Siderophores: an alternative bioremediation strategy?

Siderophores and metallophores: Metal complexation weapons to fight environmental pollution

Siderophores are small molecules of organic nature, released by bacteria to chelate iron from the surrounding environment and subsequently incorporate it into the cytoplasm. In addition to iron, these secondary metabolites can complex with a wide variety of metals, which is why they are commonly studied in the environment. Heavy metals can be very toxic when present in large amounts on the planet, affecting public health and all living organisms. The pollution caused by these toxic metals is increasing, and therefore it is urgent to find practical, sustainable, and economical solutions for remediation. One of the strategies is siderophore-assisted bioremediation, an innovative and advantageous alternative for various environmental applications. This research highlights the various uses of siderophores and metallophores in the environment, underscoring their significance to ecosystems. The study delves into the utilization of siderophores and metallophores in both marine and terrestrial settings (e.g. bioremediation, biocontrol of pathogens, and plant growth promotion), such as bioremediation, biocontrol of pathogens, and plant growth promotion, providing context for the different instances outlined in the existing literature and highlighting their relevance in each field. The study delves into the structures and types of siderophores focusing on their singular characteristics for each application and methodologies used. Focusing on recent developments over the last two decades, the opportunities and challenges associated with siderophores and metallophores applications in the environment were mapped to arm researchers in the fight against environmental pollution.

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.

N- acyl homoserine lactones (AHLs) type signal molecules produced by rhizobacteria associated with plants that growing in a metal(oids) contaminated soil: A catalyst for plant growth

The present study explores the potential of rhizobacteria isolated from Baccharis linearis and Solidago chilensis in metal(loid)-contaminated soil for producing N-acyl-homoserine lactones (AHLs)-type signal molecules and promoting plant growth. A total of 42 strains were isolated, four demonstrating the production of AHL-type signal molecules. Based on 16S rRNA gene sequencing analyses and MALDI-TOF analyses, these four isolates were identified as belonging to the Pseudomonas genus, specifically P. brassicacearum, P. frederickberguensis, P. koreensis, and P. orientalis. The four AHL-producing strains were evaluated for metal(loid)s tolerance, their plant growth promotion traits, AHL quantification, and their impact on in vitro Lactuca sativa plant growth. The study found that four strains exhibited high tolerance to metal(loid)s, particularly As, Cu, and Zn. Additionally, plant growth-promoting traits were detected in AHL-producing bacteria, such as siderophore production, ammonia production, ACC deaminase activity, and P solubilization. Notably, AHL production varied among strains isolated from B. linearis, where C7-HSL and C9-HSL signal molecules were detected, and S. chilensis, where only C7-HSL signal molecules were observed. In the presence of copper, the production of C7-HSL and C9-HSL significantly decreased in B. linearis isolates, while in S. chilensis isolates, C7-HSL production was inhibited. Further, when these strains were inoculated on lettuce seeds and in vitro plants, a significant increase in germination and plant growth was observed. Mainly, the inoculation of P. brassicacearum and P. frederickberguensis led to extensive root hair development, significantly increasing length and root dry weight. Our results demonstrate that rhizospheric strains produce AHL molecules and stimulate plant growth, primarily through root development. However, the presence of copper reduces the production of these molecules, potentially affecting the root development of non-metalloid tolerant plants such as S. chilensis, which would explain its low population in this hostile environment.

Chryseobacterium metallicongregator, sp. nov., a bacterium possessing metallophore activity towards rare earth elements

A polyphasic taxonomic study was carried out on strain ES2T, isolated from sediment of a wetland created to remediate acid drainage from a coal mine. The rod-shaped bacterium formed yellow/orange pigmented colonies and produced the pigment flexirubin. The 16S rRNA gene sequence results assigned the strain to Chryseobacterium, with 98.9 and 98.3 % similarity to Chryseobacterium vietnamense and Chryseobacterium cucumeris, respectively. Computation of the average nucleotide identity and digital DNA-DNA hybridization values with the closest phylogenetic neighbours of ES2T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The dominant fatty acids of strain ES2T were iso-C15 : 0, iso-C17 : 1 ω9c, iso C17 : 0 3-OH, and iso-C15 : 0 2-OH. The DNA G+C content was 35.5 mol%. The major polar lipid was phosphatidylethanolamine while menaquinone-6 was the only menaquinone found. This bacterium has been previously shown to possess metallophore activity towards rare earth elements, and based on genome sequencing, possesses all required genes for siderophore production/activity, possibly identifying the source of this unique ability. On the basis of the results obtained here, this bacterium is assigned to the genus Chryseobacterium as representing a new species with the name Chryseobacterium metallicongregator sp. nov., type strain ES2T (=NRRL B-65679T=KCTC 102120T).

Sasa argenteostriata - A potential plant for phytostabilization remediation of lead-zinc tailing-contaminated soil

Phytoremediation is an effective way to remediate metal-contaminated soils. During phytoremediation, plants immobilize heavy metals through the roots to reduce the mobility, toxicity and dispersal of the metals, and the changes in the activity of the roots are often accompanied by changes in the rhizosphere ecosystems, in which rhizobacteria are essential components and interact with roots to maintain the stability of the rhizosphere ecosystem and improve soil health. In this study, the phytoremediation potential of Sasa argenteostriata (Regel) E.G. Camu and the response of rhizobacteria were revealed with different levels of lead-zinc tailing contamination (Pb, Zn, and Cd concentrations of 1197.53, 3243.40, and 185.44 mg/kg for M1 and 2301.71, 6087.95, and 364.00 mg/kg for M2, respectively). The BCF of Sasa argenteostriata increased with increasing soil pollution, and the BCFPb, BCFZn, and BCFCd were 0.19, 0.27, and 0.08, respectively, under the M2 treatment; in contrast, the TF decreased with increasing soil pollution, and the TFPb, TFZn, and TFCd were 0.39, 0.85, and 0.07, respectively, under the M1 treatment. The mobility of Pb in the rhizosphere was higher than that of Zn and Cd, and the percentage of residual (Res) Zn and Cd in the rhizosphere increased, while the acid-soluble (Aci) Pb was significantly higher, leading to obvious uptake of Pb by the roots. Correlation analysis showed that Sasa argenteostriata affected the rhizobacterial community by changing the rhizosphere soil pH, the contents of organic matter and NRFM, and bacteria such as Proteobacteria and MND1, which are highly resistant to heavy metals (HMs), became the dominant species in the community. Further PICRUSt2 analysis showed that reducing metal transport across the membranes and increasing the efficiency of cellular reproduction were the main metabolic mechanisms of bacterial tolerance to HMs. Overall, the roots of Sasa argenteostriata were able to immobilize more heavy metals in PbZn tailing-contaminated soil, reducing the toxicity of HMs in the soil, and then influencing the rhizobacteria to change the community structure and metabolism mechanism to adapt to the HM-contaminated environment, and the soil fertility was increased, which together promoted the health and stability of the soil. This study is the first to illustrate the phytoremediation potential and response of the rhizobacterial community of Sasa argenteostriata under multimetal contamination of PbZn tailings. The results of the study provide some guidance for the practice of lead-zinc tailing-phytoremediation and soil health.

Functional differences of cultivable leaf-associated microorganisms in the native Andean tree Gevuina avellana Mol. (Proteaceae) exposed to atmospheric contamination

AIMS

This study aimed to evaluate and describe the functional differences of cultivable bacteria and fungi inhabiting the leaves of Gevuina avellana Mol. (Proteaceae) in an urban area with high levels of air pollution and in a native forest in the southern Andes.

METHODS AND RESULTS

Phyllosphere microorganisms were isolated from the leaves of G. avellana, their plant growth-promoting capabilities were estimated along with their biocontrol potential and tolerance to metal(loid)s. Notably, plants from the urban area showed contrasting culturable leaf-associated microorganisms compared to those from the native area. The tolerance to metal(loid)s in bacteria range from 15 to 450 mg l-1 of metal(loid)s, while fungal strains showed tolerance from 15 to 625 mg l-1, being especially higher in the isolates from the urban area. Notably, the bacterial strain Curtobacterium flaccumfaciens and the fungal strain Cladosporium sp. exhibited several plant-growth-promoting properties along with the ability to inhibit the growth of phytopathogenic fungi.

CONCLUSIONS

Overall, our study provides evidence that culturable taxa in G. avellana leaves is directly influenced by the sampling area. This change is likely due to the presence of atmospheric pollutants and diverse microbial symbionts that can be horizontally acquired from the environment.

Unveiling the Pool of Metallophores in Native Environments and Correlation with Their Potential Producers

For many organisms, metallophores are essential biogenic ligands that ensure metal scavenging and acquisition from their environment. Their identification is challenging in highly organic matter rich environments like peatlands due to low solubilization and metal scarcity and high matrix complexity. In contrast to common approaches based on sample modification by spiking of metal isotope tags, we have developed a two-dimensional (2D) Solid-phase extraction-Liquid chromatography-mass spectrometry (SPE-LC-MS) approach for the highly sensitive (LOD 40 fmol per g of soil), high-resolution direct detection and identification of metallophores in both their noncomplexed (apo) and metal-complexed forms in native environments. The characterization of peat collected in the Bernadouze (France) peatland resulted in the identification of 53 metallophores by a database mass-based search, 36 among which are bacterial. Furthermore, the detection of the characteristic (natural) metal isotope patterns in MS resulted in the detection of both Fe and Cu potential complexes. A taxonomic-based inference method was implemented based on literature and public database (antiSMASH database version 3.0) searches, enabling to associate over 40% of the identified bacterial metallophores with potential producers. In some cases, low completeness with the MIBiG reference BCG might be indicative of alternative producers in the ecosystem. Thus, coupling of metallophore detection and producers' inference could pave a new way to investigate poorly documented environment searching for new metallophores and their producers yet unknown.

Opportunities and challenges of microbial siderophores in the medical field

Siderophores are low-molecular-weight secondary metabolites that function as iron chelators. Under iron-deficiency conditions, they are produced by a wide variety of microbes, allowing them to increase their iron uptake. The primary function of these compounds is the environmental iron scavenging and its transport into the cytosol. Iron is then reduced to its ferrous form to operate as an enzymatic cofactor for various functions, including respiration, nitrogen fixation, photosynthesis, methanogenesis, and amino acid synthesis. Depending on their functional group, siderophores are classified into hydroxamate, catecholate, phenolate, carboxylate, and mixed types. They have achieved great importance in recent years due to their medical applications as antimicrobial, antimalarial, or anticancer drugs, vaccines, and drug-delivery agents. This review integrates current advances in specific healthcare applications of microbial siderophores, delineating new opportunities and challenges as viable therapies to fight against diseases that represent crucial public health problems in the medical field.Key points• Siderophores are low-molecular-weight secondary metabolites functioning as iron chelators.• The siderophore's properties offer viable options to face diverse clinical problems.• Siderophores are alternatives for the enhancement of antibiotic activities.

Selenite bioreduction with concomitant green synthesis of selenium nanoparticles by a selenite resistant EPS and siderophore producing terrestrial bacterium

Environmental bacterial isolates play a very important role in bioremediation of metals and toxic metalloids. A bacterial strain with high selenite (SeO32-) tolerance and reducing capability was isolated from electronic waste dump site in Banaras Hindu University, Varanasi, India. Based on 16 S rRNA sequencing and BLAST search, this bacterial isolate was identified as Bacillus paramycoides and designated as strain MF-14. It tolerated Sodium selenite up to 110 mM when grown aerobically in LB broth and reduced selenite into elemental selenium (Se0) significantly within 24 h with concomitant biosynthesis of selenium nanoparticles as clearly revealed by brick red precipitate and specific surface plasmon resonance peak at 210 nm using UV-Visible spectrophotometer. Scanning electron microscopy (SEM) analysis of this bacterial strain exposed to 1mM and 5 mM selenite also demonstrated morphological alterations as cell enlargement due to accumulation and bioprecipitation of elemental selenium (Se0). The FTIR analysis clearly demonstrated that functional groups present on the surface of biogenic selenium nanoparticles (SeNPs) play a significant role in the stabilization and capping of SeNPs. Furthermore, these SeNPs were characterized using spectroscopic analysis involving Dynamic light scattering, zeta potential, XPS, FTIR, XRD and Raman spectroscopy which clearly revealed particle size 10-700 nm, amorphous nature, stability as well as it's oxidation state. The biochemical studies have demonstrated that membrane bound reductase enzyme may be responsible for significant reduction of selenite into elemental selenium. Therefore, we may employ Bacillus paramycoides strain MF-14 successfully for bioremediation of selenite contaminated environmental sites with concomitant green synthesis of SeNPs.

Endophyte inoculation enhanced microbial metabolic function in the rhizosphere benefiting cadmium phytoremediation by Phytolaccaacinosa

Microbial metabolic activities in rhizosphere soil play a critical role in plant nutrient utilization and metal availability. However, its specific characteristics and influence on endophyte assisted phytoremediation remains unclear. In this study, an endophyte strain Bacillus paramycoides (B. paramycoides) was inoculated in the rhizosphere of Phytolacca acinosa (P. acinosa), and microbial metabolic characteristics of rhizosphere soils were analyzed using Biolog system to investigate how they influence phytoremediation performance of different types of cadmium contaminated soil. The results indicated that endophyte B. paramycoides inoculation enhanced bioavailable Cd percentage by 9-32%, resulting in the increased Cd uptake (32-40%) by P. acinosa. With endophyte inoculation, the utilization of carbon sources was significantly promoted by 4-43% and the microbial metabolic functional diversity increased by 0.4-36.8%. Especially, B. paramycoides enhanced the utilization of recalcitrant substrates carboxyl acids, phenolic compounds and polymers by 48.3-225.6%, 42.4-65.8% and 15.6-25.1%, respectively. Further, the microbial metabolic activities were significant correlated with rhizosphere soil microecology properties and impact phytoremediation performance. This study provided new insight into the microbial processes during endophyte assisted phytoremediation.

Interaction between a Martian Regolith Simulant and Fungal Organic Acids in the Biomining Perspective

The aim of this study was to evaluate the potential of Aspergillus tubingensis in extracting metals from rocks simulating Martian regolith through biomining. The results indicated that the fungal strain produced organic acids, particularly oxalic acid, in the first five days, leading to a rapid reduction in the pH of the culture medium. This acidic medium is ideal for bioleaching, a process that employs acidolysis and complexolysis to extract metals from rocks. Additionally, the strain synthesized siderophores, molecules capable of mobilizing metals from solid matrices, as verified by the blue CAS colorimetric test. The secretion of siderophores in the culture medium proved advantageous for biomining. The siderophores facilitated the leaching of metal ions, such as manganese, from the rock matrix into the acidified water solution. In addition, the susceptibility of the Martian regolith simulant to the biomining process was assessed by determining the particle size distribution, acid composition after treatment, and geochemical composition of the rock. Although the preliminary results demonstrate successful manganese extraction, further research is required to optimize the extraction technique. To conclude, the A. tubingensis strain exhibits promising abilities in extracting metals from rocks through biomining. Its use could prove useful in future in situ mining operations and environmental remediation efforts. Further research is required to optimize the process and evaluate its feasibility on a larger scale.

Contribution of endophytes towards improving plant bioactive metabolites: a rescue option against red-taping of medicinal plants

Medicinal plants remain a valuable source for natural drug bioprospecting owing to their multi-target spectrum. However, their use as raw materials for novel drug synthesis has been greatly limited by unsustainable harvesting leading to decimation of their wild populations coupled with inherent low concentrations of constituent secondary metabolites per unit mass. Thus, adding value to the medicinal plants research dynamics calls for adequate attention. In light of this, medicinal plants harbour endophytes which are believed to be contributing towards the host plant survival and bioactive metabolites through series of physiological interference. Stimulating secondary metabolite production in medicinal plants by using endophytes as plant growth regulators has been demonstrated to be one of the most effective methods for increasing metabolite syntheses. Use of endophytes as plant growth promotors could help to ensure continuous supply of medicinal plants, and mitigate issues with fear of extinction. Endophytes minimize heavy metal toxicity in medicinal plants. It has been hypothesized that when medicinal plants are exposed to harsh conditions, associated endophytes are the primary signalling channels that induce defensive reactions. Endophytes go through different biochemical processes which lead to activation of defence mechanisms in the host plants. Thus, through signal transduction pathways, endophytic microorganisms influence genes involved in the generation of secondary metabolites by plant cells. Additionally, elucidating the role of gene clusters in production of secondary metabolites could expose factors associated with low secondary metabolites by medicinal plants. Promising endophyte strains can be manipulated for enhanced production of metabolites, hence, better probability of novel bioactive metabolites through strain improvement, mutagenesis, co-cultivation, and media adjustment.

The potency of a liquid biofertilizer containing bacterial strains of Rhodopseudomonas spp. on recovery of soil properties damaged by Al3+ and Fe2+ toxins and enhancement of rice yield in acid sulfate soil

In the Mekong Delta Vietnam, rice is heavily affected by Al3+ and Fe2+ ions appearing in local acid sulfate soils (AAS). Therefore, the current study was carried out to assess the efficacy of a liquid biofertilizer (LB) containing nitrogen-fixing and phosphorus-solubilizing bacterial strains of Rhodopseudomonas spp. on remediation of soil characteristics and improvements of rice uptakes, growth, and yield. The experiment was designed in a randomized block design with nine treatments and four replications in an ASS. The results have shown that the LB application could contribute to the remediation of soil properties, including an increase in concentrations of NH4+ by 12.9%-19.4%, soluble P by 25.7%-42.6%, total N uptake by 40.7-64.0 kg ha-1 and total P uptake by 5.60-12.6 kg ha-1, and a decrease in concentrations of toxins, such as Al3+ by 12.1%-19.7% and Fe2+ by 16.6%-19.0%, compared to the treatment with the farmer-based fertilization. Thereby, grain yield was improved by 31.9%-32.2% with the LB versus the treatments without the bacteria and by 9.5%-11.1% compared to the commercial biofertilizer treatments. The application of LB reduced 25% N and 50% P of the recommendation versus the farmers' fertilization and improved performance of rice growth and yield cultivated on ASS which suffered from Al3+ and Fe2+ ions.

DFT-based analysis of siderophore-metal ion interaction for efficient heavy metal remediation

Siderophores have great application potential in metal pollutant remediation because of their effective cost and friendly impact on the environment. However, the practical use of siderophores in the remediation of specific metals is rather limited because of the weak nonspecific interactions between the siderophores and different metals. Thus, screening for a siderophore with optimal interaction with a specific metal would be necessary. In this study, the interaction between metal ions and moieties that donate the oxygen ligands for the coordination of four types of siderophore (hydroxamates, catecholates, phenolates, and carboxylates) was modeled and analyzed. As revealed by DFT-based analysis, the four types of siderophore generally exhibited selection preference for different metal ions in the order Ga3+  > Al3+  > Fe3+  > Cr3+  > Ni2+  > Cu2+  > Zn2+  > Co2+  > Mn2+  > Hg2+  > Pb2+  > Cd2+, which was determined mainly by the electronegativity of the siderophore functional groups, the electronegativity of the metals, and the ionic radius of the metals, as well as the interaction between the siderophores and the metals. Moreover, the effect of linear or nonlinear (cyclic) structure on the affinity of each siderophore for different metal ions was evaluated. In most situations, metal-bound cyclic siderophores were found to be more stable than their linear counterparts. Thus, proper siderophores for the remediation of metal pollution may be rapidly screened using this model.

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.

Hydrocarbon degradation strategy and pyoverdine production using the salt tolerant Antarctic bacterium Marinomonas sp. ef1

One of the most concerning environmental problems is represented by petroleum and its derivatives causing contamination of aquatic and underground environments. In this work, the degradation treatment of diesel using Antarctic bacteria is proposed. Marinomonas sp. ef1 is a bacterial strain isolated from a consortium associated with the Antarctic marine ciliate Euplotes focardii. Its potential in the degradation of hydrocarbons commonly present in diesel oil were studied. The bacterial growth was evaluated in culturing conditions that resembled the marine environment with 1% (v/v) of either diesel or biodiesel added; in both cases, Marinomonas sp. ef1 was able to grow. The chemical oxygen demand measured after the incubation of bacteria with diesel decreased, demonstrating the ability of bacteria to use diesel hydrocarbons as a carbon source and degrade them. The metabolic potential of Marinomonas to degrade aromatic compounds was supported by the identification in the genome of sequences encoding various enzymes involved in benzene and naphthalene degradation. Moreover, in the presence of biodiesel, a fluorescent yellow pigment was produced; this was isolated, purified and characterized by UV-vis and fluorescence spectroscopy, leading to its identification as a pyoverdine. These results suggest that Marinomonas sp. ef1 can be used in hydrocarbon bioremediation and in the transformation of these pollutants in molecules of interest.

Bioprospecting of the Antarctic Bacillus subtilis strain for potential application in leaching hydrocarbons and trace elements from contaminated environments based on functional and genomic analysis

The production of secondary metabolites including biosurfactants by the Bacillus subtilis ANT_WA51 and the evaluation of its ability to leach metals and petroleum derivatives from the soil, using post-culture medium was investigated. The ANT_WA51 strain isolated from a pristine, harsh Antarctic environment produces the biosurfactants surfactin and fengycin, which reduce the surface tension of molasses-based post-culture medium to 26.6 mN m^-1 at a critical micellization concentration (CMC) of 50 mg L^-1 and a critical micelle dilution (CMD) of 1:19. The presence of biosurfactants and other secondary metabolites in the post-culture medium contributed to significant removal of xenobiotics from contaminated soils in the batch washing experiment - 70% hydrocarbons and 10-23% metals (Zn, Ni and Cu). The isolate's tolerance to different abiotic stresses, including freezing, freeze-thaw cycles, salinity (up to 10%), the presence of metals - Cr(VI), Pb(II), Mn(II), As(V) (up to 10 mM) and Mo(VI) (above 500 mM) and petroleum hydrocarbons (up to 20.000 mg kg^-1) as well as the confirmed metabolic activity of these bacteria in toxic environments in the OxiTop® system indicate that they can be used directly in bioremediation. Comparative genomic analysis of this bacteria revealed a high similarity of its genome to the associated plant strains from America and Europe indicating the wide applicability of plant growth-promoting Bacillus subtilis and that the data can be extrapolated to a wide range of environmental strains. An important aspect of the study was to present the absence of inherent features which would indicate its clear pathogenicity enables its safe use in the environment. Based on the obtained results, we also conclude that the use of post-culture medium, obtained on low-cost byproducts like molasses, for leaching contaminants, especially hydrocarbons, is a promising bioremediation method that can be a replacement for the use of synthetic surfactants and provides a base for further large-scale research but the selection of an appropriate leaching may be dependent on the concentration of contaminants.

Deciphering endemic rhizosphere microbiome community's structure towards the host-derived heavy metals tolerance and plant growth promotion functions in serpentine geo-ecosystem

Environmental microbes in rhizosphere soil and surrounding plants have the potential to alter ecosystem functions. We investigated the microbial communities inhabiting the rhizosphere soils of both serpentine and non-serpentine rhizosphere zones to evaluate their heavy metal tolerance and ability to promote plant growth, utilizing 16S rRNA metabarcoding. The Biolog-EcoPlate technique was employed to determine how abiotic stress factors affect carbon utilization capacity by rhizospheric microbial communities in the serpentine geo-ecosystem. The phyla Proteobacteria, Acidobacteria, Bacteroidetes, and Nitrospirae colonized in the roots of Miscanthus sp., Biden sp., and Oryza sp. showed noticeable differences in different rhizosphere zones. The PICRUSt2-based analysis identified chromium/iron resistance genes (ceuE, chrA) and arsenic resistance genes (arsR, acr3, arsC) abundant in all the studied rhizosphere soils. Notably, nickel resistance genes (nikA, nikD, nikE, and nikR) from Arthrobacter, Microbacterium, and Streptomyces strongly correlate with functions related to solubilization of nickel and an increase in siderophore and IAA production. The abundance of Arthrobacter, Clostridium, Geobacter, Dechloromonas, Pseudomonas, and Flavobacterium was positively correlated with chromium and nickel but negatively correlated with the calcium/magnesium ratio. Our results contribute to a better understanding of the functions of plant-tolerant PGPR interaction in the heavy metal-contaminated rhizosphere and eco-physiological responses from long-term biological weathering.

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.

Drivers to improve metal(loid) phytoextraction with a focus on microbial degradation of dissolved organic matter in soils

Bioaugmentation of soils can increase the mobilization of metal(loid)s from the soil-bearing phases. However, once desorbed, these metal(loid)s are mostly complexed to the dissolved organic matter (DOM) in the soil solution, which can restrict their availability to plants (roots mainly taking up the free forms) and then the phytoextraction performances. Firstly the main drivers influencing phytoextraction are reminded, then the review focuses on the DOM role. After having reminding the origin, the chemical structure and the lability of DOM, the pool of stable DOM (the most abundant in the soil) most involved in the complexation of metal(loid)s is addressed in particular by focusing on carboxylic and/or phenolic groups and factors controlling metal(loid) complexation with DOM. Finally, this review addresses the ability of microorganisms to degrade metal(loid)-DOM complexes as an additional lever for increasing the pool of free metal(loid) ions, and then phytoextraction performances, and details the origin of microorganisms and how they are selected. The development of innovative processes including the use of these DOM-degrading microorganisms is proposed in perspectives.

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.

Plant-beneficial Streptomyces dioscori SF1 potential biocontrol and plant growth promotion in saline soil within the arid and semi-arid areas

Environmental challenges like salinity, drought, fungal phytopathogens, and pesticides directly or/and indirectly influence the environment and agricultural yields. Certain beneficial endophytic Streptomyces sp. can ameliorate environmental stresses and be utilized as crop growth promoters under adverse conditions. Herein, Streptomyces dioscori SF1 (SF1) isolated from seeds of Glycyrrhiza uralensis tolerated fungal phytopathogens and abiotic stresses (drought, salt, and acid base). Strain SF1 showed multifarious plant growth promotion characteristics, including the production of indole acetic acid (IAA), ammonia, siderophores, ACC deaminase, extracellular enzymes, the ability of potassium solubilization, and nitrogen fixation. The dual plate assay showed that strain SF1 inhibited 63.21 ± 1.53%, 64.84 ± 1.35%, and 74.19 ± 2.88% of Rhizoctonia solani, Fusarium acuminatum, and Sclerotinia sclerotiorum, respectively. The detached root assays showed that strain SF1 significantly reduced the number of rotten sliced roots, and the biological control effect on sliced roots of Angelica sinensis, Astragalus membranaceus, and Codonopsis pilosula was 93.33%, 86.67%, and 73.33%, respectively. Furthermore, the strain SF1 significantly increased the growth parameters and biochemical indicators of adversity in G. uralensis seedlings under drought and/or salt conditions, including radicle length and diameter, hypocotyl length and diameter, dry weight, seedling vigor index, antioxidant enzyme activity, and non-enzymatic antioxidant content. In conclusion, the strain SF1 can be used to develop environmental protection biological control agents, improve the anti-disease activity of plants, and promote plant growth in salinity soil within arid and semi-arid regions.

Structural Requirements for Ga3+ Coordination in Synthetic Analogues of the Siderophore Piscibactin Deduced by Chemical Synthesis and Density Functional Theory Calculations

Stereoselective total synthesis of several analogues of piscibactin (Pcb), the siderophore produced by different pathogenic Gram-negative bacteria, was performed. The acid-sensitive α-methylthiazoline moiety was replaced by a more stable thiazole ring, differing in the configuration of the OH group at the C-13 position. The ability of these Pcb analogues to form complexes with Ga³⁺ as a mimic of Fe³⁺ showed that the configuration of the hydroxyl group at C-13 as 13S is crucial for the chelation of Ga³⁺ to preserve the metal coordination, while the presence of a thiazole ring instead of the α-methylthiazoline moiety does not affect such coordination. A complete ¹H and ¹³C NMR chemical shift assignment of the diastereoisomer mixtures around C9/C10 was done for diagnostic stereochemical disposition. Additionally, density functional theory calculations were performed not only for confirming the stereochemistry of the Ga³⁺ complex among the six possible diastereoisomers but also for deducing the ability of these to form octahedral coordination spheres with gallium. Finally, the lack of antimicrobial activity of Pcb and Pcb thiazole analogue Ga³⁺ complexes against Vibrio anguillarum agrees with one of the roles of siderophores in protecting pathogens from metal ion toxicity. The efficient metal coordination shown by this scaffold suggests its possible use as a starting point for the design of new chelating agents or vectors for the development of new antibacterials that exploit the "Trojan horse" strategy using the microbial iron uptake mechanisms. The results obtained will be of great help in the development of biotechnological applications for these types of compounds.

On the coordination chemistry of a bacterial siderophore cepabactin from a theoretical perspective

Iron is one of the essential metals required by almost all living organisms. However, nature has certain constraints in distributing this element among tissues. Since polymeric oxide-bridged Fe (III) is the prominent source of Fe (III) ions, the insolubility of Fe (III) ions in aqueous systems reduces the direct uptake by cells. Secondly, the free-Fe entities which generate ^.OH radicals pave the way to the destruction of the cells. Hence, a protective coordination environment via sophisticated chemical systems is required for the acquisition of Fe, its successive transport, storage, and effective utilization in various tissues. Siderophores are polydentate ligands used by bacterial cells for Fe acquisition, with a relatively high affinity for Fe (III) ions. Secreted from the bacterial cells into the external aqueous medium, they sequester Fe to give a soluble complex which re-enters the organism at a specific receptor. Once it gets inside the cell, the Fe is released from the complex and utilized for essential biochemical reactions. The medicinal applications of these natural ligands, developing progressively in various research groups, necessitate the theoretical aspects of their coordination chemistry. This research paper deals with the coordination chemistry of one of the siderophores, cepabactin (Cep). The chemical computations confirm that the Fe^III(Cep)₃ complex is octahedral and high spin. The oxygen atoms of Cep, which are hard and negatively charged, thus act as electron donors in the Fe^III(Cep)₃ complex formation. This in turn makes the siderophores relatively less attractive towards Fe (II) ions.

A novel N-arachidonoyl-l-alanine-catabolizing strain of Serratia marcescens for the bioremediation of Cd and Cr co-contamination

Cadmium (Cd) and chromium (Cr) are widespread contaminants with a high risk to the environment and humans. Herein we isolated a novel strain of Serratia marcescens, namely strain S27, from soil co-contaminated with Cd and Cr. This strain showed strong resistance to Cd as well as Cr. S27 cells demonstrated Cd adsorption rate of 45.8% and Cr reduction capacity of 84.4% under optimal growth conditions (i.e., 30 °C, 200 rpm, and pH 7.5). Microscopic characterization of S27 cells revealed the importance of the functional groups C-O-C, C-H-O, C-C, C-H, and -OH, and also indicated that Cr reduction occurred on bacterial cell membrane. Cd(II) and Cr(VI) bioaccumulation on S27 cell surface was mainly in the form of Cd(OH)₂ and Cr₂O₃, respectively. Further, metabolomic analyses revealed that N-arachidonoyl-l-alanine was the key metabolite that promoted Cd and Cr complexation by S27; it primarily promotes γ-linolenic acid (GLA) metabolism, producing siderophores and coordinating with organic acids to enhance metal bioavailability. To summarize, our results suggest that S27 is promising for the bioremediation of environments contaminated with Cd and Cr in tropical regions.

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.

Bacteria Associated with the Roots of Common Bean (Phaseolus vulgaris L.) at Different Development Stages: Diversity and Plant Growth Promotion

Current agricultural methodologies are vulnerable to erratic climate and are dependent on cost-intensive fertilization to ensure high yields. Sustainable practices should be pursued to ensure food security. Phaseolus vulgaris L. is one of the most produced legumes worldwide and may be an alternative to reduce the environmental impact of meat production as a reliable source of high-quality protein. Plant growth-promoting rhizobacteria (PGPR) are emerging as a sustainable option to increase agricultural production. To understand the dynamics between plants and microorganisms, the culturable microbiota of bean roots was isolated and identified at distinct stages of plant development (early and late vegetative growth, flowering, and pod) and root compartments (rhizoplane, endosphere, and nodules). Diversity and abundance of bacteria associated with root compartments differed throughout the plant life cycle. Bacterial plant growth promotion (PGP) and protection abilities (indole-3-acetic acid production, siderophore synthesis, and antifungal activity) were assessed and associated with plant phenology, demonstrating that among the bacteria associated with plant roots, several strains had an active role in the response to plant biological needs at each stage. Several strains stood out for their ability to display one or more PGP traits, being excellent candidates for efficient stage-specific biostimulants for application in precision agriculture.

The hidden power of secondary metabolites in plant-fungi interactions and sustainable phytoremediation

The global environment is dominated by various small exotic substances, known as secondary metabolites, produced by plants and microorganisms. Plants and fungi are particularly plentiful sources of these molecules, whose physiological functions, in many cases, remain a mystery. Fungal secondary metabolites (SM) are a diverse group of substances that exhibit a wide range of chemical properties and generally fall into one of four main family groups: Terpenoids, polyketides, non-ribosomal peptides, or a combination of the latter two. They are incredibly varied in their functions and are often related to the increased fitness of the respective fungus in its environment, often competing with other microbes or interacting with plant species. Several of these metabolites have essential roles in the biological control of plant diseases by various beneficial microorganisms used for crop protection and biofertilization worldwide. Besides direct toxic effects against phytopathogens, natural metabolites can promote root and shoot development and/or disease resistance by activating host systemic defenses. The ability of these microorganisms to synthesize and store biologically active metabolites that are a potent source of novel natural compounds beneficial for agriculture is becoming a top priority for SM fungi research. In this review, we will discuss fungal-plant secondary metabolites with antifungal properties and the role of signaling molecules in induced and acquired systemic resistance activities. Additionally, fungal secondary metabolites mimic plant promotion molecules such as auxins, gibberellins, and abscisic acid, which modulate plant growth under biotic stress. Moreover, we will present a new trend regarding phytoremediation applications using fungal secondary metabolites to achieve sustainable food production and microbial diversity in an eco-friendly environment.

Responses of diversity and arsenic-transforming functional genes of soil microorganisms to arsenic hyperaccumulator (Pteris vittata L.)/pomegranate (Punica granatum L.) intercropping

Intercropping of arsenic (As) hyperaccumulator (Pteris vittata L.) with crops can reduce the As concentration in soil and the resulting ecological and health risks, while maintaining certain economic benefits. However, it is still unclear how As-transforming functional bacteria and dominant bacteria in the rhizosphere of P. vittata affect the microbial properties of crop rhizosphere soil, as well as how As concentration and speciation change in crop rhizosphere soil under intercropping. This is of great significance for understanding the biogeochemical cycle of As in soil and crops. This study aimed to use high-throughput sequencing and quantitative polymerase chain reaction (qPCR) to analyze the effects of different rhizosphere isolation patterns on the bacterial diversity and the copy number of As-transforming functional genes in pomegranate (Punica granatum L.) rhizosphere soil. The results showed that the abundance of bacteria in the rhizosphere soil of pomegranate increased by 16.3 %, and the soil bacterial community structure significantly changed. C_Alphaproteobacteria and o_Rhizobiales bacteria significantly accumulated in the rhizosphere of pomegranate. The copy number of As methylation (arsM) gene in pomegranate rhizosphere soil significantly increased by 63.37 %. The concentrations of nonspecifically sorbed As (F1), As associated with amorphous Fe (hydr)oxides (F3), and the total As (FT) decreased; the proportion of As (III) in pomegranate rhizosphere soil decreased; and the proportion of As (V) increased in pomegranate rhizosphere soil. c_Alphaproteobacteria and o_Rhizobiales accumulated in crop rhizosphere soil under the intercropping of P. vittata with crops. Also, the copy number of As methylation functional genes in crop rhizosphere soil significantly increased, which could reduce As (III) proportion in crop rhizosphere soil. These changes favored simultaneous agricultural production and soil remediation. The results provided the theoretical basis and practical guidance for the safe utilization of As-contaminated soil in the intercropping of As-hyperaccumulator and cash crops.

Actinomycete Potential as Biocontrol Agent of Phytopathogenic Fungi: Mechanisms, Source, and Applications

Synthetic fungicides have been the main control of phytopathogenic fungi. However, they cause harm to humans, animals, and the environment, as well as generating resistance in phytopathogenic fungi. In the last few decades, the use of microorganisms as biocontrol agents of phytopathogenic fungi has been an alternative to synthetic fungicide application. Actinomycetes isolated from terrestrial, marine, wetland, saline, and endophyte environments have been used for phytopathogenic fungus biocontrol. At present, there is a need for searching new secondary compounds and metabolites of different isolation sources of actinomycetes; however, little information is available on those isolated from other environments as biocontrol agents in agriculture. Therefore, the objective of this review is to compare the antifungal activity and the main mechanisms of action in actinomycetes isolated from different environments and to describe recent achievements of their application in agriculture. Although actinomycetes have potential as biocontrol agents of phytopathogenic fungi, few studies of actinomycetes are available of those from marine, saline, and wetland environments, which have equal or greater potential as biocontrol agents than isolates of actinomycetes from terrestrial environments.

A manganese-oxidizing bacterium-Enterobacter hormaechei strain DS02Eh01: Capabilities of Mn(II) immobilization, plant growth promotion and biofilm formation

While biogenic Mn oxides (BioMnO_x) generated by Mn(II)-oxidizing bacteria (MOB) have attracted increasing attention, a MOB strain isolated from Mn-polluted sediments was identified and assigned as Enterobacter hormaechei DS02Eh01. Its Mn(II) immobilization activity, plant growth-promoting traits, and biofilm formation capability were investigated. The results showed that strain DS02Eh01 was found to be able to tolerate Mn(II) up to 122 mM. The strain immobilized Mn(II) in aquatic media mainly through extracellular adsorption, bio-oxidation and pH-induced precipitation as well as manganese oxidation. DS02Eh01-derived BioMnO_x are negatively charged and have a larger specific surface area (86.70 m²/g) compared to the previously reported BioMnO_x. The strain can immobilize Mn(II) at extreme levels, for instance, when it was exposed to 20 mM Mn(II), about 59% of Mn(II) were found immobilized and 17% of Mn(II) were converted to MnO_x. The SEM and TEM observation revealed that the DS02Eh01-derived BioMnO_x were aggregates doped with granules and microbial pellets. The precipitated Mn(II) and the Mn(III)/Mn(IV) oxides co-existed in BioMnO_x, in which Mn(II) and Mn(IV) were found dominant with Mn(II) accounting for 49.6% and Mn(IV) accounting for 41.3%. DS02Eh01 possesses plant growth-promoting traits and biofilm formation capacity even under Mn(II) exposure. Mn(II) exposure at 5 mM was found to stimulate strain DS02Eh01 to form biofilms, from which, the extracted EPS was mainly composed of aromatic proteins. This study reveals that E. hormaechei strain DS02Eh01 possesses the potential in environmental ecoremediation via coupling processes of macrophytes extraction, biochemical immobilization and biosorption.

Effect of copper stress on Phaseolus coccineus in the presence of exogenous methyl jasmonate and/or Serratia plymuthica from the Spitsbergen soil

Copper stress in the presence of exogenous methyl jasmonate and Serratia plymuthica in a complete trifactorial design with copper (0, 50 µM), methyl jasmonate (0, 1, 10 µM) and Serratia plymuthica (without and with inoculation) was studied on the physiological parameters of Phaseolus coccineus. Copper application reduced biomass and allantoin content, but increased chlorophyll and carotenoids contents as well as catalase and peroxidases activities. Jasmonate did not modify biomass and organic acids levels under copper treatment, but additional inoculation elevated biomass and content of tartrate, malate and succinate. Jasmonate used alone or in combination with bacteria increased superoxide dismutase activity in copper application. With copper, allantoin content elevated at lower jasmonate concentration, but with additional inoculation - at higher jasmonate concentration. Under copper stress, inoculation resulted in higher accumulation of tartrate, malate and citrate contents in roots, which corresponded with lower allantoin concentration in roots. Combined with copper, inoculation reduced catalase and guaiacol peroxidase activities, whereas organic acids content was higher. Under metal stress, with bacteria, jasmonate reduced phenolics content, elevated superoxide dismutase and guaiacol peroxidase activities. The data indicate that jasmonate and S. plymuthica affected most physiological parameters of P. coccineus grown with copper and revealed some effect on biomass.

Characterization of siderophores from Escherichia coli strains through genome mining tools: an antiSMASH study

Although urinary tract infections (UTIs) affect many people, they are usually a disease observed in women. UTIs happen when exogenous and endogenous bacteria enter the urinary tract and colonize there. Cystitis and pyelonephritis occur when bacteria infect the bladder and the kidneys, respectively. UTIs become much serious if the bacteria causing the infection are antibiotic resistant. Since the pathogenic microorganisms have been adopted to current antibiotics via genetic variations, UTIs have become an even more severe health problem. Therefore, there is a great need for the discovery of novel antibiotics. Genome mining of nonpathogenic and pathogenic Escherichia coli strains for investigating secondary metabolites were conducted by the antiSMASH analysis. When the resulting secondary metabolites were examined, it was found that some of the siderophores are effective in UTIs. In conclusion, since the siderophore production in E. coli is directly related to UTIs, these molecules can be a good target for development of future pharmaceutical approaches and compounds. Siderophores can also be used in industrial studies due to their higher chelating affinity for iron.

Genome mining on nonpathogenic and pathogenic E. coli was studied.

Comprehensive and comparative analysis of siderophores were investigated.

The results may open a new gate on the development of new drugs on pathogenic E. coli-based diseases.