Spatially resolved characterization of biogenic manganese oxide production within a bacterial biofilm

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.

Organic buffers act as reductants of abiotic and biogenic manganese oxides

Proton activity is the master variable in many biogeochemical reactions. To control pH, laboratory studies involving redox-sensitive minerals like manganese (Mn) oxides frequently use organic buffers (typically Good's buffers); however, two Good's buffers, HEPES and MES, have been shown to reduce Mn(IV) to Mn(III). Because Mn(III) strongly controls mineral reactivity, avoiding experimental artefacts that increase Mn(III) content is critical to avoid confounding results. Here, we quantified the extent of Mn reduction upon reaction between Mn oxides and several Good's buffers (MES, pK_a = 6.10; PIPES, pK_a = 6.76; MOPS, pK_a = 7.28; HEPES, pK_a = 7.48) and TRIS (pK_a = 8.1) buffer. For δ-MnO₂, Mn reduction was rapid, with up to 35% solid-phase Mn(III) generated within 1 h of reaction with Good's buffers; aqueous Mn was minimal in all Good's buffers experiments except those where pH was one unit below the buffer pK_a and the reaction proceeded for 24 h. Additionally, the extent of Mn reduction after 24 h increased in the order MES < MOPS < PIPES < HEPES << TRIS. Of the variables tested, the initial Mn(II,III) content had the greatest effect on susceptibility to reduction, such that Mn reduction scaled inversely with the initial average oxidation number (AMON) of the oxide. For biogenic Mn oxides, which consist of a mixture of Mn oxides, bacterial cells and extracelluar polymeric substances, the extent of Mn reduction was lower than predicted from experiments using abiotic analogs and may result from biotic re-oxidation of reduced Mn or a difference in the reducibility of abiotic versus biogenic oxides. The results from this study show that organic buffers, including morpholinic and piperazinic Good's buffers and TRIS, should be avoided for pH control in Mn oxide systems due to their ability to transfer electrons to Mn, which modifies the composition and reactivity of these redox-active minerals.

Chemical-state distributions in charged LiCoO2 cathode particles visualized by soft X-ray spectromicroscopy

Lithium-ion deintercalation/intercalation during charge/discharge processes is one of the essential reactions that occur in the layered cathodes of lithium-ion batteries, and the performance of the cathode can be expressed as the sum of the reactions that occur in the local area of the individual cathode particles. In this study, the spatial distributions of the chemical states present in prototypical layered LiCoO₂ cathode particles were determined at different charging conditions using scanning transmission X-ray microscopy (STXM) with a spatial resolution of approximately 100 nm. The Co L₃- and O K-edge X-ray absorption spectroscopy (XAS) spectra, extracted from the same area of the corresponding STXM images, at the initial state as well as after charging to 4.5 V demonstrate the spatial distribution of the chemical state changes depending on individual particles. In addition to the Co L₃-edge XAS spectra, the O K-edge XAS spectra of the initial and charged LiCoO₂ particles are different, indicating that both the Co and O sites participate in charge compensation during the charging process possibly through the hybridization between the Co 3d and O 2p orbitals. Furthermore, the element maps of both the Co and O sites, derived from the STXM stack images, reveal the spatial distribution of the chemical states inside individual particles after charging to 4.5 V. The element mapping analysis suggests that inhomogeneous reactions occur on the active particles and confirm the existence of non-active particles. The results of this study demonstrate that an STXM-based spatially resolved electronic structural analysis method is useful for understanding the charging and discharging of battery materials.

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.

Diversity of Mixotrophic Neutrophilic Thiosulfate- and Iron-Oxidizing Bacteria from Deep-Sea Hydrothermal Vents

At deep-sea hydrothermal vents, sulfur oxidation and iron oxidation are of the highest importance to microbial metabolisms, which are thought to contribute mainly in chemolithoautotrophic groups. In this study, 17 mixotrophic neutrophilic thiosulfate- and iron-oxidizing bacteria were isolated from hydrothermal fields on the Carlsberg Ridge in the Indian Ocean, nine to the γ-proteobacteria (Halomonas (4), Pseudomonas (2), Marinobacter (2), and Rheinheimera (1)), seven to the α-proteobacteria (Thalassospira, Qipengyuania, Salipiger, Seohaeicola, Martelella, Citromicrobium, and Aurantimonas), and one to the Actinobacteria (Agromyces), as determined by their 16S rRNA and genome sequences. The physiological characterization of these isolates revealed wide versatility in electron donors (Fe(II) and Mn(II), or thiosulfate) and a variety of lifestyles as lithotrophic or heterotrophic, microaerobic, or anaerobic. As a representative strain, Pseudomonas sp. IOP_13 showed its autotrophic gowth from 10⁵ cells/ml to 10⁷ cells/ml;carbon dioxide fixation capacity with the δ13C_VPDB in the biomass increased from -27.42‱ to 3460.06‱; the thiosulfate-oxidizing ability with produced SO₄^2- increased from 60 mg/L to 287 mg/L; and the iron-oxidizing ability with Fe(II) decreased from 10 mM to 5.2 mM. In addition, iron-oxide crust formed outside the cells. Gene coding for energy metabolism involved in possible iron, manganese, and sulfur oxidation, and denitrification was identified by their genome analysis. This study sheds light on the function of the mixotrophic microbial community in the iron/manganese/sulfur cycles and the carbon fixation of the hydrothermal fields.

A Critical Review on the Multiple Roles of Manganese in Stabilizing and Destabilizing Soil Organic Matter

Manganese (Mn) is a biologically important and redox-active metal that may exert a poorly recognized control on carbon (C) cycling in terrestrial ecosystems. Manganese influences ecosystem C dynamics by mediating biochemical pathways that include photosynthesis, serving as a reactive intermediate in the breakdown of organic molecules, and binding and/or oxidizing organic molecules through organo-mineral associations. However, the potential for Mn to influence ecosystem C storage remains unresolved. Although substantial research has demonstrated the ability of Fe- and Al-oxides to stabilize organic matter, there is a scarcity of similar information regarding Mn-oxides. Furthermore, Mn-mediated reactions regulate important litter decomposition pathways, but these processes are poorly constrained across diverse ecosystems. Here, we discuss the ecological roles of Mn in terrestrial environments and synthesize existing knowledge on the multiple pathways by which biogeochemical Mn and C cycling intersect. We demonstrate that Mn has a high potential to degrade organic molecules through abiotic and microbially mediated oxidation and to stabilize organic molecules, at least temporarily, through organo-mineral associations. We outline research priorities needed to advance understanding of Mn-C interactions, highlighting knowledge gaps that may address key uncertainties in soil C predictions.

Characterization and mechanism of Mn(II)-based mixotrophic denitrifying bacterium (Cupriavidus sp. HY129) in remediation of nitrate (NO3--N) and manganese (Mn(II)) contaminated groundwater

The co-contamination of groundwater with nitrate (NO₃^--N) and manganese (Mn(II)) is a global issue that needs to be efficiently remediated. In this research, a novel denitrifying and manganese-oxidizing strain HY129 was isolated from the sediments sample of a drinking water and identified as Cupriavidus sp. HY129. The remediation ability of strain HY129 regarding the nitrate and Mn(II) pollution were investigated. The removal efficiency of nitrate and Mn(II) were 99.81% (0.229 mgL^-1 h^-1) and 87.24% (0.233 mgL^-1 h^-1) in bacterial culture after 72 h, respectively. Moreover, the addition of Mn(II) significantly enhanced the denitrification process, while excessive concentration of Mn(II) caused more NO₂^--N accumulation. The impacts of adsorption and oxidation activity on Mn(II) removal were investigated. Protein in extracellular polymeric substance (EPS) which produced in the Mn-oxidizing process was speculated to be the main cause of extracellular adsorption of Mn(II). Characterization of biogenic manganese oxides (BMO) confirmed the formation of high-valent manganese and the trapping experiment with sodium pyrophosphate (NaPP) demonstrated the existence of Mn(III)-intermediates. Furthermore, multicopper oxidase gene amplification provided evidence for the molecular biology of Mn(II) oxidation by strain HY129.

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.

Mn oxide formation by phototrophs: Spatial and temporal patterns, with evidence of an enzymatic superoxide-mediated pathway

Manganese (Mn) oxide minerals influence the availability of organic carbon, nutrients and metals in the environment. Oxidation of Mn(II) to Mn(III/IV) oxides is largely promoted by the direct and indirect activity of microorganisms. Studies of biogenic Mn(II) oxidation have focused on bacteria and fungi, with phototrophic organisms (phototrophs) being generally overlooked. Here, we isolated phototrophs from Mn removal beds in Pennsylvania, USA, including fourteen Chlorophyta (green algae), three Bacillariophyta (diatoms) and one cyanobacterium, all of which consistently formed Mn(III/IV) oxides. Isolates produced cell-specific oxides (coating some cells but not others), diffuse biofilm oxides, and internal diatom-specific Mn-rich nodules. Phototrophic Mn(II) oxidation had been previously attributed to abiotic oxidation mediated by photosynthesis-driven pH increases, but we found a decoupling of Mn oxide formation and pH alteration in several cases. Furthermore, cell-free filtrates of some isolates produced Mn oxides at specific time points, but this activity was not induced by Mn(II). Manganese oxide formation in cell-free filtrates occurred via reaction with the oxygen radical superoxide produced by soluble extracellular proteins. Given the known widespread ability of phototrophs to produce superoxide, the contribution of phototrophs to Mn(II) oxidation in the environment may be greater and more nuanced than previously thought.

Portraying manganese biofilms via a merger of EPR spectroscopy and cathodic polarization

Microbial biofilms on stainless steel surfaces exposed to water from a freshwater pond were dominated by manganese-oxidizing bacteria, as initially diagnosed by microscopy and elemental analysis. The application of electron paramagnetic resonance (EPR) spectroscopy revealed conspicuous sextet (six-line) patterns that intensified with immersion time, implying the gradual accumulation of Mn(II) in the biofilms. Correspondingly, cathodic polarization designated the manganese oxide (MnO_x) reduction peak in the form of a distinctive 'nose', which grew increasingly more negative with biofilm growth. The progressive expansion of cathodic current densities and the concurrent area-under-the-curve also allowed the quantification of microbially mediated MnO_x deposition_. Furthermore, the merger of EPR and cathodic polarization techniques yielded key insights, in tandem with Mn speciation data, into the pathways of microbial manganese transformations in biofilms, besides providing meaningful interpretations of prevailing literature. Accordingly, the natural freshwater biofilm was inferred as one supporting a complete manganese cycle encompassing multiple redox states.

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.

Preliminary study on the tick population of Benin wildlife at the moment of its invasion by the Rhipicephalus microplus tick (Canestrini, 1888)

BACKGROUND AND AIM

Rhipicephalus microplus (Rm) is one of the most problematic livestock tick species in the world. Its rapid propagation and resistance to acaricides make it control difficult in the sub-region and Benin particularly. The aim of this work was to check its presence in wildlife and to confirm the possible role of reservoir wildlife may play in the propagation of the parasite. This will help to design more efficient control strategy.

MATERIALS AND METHODS

This study was conducted from February to March 2017 in the National Parks of Benin (Pendjari and W Park) and wildfowl's assembly and selling point in Benin. Ticks were manually picked with forceps from each animal after slaughtering by hunters then stored in 70° ethanol. Collected ticks were counted and identified in the laboratory using the identification key as described by Walker.

RESULTS

Overall, seven species of ticks (Amblyomma variegatum, Boophilus decoloratus, Rm, Boophilus spp., Hyalomma spp., Rhipicephalus sanguineus, Rhipicephalus spp.) were identified on nine wild animal species sampled (Cane rat, wildcat, Hare, Doe, Cricetoma, Buffalo, Buffon Cobe, and Bushbuck and Warthog). The average number of ticks varies from 3 to 6 between animal species, 3 to 7 between localities visited, and 2 to 5 between tick species. However, these differences are statistically significant only for localities. Considering tick species and animal species, the parasite load of Rm and Rhipicephalus spp. is higher; the buffalo being more infested. The analysis of deviance reveals that the abundance of ticks observed depends only on the observed localities (p>0.05). However, the interactions between animal species and localities on the one hand and between animal and tick species on the other hand, although not significant, have influenced the abundance of ticks as they reduce the residual deviance after their inclusion in the model.

CONCLUSIONS

This study reported the presence of Rm in wildlife of Benin and confirmed its role in the maintenance and spread of the parasites. It is, therefore, an important risk factor that we must not neglect in the epidemiological surveillance and ticks control strategies in the West African sub-region and particularly in Benin.

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.

Recrystallization of Manganite (γ-MnOOH) and Implications for Trace Element Cycling

The recrystallization of Mn(III,IV) oxides is catalyzed by aqueous Mn(II) (Mn(II)_aq) during (bio)geochemical Mn redox cycling. It is poorly understood how trace metals associated with Mn oxides (e.g., Ni) are cycled during such recrystallization. Here, we use X-ray absorption spectroscopy (XAS) to examine the speciation of Ni associated with Manganite (γ-Mn(III)OOH) suspensions in the presence or absence of Mn(II)_aq under variable pH conditions (pH 5.5 and 7.5). In a second set of experiments, we used a ⁶²Ni isotope tracer to quantify the amount of dissolved Ni that exchanges with Ni incorporated in the Manganite crystal structure during reactions in 1 mM Mn(II)_aq and in Mn(II)-free solutions. XAS spectra show that Ni is initially sorbed on the Manganite mineral surface and is progressively incorporated into the mineral structure over time (13% after 51 days) even in the absence of dissolved Mn(II). The amount of Ni incorporation significantly increases to about 40% over a period of 51 days when Mn(II)_aq is present in solution. Similarly, Mn(II)_aq promotes Ni exchange between Ni-substituted Manganite and dissolved Ni(II), with around 30% of Ni exchanged at pH 7.5 over the duration of the experiment. No new mineral phases are detected following recrystallization as determined by X-ray diffraction and XAS. Our results reveal that Mn(II)-catalyzed mineral recrystallization partitions Ni between Mn oxides and aqueous fluids and can therefore affect Ni speciation and mobility in the environment.

Biogenic manganese oxides as reservoirs of organic carbon and proteins in terrestrial and marine environments

Manganese (Mn) oxides participate in a range of interactions with organic carbon (OC) that can lead to either carbon degradation or preservation. Here, we examine the abundance and composition of OC associated with biogenic and environmental Mn oxides to elucidate the role of Mn oxides as a reservoir for carbon and their potential for selective partitioning of particular carbon species. Mn oxides precipitated in natural brackish waters and by Mn(II)-oxidizing marine bacteria and terrestrial fungi harbor considerable levels of organic carbon (4.1-17.0 mol OC per kg mineral) compared to ferromanganese cave deposits which contain 1-2 orders of magnitude lower OC. Spectroscopic analyses indicate that the chemical composition of Mn oxide-associated OC from microbial cultures is homogeneous with bacterial Mn oxides hosting primarily proteinaceous carbon and fungal Mn oxides containing both protein- and lipopolysaccharide-like carbon. The bacterial Mn oxide-hosted proteins are involved in both Mn(II) oxidation and metal binding by these bacterial species and could be involved in the mineral nucleation process as well. By comparison, the composition of OC associated with Mn oxides formed in natural settings (brackish waters and particularly in cave ferromanganese rock coatings) is more spatially and chemically heterogeneous. Cave Mn oxide-associated organic material is enriched in aliphatic C, which together with the lower carbon concentrations, points to more extensive microbial or mineral processing of carbon in this system relative to the other systems examined in this study, and as would be expected in oligotrophic cave environments. This study highlights Mn oxides as a reservoir for carbon in varied environments. The presence and in some cases dominance of proteinaceous carbon within the biogenic and natural Mn oxides may contribute to preferential preservation of proteins in sediments and dominance of protein-dependent metabolisms in the subsurface biosphere.

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.

DGGE diversity of manganese mine samples and isolation of a Lysinibacillus sp. efficient in removal of high Mn (II) concentrations

Manganese contamination has become a serious environmental problem in the world and bacterial removal plays an important role in global cycling of manganese. In this study, microorganism distribution within samples from a manganese mine was analyzed with PCR-DGGE technology. The results suggested that Manganese oxidizing bacteria (such as Bacillus, Hyphomicrobiaceae and Erythrobacter) were dominant in the soil. In addition, a Lysinibacillus sp. Isolate, strain MK-1, revealed robust growth at high Mn(II) concentrations up to 1 mM. At that concentration, 55.94% of added Mn(II) was oxidized and 36.23% of the Mn(II) was adsorbed by MK-1(total manganese removal reached 94.67%) after 7 days of culturing. By measuring its metabolic process, the great role of biological adsorption was found. Additionally, the spectroscopic result demonstrated that Mn(III) was an intermediate during the biological oxidation process. These findings increase the knowledge of biological manganese removal mechanisms and show some potentials to the operation of manganese treatment.

Oxygen Isotope Evidence for Mn(II)-Catalyzed Recrystallization of Manganite (γ-MnOOH)

Manganese is biogeochemically cycled between aqueous Mn(II) and Mn(IV) oxides. Aqueous Mn(II) often coexists with Mn(IV) oxides, and redox reactions between the two (e.g., comproportionation) are well known to result in the formation of Mn(III) minerals. It is unknown, however, whether aqueous Mn(II) exchanges with structural Mn(III) in manganese oxides in the absence of any mineral transformation (similar to what has been reported for aqueous Fe(II) and some Fe(III) minerals). To probe whether atoms exchange between a Mn(III) oxide and water, we use a (17)O tracer to measure oxygen isotope exchange between structural oxygen in manganite (γ-MnOOH) and water. In the absence of aqueous Mn(II), about 18% of the oxygen atoms in manganite exchange with the aqueous phase, which is close to the estimated surface oxygen atoms (∼11%). In the presence of aqueous Mn(II), an additional 10% (for a total of 28%) of the oxygen atoms exchange with water, suggesting that some of the bulk manganite mineral (i.e., beyond surface) is exchanging with the fluid. Exchange of manganite oxygen with water occurs without any observable change in mineral phase and appears to be independent of the rapid Mn(II) sorption kinetics. These experiments suggest that Mn(II) catalyzes manganese oxide recrystallization and illustrate a new pathway by which these ubiquitous minerals interact with their surrounding fluid.

Deciphering the Complex Chemistry of Deep-Ocean Particles Using Complementary Synchrotron X-ray Microscope and Microprobe Instruments

The reactivity and mobility of natural particles in aquatic systems have wide ranging implications for the functioning of Earth surface systems. Particles in the ocean are biologically and chemically reactive, mobile, and complex in composition. The chemical composition of marine particles is thought to be central to understanding processes that convert globally relevant elements, such as C and Fe, among forms with varying bioavailability and mobility in the ocean. The analytical tools needed to measure the complex chemistry of natural particles are the subject of this Account. We describe how a suite of complementary synchrotron radiation instruments with nano- and micrometer focusing, and X-ray absorption spectroscopy (XAS) and X-ray diffraction (XRD) capabilities are changing our understanding of deep-ocean chemistry and life. Submarine venting along mid-ocean ridges creates hydrothermal plumes where dynamic particle-forming reactions occur as vent fluids mix with deep-ocean waters. Whether plumes are net sources or sinks of elements in ocean budgets depends in large part on particle formation, reactivity, and transport properties. Hydrothermal plume particles have been shown to host microbial communities and exhibit complex size distributions, aggregation behavior, and composition. X-ray microscope and microprobe instruments can address particle size and aggregation, but their true strength is in measuring chemical composition. Plume particles comprise a stunning array of inorganic and organic phases, from single-crystal sulfides to poorly ordered nanophases and polymeric organic matrices to microbial cells. X-ray microscopes and X-ray microprobes with elemental imaging, XAS, and XRD capabilities are ideal for investigating these complex materials because they can (1) measure the chemistry of organic and inorganic constituents in complex matrices, usually within the same particle or aggregate, (2) provide strong signal-to-noise data with exceedingly small amounts of material, (3) simplify the chemical complexity of particles or sets of particles with a focused-beam, providing spatial resolution over 6 orders of magnitude (nanometer to millimeter), (4) provide elemental specificity for elements in the soft-, tender-, and hard-X-ray energies, (5) switch rapidly among elements of interest, and (6) function in the presence of water and gases. Synchrotron derived data sets are discussed in the context of important advances in deep-ocean technology, sample handling and preservation, molecular microbiology, and coupled physical-chemical-biological modeling. Particle chemistry, size, and morphology are all important in determining whether particles are reactive with dissolved constituents, provide substrates for microbial respiration and growth, and are delivered to marine sediments or dispersed by deep-ocean currents.

Preparation and representation of recombinant Mn-ferritin flower-like spherical aggregates from marine invertebrates

Ferritin has important functions in the transition and storage of toxic metal ions, but its regulation and function in many invertebrate species are still largely unknown. In our previous work, the cDNA sequence of Sinonovacula constricta, Apostichopus japonicas and Acaudina leucoprocta were constructed and efficiently expressed in E. Coli BL21 under IPTG induction. In this follow-up study, the recombinant ferritins were exposed to heavy metal manganese. The manganese concentration levels in three recombinant ferritins were greater than horse spleen ferritin (HSF). Compared with HSF, the amount of manganese enrichment in the three recombinant ferritins was 1.75-fold, 3.25-fold and 2.42-fold increases in ScFER, AjFER, and AlFER, respectively. After phosphate stimulation, the concentration of manganese increased and was higher than the ordinary dialysis control groups. The ScFER was four times its baseline value. The AjFER and AlFER were 1.4- and 8-fold higher, respectively. The AlFER sample stimulated by phosphate was 22-fold that of HSF. The morphologies of the resulting Mn-Ferritin from different marine invertebrates were characterized with scanning electron microscopy. Surface morphologies were lamella flower-like and are consistent with changes in surface morphologies of the standard Mn-HSF. Invertebrate recombinant ferritin and HSF both can uptake manganese. We found that the structure of A. leucoproctarecombinant Mn-Ferritin aggregate changed over time. The surface formed lamella flower-like aggregate, but gradually merged to create a relatively uniform plate-like phase of aggregate spherically and fused without clear boundaries.

A comparison of the sorption reactivity of bacteriogenic and mycogenic Mn oxide nanoparticles

Biogenic MnO2 minerals affect metal fate and transport in natural and engineered systems by strongly sorbing metals ions. The ability to produce MnO2 is widely dispersed in the microbial tree of life, leading to potential differences in the minerals produced by different organisms. In this study, we compare the structure and reactivity of biogenic Mn oxides produced by the biofilm-forming bacterium Pseudomonas putida GB-1 and the white-rot fungus Coprinellus sp. The rate of Mn(II) oxidation, and thus biomineral production, was 45 times lower for Coprinellus sp. (5.1 × 10(-2) mM d(-1)) than for P. putida (2.32 mM d(-1)). Both organisms produced predominantly Mn(IV) oxides with hexagonal-sheet symmetry, low sheet stacking, small particle size, and Mn(II/III) in the interlayer. However, we found that mycogenic MnO2 could support a significantly lower quantity of Ni sorbed via inner-sphere coordination at vacancy sites than the bacteriogenic MnO2: 0.09 versus 0.14 mol Ni mol(-1) Mn. In addition, 50-100% of the adsorbed Ni partitioned to the MnO2, which accounts for less than 20% of the sorbent on a mass basis. The vacancy content, which appears to increase with the kinetics of MnO2 precipitation, exerts significant control on biomineral reactivity.

Quantitative study of contrast enhancement in soft X-ray micrographs of insect eyes by tissue selective mass loss

Quantitative studies of soft X-ray induced radiation damage in zone-plate-based X-ray microspectroscopy have so far concentrated on investigations of homogeneous specimens. However, more complex materials can show unexpected radiation-induced behaviour. Here a quantitative radiochemical analysis of biological tissue from Xantophan morganii praedicta eyes is presented. Contrast enhancement due to tissue selective mass loss leading to a significant improvement of imaging quality is reported. Since conventional quantitative analysis of the absorbed dose cannot conclusively explain the experimental observations on photon-energy-dependent radiation damage, a significant contribution of photo- and secondary electrons to soft matter damage for photon energies above the investigated absorption edge is proposed.

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.

Pyoverdine synthesis by the Mn(II)-oxidizing bacterium Pseudomonas putida GB-1

When iron-starved, the Mn(II)-oxidizing bacteria Pseudomonas putida strains GB-1 and MnB1 produce pyoverdines (PVDGB-1 and PVDMnB1), siderophores that both influence iron uptake and inhibit manganese(II) oxidation by these strains. To explore the properties and genetics of a PVD that can affect manganese oxidation, LC-MS/MS, and various siderotyping techniques were used to identify the peptides of PVDGB-1 and PVDMnB1 as being (for both PVDs): chromophore-Asp-Lys-OHAsp-Ser-Gly-aThr-Lys-cOHOrn, resembling a structure previously reported for P. putida CFML 90-51, which does not oxidize Mn. All three strains also produced an azotobactin and a sulfonated PVD, each with the peptide sequence above, but with unknown regulatory or metabolic effects. Bioinformatic analysis of the sequenced genome of P. putida GB-1 suggested that a particular non-ribosomal peptide synthetase (NRPS), coded by the operon PputGB1_4083-4086, could produce the peptide backbone of PVDGB-1. To verify this prediction, plasmid integration disruption of PputGB1_4083 was performed and the resulting mutant failed to produce detectable PVD. In silico analysis of the modules in PputGB1_4083-4086 predicted a peptide sequence of Asp-Lys-Asp-Ser-Ala-Thr-Lsy-Orn, which closely matches the peptide determined by MS/MS. To extend these studies to other organisms, various Mn(II)-oxidizing and non-oxidizing isolates of P. putida, P. fluorescens, P. marincola, P. fluorescens-syringae group, P. mendocina-resinovorans group, and P. stutzerii group were screened for PVD synthesis. The PVD producers (12 out of 16 tested strains) were siderotyped and placed into four sets of differing PVD structures, some corresponding to previously characterized PVDs and some to novel PVDs. These results combined with previous studies suggested that the presence of OHAsp or the flexibility of the pyoverdine polypeptide may enable efficient binding of Mn(III).

Development of a New Decision Tree to Rapidly Screen Chemical Estrogenic Activities of Xenopus laevis

During the last past decades, there is an increasing number of studies about estrogenic activities of the environmental pollutants on amphibians and many determination methods have been proposed. However, these determination methods are time-consuming and expensive, and a rapid and simple method to screen and test the chemicals for estrogenic activities to amphibians is therefore imperative. Herein is proposed a new decision tree formulated not only with physicochemical parameters but also a biological parameter that was successfully used to screen estrogenic activities of the chemicals on amphibians. The biological parameter, CDOCKER interaction energy (Ebinding ) between chemicals and the target proteins was calculated based on the method of molecular docking, and it was used to revise the decision tree formulated by Hong only with physicochemical parameters for screening estrogenic activity of chemicals in rat. According to the correlation between Ebinding of rat and Xenopus laevis, a new decision tree for estrogenic activities in Xenopus laevis is finally proposed. Then it was validated by using the randomly 8 chemicals which can be frequently exposed to Xenopus laevis, and the agreement between the results from the new decision tree and the ones from experiments is generally satisfactory. Consequently, the new decision tree can be used to screen the estrogenic activities of the chemicals, and combinational use of the Ebinding and classical physicochemical parameters can greatly improves Hong's decision tree.

3D chemical mapping: application of scanning transmission (soft) X-ray microscopy (STXM) in combination with angle-scan tomography in bio-, geo-, and environmental sciences

The identification of environmental processes and mechanisms often requires information on the organochemical and inorganic composition of specimens at high spatial resolution. X-ray spectroscopy (XAS) performed in the soft X-ray range (100-2,200 eV) provides chemical speciation information for elements that are of high biogeochemical relevance such as carbon, nitrogen, and oxygen but also includes transition metals such as iron, manganese, or nickel. Synchrotron-based scanning transmission X-ray microscopy (STXM) combines XAS with high resolution mapping on the 20-nm scale. This provides two-dimensional (2D) quantitative information about the distribution of chemical species such as organic macromolecules, metals, or mineral phases within environmental samples. Furthermore, the combination of STXM with angle-scan tomography allows for three-dimensional (3D) spectromicroscopic analysis of bio-, geo-, or environmental samples. For the acquisition of STXM tomography data, the sample is rotated around an axis perpendicular to the X-ray beam. Various sample preparation approaches such as stripes cut from TEM grids or the preparation of wet cells allow for preparing environmentally relevant specimens in a dry or in a fully hydrated state for 2D and 3D STXM measurements. In this chapter we give a short overview about the principles of STXM, its application to environmental sciences, different preparation techniques, and the analysis and 3D reconstruction of STXM tomography data.

Constraints on superoxide mediated formation of manganese oxides

Manganese (Mn) oxides are among the most reactive sorbents and oxidants within the environment, where they play a central role in the cycling of nutrients, metals, and carbon. Recent discoveries have identified superoxide (O2−) both of biogenic and abiogenic origin as an effective oxidant of Mn(II) leading to the formation of Mn oxides. Here we examined the conditions under which abiotically produced superoxide led to oxidative precipitation of Mn and the solid-phases produced. Oxidized Mn, as both aqueous Mn(III) and Mn(III/IV) oxides, was only observed in the presence of active catalase, indicating that hydrogen peroxide (H₂O₂), a product of the reaction of O2− with Mn(II), inhibits the oxidation process presumably through the reduction of Mn(III). Citrate and pyrophosphate increased the yield of oxidized Mn but decreased the amount of Mn oxide produced via formation of Mn(III)-ligand complexes. While complexing ligands played a role in stabilizing Mn(III), they did not eliminate the inhibition of net Mn(III) formation by H₂O₂. The Mn oxides precipitated were highly disordered colloidal hexagonal birnessite, similar to those produced by biotically generated superoxide. Yet, in contrast to the large particulate Mn oxides formed by biogenic superoxide, abiotic Mn oxides did not ripen to larger, more crystalline phases. This suggests that the deposition of crystalline Mn oxides within the environment requires a biological, or at least organic, influence. This work provides the first direct evidence that, under conditions relevant to natural waters, oxidation of Mn(II) by superoxide can occur and lead to formation of Mn oxides. For organisms that oxidize Mn(II) by producing superoxide, these findings may also point to other microbially mediated processes, in particular enzymatic hydrogen peroxide degradation and/or production of organic ligand metabolites, that allow for Mn oxide formation.

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.

Enigmatic reticulated filaments in subsurface granite

In the last few years, geomicrobiologists have focused their researches on the nature and origin of enigmatic reticulated filaments reported in modern and fossil samples from limestone caves and basalt lava tubes. Researchers have posed questions on these filaments concerning their nature, origin, chemistry, morphology, mode of formation and growth. A tentative microbial origin has been elusive since these filaments are found as hollow tubular sheaths and could not be affiliated to any known microorganism. We describe the presence of similar structures in a 16th century granite tunnel in Porto, Northwest Portugal. The reticulated filaments we identify exhibit fine geometry surface ornamentation formed by cross-linked Mn-rich nanofibres, surrounded by a large amount of extracellular polymeric substances. Within these Mn-rich filaments we report for the first time the occurrence of microbial cells.

Characterisation of the dissimilatory reduction of Fe(III)-oxyhydroxide at the microbe-mineral interface: the application of STXM-XMCD

A combination of scanning transmission X-ray microscopy and X-ray magnetic circular dichroism was used to spatially resolve the distribution of different carbon and iron species associated with Shewanella oneidensis MR-1 cells. S. oneidensis MR-1 couples the reduction of Fe(III)-oxyhydroxides to the oxidation of organic matter in order to conserve energy for growth. Several potential mechanisms may be used by S. oneidensis MR-1 to facilitate Fe(III)-reduction. These include direct contact between the cell and mineral surface, secretion of either exogenous electron shuttles or Fe-chelating agents and the production of conductive 'nanowires'. In this study, the protein/lipid signature of the bacterial cells was associated with areas of magnetite (Fe₃O₄), the product of dissimilatory Fe(III) reduction, which was oversaturated with Fe(II) (compared to stoichiometric magnetite). However, areas of the sample rich in polysaccharides, most likely associated with extracellular polymeric matrix and not in direct contact with the cell surface, were undersaturated with Fe(II), forming maghemite-like (γ-Fe₂O₃) phases compared to stoichiometric magnetite. The reduced form of magnetite will be much more effective in environmental remediation such as the immobilisation of toxic metals. These findings suggest a dominant role for surface contact-mediated electron transfer in this study and also the inhomogeneity of magnetite species on the submicron scale present in microbial reactions. This study also illustrates the applicability of this new synchrotron-based technique for high-resolution characterisation of the microbe-mineral interface, which is pivotal in controlling the chemistry of the Earth's critical zone.

Electron energy-loss safe-dose limits for manganese valence measurements in environmentally relevant manganese oxides

Manganese (Mn) oxides are among the strongest mineral oxidants in the environment and impose significant influence on mobility and bioavailability of redox-active substances, such as arsenic, chromium, and pharmaceutical products, through oxidation processes. Oxidizing potentials of Mn oxides are determined by Mn valence states (2+, 3+, 4+). In this study, the effects of beam damage during electron energy-loss spectroscopy (EELS) in the transmission electron microscope have been investigated to determine the "safe dose" of electrons. Time series analyses determined the safe dose fluence (electrons/nm(2)) for todorokite (10(6) e/nm(2)), acid birnessite (10(5)), triclinic birnessite (10(4)), randomly stacked birnessite (10(3)), and δ-MnO(2) (<10(3)) at 200 kV. The results show that meaningful estimates of the mean Mn valence can be acquired by EELS if proper care is taken.

Role of bacterial biomass in the sorption of Ni by biomass-birnessite assemblages

Birnessites precipitated by bacteria are typically poorly crystalline Mn(IV) oxides enmeshed within biofilms to form complex biomass-birnessite assemblages. The strong sorption affinity of bacteriogenic birnessites for environmentally important trace metals is relatively well understood mechanistically, but the role of bacterial cells and extracellular polymeric substances appears to vary among trace metals. To assess the role of biomass definitively, comparison between metal sorption by biomass at high metal loadings in the presence and absence of birnessite is required. We investigated the biomass effect on Ni sorption through laboratory experiments utilizing the birnessite produced by the model bacterium, Pseudomonas putida. Surface excess measurements at pH 6-8 showed that birnessite significantly enhanced Ni sorption at high loadings (up to nearly 4-fold) relative to biomass alone. This apparent large difference in affinity for Ni between the organic and mineral components was confirmed by extended X-ray absorption fine structure spectroscopy, which revealed preferential Ni binding to birnessite cation vacancy sites. At pH ≥ 7, Ni sorption involved both adsorption and precipitation reactions. Our results thus support the view that the biofilm does not block reactive mineral surface sites; instead, the organic material contributes to metal sorption once high-affinity sites on the mineral are saturated.

Synthesis and characterization of a novel extracellular biogenic manganese oxide (bixbyite-like Mn₂O₃) nanoparticle by isolated Acinetobacter sp

Recently, manganese oxides have been considered in the environmental remediation, MRI diagnosis and drug and pharmaceutical industries. Different numbers of physicochemical and biological methods have been reported for the preparation of nanoscale manganese oxides. Although manganese oxide biogenesis by bacterial species has been recognized as the major Mn-oxidizing agent in nature, in this research, for first time, we demonstrated the process which used to produce bixbyite-like Mn(2)O(3) nanoparticles by isolated aerobic bacterium from Persian Gulf water. The 16SRNA sequencing showed that this isolate belong to a gram-negative Acinetobacter which produced nano Mn-oxide crystal particle. Characterization of complement morphology, size and chemical structure of these particles were determined by TEM, SEM, EDAX, XRD and FTIR. The data showed that this bacterium could produce nanosized extracellular bixbyite-like Mn(2)O(3) which depend on enzymatic pathway.

Sorption and distribution of copper in unsaturated Pseudomonas putida CZ1 biofilms as determined by X-ray fluorescence microscopy

The spatial and temporal distribution of metals in unsaturated Pseudomonas putida CZ1 biofilms was determined using synchrotron-based X-ray fluorescence microscopy (XRF). It was found that Fe, Mn, and Ca were mainly distributed near the air-biofilm interface of a biofilm grown on 40 mM citrate, while there were two Fe-, Mn-, and Ca-rich layers within a biofilm grown on 10 mM citrate. The sorption of copper by biofilm grown in medium containing 10 mM citrate was rapid, with copper being found throughout the biofilm after only 1 h of exposure. Copper initially colocalized with Fe and Mn element layers in the biofilm and then precipitated in a 40-μm-thick layer near the air-biofilm interface when exposed for 12 h. Cu K-edge X-ray absorption near edge structure (XANES) analysis revealed that Cu was primarily bound with citrate within the biofilm, and the precipitate formed in the biofilm exposed to copper for 12 h was most similar to copper phosphate. LIVE/DEAD staining revealed that cells at the biofilm-membrane interface were mostly alive even when the copper concentration reached 80.5 mg copper g(-1) biomass. This suggests that the biofilm matrix provided significant protection for cells in this area. These results significantly improve our understanding of metal acquisition, transportation, and immobilization in unsaturated biofilm systems.

Carbon K-edge spectra of carbonate minerals

Carbon K-edge X-ray spectroscopy has been applied to the study of a wide range of organic samples, from polymers and coals to interstellar dust particles. Identification of carbonaceous materials within these samples is accomplished by the pattern of resonances in the 280-320 eV energy region. Carbonate minerals are often encountered in the study of natural samples, and have been identified by a distinctive resonance at 290.3 eV. Here C K-edge and Ca L-edge spectra from a range of carbonate minerals are presented. Although all carbonates exhibit a sharp 290 eV resonance, both the precise position of this resonance and the positions of other resonances vary among minerals. The relative strengths of the different carbonate resonances also vary with crystal orientation to the linearly polarized X-ray beam. Intriguingly, several carbonate minerals also exhibit a strong 288.6 eV resonance, consistent with the position of a carbonyl resonance rather than carbonate. Calcite and aragonite, although indistinguishable spectrally at the C K-edge, exhibited significantly different spectra at the Ca L-edge. The distinctive spectral fingerprints of carbonates provide an identification tool, allowing for the examination of such processes as carbon sequestration in minerals, Mn substitution in marine calcium carbonates (dolomitization) and serpentinization of basalts.

Diclofenac oxidation by biogenic manganese oxides

Diclofenac, a nonsteroidal anti-inflammatory drug, is one of the most commonly detected pharmaceuticals in sewage treatment plant (STP) effluents. In this work, biologically produced manganese oxides (BioMnOx) were investigated to remove diclofenac. At neutral pH, the diclofenac oxidation with BioMnOx was 10-fold faster than with chemically produced MnO(2). The main advantage of BioMnOx over chemical MnO(2) is the ability of the bacteria to reoxidize the formed Mn(2+), which inhibits the oxidation of diclofenac. Diclofenac-2,5-iminoquinone was identified as a major transformation product, accounting for 5-10% of the transformed diclofenac. Except for 5-hydroxydiclofenac, which was identified as an intermediate, no other oxidation products were detected. Diclofenac oxidation was proportional to the amount of BioMnOx dosed, and the pseudo first order rate constant k was 6-fold higher when pH was decreased from 6.8 to 6.2. The Mn(2+) levels remained below the drinking water limit (0.05 mg L(-1)), thus indicating the efficient in situ microbiological regeneration of the oxidant. These results combined with previous studies suggest the potential of BioMnOx for STP effluent polishing.

Advanced imaging techniques for assessment of structure, composition and function in biofilm systems

Scientific imaging represents an important and accepted research tool for the analysis and understanding of complex natural systems. Apart from traditional microscopic techniques such as light and electron microscopy, new advanced techniques have been established including laser scanning microscopy (LSM), magnetic resonance imaging (MRI) and scanning transmission X-ray microscopy (STXM). These new techniques allow in situ analysis of the structure, composition, processes and dynamics of microbial communities. The three techniques open up quantitative analytical imaging possibilities that were, until a few years ago, impossible. The microscopic techniques represent powerful tools for examination of mixed environmental microbial communities usually encountered in the form of aggregates and films. As a consequence, LSM, MRI and STXM are being used in order to study complex microbial biofilm systems. This mini review provides a short outline of the more recent applications with the intention to stimulate new research and imaging approaches in microbiology.

Soft X-ray spectromicroscopy of nickel sorption in a natural river biofilm

Scanning transmission X-ray microscopy (STXM) at the C 1s, O 1s, Ni 2p, Ca 2p, Mn 2p, Fe 2p, Mg 1s, Al 1s and Si 1s edges was used to study Ni sorption in a complex natural river biofilm. The 10-week grown river biofilm was exposed to 10 mg L(-1) Ni(2+) (as NiCl(2)) for 24 h. The region of the biofilm examined was dominated by filamentous structures, which were interpreted as the discarded sheaths of filamentous bacteria, as well as a sparse distribution of rod-shaped bacteria. The region also contained discrete particles with spectra similar to those of muscovite, SiO(2) and CaCO(3). The Ni(II) ions were selectively adsorbed by the sheaths of the filamentous bacteria. The sheaths were observed to be metal rich with significant amounts of Ca, Fe and Mn, along with the Ni. In addition, the sheaths had a large silicate content but little organic material. The metal content of the rod-shaped bacterial cells was much lower. The Fe on the sheath was mainly in the Fe(III) oxidation state. Mn was found in II, III and IV oxidation states. The Ni was likely sorbed to Mn-Fe minerals on the sheath. These STXM results have probed nano-scale biogeochemistry associated with bacterial species in a complex, natural biofilm community. They have implications for selective Ni contamination of the food chain and for developing bioremediation strategies.

Removal of multi-heavy metals using biogenic manganese oxides generated by a deep-sea sedimentary bacterium – Brachybacterium sp. strain Mn32

A deep-sea manganese-oxidizing bacterium,Brachybacteriumsp. strain Mn32, showed high Mn(II) resistance (MIC 55 mM) and Mn(II)-oxidizing/removing abilities. Strain Mn32 removed Mn(II) by two pathways: (1) oxidizing soluble Mn(II) to insoluble biogenic Mn oxides – birnessite (δ-MnO2group) and manganite (γ-MnOOH); (2) the biogenic Mn oxides further adsorb more Mn(II) from the culture. The generated biogenic Mn oxides surround the cell surfaces of strain Mn32 and provide a high capacity to adsorb Zn(II) and Ni(II). Mn(II) oxidation by strain Mn32 was inhibited by both sodium azide ando-phenanthroline, suggesting the involvement of a metalloenzyme which was induced by Mn(II). X-ray diffraction analysis showed that the crystal structures of the biogenic Mn oxides were different from those of commercial pyrolusite (β-MnO2group) and fresh chemically synthesized vernadite (δ-MnO2group). The biogenic Mn oxides generated by strain Mn32 showed two to three times higher Zn(II) and Ni(II) adsorption abilities than commercial and fresh synthetic MnO2. The crystal structure and the biogenic MnO2types may be important factors for the high heavy metal adsorption ability of strain Mn32. This study provides potential applications of a new marine Mn(II)-oxidizing bacterium in heavy metal bioremediation and increases our basic knowledge of microbial manganese oxidation mechanisms.

First direct imaging of electrolyte-induced deswelling behavior of pH-responsive microgels in aqueous media using scanning transmission X-ray microscopy

Lightly cross-linked sterically stabilized poly(2-vinylpyridine) latexes exhibit pH-responsive behavior, undergoing a latex-to-microgel transition below pH 4.1 as a result of protonation of the pyridine pendent groups. We have examined both the latex and microgel states of such particles directly in aqueous solution using scanning transmission X-ray microscopy (STXM). Moreover, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy studies confirm that the nitrogen atoms of the microgel particles are fully protonated at low pH. The addition of salt causes partial deswelling of these microgel particles, but spectroscopic analysis confirms the retention of their cationic character. This is the first direct visualization of the effect of electrolyte screening on microgel dimensions in aqueous solution. In each case, the observed particle dimensions are consistent with dynamic light scattering characterization, especially when polydispersity effects are taken into consideration.

Biogenic origin of polymetallic nodules from the Clarion-Clipperton Zone in the Eastern Pacific Ocean: electron microscopic and EDX evidence

Polymetallic/ferromanganese nodules (Mn-nodules) have been assigned a huge economic potential since they contain considerable concentrations of manganese, copper, nickel, iron, and cobalt. It has been assumed that they are formed by, besides hydrogenous, nonbiogenic processes, biogenic processes based on metabolic processes driven by microorganisms. In the present study, we applied the techniques of digital optical microscopy and high-resolution scanning electron microscopy to search for microorganisms in Mn-nodules. They were collected from the Clarion-Clipperton Zone in the Eastern Pacific Ocean and are composed of Mn (23.9%), Cu (0.69%), Ni (1.02%), Fe (10.9%), and Co (0.29%). These Mn-nodules, between 2.3 and 4.8 cm, show a distinct lamination; they are composed of small-sized micronodules, 100 to 450 microm in size, which are bound together by an interstitial whitish material. In the micronodules, a dense accumulation of microorganisms/bacteria could be visualized. Only two morphotypes exist: (1) round-shaped cocci and (2) elongated rods. The cocci (diameter: approximately 3.5 microm) are arranged in bead-like chains, while the rods (approximately 2 x 0.4 microm) are arranged either as palisades or in a linear row. Energy-dispersive X-ray spectroscopy analyses showed that the areas rich in microorganisms/bacteria are also rich in Mn, while in regions where no microorganisms are found, the element Si is dominant. We suggest that growth of the Mn-nodules starts with the formation of "micronodules." The formation of micronodules is assumed to be mediated by microorganisms. After accretion of biogenic and additional nonbiogenic minerals, the micronodules assemble to large nodules on the sea floor through additional inclusion of nonbiogenic material.

Mapping the speciation of iron in Pseudomonas aeruginosa biofilms using scanning transmission X-ray microscopy

An important feature of microbial communities is the spatial heterogeneity of extracellular chemistry. Scanning transmission X-ray microscopy (STXM) was used to map the spatial distribution of iron speciesthroughout Pseudomonas aeruginosa biofilms to assess the influence of chemical heterogeneity on biomineralization. P. aeruginosa biofilms were treated with Fe(III)-amended media. Speciation and quantitative mapping using STXM image sequences in the Fe 2p(3/2) (L3) absorption edge region revealed both Fe(II) and Fe(III) in localized microenvironments. Fe(III) was mainly associated with cell surfaces, while small amounts of Fe(II) was found in the extracellular space. Biofilms were also characterized using C 1s edge STXM image sequences. Anaerobic growth assays and confocal microscopy revealed the inability of P. aeruginosa to directly reduce Fe(III), implicating indirect iron reduction mechanisms in the formation of fine-grained, multivalent minerals. These studies suggest that geochemical microenvironments found throughout microbial communities are even more complex than previously believed.

Multimetal resistance and tolerance in microbial biofilms

Geochemical cycling and industrial pollution have made toxic metal ions a pervasive environmental pressure throughout the world. Biofilm formation is a strategy that microorganisms might use to survive a toxic flux in these inorganic compounds. Evidence in the literature suggests that biofilm populations are protected from toxic metals by the combined action of chemical, physical and physiological phenomena that are, in some instances, linked to phenotypic variation among the constituent biofilm cells. Here, we propose a multifactorial model by which biofilm populations can withstand metal toxicity by a process of cellular diversification.

Production of biogenic manganese oxides by repeated-batch cultures of laboratory microcosms

We investigated the production of manganese (Mn) oxides using repeated-batch bioreactors maintained over long periods under laboratory conditions. Freshwater epilithic biofilms were used as the initial inocula. The bioreactors yielded suspended solids that could remove 0.1 mM dissolved Mn(II) within a few days. Chemical titration, X-ray absorption near-edge structure spectroscopy, and X-ray diffraction analysis revealed that the Mn(II) had been converted to poorly crystallized layer-type Mn(IV) oxides, which were similar to known biogenic Mn oxides from pure bacterial cultures. Spherical or rod-shaped Mn microconcretions occurred in the suspended solids; transmission electron microscopy showed that these structures likely resulted from the microbial activity but not represent living cells. Instead, the presence of encapsulated, sheathed, and hyphal budding cells in the suspended solids indicated that a range of Mn-depositing bacteria contributed to the Mn oxide formation. To our knowledge, our data represent the first observation of production of such Mn oxides in a laboratory microcosm wherein a range of Mn-depositing bacteria coexist. The fact that sorption of trace Zn(II) and Ni(II) ions onto the suspended solids co-occurred with the removal of dissolved Mn(II) emphasizes the important role of Mn-oxidizing microorganisms in the fates of trace or contaminant metals in the aquatic environment.

Speciation and quantitative mapping of metal species in microbial biofilms using scanning transmission X-ray microscopy

A scanning transmission X-ray microscope illuminated with synchrotron light was used to investigate the speciation and spatial distributions of metals in a microbial biofilm cultivated from river water. Metal 2p absorption edge signals were used to provide metal speciation (through shapes of the absorption spectra) and quantitative spatial distributions of the metal species. This paper presents sample data and describes methods for extracting quantitative maps of metal species from image sequences recorded in the region of the metal 2p edges. Comparisons were made with biochemical characterization of the same region using images recorded at the C 1s and O 1s edges. The method is applied to detailed quantitative analysis of ferrous and ferric iron in a river biofilm, in concert with mapping Ni(II) and Mn(II) species in the same region. The distributions of the metal species are discussed in the context of the biofilm structure. These results demonstrate that soft X-ray STXM measurements at the metal 2p absorption edges can be used to speciate metals and to provide quantitative spatial distribution maps for metal species in environmental samples with 50 nm spatial resolution.

Manganese oxidation by bacterial isolates from the Indian ridge system

The abundance and activity of culturable manganese-oxidizing bacteria were assessed from near-bottom water samples of the tectonically active Carlsberg Ridge. Retrievable counts as colony forming units (CFU) on dilute nutrient agar medium (dilNA=2 gm l(-1) nutrient broth+2% agar) and on dilNA supplemented with 1, 2 and 3 mM MnCl(2).4H(2)O were in the order of 10(6) CFU l(-1). Retrievability of heterotrophs ranged from non-detectable levels (ND) to 2.82 x 10(6) CFU l(-1). The retrievable counts on Mn amended dilNA ranged from ND to 3.21 x 10(6), 1.47 x 10(6) and 1.45 x 10(6) CFU l(-1) on 1, 2 and 3 mM, respectively. About 87% of the Mn tolerant isolates (n=39) showed taxonomic affinities to Pseudomonas I and II sp. Two representative strains CR35 and CR48 (CR-Carlsberg Ridge) isolated on manganese-supplemented media were tested for their ability to tolerate a range of Mn amendments from 1 nM to 100 mM in terms of growth and respiration. CR35 represents 66% of the total CFU (3.04 x 10(6) CFU l(-1)), while CR48 represented only 6% of the total CFU (1.05 x 10(6) CFU l(-1)). The colonies of these two isolates were dark brown in color suggesting precipitation of Mn as oxide. Tests for the effect on growth and respiration were conducted in media simulating heterotrophic (amended with 0.01% glucose) and lithotrophic (unamended) conditions. Maximum stimulation in growth and respiration of CR35 occurred at 100 microM Mn both in unamended and amended media. At levels of Mn greater than 100 microM the counts decreased steadily. Total respiring cells of CR48 were stimulated to a maximum at 1 microM Mn in unamended medium and 1 nM in amended medium. Total cells counts for the same decreased beyond 100 microM Mn in unamended and 1 nM in amended medium. The isolates were tested for their ability to oxidize Mn amendments from 1 microM to 10 mM Mn. At the end of a 76-day incubation period, there was evidence of manganese oxide precipitation at high Mn concentrations (>or=1 mM) as a dark brown coloration on the sides of culture tubes. Highest Mn oxidation rates were observed at 10 mM Mn(II) concentration with CR35 oxidizing 27 and 25 microM Mn day(-1) in unamended and amended condition, respectively. CR48 oxidized Mn at the rate of 26 microM Mn day(-1) in unamended medium and 35 microM Mn day(-1) in amended medium. Scanning electron microscope (SEM) observations of both isolates revealed free-living cells in clustered matrices approximately 2 microm diameter. Energy dispersive spectrum of the cell matrix of CR35 cultured in 1 mM Mn detected 30% Mn, while the cell aggregates of CR48 harbored 7-10% Mn. The relatively high specific activity of these mixotrophic bacteria under relatively oligotrophic conditions suggests that they may be responsible for scavenging dissolved Mn from the Carlsberg Ridge waters and could potentially participate in oxidation.