.

A Review of Pseudomonas aeruginosa Metallophores: Pyoverdine, Pyochelin and Pseudopaline

P. aeruginosa is a common Gram-negative bacterium found in nature that causes severe infections in humans. As a result of its natural resistance to antibiotics and the ability of biofilm formation, the infection with this pathogen can be therapeutic challenging. During infection, P. aeruginosa produces secondary metabolites such as metallophores that play an important role in their virulence. Metallophores are metal ions chelating molecules secreted by bacteria, thus allowing them to survive in the host under metal scarce conditions. Pyoverdine, pyochelin and pseudopaline are the three metallophores secreted by P. aeruginosa. Pyoverdines are the primary siderophores that acquire iron from the surrounding medium. These molecules scavenge and transport iron to the bacterium intracellular compartment. Pyochelin is another siderophore produced by this bacterium, but in lower quantities and its affinity for iron is less than that of pyoverdine. The third metallophore, pseudopaline, is an opine narrow spectrum ion chelator that enables P. aeruginosa to uptake zinc in particular but can transport nickel and cobalt as well. This review describes all the aspects related to these three metallophore, including their main features, biosynthesis process, secretion and uptake when loaded by metals, in addition to the genetic regulation responsible for their synthesis and secretion.

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.

Bacterial Siderophores: Structure, Functions, and Role in the Pathogenesis of Infections

This review systematizes and analyzes the data published over the past decade, devoted to the study of low-molecular-weight high affinity iron chelators – siderophores. Siderophores, which are found in bacteria, fungi and mammals, are able to extract iron from insoluble inorganic compounds, and in the host organism – from complexes with proteins that perform the function of nonspecific protection of mammals from infections. The extracted iron is delivered to cells through surface protein receptors specific for each siderophore, as well as various protein transport systems that make up membranes. Siderophores play an important role in virulence in pathogenic bacteria, performing many functions in the host organism, in addition to providing microbes with iron and other biological metals. They participate in the storage of excess iron, toxic to cells, protect bacteria from reactive oxygen compounds, compete for iron with phagocytes, and have a harmful effect on host cells, acting as secreted bacterial toxin in some cases. Bacterial siderophores perform a signaling function and regulate both, their own synthesis and the synthesis of other virulence factors. Many pathogenic bacteria produce several siderophores that are active under different conditions, against various sources of iron in the host organism and at different stages of infectious process. The review presents the results of the experimental studies aimed at elucidating the structure and diverse functions of bacterial siderophores, the mechanisms of their biosynthesis and regulation of expression, as well as the role of these molecules in the physiology and virulence of pathogenic bacteria. Special emphasis is put on siderophores of bacteria causing particularly dangerous infections.

Role of Exopolysaccharides of Pseudomonas in Heavy Metal Removal and Other Remediation Strategies

Pseudomonas biofilms have been studied intensively for several decades and research outcomes have been successfully implemented in various medical and agricultural applications. Research on biofilm synthesis and composition has also overlapped with the objectives of environmental sciences, since biofilm components show exceptional physicochemical properties applicable to remediation techniques. Especially, exopolysaccharides (ExPs) have been at the center of scientific interest, indicating their potential in solving the environmental issues of heavy metal land and water contamination via sorptive interactions and flocculation. Since exposure to heavy metal via contaminated water or soil poses an imminent risk to the environment and human health, ExPs provide an interesting and viable solution to this issue, alongside other effective and green remedial techniques (e.g., phytostabilization, implementation of biosolids, and biosorption using agricultural wastes) aiming to restore contaminated sites to their natural, pollution-free state, or to ameliorate the negative impact of heavy metals on the environment. Thus, we discuss the plausible role and performance of Pseudomonas ExPs in remediation techniques, aiming to provide the relevant available and comprehensive information on ExPs’ biosynthesis and their usage in heavy metal remediation or other environmental applications, such as wastewater treatment via bioflocculation and soil remediation.

Lead removal in flue gas from sludge incineration by denitrification: Insights from metagenomics and metaproteomics

Flue gas lead emission during sludge incineration damages to human health and ecological environment seriously. Therefore, a denitrifying bio-trickling filter (DNBTF) for lead removal in flue gas from sludge incineration was investigated. Lead removal efficiency was up to 90.7% in 60 days' operation. Lead speciation in biofilms of DNBTF consists of 84.27% residue lead, 15.18% organic bound lead, and less than 1% exchangeable and reducible lead. Lead resistant bacteria and lead resistant-denitrifying bacteria accounted for 85.04% and 58.25%, respectively. Lead resistant microorganisms(Pseudomonas, Azoarcus, Stappia, Pararhodobacter, Paracoccus, Azospirillum, Hyphomonas, Rhodobacter, Polymorphum, Brevunimonas, Stenotrophomonas) could resist the toxicity of Pb²⁺ in flue gas by transport protein and binding protein, and detoxify Pb²⁺ in flue gas by extracellular polymeric substances (EPS) adsorption, protein binding and precipitation under the action of resistance genes, such as pbrAB, golT, troABCD, znuABC, czcABCD, pcoB, copA, as shown by integrated metagenomic and metaproteomic analyses. The biofilm was characterized by FTIR, XRD, 3D-EEM, and SEM-EDS. XRD and SEM-EDS spectra indicated the formation of pyromorphite from bioconversion of lead in flue gas. Lead-containing flue gas was bio-stabilized in the form of pyromorphite and HA-Pb via complexation of humic acids in extracellular polymeric substances (EPS), biosorption and biodeposition. This provides a new way of sludge incineration flue gas lead removal using a denitrifying biotricking filter.

Primary Succession Changes the Composition and Functioning of the Protist Community on Mine Tailings, Especially Phototrophic Protists

Primary succession in mine tailings is a prerequisite for tailing vegetation. Microorganisms, including bacteria, fungi, and protists, play an important role in this process in the driving force for improving the nutritional status. Compared to bacteria and fungi, protist populations have rarely been investigated regarding their role in mine tailings, especially for those inhabiting tailings associated with primary succession. Protists are the primary consumers of fungi and bacteria, and their predatory actions promote the release of nutrients immobilized in the microbial biomass, as well as the uptake and turnover of nutrients, affecting the functions of the wider ecosystems. In this study, three different types of mine tailings associated with three successional stages (original tailings, biological crusts, and Miscanthus sinensis grasslands) were selected to characterize the protistan community diversity, structure, and function during primary succession. Some members classified as consumers dominated the network of microbial communities in the tailings, especially in the original bare land tailings. The keystone phototrophs of Chlorophyceae and Trebouxiophyceae showed the highest relative abundance in the biological crusts and grassland rhizosphere, respectively. In addition, the co-occurrences between protist and bacterial taxa demonstrated that the proportion of protistan phototrophs gradually increased during primary succession. Further, the metagenomic analysis of protistan metabolic potential showed that abundances of many functional genes associated with photosynthesis increased during the primary succession of tailings. Overall, these results suggest that the primary succession of mine tailings drives the changes observed in the protistan community, and in turn, the protistan phototrophs facilitate the primary succession of tailings. This research offers an initial insight into the changes in biodiversity, structure, and function of the protistan community during ecological succession on tailings.

Differential toxicity of potentially toxic elements to human gut microbes

Specific microorganisms in the human gut (i.e., gut microbes) provide mutually beneficial outcomes such as microbial balance by inhibiting the growth of pathogenic organisms, immune system modulation, fermentation of ingested products, and vitamin production. The intake of contaminants including potenially toxic elements (PTEs) can occur through food, air, water and some medicines. The gut microbes not only can be affected by environmental contaminants but they themselves can alter the speciation and bioavailability of these contaminants. This research work was designed to demonstrate the relationship between increasing level of selected PTEs including As, Cd, Pb and Hg on the growth of selected gut microbes. The toxicity of above mentioned PTEs to three gut bacteria (Lactobacillus rhamnosus, Lactobacillus acidophilus and Escherichia coli) was examined. While the toxicity of all the cationic PTEs including Cd, Pb and Hg towards gut bacteria decreased with increasing pH, the anionic As species exhibited an opposite effect. The order of toxicity was Hg > Cd > Pb > As(III)>As(V) for E. coli; and Hg > Cd > As(III)>Pb > As(V) for the two Lactobacillus sp. Arsenite (AsIII) showed higher toxicity than arsenate (AsV) to gut bacteria. While As is an anion, Cd, Pb and Hg are cations and hence their binding capacity to the bacterial cell wall varied based on the charge dependent functional groups. However, the toxic effects of PTEs for a bacteria are controlled by their speciation and bioavailability.