Manganese oxidation by Leptothrix discophora

Microbial consortium involved in ferromanganese and francolite biomineralization in an anchialine environment (Zinzulùsa Cave, Castro, Italy)

Tidally-influenced subterranean settings represent natural geomicrobiological laboratories, relatively unexplored, that facilitate the investigation of new biomineralization processes. The unusual water chemistry of Zinzulùsa Cave and its oligotrophic and aphotic conditions have allowed the development of a unique ecosystem in which complex bacterial activities induce rare biomineralization processes. A diversified microbial community develops on centimeter-thick crusts that form in the submerged part of the cave. The crusts are formed of Ca-phosphate minerals, mostly carbonate-fluoroapatite (francolite), covered by a black crust, few microns in thickness, composed of ferromanganiferous oxides (hematite and vernadite). Diffuse coccoidal and filamentous bacteria and amorphous organic matter are mixed with the minerals. The micromorphologies and comparative 16S rRNA gene-based metabarcoding analyses identify a "core microbiota" also common to other natural environments characterized by FeMn and Ca-phosphate mineralization. The microbiota is characterized by nitrifying, sulfide/sulfur/thiosulfate-oxidizing and sulfate/thiosulfate/sulfur-reducing bacteria. In addition, manganese-oxidizing bacteria include the recently described "Ca. Manganitrophus noduliformans" and an abundance of bacteria belonging to the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum, as well as Haliangiales (fruiting body-forming bacteria) and Hyphomicrobiales (stalked and budding bacteria) that are known to produce extracellular polymers that trap iron and manganese oxides. 16S rRNA gene metabarcoding analysis showed the presence of bacteria able to utilize many organic P substrates, including Ramlibacter, and SEM images revealed traces of fossilized microorganisms resembling "cable bacteria", which may play a role in Ca-phosphate biomineralization. Overall, the data indicate biomineralization processes induced by microbial metabolic activities for both ferromanganiferous oxide and francolite components of these crusts.

Nonribosomal Peptide Synthetase Specific Genome Amplification Using Rolling Circle Amplification for Targeted Gene Sequencing

Next-generation sequencing has transformed the acquisition of vast amounts of genomic information, including the rapid identification of target gene sequences in metagenomic databases. However, dominant species can sometimes hinder the detection of rare bacterial species. Therefore, a highly sensitive amplification technique that can selectively amplify bacterial genomes containing target genes of interest was developed in this study. The rolling circle amplification (RCA) method can initiate amplification from a single locus using a specific single primer to amplify a specific whole genome. A mixed cell suspension was prepared using Pseudomonas fluorescens ATCC17400 (targeting nonribosomal peptide synthetase [NRPS]) and Escherichia coli (non-target), and a specific primer designed for the NRPS was used for the RCA reaction. The resulting RCA product (RCP) amplified only the Pseudomonas genome. The NRPS was successfully amplified using RCP as a template from even five cells, indicating that the single-priming RCA technique can specifically enrich the target genome using gene-specific primers. Ultimately, this specific genome RCA technique was applied to metagenomes extracted from sponge-associated bacteria, and NRPS sequences were successfully obtained from an unknown sponge-associated bacterium. Therefore, this method could be effective for accessing species-specific sequences of NRPS in unknown bacteria, including viable but non-culturable bacteria.

Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India

BACKGROUND

The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge.

RESULTS

To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances.

CONCLUSION

Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section.

Characterization of Mn3 O4 -MnO2 nanocomposites biosynthesized by cell lysate of Haloferax alexandrinus GUSF-1

Manganese oxide nanocomposites attract huge attention in various biotechnological fields due to their extensive catalytic properties. This study reports an easy, rapid, and cost-effective method of using the cell lysate of haloarchaeon, Haloferax alexandrinus GUSF-1 for the synthesis of manganese oxide nanoparticles. The reaction between the cell lysate and manganese sulfate resulted in the formation of a dark brown precipitate within 48 h at room temperature. The X-ray diffraction pattern showed the existence of Mn3 O4 and MnO2 phases consistent with the JCPDS card no. (01-075-1560 and 00-050-0866). The dark brown colloidal suspension of MnO3 -MnO2 in methanol showed maximum absorption between 220 and 260 nm. The EDX spectrum confirmed the presence of manganese and oxygen. The Transmission electron microscopy revealed the spherical morphology with an average particle size between 30 and 60 nm. The magnetic moment versus magnetic field (MH) curve, at room temperature (300 K) did not saturate even at a high magnetic field (±3T) indicating the paramagnetic nature of the prepared nanocomposite. The Atomic Emission Spectroscopic analysis showed a negligible amount of soluble manganese (0.03 ppm in 50 ppm) in the Mn3 O4 -MnO2 suspension suggesting the maximum stability of the material in the solvent over time. Interstingly, Mn3 O4 -MnO2 nanocomposites evidenced antimicrobial activity in the order of Pseudomonas aeruginosa > Salmonella typhi > Escherichia coli > Proteus vulgaris > Candida albicans > Staphylococcus aureus. Conclusively, this is the first report on the formation of Mn3 O4 -MnO2 nanocomposites using cell lysate of salt pan haloarcheon Haloferax alexandrinus GUSF-1 with antimicrobial potential.

Effects of Algal Extracellular Polysaccharides on the Formation of Filamentous Manganese Oxide Particles in the Near-Bottom Layer of Lake Biwa

Filamentous manganese (Mn) oxide particles, which occur in the suboxic zone of stratified waterbodies, are important drivers of diverse elemental cycles. These particles are considered to be bacteriogenic; despite the importance of biogeochemical implications, however, the environmental factor responsible for their formation has not been identified. The aim of this study was to demonstrate the involvement of algal extracellular polysaccharides in Mn oxide particle formation. Based on this study of laboratory cultures of a model Mn(II)-oxidizing bacterium, the supply of algal extracellular mucilage was shown to stimulate Mn(II) oxidation and thus the production of filamentous Mn oxide particles. This observation was consistent with the results obtained for naturally occurring particles collected from a near-bottom layer (depth of approximately 90 m) in the northern basin of Lake Biwa, Japan, that is, most Mn particles resembling δ-MnO₂ were associated with an extracellular mucilage-like gelatinous matrix, which contained dead algal cells and was lectin-stainable. In the lake water column, polysaccharides produced by algal photosynthesis sank to the bottom layer. The analysis of the quality of water samples, which have been collected from the study site for 18 years, reveals that the annual average total phytoplankton biovolume in the surface layer correlates with the density of filamentous Mn particles in the near-bottom layer. Among different phytoplankton species, green algae appeared to be the key species. The results of this study suggest that algal extracellular polysaccharides serve as an important inducer for the formation of filamentous Mn oxide particles in the near-bottom layer of the northern basin of Lake Biwa.

Complete oxidative degradation of diclofenac via coupling free radicals and oxygenases of a micro/nanostructured biogenic Mn oxide composite from engineered Pseudomonas sp. MB04R-2

Oxidative degradation can effectively degrade aromatic emerging contaminants (ECs). However, the degradability of lone inorganic/biogenic oxides or oxidases is typically limited when treating polycyclic ECs. Herein, we report a dual-dynamic oxidative system comprising engineered Pseudomonas and biogenic Mn oxides (BMO), which completely degrades diclofenac (DCF), a representative halogen-containing polycyclic EC. Correspondingly, recombinant Pseudomonas sp. MB04R-2 was constructed via gene deletion and chromosomal insertion of a heterologous multicopper oxidase cotA, allowing for enhanced Mn(II)-oxidizing activity and rapid formation of the BMO aggregate complex. Additionally, we characterized it as a micro/nanostructured ramsdellite (MnO₂) composite using multiple-phase composition and fine structure analyses. Furthermore, using real-time quantitative polymerase chain reaction, gene knockout, and expression complementation of oxygenase genes, we demonstrated the central and associative roles of intracellular oxygenases and cytogenic/BMO-derived free radicals (FRs) in degrading DCF and determined the effects of FR excitation and quenching on the DCF degradation efficiency. Finally, after identifying the degraded intermediates of ²H-labeled DCF, we constructed the DCF metabolic pathway. In addition, we evaluated the degradation and detoxification effects of the BMO composite on DCF-containing urban lake water and on biotoxicity in zebrafish embryos. Based on our findings, we proposed a mechanism for oxidative degradation of DCF by associative oxygenases and FRs.

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.

Synthesis, optimization, and characterization of biogenic manganese oxide (BioMnOx) by bacterial isolates from mangrove soils with sorbents property towards different toxic metals

Manganese oxidizing bacteria, Bacillus mycoides and Bacillus subtilis were isolated from mangrove soils and optimized for the removal of Mn(II) with simultaneous production of biogenic manganese oxide (BioMnOx). The removal rate of Mn(II) was 90% in 48 h for B. mycoides and 72 h for B. subtilis under the optimized conditions at pH 7, temperature 37 °C, 120 rpm, with 1% inoculum containing 10 mM MnCl₂. Scanning electron microscopy (SEM), Transmission electron microscopy (TEM), Energy dispersive X-Ray analysis (EDAX), Fourier-transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) were used to characterize the synthesized biogenic manganese oxide. BioMnOx by Bacillus mycoides and Bacillus subtilis were identified as Bixbyite (Mn₂O₃) and Hausmannite (Mn₃O₄), respectively, with nano-sized monocrystalline nature. BioMnOx of Bacillus subtilis strain was more efficient in the removal of metals Zn and Co than BioMnOx of Bacillus mycoides except for mercury. The removal property of synthesized BioMnOx could be applied to treat multi-metal containing wastewater.

Challenges of Measuring Soluble Mn(III) Species in Natural Samples

Soluble Mn(III)-L complexes appear to constitute a substantial portion of manganese (Mn) in many environments and serve as critical high-potential species for biogeochemical processes. However, the inherent reactivity and lability of these complexes-the same chemical characteristics that make them uniquely important in biogeochemistry-also make them incredibly difficult to measure. Here we present experimental results demonstrating the limits of common analytical methods used to quantify these complexes. The leucoberbelin-blue method is extremely useful for detecting many high-valent Mn species, but it is incompatible with the subset of Mn(III) complexes that rapidly decompose under low-pH conditions-a methodological requirement for the assay. The Cd-porphyrin method works well for measuring Mn(II) species, but it does not work for measuring Mn(III) species, because additional chemistry occurs that is inconsistent with the proposed reaction mechanism. In both cases, the behavior of Mn(III) species in these methods ultimately stems from inter- and intramolecular redox chemistry that curtails the use of these approaches as a reflection of ligand-binding strength. With growing appreciation for the importance of high-valent Mn species and their cycling in the environment, these results underscore the need for additional method development to enable quantifying such species rapidly and accurately in nature.

Complete Degradation and Detoxification of Ciprofloxacin by a Micro-/Nanostructured Biogenic Mn Oxide Composite from a Highly Active Mn2+-Oxidizing Pseudomonas Strain

Ciprofloxacin (CIP), as a representative broad-spectrum antibiotic, poses a major threat to human health and the ecological environment as a result of its abuse and emissions. In this study, a highly active Mn²⁺-oxidizing bacterium, Pseudomonas sp. CCTCC M2014168, was induced to form micro-/nanostructured biogenic Mn oxide (BMO) aggregates through continuous culturing with 1 mmoL^-1 Mn²⁺. Following the characterization of Mn⁴⁺ oxides and the micro-/nanostructures by scanning electron microscopy, high-resolution transmission electron microscopy and X-ray diffraction assays, the BMO composites were subjected to CIP degradation and detoxification in laboratory trials. High-performance liquid chromatograph (HPLC) analysis identified that the BMO composites were capable of completely degrading CIP, and HPLC with a mass spectrometer (LC/MS) assays identified three intermediates in the degradation pathway. The reaction temperature, pH and initial ciprofloxacin concentration substantially affected the degradation efficiency of CIP to a certain extent, and the metal ions Mg²⁺, Cu²⁺, Ni²⁺ and Co²⁺ exerted significant inhibitory effects on CIP degradation. A toxicity test of the degradation products showed that CIP was completely detoxified by degradation. Moreover, the prepared BMO composite exhibited a high capacity for repeated degradation and good performance in continuous degradation cycles, as well as a high capacity to degrade CIP in real natural water.

Biogenic manganese oxides combined with 1-hydroxybenzotriazol and an Mn(II)-oxidizing enzyme from Pleosporales sp. Mn1 oxidize 3,4-dimethoxytoluene to yield 3,4-dimethoxybenzaldehyde

Using soil samples, we screened for microbes that produce biogenic manganese oxides (BMOs) and isolated Mn(II)-oxidizing fungus, namely Pleosporales sp. Mn1 (Mn1). We purified the Mn(II)-oxidizing enzyme from intracellular extracts of Mn1. The enzyme oxidized Mn(II) most effectively at pH 7.0 and 45 °C. The N-terminal amino acid sequence of the purified enzyme possessed homology with multicopper oxidases in fungi. The properties of the enzyme and the effects of the pH and inhibitors on the Mn(II)-oxidization activity suggested that the enzyme is a member of the multicopper oxidase family. The X-ray diffraction pattern of the BMOs produced by Mn1 showed a strong correlation with that of a typical poorly crystalized vernadite (δ-MnO₂). Since BMOs are some of the most reactive materials in the environment, we investigated a potential new application of BMOs as oxidation catalysts. We confirmed that BMOs oxidized aromatic methyl groups when combined with the purified enzyme and a mediator, 1-hydroxybenzotriazole (HBT). BMO oxidation of 3,4-dimethoxytoluene achieved a better yield than that of abiotic MnO₂ and white-rot fungus laccase under acidic and neutral pH conditions. Under neutral pH, the BMOs oxidized 3,4-dimethoxytoluene to yield 200-fold more 3,4-dimethoxybenzaldehyde than that of abiotic MnO₂. This is the first report to reveal that BMOs combined with a Mn(II)-oxidizing enzyme and mediator can oxidize aromatic hydrocarbons to yield corresponding aldehydes.

Molecular Cloning and Heterologous Expression of Manganese(II)-Oxidizing Enzyme from Acremonium strictum Strain KR21-2

Diverse ascomycete fungi oxidize manganese(II) [Mn(II)] and produce Mn(III, IV) oxides in terrestrial and freshwater environments. Although multicopper oxidase (MCO) is considered to be a key catalyst in mediating Mn(II) oxidation in ascomycetes, the responsible gene and its product have not been identified. In this study, a gene, named mco1, encoding Mn(II)-oxidizing MCO from Acremonium strictum strain KR21-2 was cloned and heterologously expressed in the methylotrophic yeast Pichia pastoris. Based on the phylogenetic relationship, similarity of putative copper-binding motifs, and homology modeling, the gene product Mco1 was assigned to a bilirubin oxidase. Mature Mco1 was predicted to be composed of 565 amino acids with a molecular mass of 64.0 kDa. The recombinant enzyme oxidized Mn(II) to yield spherical Mn oxides, several micrometers in diameter. Zinc(II) ions added to the reaction mixture were incorporated by the Mn oxides at a Zn/Mn molar ratio of 0.36. The results suggested that Mco1 facilitates the growth of the micrometer-sized Mn oxides and affects metal sequestration through Mn(II) oxidation. This is the first report on heterologous expression and identification of the Mn(II) oxidase enzyme in Mn(II)-oxidizing ascomycetes. The cell-free, homogenous catalytic system with recombinant Mco1 could be useful for understanding Mn biomineralization by ascomycetes and the sequestration of metal ions in the environment

Manganese(II) Oxidizing Bacteria as Whole-Cell Catalyst for β-Keto Ester Oxidation

Manganese oxidizing bacteria can produce biogenic manganese oxides (BMO) on their cell surface and have been applied in the fields of agriculture, bioremediation, and drinking water treatment to remove toxic contaminants based on their remarkable chemical reactivity. Herein, we report for the first time the synthetic application of the manganese oxidizing bacteria, Pseudomonas putida MnB1 as a whole-cell biocatalyst for the effective oxidation of β-keto ester with excellent yield. Differing from known chemical protocols toward this transformation that generally necessitate the use of organic solvents, stoichiometric oxygenating agents and complex chemical catalysts, our strategy can accomplish it simply under aqueous and mild conditions with higher efficiency than that provided by chemical manganese oxides. Moreover, the live MnB1 bacteria are capable of continuous catalysis for this C-O bond forming reaction for several cycles and remain proliferating, highlighting the favorable merits of this novel protocol for sustainable chemistry and green synthesis.

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.

Metal distribution and biological diversity of crusts in paddy fields polluted with different levels of cadmium

The paddy-crusts (PCs) play an important pole in the transformation and transfer of heavy metal in paddy. Different PCs were collected from paddy fields whose soils contained cadmium (Cd) at four concentration levels (0.61, 0.71, 1.53, and 7.08 mg/kg) in Hunan Province, China P.R. at Sep 2017. This metal's distribution among and biological community structures of PCs were both measured. Our results indicated that PCs were able to accumulate Cd from irrigation water and soil. With greater Cd levels in paddy fields, the weak EPS-binding Cd fraction decreased whereas the non-EDTA-exchangeable Cd fraction increased. The sorbed Cd fraction was initially enhanced at low-to mid-level Cd concentrations, but then gradually declined. Biomineralization was shown to function as the dominant Cd accumulation mechanism in non-EDTA-exchangeable fractions. The biological diversity of soil microbes decreased with more Cd in soil, and the Proteobacteria, Bacteroidetes, and Cyanobacteria were the dominant phyla in all the sampled PCs. Canonical correspondence analysis (CCA) between the composition of microbial communities and soil chemical variables in the PCs clustered all samples based on the Cd-contaminated level, and demonstrated that Cd, Mn, and Fe all significantly influenced the microbial communities. In particular, the Alphaproteobacteria and Chloroplast classes of bacteria may play a significant role in Cd accumulation via the bio-mineralization process. Taken together, our results provide basic empirical information to better understand the heavy metal speciation transformation mechanisms of PCs upon Cd-contaminated paddy fields.

Concentrations of reactive Mn(III)-L and MnO2 in estuarine and marine waters determined using spectrophotometry and the leuco base, leucoberbelin blue

In terms of its oxidative strength, the MnO₂/Mn²⁺ couple is one of the strongest in the aquatic environment. The intermediate oxidation state, manganese(III), is stabilized by a range of organic ligands (Mn(III)-L) and some of these complexes are also strong oxidants or reductants. Here, we present improved methods for quantifying soluble reactive oxidized manganese(III) and particulate reactive oxidized manganese at ultra-low concentrations; the respective detection limits are 6.7 nM and 7 pM (100-cm spectrophotometric path length) and 260 nM and 2.6 nM (1-cm path length). The methods involve a simple, specific, spectrophotometric technique using a water-soluble leuco base (leucoberbelin blue; LBB). LBB is oxidized by manganese through a hydrogen atom transfer reaction forming a colored complex that is stoichiometrically related to the oxidation state of the manganese, either Mn(III)-L or manganese(III,IV) oxides (MnO_x). At the concentration of LBB used in this study, nitrite may be a minor interference, so we provide concentration ranges over which it interferes and suggest potential strategies to mitigate the interference. Unlike previous methods devised to quantify Mn(III)-L, which use ligand exchange reactions, the LBB oxidation requires an electron and therefore needs to physically contact manganese(III) for inner-sphere electron transfer to occur. The method for measuring soluble Mn(III)-L was evaluated in the laboratory, and LBB was found to be oxidized by an extensive suite of weak Mn(III)-L complexes, as it is by MnO_x, but could not react with or reacted very slowly with strong Mn(III)-L complexes. According to the molecular structures of the Mn(III)-L complexes tested, LBB can also be used to qualitatively assess the binding strength of Mn(III)-L complexes based on metal-chelate structural considerations. The assays for soluble Mn(III)-L (membrane filtered) and particulate manganese oxides (trapped by membrane filters) were applied to the well-oxygenated estuarine waters of the Saguenay Fjord, a major tributary of the Lower St. Lawrence Estuary, and to Western North Atlantic oceanic waters, off the continental shelf, where there is an oxygen minimum zone (< 67% O₂ saturation). The methods applied can be used in the field or onboard ships and provide important new insights into oxidized manganese speciation.

Blackening and odorization of urban rivers: a bio-geochemical process

Urban rivers constitute a major part of urban drainage systems, and play critical roles in connecting other surface waters in urban areas. Black-odorous urban rivers are widely found in developing countries experiencing rapid urbanization, and the mismatch between urbanization and sewage treatment is thought to be the reason. The phenomena of blackening and odorization are likely complex bio-geochemical processes of which the microbial interactions with the environment are not fully understood. Here, we provide an overview of the major chemical compounds, such as iron and sulfur, and their bio-geochemical conversions during blackening and odorization of urban rivers. Scenarios explaining the formation of black-odorous urban rivers are proposed. Finally, we point out knowledge gaps in mechanisms and microbial ecology that need to be addressed to better understand the development of black-odorous urban rivers.

Environmental Bacteria Involved in Manganese(II) Oxidation and Removal From Groundwater

The presence of iron (Fe) and manganese (Mn) in groundwater is an important concern in populations that use it as source of drinking water. The ingestion of high concentrations of these metals may affect human health. In addition, these metals cause aesthetic and organoleptic problems that affect water quality and also induce corrosion in distribution networks, generating operational and system maintenance problems. Biological sand filter systems are widely used to remove Fe and Mn from groundwater since they are a cost-effective technology and minimize the use of chemical oxidants. In this work, the bacterial communities of two biological water treatment plants from Argentina, exposed to long term presence of Mn(II) and with a high Mn(II) removal efficiency, were characterized using 16S rRNA gene Illumina sequencing. Several selective media were used to culture Mn-oxidizing bacteria (MOB) and a large number of known MOB and several isolates that have never been reported before as MOB were cultivated. These bacteria were characterized to select those with the highest Mn(II) oxidation and biofilm formation capacities and also those that can oxidize Mn(II) at different environmental growth conditions. In addition, studies were performed to determine if the selected MOB were able to oxidize Mn(II) present in groundwater while immobilized on sand. This work allowed the isolation of several bacterial strains adequate to develop an inoculum applicable to improve Mn(II) removal efficiency of sand filter water treatment plants.

Electrochemical Bioreactor Technology for Biocatalysis and Microbial Electrosynthesis

Two seemingly distinct fields, industrial biocatalysis and microbial electrosynthesis, can be viewed together through the lens of electrochemical bioreactor technology in order to highlight the challenges that exist in creating a versatile platform technology for use in chemical and biological applications. Industrial biocatalysis applications requiring NAD(P)H to perform redox transformations often necessitate convoluted coupled-enzyme regeneration systems to regenerate reduced cofactor, NAD(P)H from oxidized cofactor, NAD(P). Renewed interest in continuously recycling the cofactor via electrochemical reduction is motivated by the low cost of performing electrochemical reactions, easy monitoring of the reaction progress, and straightforward product recovery. However, electrochemical cofactor regeneration methods invariably produce adventitious reduced cofactor side products which result in unproductive loss of input NAD(P). Microbial electrosynthesis is a form of microbially driven catalysis in which electricity is supplied to living microorganisms for the production of industrially relevant chemical products at higher carbon efficiencies and yields compared with traditional, nonelectrically driven, fermentations. The fundamental biochemistry of these organisms as related to selected biochemical redox processes will be explored in order to highlight opportunities to devise strategies for taking advantage of these biochemical processes in engineered systems.

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.

bifA Regulates Biofilm Development of Pseudomonas putida MnB1 as a Primary Response to H2O2 and Mn2

Pseudomonas putida (P. putida) MnB1 is a widely used model strain in environment science and technology for determining microbial manganese oxidation. Numerous studies have demonstrated that the growth and metabolism of P. putida MnB1 are influenced by various environmental factors. In this study, we investigated the effects of hydrogen peroxide (H₂O₂) and manganese (Mn²⁺) on proliferation, Mn²⁺ acquisition, anti-oxidative system, and biofilm formation of P. putida MnB1. The related orthologs of 4 genes, mco, mntABC, sod, and bifA, were amplified from P. putida GB1 and their involvement were assayed, respectively. We found that P. putida MnB1 degraded H₂O₂, and quickly recovered for proliferation, but its intracellular oxidative stress state was maintained, with rapid biofilm formation after H₂O₂ depletion. The data from mco, mntABC, sod and bifA expression levels by qRT-PCR, elucidated a sensitivity toward bifA-mediated biofilm formation, in contrary to intracellular anti-oxidative system under H₂O₂ exposure. Meanwhile, Mn²⁺ ion supply inhibited biofilm formation of P. putida MnB1. The expression pattern of these genes showed that Mn²⁺ ion supply likely functioned to modulate biofilm formation rather than only acting as nutrient substrate for P. putida MnB1. Furthermore, blockade of BifA activity by GTP increased the formation and development of biofilms during H₂O₂ exposure, while converse response to Mn²⁺ ion supply was evident. These distinct cellular responses to H₂O₂ and Mn²⁺ provide insights on the common mechanism by which environmental microorganisms may be protected from exogenous factors. We postulate that BifA-mediated biofilm formation but not intracellular anti-oxidative system may be a primary protective strategy adopted by P. putida MnB1. These findings will highlight the understanding of microbial adaptation mechanisms to distinct environmental stresses.

Biogenic manganese oxide nanoparticle formation by a multimeric multicopper oxidase Mnx

Bacteria that produce Mn oxides are extraordinarily skilled engineers of nanomaterials that contribute significantly to global biogeochemical cycles. Their enzyme-based reaction mechanisms may be genetically tailored for environmental remediation applications or bioenergy production. However, significant challenges exist for structural characterization of the enzymes responsible for biomineralization. The active Mn oxidase in Bacillus sp. PL-12, Mnx, is a complex composed of a multicopper oxidase (MCO), MnxG, and two accessory proteins, MnxE and MnxF. MnxG shares sequence similarity with other, structurally characterized MCOs. MnxE and MnxF have no similarity to any characterized proteins. The ~200 kDa complex has been recalcitrant to crystallization, so its structure is unknown. Here, we show that native mass spectrometry defines the subunit topology and copper binding of Mnx, while high-resolution electron microscopy visualizes the protein and nascent Mn oxide minerals. These data provide critical structural information for understanding Mn biomineralization by such unexplored enzymes.

Significant challenges exist for structural characterization of enzymes responsible for biomineralization. Here the authors show that native mass spectrometry and high resolution electron microscopy can define the subunit topology and copper binding of a manganese oxidizing complex, and describe early stage formation of its mineral products

The key role of biogenic manganese oxides in enhanced removal of highly recalcitrant 1,2,4-triazole from bio-treated chemical industrial wastewater

The secondary effluent from biological treatment process in chemical industrial plant often contains refractory organic matter, which deserves to be further treated in order to meet the increasingly stringent environmental regulations. In this study, the key role of biogenic manganese oxides (BioMnOx) in enhanced removal of highly recalcitrant 1,2,4-triazole from bio-treated chemical industrial wastewater was investigated. BioMnOx production by acclimated manganese-oxidizing bacterium (MOB) consortium was confirmed through scanning electronic microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and X-ray diffraction (XRD) analysis. Pseudomonas and Bacillus were found to be the most predominant species in acclimated MOB consortium. Mn²⁺ could be oxidized optimally at neutral pH and initial Mn²⁺ concentration below 33 mg L^-1. However, 1,2,4-triazole removal by BioMnOx produced occurred optimally at slightly acidic pH. High dosage of both Mn²⁺ and 1,2,4-triazole resulted in decreased 1,2,4-triazole removal. In a biological aerated filter (BAF) coupled with manganese oxidation, 1,2,4-triazole and total organic carbon removal could be significantly enhanced compared to the control system without the participation of manganese oxidation, confirming the key role of BioMnOx in the removal of highly recalcitrant 1,2,4-triazole. This study demonstrated that the biosystem coupled with manganese oxidation had a potential for the removal of various recalcitrant contaminants from bio-treated chemical industrial wastewater.

Physiological and transcriptional approaches reveal connection between nitrogen and manganese cycles in Shewanella algae C6G3

To explain anaerobic nitrite/nitrate production at the expense of ammonium mediated by manganese oxide (Mn(IV)) in sediment, nitrate and manganese respirations were investigated in a strain (Shewanella algae C6G3) presenting these features. In contrast to S. oneidensis MR-1, a biotic transitory nitrite accumulation at the expense of ammonium was observed in S. algae during anaerobic growth with Mn(IV) under condition of limiting electron acceptor, concomitantly, with a higher electron donor stoichiometry than expected. This low and reproducible transitory accumulation is the result of production and consumption since the strain is able to dissimilative reduce nitrate into ammonium. Nitrite production in Mn(IV) condition is strengthened by comparative expression of the nitrate/nitrite reductase genes (napA, nrfA, nrfA-2), and rates of the nitrate/nitrite reductase activities under Mn(IV), nitrate or fumarate conditions. Compared with S. oneidensis MR-1, S. algae contains additional genes that encode nitrate and nitrite reductases (napA-α and nrfA-2) and an Outer Membrane Cytochrome (OMC)(mtrH). Different patterns of expression of the OMC genes (omcA, mtrF, mtrH and mtrC) were observed depending on the electron acceptor and growth phase. Only gene mtrF-2 (SO1659 homolog) was specifically expressed under the Mn(IV) condition. Nitrate and Mn(IV) respirations seem connected at the physiological and transcriptional levels.

Hexavalent Chromium Generation within Naturally Structured Soils and Sediments

Chromium(VI) produced from the oxidation of indigenous Cr(III) minerals is increasingly being recognized as a threat to groundwater quality. A critical determinant of Cr(VI) generation within soils and sediments is the necessary interaction of two low-solubility phases-Cr(III) silicates or (hydr)oxides and Mn(III/IV) oxides-that lead to its production. Here we investigate the potential for Cr(III) oxidation by Mn oxides within fixed solid matrices common to soils and sediments. Artificial aggregates were constructed from Cr(OH)₃- and Cr_0.25Fe_0.75(OH)₃-coated quartz grains and either mixed with synthetic birnessite or inoculated with the Mn(II)-oxidizing bacterium Leptothrix cholodnii. In aggregates simulating low organic carbon environments, we observe Cr(VI) concentrations within advecting solutes at levels more than twenty-times the California drinking water standard. Chromium(VI) production is highly dependent on Cr-mineral solubility; increasing Fe-substitution (x = 0 to x = 0.75) decreases the solubility of the solid and concomitantly decreases total Cr(VI) generation by 37%. In environments with high organic carbon, reducing conditions within aggregate cores (microbially) generate sufficient Fe(II) to suppress Cr(VI) efflux. Our results illustrate Cr(VI) generation from reaction with Mn oxides within structured media simulating soils and sediments and provide insight into how fluctuating hydrologic and redox conditions impact coupled processes controlling Cr and Mn cycling.

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.

Effectiveness of hypolimnetic oxygenation for preventing accumulation of Fe and Mn in a drinking water reservoir

The accumulation of Fe and Mn in seasonally stratified drinking water reservoirs adversely impacts water quality. To control issues with Fe and Mn at the source, some drinking water utilities have deployed hypolimnetic oxygenation systems to create well-oxygenated conditions in the water column that are favorable for the oxidation, and thus removal, of Fe and Mn. However, in addition to being controlled by dissolved oxygen (DO), Fe and Mn concentrations are also influenced by pH and metal-oxidizing microorganisms. We studied the response of Fe and Mn concentrations to hypolimnetic oxygenation in a shallow drinking water reservoir in Vinton, Virginia, USA by sequentially activating and deactivating an oxygenation system over two summers. We found that maintaining well-oxygenated conditions effectively prevented the accumulation of soluble Fe in the hypolimnion. However, while the rate of Mn oxidation increased under well-oxygenated conditions, soluble Mn still accumulated in the slightly acidic to neutral (pH 5.6 to 7.5) hypolimnion. In parallel, we conducted laboratory incubation experiments, which showed that the presence of Mn-oxidizing microorganisms increased the rate of Mn oxidation in comparison with rates under oxic, abiotic conditions. Combined, our field and laboratory results demonstrate that increasing DO concentrations in the water column is important for stimulating the oxidation of Fe and Mn, but that the successful management of Mn is also tied to the activity of Mn-oxidizing organisms in the water column and favorable (neutral to alkaline) pH.

Biogenic nanosized iron oxides obtained from cultivation of iron bacteria from the genus Leptothrix

A detailed investigation of nanostructured iron oxides/(oxy)hydroxides gathered after cultivation of bacteria from the genus Leptothrix as iron (II) oxidizers is presented. A specific type of medium is selected for the cultivation of the bacteria. Results for sediment powder and bio-film on glass substrate samples from the same media are discussed. XRD, Raman spectroscopy, SEM, and TEM images and PPMS measurements are used to prove the exact composition of the biogenic products and to interpret the oxidation process. Analysis of the data collected shows that around 80 % of the iron (II) from the growth medium has been transformed into iron (III) in the form of different (oxy)hydroxides, with the rest found to be in a mixed 2,5 valence in magnetite. Our investigation shows that the bio-film sample has a phase content different from that of the powdered biomass and that lepidocrocite (γ-FeOOH) is the predominant and the initial biogenic phase in both samples. Magnetite nanoparticles are a secondary product in the bio-film, part of which possesses a defective quasi-maghemite surface layer. In the powdered biomass, the oxidation steps are not fully completed. The initial products are non-stoichiometric and due to the mixed ferric and ferrous ions present, they develop into: (i) lepidocrocite (γ-FeOOH) as a basic sediment, (ii) magnetite (Fe₃O₄) and (iii) goethite (α-FeOOH) in small quantities. The average size of all iron-bearing particles is found to be below 30 nm. The magnetic measurements performed show a superparamagnetic behavior of the material at room temperature.

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.

Abiotic Deposition of Fe Complexes onto Leptothrix Sheaths

Bacteria classified in species of the genus Leptothrix produce extracellular, microtubular, Fe-encrusted sheaths. The encrustation has been previously linked to bacterial Fe oxidases, which oxidize Fe(II) to Fe(III) and/or active groups of bacterial exopolymers within sheaths to attract and bind aqueous-phase inorganics. When L. cholodnii SP-6 cells were cultured in media amended with high Fe(II) concentrations, Fe(III) precipitates visibly formed immediately after addition of Fe(II) to the medium, suggesting prompt abiotic oxidation of Fe(II) to Fe(III). Intriguingly, these precipitates were deposited onto the sheath surface of bacterial cells as the population was actively growing. When Fe(III) was added to the medium, similar precipitates formed in the medium first and were abiotically deposited onto the sheath surfaces. The precipitates in the Fe(II) medium were composed of assemblies of globular, amorphous particles (ca. 50 nm diameter), while those in the Fe(III) medium were composed of large, aggregated particles (≥3 µm diameter) with a similar amorphous structure. These precipitates also adhered to cell-free sheaths. We thus concluded that direct abiotic deposition of Fe complexes onto the sheath surface occurs independently of cellular activity in liquid media containing Fe salts, although it remains unclear how this deposition is associated with the previously proposed mechanisms (oxidation enzyme- and/or active group of organic components-involved) of Fe encrustation of the Leptothrix sheaths.

The Role of Bacterial Spores in Metal Cycling and Their Potential Application in Metal Contaminant Bioremediation

Bacteria are one of the premier biological forces that, in combination with chemical and physical forces, drive metal availability in the environment. Bacterial spores, when found in the environment, are often considered to be dormant and metabolically inactive, in a resting state waiting for favorable conditions for them to germinate. However, this is a highly oversimplified view of spores in the environment. The surface of bacterial spores represents a potential site for chemical reactions to occur. Additionally, proteins in the outer layers (spore coats or exosporium) may also have more specific catalytic activity. As a consequence, bacterial spores can play a role in geochemical processes and may indeed find uses in various biotechnological applications. The aim of this review is to introduce the role of bacteria and bacterial spores in biogeochemical cycles and their potential use as toxic metal bioremediation agents.

Celeribacter manganoxidans sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediment of a polymetallic nodule province

A Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, manganese-oxidizing bacterial strain, designated DY2-5T, was isolated from surface sediment of Pacific Clarion-Clipperton Fracture Zone (CCFZ). Growth occurred at 0-37 °C (optimum 28 °C), pH 6.5-9.0 (optimum pH 7.0-7.5) and in the presence of 1-11% (w/v) NaCl (optimum 3-4%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that the novel strain was most closely related to Celeribacter halophilus ZXM137T with 96.13% sequence similarity, and had 16S rRNA gene sequence similarities in the range 93.89-95.87% with other species of the genus Celeribacter. The dominant fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C16:0. The polar lipids of strain DY2-5T comprised phosphatidylglycerol, phosphatidylcholine and two unknown aminolipids. The major respiratory quinone was ubiquinone-10 (Q-10). The DNA G+C content of strain DY2-5T was 64.8 mol%. On the basis of the phenotypic, genotypic and physiological evidence, strain DY2-5T represents a novel species of the genus Celeribacter, for which the name Celeribacter manganoxidans sp. nov. is proposed. The type strain is DY2-5T ( = JCM 19384T = KCTC 32473T).

Surface Mn(II) oxidation actuated by a multicopper oxidase in a soil bacterium leads to the formation of manganese oxide minerals

In this manuscript, we report that a bacterial multicopper oxidase (MCO266) catalyzes Mn(II) oxidation on the cell surface, resulting in the surface deposition of Mn(III) and Mn(IV) oxides and the gradual formation of bulky oxide aggregates. These aggregates serve as nucleation centers for the formation of Mn oxide micronodules and Mn-rich sediments. A soil-borne Escherichia coli with high Mn(II)-oxidizing activity formed Mn(III)/Mn(IV) oxide deposit layers and aggregates under laboratory culture conditions. We engineered MCO266 onto the cell surfaces of both an activity-negative recipient and wild-type strains. The results confirmed that MCO266 governs Mn(II) oxidation and initiates the formation of deposits and aggregates. By contrast, a cell-free substrate, heat-killed strains, and intracellularly expressed or purified MCO266 failed to catalyze Mn(II) oxidation. However, purified MCO266 exhibited Mn(II)-oxidizing activity when combined with cell outer membrane component (COMC) fractions in vitro. We demonstrated that Mn(II) oxidation and aggregate formation occurred through an oxygen-dependent biotic transformation process that requires a certain minimum Mn(II) concentration. We propose an approximate electron transfer pathway in which MCO266 transfers only one electron to convert Mn(II) to Mn(III) and then cooperates with other COMC electron transporters to transfer the other electron required to oxidize Mn(III) to Mn(IV).

Biological and physico-chemical formation of Birnessite during the ripening of manganese removal filters

The efficiency of manganese removal in conventional groundwater treatment consisting of aeration followed by rapid sand filtration, strongly depends on the ability of filter media to promote auto-catalytic adsorption of dissolved manganese and its subsequent oxidation. Earlier studies have shown that the compound responsible for the auto-catalytic activity in ripened filters is a manganese oxide called Birnessite. The aim of this study was to determine if the ripening of manganese removal filters and the formation of Birnessite on virgin sand is initiated biologically or physico-chemically. The ripening of virgin filter media in a pilot filter column fed by pre-treated manganese containing groundwater was studied for approximately 600 days. Samples of filter media were taken at regular time intervals, and the manganese oxides formed in the coating were analysed by Raman spectroscopy, Electron Paramagnetic Resonance (EPR) and Scanning Electron Microscopy (SEM). From the EPR analyses, it was established that the formation of Birnessite was most likely initiated via biological activity. With the progress of filter ripening and development of the coating, Birnessite formation became predominantly physico-chemical, although biological manganese oxidation continued to contribute to the overall manganese removal. The knowledge that manganese removal in conventional groundwater treatment is initiated biologically could be of help in reducing typically long ripening times by creating conditions that are favourable for the growth of manganese oxidizing bacteria.

Pyrosequencing revealed highly microbial phylogenetic diversity in ferromanganese nodules from farmland

There is renewed interest in the origin and makeup of ferromanganese nodules (FMNs), long known to soil mineralogists as unusual secondary minerals. However, new evidence suggests that microorganisms play a significant role in the generation of FMNs. The biogenic origin of nodules has remained elusive because until recently, little has been known about the overall microbial community structure in their microbiota. To learn more about the microbial community and to determine the relative abundance, diversity, and composition of the microbial communities present in FMNs and their surrounding soil, we used pyrosequencing to investigate 16S rRNA genes obtained from vertical soil profiles of both paddy fields and sugarcane fields. Using pyrotaq 16S rRNA gene sequencing, we show that the microbial phylogenetic diversity of nodules was higher than those reported in previous studies of this biosphere, and we identified many previously unidentified microorganisms. Here, we show that the microbial community of these nodules is dominated by Burkholderiales, Rhodocyclales, Acidobacteriales, Desulfuromonales, and Clostridiales, and there were no statistically significant differences found when comparing the microbial community structures of FMNs obtained from vertical soil sequences. Although the microbial composition was markedly different between the surrounding soil and the FMNs, the microbes found within the FMNs were very similar to other FMNs from both field types examined here. In addition to their geochemical properties and the microbial community composition of FMNs, we found that the levels of iron (Fe), manganese (Mn), and SiO2 greatly impact the microbial diversity among FMN communities. Our results indicate that the FMN microbial communities from different land-use types are very similar and suggest that natural selection of these microbes is based on the oligotrophic conditions and the high metal content. Researching FMNs in these two land-use patterns, which represent two different redox potentials, deepens our understanding of Fe-Mn biogeochemical cycling in these oligotrophic biospheres and suggests a biogenetical origin for these nodules.

Effect of drinking water treatment process parameters on biological removal of manganese from surface water

Soluble manganese (Mn) presents a significant treatment challenge to many water utilities, causing aesthetic and operational concerns. While application of free chlorine to oxidize Mn prior to filtration can be effective, this is not feasible for surface water treatment plants using ozonation followed by biofiltration because it inhibits biological removal of organics. Manganese-oxidizing bacteria (MOB) readily oxidize Mn in groundwater treatment applications, which normally involve pH > 7.0. The purpose of this study was to evaluate the potential for biological Mn removal at the lower pH conditions (6.2-6.3) often employed in enhanced coagulation to optimize organics removal. Four laboratory-scale biofilters were operated over a pH range of 6.3-7.3. The biofilters were able to oxidize Mn at a pH as low as pH 6.3 with greater than 98% Mn removal. Removal of simulated organic ozonation by-products was also greater than 90% in all columns. Stress studies indicated that well-acclimated MOB can withstand variations in Mn concentration (e.g., 0.1-0.2 mg/L), hydraulic loading rate (e.g., 2-4 gpm/ft(2); 1.36 × 10(-3)-2.72 × 10(-3) m/s), and temperature (e.g., 7-22 °C) typically found at surface water treatment plants at least for relatively short (1-2 days) periods of time.

Earth history. Low mid-Proterozoic atmospheric oxygen levels and the delayed rise of animals

The oxygenation of Earth's surface fundamentally altered global biogeochemical cycles and ultimately paved the way for the rise of metazoans at the end of the Proterozoic. However, current estimates for atmospheric oxygen (O2) levels during the billion years leading up to this time vary widely. On the basis of chromium (Cr) isotope data from a suite of Proterozoic sediments from China, Australia, and North America, interpreted in the context of data from similar depositional environments from Phanerozoic time, we find evidence for inhibited oxidation of Cr at Earth's surface in the mid-Proterozoic (1.8 to 0.8 billion years ago). These data suggest that atmospheric O2 levels were at most 0.1% of present atmospheric levels. Direct evidence for such low O2 concentrations in the Proterozoic helps explain the late emergence and diversification of metazoans.

Effects of exogenous pyoverdines on Fe availability and their impacts on Mn(II) oxidation by Pseudomonas putida GB-1

Pseudomonas putida GB-1 is a Mn(II)-oxidizing bacterium that produces pyoverdine-type siderophores (PVDs), which facilitate the uptake of Fe(III) but also influence MnO₂ formation. Recently, a non-ribosomal peptide synthetase mutant that does not synthesize PVD was described. Here we identified a gene encoding the PVD_GB-1 (PVD produced by strain GB-1) uptake receptor (PputGB1_4082) of strain GB-1 and confirmed its function by in-frame mutagenesis. Growth and other physiological responses of these two mutants and of wild type were compared during cultivation in the presence of three chemically distinct sets of PVDs (siderotypes n°1, n°2, and n°4) derived from various pseudomonads. Under iron-limiting conditions, Fe(III) complexes of various siderotype n°1 PVDs (including PVD_GB-1) allowed growth of wild type and the synthetase mutant, but not the receptor mutant, confirming that iron uptake with any tested siderotype n°1 PVD depended on PputGB1_4082. Fe(III) complexes of a siderotype n°2 PVD were not utilized by any strain and strongly induced PVD synthesis. In contrast, Fe(III) complexes of siderotype n°4 PVDs promoted the growth of all three strains and did not induce PVD synthesis by the wild type, implying these complexes were utilized for iron uptake independent of PputGB1_4082. These differing properties of the three PVD types provided a way to differentiate between effects on MnO₂ formation that resulted from iron limitation and others that required participation of the PVD_GB-1 receptor. Specifically, MnO₂ production was inhibited by siderotype n°1 but not n°4 PVDs indicating PVD synthesis or PputGB1_4082 involvement rather than iron-limitation caused the inhibition. In contrast, iron limitation was sufficient to explain the inhibition of Mn(II) oxidation by siderotype n°2 PVDs. Collectively, our results provide insight into how competition for iron via siderophores influences growth, iron nutrition and MnO₂ formation in more complex environmental systems.

Microbial engineering of floc Fe and trace element geochemistry in a circumneutral, remote lake

Evaluation of lacustrine floc Fe, Pb, and Cd biogeochemistry over seasonal (summer, winter) and water column depth (metalimnetic, hypolimnetic) scales reveals depth-independent seasonally significant differences in floc Fe biominerals and trace element (TE: Pb, Cd) sequestration, driven by floc microbial community shifts. Winter floc [TE] were significantly lower than summer [TE], driven by declining abundance and reactivity of floc amorphous Fe((III))-(oxy)hydroxide (FeOOH) phases under ice ([FeOOH](summer) = 37-77 mgg(-1) vs [FeOOH](winter) = 0.3-7 mgg(-1)). Further, while high summer floc [FeOOH] was observed at both water column depths, winter floc was dominated by Fe((II)) phases. However, the observed seasonal change in the nature and concentrations of floc Fe-phases was independent of water column [Fe], O2, and pH and, instead, significantly correlated to floc bacterial community membership. Bioinformatic modeling (Unifrac, PCA analyses) of in situ and experimental microcosm results identified a temperature-driven seasonal turnover of floc microbial communities, shifting from dominantly putative Fe metabolisms within summer floc to wintertime ancillary Fe reducing and S metabolizing bacteria. This seasonal shift of floc microbial community functioning, significantly the wintertime loss of microbial Fe((II))-oxidizing capability and concomitant increases of sulfur-reducing bacteria, alters dominant floc Fe minerals from Fe((III)) to Fe((II)) phases. This resulted in decreased winter floc [TE], not predicted by water column geochemistry.

Identification of Mn(II)-oxidizing bacteria from a low-pH contaminated former uranium mine

Biological Mn oxidation is responsible for producing highly reactive and abundant Mn oxide phases in the environment that can mitigate metal contamination. However, little is known about Mn oxidation in low-pH environments, where metal contamination often is a problem as the result of mining activities. We isolated two Mn(II)-oxidizing bacteria (MOB) at pH 5.5 (Duganella isolate AB_14 and Albidiferax isolate TB-2) and nine strains at pH 7 from a former uranium mining site. Isolate TB-2 may contribute to Mn oxidation in the acidic Mn-rich subsoil, as a closely related clone represented 16% of the total community. All isolates oxidized Mn over a small pH range, and isolates from low-pH samples only oxidized Mn below pH 6. Two strains with different pH optima differed in their Fe requirements for Mn oxidation, suggesting that Mn oxidation by the strain found at neutral pH was linked to Fe oxidation. Isolates tolerated Ni, Cu, and Cd and produced Mn oxides with similarities to todorokite and birnessite, with the latter being present in subsurface layers where metal enrichment was associated with Mn oxides. This demonstrates that MOB can be involved in the formation of biogenic Mn oxides in both moderately acidic and neutral pH environments.

Characterization and reactivity of biogenic manganese oxides for ciprofloxacin oxidation

Biogenic manganese oxides (BioMnOx) were synthesized by the oxidation of Mn(II) with Mn-oxidizing bacteria Pseudomonas sp. G7 under different initial pH values and Mn(II) dosages, and were characterized by X-ray diffraction, X-ray photoelectron spectroscopy, and UV-Vis absorption spectroscopy. The crystal structure and Mn oxidation states of BioMnOx depended on the initial pH and Mn(II) dosages of the medium. The superoxide radical (O(·-)2) was observed in Mn-containing (III/IV) BioMnOx suspensions by electron spin resonance measurements. BioMnOx(0.4)-7, with mixed valence of Mn(II/III/IV) and the strongest O(·-)2 signals, was prepared in the initial pH 7 and Mn(II) dosage of 0.4 mmol/L condition, and exhibited the highest activity for ciprofloxacin degradation and no Mn(II) release. During the degradation of ciprofloxacin, the oxidation of the Mn(II) formed came from biotic and abiotic reactions in BioMnOx suspensions on the basis of the Mn(II) release and O(·-)2 formation from different BioMnOx. The degradation process of ciprofloxacin was shown to involve the cleavage of the hexatomic ring having a secondary amine and carbon-carbon double bond connected to a carboxyl group, producing several compounds containing amine groups as well as small organic acids.

Manganese (Mn) oxidation increases intracellular Mn in Pseudomonas putida GB-1

Bacterial manganese (Mn) oxidation plays an important role in the global biogeochemical cycling of Mn and other compounds, and the diversity and prevalence of Mn oxidizers have been well established. Despite many hypotheses of why these bacteria may oxidize Mn, the physiological reasons remain elusive. Intracellular Mn levels were determined for Pseudomonas putida GB-1 grown in the presence or absence of Mn by inductively coupled plasma mass spectrometry (ICP-MS). Mn oxidizing wild type P. putida GB-1 had higher intracellular Mn than non Mn oxidizing mutants grown under the same conditions. P. putida GB-1 had a 5 fold increase in intracellular Mn compared to the non Mn oxidizing mutant P. putida GB-1-007 and a 59 fold increase in intracellular Mn compared to P. putida GB-1 ∆2665 ∆2447. The intracellular Mn is primarily associated with the less than 3 kDa fraction, suggesting it is not bound to protein. Protein oxidation levels in Mn oxidizing and non oxidizing cultures were relatively similar, yet Mn oxidation did increase survival of P. putida GB-1 when oxidatively stressed. This study is the first to link Mn oxidation to Mn homeostasis and oxidative stress protection.

Fungal mn oxides supporting Mn(II) oxidase activity as effective Mn(II) sequestering materials

We examined the Mn(II)-oxidizing ability of the biogenic Mn oxide (BMO) formed in cultures ofa Mn(II)-oxidizing fungus, Acremonium strictum strain KR21-2. The newly formed BMO effectively sequestered dissolved Mn(II) mainly by oxidizing Mn(II) to insoluble Mn under air-equilibrated conditions, and this ability lasted for at least 8 days. Deaerating the BMOs, poisoning them with NaN3, or heating them all readily weakened their Mn(II) oxidation ability, indicating the involvement of enzymatic Mn(II) oxidation. There was no Mn(II)-oxidizing ability observed for mycelia cultivated without Mn(II) or for residual mycelia after the BMO phase was dissolved, suggesting the need for the oxide phase. A sodium dodecyl sulphate-polyacrylamide gel electrophoresis assay demonstrated that the oxide phase embeds the Mn(II) oxidase and thereby maintains the enzymatic activity in BMOs. Freezing at -80 degrees C preserved the Mn(II)-oxidizing ability in BMOs for at least 4 weeks, while lyophilization caused a complete loss of this ability. Based on these results, we propose that fungal Mn oxides supporting Mn(II) oxidase activity are an effective Mn(II)-sequestering material capable of oxidizing Mn(II) continuously from solutions containing no additional nutrients to maintain biological activity.

Widespread production of extracellular superoxide by heterotrophic bacteria

Superoxide and other reactive oxygen species (ROS) originate from several natural sources and profoundly influence numerous elemental cycles, including carbon and trace metals. In the deep ocean, the permanent absence of light precludes currently known ROS sources, yet ROS production mysteriously occurs. Here, we show that taxonomically and ecologically diverse heterotrophic bacteria from aquatic and terrestrial environments are a vast, unrecognized, and light-independent source of superoxide, and perhaps other ROS derived from superoxide. Superoxide production by a model bacterium within the ubiquitous Roseobacter clade involves an extracellular oxidoreductase that is stimulated by the reduced form of nicotinamide adenine dinucleotide (NADH), suggesting a surprising homology with eukaryotic organisms. The consequences of ROS cycling in immense aphotic zones representing key sites of nutrient regeneration and carbon export must now be considered, including potential control of carbon remineralization and metal bioavailability.

A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera

A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1(T), was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0-3.0 µm straight rods, often observed with round endospores. Strain KKC1(T) grew at 55-68 °C, pH 5.2-9.2 and 0.8-14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0-7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1(T) grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1(T) was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1(T) ( = DSM 26464(T) = NBRC 109353(T)).

CotA, a multicopper oxidase from Bacillus pumilus WH4, exhibits manganese-oxidase activity

Multicopper oxidases (MCOs) are a family of enzymes that use copper ions as cofactors to oxidize various substrates. Previous research has demonstrated that several MCOs such as MnxG, MofA and MoxA can act as putative Mn(II) oxidases. Meanwhile, the endospore coat protein CotA from Bacillus species has been confirmed as a typical MCO. To study the relationship between CotA and the Mn(II) oxidation, the cotA gene from a highly active Mn(II)-oxidizing strain Bacillus pumilus WH4 was cloned and overexpressed in Escherichia coli strain M15. The purified CotA contained approximately four copper atoms per molecule and showed spectroscopic properties typical of blue copper oxidases. Importantly, apart from the laccase activities, the CotA also displayed substantial Mn(II)-oxidase activities both in liquid culture system and native polyacrylamide gel electrophoresis. The optimum Mn(II) oxidase activity was obtained at 53°C in HEPES buffer (pH 8.0) supplemented with 0.8 mM CuCl2. Besides, the addition of o-phenanthroline and EDTA both led to a complete suppression of Mn(II)-oxidizing activity. The specific activity of purified CotA towards Mn(II) was 0.27 U/mg. The Km, Vmax and kcat values towards Mn(II) were 14.85±1.17 mM, 3.01×10(-6)±0.21 M·min(-1) and 0.32±0.02 s(-1), respectively. Moreover, the Mn(II)-oxidizing activity of the recombinant E. coli strain M15-pQE-cotA was significantly increased when cultured both in Mn-containing K liquid medium and on agar plates. After 7-day liquid cultivation, M15-pQE-cotA resulted in 18.2% removal of Mn(II) from the medium. Furthermore, the biogenic Mn oxides were clearly observed on the cell surfaces of M15-pQE-cotA by scanning electron microscopy. To our knowledge, this is the first report that provides the direct observation of Mn(II) oxidation with the heterologously expressed protein CotA, Therefore, this novel finding not only establishes the foundation for in-depth study of Mn(II) oxidation mechanisms, but also offers a potential biocatalyst for Mn(II) removal.

The effect of Ca2+ ions and ionic strength on Mn(II) oxidation by spores of the marine Bacillus sp. SG-1

Manganese(IV) oxides, believed to form primarily through microbial activities, are extremely important mineral phases in marine environments where they scavenge a variety of trace elements and thereby control their distributions. The presence of various ions common in seawater are known to influence Mn oxide mineralogy yet little is known about the effect of these ions on the kinetics of bacterial Mn(II) oxidation and Mn oxide formation. We examined factors affecting bacterial Mn(II) oxidation by spores of the marine Bacillus sp. strain SG-1 in natural and artificial seawater of varying ionic conditions. Ca²⁺ concentration dramatically affected Mn(II) oxidation, while Mg²⁺, Sr²⁺, K⁺, Na⁺ and NO₃^- ions had no effect. The rate of Mn(II) oxidation at 10mM Ca²⁺ (seawater composition) was four or five times that without Ca²⁺. The relationship between Ca²⁺ content and oxidation rate demonstrates that the equilibrium constant is small (on the order of 0.1) and the binding coefficient is 0.5. The pH optimum for Mn(II) oxidation changed depending on the amount of Ca²⁺ present, suggesting that Ca²⁺ exerts a direct effect on the enzyme perhaps as a stabilizing bridge between polypeptide components. We also examined the effect of varying concentrations of NaCl or KNO₃ (0 mM - 2000 mM) on the kinetics of Mn(II) oxidation in solutions containing 10 mM Ca²⁺. Mn(II) oxidation was unaffected by changes in ionic strength (I) below 0.2, but it was inhibited by increasing salt concentrations above this value. Our results suggest that the critical coagulation concentration is around 200 mM of salt (I = ca. 0.2), and that the ionic strength of seawater (I > 0.2) accelerates the precipitation of Mn oxides around the spores. Under these conditions, the aggregation of Mn oxides reduces the supply of dissolved O₂ and/or Mn²⁺ and inhibits the Mn(II) -> Mn(III) step controlling the enzymatic oxidation of Mn(II). Our results suggest that the hardness and ionic strength of the aquatic environment at circumneutral pH strongly influences the rate of biologically mediated Mn(II) oxidation.