Metal homeostasis and resistance in bacteria

Effect of nanomaterials on microbial metabolism and their applications in fermentative hydrogen production: A review

Recent developments in nanomaterial-microbe hybrid systems have combined the unique physicochemical properties of nanomaterials with the biocatalytic capabilities of microorganisms. These hybrid systems have seen extensive use in energy production, particularly in enhancing hydrogen generation. Researchers have incorporated nanomaterials into microbial cultures, achieving significant improvements in the hydrogen production efficiency of microbes across various environments and bacterial strains. However, challenges such as the biological toxicity of nanomaterials pose obstacles to their broader application in microbial energy production. This review examines the effects of nanomaterials on microorganisms, focusing on both their positive and negative effects on microbial growth and metabolism. It also summarizes the applications of nanomaterials in microbial fermentation for hydrogen production. Additionally, it highlights the importance of understanding and balancing these effects when introducing nanomaterials, offering guidance for developing more efficient nanomaterial-microbial hybrid hydrogen production systems.

Molecular insights into cobalt homeostasis in estuarine microphytobenthos: A meta-transcriptomics and biogeochemical approach

Meta-transcriptomics data supported by biofilm physico-chemical parameters unravelled the molecular and biochemical processes utilized by multicomponent intertidal biofilms to endure cobalt toxicity. Findings indicated activation of influx (BtuB, ABC-type transporters) and efflux pumps (RND, CZC) to maintain metal ion homeostasis. Enhanced specific activity of antioxidant enzymes namely catalases and peroxidases (KatG, SodA) mitigated oxidative damage. Heightened synthesis of capsular polysaccharide components, specifically uronic acid and carbohydrate via PEP-CTERM sorting system, wzy pathway and glycosyltransferases protected biofilms against cobalt exposure. Despite chlorophyll biosynthesis genes being upregulated, metal toxicity impeded chlorophyll replenishment. Principal pathways associated with iron acquisition (AfuA), energy metabolism (AtpG), general metabolic activities (FruK, NifD, coABC) and central dogma regulation (DPS, AsrR, RRM) were activated to combat cobalt toxicity. This investigation offered novel insights into the regulatory network employed by intertidal microphytobenthic communities for maintaining cobalt homeostasis and underlined the basis for their application as biomarkers for estuarine cobalt pollution.

Janus PEGylated CuS-engineered Lactobacillus casei combats biofilm infections via metabolic interference and innate immunomodulation

Bacterial implant-associated infections predominantly contribute to the failure of prosthesis implantation. The local biofilm microenvironment (BME), characterized by its hyperacidic condition and high hydrogen peroxide (H2O2) level, inhibits the host's immune response, thereby facilitating recurrent infections. Here, a Janus PEGylated CuS nanoparticle (CuPen) armed engineered Lactobacillus casei (L. casei) denoted as LC@CuPen, is proposed to interfere with bacterial metabolism and arouse macrophage antibiofilm function. Once LC@CuPen reached the BME, NIR irradiation-activated mild heat damages L. casei and biofilm structure. Meanwhile, the BME-responsive LC@CuPen can catalyze local H2O2 to produce toxic •OH, whereas in normal tissues, the effect of •OH production is greatly reduced due to the higher pH and lower H2O2 concentration. The released bacteriocin from damaged L. casei can destroy the bacterial membrane to enhance the penetration of •OH into damaged biofilm. Excessive •OH interferes with normal bacterial metabolism, resulting in reduced resistance of bacteria to heat stress. Finally, under the action of mild heat treatment, the bacterial biofilm lysed and died. Furthermore, the pathogen-associated molecular patterns (PAMPs) in LC@CuPen can induce M1 polarization of macrophages through NF-κB pathway and promote the release of inflammatory factors. Inflammatory factors enhance the migration of macrophages to the site of infection and phagocytose bacteria, thereby inhibiting the recurrence of infection. Generally, this engineered L. casei program presents a novel perspective for the treatment of bacterial implant-associated infections and serves as a valuable reference for future clinical applications of engineered probiotics.

Iron Modulates the Growth and Activity of Nitrate-Dependent Methanotrophic Bacteria by Reprogramming Carbon Metabolism

Iron is indispensable for literally all microorganisms, yet becomes toxic at elevated levels. Protein-based iron storage compartments, such as ferritins, play a key role in maintaining iron homeostasis when the iron level surpasses microbial requirements. However, the energy-intensive nature of iron storage raises questions about how microbes balance this bioprocess between growth and metabolism. Here, using nitrate-dependent methanotrophic bacteria with the simplified metabolic system as a model, we propose a novel metabolic reprogramming pathway regulated by iron storage that controls the balance between growth and activity. Isotopic labeling and meta-omics analyses revealed a striking contrast between bacterial abundance and methane-dependent denitrification activity in "Ca. M. sinica". Using microscopy and energy dispersive spectroscopy, we identified iron-rich nanoparticles within cells exposed to 40 μM Fe2+, alongside increased expression of genes involved in iron metabolism and methane oxidation coupled with denitrification. Additionally, we observed a shift from the energy-demanding Calvin cycle to the more energy-efficient serine pathway for carbon fixation, promoting the synthesis of glycine and succinyl-CoA, which serve as key precursors for iron storage proteins. These metabolic adjustments highlight a strategy for coordinating both substance and energy metabolism in nitrate-dependent methanotrophic bacteria, thereby enhancing their capacity for simultaneous nitrogen and carbon removal. Our findings reveal that iron may act as a metabolic "switch" in microorganisms, offering new insights into the targeted manipulation of microbial metabolism to maximize their beneficial functions in both engineered and natural environments.

Compatibility of intracellular binding: Evolutionary design principles for metal sensors

In the common cellular space, hundreds of binding reactions occur reliably and simultaneously without disruptive mutual interference. The design principles that enable this remarkable compatibility have not yet been adequately elucidated. In order to delineate these principles, we consider the intracellular sensing of transition metals in bacteria-an integral part of cellular metal homeostasis. Protein cytosolic sensors typically interact with metals through three types of lateral chain residues, containing oxygen, nitrogen, or sulfur. The very existence of complete sets of mutually compatible sensors is a nontrivial problem solved by evolution, since each metal sensor has to bind to its cognate metal without being "mismetallated" by noncognate competitors. Here, based solely on theoretical considerations and limited information about binding constants for metal-amino acid interactions, we are able to predict possible "sensor compositions," i.e., the residues forming the binding sites. We find that complete transition-metal sensor sets are severely limited in their number by compatibility requirements, leaving only a handful of possible sensor compositions for each transition metal. Our theoretical results turn out to be broadly consistent with experimental data on known bacterial sensors. If applicable to other cytosolic binding interactions, the results generated by our approach imply that compatibility requirements may play a crucial role in the organization and functioning of intracellular processes.

High-Throughput Tn-Seq Screens Identify Both Known and Novel Pseudomonas putida KT2440 Genes Involved in Metal Tolerance

Industrial and urban activities release toxic chemical waste into the environment. Pseudomonas putida, a soil bacterium, is known to degrade hydrocarbons and xenobiotics, and possesses numerous genes associated with heavy metal tolerance. Most studies on metal tolerance in P. putida focus solely on over- or underexpressed genes, potentially overlooking important genes with unchanged expression. This study employed a Tn-seq approach to identify the essential genes required for P. putida growth under metal stress. This method enables the identification of mutants with altered fitness in the presence of excess metals. The screen successfully identified a number of known genes implicated in metal resistance, including czcA-1, cadA-3, cadR, and pcoA2, thereby validating the approach. Further analyses using targeted mutagenesis and complementation assays revealed PP_5337 as a putative transcriptional regulator involved in copper tolerance and the two-component system RoxSR (PP_0887/PP_0888) as a key determinant of cadmium tolerance. Additionally, PP_1663 and PP_5002 were identified as contributing to cadmium and cobalt tolerance, respectively. This study provides the first evidence linking these genes to metal tolerance, highlighting gaps in our understanding of metal tolerance mechanisms in P. putida and demonstrating the utility of Tn-seq for identifying novel tolerance determinants.

Enhanced methanogenesis of wastewater anaerobic digestion by nanoscale zero-valent iron: Mechanism on intracellular energy conservation and amino acid metabolism

Nanoscale zero-valent iron (nZVI)-mediated anaerobic digestion commonly focuses on electron transfer between syntrophic bacteria, neglecting intracellular energy conservation strategies and amino acid metabolism. In this study, F420H2 dehydrogenase abundance increased by 5.1 %, 27.0 %, and 31.5 % at 10 mM, mM， 30 mM, and 50 mM nZVI dosing, respectively, enabling an efficient transmembrane proton-coupled electron transfer mode. Electron bifurcation (EB) enzymes involved in methanogenesis responded differently to nZVI, with HdrA2B2C2 initially increasing at 10 mM and decreasing at 30 mM and 50 mM, while MvhADG-HdrABC was completely down-regulated. Metabolomics further demonstrated that nZVI reduced riboflavin and flavin mononucleotide content, which is detrimental to the EB. Instead, an alternative measure to maintain electron flow and energy conservation under high nZVI exposure is high expression of ndh and F-type or V/A-type ATPase genes. Additionally, enhancing C1-unit carrier expression through amino acid metabolism regulation emerged as a key strategy. This study provides new perspectives on nZVI-mediated anaerobic digestion.

A novel Zn (II)/Cd (II)/Pb (II)-translocating PIB-type ATPase mediates metal resistance in Chryseobacterium sp. strain PMSZPI in metal-enriched soil of uranium ore deposit

Transition metals at higher concentrations are toxic to the cells. Membrane bound, ATP-driven efflux pumps belonging to the P-type ATPase superfamily maintain metal homeostasis by transporting metals/ions across the biological membranes. A soil bacterium, Chryseobacterium sp. strain PMSZPI, residing in metal enriched environment of uranium ore deposit exhibited high tolerance to multiple heavy metals. In an attempt to unveil one of the molecular determinants of metal resistance in PMSZPI, we characterized an unannotated, novel metal exporting PIB-2-ATPase that was categorized as Zn (II)/Cd (II)/Pb(II) PIB-2-ATPase based on amino-acid sequence alignment and the substrate specificities. The heterologously expressed and purified PIB-2-ATPase exhibited zinc/cadmium/lead dependent ATP hydrolysis activity, ATP dependent phosphorylation and activity inhibition in the presence of vanadate. In-vivo metal tolerance assays and analysis of intracellular metal contents indicated involvement of PIB-2-ATPase in metal efflux. The disordered N-terminal metal binding domain of PIB-2-ATPase was found to be inconsequential for its function. Mutagenesis studies revealed the role of the conserved transmembrane (TM) residues (cysteine, aspartate and lysine) in metal translocation. Overall, our data establishes the vital role of Zn(II)/Cd(II)/Pb(II) PIB-2-ATPase in conferring metal resistance in PMSZPI.

Food, Health, and Environmental Impact of Lactic Acid Bacteria: The Superbacteria for Posterity

Lactic acid bacteria (LAB) are Gram-positive cocci or rods that do not produce spores or respire. Their primary function is to ferment carbohydrates and produce lactic acid. The two primary forms of LAB that are currently recognized are homofermentative and heterofermentative. This review discusses the evolutionary diversity and the biochemical and biophysical conditions required by LAB for their metabolism. Next, it concentrates on the applications of these bacteria in gut health, cancer prevention, and overall well-being and food systems. There are numerous uses for LAB, including the food and dairy sectors, as probiotics to improve human and animal gut-health, as anti-carcinogenic agents, and in food safety as biopreservatives, pathogen inhibitors, and reducers of anti-nutrients in foods. The group included many genera, including Aerococcus, Carnobacterium, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Streptococcus, Tetragenococcus, Vagococcus, and Weissella. Numerous species of Lactobacillus and Bifidobacterium genera as well as other microbes have been suggested as probiotic strains, or live microorganisms added to meals to improve health. LAB can colonize the intestine and take part in the host's physiological processes. This review briefly highlights the role of these bacteria in food safety and security as well as aspects of regulation and consumer acceptance. Finally, the recent innovations in LAB fermentations and the limitations and challenges of the applications of LAB in the food industry are discussed. Notwithstanding recent developments, the study of LAB and their functional components is still an emerging topic of study that has not yet realized its full potential.

Unraveling the genetic basis of microbial metal resistance: Shift from mendelian to systems biology

Microbial metal resistance, a trait that enables microorganisms to withstand high levels of toxic metals, has been studied for over a century. The significance of uncovering these mechanisms goes beyond basic science as they have implications for human health through their connection to microbial pathogenesis, metal bioremediation, and biomining. Recent advances in analytical chemistry and molecular biology have accelerated the discovery and understanding of genetic mechanisms underlying microbial metal resistance, identifying specific metal resistance genes and their operons. The emergence of omics tools has further propelled research towards a comprehensive understanding of how cells respond to metal stress at the systemic level, revealing the complex regulatory networks and evolutionary dynamics that drive microbial adaptation to metal-rich environments. In this article, we present a historical overview of the evolving understanding of the genetic determinants of metal resistance in microbes. Through multiple narrative threads, we illustrate how our knowledge of microbial metal resistance and genetics has interacted with genetic tools and concept development. This review also discusses how our understanding of microbial metal resistance has progressed from the Mendelian perspective to the current systems biology viewpoint, particularly as omics approaches have considerably enhanced our understanding. This system-level understanding has opened new possibilities for genetically engineered microorganisms to regulate metal homeostasis.

Iron-based microbial interactions: the role of iron metabolism in the cheese ecosystem

Iron is involved in various microbial metabolisms and interactions and is an essential micronutrient for most microorganisms. This review focuses on the cheese ecosystem, in which iron is sparse (median concentration of 2.9 mg/kg based on a literature survey) and of limited bioavailability due to the presence of various metal-binding agents in the cheese matrix. Cheese microorganisms overcome this low bioavailability of iron by producing and/or importing ferric iron-specific chelators called siderophores. We introduce these siderophores and their specific transporters, which play a key role in ecological interactions and microbial metabolism. We discuss the impact of iron on all the major taxa (fungi, bacteria, and viruses) and functional groups (starters, ripening microorganisms, and pathogens) present and interacting in cheese, from the community to individual levels. We describe the ways in which cheese-ripening microorganisms use iron and the effects of iron limitation on major metabolic pathways, including the tricarboxylic acid (TCA) cycle and amino-acid biosynthesis. The cheese ecosystem is a relevant in situ model for improving our understanding of iron biochemistry and its putative role in microbe-microbe interactions. Yet, this review highlights critical gaps in our understanding of iron's role in cheese from fundamental ecological and biochemical perspectives to applied microbiology, with broader implications for the quality, safety, and organoleptic properties of cheese.

Distinct response of nitrogen metabolism to exogenous cadmium (Cd) in river sediments with and without Cd contamination history

The role of metal resistance on nitrogen metabolism function and community resilience against Cd is important for elucidating the evolutionary dynamics of key ecological functions in river ecosystems. In this study, the response of nitrogen transforming function to Cd exposure in river sediments from the Yangtze River Basin with varying levels of heavy metal contamination history (Cd-contaminated and Cd-free sediments) was compared to understand how Cd influenced nitrogen metabolism under varying metal resistance conditions. The results showed that chronic and persistent Cd pollution of sediments caused an elevation of transport efflux metal resistance genes (MRGs) and a reduction in the uptake MRGs, leading to a stronger tolerance to Cd for Cd-contaminated sediment than Cd-free ones. Specifically, denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) respectively responded to Cd through different mechanisms. Exogenous Cd (5-100 mg kg-1) influenced denitrification rates (-70 %-100 % deviation to control group) by regulating key genera (Thiobacillus, Magnetospirillum, Sideroxydans etc.) and gene clusters for denitrification. Both adaptive nature of anammox bacteria and co-regulation of key genera (Candidatus_Scalindua, Candidatus_Jettenia, Planctomyces etc.) and gene hzsA were drivers of differential responses in sediments from various contamination history. Environmental factors rather than contamination history, key genera or genes were probably critical ones determining Cd-resistance in DNRA, being more tolerant to Cd in sediments with higher TOC and NH4+. Stimulation of N2O reduction process (genera Gemmatimonas and Gemmatirosa and genes nosZ) in Cd-contaminated sediments by exogenous Cd lowered N2O emission risk, whereas the reverse was true for Cd-free sediments. These results enrich our understanding about the linkages among MRGs and nitrogen reduction functions in river.

Molecular basis of protein-DNA interactions between Halalkalibacterium halodurans MntR and its DNA operator sequence

Transition metals such as iron, zinc and manganese are essential for bacterial survival. A pivotal role in regulation of manganese homeostasis in bacterium Halalkalibacterium halodurans has MntR protein (HhMntR). In this work, molecular dynamics simulations of holoprotein (with Mn2+) and apoprotein (without Mn2+) HhMntR in complex with DNA mntA operator were conducted and enabled understanding of interaction between HhMntR and DNA on molecular level. Molecular mechanism through which affinity of HhMntR towards DNA is increased upon Mn2+ binding was revealed. Holoprotein binds DNA through stable and consistent noncovalent interactions, while apoprotein shows highly dynamic behavior, attaching to and detaching from the DNA backbone and inner grooves on a nanosecond time scale. The same observations are seen even during the simulations that started with protein and DNA separated from the complex. Additionally, key amino acids involved in the formation of the HhMntR-DNA complex were identified, leading to the proposal of a molecular framework that allows HhMntR to perform its biological function as a transcription factor. Overall, observed behaviors promote the lateral movement of HhMntR along the DNA sequence, enabling the protein to remain close to the DNA while it seeks out specific base pairs for strong binding upon activation by Mn2+.

Heme and iron limitation in a GI-tract foundation species leads to a reshuffling of the metalloproteome and a shift toward manganese usage

The metal-binding complement of the cellular proteome (the metalloproteome) depends on metal availability in the cellular environment and drives cellular metabolism. Bacteroides thetaiotaomicron (Bacteroides theta) is a foundational species in the anaerobic gut microbiome and a heme auxotroph, though little is known about why it requires heme. We hypothesized that B. theta would overproduce heme-binding proteins in response to limitations in non-heme iron, and reciprocally, activate non-heme iron pathways when heme was growth limiting. Here we showed that heme and/or non-heme iron scarcity triggers a more holistic reorganization of its metallome and metalloproteome. Under non-heme iron limitation induced by an Fe(II)-specific chelator, manganese supplementation restored growth, suggesting manganese can partly compensate for non-heme iron. Metalloproteomic analyses using tandem HPLC-ICP-MS revealed significant changes in the distribution of zinc, manganese, and iron in response to varying iron or heme availability. These findings highlight the interplay between heme/non-heme iron and the metallome in bacterial growth regulation, and they underscore a role for manganese under iron scarcity.

Lead (Pb2+) biosorption and bioaccumulation efficiency of Enterobacter chuandaensis DGI-2: Isotherm, kinetics and mechanistic study for bioremediation

Heavy metal (HM) contamination, particularly lead (Pb²⁺), threatens environmental and agricultural sustainability, necessitating effective remediation strategies. This study evaluates the Pb²⁺ sequestration potential of Enterobacter chuandaensis DGI-2, an HM-tolerant rhizobacterium isolated from a Pb-contaminated rhizosphere. DGI-2 exhibited high Pb²⁺ removal efficiency, achieving 94.73 % removal at 100 µg/mL and 69.09 % at 750 µg/mL over 96 h, primarily through cell surface and exopolysaccharide (EPS) adsorption. Biosorption studies demonstrated higher Pb²⁺ uptake in living biomass (102.95 mg/g, 68.63 %) than in dead biomass (98.61 mg/g, 65.74 %) under controlled conditions (0.5 g/L biomass, pH-6.5, 720 min). Mechanistic analyses revealed that Pb²⁺ adsorption primarily involved interactions with -OH, -COOH, and -PO₄³ ⁻ functional groups, facilitated by multilayer sorption, complexation, and ion exchange. Moreover, a 210.66 % increase in phosphatase activity promoted Pb²⁺ precipitation, forming stable Pb-phosphate minerals (e.g., Pb₅(PO₄)₃Cl, Pb₁₀(PO₄)₆(OH)₂), as confirmed by X-ray diffraction (XRD), significantly contributing to Pb sequestration. Regeneration studies demonstrated the biomass' reusability over four cycles. Soil microcosm experiments showed an 11.7-13.1 % reduction in bioavailable Pb, with greater stabilization in non-sterile soils, suggesting synergistic effects with native microbiota. Additionally, DGI-2 exhibited plant growth-promoting (PGP) traits, reducing phytotoxicity, enhancing soil health and phytostabilization potential, positioning it as a sustainable biosorbent for Pb²⁺ remediation.

Antibiotic-free responsive biomaterials for specific and targeted Helicobacter pylori eradication

Gastric cancer is highly correlated with Helicobacter pylori (H. pylori) infection. Approximately 50 % of the population worldwide is infected with H. pylori. However, current treatment regimens face severe challenges including drug resistance and gut microbiota disruption. An integrative treatment with slight negative influences on intestinal flora, conforming with concepts of integrative prevention of gastric cancer, is urgently needed. Non-antibiotic responsive biomaterials can respond to different stimuli, including pH, enzymes, light, ultrasound and magnetism, under which biomaterials are specifically activated to perform antibacterial capabilities, while neutral intestinal microenvironments differ from gastric microenvironments or inflammatory sites and have no or minimal irradiation via precisely controlled exogenous stimuli, which may not only overcome antibiotic resistance but also avoid gut microbiota disorders. First, the latest progress in responsive biomaterials against H. pylori without gut microbiome disturbance and their anti-H. pylori performances are profoundly summarized. Second, the mechanisms against planktonic bacteria, biofilms and intracellular bacteria are discussed respectively. Finally, the strategies of specific and targeted H. pylori elimination by responsive biomaterials are introduced. Additionally, the challenges and the focus of future research on translation into clinical application are fully proposed. Antibiotic-free responsive biomaterials for specific and targeted H. pylori eradication represent an innovative approach.

Structural basis for transcription activation through cooperative recruitment of MntR

Bacillus subtilis MntR is a dual regulatory protein that responds to heightened Mn2+ availability in the cell by both repressing the expression of uptake transporters and activating the expression of efflux proteins. Recent work indicates that, in its role as an activator, MntR binds several sites upstream of the genes encoding Mn2+ exporters, leading to a cooperative response to manganese. Here, we use cryo-EM to explore the molecular basis of gene activation by MntR and report a structure of four MntR dimers bound to four 18-base pair sites across an 84-base pair regulatory region of the mneP promoter. Our structures, along with solution studies including mass photometry and in vivo transcription assays, reveal that MntR dimers employ polar and non-polar contacts to bind cooperatively to an array of low-affinity DNA-binding sites. These results reveal the molecular basis for cooperativity in the activation of manganese efflux.

Rational design of peptides to overcome drug resistance by metabolic regulation

Chemotherapy is widely used clinically, however, its efficacy is often compromised by the development of drug resistance, which arises from prolonged administration of drugs or other stimuli. One of the driven causes of drug resistance in tumors or bacterial infections is metabolic reprogramming, which alters mitochondrial metabolism, disrupts metabolic pathways and causes ion imbalance. Bioactive peptide materials, due to their biocompatibility, diverse bioactivities, customizable sequences, and ease of modification, have shown promise in overcoming drug resistance. This review provides an in-depth analysis of metabolic reprogramming and associated microenvironmental changes that contribute to drug resistance in common tumors and bacterial infections, suggesting potential therapeutic targets. Additionally, we explore peptide-based materials for regulating metabolism and their potential synergic effect with other therapies, highlighting the mechanisms by which these peptides reverse drug resistance. Finally, we discuss future perspectives and the clinical challenges in peptide-based treatments, aiming to offer insights for overcoming drug-resistant diseases.

Characterization of antibiotic determinants and heavy metal resistance genes in Escherichia coli from pigs in Catalonia

More antibiotics are administered to livestock animals than to treat human infections. Industrialization, large animal densities and early weaning mean pigs are exposed to more antibiotics than any other livestock animal. Consequently, antimicrobial resistance (AMR) is common among commensal and pathogenic bacteria. Heavy metals (HMs) are also often used as feed additives for growth promotion and infection prevention alongside antimicrobials, and increased exposure to copper, zinc and cadmium can further encourage AMR through co-selection. In this study, we sequenced an archived collection of 112 Escherichia coli isolates from pigs in Catalonia using short- and long-read sequencing methods to detect AMR and HM tolerance genes. The most common AMR genes were mdfA (84.8%), aph(3″)-Ib (52.7%), bla TEM-1B (45.6%) and aph(6)-Id (45.6%). Genes relevant to public health, such as the extended-spectrum β-lactamases (15.4%), bla CTX-M type or bla SHV, or mobile colistin resistance (mcr) genes (13.4%), such as mcr-1, were also found. HM tolerance genes were present in almost every genome but were rarely located in plasmids, and, in most cases, AMR and HM tolerance genes were not located on the same plasmids. Of the genes predicted to increase tolerance to HMs, only those with activity to mercury were co-located on plasmids alongside other AMR determinants. However, mercury is rarely used in pig farming and does not support a scenario where AMR and HM genes are co-selected. Finally, we identified the exclusive association between mcr-4 and ColE10 plasmid, which may help target interventions to curtail its spread among pig Escherichia coli.

Biosynthesis of Gold Nanostructures and Their Virucidal Activity Against Influenza A Virus

Bacteria in natural environments often encounter high concentrations of metal ions, leading to the development of defense mechanisms such as chemical reduction. This process can result in the formation of nanostructures (NS) ranging from 1-100 nm, which have valuable properties for various applications, including as virucidal agents. Currently, metallic NS with virucidal activity are used in disinfectants and surface protection products. However, their production mainly relies on physical and chemical methods, which are often complex, toxic, and energy-intensive. A sustainable alternative is the biosynthesis of nanostructures. Our research focuses on the biosynthesis of gold nanostructures (AuNS) using environmental bacteria and their proteins, with the aim of exploring their potential as agents to destroy the influenza A virus. We screened bacteria under conditions with HAuCl4, identifying eight microorganisms capable of growing in high gold concentrations. Staphylococcus haemolyticus BNF01 showed the highest resistance and Au(III) reduction, growing up to 0.25 mM in HAuCl4. Bioinformatic analysis revealed five proteins with potential Au(III)-reductase activity, which were cloned and expressed in Escherichia coli. These proteins reduced gold to form AuNPs, which were purified, characterized for size, shape, and surface charge, and tested against influenza A, showing significant virucidal effects, likely due to interactions with viral proteins.

Synergistic effects of indigenous bacterial consortia on heavy metal tolerance and reduction

Heavy metal contamination represents a critical environmental and public health challenge, necessitating effective remediation approaches. This study examines the bioremediation potential of three indigenous bacterial strains Aeromonas caviae KQ_21, Aeromonas hydrophila AUoR_24, and Shewanella putrefaciens SUoR_24 evaluated both individually and in consortia for their capacity to remove heavy metals. Tolerance assessments demonstrated that the coculture of these strains exhibited superior resistance to copper (Cu), zinc (Zn), and nickel (Ni), with optimal growth observed up to 6 mM for Cu, 9 mM for Zn, and 5 mM for Ni, outperforming the monocultures. The co-culture system also achieved higher metal reduction efficiencies, with reductions of 47.02% for Cu, 61.49% for Ni, and 61.93% for Zn, in contrast to lower reductions observed in individual strains. The study further explored the impact of environmental conditions on bioremediation efficiency. Optimal temperature for both monoculture and coculture setups was found to be 30 °C. pH and salt concentration variations significantly affected bacterial growth and metal reduction, highlighting the necessity of tailored conditions for enhanced bioremediation. In terms of metal removal mechanisms, the results demonstrated that nickel (Ni) removal occurred primarily through bioaccumulation, while copper (Cu) removal involved both biosorption and bioaccumulation. Zinc (Zn) removal was facilitated through biosorption, bioaccumulation, and biotransformation. These findings underscore the effectiveness of bacterial consortia, particularly indigenous strains, in improving heavy metal tolerance and reduction through synergistic interactions and cooperative metabolic processes. This research offers valuable insights into optimizing bacterial consortia for environmental cleanup and advances the application of indigenous bacteria in bioremediation strategies. Future investigations should focus on exploring additional microbial species and further elucidating the molecular mechanisms that contribute to enhanced bioremediation efficacy.

First evidence of off-flavour haloanisoles production by dormant fungal spores in drinking water: Formation pattern, influencing factors and transcriptome analysis

Fungi are major producers of off-flavour haloanisoles (HAs) in drinking water supply systems. However, evidence of HA production by dormant fungal spores remains unclear. This study investigated the microbial O-methylation of dormant spores of a fungus Aspergillus sp. from drinking water treatment plants. Dormant spores were capable of O-methylating 2,4,6-trichlorophenol (2,4,6-TCP) to produce 2,4,6-trichloroanisole (2,4,6-TCA). A pronounced linear correlation was identified between the precursor load and the 2,4,6-TCA formation capability, with a function lg(y)= 0.542lg(x) - 4.28 (R2 = 0.838). The effects of metal ions on fungal spore O-methylation were multifaceted and highly concentration-dependent. Natural organic matters could inhibit 2,4,6-TCA formation. NH2Cl presented higher efficacy than free chlorine in inhibiting spore O-methylation. However, O-methylation inhibition rates were lower than spore inactivation rates, suggesting spores in viable but non-culturable state still possessed partial ability to form 2,4,6-TCA. Transcriptome analysis revealed that 50 nM 2,4,6-TCP treatment had no impact on the spore's transcriptional profile, whereas 1 mM Cu2+ treatment significantly inhibited O-methylation process by down-regulating genes involved in ATP generation. This study provides a first evidence that dormant fungal spores are capable of producing 2,4,6-TCA, raising concerns about the potential off-flavour risk and the development of targeted control strategies in drinking water systems.

Nanozyme-Based Strategies against Bone Infection

Nanozymes are a class of nanomaterials that exhibit catalytic functions analogous to those of natural enzymes. They demonstrate considerable promise in the biomedical field, particularly in the treatment of bone infections, due to their distinctive physicochemical properties and adjustable catalytic activities. Bone infections (e.g., periprosthetic infections and osteomyelitis) are infections that are challenging to treat clinically. Traditional treatments often encounter issues related to drug resistance and suboptimal anti-infection outcomes. The advent of nanozymes has brought with it a new avenue of hope for the treatment of bone infections.

Enrichment, Isolation and Characterization of Heavy Metal-Tolerant Bacteria from Polar Lacustrine Sediments

Polar areas are not exempt from anthropogenic pollution. Heavy metals have been detected in Arctic and Antarctic lakes. Bacteria, at the base of the food web, can possess the ability to adsorb or immobilize heavy metals in the environment and reduce their concentration in the water column. However, several gaps exist in our knowledge of bacterial tolerance to heavy metals in polar systems, especially in lakes. Heavy metal-tolerant bacteria from polar lacustrine sediments were selectively enriched and subsequently isolated and identified. Their growth at increasing concentrations of different heavy metals (iron, copper, and mercury) was evaluated. Selected isolates were tested for sequestration of iron and mercury. A total of 101 bacterial isolates were obtained from metal-enriched cultures. Gammaproteobacteria and Actinomycetota isolates were most abundant in Arctic and Antarctic enrichments, respectively. Iron was the most tolerated metal. Mercury and iron were sequestered by the isolates by up to 14.2 and 13.4%, respectively. The results from this study contribute to our understanding of heavy metal-tolerant bacteria from cold environments and their potential use in biotechnological applications.

Metals in Motion: Understanding Labile Metal Pools in Bacteria

Metal ions are essential for all life. In microbial cells, potassium (K+) is the most abundant cation and plays a key role in maintaining osmotic balance. Magnesium (Mg2+) is the dominant divalent cation and is required for nucleic acid structure and as an enzyme cofactor. Microbes typically require the transition metals manganese (Mn), iron (Fe), copper (Cu), and zinc (Zn), although the precise set of metal ions needed to sustain life is variable. Intracellular metal pools can be conceptualized as a chemically complex mixture of rapidly exchanging (labile) ions, complemented by those reservoirs that exchange slowly relative to cell metabolism (sequestered). Labile metal pools are buffered by transient interactions with anionic metabolites and macromolecules, with the ribosome playing a major role. Sequestered metal pools include many metalloproteins, cofactors, and storage depots, with some pools redeployed upon metal depletion. Here, I review the size, composition, and dynamics of intracellular metal pools and highlight the major gaps in understanding.

Structurally distinct manganese-sensing riboswitch aptamers regulate diverse expression platform architectures

Manganese (Mn)-sensing riboswitches protect bacteria from Mn toxicity by upregulating expression of Mn exporters. The Mn aptamers share key features but diverge in other important elements, including within the metal-binding core. Although X-ray crystal structures of isolated aptamers exist, these structural snapshots lack crucial details about how the aptamer communicates the presence or absence of ligand to the expression platform. In this work, we investigated the Mn-sensing translational riboswitches in E. coli ( mntP and alx ), which differ in aptamer secondary structure, nucleotide sequence, and pH-dependence of Mn response. We performed co-transcriptional RNA chemical probing, allowing us to visualize RNA folding intermediates that form and resolve en route to the final folded riboswitch. For the first time, we report that sampling of metal ions by the RNA begins before the aptamer synthesis and folding are complete. At a single-nucleotide resolution, we pinpoint the transcription window where "riboswitching" occurs in response to Mn binding and uncover key differences in how the alx and mntP riboswitches fold. Finally, we describe riboswitch-specific effects of pH, providing insights into how two members of the same riboswitch family differentially sense two distinct environmental cues: concentration of Mn and pH.

GRAPHICAL ABSTRACT

Metal compounds as antimicrobial agents: 'smart' approaches for discovering new effective treatments

Due to their considerable chemical diversity, metal compounds are attracting increasing and renewed attention from the scientific and medical communities as potential antimicrobial agents to combat the growing problem of antibiotic resistance. The development of metal compounds as antimicrobial agents typically follows classical drug discovery procedures and suffers from the same problems; indeed, these procedures can be very expensive and time-consuming, and carry an intrinsically high risk of failure. Here, we show how some established drug discovery approaches can be conveniently and successfully applied to antimicrobial metal compounds to provide some shortcuts for faster clinical translation of new treatments. Specifically, we refer to (i) drug repurposing, (ii) drug combination and (iii) drug targeting by bioconjugation; some relevant examples will be illustrated.

Changes of shrimp myofibrillar proteins hydrolyzed by Virgibacillus proteases: Structural characterization, mechanism visualization, and flavor compound formation

To explore the mechanism of Virgibacillus proteases on hydrolysis of shrimp myofibrillar protein (SMP) and formation of volatile compounds, the fermented broth of Virgibacillus halodenitrificans was purified and the protease was identified as peptidase S8. The enzyme had optimum activity at pH 7.0-8.5 and 40-50 °C, and showed good stability at pH 6.5-8.5 and 20-50 °C. The enzyme showed certain salt and metal ion tolerance. Inhibitor results indicated that the enzyme might belong to the serine protease family. V. halodenitrificans proteases (BP) had a stronger ability to degrade SMP compared to Bacillus subtilis proteases (BS). After 60 min of hydrolysis, the hydrolysis index and surface hydrophobicity value of the BP sample were 36.7 % and 177.5 higher than those of the BS sample, respectively. Various spectral measurement results showed that the structural conformation of the BP-treated SMP was significantly changed, with a smaller particle size (510.4 nm) and a lower zeta potential (-27.7 mV). Molecular docking results showed that the enzyme had the highest degradation capacity for myofibrillar heavy chains, followed by actin, and the lowest for myofibrillar light chains, with the interaction forces being hydrogen bonding and hydrophobic interactions. In addition, BP-treated SMP had higher levels of peptides, small molecular weight peptides (<1 kDa), and umami amino acids compared to the BS sample. Solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) results showed that BP hydrolysates contained more volatile compounds and key volatile compounds than BS hydrolysates. Pyrazines and alcohols were the main volatile flavor compounds in BS and BP hydrolysates, respectively.

Control of iron acquisition by multiple small RNAs unravels a new role for transcriptional terminator loops in gene regulation

Small RNAs (sRNAs) controlling gene expression by imperfect base-pairing with mRNA(s) are widespread in bacteria. They regulate multiple genes, including genes involved in iron homeostasis, through a wide variety of mechanisms. We previously showed that OmrA and OmrB sRNAs repress the synthesis of the Escherichia coli FepA receptor for iron-enterobactin complexes. We now report that five additional sRNAs, namely RprA, RybB, ArrS, RseX and SdsR, responding to different environmental cues, also repress fepA, independently of one another. While RprA follows the canonical mechanism of pairing with the translation initiation region, repression by ArrS or RseX requires a secondary structure far upstream within the long fepA 5' untranslated region. We also demonstrate a dual action of SdsR, whose 5'-part pairs with the fepA translation initiation region while its 3'-end behaves like ArrS or RseX. Strikingly, mutation analysis shows a key role for the loops of these sRNAs' intrinsic terminators in the regulation. Furthermore, regulation depends on both the Hfq chaperone and the RNase E endonuclease. Overall, our data strongly suggest that FepA levels must be tightly controlled under a variety of conditions and highlight the diversity of mechanisms that underly the regulation of gene expression by sRNAs in bacteria.

Pathogenicity and virulence of Acinetobacter baumannii: Factors contributing to the fitness in healthcare settings and the infected host

Acinetobacter baumannii is a common cause of healthcare-associated infections and hospital outbreaks, particularly in intensive care units. Much of the success of A. baumannii relies on its genomic plasticity, which allows rapid adaptation to adversity and stress. The capacity to acquire novel antibiotic resistance determinants and the tolerance to stresses encountered in the hospital environment promote A. baumannii spread among patients and long-term contamination of the healthcare setting. This review explores virulence factors and physiological traits contributing to A. baumannii infection and adaptation to the hospital environment. Several cell-associated and secreted virulence factors involved in A. baumannii biofilm formation, cell adhesion, invasion, and persistence in the host, as well as resistance to xeric stress imposed by the healthcare settings, are illustrated to give reasons for the success of A. baumannii as a hospital pathogen.

Single cell-inductively coupled plasma-mass spectrometry (SC-ICP-MS) reveals metallic heterogeneity in a macrophage model of infectious diseases

Single cell-inductively coupled plasma-mass spectrometry (SC-ICP-MS) offers an attractive option for rapidly measuring trace metal heterogeneity at the single cell level. Chemical fixation has been previously applied to mammalian cells prior to sample introduction so that they can be resuspended in a solution suitable for SC-ICP-MS. However, the effect of fixation on the elemental composition of suspended cells is unknown, and robust methodologies are urgently needed so that the community can measure the effects of intracellular pathogens on elemental composition of their host cells. We demonstrate that different fixatives impact measured cell elemental composition. We have compared suspensions treated using different fixatives (methanol 60-100% in H2O and 4% paraformaldehyde in phosphate-buffered saline solution), and the number of distinguishable single cell events, keeping a constant particle number concentration. Significantly more single cell events (n = 3, P ≤ 0.05) were observed for Ca and Mg when cells were fixed in 4% paraformaldehyde than for the methanol-based fixatives, confirming the hypothesis that methanol fixatives cause leaching of these elements from the cells. The impact of fixation on Mn and Zn was less pronounced. Microbial and viral infection of eukaryotic cells can have profound effects on their elemental composition, but chemical fixation is necessary to render infected cells safe before analysis. We have successfully applied our methodology to a macrophage model of tuberculosis demonstrating utility in understanding metal homeostasis during microbial infection of mammalian cells.

Adaptation to zinc restriction in Streptococcus agalactiae: role of the ribosomal protein and zinc-importers regulated by AdcR

Zinc (Zn) is an essential cofactor for numerous bacterial proteins and altering Zn availability is an important component of host innate immunity. During infection, adaptation to both Zn deprivation and excess is critical for pathogenic bacteria development. To understand the adaptive responses to Zn availability of Streptococcus agalactiae, a pathogen causing invasive infections of neonates, global transcriptional profiling was conducted. Results highlight that in response to Zn limitation, genes belonging to the AdcR regulon, the master regulator of Zn homeostasis in streptococci, were overexpressed. Through a combination of in silico analysis and experimental validation, new AdcR-regulated targets were identified. Among them, we identified a duplicated ribosomal protein, RpsNb, and an ABC transporter, and examined the role of these genes in bacterial growth under Zn-restricted conditions. Our results indicated that, during Zn restriction, both the RpsNb protein and a potential secondary Zn transporter are important for S. agalactiae adaptation to Zn deficiency.

IMPORTANCE

Streptococcus agalactiae is a bacterial human pathobiont causing invasive diseases in neonates. Upon infection, S. agalactiae is presented with Zn limitation and excess but the genetic systems that allow bacterial adaptation to these conditions remain largely undefined. A comprehensive analysis of S. agalactiae global transcriptional response to Zn availability shows that this pathogen manages Zn limitation mainly through upregulation of the AdcR regulon. We demonstrate that several AdcR-regulated genes are important for bacterial growth during Zn deficiency, including human biological fluids. Taken together, these findings reveal new mechanisms of S. agalactiae adaptation under conditions of metal deprivation.

Inactivation of bacteria using synergistic hydrogen peroxide with split-dose nanosecond pulsed electric field exposures

The use of pulsed electric fields (PEF) as a nonthermal technology for the decontamination of foods is of growing interest. This study aimed to enhance the inactivation of Escherichia coli, Listeria innocua, and Salmonella enterica in Gomori buffer using a combination of nsPEF and hydrogen peroxide (H2O2). Three sub-MIC concentrations (0.1, 0.3, and 0.5%) of H2O2 and various contact times ranging from 5-45 min were tested. PEF exposures as both single (1000 pulse) and split-dose (500+500 pulse) trains were delivered via square-wave, monopolar, 600 ns pulses at 21 kV/cm and 10 Hz. We demonstrate that >5 log CFU/mL reduction can be attained from combination PEF/H2O2 treatments with a 15 min contact time for E. coli (0.1%) and a 30 min contact time for L. innocua and S. enterica (0.5%), despite ineffective results from either individual treatment alone. A 5 log reduction in microbial population is generally the lowest acceptable level in consideration of food safety and represents inactivation of 99.999% of bacteria. Split-dose PEF exposures enhance lethality for several tested conditions, indicating greater susceptibility to PEF after oxidative damage has occurred.

The Coexistence of Klebsiella pneumoniae and Candida albicans Enhanced Biofilm Thickness but Induced Less Severe Neutrophil Responses and Less Inflammation in Pneumonia Mice Than K. pneumoniae Alone

Due to the possible coexistence of Klebsiella pneumoniae (KP) and Candida albicans (CA), strains of KP and CA with biofilm production properties clinically isolated from patients were tested. The production of biofilms from the combined organisms (KP+CA) was higher than the biofilms from each organism alone, as indicated by crystal violet and z-stack immunofluorescence. In parallel, the bacterial abundance in KP + CA was similar to KP, but the fungal abundance was higher than CA (culture method), implying that CA grows better in the presence of KP. Proteomic analysis was performed to compare KP + CA biofilm to KP biofilm alone. With isolated mouse neutrophils (thioglycolate induction), KP + CA biofilms induced less prominent responses than KP biofilms, as determined by (i) neutrophilic supernatant cytokines (ELISA) and (ii) neutrophil extracellular traps (NETs), using immunofluorescent images (neutrophil elastase, myeloperoxidase, and citrullinated histone 3), peptidyl arginine deiminase 4 (PAD4) expression, and cell-free DNA. Likewise, intratracheal KP + CA in C57BL/6 mice induces less severe pneumonia than KP alone, as indicated by organ injury (serum creatinine and alanine transaminase) (colorimetric assays), cytokines (ELISA), bronchoalveolar lavage fluid parameters (bacterial culture and neutrophil abundances using a hemocytometer), histology score (H&E stains), and NETs (immunofluorescence on the lung tissue). In conclusion, the biofilm biomass of KP + CA was mostly produced from CA with less potent neutrophil activation and less severe pneumonia than KP alone. Hence, fungi in the respiratory tract might benefit the host in some situations, despite the well-known adverse effects of fungi.

Cholesterol metabolism and intrabacterial potassium homeostasis are intrinsically related in Mycobacterium tuberculosis

Potassium (K+) is the most abundant intracellular cation, but much remains unknown regarding how K+ homeostasis is integrated with other key bacterial biology aspects. Here, we show that K+ homeostasis disruption (CeoBC K+ uptake system deletion) impedes Mycobacterium tuberculosis (Mtb) response to, and growth in, cholesterol, a critical carbon source during infection, with K+ augmenting activity of the Mtb ATPase MceG that is vital for bacterial cholesterol import. Reciprocally, cholesterol directly binds to CeoB, modulating its function, with a residue critical for this interaction identified. Finally, cholesterol binding-deficient CeoB mutant Mtb are attenuated for growth in lipid-rich foamy macrophages and in vivo colonization. Our findings raise the concept of a role for cholesterol as a key co-factor, beyond its role as a carbon source, and illuminate how changes in bacterial intrabacterial K+ levels can act as part of the metabolic adaptation critical for bacterial survival and growth in the host.

Investigating MerR's Selectivity: The Crosstalk Between Cadmium and Copper Under Elevated Stress Conditions

Bacteria respond to metal pollution through sensors that control the uptake and the detoxification machineries. Specificity in metal recognition is therefore a prerequisite for triggering the appropriate response, particularly when facing a mixture of metals. In response to Cu+, the purple bacterium Rubrivivax gelatinosus induces the efflux Cu+-ATPase CopA by the Cu+ regulator CopR. However, genetic analyses have suggested the presence of additional regulators. Here, we show that CadR, the Cd2+ sensor, is involved in Cd2+ and Cu+ tolerance and demonstrate that CopR and CadR share common target genes. Interestingly, expression of the Cu+ detoxification and efflux (CopI/CopA) system was induced by Cd2+ and downregulated in the double mutant copRcadR-. This double mutant was more sensitive to low Cu+ concentration than the single copR- mutant, and accumulation of coproporphyrin III pointed to a significantly decreased expression of CopA. Furthermore, analyses of Cd2+ toxicity in the cadR- mutant suggested that although CopR is Cu+ selective, CopR is involved in Cd2+ response since the addition of Cu+ alleviates Cd2+ toxicity. Based on our current knowledge of metal transport across the inner membrane, Cd2+ and Cu+ do not share common efflux routes nor do they share common regulators. Nevertheless, the crosstalk between Cd2+ and Cu+ tolerance systems is demonstrated in the present study. The modulation of Cu+ detoxification by a Cd2+ regulator in vivo places emphasis on the relaxed selectivity, under elevated metal concentration, in MerR regulators.

The Effects of Seed Inoculation with Bacterial Biofilm on the Growth and Elemental Composition of Tomato (Solanum lycopersicum L.) Cultivated on a Zinc-Contaminated Substrate

Biofilm obtained from Bacillus subtilis subsp. spizizenii inoculated on vegetable seeds has been shown to have plant growth-promoting capacity. Seed inoculation with biofilm produced by this strain could also reduce the adverse effects on plant growth caused by soil or substrate heavy metal overabundance. Therefore, the objective of this work was to evaluate the impact of biofilm inoculated on tomato (Solanum lycopersicum L.) seeds, which were planted on a substrate with artificially added zinc. First, seeds of the Río Grande tomato variety were exposed to increasing zinc concentrations, namely: 50, 100, 200, and 400 ppm, with and without bacterial biofilm inoculation. Zinc addition and seed inoculation affected germination parameters. For example, an extra 200 and 400 ppm of zinc led to high toxicity. Biofilm inoculation, however, reduced the noxious effects of excess zinc, bringing acute toxicity down to moderate. Then, tomato plants growing from inoculated and non-inoculated seeds were cropped for 4 months in both substrates with 400 ppm zinc and without added zinc. Extra zinc addition significantly (p < 0.05) reduced tomato root and shoot biomass, plant height, and fruit number at harvest time. However, seed biofilm inoculation avoided the harmful effect of zinc on plant growth parameters, fruit yield, and fruit quality. The roots and shoots of plants growing on contaminated substrates showed very noticeable increases in zinc levels compared to the control, while fruits only showed a much weaker zinc gain, even if this was significant (p < 0.05). Moreover, root shoot and fruit concentrations of elements other than zinc, (nitrogen, phosphorus, potassium, calcium, magnesium, sulfur, iron, manganese, copper, lead, and cadmium) were not or only weakly affected by the addition of this metal to the substrate. In summary, the biofilm of B. subtilis proved to be effective as a bioinoculant to alleviate negative effects on tomatoes cropped in a substrate with excess zinc.

Methanobactins: Structures, Biosynthesis, and Microbial Diversity

Methanobactins (Mbns) are ribosomally synthesized and posttranslationally modified peptide natural products released by methanotrophic bacteria under conditions of copper scarcity. Mbns bind Cu(I) with high affinity via nitrogen-containing heterocycles and thioamide groups installed on a precursor peptide, MbnA, by a core biosynthetic enzyme complex, MbnBC. Additional stabilizing modifications are enacted by other, less universal biosynthetic enzymes. Copper-loaded Mbn is imported into the cell by TonB-dependent transporters called MbnTs, and copper is mobilized by an unknown mechanism. The machinery to biosynthesize and transport Mbn is encoded in operons that are also found in the genomes of nonmethanotrophic bacteria. In this review, we provide an update on the state of the Mbn field, highlighting recent discoveries regarding Mbn structure, biosynthesis, and handling as well as the emerging roles of Mbns in the environment and their potential use as therapeutics.

Metalation of Extracytoplasmic Proteins and Bacterial Cell Envelope Homeostasis

Cell physiology requires innumerable metalloenzymes supported by the selective import of metal ions. Within the crowded cytosol, most enzymes acquire their cognate cofactors from a buffered labile pool. Metalation of membrane-bound and secreted exoenzymes is more problematic since metal concentrations are highly variable outside the cell. Here, we focus on metalloenzymes involved in cell envelope homeostasis. Peptidoglycan synthesis often relies on Zn-dependent hydrolases, and metal-dependent β-lactamases play important roles in antibiotic resistance. In gram-positive bacteria, lipoteichoic acid synthesis requires Mn, with TerC family Mn exporters in a supporting role. For some exoenzymes, metalation occurs in the cytosol, and metalated enzymes are exported through the TAT secretion system. For others, metalation is facilitated by metal exporters, metallochaperones, or partner proteins that enhance metal affinity. To help ensure function, some metalloenzymes can function with multiple metals. Thus, cells employ a diversity of strategies to ensure metalation of enzymes functioning outside the cytosol.

Changes in Cd forms and Cd resistance genes in municipal sludge during coupled earthworm and biochar composting

There is a close relationship between microbial activity and the bioavailability of heavy metals, and heavy metal resistance genes can affect the activity of heavy metals. To evaluate the effects of coupled earthworm and biochar composting on Cd forms and Cd resistance genes in sludge, the BCR continuous extraction method was applied to classify the Cd forms, and Cd resistance genes were quantitatively determined with heavy metal gene chip technology. The results showed that the changes in earthworm biomass during composting were sufficiently fitted by logistic models and that adding biochar effectively increased earthworm biomass. The coupled treatment of earthworms and biochar promoted the degradation of sludge. The coupled treatment of earthworms and biochar reduced the proportion of acid-extractable and reducible Cd relative to total Cd, increased the proportion of oxidized and residual Cd relative to total Cd, transformed Cd forms from active to inert, and reduced the gene copy number of Cd resistance genes (czcA, czcB, czcC, czcD, czcS, czrA, czrR, cadA, and zntA). czcB was identified as a key gene that affected acid-extractable Cd and residual Cd contents; czcA, czcB, czcD, and czcS were identified as key genes that affected the reducible Cd content; czrR and cadA were identified as key genes that affected the oxidized Cd content; and czcC was identified as a key gene that affected the total Cd content. Cd resistance genes could directly affect the Cd form or indirectly affect Cd form through their interactions with each other.

Exploring resource competition by protective lactic acid bacteria cultures to control Salmonella in food: an Achilles' heel to target?

Salmonella is a pathogenic bacterium, being the second most commonly reported foodborne pathogen in Europe, due to the ability of its different serovars to contaminate a wide variety of foods, with differences among countries. Common chemical or physical control methods are not always effective, eco-sustainable and adapted to the diversity of Salmonella serovars. Thus, great attention is given to developing complementary or alternative control methods that can be tailor made for specific situations. One of these methods is biopreservation using lactic acid bacteria, with most studies on their antagonistic activity focused on the production of antimicrobials. Less attention has been given to competition by exploitation of nutrients. This review is thus set to investigate and highlight limiting resources that may be involved in the competitive exclusion of Salmonella in food matrices. To do this the needs for nutrients and microelements and the known homeostatic pathways of Salmonella and lactic acid bacteria are examined. Finally, milk, intended for the manufacture of fermented dairy foods, is pointed out as an example of food to investigate the bioavailable macronutrients, metals and vitamins that could be involved in competition between the different species and serovars, and could be exploited for targeted biopreservation.

Investigation of Zur-regulated metal transport systems reveals an unexpected role of pyochelin in zinc homeostasis

Limiting the availability of transition metals at infection sites serves as a critical defense mechanism employed by the innate immune system to combat microbial infections. Pseudomonas aeruginosa exhibits a remarkable ability to thrive in zinc-deficient environments, facilitated by intricate cellular responses governed by numerous genes regulated by the zinc-responsive transcription factor Zur. Many of these genes have unknown functions, including those within the predicted PA2911-PA2914 and PA4063-PA4066 operons. A structural bioinformatics investigation revealed that PA2911-PA2914 comprises a TonB-dependent outer membrane receptor and inner membrane ABC-permeases responsible for importing metal-chelating molecules, whereas PA4063-PA4066 contains genes encoding a MacB transporter, likely involved in the export of large molecules. Molecular genetics and biochemical experiments, feeding assays, and intracellular metal content measurements support the hypothesis that PA2911-PA2914 and PA4063-PA4066 are engaged in the import and export of the pyochelin-cobalt complex, respectively. Notably, cobalt can reduce zinc demand and promote the growth of P. aeruginosa strains unable to import zinc, highlighting pyochelin-mediated cobalt import as a novel bacterial strategy to counteract zinc deficiency. These results unveil an unexpected role for pyochelin in zinc homeostasis and challenge the traditional view of this metallophore exclusively as an iron transporter.

IMPORTANCE

The mechanisms underlying the remarkable ability of Pseudomonas aeruginosa to resist the zinc sequestration mechanisms implemented by the vertebrate innate immune system to control bacterial infections are still far from being fully understood. This study reveals that the Zur-regulated gene clusters PA2911-2914 and PA4063-PA4066 encode systems for the import and export of cobalt-bound pyochelin, respectively. This proves to be a useful strategy to counteract conditions of severe zinc deficiency since cobalt can replace zinc in many proteins. The discovery that pyochelin may contribute to cellular responses to zinc deficiency leads to a reevaluation of the paradigm that pyochelin is a siderophore involved exclusively in iron acquisition and suggests that this molecule has a broader role in modulating the homeostasis of multiple metals.

Iron homeostasis as a cell detoxification mechanism in Mesorhizobium qingshengii J19 under yttrium exposure

Yttrium (Y), an important rare earth element (REE), is increasingly prevalent in the environment due to industrial activities, raising concerns about its toxicity. Understanding the effects of Y on microorganisms is essential for bioremediation and biorecovery processes. This study investigates how Mesorhizobium qingshengii J19, a strain with notable resistance to Y, manages iron homeostasis as a detoxifying mechanism under Y stress. Using comparative genomic and transcriptomic analyses, we explored the gene expression profile of strain J19 to identify the mechanisms underlying its high Y resistance and effective Y removal from the medium. Genome-wide transcriptional profiling revealed 127 significantly differentially expressed genes out of 6,343 under Y stress, with 36.2 % up-regulated and 63.8 % down-regulated. Notably, Y exposure significantly affects cellular iron homeostasis and activates arsenic detoxifying mechanisms. A key finding was the 7.6-fold up-regulation of a TonB transporter gene, indicating its crucial role in Y detoxification. Real-time PCR (RT-PCR) analysis of the selected gene confirmed the accuracy of RNA sequencing results. Further validation showed that iron supplementation mitigates Y-induced growth inhibition, leading to reduced ROS production in strain J19. This study elucidates the molecular mechanisms by which strain M. qingshengii J19 adapts to Y stress, emphasizing the importance of iron in controlling ROS and protecting against Y toxicity. It also highlights critical pathways and adaptive responses involved in the strain's resilience to metal stress.

Metal(loid)-gut microbiota interactions and microbiota-related protective strategies: A review

Human exposure to metal(loid)s has dramatically increased over the past five decades, which has triggered public concern worldwide. Recently, gut microbiota has been considered a target for metal(loid)s, and some literature has reviewed the interactions between gut microbiota and heavy metal(loid)s (HMs) with high toxicity. However, whether there is an interaction between gut microbiota and metal(loid)s with essential roles or some normal functions are far from clear to date. Importantly, in addition to traditional probiotics that have been clarified to alleviate the adverse effect of HMs on the body, some novel probiotics, prebiotics, synbiotics, and postbiotics may also exhibit comparable or even better abilities of metal(loid) remediation. In this review, we mainly outline and discuss recent research findings on the metal(loid)-gut microbiota interactions and microbiota-related protective strategies.

Mechanistic insights and in vivo efficacy of thiosemicarbazones against methicillin-resistant Staphylococcus aureus

Staphylococcus aureus poses a significant threat in both community and hospital settings due to its infective and pathogenic nature combined with its ability to resist the action of chemotherapeutic agents. Methicillin-resistant S. aureus (MRSA) represents a critical challenge. Metal-chelating thiosemicarbazones (TSCs) have shown promise in combating MRSA and while previous studies hinted at the antimicrobial potential of TSCs, their mechanisms of action against MRSA are still under investigation. We screened a chemical library for anti-staphylococcal compounds and identified a potent molecule named R91 that contained the NNSN structural motif found within TSCs. We identified that R91 and several structural analogs exhibited antimicrobial activity against numerous S. aureus isolates as well as other Gram-positive bacteria. RNAseq analysis revealed that R91 induces copper and oxidative stress responses. Checkerboard assays demonstrated synergy of R91 with copper, nickel, and zinc. Mutation of the SrrAB two-component regulatory system sensitizes S. aureus to R91 killing, further linking the oxidative stress response to R91 resistance. Moreover, R91 was found to induce hydrogen peroxide production, which contributed to its antimicrobial activity. Remarkably, no mutants with elevated R91 resistance were identified, despite extensive attempts. We further demonstrate that R91 can be used to effectively treat an intracellular reservoir of S. aureus in cell culture and can reduce bacterial burdens in a murine skin infection model. Combined, these data position R91 as a potent TSC effective against MRSA and other Gram-positive bacteria, with implications for future therapeutic development.

ZIP8 A391T Crohn's Disease-Linked Risk Variant Induces Colonic Metal Ion Dyshomeostasis, Microbiome Compositional Shifts, and Inflammation

BACKGROUND

The pathogenesis of Crohn's disease involves genetic and environmental factors, with the gut microbiome playing a crucial role. The Crohn's disease-associated variant rs13107325 in the SLC39A8 gene results in an A391T substitution in the ZIP8 metal ion transporter and has previously been linked to alterations in the colonic microbiome in variant carriers. We hypothesized that the A391T substitution alters metal ion homeostasis in the colonic mucosal-luminal interface, thereby inducing dysbiosis which may promote intestinal inflammation.

METHODS

To evaluate this hypothesis, we generated a SLC39A8 A393T mouse model (matching human A391T). We first examined trace element abundance in the colonic mucosal epithelium and lumen of homozygous A393T and wild-type (WT) mice to determine if the variant affected metal distribution. We also performed 16S rRNA gene sequencing on colon samples at 2 months, 3-4 months, and 12 months of age, and conducted histological scoring of colon tissue collected from 5-month and 10-month old mice.

RESULTS

Consistent with an effect of the variant on ZIP8 function, homozygous A393T mice exhibited increased cobalt in the colonic mucosa, but reduced iron, zinc, manganese, cobalt, copper, and cadmium in the colonic lumen. 16S rRNA gene sequencing of colon samples revealed variant-linked effects on microbiome beta diversity in 2-month-, 3-4-month-, and 12-month-old mice. Histological scoring showed spontaneous intestinal inflammation in 10-month but not in 5-month-old mice. Lastly, predicted pathway analysis of the microbiome samples revealed differential enrichment of iron-, zinc-, and cobalt-dependent pathways in A393T mice compared to wild-type controls.

CONCLUSION

These results suggest that the variant in SLC39A8 primarily restricts metal availability to the microbiota, resulting in compositions that can adapt to the environment and that A393T-linked dysbiosis occurs prior to the onset of inflammation. This study paves the way for future studies investigating risk variants as microbiome-disease modifiers.

Transition metal homoeostasis is key to metabolism and drug tolerance of Mycobacterium abscessus

Antimicrobial resistance (AMR) is one of the major challenges humans are facing this century. Understanding the mechanisms behind the rise of AMR is therefore crucial to tackling this global threat. The presence of transition metals is one of the growth-limiting factors for both environmental and pathogenic bacteria, and the mechanisms that bacteria use to adapt to and survive under transition metal toxicity resemble those correlated with the rise of AMR. A deeper understanding of transition metal toxicity and its potential as an antimicrobial agent will expand our knowledge of AMR and assist the development of therapeutic strategies. In this study, we investigate the antimicrobial effect of two transition metal ions, namely cobalt (Co2+) and nickel (Ni2+), on the non-tuberculous environmental mycobacterium and the opportunistic human pathogen Mycobacterium abscessus. The minimum inhibitory concentrations of Co2+ and Ni2+ on M. abscessus were first quantified and their impact on the bacterial intracellular metallome was investigated. A multi-omics strategy that combines transcriptomics, bioenergetics, metabolomics, and phenotypic assays was designed to further investigate the mechanisms behind the effects of transition metals. We show that transition metals induced growth defect and changes in transcriptome and carbon metabolism in M. abscessus, while the induction of the glyoxylate shunt and the WhiB7 regulon in response to metal stresses could be the key response that led to higher AMR levels. Meanwhile, transition metal treatment alters the bacterial response to clinically relevant antibiotics and enhances the uptake of clarithromycin into bacterial cells, leading to increased efficacy. This work provides insights into the tolerance mechanisms of M. abscessus to transition metal toxicity and demonstrates the possibility of using transition metals to adjuvant the efficacy of currently using antimicrobials against M. abscessus infections.

Metal chelation as an antibacterial strategy for Pseudomonas aeruginosa and Acinetobacter baumannii

It is estimated that by 2050, bacterial infections will cause 1.8 million more deaths than cancer annually, and the current lack of antibiotic drug discovery is only exacerbating the crisis. Two pathogens in particular, Gram-negative bacteria A. baumannii and P. aeruginosa, are of grave concern because of their heightened multi-drug resistance due to a dense, impermeable outer membrane. However, targeting specific cellular processes may prove successful in overcoming bacterial resistance. This review will concentrate on a novel approach to combatting pathogenicity by disarming bacteria through the disruption of metal homeostasis to reduce virulence and enhance antibiotic uptake. The varying levels of success in bringing metallophores to clinical trials, with currently only one FDA-approved siderophore antibiotic to date, will also be detailed.

Biodegradable oxygen-evolving metalloantibiotics for spatiotemporal sono-metalloimmunotherapy against orthopaedic biofilm infections

Pathogen-host competition for manganese and intricate immunostimulatory pathways severely attenuates the efficacy of antibacterial immunotherapy against biofilm infections associated with orthopaedic implants. Herein, we introduce a spatiotemporal sono-metalloimmunotherapy (SMIT) strategy aimed at efficient biofilm ablation by custom design of ingenious biomimetic metal-organic framework (PCN-224)-coated MnO2-hydrangea nanoparticles (MnPM) as a metalloantibiotic. Upon reaching the acidic H2O2-enriched biofilm microenvironment, MnPM can convert abundant H2O2 into oxygen, which is conducive to significantly enhancing the efficacy of ultrasound (US)-triggered sonodynamic therapy (SDT), thereby exposing bacteria-associated antigens (BAAs). Moreover, MnPM disrupts bacterial homeostasis, further killing more bacteria. Then, the Mn ions released from the degraded MnO2 can recharge immune cells to enhance the cGAS-STING signaling pathway sensing of BAAs, further boosting the immune response and suppressing biofilm growth via biofilm-specific T cell responses. Following US withdrawal, the sustained oxygenation promotes the survival and migration of fibroblasts, stimulates the expression of angiogenic growth factors and angiogenesis, and neutralizes excessive inflammation. Our findings highlight that MnPM may act as an immune costimulatory metalloantibiotic to regulate the cGAS-STING signaling pathway, presenting a promising alternative to antibiotics for orthopaedic biofilm infection treatment and pro-tissue repair.