Atomic-scale structure of biogenic materials by total X-ray diffraction: a study of bacterial and fungal MnOx

Biological Oxidation of Manganese Mediated by the Fungus Neoroussoella solani MnF107

Manganese oxides are highly reactive minerals and influence the geochemical cycling of carbon, nutrients, and numerous metals in natural environments. Natural Mn oxides are believed to be dominantly formed by biotic processes. A marine Mn-oxidizing fungus Neoroussoella solani MnF107 was isolated and characterized in this study. SEM observations show that the Mn oxides are formed on the fungal hyphal surfaces and parts of the hypha are enveloped by Mn oxides. TEM observations show that the Mn oxides have a filamentous morphology and are formed in a matrix of EPS enveloping the fungal cell wall. Mineral phase analysis of the fungal Mn oxides by XRD indicates that it is poorly crystalline. Chemical oxidation state analysis of the fungal Mn oxides confirms that it is predominantly composed of Mn(IV), indicating that Mn(II) has been oxidized to Mn (IV) by the fungus.

Intrinsic enzyme-like activity of magnetite particles is enhanced by cultivation with Trichoderma guizhouense

Fungal-mineral interactions can produce large amounts of biogenic nano-size (~ 1-100 nm) minerals, yet their influence on fungal physiology and growth remains largely unexplored. Using Trichoderma guizhouense NJAU4742 and magnetite (Mt) as a model fungus and mineral system, we have shown for the first time that biogenic Mt nanoparticles formed during fungal-mineral cultivation exhibit intrinsic peroxidase-like activity. Specifically, the average peroxidase-like activity of Mt nanoparticles after 72 h cultivation was ~ 2.4 times higher than that of the original Mt. Evidence from high resolution X-ray photoelectron spectroscopy analyses indicated that the unique properties of magnetite nanoparticles largely stemmed from their high proportion of surface non-lattice oxygen, through occupying surface oxygen-vacant sites, rather than Fe redox chemistry, which challenges conventional Fenton reaction theories that assume iron to be the sole redox-active centre. Nanoscale secondary ion mass spectrometry with a resolution down to 50 nm demonstrated that a thin (< 1 μm) oxygen-film was present on the surface of fungal hyphae. Furthermore, synchrotron radiation-based micro-FTIR spectra revealed that surface oxygen groups corresponded mainly to organic OH, mineral OH and carbonyl groups. Together, these findings highlight an important, but unrecognized, catalytic activity of mineral nanoparticles produced by fungal-mineral interactions and contribute substantially to our understanding of mineral nanoparticles in natural ecosystems.

Biogenic Metal Oxides

Biogenic metal oxides (MxOy) feature structures as highly functional and unique as the organisms generating them. They have caught the attention of scientists for the development of novel materials by biomimicry. In order to understand how biogenic MxOy could inspire novel technologies, we have reviewed examples of all biogenic MxOy, as well as the current state of understanding of the interactions between the inorganic MxOy and the biological matter they originate from and are connected to. In this review, we first summarize the origins of the precursors that living nature converts into MxOy. From the point-of-view of our materials chemists, we present an overview of the biogenesis of silica, iron and manganese oxides, as the only reported biogenic MxOy to date. These MxOy are found across all five kingdoms (bacteria, protoctista, fungi, plants and animals). We discuss the key molecules involved in the biosynthesis of MxOy, the functionality of the MxOy structures, and the techniques by which the biogenic MxOy can be studied. We close by outlining the biomimetic approaches inspired by biogenic MxOy materials and their challenges, and we point at promising directions for future organic-inorganic materials and their synthesis.

Crystal engineering in 3D: converting nanoscale lamellar manganese oxide to cubic spinel while affixed to a carbon architecture

By applying differential pair distribution function analyses to MnO_x-painted carbon nanofoam papers, we quantify the manganese oxide speciation as the nanoscale oxide transitions from disordered NaMnO_x to spinel LiMn₂O₄.

Nutrient input influences fungal community composition and size and can stimulate manganese (II) oxidation in caves

Little is known about the fungal role in biogeochemical cycling in oligotrophic ecosystems. This study compared fungal communities and assessed the role of exogenous carbon on microbial community structure and function in two southern Appalachian caves: an anthropogenically impacted cave and a near-pristine cave. Due to carbon input from shallow soils, the anthropogenically impacted cave had an order of magnitude greater fungal and bacterial quantitative-polymerase chain reaction (qPCR) gene copy numbers, had significantly greater community diversity, and was dominated by ascomycotal phylotypes common in early phase, labile organic matter decomposition. Fungal assemblages in the near-pristine cave samples were dominated by Basidiomycota typically found in deeper soils (and/or in late phase, recalcitrant organic matter decomposition), suggesting more oligotrophic conditions. In situ carbon and manganese (II) [Mn(II)] addition over 10 weeks resulted in growth of fungal mycelia followed by increased Mn(II) oxidation. A before/after comparison of the fungal communities indicated that this enrichment increased the quantity of fungal and bacterial cells, yet decreased overall fungal diversity. Anthropogenic carbon sources can therefore dramatically influence the diversity and quantity of fungi, impact microbial community function, and stimulate Mn(II) oxidation, resulting in a cascade of changes that can strongly influence nutrient and trace element biogeochemical cycles in karst aquifers.

Solving the nanostructure problem: exemplified on metallic alloy nanoparticles

With current technology moving rapidly toward smaller scales nanometer-size materials, hereafter called nanometer-size particles (NPs), are being produced in increasing numbers and explored for various useful applications ranging from photonics and catalysis to detoxification of wastewater and cancer therapy. Nature also is a prolific producer of useful NPs. Evidence can be found in ores on the ocean floor, minerals and soils on land and in the human body that, when water is excluded, is mostly made of proteins that are 6-10 nm in size and globular in shape. Precise knowledge of the 3D atomic-scale structure, that is how atoms are arranged in space, is a crucial prerequisite for understanding and so gaining more control over the properties of any material, including NPs. In the case of bulk materials such knowledge is fairly easy to obtain by Bragg diffraction experiments. Determining the 3D atomic-scale structure of NPs is, however, still problematic spelling trouble for science and technology at the nanoscale. Here we explore this so-called "nanostructure problem" from a practical point of view arguing that it can be solved when its technical, that is the inapplicability of Bragg diffraction to NPs, and fundamental, that is the incompatibility of traditional crystallography with NPs, aspects are both addressed properly. As evidence we present a successful and broadly applicable, 6-step approach to determining the 3D atomic-scale structure of NPs based on a suitable combination of a few experimental and computational techniques. This approach is exemplified on 5 nm sized Pd(x)Ni(100-x) particles (x = 26, 56 and 88) explored for catalytic applications. Furthermore, we show how once an NP atomic structure is determined precisely, a strategy for improving NP structure-dependent properties of particular interest to science and technology can be designed rationally and not subjectively as frequently done now.

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.

Short-range and long-range order of phyllomanganate nanoparticles determined using high-energy X-ray scattering

High-energy X-ray scattering (HEXS) is used to explore the pH-dependent structure of randomly stacked manganese oxide nanosheets of nominal formula δ-MnO2. Data are simulated in real space by pair distribution function (PDF) analysis and in reciprocal space by both the Bragg-rod method and the Debye equation in order to maximize the information gained from the total scattering measurements. The essential new features of this triple-analysis approach are (1) the use of a two-dimensional supercell in PDF modeling to describe local distortions around Mn layer vacancies, (2) the implementation in Bragg-rod calculations of a lognormal crystal size distribution in the layer plane and an empirical function for the effect of strain, and (3) the incorporation into the model used with the Debye equation of an explicit elastic deformation of the two-dimensional nanocrystals. The PDF analysis reveals steady migration at acidic pH of the Mn atoms from layer to interlayer sites, either above or below the Mn layer vacancies, and important displacement of the remaining in-layer Mn atoms toward vacancies. The increased density of the vacancy–interlayer Mn pairs at low pH causes their mutual repulsion and results in short-range ordering. The layer microstructure, responsible for the long-range lateral disorder, is modeled with spherically and cylindrically bent crystallites having volume-averaged radii of 20–40 Å. Thebunit-cell parameter from the hexagonal layer has different values in PDF, Bragg-rod and Debye equation modeling, because of the use of different weighting contributions from long-range and short-range distances in each method. The PDFbparameter is in effect a measure of the average inlayer Mn...Mn distance and consistently deviates from the average structure value determined by the Bragg-rod method by 0.02 Å at low pH, as a result of the local relaxation induced by vacancies. The layer curvature increases the Bragg-rod value by 0.01–0.02 Å with the cylindrical model and as much as 0.04–0.05 Å with the spherical model. Therefore, in principle, the diffraction alone can unambiguously determine with good accuracy only a volume-averaged apparent layer dimension of the manganese oxide nanosheets. Thebparameter is model dependent and has no single straightforward interpretation, so comparison ofbbetween different samples only makes sense if done in the context of a single specified model.

Fungal oxidative dissolution of the Mn(II)-bearing mineral rhodochrosite and the role of metabolites in manganese oxide formation

Microbially mediated oxidation of Mn(II) to Mn(III/IV) oxides influences the cycling of metals and remineralization of carbon. Despite the prevalence of Mn(II)-bearing minerals in nature, little is known regarding the ability of microbes to oxidize mineral-hosted Mn(II). Here, we explored oxidation of the Mn(II)-bearing mineral rhodochrosite (MnCO3 ) and characteristics of ensuing Mn oxides by six Mn(II)-oxidizing Ascomycete fungi. All fungal species substantially enhanced rhodochrosite dissolution and surface modification. Mineral-hosted Mn(II) was oxidized resulting in formation of Mn(III/IV) oxides that were all similar to δ-MnO2 but varied in morphology and distribution in relation to cellular structures and the MnCO3 surface. For four fungi, Mn(II) oxidation occurred along hyphae, likely mediated by cell wall-associated proteins. For two species, Mn(II) oxidation occurred via reaction with fungal-derived superoxide produced at hyphal tips. This pathway ultimately resulted in structurally unique Mn oxide clusters formed at substantial distances from any cellular structure. Taken together, findings for these two fungi strongly point to a role for fungal-derived organic molecules in Mn(III) complexation and Mn oxide templation. Overall, this study illustrates the importance of fungi in rhodochrosite dissolution, extends the relevance of biogenic superoxide-based Mn(II) oxidation and highlights the potential role of mycogenic exudates in directing mineral precipitation.

Metals, minerals and microbes: geomicrobiology and bioremediation

Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and 'higher organisms', can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social and economic consequences. The ubiquity and importance of microbes in biosphere processes make geomicrobiology one of the most important concepts within microbiology, and one requiring an interdisciplinary approach to define environmental and applied significance and underpin exploitation in biotechnology.