Arsenite Oxidation Using Biogenic Manganese Oxides Produced by a Deep-Sea Manganese-Oxidizing Bacterium,Marinobacter sp. MnI7-9

Marinobacter sp. MnI7-9, a deep-sea manganese [Mn(II)]-oxidizing bacterium isolated from the Indian Ocean, showed a high resistance to Mn(II) and other metals or metalloids and high Mn(II) oxidation/removal abilities. This strain was able to grow well when the Mn(II) concentration reached up to 10 mM, and at that concentration, 76.4% of the added Mn(II) was oxidized and 23.4% of the Mn(II) was adsorbed by the generated biogenic Mn oxides (total 99.9% Mn removal). Scanning electron microscope observation and X-ray diffraction analysis showed that the biogenic Mn oxides were in stick shapes, adhered to the cell surface, and contained two typical crystal structures of γ-MnOOH and δ-MnO₂. In addition, the biogenic Mn oxides generated by strain MnI7-9 showed abilities to oxidize the highly toxic As(III) to the less toxic As(V), in both co-culture and after-collection systems. In the co-culture system containing 10 mM Mn(II) and 55 μM As(III), the maximum percentage of As(III) oxidation was 83.5%. In the after-collection system using the generated biogenic Mn oxides, 90% of the As(III) was oxidized into As(V), and the concentration of As(III) decreased from 55.02 to 5.55 μM. This study demonstrates the effective bioremediation by a deep-sea Mn(II)-oxidizing bacterium for the treatment of As-containing water and increases the knowledge of deep-sea bacterial Mn(II) oxidation mechanisms. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.     

Production of Biogenic Manganese Oxides by Anamorphic Ascomycete Fungi Isolated from Streambed Pebbles

We characterized the production of biogenic Mn oxides by four anamorphic ascomycete fungi isolated from streambed pebbles with Mn oxide coatings. Based on the 18S rRNA gene sequences, one strain was related to members of the order Xylariales and the other three were within distinct lineages of the Pleosporales. These strains oxidized Mn(II) to deposit Mn oxides when their growth approached the stationary phase. The fungal Mn oxides showed X-ray diffraction patterns typical of poorly crystalline vernadite (δ -MnO₂), and X-ray absorption near-edge structure spectroscopy confirmed that the Mn phases consisted predominantly of Mn(IV). Mn(II) oxidation in the four strains proceeded enzymatically. The Mn(II)-oxidizing proteins were inhibited by azide and o-phenanthroline, and the proteins also oxidized typical laccase substrates including 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), showing the role of laccase or a laccase-like metalloenzyme. The mineralogical traits of the biogenic Mn oxides, and the participation of laccase-like enzymes, are in accordance with our previous results obtained with one Hypocreales ascomycete. In conclusion, phylogenetically diverse ascomycetes may use this common enzymatic system to produce solid Mn phases similar to δ -MnO₂.     

Spatially Resolved Characterization of Biogenic Manganese Oxide Production within a Bacterial Biofilm

Pseudomonas putida strain MnB1, a biofilm-forming bacterial culture, was used as a model for the study of bacterial Mn oxidation in freshwater and soil environments. The oxidation of aqueous Mn⁺² [Mn⁺²_(aq)] by P. putida was characterized by spatially and temporally resolving the oxidation state of Mn in the presence of a bacterial biofilm, using scanning transmission X-ray microscopy (STXM) combined with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at the Mn L_2,3 absorption edges. Subsamples were collected from growth flasks containing 0.1 and 1 mM total Mn at 16, 24, 36, and 48 h after inoculation. Immediately after collection, the unprocessed hydrated subsamples were imaged at a 40-nm resolution. Manganese NEXAFS spectra were extracted from X-ray energy sequences of STXM images (stacks) and fit with linear combinations of well-characterized reference spectra to obtain quantitative relative abundances of Mn(II), Mn(III), and Mn(IV). Careful consideration was given to uncertainty in the normalization of the reference spectra, choice of reference compounds, and chemical changes due to radiation damage. The STXM results confirm that Mn⁺²_(aq) was removed from solution by P. putida and was concentrated as Mn(III) and Mn(IV) immediately adjacent to the bacterial cells. The Mn precipitates were completely enveloped by bacterial biofilm material. The distribution of Mn oxidation states was spatially heterogeneous within and between the clusters of bacterial cells. Scanning transmission X-ray microscopy is a promising tool for advancing the study of hydrated interfaces between minerals and bacteria, particularly in cases where the structure of bacterial biofilms needs to be maintained.     

Enhancing Manganese Recovery from Low-Grade Ores by Using Mixed Culture of Indigenously Isolated Bacterial Strains

Conventional leaching methods for manganese (Mn) recovery require strong acids and are threatening to the environment. Alternatively, the use of microbes for Mn recovery is environment friendly in nature. The present investigation compares the capacity of pure and mixed cultures of native bacterial strains for bioleaching of low-grade Mn ores. The ability of the isolated microorganisms to recover Mn was evaluated in shake flasks for 20 days under optimized conditions of pulp density (2%), sucrose concentration (2 g/100 mL), initial pH 6.5, and 30°C incubation temperature. In pure culture form, Acinetobacter sp. MSB 5 (70%) was found to have a higher bioleaching potential than Lysinibacillus sp. MSB 11 (67%). Mixed culture of Acinetobacter sp. MSB 5 and Lysinibacillus sp. MSB 11 was found to perform better than the pure cultures with 74% extraction of Mn. The presence of mixed culture increased the dissolution rate and the recovery percentage of Mn. The respective growth pattern of the cultures was in synchronization to their Mn bioleaching performances. This study underlines the importance of mixed cultures and Mn solubilizing activity of native bacterial strains for efficient Mn biorecovery.     

五株产MnCO3细菌的除锰特性

本研究从湖南省某锌锰矿矿口和天津市西青玛钢厂锰原料仓库土样中富集分离获得5株对锰有去除能力的抗锰细菌, 将其命名为J2-3、J4-3、J12-1、JM3-2和JD。形态学、生理生化分析和16S rRNA基因测序等结果表明它们分别归属为氢噬孢菌属、分枝杆菌属、红球菌属、不动杆菌属和芽孢杆菌属。JD和JM3-2菌的Mn(Ⅱ)抗性最低抑制浓度(MIC)为2 mmol/L, J2-3、J4-3和J12-1菌为12 mmol/L。X射线晶体衍射分析表明这5株抗锰菌随生长生成了MnCO3沉淀而将Mn(Ⅱ) 从溶液中去除。其中JD和JM3-2的锰去除率分别为94.28% ± 0.1%和93.10% ± 3.1%。其他菌的锰去除率也均在85%以上。研究发现培养基的pH由起始的7.0变为最终8.5以上, 推测其除锰原理可能是由于菌体代谢改变了培养基pH而将可溶的MnCl2转化为不溶的MnCO3沉淀。本研究证实了和以往报道的锰氧化细菌不同的新型除锰细菌。     

Structural Influences of Sodium and Calcium Ions on the Biogenic Manganese Oxides Produced by the Marine Bacillus Sp., Strain SG-1

Natural manganese oxide nanoparticles and grain coatings profoundly impact contaminant cycling in the environment through their ability to degrade organic compounds and sequester metal ions. Previous studies of biogenic manganese oxides have shown that the interlayer cation may have an important effect on the resulting oxide structure. The effect of Na and Ca ions was investigated to determine their fundamental roles in the stabilization of the phyllomanganate biooxide structure, its unit cell symmetry, and order/disorder relations. Biogenic oxides were created by incubating Mn(II) with spores of the marine Bacillus sp., strain SG-1 and the resulting oxide structures examined using X-ray absorption spectroscopy and X-ray diffraction to determine the short-range and long-range atomic structure. Phyllomanganates were observed exclusively, with differing degrees of layer stacking disorder, degree of crystallinity, and layer symmetry, depending on the cation present. In general, Ca was found to promote biooxide long-range order. We conclude that the presence of Ca in these oxides will confer greater stability to these bacteriogenic manganese bioxodes.     

Enhanced Staining of Bacterial Flagella Using Aged Mordant in the Silver Stain

Intensity of bacterial flagella staining using a modified silver stain was increased by aging the mordant for one week at room temperature. The use of aged mordant increased the apparent diameters of stained flagella and resulted in a darker stain. The mordant remained stable for at least four months at room temperature. The staining protocol presented allows application to liquid or solid cultures.     

Biochemical Function and Ecological Significance of Novel Bacterial Lipids in Deep-Sea Procaryotes

The fatty acid composition of the membrane lipids in 11 deep-sea bacterial isolates was determined. The fatty acids observed were typical of marine vibrios except for the presence of large amounts of long-chain polyunsaturated fatty acids (PUFAs). These long-chain PUFAs were previously thought to be absent in procaryotes, with the notable exception of a single marine Flexibacter sp. In three barophilic strains tested at 2°C, there was a general increase in the relative amount of PUFAs as pressure was increased from a low growth pressure towards the optimal growth pressure. In Vibrio marinus MP-1, a psychrophilic strain, PUFAs were found to increase as a function of decreasing temperature at constant atmospheric pressure. These results suggest the involvement of PUFAs in the maintenance of optimal membrane fluidity and function over environmentally relevant temperatures and pressures. Furthermore, since these lipids are essential nutrients for higher taxa and are found in large amounts in the lipids of deep-sea vertebrates and invertebrates, an important, specific role for deep-sea bacteria in abyssal food webs is implicated.     

Recovery of Nuclease Produced by Lactococcus Lactis Using Expanded Bed Ion Exchange Chromatography

Expanded bed-ionic exchange chromatography (EB-IEC) was used for the recovery and purification of recombinant staphylococcal nuclease secreted by Lactococcus lactis. At the end of the fermentation process, the nuclease activity reached 39 U ml⁻¹. The EB-IEC performances were firstly evaluated with clarified culture broth. The isocratic elution with 0.5 M NaCl led to approximately 80% of nuclease recovery. Proceeding with 3-fold bed expansion resulted in a reduction of the resin capacity by a factor of 32% compared to the process in a packed bed configuration. Simplification of the early purification steps was reached by loading immediately the unclarified culture broth previously diluted to reduce conductivity. Presence of Cells did not affect the chromatography performances resulting in 55-fold purification with the same yield.     

Clustering of Silver Nanoclusters Embedded in Soda Lime Glasses Using Ionic Exchange and Helium Ion Bombardment

Silver nanocluster precipitation in AR Schott glass by subsequently silver ionic exchange and helium bombardment was investigated by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and UV-visible optical absorption. Helium ion bombardment was used to induce local defects in the matrix and to promote the growth of the silver nano-aggregates. The typical implantation depth was estimated at 1 μm by Trim simulation. SEM investigations give us the concentration profile of the exchanged samples and the maximum depth. Optical absorption was performed to visualize the effect of the He⁺ fluence on the ion exchanged sample spectra and compared to the Drude model varying size and matrix refractive index. TEM was used to evaluate the distribution size of the silver nanoparticles, their structure by diffraction pattern, size, and shape and to correlate it to the experimental and theoretical absorption curves. The TEM observations prove that we are in a confinement regime with a particle size below the mean free path of the silver bulk metal.     

Difference Between Manganese Ion Requirements of Pediococci and Enterococci

For maximal turbidity and dissimilatory activity, three strains of pediococci required the addition of Mn(2+) to Rogosa basal medium. Twenty-two strains of enterococci proved indifferent to this supplement.     

Neutron Activation Analysis of Manganese and Sodium in Bacterial Cells

The application of neutron activation analysis for mineral determinations in bacteria was investigated. Elements considered here were manganese and sodium. The sporeformer Bacillus megaterium ATCC 19213 was utilized. With this method, the manganese and sodium levels of whole and ashed vegetative cells, sporulating cells, and free spores were determined. The culture medium was also analyzed for these two elements. The results indicate that neutron activation analysis is readily applicable to the study of mineral content of bacterial cells, spores, and culture media. The method has been shown to be ideal for the study of incorporation and egression of mineral elements during vegetative growth and secondary metabolism of sporulation.     

Zinc Sorption During Bio-oxidation and Precipitation of Manganese Modifies the Layer Stacking of Biogenic Birnessite

The formation and structural evolution of fungal mediate biogenic birnessite are dynamic processes. Although the associations of Zn with the pre-formed biogenic Mn oxides are relatively well understood, the reactivity of the intermediate precipitate at the initial stage of Mn bio-oxidation appears to differ from the final precipitate. In the present work, Zn sorption during precipitation of biogenic Mn oxides was investigated contrasting Zn sorption to pre-formed biogenic Mn oxides, using the Mn-oxidizing fungus Paraconiothyrium sp. WL-2. A substantially higher Zn uptake was found during precipitation of biogenic Mn oxides compared to Zn sorption to pre-formed biogenic Mn oxides. The presence of Zn during Mn oxidation resulted in a biogenic Mn oxide with reduced ordering in the c-axis. The precipitate was identified by X-ray diffraction (XRD) as a layer-type Mn oxide with structural properties similar to hexagonal birnessite. Extended X-ray absorption fine structure (EXAFS) spectroscopy showed that Zn forms triple-corner-sharing tetrahedral coordination (^IVTCS-Zn) complexes on the surface of birnessite, which may inhibited layer stacking of birnessite in the final products. This study emphasizes the importance of the intermediate precipitates on Zn sorption, and provides insight regarding the dynamic interaction between Zn and Mn oxide in the process of microbiological oxidation. Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.     

Removal of Contaminating Metals from Soil by Sulfur-Based Bioleaching and Biogenic Sulfide-Based Precipitation

The potential of a hybrid process incorporating sulfur-based bioleaching and sulfide-based precipitation for treatment of metal-contaminated soil was examined in batch-type experiments. The sulfur-based soil bioleaching process with Acidithiobacillus sp. could be initiated at a wide range of initial pH from 4.0 to 6.3. After 15 days, 98% of Zn, 89% of Cu and 79% of Cd was bioleached. The gaseous sulfides recycling from Desulfovibrio sp.-mediated sulfate-reducing reactor via N₂ sparging efficiently treated metal-loaded soil leachate. With a sulfide/metal ratio of 3.0, 88% of Zn, 100% of Cu and 95% of Cd were precipitated, resulting in effluent metal concentrations of 3.5 mg Zn²⁺/L, 0.2 mg Cu²⁺/L and 0.03 mg Cd²⁺/L.

Supplemental materials are available for this article. Go to the publisher's online edition of Geomicrobiology Journal to view the supplemental file.     

Influence of Artifact Removal on Rare Species Recovery in Natural Complex Communities Using High-Throughput Sequencing

Large-scale high-throughput sequencing techniques are rapidly becoming popular methods to profile complex communities and have generated deep insights into community biodiversity. However, several technical problems, especially sequencing artifacts such as nucleotide calling errors, could artificially inflate biodiversity estimates. Sequence filtering for artifact removal is a conventional method for deleting error-prone sequences from high-throughput sequencing data. As rare species represented by low-abundance sequences in datasets may be sensitive to artifact removal process, the influence of artifact removal on rare species recovery has not been well evaluated in natural complex communities. Here we employed both internal (reliable operational taxonomic units selected from communities themselves) and external (indicator species spiked into communities) references to evaluate the influence of artifact removal on rare species recovery using 454 pyrosequencing of complex plankton communities collected from both freshwater and marine habitats. Multiple analyses revealed three clear patterns: 1) rare species were eliminated during sequence filtering process at all tested filtering stringencies, 2) more rare taxa were eliminated as filtering stringencies increased, and 3) elimination of rare species intensified as biomass of a species in a community was reduced. Our results suggest that cautions be applied when processing high-throughput sequencing data, especially for rare taxa detection for conservation of species at risk and for rapid response programs targeting non-indigenous species. Establishment of both internal and external references proposed here provides a practical strategy to evaluate artifact removal process.     

Efficiencies of Recovery of Bdellovibrios from Brackish- Water Environments by Using Various Bacterial Species as Prey

A total of 44 bacterial species subdivided into 10 trial experiments have been used as prey for the recovery of bdellovibrios from samples of water from a brackish tidal pond and an aquarium saltwater tank. In an initial investigation, the recovery efficiency of each of the test bacterial species was compared with that of a designated standard prey, Vibrio parahaemolyticus P-5. The results revealed that in each case strain P-5 yielded an equal or significantly greater number of plaques of bdellovibrios than the test prey with but a single exception, strain CS5. In repeat experiments, CS5 yielded fewer plaques than P-5. To determine whether the use of multiple bacterial species compared with a single species as prey would increase the number of PFU of bdellovibrios recovered, material from plaques appearing on each of the test prey in the respective trials was sequentially subcultured onto two respective agar plates, the first containing as prey V. parahaemolyticus P-5 and the second containing the initial test organism. In nearly every case, subculture of plaques from lawns of the test prey to P-5 resulted in plaque formation. On the basis of the results, the use of several test prey and P-5 did not result in the recovery of any more bdellovibrio PFU than the use of P-5 alone. In this study, V. parahaemolyticus P-5 was observed to be the most efficient prey for the recovery of bdellovibrios from moderate salt water.     

On Comparison Between Fungal and Bacterial Pretreatment of Coal for Enhanced Biogenic Methane Generation

Owing to better understanding of subsurface geochemical carbon recycling and real-time active methanogenesis in major coal basins around the globe, substantial share of subsurface methane generation is attributed to biogenic origin. Since coal, being complex geopolymer, does not appear to be a favorable microbial substrate, enhancement in biogenic methane yield depends on its degradation into simpler organic substrates. This review puts forward a comparative analysis of fungal and bacterial pretreatment for determining the extent of facilitation in initial degradation of coal, which is still rate limiting step in overall conversion of coal into methane. Primarily, the initial fungal degradation of coal differs from bacterial pretreatment of coal in terms of the nature of released organics. On the basis of previous reports, fungal pretreatment of coal yields, majorly, polyaromatic hydrocarbons, however, bacterial pretreatment results in the generation of mixed organics pool of aromatics and aliphatics. The presence of aliphatics may be prospected for achieving greater conversion rates of coal conversion into methane. Considering the criticality of preliminary degradation of coal and associated issues, the fate of commercial biogenic methane generation would be dictated by the factors pertaining to geological considerations and reservoir geology, chemistry of coal and associated water tables, geomicrobial considerations and economic viability.     

Toxic Effects and Detection of Oxygen Free Radicals on Cultured Articular Chondrocytes Generated by Menadione

The aim of this work was to study the proliferation pathological perturbations of cultured chondrocytes in response to menadione, an oxygen free radicals producing drug. Rabbit articular chondrocytes in monolayer culture were treated with 10^-5, 1.5.M^-5 and 2.10^-5M of menadione during three days. A dose dependent decrease of the proliferative capacity was observed. Flow cytometry analysis revealed a perturbation of the cell cycle progression consisting in an accumulation of cells in the S and G2 + M phases. This growth perturbation was due to oxygen radicals production since a treatment with catalase suppressed these toxic effects. Furthermore, to identify oxygen derived radicals in the cellular suspension of cultures treated with menadione, we used a technique of spin-trapping coupled with electron spin resonance (ESR). The ESR signal corresponding to the DMPO hydroxyl radical adduct (DMPO-OH) has been detected. The spectra observation indicated the actual production of hydroxyl radical. However, superoxide anions have not been identified; this fact can be explained by the low reactivity of these anions with DMPO and by the decomposition of signal DMPO-OOH to DMPO-OH.     

Resveratrol Antagonizes Antimicrobial Lethality and Stimulates Recovery of Bacterial Mutants

Reactive oxygen species (ROS; superoxide, peroxide, and hydroxyl radical) are thought to contribute to the rapid bactericidal activity of diverse antimicrobial agents. The possibility has been raised that consumption of antioxidants in food may interfere with the lethal action of antimicrobials. Whether nutritional supplements containing antioxidant activity are also likely to interfere with antimicrobial lethality is unknown. To examine this possibility, resveratrol, a popular antioxidant dietary supplement, was added to cultures of Escherichia coli and Staphylococcus aureus that were then treated with antimicrobial and assayed for bacterial survival and the recovery of mutants resistant to an unrelated antimicrobial, rifampicin. Resveratrol, at concentrations likely to be present during human consumption, caused a 2- to 3-fold reduction in killing during a 2-hr treatment with moxifloxacin or kanamycin. At higher, but still subinhibitory concentrations, resveratrol reduced antimicrobial lethality by more than 3 orders of magnitude. Resveratrol also reduced the increase in reactive oxygen species (ROS) characteristic of treatment with quinolone (oxolinic acid). These data support the general idea that the lethal activity of some antimicrobials involves ROS. Surprisingly, subinhibitory concentrations of resveratrol promoted (2- to 6-fold) the recovery of rifampicin-resistant mutants arising from the action of ciprofloxacin, kanamycin, or daptomycin. This result is consistent with resveratrol reducing ROS to sublethal levels that are still mutagenic, while the absence of resveratrol allows ROS levels to high enough to kill mutagenized cells. Suppression of antimicrobial lethality and promotion of mutant recovery by resveratrol suggests that the antioxidant may contribute to the emergence of resistance to several antimicrobials, especially if new derivatives and/or formulations of resveratrol markedly increase bioavailability.     

Systematic Modeling Approach to Selective Plugging Using In Situ Bacterial Biopolymer Production and Its Potential for Microbial-enhanced Oil Recovery

This study presents a systematic modeling approach for examining the efficiency of the MEOR process based on in situ selective plugging by bacterial biopolymer production and optimization of the nutrient injection strategy to yield the maximum oil recovery. This study focuses on modeling in situ selective plugging by the bacterial biopolymer dextran that is generated by Leuconostoc mesenteroides. Bacterial growth and dextran generation were described by a stoichiometric equation and kinetic reactions using batch model simulation. Based on the parameters for permeability reduction obtained from the sandpack model, the MEOR process was implemented in a pilot-scale system that included a highly permeable thief zone in a low-permeability reservoir. The base MEOR design yielded a 61.5% improvement of the recovery factor compared to that obtained with waterflooding. The parametric simulations revealed that the recovery efficiency was influenced by the amount of dextran, as well as the distribution of dextran, and thus, the injection strategy is critical for controlling the dextran distribution. By incorporating the results from the sensitivity analysis and optimization to determine the optimal design parameters, a 36.7% improvement of the oil recovery was achieved with the optimized MEOR process in comparison with the base case.