Elimination of manganese(II,III) oxidation in Pseudomonas putida GB-1 by a double knockout of two putative multicopper oxidase genes

Can xenobiotics support the growth of Mn(II)-oxidizing bacteria (MnOB)? A case of phenol-utilizing bacteria Pseudomonas sp. AN-1

Biogenic manganese oxides (BioMnOx) produced by Mn(II)-oxidizing bacteria (MnOB) have garnered considerable attention for their exceptional adsorption and oxidation capabilities. However, previous studies have predominantly focused on the role of BioMnOx, neglecting substantial investigation into MnOB themselves. Meanwhile, whether the xenobiotics could support the growth of MnOB as the sole carbon source remains uncertain. In this study, we isolated a strain termed Pseudomonas sp. AN-1, capable of utilizing phenol as the sole carbon source. The degradation of phenol took precedence over the accumulation of BioMnOx. In the presence of 100 mg L-1 phenol and 100 µM Mn(II), phenol was entirely degraded within 20 h, while Mn(II) was completely oxidized within 30 h. However, at the higher phenol concentration (500 mg L-1), phenol degradation reduced to 32% and Mn(II) oxidation did not appear to occur. TOC determination confirmed the ability of strain AN-1 to mineralize phenol. Based on the genomic and proteomics studies, the Mn(II) oxidation and phenol mineralization mechanism of strain AN-1 was further confirmed. Proteome analysis revealed down-regulation of proteins associated with Mn(II) oxidation, including MnxG and McoA, with increasing phenol concentration. Notably, this study observed for the first time that the expression of Mn(II) oxidation proteins is modulated by the concentration of carbon sources. This work provides new insight into the interaction between xenobiotics and MnOB, thus revealing the complexity of biogeochemical cycles of Mn and C.

Corroded iron pipe inhibits microbial-mediated Mn(II) oxidation and MnOx accumulation compared to PVC pipe

MnOx deposits in distribution pipes can cause severe discoloration problems in drinking water. However, the impact of pipe materials on Mn(II) oxidation and MnOx accumulation remains unclear. This study investigated microbial-mediated Mn(II) oxidation and deposit formation through 300-day pipe loop experiments with corroded galvanized steel pipes (DN100) and new polyvinyl chloride (PVC) pipes (DN100). The results showed that influent Mn(II) was entirely oxidized within 48 h in the PVC pipes with biofilms in the absence of chlorine, while most influent Mn(II) remained unoxidized in the iron pipes. Dissolved oxygen (DO) monitoring showed that the DO in the PVC pipes was consistently higher than 8.0 mg/L, but that in the iron pipes dropped to 6.5 mg/L. Microbial analysis revealed that the abundance of potential Mn(II)-oxidizing bacteria in the low-DO iron pipes was less than that in the PVC pipes. Analysis of the Mn(II) concentration dynamics in different pipes revealed that the early Mn(II) disappearance in the iron pipes was contributed mainly to Mn(II) adsorption by iron corrosion products rather than microbial Mn(II) oxidation. When aeration was performed to increase the DO concentration to 8.0 mg/L in the iron pipes, complete Mn(II) oxidation occurred. This study provides insights into Mn(II) transformation in different pipes and highlights the critical role of DO in microbial Mn(II) oxidation in drinking water pipes.

Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field

IMPORTANCE

Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.

Sublethal nickel toxicity shuts off manganese oxidation and pellicle biofilm formation in Pseudomonas putida GB-1

In sediments, the bioavailability and toxicity of Ni are strongly influenced by its sorption to manganese (Mn) oxides, which largely originate from the redox metabolism of microbes. However, microbes are concurrently susceptible to the toxic effects of Ni, which establishes complex interactions between toxicity and redox processes. This study measured the effect of Ni on growth, pellicle biofilm formation and oxidation of the Mn-oxidizing bacteria Pseudomonas putida GB-1. In liquid media, Ni exposure decreased the intrinsic growth rate but allowed growth to the stationary phase in all intermediate treatments. Manganese oxidation was 67% less than control for bacteria exposed to 5 μM Ni and completely ceased in all treatments above 50 μM. Pellicle biofilm development decreased exponentially with Ni concentration (maximum 92% reduction) and was replaced by planktonic growth in higher Ni treatments. In solid media assays, growth was unaffected by Ni exposure, but Mn oxidation completely ceased in treatments above 10 μM of Ni. Our results show that sublethal Ni concentrations substantially alter Mn oxidation rates and pellicle biofilm development in P. putida GB-1, which has implications for toxic metal bioavailability to the entire benthic community and the environmental consequences of metal contamination.

Characterization on nicotine degradation and research on heavy metal resistance of a strain Pseudomonas sp. NBB

The remediation of polluted sites containing multiple contaminants like nicotine and heavy metals poses significant challenges, due to detrimental effects like cell death. In this study, we isolated a new strain Pseudomonas sp. NBB capable of efficiently degrading nicotine even in high level of heavy metals. It degraded nicotine through pyrrolidine pathway and displayed minimum inhibitory concentrations of 2 mM for barium, copper, and lead, and 5 mM for manganese. In the presence of 2 mM Ba2+ or Pb2+, 3 g L-1 nicotine could be completely degraded within 24 h. Moreover, under 0.5 mM Cu2+ or 5 mM Mn2+ stress, 24.13% and 72.56% of nicotine degradation were achieved in 60 h, respectively. Strain NBB tolerances metal stress by various strategies, including morphological changes, up-regulation of macromolecule transporters, cellular response to DNA damage, and down-regulation of ABC transporters. Notably, among the 153 up-regulated genes, cds_821 was identified as manganese exporter (MneA) after gene disruption and recovery experiments. This study presents a novel strain capable of efficiently degrading nicotine and displaying remarkable resistance to heavy metals. The findings of this research provide valuable insights into the potential application of nicotine bioremediation in heavy metal-contaminated areas.

Sequestration and oxidation of heavy metals mediated by Mn(II) oxidizing microorganisms in the aquatic environment

Microorganisms can oxidize Mn(II) to biogenic Mn oxides (BioMnOx), through enzyme-mediated processes and non-enzyme-mediated processes, which are generally considered as the source and sink of heavy metals due to highly reactive to sequestrate and oxidize heavy metals. Hence, the summary of interactions between Mn(II) oxidizing microorganisms (MnOM) and heavy metals is benefit for further work on microbial-mediated self-purification of water bodies. This review comprehensively summarizes the interactions between MnOM and heavy metals. The processes of BioMnOx production by MnOM has been firstly discussed. Moreover, the interactions between BioMnOx and various heavy metals are critically discussed. On the one hand, modes for heavy metals adsorbed on BioMnOx are summarized, such as electrostatic attraction, oxidative precipitation, ion exchange, surface complexation, and autocatalytic oxidation. On the other hand, adsorption and oxidation of representative heavy metals based on BioMnOx/Mn(II) are also discussed. Thirdly, the interactions between MnOM and heavy metals are also focused on. Finally, several perspectives which will contribute to future research are proposed. This review provides insight into the sequestration and oxidation of heavy metals mediated by Mn(II) oxidizing microorganisms. It might be helpful to understand the geochemical fate of heavy metals in the aquatic environment and the process of microbial-mediated water self-purification.

Biologically Assisted One-Step Synthesis of Electrode Materials for Li-Ion Batteries

Mn(II)-oxidizing organisms promote the biomineralization of manganese oxides with specific textures, under ambient conditions. Controlling the phases formed and their texture on a larger scale may offer environmentally relevant routes to manganese oxide synthesis, with potential technological applications, for example, for energy storage. In the present study, we sought to use biofilms to promote the formation of electroactive minerals and to control the texture of these biominerals down to the electrode scale (i.e., cm scale). We used the bacterium Pseudomonas putida strain MnB1 which can produce manganese oxide in a biofilm. We characterized the biofilm–mineral assembly using a combination of electron microscopy, synchrotron-based X-ray absorption spectroscopy, X-ray diffraction, thermogravimetric analysis and electron paramagnetic resonance spectroscopy. Under optimized conditions of biofilm growth on the surface of current collectors, mineralogical characterizations revealed the formation of several minerals including a slightly crystalline MnOx birnessite. Electrochemical measurements in a half-cell against Li(0) revealed the electrochemical signature of the Mn4+/Mn3+ redox couple indicating the electroactivity of the biomineralized biofilm without any post-synthesis chemical, physical or thermal treatment. These results provide a better understanding of the properties of biomineralized biofilms and their possible use in designing new routes for one-pot electrode synthesis.

Direct observation of Mn distribution/speciation within and surrounding a basidiomycete fungus in the production of Mn-oxides important in toxic element containment

Biogenic manganese (Mn) oxides occur ubiquitously in the environment including the uranium (U) mill tailings at the Ningyo-toge U mine in Okayama, Japan, being important in the sequestration of radioactive radium. To understand the nanoscale processes in Mn oxides formation at the U mill tailings site, Mn²⁺ absorption by a basidiomycete fungus, Coprinopsis urticicola, isolated from Ningyo-toge mine water samples, was investigated in the laboratory under controlled conditions utilizing electron microscopy, synchrotron-based X-ray analysis, and fluorescence microscopy with a molecular pH probe. The fungus' growth was first investigated in an agar-solidified medium supplemented with 1.0 mmol/L Mn²⁺, and Cu²⁺ (0-200 μM), Zn²⁺ (0-200 μM), or diphenyleneiodonium (DPI) chloride (0-100 μM) at 25 °C. The results revealed that Zn²⁺ has no significant effects on Mn oxide formation, whereas Cu²⁺ and DPI significantly inhibit both fungal growth and Mn oxidation, indicating superoxide-mediated Mn oxidation. Indeed, nitroblue tetrazolium and diaminobenzidine assays on the growing fungus revealed the production of superoxide and peroxide. During the interaction of Mn²⁺ with the fungus in solution medium at the initial pH of 5.67, a small fraction of Mn²⁺ infiltrated the fungal hyphae within 8 h, forming a few tens of nm-sized concentrates of soluble Mn²⁺ in the intracellular pH of ∼6.5. After 1 day of incubation, Mn oxides began to precipitate on the hyphae, which were characterized as fibrous nanocrystals with a hexagonal birnessite-structure, these forming spherical aggregates with a diameter of ∼1.5 μm. These nanoscale processes associated with the fungal species derived from the Ningyo-toge mine area provide additional insights into the existing mechanisms of Mn oxidation by filamentous fungi at other U mill tailings sites under circumneutral pH conditions. Such processes add to the class of reactions important to the sequestration of toxic elements.

Coupling and environmental implications of in situ formed biogenic Fe-Mn minerals induced by indigenous bacteria and oxygen perturbations for As(III) immobilization in groundwater

Iron (Fe)-manganese (Mn) minerals formed in situ can be used for the natural remediation of the primary poor-quality groundwater with coexistence of arsenite [As(III)], Mn(II), and Fe(II) (PGAMF). However, the underlying mechanisms of immobilization and coupling of As, Mn, and Fe during in-situ formation of Fe-Mn minerals in PGAMF remains unclear. The simultaneous immobilization and coupling of arsenic (As), Mn, and Fe in PGAMF during in-situ formation of biogenic Fe-Mn minerals induced by O₂ perturbations and indigenous bacteria (Comamonas sp. RM6) were investigated at the different molar ratios of Fe(II):Mn(II) (1:1, 2:1, and 3:1). Compared with systems without Fe(II) in the presence of Mn(II), the coexisted Fe(II) significantly enhanced Mn(II) bio-oxidation and mineral precipitation, resulting in As immobilization increased by 5, 7, and 7 times at initial Fe(II) concentration of 0.3, 0.6, and 0.9 mM, respectively. Moreover, the As(III) immobilization efficiencies in Mn(II) and Fe(II) mixed system at initial Fe(II) concentration of 0.3, 0.6, and 0.9 mM were 73%, 91%, and 92%, respectively, that were significantly higher than those of single Fe(II) system (30%, 59%, and 74%) and those of single Mn(II) system (12%), indicating that Fe(II) and Mn(II) oxidation synergically enhanced As(III) immobilization. This was mainly attributed to the formation and As adsorption capacity of biogenic Fe-Mn minerals (BFMM). The formed BFMM significantly facilitated simultaneous immobilization of Fe, Mn, and As in PGAMF by oxidation, adsorption, and precipitation/coprecipitation, a coupling of biological, physical, and chemical processes. Fe component was mainly responsible for As fixation, and Mn component dominated As(III) oxidation. Based on the results from this work, biostimulation and bioaugmentation techniques can be developed for in-situ purification and remediation of PGAMF. This work provides insights into the simultaneous immobilization of pollutants in PGAMF, as well as promising strategies for in-situ purification and remediation of PGAMF.

Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel

The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.

Cyclic di-GMP Signaling Links Biofilm Formation and Mn(II) Oxidation in Pseudomonas resinovorans

Bioaugmentation of biological sand filters with Mn(II)-oxidizing bacteria (MOB) is used to increase the efficiency of Mn removal from groundwater. While the biofilm-forming ability of MOB is important to achieve optimal Mn filtration, the regulatory link between biofilm formation and Mn(II) oxidation remains unclear. Here, an environmental isolate of Pseudomonas resinovorans strain MOB-513 was used as a model to investigate the role of c-di-GMP, a second messenger crucially involved in the regulation of biofilm formation by Pseudomonas, in the oxidation of Mn(II). A novel role for c-di-GMP in the upregulation of Mn(II) oxidation through induction of the expression of manganese-oxidizing peroxidase enzymes was revealed. MOB-513 macrocolony biofilms showed a strikingly stratified pattern of biogenic Mn oxide (BMnOx) accumulation in a localized top layer. Remarkably, elevated cellular levels of c-di-GMP correlated not only with increased accumulation of BMnOx in the same top layer but also with the appearance of a second BMnOx stratum in the bottom region of macrocolony biofilms, and the expression of mop genes correlated with this pattern. Proteomic analysis under Mn(II) conditions revealed changes in the abundance of a PilZ domain protein. Subsequent analyses supported a model in which this protein sensed c-di-GMP and affected a regulatory cascade that ultimately inhibited mop gene expression, providing a molecular link between c-di-GMP signaling and Mn(II) oxidation. Finally, we observed that high c-di-GMP levels were correlated with higher lyophilization efficiencies and higher groundwater Mn(II) oxidation capacities of freeze-dried bacterial cells, named lyophiles, showing the biotechnological relevance of understanding the role of c-di-GMP in MOB-513. IMPORTANCE The presence of Mn(II) in groundwater, a common source of drinking water, is a cause of water quality impairment, interfering with its disinfection, causing operation problems, and affecting human health. Purification of groundwater containing Mn(II) plays an important role in environmental and social safety. The typical method for Mn(II) removal is based on bacterial oxidation of metals to form insoluble oxides that can be filtered out of the water. Evidence of reducing the start-up periods and enhancing Mn removal efficiencies through bioaugmentation with appropriate biofilm-forming and MOB has emerged. As preliminary data suggest a link between these two phenotypes in Pseudomonas strains, the need to investigate the underlying regulatory mechanisms is apparent. The significance of our research lies in determining the role of c-di-GMP for increased biofilm formation and Mn(II)-oxidizing capabilities in MOB, which will allow the generation of super-biofilm-elaborating and Mn-oxidizing strains, enabling their implementation in biotechnological applications.

Manganese oxidation counteracts the deleterious effect of low temperatures on biofilm formation in Pseudomonas sp. MOB-449

Mn removal from groundwater by biological sand filter technology is negatively impacted by low temperatures in winter periods. Therefore, the need to study Mn(II)-oxidizing bacteria (MOB) having the potential to oxidize Mn(II) and form biofilms at low temperatures is imperative. These MOB can have potential as inocula for sand filter bioaugmentation strategies to optimize Mn removal during winter periods. We previously showed that a Pseudomonas sp. MOB-449 (MOB-449), isolated from a Mn biofilter, oxidizes Mn(II) in a biofilm-dependent way at low temperatures. In this work, MOB-449 Mn(II) oxidation and growth capacities were evaluated under planktonic and biofilm conditions at different temperatures. At 18°C, MOB-449 showed enhanced biofilm formation due to the addition of Mn(II) to the medium correlating with Mn(II) oxidation, compared to biofilms grown in control medium. Moreover, this enhancement on biofilm formation due to the addition of Mn(II) was only observed at 18°C. At this temperature, Mn(II) oxidation in membrane fractions collected from biofilms was induced by uncoupling oxidative phosphorylation from the electron transport chain with 2,4-Dinitrophenol. In Pseudomonas, a role for c-type cytochrome in Mn(II) oxidation has been demonstrated. Accordingly, transcriptional profiles of all terminal oxidases genes found in MOB-449 showed an induction of cytochrome c terminal oxidases expression mediated by Mn(II) oxidation at 18°C. Finally, heme peroxidase activity assays and MS analysis revealed that PetC, a cytochrome c5, and also CcmE, involved in the cytochrome c biogenesis machinery, are induced at 18°C only in the presence of Mn(II). These results present evidence supporting that cytochromes c and also the cytochrome c terminal oxidases are activated at low temperatures in the presence of Mn(II). Overall, this work demonstrate that in MOB-449 Mn(II) oxidation is activated at low temperatures to gain energy, suggesting that this process is important for survival under adverse environmental conditions and contributing to the understanding of the physiological role of bacterial Mn(II) oxidation.

Fe(II) oxygenation inhibits bacterial Mn(II) oxidation by P. putida MnB1 in groundwater under O2-perturbed conditions

Bacterial Mn(II) oxidation plays a crucial role in Mn cycling and the associated biogeochemistry in natural waters and is of practical concern in the clean-up of excess Mn from drinking water. Fe(II) usually occurring together with Mn(II) in groundwater is oxidized prior to Mn(II) when perturbed by O₂, but the impact of Fe(II) oxygenation on the subsequent bacterial Mn(II) oxidation remains unknown. Here we demonstrated that Fe(II) oxygenation largely inhibited the Mn(II)-oxidizing ability of MnB1 belong to Pseudomonas putida which is ubiquitous in groundwater. The mechanisms of the inhibition varied under different Fe(II) concentrations. At high Fe(II) concentrations (≥ 1 mM), the inhibition of bacterial Mn(II) oxidation was mainly because of cell death caused by intracelluar reactive oxygen species. At low Fe(II) concentrations (≤ 0.05 mM), the inhibition of bacterial Mn(II) oxidation was attributed to Fe(III) oxyhydroxides generated from Fe(II) oxygenation. Fe(III) oxyhydroxides attached to cell surface and damaged the cell membrane, resulting in the influx of dissolved Fe into the cell. Transcriptomic analysis revealed that the intracellular Fe suppressed the transcription initiation process and the subsequent generation of multicopper oxidases which were responsible for Mn(II) oxidation. These findings implicate that the inhibition effect of Fe(II) oxygenation on bacterial Mn(II) oxidation should be considered in groundwater-surface water interaction zone and the biological treatment of Fe-Mn containing drinking water.

Mineralogical and Genomic Constraints on the Origin of Microbial Mn Oxide Formation in Complexed Microbial Community at the Terrestrial Hot Spring

Manganese (Mn) oxides are widespread on the surface environments of the modern Earth. The role of microbial activities in the formation of Mn oxides has been discussed for several decades. However, the mechanisms of microbial Mn oxidation, and its role in complex microbial communities in natural environments, remain uncertain. Here, we report the geochemical, mineralogical, and metagenomic evidence for biogenic Mn oxides, found in Japanese hot spring sinters. The low crystallinity of Mn oxides, and their spatial associations with organic matter, support the biogenic origin of Mn oxides. Specific multicopper oxidases (MCOs), which are considered Mn-oxidizing enzymes, were identified using metagenomic analyses. Nanoscale nuggets of copper sulfides were, also, discovered in the organic matter in Mn-rich sinters. A part of these copper sulfides most likely represents traces of MCOs, and this is the first report of traces of Mn-oxidizing enzyme in geological samples. Metagenomic analyses, surprisingly, indicated a close association of Mn oxides, not only in aerobic but also in anaerobic microbial communities. These new findings offer the unique and unified positions of Mn oxides, with roles that have not been ignored, to sustain anaerobic microbial communities in hot spring environments.

Structure of dye-decolorizing peroxidase from Bacillus subtilis in complex with veratryl alcohol

Dye-decolorizing peroxidases (DyPs) are heme-containing peroxidases, which have promising application in biodegradation of phenolic lignin compounds and in detoxification of dyes. In this study, the crystal structure of BsDyP- veratryl alcohol (VA) complex delves deep into the binding of small substrate molecules within the DyP heme cavity. The biochemical analysis shows that BsDyP oxidizes the VA with a turnover number of 0.065 s^-1, followed by the oxidation of 2,6-dimethoxyphenol (DMP) and guaiacol with a comparable turnover number (k_cat) of 0.07 s^-1 and 0.07 s^-1, respectively. Moreover, biophysical and computational studies reveal the comparable binding affinity of substrates to BsDyP and produce lower-energy stable BsDyP-ligand(s) complexes. All together with our previous findings, we are providing a complete structural description of substrate-binding sites in DyP. The structural insight of BsDyP helps to modulate its engineering to enhance the activity towards the oxidation of a wide range of substrates.

Manganese Stress Adaptation Mechanisms of Bacillus safensis Strain ST7 From Mine Soil

The mechanism of bacterial adaption to manganese-polluted environments was explored using 50 manganese-tolerant strains of bacteria isolated from soil of the largest manganese mine in China. Efficiency of manganese removal by the isolated strains was investigated using atomic absorption spectrophotometry. Bacillus safensis strain ST7 was the most effective manganese-oxidizing bacteria among the tested isolates, achieving up to 82% removal at a Mn(II) concentration of 2,200 mg/L. Bacteria-mediated manganese oxide precipitates and high motility were observed, and the growth of strain ST7 was inhibited while its biofilm formation was promoted by the presence of Mn(II). In addition, strain ST7 could grow in the presence of high concentrations of Al(III), Cr(VI), and Fe(III). Genome-wide analysis of the gene expression profile of strain ST7 using the RNA-seq method revealed that 2,580 genes were differently expressed under Mn(II) exposure, and there were more downregulated genes (n = 2,021) than upregulated genes (n = 559) induced by Mn stress. KAAS analysis indicated that these differently expressed genes were mainly enriched in material metabolisms, cellular processes, organism systems, and genetic and environmental information processing pathways. A total of twenty-six genes from the transcriptome of strain ST7 were involved in lignocellulosic degradation. Furthermore, after 15 genes were knocked out by homologous recombination technology, it was observed that the transporters, multicopper oxidase, and proteins involved in sporulation and flagellogenesis contributed to the removal of Mn(II) in strain ST7. In summary, B. safensis ST7 adapted to Mn exposure by changing its metabolism, upregulating cation transporters, inhibiting sporulation and flagellogenesis, and activating an alternative stress-related sigB pathway. This bacterial strain could potentially be used to restore soil polluted by multiple heavy metals and is a candidate to support the consolidated bioprocessing community.

Oligo-heterotrophic Activity of Marinobacter subterrani Creates an Indirect Fe(II) Oxidation Phenotype in Gradient Tubes

Autotrophic bacteria utilizing Fe(II) as their energy and electron sources for growth affect multiple biogeochemical cycles. Some chemoheterotrophic bacteria have also been considered to exhibit an Fe(II) oxidation phenotype. For example, several Marinobacter strains have been reported to oxidize Fe(II) based on formation of oxidized iron bands in semi-solid gradient tubes that produce opposing concentration gradients of Fe(II) and oxygen. While gradient tubes are a simple and visually compelling method to test for Fe(II) oxidation, this method alone cannot confirm if, and to what extent, Fe(II) oxidation is linked to metabolism in chemoheterotrophic bacteria. Here we probe the possibility of protein-mediated and metabolic by-product-mediated Fe(II) oxidation in Marinobacter subterrani JG233, a chemoheterotroph previously proposed to oxidize Fe(II). Results from conditional and mutant studies, along with measurements of Fe(II) oxidation rates, suggest M. subterrani is unlikely to facilitate Fe(II) oxidation under microaerobic conditions. We conclude that the Fe(II) oxidation phenotype observed in gradient tubes inoculated with M. subterrani JG233 is a result of oligo-heterotrophic activity, shifting the location where oxygen dependent chemical Fe(II) oxidation occurs, rather than a biologically mediated process. IMPORTANCE Gradient tubes are the most commonly used method to isolate and identify neutrophilic Fe(II)-oxidizing bacteria. The formation of oxidized iron bands in gradient tubes provides a compelling assay to ascribe the ability to oxidize Fe(II) to autotrophic bacteria whose growth is dependent on Fe(II) oxidation. However, the physiological significance of Fe(II) oxidation in chemoheterotrophic bacteria is less well understood. Our work suggests that oligo-heterotrophic activity of certain bacteria may create a false-positive phenotype in gradient tubes by altering the location of the abiotic, oxygen-mediated oxidized iron band. Based on the results and analysis presented here, we caution against utilizing gradient tubes as the sole evidence for the capability of a strain to oxidize Fe(II) and that additional experiments are necessary to ascribe this phenotype to new isolates.

Manganese-Oxidizing Antarctic Bacteria (Mn-Oxb) Release Reactive Oxygen Species (ROS) as Secondary Mn(II) Oxidation Mechanisms to Avoid Toxicity

Manganese (Mn) oxidation is performed through oxidative Mn-oxidizing bacteria (MnOxb) as the main bio-weathering mechanism for Mn(III/IV) deposits during soil formation. However, with an increase in temperature, the respiration rate also increases, producing Reactive Oxygen Species (ROS) as by-products, which are harmful to microbial cells. We hypothesize that bacterial ROS oxidize Mn(II) to Mn(III/IV) as a secondary non-enzymatic temperature-dependent mechanism for cell protection. Fourteen MnOxb were isolated from Antarctic soils under the global warming effect, and peroxidase (PO) activity, ROS, and Mn(III/IV) production were evaluated for 120 h of incubation at 4 °C, 15 °C, and 30 °C. ROS contributions to Mn oxidation were evaluated in Arthrobacter oxydans under antioxidant (Trolox) and ROS-stimulated (menadione) conditions. The Mn(III/IV) concentration increased with temperature and positively correlated with ROS production. ROS scavenging with Trolox depleted the Mn oxidation, and ROS-stimulant increased the Mn precipitation in A. oxydans. Increasing the Mn(II) concentration caused a reduction in the membrane potential and bacterial viability, which resulted in Mn precipitation on the bacteria surface. In conclusion, bacterial ROS production serves as a complementary non-enzymatic temperature-dependent mechanism for Mn(II) oxidation as a response in warming environments.

Metallo-inhibition of Mnx, a bacterial manganese multicopper oxidase complex

The manganese oxidase complex, Mnx, from Bacillus sp. PL-12 contains a multicopper oxidase (MCO) and oxidizes dissolved Mn(II) to form insoluble manganese oxide (MnO₂) mineral. Previous kinetic and spectroscopic analyses have shown that the enzyme's mechanism proceeds through an activation step that facilitates formation of a series of binuclear Mn complexes in the oxidation states II, III, and IV on the path to MnO₂ formation. We now demonstrate that the enzyme is inhibited by first-row transition metals in the order of the Irving-Williams series. Zn(II) strongly (K_i ~ 1.5 μM) inhibits both activation and turnover steps, as well as the rate of Mn(II) binding. The combined Zn(II) and Mn(II) concentration dependence establishes that the inhibition is non-competitive. This result is supported by electron paramagnetic resonance (EPR) spectroscopy, which reveals unaltered Mnx-bound Mn(II) EPR signals, both mono- and binuclear, in the presence of Zn(II). We infer that inhibitory metals bind at a site separate from the substrate sites and block the conformation change required to activate the enzyme, a case of allosteric inhibition. The likely biological role of this inhibitory site is discussed in the context of Bacillus spore physiology. While Cu(II) inhibits Mnx strongly, in accord with the Irving-Williams series, it increases Mnx activation at low concentrations, suggesting that weakly bound Cu, in addition to the four canonical MCO-Cu, may support enzyme activity, perhaps as an electron transfer agent.

Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation

BACKGROUND

Cylindrospermopsin is a highly persistent cyanobacterial secondary metabolite toxic to humans and other living organisms. Strain OF001 and A210 are manganese-oxidizing bacteria (MOB) able to transform cylindrospermopsin during the oxidation of Mn²⁺. So far, the enzymes involved in manganese oxidation in strain OF001 and A210 are unknown. Therefore, we analyze the genomes of two cylindrospermopsin-transforming MOB, Pseudomonas sp. OF001 and Rubrivivax sp. A210, to identify enzymes that could catalyze the oxidation of Mn²⁺. We also investigated specific metabolic features related to pollutant degradation and explored the metabolic potential of these two MOB with respect to the role they may play in biotechnological applications and/or in the environment.

RESULTS

Strain OF001 encodes two multicopper oxidases and one haem peroxidase potentially involved in Mn²⁺ oxidation, with a high similarity to manganese-oxidizing enzymes described for Pseudomonas putida GB-1 (80, 83 and 42% respectively). Strain A210 encodes one multicopper oxidase potentially involved in Mn²⁺ oxidation, with a high similarity (59%) to the manganese-oxidizing multicopper oxidase in Leptothrix discophora SS-1. Strain OF001 and A210 have genes that might confer them the ability to remove aromatic compounds via the catechol meta- and ortho-cleavage pathway, respectively. Based on the genomic content, both strains may grow over a wide range of O₂ concentrations, including microaerophilic conditions, fix nitrogen, and reduce nitrate and sulfate in an assimilatory fashion. Moreover, the strain A210 encodes genes which may convey the ability to reduce nitrate in a dissimilatory manner, and fix carbon via the Calvin cycle. Both MOB encode CRISPR-Cas systems, several predicted genomic islands, and phage proteins, which likely contribute to their genome plasticity.

CONCLUSIONS

The genomes of Pseudomonas sp. OF001 and Rubrivivax sp. A210 encode sequences with high similarity to already described MCOs which may catalyze manganese oxidation required for cylindrospermopsin transformation. Furthermore, the analysis of the general metabolism of two MOB strains may contribute to a better understanding of the niches of cylindrospermopsin-removing MOB in natural habitats and their implementation in biotechnological applications to treat water.

Microbially Induced Mineralization of Layered Mn Oxides Electroactive in Li Batteries

Nanoparticles produced by bacteria, fungi, or plants generally have physicochemical properties such as size, shape, crystalline structure, magnetic properties, and stability which are difficult to obtain by chemical synthesis. For instance, Mn(II)-oxidizing organisms promote the biomineralization of manganese oxides with specific textures under ambient conditions. Controlling their crystallinity and texture may offer environmentally relevant routes of Mn oxide synthesis with potential technological applications, e.g., for energy storage. However, whereas the electrochemical activity of synthetic (abiotic) Mn oxides has been extensively studied, the electroactivity of Mn biominerals has been seldom investigated yet. Here we evaluated the electroactivity of biologically induced biominerals produced by the Mn(II)-oxidizer bacteria Pseudomonas putida strain MnB1. For this purpose, we explored the mechanisms of Mn biomineralization, including the kinetics of Mn(II) oxidation, under different conditions. Manganese speciation, biomineral structure, and texture as well as organic matter content were determined by a combination of X-ray diffraction, electron and X-ray microscopies, and thermogravimetric analyses coupled to mass spectrometry. Our results evidence the formation of an organic–inorganic composite material and a competition between the enzymatic (biotic) oxidation of Mn(II) to Mn(IV) yielding MnO₂ birnessite and the abiotic formation of Mn(III), of which the ratio depends on oxygenation levels and activity of the bacteria. We reveal that a subtle control over the conditions of the microbial environment orients the birnessite to Mn(III)-phases ratio and the porosity of the assembly, which both strongly impact the bulk electroactivity of the composite biomineral. The electrochemical properties were tested in lithium battery configuration and exhibit very appealing performances (voltage, capacity, reversibility, and power capability), thanks to the specific texture resulting from the microbially driven synthesis route. Given that such electroactive Mn biominerals are widespread in the environment, our study opens an alternative route for the synthesis of performing electrode materials under environment-friendly conditions.

A non-blue laccase of Bacillus sp. GZB displays manganese-oxidase activity: A study of laccase characterization, Mn(II) oxidation and prediction of Mn(II) oxidation mechanism

Laccase, a unique class of multicopper oxidase, presents promising potential as a biocatalyst in many industrial and biotechnological applications. Recently, it has been significantly applied in many metal-polluted sites due to its Manganese (Mn)-oxidation ability. Here, we demonstrate the Mn(II)-oxidase activity of laccase obtained from Bacillus sp. GZB. The CotA gene of GZB was transformed in E. coli BL21 and overexpressed. The purified laccase (LACREC3-laccase) displayed the absence of a peak at 610 nm that is usually found in blue-laccase. Further, the LACREC3-laccase exhibited high activity and stability at different pH and temperatures with substrates 2, 2'-Azino-bis (3-ethylbenzothiazoline-6-sulfonate) and syringaldazine, respectively. It also functioned in the presence of various metals and enzyme inhibitors. Most notably, LACREC3-laccase formed insoluble brown Mn(III)/Mn(IV)-oxide particles from Mn(II) mineral, exhibiting its Mn(II)-oxidase activity. In addition to native polyacrylamide gel electrophoresis and buffer test, we developed an 'agarose gel plate' assay to evaluate Mn(II) oxidation activity of laccase. Furthermore, using the leucoberbelin blue assay, a total of 44.45 ± 0.45% Mn(IV)-oxides were quantified, in which 5.87 ± 0.61% autoxidized after 24 h. The Mn(II) oxidation mechanisms were further predicted by trapping Mn(III) using pyrophosphate during Mn(II) to Mn(IV) conversion by LACREC3-laccase. Overall, the laccase of GZB has excellent activity and stability plus an ability to oxidize Mn(II). This study is the first report on a non-blue laccase, exhibiting Mn(II)-oxidase activity. Thus, it offers a novel finding of the Mn(II) oxidation processes that can be a valuable way of Mn(II)-mineralization in various metal-polluted environments.

Anti-bacterial Effects of MnO2 on the Enrichment of Manganese-oxidizing Bacteria in Downflow Hanging Sponge Reactors

We focused on the use of abiotic MnO2 to develop reactors for enriching manganese-oxidizing bacteria (MnOB), which may then be used to treat harmful heavy metal-containing wastewater and in the recovery of useful minor metals. Downflow hanging sponge (DHS) reactors were used under aerobic and open conditions to investigate the potential for MnOB enrichment. The results of an experiment that required a continuous supply of organic feed solution containing Mn(II) demonstrated that MnOB enrichment and Mn(II) removal were unsuccessful in the DHS reactor when plain sponge cubes were used. However, MnOB enrichment was successful within a very short operational period when sponge cubes initially containing abiotic MnO2 were installed. The results of a microbial community analysis and MnOB isolation revealed that MnOB belonging to Comamonadaceae or Pseudomonas played a major role in Mn(II) oxidation. Successful MnOB enrichment was attributed to several unidentified species of Chitinophagaceae and Gemmataceae, which were estimated to be intolerant of MnO2, being unable to grow on sponge cubes containing MnO2. The present results show that MnO2 exerted anti-bacterial effects and inhibited the growth of certain non-MnOB groups that were intolerant of MnO2, thereby enabling enriched MnOB to competitively consume more substrate than MnO2-intolerant bacteria.

Comparative genomic and metabolic analysis of manganese-oxidizing mechanisms in Celeribacter manganoxidans DY25T: Its adaptation to the environment of polymetallic nodules

Manganese (Mn) nodule is one of the ubiquitous polymetallic concretions and mainly consists of Mn - Fe oxi-hydroxide precipitations. A primary oxidation of Mn(II) to MnO₂, in which microorganisms may play important roles, is followed by agglomeration of MnO₂ into nodules. Celeribater manganoxidans DY25^T, belonging to family Rhodobacteraceae, has ability to catalyze the formation of MnO₂ [1]. The concentration of MnO₂ formed by harvested cells reached 7.08 μM after suspended in 10 mM HEPES (pH 7.5). Genomic and physiological characteristics of strain DY25^T provided a better understanding of its Mn-oxidizing mechanism. Fifteen genes (including four multicopper oxidases) may be involved in Mn(II)-oxidation, whereas only three of them can promote this process. Sulfur-oxidizing activity was detected, which may be associated with manganese oxidation. Genes involved in import and export of primary elemental ingredients (C, N, P and S) and metallic elements (e.g. Mn) were discovered, demonstrating its potential roles in the biogeochemical cycle.

Removal of Manganese(II) from Acid Mine Wastewater: A Review of the Challenges and Opportunities with Special Emphasis on Mn-Oxidizing Bacteria and Microalgae

Many global mining activities release large amounts of acidic mine drainage with high levels of manganese (Mn) having potentially detrimental effects on the environment. This review provides a comprehensive assessment of the main implications and challenges of Mn(II) removal from mine drainage. We first present the sources of contamination from mineral processing, as well as the adverse effects of Mn on mining ecosystems. Then the comparison of several techniques to remove Mn(II) from wastewater, as well as an assessment of the challenges associated with precipitation, adsorption, and oxidation/filtration are provided. We also critically analyze remediation options with special emphasis on Mn-oxidizing bacteria (MnOB) and microalgae. Recent literature demonstrates that MnOB can efficiently oxidize dissolved Mn(II) to Mn(III, IV) through enzymatic catalysis. Microalgae can also accelerate Mn(II) oxidation through indirect oxidation by increasing solution pH and dissolved oxygen production during its growth. Microbial oxidation and the removal of Mn(II) have been effective in treating artificial wastewater and groundwater under neutral conditions with adequate oxygen. Compared to physicochemical techniques, the bioremediation of manganese mine drainage without the addition of chemical reagents is relatively inexpensive. However, wastewater from manganese mines is acidic and has low-levels of dissolved oxygen, which inhibit the oxidizing ability of MnOB. We propose an alternative treatment for manganese mine drainage that focuses on the synergistic interactions of Mn in wastewater with co-immobilized MnOB/microalgae.

How manganese empowered life with dioxygen (and vice versa)

Throughout the history of life on Earth, abiotic components of the environment have shaped the evolution of life, and in turn life has shaped the environment. The element manganese embodies a special aspect of this collaboration; its history is closely entwined with those of photosynthesis and O₂-two reigning features that characterize the biosphere today. Manganese chemistry was central to the environmental context and evolutionary innovations that enabled the origin of oxygenic photosynthesis and the ensuing rise of O₂. It was also manganese chemistry that provided an early, fortuitous antioxidant system that was instrumental in how life came to cope with oxidative stress and ultimately thrive in an aerobic world. Subsequently, the presence of O₂ transformed the biogeochemical dynamics of the manganese cycle, enabling a rich suite of environmental and biological processes involving high-valent manganese and manganese redox cycling. Here, we describe insights from chemistry, biology, and geology, to examine manganese dynamics in the environment, and its unique role in the history of life.

Biogenic and Synthetic MnO2 Nanoparticles: Size and Growth Probed with Absorption and Raman Spectroscopies and Dynamic Light Scattering

MnO₂ nanoparticles, similar to those found in soils and sediments, have been characterized via their UV-visible and Raman spectra, combined with dynamic light scattering and reactivity measurements. Synthetic colloids were prepared by thiosulfate reduction of permanganate, their sizes controlled with adsorbates acting as capping agents: bicarbonate, phosphate, and pyrophosphate. Biogenic colloids, products of the manganese oxidase, Mnx, were similarly characterized. The band-gap energies of the colloids were found to increase with decreasing hydrodynamic diameter, D_h, and were proportional to 1/ D_h², as predicted from quantum confinement theory. The intensity ratio of the two prominent Mn-O stretching Raman bands also varied with particle size, consistent with the ratio of edge to bulk Mn atoms. Reactivity of the synthetic colloids toward reduction by Mn²⁺, in the presence of pyrophosphate to trap the Mn³⁺ product, was proportional to the surface to volume ratio, but showed surprising complexity. There was also a remnant unreactive fraction, likely attributable to Mn(III)-induced surface passivation. The band gap was similar for biogenic and synthetic colloids of similar size, but decreased when the enzyme solution contained pyrophosphate, which traps the intermediate Mn(III) and slows MnO₂ growth. The band gap/size correlation was used to analyze the growth of the enzymatically produced MnO₂ oxides.

Natural Attenuation of Mn(II) in Metal Refinery Wastewater: Microbial Community Structure Analysis and Isolation of a New Mn(II)-Oxidizing Bacterium Pseudomonas sp. SK3

Natural attenuation of Mn(II) was observed inside the metal refinery wastewater pipeline, accompanying dark brown-colored mineralization (mostly MnIVO2 with some MnIII2O3 and Fe2O3) on the inner pipe surface. The Mn-deposit hosted the bacterial community comprised of Hyphomicrobium sp. (22.1%), Magnetospirillum sp. (3.2%), Geobacter sp. (0.3%), Bacillus sp. (0.18%), Pseudomonas sp. (0.03%), and non-metal-metabolizing bacteria (74.2%). Culture enrichment of the Mn-deposit led to the isolation of a new heterotrophic Mn(II)-oxidizer Pseudomonas sp. SK3, with its closest relative Ps. resinovorans (with 98.4% 16S rRNA gene sequence identity), which was previously unknown as an Mn(II)-oxidizer. Oxidation of up to 100 mg/L Mn(II) was readily initiated and completed by isolate SK3, even in the presence of high contents of MgSO4 (a typical solute in metal refinery wastewaters). Additional Cu(II) facilitated Mn(II) oxidation by isolate SK3 (implying the involvement of multicopper oxidase enzyme), allowing a 2-fold greater Mn removal rate, compared to the well-studied Mn(II)-oxidizer Ps. putida MnB1. Poorly crystalline biogenic birnessite was formed by isolate SK3 via one-electron transfer oxidation, gradually raising the Mn AOS (average oxidation state) to 3.80 in 72 h. Together with its efficient in vitro Mn(II) oxidation behavior, a high Mn AOS level of 3.75 was observed with the pipeline Mn-deposit sample collected in situ. The overall results, including the microbial community structure analysis of the pipeline sample, suggest that the natural Mn(II) attenuation phenomenon was characterized by robust in situ activity of Mn(II) oxidizers (including strain SK3) for continuous generation of Mn(IV). This likely synergistically facilitated chemical Mn(II)/Mn(IV) synproportionation for effective Mn removal in the complex ecosystem established in this artificial pipeline structure. The potential utility of isolate SK3 is illustrated for further industrial application in metal refinery wastewater treatment processes.

MopA, the Mn Oxidizing Protein From Erythrobacter sp. SD-21, Requires Heme and NAD+ for Mn(II) Oxidation

Bacterial manganese (Mn) oxidation is catalyzed by a diverse group of microbes and can affect the fate of other elements in the environment. Yet, we understand little about the enzymes that catalyze this reaction. The Mn oxidizing protein MopA, from Erythrobacter sp. strain SD-21, is a heme peroxidase capable of Mn(II) oxidation. Unlike Mn oxidizing multicopper oxidase enzymes, an understanding of MopA is very limited. Sequence analysis indicates that MopA contains an N-terminal heme peroxidase domain and a C-terminal calcium binding domain. Heterologous expression and nickel affinity chromatography purification of the N-terminal peroxidase domain (MopA-hp) from Erythrobacter sp. strain SD-21 led to partial purification. MopA-hp is a heme binding protein that requires heme, NAD⁺, and calcium (Ca²⁺) for activity. Mn oxidation is also stimulated by the presence of pyrroloquinoline quinone. MopA-hp has a K_M for Mn(II) of 154 ± 46 μM and k_cat = 1.6 min⁻¹. Although oxygen requiring MopA-hp is homologous to peroxidases based on sequence, addition of hydrogen peroxide and hydrogen peroxide scavengers had little effect on Mn oxidation, suggesting this is not the oxidizing agent. These studies provide insight into the mechanism by which MopA oxidizes Mn.

Continuous degradation of ciprofloxacin in a manganese redox cycling system driven by Pseudomonas putida MnB-1

Ciprofloxacin (CIP), as an extensively used antibiotic, has been widely detected at a high level in the environment and has raised environmental pollution concerns. Thus, efficient and cost-effective methods for CIP degradation are highly desired. Biologically produced manganese oxides (BioMnO_x) offer a promising perspective for CIP degradation because of their catalytic reactivity and cost-effectiveness. However, the release of Mn(II) from BioMnO_x prevents the further oxidation of pollutants. As a consequence, continuous CIP degradation by BioMnO_x is not feasible. In this work, a manganese redox cycling system driven by Pseudomonas putida MnB-1 was constructed for continuous degradation of CIP. In such a system CIP was oxidized continuously and rapidly by re-oxidizing the formed Mn(II) to regenerate reactive BioMnO_x, which also protected the strain from CIP toxicity. CIP was degraded through N-dealkylation passway. No significant loss of BioMnO_x reactivity was observed in three-cycle CIP degradation process, suggesting the stability of this system. An overlooked intracellular BioMnO_x, which was involved in CIP degradation, was discovered in P. putida MnB-1. Moreover, the important role of Mn(III) in facilitating CIP removal in this system was also identified. This work provides useful information to better understand the degradation of antibiotic compounds mediated by microbes in environments.

Characterization of manganese oxidation by Brevibacillus at different ecological conditions

Bacterial Mn(II) oxidation plays an important role in the biogeochemical cycling of manganese and many trace metals. This study describes Mn(II) oxidation by two isolated manganese (Mn)-oxidizing strains that were identified and assigned as Brevibacillus brevis MO1 and Brevibacillus parabrevis MO2 based on physiochemical and phylogenetic characterizations. The ecological conditions influenced Mn(II) oxidation by both strains. Mn(II) stimulated the growth of strain MO2 while slightly inhibiting strain MO1. Mn(II)-oxidizing activity of two strains was enhanced with increase of initial pH, and maximum Mn(II)-oxidizing activity occurred at pH 8 for both strains (93.5%-94.0%). Brevibacillus showed the capability of mesophilic and psychrophilic Mn(II) oxidation. X-ray photoelectron spectroscopy (XPS) analysis indicated that the biogenic manganese oxides had an intermediate valence between 3 and 4. These results demonstrated that Brevibacillus, which is capable of oxidizing dissolved Mn(II), will be a suitable strain for exploring the mechanism of manganese oxidation in engineered and natural environments.

Oxidative Formation and Removal of Complexed Mn(III) by Pseudomonas Species

The observation of significant concentrations of soluble Mn(III) complexes in oxic, suboxic, and some anoxic waters has triggered a re-evaluation of the previous Mn paradigm which focused on the cycling between soluble Mn(II) and insoluble Mn(III,IV) species as operationally defined by filtration. Though Mn(II) oxidation in aquatic environments is primarily bacterially-mediated, little is known about the effect of Mn(III)-binding ligands on Mn(II) oxidation nor on the formation and removal of Mn(III). Pseudomonas putida GB-1 is one of the most extensively investigated of all Mn(II) oxidizing bacteria, encoding genes for three Mn oxidases (McoA, MnxG, and MopA). P. putida GB-1 and associated Mn oxidase mutants were tested alongside environmental isolates Pseudomonas hunanensis GSL-007 and Pseudomonas sp. GSL-010 for their ability to both directly oxidize weakly and strongly bound Mn(III), and to form these complexes through the oxidation of Mn(II). Using Mn(III)-citrate (weak complex) and Mn(III)-DFOB (strong complex), it was observed that P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 and mutants expressing only MnxG and McoA were able to directly oxidize both species at varying levels; however, no oxidation was detected in cultures of a P. putida mutant expressing only MopA. During cultivation in the presence of Mn(II) and citrate or DFOB, P. putida GB-1, P. hunanensis GSL-007 and Pseudomonas sp. GSL-010 formed Mn(III) complexes transiently as an intermediate before forming Mn(III/IV) oxides with the overall rates and extents of Mn(III,IV) oxide formation being greater for Mn(III)-citrate than for Mn(III)-DFOB. These data highlight the role of bacteria in the oxidative portion of the Mn cycle and suggest that the oxidation of strong Mn(III) complexes can occur through enzymatic mechanisms involving multicopper oxidases. The results support the observations from field studies and further emphasize the complexity of the geochemical cycling of manganese.

Draft Genome Sequence of Mn(II)-Oxidizing Pseudomonas resinovorans Strain MO-1

Pseudomonas resinovorans strain MO-1, which possesses a high ability to oxidize Mn(II), has been isolated from oligotrophic pond sediment. The draft genome sequence consists of 6,252,942 bp and has a G+C content of 63.4%. Strain MO-1 has 5,694 coding sequences, including 13 putative Mn(II) oxidation genes.

Synergistic effects of biogenic manganese oxide and Mn(II)-oxidizing bacterium Pseudomonas putida strain MnB1 on the degradation of 17 α-ethinylestradiol

While biogenic manganese oxide (BMO) generated via the oxidation of Mn(II) by the Mn-oxidizing bacteria (MOB) have received attention, the relative roles of biological activity by MOB themselves were not clearly investigated. In this study, the synergistic effects of BMO and MOB Pseudomonas putida strain MnB1 on the degradation of 17α-ethinylestradiol (EE2) was investigated. Experiments with BMO in the presence of P. putida MnB1 showed 15-fold higher removal than that with BMO alone, suggesting that EE2 degradation was mediated by the biological activity of MOB as well as abiotic reaction by BMO. Trapping experiments with pyrophosphate (PP) proved that Mn(III) intermediate formed during the biological process from Mn (II) to Mn (IV) contribute much to the EE2 removal. Also, sharp decreases in EE2 removal were observed when microbial activity was inactivated by heat treatment or sodium azide. From this study, the EE2 removal mechanisms by BMO in the presence P. putida MnB1 are described as follows: (1) abiotic oxidation of EE2 by BMO occurs. (2) P. putida MnB1 indirectly oxidizes EE2 by transferring electrons from the Mn (III) intermediate. (3) P. putida MnB1 continuously re-oxidizes the Mn(II) released from the oxidative degradation of EE2 by BMO, generating new Mn(III)-intermediates or BMO.

Molecular dynamics simulation studies suggests unconventional roles of non-secretary laccases from enteropathogenic gut bacteria and Cryptococcus neoformans serotype D

Laccase in Cryptococcus neoformans is covalently linked to the carbohydrate moiety of the cell wall, which allows it to get access to the different substrates for catalyzing their oxidation and therefore plays a vital role in the virulence. The laccase gene (3.0 kb) from C. neoformans serotype D was amplified, cloned and sequenced for protein modeling, docking and simulation studies. The three dimensional homology models of laccase protein from C. neoformans and other pathogenic gut bacteria were docked with selected biomolecules like prostaglandins (PG), membrane phospholipids, neurotransmitters (serotonin) using GOLD software. The GOLDscore values of laccase from C. neoformans docked with prostaglandinH₂ (59.76), prostaglandinG₂ (59.45), prostaglandinE₂ (60.99), phosphatidylinositol (54.95), phosphatidylcholine (46.26), phosphatidylserine (55.26), arachidonic acid (53.08) and serotonin (46.22) were similar to the laccase from enteropathogenic bacteria but showed a better binding affinity as compared to that of the non-pathogenic bacteria (e.g. Bacillus safensis, Bacillus pumilus and Bacillus subtilis). The RMSD of MD simulation study done for 25 ns using laccase protein from C. neoformans complexed with phosphatidylcholine was found to be highly stable, followed by the laccase-PGE₂ and laccase-serotonin complexes. Furthermore, the binding free energy results were found to support the docking and MD simulation results. The present study implies that few candidate ligands can be intermediate substrate in the catalysis of microbial laccases, which can further play some crucial role in the cell signaling and pathogenesis of enteropathogenic gut micro flora and C. neoformans.

High Manganese Tolerance and Biooxidation Ability of Serratia marcescens Isolated from Manganese Mine Water in Minas Gerais, Brazil

Manganese is an important metal for the maintenance of several biological functions, but it can be toxic in high concentrations. One of the main forms of human exposure to metals, such as manganese (Mn), is the consumption of solar salt contaminated. Mn-tolerant bacteria could be used to decrease the concentration of this metal from contaminated sites through safer environmental-friendly alternative technology in the future. Therefore, this study was undertaken to isolate and identify Mn resistant bacteria from water samples collected from a Mn mine in the Iron Quadrangle region (Minas Gerais, Brazil). Two bacterial isolates were identified as Serratia marcescens based on morphological, biochemical, 16S rDNA gene sequencing and phylogeny analysis. Maximum resistance of the selected isolates against increasing concentrations of Mn(II), up to 1200 mg L^-1 was determined in solid media. A batch assay was developed to analyze and quantify the Mn removal capacities of the isolates. Biological Mn removal capacities of over 55% were detected for both isolates. Whereas that mechanism like biosorption, precipitation and oxidation could be explaining the Mn removal, we seek to give an insight into some of the molecular mechanisms adopted by S. marcescens isolates. For this purpose, the following approaches were adopted: leucoberbelin blue I assay, Mn(II) oxidation by cell-free filtrate and electron microscopy and energy-dispersive X-ray spectroscopy analyses. Overall, these results indicate that S. marcescens promotes Mn removal in an indirect mechanism by the formation of Mn oxides precipitates around the cells, which should be further explored for potential biotechnological applications for water recycling both in hydrometallurgical and mineral processing operations.

From the Surface to the Deep-Sea: Bacterial Distributions across Polymetallic Nodule Fields in the Clarion-Clipperton Zone of the Pacific Ocean

Marine bacteria regulate fluxes of matter and energy essential for pelagic and benthic organisms and may also be involved in the formation and maintenance of commercially valuable abyssal polymetallic nodules. Future mining of these nodule fields is predicted to have substantial effects on biodiversity and physicochemical conditions in mined areas. Yet, the identity and distributions of bacterial populations in deep-sea sediments and associated polymetallic nodules has received relatively little attention. We examined bacterial communities using high-throughput sequencing of bacterial 16S rRNA gene fragments from samples collected in the water column, sediment, and polymetallic nodules in the Pacific Ocean (bottom depth ≥4,000 m) in the eastern Clarion-Clipperton Zone. Operational taxonomic units (OTUs; defined at 99% 16S rRNA gene identity) affiliated with JTB255 (Gammaproteobacteria) and Rhodospirillaceae (Alphaproteobacteria) had higher relative abundances in the nodule and sediment habitats compared to the water column. Rhodobiaceae family and Vibrio OTUs had higher relative abundance in nodule samples, but were less abundant in sediment and water column samples. Bacterial communities in sediments and associated with nodules were generally similar; however, 5,861 and 6,827 OTUs found in the water column were retrieved from sediment and nodule habitats, respectively. Cyanobacterial OTUs clustering among Prochlorococcus and Synechococcus were detected in both sediments and nodules, with greater representation among nodule samples. Such results suggest that vertical export of typically abundant photic-zone microbes may be an important process in delivery of water column microorganisms to abyssal habitats, potentially influencing the structure and function of communities in polymetallic nodule fields.

Mn(II) Oxidation by the Multicopper Oxidase Complex Mnx: A Binuclear Activation Mechanism

The bacterial protein complex Mnx contains a multicopper oxidase (MCO) MnxG that, unusually, catalyzes the two-electron oxidation of Mn(II) to MnO₂ biomineral, via a Mn(III) intermediate. Although Mn(III)/Mn(II) and Mn(IV)/Mn(III) reduction potentials are expected to be high, we find a low reduction potential, 0.38 V (vs Normal Hydrogen Electrode, pH 7.8), for the MnxG type 1 Cu²⁺, the electron acceptor. Indeed the type 1 Cu²⁺ is not reduced by Mn(II) in the absence of molecular oxygen, indicating that substrate oxidation requires an activation step. We have investigated the enzyme mechanism via electronic absorption spectroscopy, using chemometric analysis to separate enzyme-catalyzed MnO₂ formation from MnO₂ nanoparticle aging. The nanoparticle aging time course is characteristic of nucleation and particle growth; rates for these processes followed expected dependencies on Mn(II) concentration and temperature, but exhibited different pH optima. The enzymatic time course is sigmoidal, signaling an activation step, prior to turnover. The Mn(II) concentration and pH dependence of a preceding lag phase indicates weak Mn(II) binding. The activation step is enabled by a pK_a > 8.6 deprotonation, which is assigned to Mn(II)-bound H₂O; it induces a conformation change (consistent with a high activation energy, 106 kJ/mol) that increases Mn(II) affinity. Mnx activation is proposed to decrease the Mn(III/II) reduction potential below that of type 1 Cu(II/I) by formation of a hydroxide-bridged binuclear complex, Mn(II)(μ-OH)Mn(II), at the substrate site. Turnover is found to depend cooperatively on two Mn(II) and is enabled by a pK_a 7.6 double deprotonation. It is proposed that turnover produces a Mn(III)(μ-OH)₂Mn(III) intermediate that proceeds to the enzyme product, likely Mn(IV)(μ-O)₂Mn(IV) or an oligomer, which subsequently nucleates MnO₂ nanoparticles. We conclude that Mnx exploits manganese polynuclear chemistry in order to facilitate an otherwise difficult oxidation reaction, as well as biomineralization. The mechanism of the Mn(III/IV) conversion step is elucidated in an accompanying paper .

Mechanistic insights into manganese oxidation of a soil-borne Mn(II)-oxidizing Escherichia coli strain by global proteomic and genetic analyses

An iTRAQ-based comparative and quantitative proteomics analysis of a soil-borne Mn(II)-oxidizing bacterium, Escherichia coli MB266, was conducted during the exponential and stationary growth phases. A total of 1850 proteins were identified in 4 samples, of which 373 and 456 proteins were significantly up- or down-regulated in at least one pairwise comparison, respectively. The iTRAQ data indicated that several enzymes involved in fatty acid metabolism (i.e., FabA, FabD and FabZ) and pyruvate metabolism (particularly pyruvate oxidase PoxB) were significantly up-regulated, while those related to the tricarboxylic acid cycle (such as FrdB, FumB and AcnA) and methylcitrate cycle (i.e., PrpC) were inactivated in the presence of 1 mM Mn(II); the amounts of some stress response and signal transduction system-related proteins (i.e., Spy) were remarkably increased, and the cold shock protein CspD was significantly up-regulated during the exponential growth phase. However, all verified heat shock proteins remained unchanged. The reactive oxygen species response and some redox enzymes might also be involved in Mn oxidation processes. The involvement of several cellular proteins in Mn(II) oxidation, including PoxB, Spy and MCO266, was further confirmed by gene disruption and expression complementation experiments. Based on these results, a signal transduction mechanism coupled to Mn oxidation was proposed.

Biotechnological and Biochemical Utilization of Lignin

This chapter provides an overview of the biosynthesis and structure of lignin. Moreover, examples of the commercial use of lignin and its promising future implementation are briefly described. Many applications are still hampered by the properties of technical lignins. Thus, the major challenge is the conversion of lignins into suitable building blocks or aromatics in order to open up new avenues for the usage of this renewable raw material. This chapter focuses on details about natural lignin degradation by fungi and bacteria, which harbor potential tools for lignin degradation and modification, which might help to develop eco-efficient processes for lignin utilization.

Manganese in Marine Microbiology

The importance of manganese in the physiology of marine microbes, the biogeochemistry of the ocean and the health of microbial communities of past and present is emerging. Manganese is distributed widely throughout the global ocean, taking the form of an essential antioxidant (Mn²⁺), a potent oxidant (Mn³⁺) and strong adsorbent (Mn oxides) sequestering disproportionately high levels of trace metals and nutrients in comparison to the surrounding seawater. Manganese is, in fact, linked to nearly all other elemental cycles and intricately involved in the health, metabolism and function of the ocean's microbiome. Here, we briefly review the diversity of microbes and pathways responsible for the transformation of Mn within the three Mn pools and their distribution within the marine environment. Despite decades of interrogation, we still have much to learn about the players, mechanisms and consequences of the Mn cycle, and new and exciting discoveries are being made at a rapid rate. What is clear is the dynamic and ever-inspiring complexity of reactions involving Mn, and the acknowledgement that microorganisms are the catalytic engine driving the Mn cycle.

Identification of a Third Mn(II) Oxidase Enzyme in Pseudomonas putida GB-1

The oxidation of soluble Mn(II) to insoluble Mn(IV) is a widespread bacterial activity found in a diverse array of microbes. In the Mn(II)-oxidizing bacterium Pseudomonas putida GB-1, two Mn(II) oxidase genes, named mnxG and mcoA, were previously identified; each encodes a multicopper oxidase (MCO)-type enzyme. Expression of these two genes is positively regulated by the response regulator MnxR. Preliminary investigation into putative additional regulatory pathways suggested that the flagellar regulators FleN and FleQ also regulate Mn(II) oxidase activity; however, it also revealed the presence of a third, previously uncharacterized Mn(II) oxidase activity in P. putida GB-1. A strain from which both of the Mn(II) oxidase genes and fleQ were deleted exhibited low levels of Mn(II) oxidase activity. The enzyme responsible was genetically and biochemically identified as an animal heme peroxidase (AHP) with domain and sequence similarity to the previously identified Mn(II) oxidase MopA. In the ΔfleQ strain, P. putida GB-1 MopA is overexpressed and secreted from the cell, where it actively oxidizes Mn. Thus, deletion of fleQ unmasked a third Mn(II) oxidase activity in this strain. These results provide an example of an Mn(II)-oxidizing bacterium utilizing both MCO and AHP enzymes.

IMPORTANCE

The identity of the Mn(II) oxidase enzyme in Pseudomonas putida GB-1 has been a long-standing question in the field of bacterial Mn(II) oxidation. In the current work, we demonstrate that P. putida GB-1 employs both the multicopper oxidase- and animal heme peroxidase-mediated pathways for the oxidation of Mn(II), rendering this model organism relevant to the study of both types of Mn(II) oxidase enzymes. The presence of three oxidase enzymes in P. putida GB-1 deepens the mystery of why microorganisms oxidize Mn(II) while providing the field with the tools necessary to address this question. The initial identification of MopA as a Mn(II) oxidase in this strain required the deletion of FleQ, a regulator involved in both flagellum synthesis and biofilm synthesis in Pseudomonas aeruginosa Therefore, these results are also an important step toward understanding the regulation of Mn(II) oxidation.

Biological Low-pH Mn(II) Oxidation in a Manganese Deposit Influenced by Metal-Rich Groundwater

The mechanisms, key organisms, and geochemical significance of biological low-pH Mn(II) oxidation are largely unexplored. Here, we investigated the structure of indigenous Mn(II)-oxidizing microbial communities in a secondary subsurface Mn oxide deposit influenced by acidic (pH 4.8) metal-rich groundwater in a former uranium mining area. Microbial diversity was highest in the Mn deposit compared to the adjacent soil layers and included the majority of known Mn(II)-oxidizing bacteria (MOB) and two genera of known Mn(II)-oxidizing fungi (MOF). Electron X-ray microanalysis showed that romanechite [(Ba,H2O)2(Mn(4+),Mn(3+))5O10] was conspicuously enriched in the deposit. Canonical correspondence analysis revealed that certain fungal, bacterial, and archaeal groups were firmly associated with the autochthonous Mn oxides. Eight MOB within the Proteobacteria, Actinobacteria, and Bacteroidetes and one MOF strain belonging to Ascomycota were isolated at pH 5.5 or 7.2 from the acidic Mn deposit. Soil-groundwater microcosms demonstrated 2.5-fold-faster Mn(II) depletion in the Mn deposit than adjacent soil layers. No depletion was observed in the abiotic controls, suggesting that biological contribution is the main driver for Mn(II) oxidation at low pH. The composition and species specificity of the native low-pH Mn(II) oxidizers were highly adapted to in situ conditions, and these organisms may play a central role in the fundamental biogeochemical processes (e.g., metal natural attenuation) occurring in the acidic, oligotrophic, and metalliferous subsoil ecosystems.

IMPORTANCE

This study provides multiple lines of evidence to show that microbes are the main drivers of Mn(II) oxidation even at acidic pH, offering new insights into Mn biogeochemical cycling. A distinct, highly adapted microbial community inhabits acidic, oligotrophic Mn deposits and mediates biological Mn oxidation. These data highlight the importance of biological processes for Mn biogeochemical cycling and show the potential for new bioremediation strategies aimed at enhancing biological Mn oxidation in low-pH environments for contaminant mitigation.

Molecular and biochemical characterization of a new thermostable bacterial laccase from Meiothermus ruber DSM 1279

A new bacterial laccase gene (mrlac) fromMeiothermus ruberDSM 1279 was successfully overexpressed to produce a laccase (Mrlac) in soluble form inEscherichia coliduring simultaneous overexpression of a chaperone protein (GroEL/ES).

Indirect Manganese Removal by Stenotrophomonas sp. and Lysinibacillus sp. Isolated from Brazilian Mine Water

Manganese is a contaminant in the wastewaters produced by Brazilian mining operations, and the removal of the metal is notoriously difficult because of the high stability of the Mn(II) ion in aqueous solutions. To explore a biological approach for removing excessive amounts of aqueous Mn(II), we investigated the potential of Mn(II) oxidation by both consortium and bacterial isolates from a Brazilian manganese mine. A bacterial consortium was able to remove 99.7% of the Mn(II). A phylogenetic analysis of isolates demonstrated that the predominant microorganisms were members of Stenotrophomonas, Bacillus, and Lysinibacillus genera. Mn(II) removal rates between 58.5% and 70.9% were observed for Bacillus sp. and Stenotrophomonas sp. while the Lysinibacillus isolate 13P removes 82.7%. The catalytic oxidation of Mn(II) mediated by multicopper oxidase was not properly detected; however, in all of the experiments, a significant increase in the pH of the culture medium was detected. No aggregates inside the cells grown for a week were found by electronic microscopy. Nevertheless, an energy-dispersive X-ray spectroscopy of the isolates revealed the presence of manganese in Stenotrophomonas sp. and Lysinibacillus sp. grown in K medium. These results suggest that members of Stenotrophomonas and Lysinibacillus genera were able to remove Mn(II) by a nonenzymatic pathway.