Environmental oxidation rate of manganese(II): bacterial catalysis

A simple mass balance for dissolved manganese(II) in waters containing low levels of oxygen in Saanich Inlet indicates that the residence time for Mn(II) removal to the solid phase is on the order of a few days. The average oxidation state of Mn in particulate material sampled from the region of Mn removal was 2.3–2.7, and electron micrographs revealed structures characteristic of bacterially formed Mn precipitates. Radiotracer experiments utilizing ⁵⁴Mn(II) indicated that removal of Mn from solution in the region of active uptake was substantially blocked by a poison mixture, demonstrating that Mn(II) binding to particulates is catalyzed by bacteria in this environment.     

Viking's Experiments and Hypothesis that Fe(VI) Is a Possible Candidate as a Martian Oxidant

In this rebuttal to G. Levin's critique of our previous publication, we claim again that iron(VI) is a very good candidate as a martian oxidant. Our experiments cannot be explained as a result of microbial activities, as we showed that Fe(VI) could be used as a sterilizing agent for destroying microorganisms, nucleic acids, and proteins.     

Energy dispersive X-ray analysis of the surface of a deep-sea ferromanganese nodule

In an effort to elucidate the mechanism of formation and accretion of ferromanganese nodules, transverse sections of undisturbed botryoid surfaces of nodules from the abyssal central North Pacific were examined by X-ray analyses both by multiple replicate sample transects and mapping. Surface concentrations of Mn and Fe were found of the size and shape of microorganisms. Abundant microorganism-like objects covering the surface and the apparent absence of Si (i.e. no sediment) with the Mn and Fe concentrations suggests microorganisms may be involved either in the selective accretion or removal of these metals. If metal accretion was simply physicochemical, one would expect a more or less even distribution of Mn and Fe on the botryoid surfaces.The replicate X-ray sample transects showed that Mn and Fe have a distribution corresponding to botryoid zonation. Areas of high Mn X-ray intensity were found associated with the cap and equatorial zones of the botryoid. Most of the valley zone of the botryoid show a more or less even Mn distribution and an increase in Fe X-ray intensity. At the base of the botryoid both metals apparently precipitously decrease.     

Manganese oxidation in pH and O2 microenvironments produced by phytoplankton

Pure cultures of Chlorella sp. catalyzed the oxidation of soluble Mn(II) to particulate, extracellular, manganic oxides. Manganese oxidation was dependent on photosynthetic activity: no oxidation was observed in the dark when cells were grown heterotrophically on glucose, or in the light when photosystem II was inhibited by the addition of DCMU. Manganates were not formed when media were buffered below pH 8.0, suggesting that an important driving force for manganese oxidation was the high pH resulting from photosynthesis. Field studies with minielectrodes in Oneida Lake, New York, demonstrated steep gradients of O2 and pH and the presence of particulate manganic oxides associated with pelagic aggregates of the cyanobacterium Microcystis sp. The manganese oxidation reaction apparently occurs only when photosynthesizing algae are present as dense populations that can generate microenvironments of high (>9.0) pH, either as aggregates in the pelagic zone or concentrated cell cultures in the laboratory. A large-scale transition from soluble to particulate manganese was measured in the surface waters of Oneida Lake throughout summer 1986. Removal of Mn(II) was correlated with the presence of aggregate-forming cyanobacteria that oxidize Mn(II) by the mechanism described above.     

Seeing through porous media: An experimental study for unveiling interstitial flows

We describe a novel inexpensive method, utilizing particle image velocimetry (PIV) and refractive index‐matching (RIM) for visualizing and quantifying the flow field within bio‐amended porous media. To date, this technique has been limited to idealized particles, whose refractive index does not match that of fresh water and thus requires specialized and often toxic or hazardous fluids. Here, we use irregularly shaped grains made of hydrogel as the solid matrix and water as the fluid. The advantage of using water is that it provides, for the first time, the opportunity to study both hydraulic and biological processes, which typically occur in soils and streambeds. By using RIM coupled with PIV (RIM‐PIV), we measured the interstitial flow field within a cell packed with granular material consisting of hydrogel grains in a size range of 1–8 mm, both in the presence and in the absence of Sinorhizobium meliloti bacteria (strain Rm8530). We also performed experiments with fluorescent tracer (fluorescein) and fluorescent microbes (Shewanella GPF MR‐1) to test the capability of visualizing solute transport and microbial movements. Results showed that the RIM‐PIV can measure the flow field for both biofilm‐free and biofilm‐covered hydrogel grains. The fluorescent tracer injection showed the ability to visualize both physical (concave surfaces and eddies) and biological (biofilms) transient storage zones, whereas the fluorescent microbe treatment showed the ability to track microbial movements within fluids. We conclude that the proposed methodology is a promising tool to visualize and quantify biofilm attachment, growth, and detachment in a system closer to natural conditions than a 2D flow cell experiment.     

Culture-dependent and independent analyses of subsurface microbial communities in oil-bearing strata of the Sagara oil reservoir

Abstract   Culture-dependent and independent methods were used to evaluate the microbial communities in cores collected at depths up to 200 m in oil-bearing and oil-free strata near the Sagara oil reservoir near Shizuoka, Japan. Direct microbial counts revealed much higher numbers (2.2 × 10⁴−7.9 × 10⁶/g) of microbes in the oil-bearing strata than in the oil-free zones, where counts were uniform at approximately 1.0 × 10⁴/g. Molecular taxonomic analyses via 16S rRNA gene sequence comparisons showed that the oil-free strata were dominated by members of the γ-Proteobacteria including Pseudomonas , Stenotrophomonas and Sphingomonas , whereas the oil-bearing strata were dominated by a single species closely related to Pseudomonas stutzeri . All archaeal clones were phylogenetically affiliated with the uncultured soil group in Crenarchaeota with the exception of a single phylotype that belonged to the genus Thermococcus . Culture-dependent analysis was carried out by most-probable-number culturing as well as direct plating to determine viable cell counts, using both complex organic substrates or native oil and autotrophic media. Both culture-dependent and independent methods revealed the abundant cultivable member was the aerobic oil-degrading bacterium Pseudomonas stutzeri and neither autotrophs nor anaerobic heterotrophs could be detected in the oil-bearing strata.     

Isotopic fractionation associated with biosynthesis of fatty acids by a marine bacterium under oxic and anoxic conditions

Shewanella putrefaciens (Strain MR-4), a gram negative facultative marine bacterium, was grown to stationary phase under both aerobic and anaerobic conditions using lactate as the sole carbon source. Aerobically-produced cells were slightly enriched in ¹³C (+1.5‰) relative to the lactate carbon source, whereas those from anaerobic growth were depleted in ¹³C (−2.2‰). The distribution of fatty acids produced under aerobic conditions was similar to that resulting from anaerobic growth, being dominated by C_16:1 ω7 and C_16:0 fatty acids with a lesser amount of the C_18:1 ω7 component. Low concentrations of saturated even numbered normal fatty acids in the C₁₄ to C₁₈ range, and iso-C_15:0 were synthesized under both conditions. Fatty acids from anaerobic cultures (average δ¹³C=−37.8‰) were considerably depleted in ¹³C relative to their aerobically-synthesized counterparts (−28.8‰). The distinct differences in isotopic composition of both whole cells and individual fatty acid components result from differences in assimilation pathways. Under aerobic conditions, the primary route of assimilation involves the pyruvate dehydrogenase enzyme complex which produces acetyl-CoA, the precursor to lipid synthesis. In contrast, under anaerobic conditions formate, and not acetate, is the central intermediate in carbon assimilation with the precursors to fatty acid synthesis being produced via the serine pathway. Anaerobically-produced bacterial fatty acids were depleted by up to 12‰ relative to the carbon source. Therefore, detection of isotopically depleted fatty acids in sediments may be falsely attributed to a terrestrial origin, when in fact they are the result of bacterial resynthesis.     

Principal component analysis and neural networks for detection of amino acid biosignatures

We examine the applicability of Principal Component Analysis (PCA) and Artificial Neural Network (ANN) methods of data analysis to biosignature detection. These techniques show promise in classifying and simplifying the representation of patterns of amino acids resulting from biological and non-biological syntheses. PCA correctly identifies glycine and alanine as the amino acids contributing the most information to the task of discriminating biotic and abiotic samples. Trained ANNs correctly classify between 86.1 and 99.5% of a large set of amino acid samples as biotic or abiotic. These and similar techniques are important in the design of automated data analysis systems for robotic missions to distant planetary bodies. Both techniques are robust with respect to noisy and incomplete data. Analysis of the performance of PCA and ANNs also lends insight into the localization of useful information within a particular data set, a feature that may be exploited in the selection of experiments for efficient mission design.     

Reduction of iodate in seawater during Arabian Sea shipboard incubations and in laboratory cultures of the marine bacterium Shewanella putrefaciens strain MR-4

Shipboard incubations from the US JGOFS cruise to the Arabian Sea (TN045) March, 1995 showed evidence of iodate reduction in 0.45 μ (Gelman Supor membrane) filtered seawater samples collected from intermediate depths (200–600 m) within the oxygen minimum zone (OMZ). Inorganic chemical reduction of iodate in these samples was ruled out as no free sulfide was measurable and concentrations of ammonia and nitrite were found to be less than 5 μM. To examine whether the reduction of iodate observed at sea could have been the result of bacterial metabolism, reduction of iodate (IO₃⁻) to iodide (I⁻) by Shewanella putrefaciens strain MR-4 was studied in artificial seawater using electrochemical methods. MR-4 is a ubiquitous marine bacterium which may be of considerable importance when considering redox zonation in the water column because it is a facultative anaerobe and may switch amongst a suite of electron acceptors to support metabolism. In all experiments MR-4 reduced all iodate to iodide. The rate of formation of [I⁻]in the culture followed pseudo-first order kinetics. This is the first report of the marine bacterial reduction of iodate where the concentrations of iodide and iodate were measured directly. Our results may help to explain the depth distribution of iodine speciation reported in productive waters like the Arabian Sea and for the first time couple iodine speciation with bacterial productivity in the ocean.