Importance of inner-sphere P-O-Fe bonds in natural and synthetic mineral-organic associations.

Sorption of organic molecules on mineral surfaces can occur through several binding mechanisms of varying strength. Here, we investigated the importance of inner-sphere P-O-Fe bonds in synthetic and natural mineral-organic associations. Natural organic matter such as water extracted soil organic matter (WESOM) and extracellular polymeric substances (EPS) from liquid bacterial cultures were adsorbed to goethite and examined by FTIR spectroscopy and P K-edge NEXAFS spectroscopy. Natural particles from a Bg soil horizon (Gleysol) were subjected to X-ray fluorescence (XRF) mapping, NanoSIMS imaging, and NEXAFS spectro-microscopy at the P K-edge. Inner-sphere P-O-Fe bonds were identified for both, adsorbed EPS extracts and adsorbed WESOMs. Characteristic infrared peaks for P-O-Fe stretching vibrations are present but cannot unambiguously be interpreted due to possible interferences with mono- and polysaccharides. For the Bg horizon, P was only found on Fe oxides, covering the entire surface at different concentrations, but not on clay minerals. Linear combination fitting of NEXAFS spectra indicates that this adsorbed P is mainly a mixture of orthophosphate and organic P compounds. By combining atomic force microscopy (AFM) images with STXM-generated C and Fe distribution maps, we show that the Fe oxide surfaces were fully coated with organic matter. In contrast, clay minerals revealed a much lower C signal. The C NEXAFS spectra taken on the Fe oxides had a substantial contribution of carboxylic C, aliphatic C, and O-alkyl C, which is a composition clearly different from pure adsorbed EPS or aromatic-rich lignin-derived compounds. Our data show that inner-sphere P-O-Fe bonds are important for the association of Fe oxides with soil organic matter. In the Bg horizon, carboxyl groups and orthophosphate compete with the organic P compounds for adsorption sites.

High-Resolution Table-Top NEXAFS Spectroscopy.

A table-top near-edge X-ray absorption fine structure (NEXAFS) spectroscopy system consisting of a soft X-ray source and an integrated spectrometer with a significantly improved resolution is presented. The soft X-ray source is based on a long-term stable and nearly debris-free picosecond laser-induced plasma generated in a pulsed krypton gas jet target. Photon energies ranging from 250 to 1000 eV can be used for the absorption spectroscopy of thin samples. The newly designed spectrometer accomplishes a spectral resolution of E/ΔE = 1535 at 430 eV, being close to typical synchrotron setups. Moreover, a simultaneous multi-edge analysis is possible. The performance of the new system is demonstrated by investigating the fine structure of the K- and L-absorption edges of various elements (carbon, calcium, oxygen, iron, nickel, and copper) for different types of samples. An excellent agreement with synchrotron spectra is achieved.

Oxygen-dependent niche formation of a pyrite-dependent acidophilic consortium built by archaea and bacteria.

Biofilms can provide a number of different ecological niches for microorganisms. Here, a multispecies biofilm was studied in which pyrite-oxidizing microbes are the primary producers. Its stability allowed not only detailed fluorescence in situ hybridization (FISH)-based characterization of the microbial population in different areas of the biofilm but also to integrate these results with oxygen and pH microsensor measurements conducted before. The O2 concentration declined rapidly from the outside to the inside of the biofilm. Hence, part of the population lives under microoxic or anoxic conditions. Leptospirillum ferrooxidans strains dominate the microbial population but are only located in the oxic periphery of the snottite structure. Interestingly, archaea were identified only in the anoxic parts of the biofilm. The archaeal community consists mainly of so far uncultured Thermoplasmatales as well as novel ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganism) species. Inductively coupled plasma analysis and X-ray absorption near edge structure spectra provide further insight in the biofilm characteristics but revealed no other major factors than oxygen affecting the distribution of bacteria and archaea. In addition to catalyzed reporter deposition FISH and oxygen microsensor measurements, microautoradiographic FISH was used to identify areas in which active CO2 fixation takes place. Leptospirilla as well as acidithiobacilli were identified as primary producers. Fixation of gaseous CO2 seems to proceed only in the outer rim of the snottite. Archaea inhabiting the snottite core do not seem to contribute to the primary production. This work gives insight in the ecological niches of acidophilic microorganisms and their role in a consortium. The data provided the basis for the enrichment of uncultured archaea.

STXM and NanoSIMS investigations on EPS fractions before and after adsorption to goethite.

Extracellular polymeric substances (EPS) are expected to be an important source for the formation of mineral-organic associations in soil. Because such formations affect the composition of mobile and immobile organic matter as well as the reactivity of minerals, we investigated the composition of EPS before and after adsorption to goethite. Raman measurements on EPS extracted from Bacillus subtilis distinguished four fractions rich in proteins, polysaccharides, lipids, or lipids and proteins. Scanning transmission X-ray microscopy identified three different EPS-fractions that varied in their composition in proteins, nonaromatic proteins, and polysaccharides. Reaction of EPS with goethite led to a preferential adsorption of lipids and proteins. The organic coverage was heterogeneous, consisting of ~100 × 200 nm large patches of either lipid-rich or protein-rich material. Nanoscale secondary ion mass spectrometry showed a strong S enrichment in aggregates of ~400 nm in the goethite adsorbed EPS. From our simplified model system, we learned that only a small portion (<10%) of EPS was immobilized via adsorption to goethite. This fraction formed a coating of subµm spaced protein-rich and lipid-rich domains, i.e., of two materials which will strongly differ in their reactive sites. This will finally affect further adsorption, the particle mobility and eventually also colloidal stability.

Calcite biomineralization by bacterial isolates from the recently discovered pristine karstic herrenberg cave.

Karstic caves represent one of the most important subterranean carbon storages on Earth and provide windows into the subsurface. The recent discovery of the Herrenberg Cave, Germany, gave us the opportunity to investigate the diversity and potential role of bacteria in carbonate mineral formation. Calcite was the only mineral observed by Raman spectroscopy to precipitate as stalactites from seepage water. Bacterial cells were found on the surface and interior of stalactites by confocal laser scanning microscopy. Proteobacteria dominated the microbial communities inhabiting stalactites, representing more than 70% of total 16S rRNA gene clones. Proteobacteria formed 22 to 34% of the detected communities in fluvial sediments, and a large fraction of these bacteria were also metabolically active. A total of 9 isolates, belonging to the genera Arthrobacter, Flavobacterium, Pseudomonas, Rhodococcus, Serratia, and Stenotrophomonas, grew on alkaline carbonate-precipitating medium. Two cultures with the most intense precipitate formation, Arthrobacter sulfonivorans and Rhodococcus globerulus, grew as aggregates, produced extracellular polymeric substances (EPS), and formed mixtures of calcite, vaterite, and monohydrocalcite. R. globerulus formed idiomorphous crystals with rhombohedral morphology, whereas A. sulfonivorans formed xenomorphous globular crystals, evidence for taxon-specific crystal morphologies. The results of this study highlighted the importance of combining various techniques in order to understand the geomicrobiology of karstic caves, but further studies are needed to determine whether the mineralogical biosignatures found in nutrient-rich media can also be found in oligotrophic caves.

Fractionation of organic matter due to reaction with ferrihydrite: coprecipitation versus adsorption.

In soil and water, ferrihydrite frequently forms in the presence of dissolved organic matter. This disturbs crystal growth and gives rise to coprecipitation of ferrihydrite and organic matter. To compare the chemical fractionation of organic matter during coprecipitation with the fractionation involved in adsorption onto pristine ferrihydrite surfaces we prepared ferrihydrite-organic matter associations by adsorption and coprecipitation using (i) a forest-floor extract or (ii) a sulfonated lignin. The reaction products were studied by (13)C CPMAS NMR, FTIR, and analysis of hydrolyzable neutral polysaccharides. Relative to the original forest-floor extract, the ferrihydrite-associated organic matter was enriched in polysaccharides, especially when adsorption took place. Moreover, mannose and glucose were bound preferentially to ferrihydrite, while fucose, arabinose, xylose, and galactose accumulated in the supernatant. This fractionation of sugar monomers was more pronounced during coprecipitation and led to an enhanced ratio of (galactose + mannose)/(arabinose + xylose). Experiments with lignin revealed that the ferrihydrite-associated material was enriched in its aromatic components but had a lower ratio of phenolic C to aromatic C than the original lignin. A compositional difference between the adsorbed and coprecipitated lignin is obvious from a higher contribution of methoxy C in the coprecipitated material. Coprecipitated organic matter may thus differ in amount and composition from adsorbed organic matter.

Acid-tolerant microaerophilic Fe(II)-oxidizing bacteria promote Fe(III)-accumulation in a fen.

The ecological importance of Fe(II)-oxidizing bacteria (FeOB) at circumneutral pH is often masked in the presence of O(2) where rapid chemical oxidation of Fe(II) predominates. This study addresses the abundance, diversity and activity of microaerophilic FeOB in an acidic fen (pH ∼ 5) located in northern Bavaria, Germany. Mean O(2) penetration depth reached 16 cm where the highest dissolved Fe(II) concentrations (up to 140 µM) were present in soil water. Acid-tolerant FeOB cultivated in gradient tubes were most abundant (10(6) cells g(-1) peat) at the 10-20 cm depth interval. A stable enrichment culture was active at up to 29% O(2) saturation and Fe(III) accumulated 1.6 times faster than in abiotic controls. An acid-tolerant, microaerophilic isolate (strain CL21) was obtained which was closely related to the neutrophilic, lithoautotrophic FeOB Sideroxydans lithotrophicus strain LD-1. CL21 oxidized Fe(II) between pH 4 and 6.0, and produced nanoscale-goethites with a clearly lower mean coherence length (7 nm) perpendicular to the (110) plane than those formed abiotically (10 nm). Our results suggest that an acid-tolerant population of FeOB is thriving at redox interfaces formed by diffusion-limited O(2) transport in acidic peatlands. Furthermore, this well-adapted population is successfully competing with chemical oxidation and thereby playing an important role in the microbial iron cycle.

Characterization of ferrihydrite-soil organic matter coprecipitates by X-ray diffraction and Mössbauer spectroscopy.

In soils and sediments ferrihydrite often precipitates from solutions containing dissolved organic matter, which affects its crystallinity. To simulate this process we prepared a series of 2-line ferrihydrite-organic matter coprecipitates using water extractable organic matter (OM) from a forest topsoil. The products were characterized byX-ray diffraction, Mössbauer spectroscopy, N2-gas adsorption and transmission electron microscopy. With increasing C/Fe ratios of the initial solution the d-spacings of the two major XRD peaks increased, while peak shoulders at 0.22 and 0.16 nm weakened. The asymmetry of the 0.26 nm peak decreased and disappeared at a C/Fe ratio of 0.78. The quadrupole splitting of the Mössbauer spectra at 300 K increased from 0.78 to 0.90 mm s(-1), the mean magnetic hyperfine field at 4.2 K dropped from 49.5 to 46.0 T, and the superparamagnetic collapse of the magnetic hyperfine splitting was shifted toward lower temperatures. These data reflect a strong interference of OM with crystal growth leading to smaller ferrihydrite crystals, increased lattice spacings, and more distorted Fe(O,OH)6 octahedra. Even small amounts of OM significantly change particle size and structural order of ferrihydrite. Crystallinity and reactivity of natural ferrihydrites will therefore often differ from their synthetic counterparts, formed in the absence of OM.