Further reading in geomicrobiology

In the wetland rhizosphere, high densities of lithotrophic Fe(II)-oxidizing bacteria (FeOB) and a favorable environment (i.e., high Fe(II) availability and microaerobic conditions) suggest that these organisms are actively contributing to the formation of Fe plaque on plant roots. We manipulated the presence/absence of an Fe(II)-oxidizing bacterium (Sideroxydans paludicola, strain BrT) in axenic hydroponic microcosms containing the roots of intact Juncus effusus (soft rush) plants to determine if FeOB affected total rates of rhizosphere Fe(II) oxidation and Fe plaque accumulation. Our experimental data highlight the importance of both FeOB and plants in influencing short-term rates of rhizosphere Fe oxidation. Over time scales ca. 1 wk, the FeOB increased Fe(II) oxidation rates by 1.3 to 1.7 times relative to FeOB-free microcosms. Across multiple experimental trials, Fe(II) oxidation rates were significantly correlated with root biomass, reflecting the importance of radial O ₂ loss in supporting rhizosphere Fe(II) oxidation. Rates of root Fe(III) plaque accumulation (time scales: 3 to 6 wk) were ～ 70 to 83% lower than expected based on the short-term Fe(II) oxidation rates and were unaffected by the presence/absence of FeOB. Decreasing rates of Fe(II) oxidation and Fe(III) plaque accumulation with increasing time scales indicate changes in rates of Fe(II) diffusion and radial O ₂ loss, shifts in the location of Fe oxide accumulation, or temporal changes in the microbial community within the microcosms. The microcosms used herein replicated many of the environmental characteristics of wetland systems and allowed us to demonstrate that FeOB can stimulate rates of Fe(II) oxidation in the wetland rhizosphere, a finding that has implications for the biogeochemical cycling of carbon, metals, and nutrients in wetland ecosystems.     

Diversity of Ferrous Iron-Oxidizing,Nitrate-Reducing Bacteria and their Involvement in Oxygen-Independent Iron Cycling

In previous studies, three different strains (BrG1, BrG2, and BrG3) of ferrous iron-oxidizing, nitrate-reducing bacteria were obtained from freshwater sediments. All three strains were facultative anaerobes and utilized a variety of organic substrates and molecular hydrogen with nitrate as electron acceptor. In this study, analyses of 16S rDNA sequences showed that strain BrG1 was affiliated with the genus Acidovorax, strain BrG2 with the genus Aquabacterium, and strain BrG3 with the genus Thermomonas. Previously, bacteria similar to these three strains were detected with molecular techniques in MPN dilution series for ferrous iron-oxidizing, nitrate-reducing bacteria inoculated with different freshwater sediment samples. In the present study, further molecular analyses of these MPN cultures indicated that the ability to oxidize ferrous iron with nitrate is widespread amongst the Proteobacteria and may also be found among the Gram-positive bacteria with high GC content of DNA. Nitrate-reducing bacteria oxidized ferrous iron to poorly crystallized ferrihydrite that was suitable as an electron acceptor for ferric iron-reducing bacteria. Biologically produced ferrihydrite and synthetically produced ferrihydrite were both well suited as electron acceptors in MPN dilution cultures. Repeated anaerobic cycling of iron was shown in a coculture of ferrous iron-oxidizing bacteria and the ferric iron-reducing bacterium Geobacter bremensis. The results indicate that iron can be cycled between its oxidation states +II and +III by microbial activities in anoxic sediments.     

Characterization of Neutrophilic Fe(II)-Oxidizing Bacteria Isolated from the Rhizosphere of Wetland Plants and Description of Ferritrophicum radicicola gen. nov. sp. nov., and Sideroxydans paludicola sp. nov.

Iron deposits (Fe plaque) on wetland plant roots contain abundant microbial populations, including Fe(II)-oxidizing bacteria (FeOB) that have not been cultured previously. In this study, 4 strains of Fe plaque-associated FeOB were isolated from 4 species of wetland plants. All 4 isolates grew in tight association with Fe-oxides, but did not form any identifiable Fe-oxide structures. All strains were obligate lithotrophic Fe(II)-oxidizers that were microaerobic, and were unable to use other inorganic or organic energy sources. One strain, BrT, was shown to fix ¹⁴ CO ₂ at a rate consistent with its requirement for total cell carbon. The doubling times for the strains varied between 9.5 and 15.8 hours. The fatty acid methyl ester (FAME) profiles of 2 strains, BrT and CCJ, revealed that 16:0, 15:1 isoG, and 14:0 were dominant fatty acids. Phylogenetic analysis of the 16S rRNA gene indicated that all the strains were Betaproteobacteria. Two of the strains, BrT and Br-1 belong to a new species, Sideroxydans paludicola; a third strain, LD-1, is related to Sideroxydans lithotrophicus, a recently described species of FeOB. The fourth isolate, Ferritrophicum radicicola, represented a new genus in a new order of Betaproteobacteria, the Ferritrophicales. There are no other cultured isolates in this order. A small subunit rRNA gene-based, cultivation-independent analysis of Typha latifolia collected from a wetland revealed terminal restriction fragment profiles (tRFLP) consistent with the presence of these bacteria in the rhizosphere. These novel organisms likely play an important role in Fe(II) oxidation kinetics and Fe cycling within many terrestrial and freshwater environments.     

The Gibbs Free Energy Threshold for the Invasion of a Microbial Population Under Kinetic Constraints

Possible chemotrophic metabolism at a site of interest is controlled not only by the catabolic energy expressed as the Gibbs energy of reaction (Δ_rG) but also by the kinetic constraints due to the availability of electron acceptors and donors. We introduced graphical and stochastic approaches for determining the Δ_rG threshold required to support a microbial population with a specific catabolic strategy under kinetic constraints. Invasibility as an indicator of the present reproductive ability of a microbial population was evaluated by simultaneously calculating Δ_rG for the catabolic reaction and the microbial catalytic rate. For example, the neutrophilic iron-oxidizing bacteria's invasibility was calculated by randomly choosing the Fe²⁺ and O₂ concentrations between 10^?8 and 10^?2 mol L^?1, and pH between 4 and 8, to determine the Δ_rG threshold for invasion. Parameters were estimated from batch experiments of neutrophilic iron-oxidizing bacteria reported in previous studies. Under the given conditions, the stochastic approach predicted that the neutrophilic iron-oxidizing bacteria can always invade a system in which the Δ_rG for Fe oxidation is below ?90 kJ mol Fe^?1, can occasionally invade if Δ_rG is between ?45 and ?90 kJ mol Fe^?1, and can never invade if Δ_rG is above ?45 kJ mol Fe^?1. The Δ_rG threshold for invasion is sifted by the growth yield coefficient, the loss rate of cells, the maximum cell-specific Fe oxidation rate constant, and the temperature. The Δ_rG threshold for invasion may be unable to rigorously predict the stable dominance of microbial metabolism, but can provide a rough indication for the possible microbial metabolism under current conditions.     

海底热液环境中嗜中性微需氧铁氧化菌的多样性、生物矿化作用及其代谢特征

铁元素是深海热液活动产物的主要成分之一,也是热液喷口处化能自养微生物生态系统的重要驱动元素。以Zetaproteobacteria为典型代表的嗜中性微需氧铁氧化菌是海底喷口及其周围环境中生物介导的Fe²⁺氧化这一生物矿化作用的主要驱动者。这些铁氧化菌通过氧化Fe²⁺获取维持自身代谢所必需的能量,同时分泌有机质将氧化后的不溶铁（氧化物或氢氧化物）沉淀于细胞外,形成具有螺旋丝带状、中空长杆状、分叉管状以及其他具有特殊形貌特征的显微结构体,进而堆积成广泛分布于海底的富铁氧化物/氢氧化物。越来越多的研究表明,编码细胞色素孔蛋白的cyc2基因是Zetaproteobacteria铁氧化菌进行Fe²⁺氧化的关键基因,而细胞色素c或其他周质细胞色素则是Fe²⁺氧化过程中的关键电子传递载体。基于宏基因组分析的系列研究揭示了Zetaproteobacteria普遍具有多种与氮、硫、氢以及砷元素循环密切相关的功能基因与代谢途径,暗示了其在上述元素循环过程中的潜在作用。本文系统地总结了海底热液喷口及其周围环境中发现的嗜中...     

Relating Microbial Community Structure and Geochemistry in Deep Regolith Developed on Volcaniclastic Rock in the Luquillo Mountains,Puerto Rico

Fe oxidation is often the first chemical reaction that initiates weathering and disaggregation of intact bedrock into regolith. Here we explore the use of pyrosequencing tools to test for evidence that bacteria participate in these reactions in deep regolith. We analyze regolith developed on volcaniclastic rocks of the Fajardo formation in a ridgetop within the rainforest of the Luquillo Mountains of Puerto Rico. In the 9-m-deep regolith profile, the primary minerals chlorite, feldspar, and pyroxene are detected near 8.3 m but weather to kaolinite and Fe oxides found at shallower depths. Over the regolith profile, both total and heterotrophic bacterial cell counts generally increase from the bedrock to the surface. Like other soil microbial studies, the dominant phyla detected are Proteobacteria, Acidobacteria, Planctomycetes, and Actinobacteria. Proteobacteria (α, β, γ and δ) were the most abundant at depth (6.8–9 m, 41–44%), while Acidobacteria were the most abundant at the surface (1.4–4.4 m, 37–43%). Despite the fact that Acidobacteria dominated surficial communities while Proteobacteria dominated near bedrock, the near-surface and near-bedrock communities were not statistically different in structure but were statistically different from mid-depth communities. Approximately 21% of all sequences analyzed did not match known sequences: the highest fraction of unmatched sequences was greatest at mid-depth (45% at 4.4 m). At the regolith-bedrock interface where weathering begins, several lines of evidence are consistent with biotic Fe oxidation. At that interface, iron-related bacterial activity tests and culturing indicate the presence of iron-related bacteria, and phylogenetic analyses identified sub-phyla containing known iron-oxidizing microorganisms. Cell densities of iron-oxidizers in the deep saprolite were estimated to be on the order of 10⁵ cells g^?1. Overall Fe loss was also observed at the regolith-bedrock interface, consistent with bacterial production of organic acids and leaching of Fe-organic complexes. Fe-organic species were also detected to be enriched near the bedrock-regolith interface. In this and other deep weathering profiles, chemolithoautotrophic bacteria that use Fe for energy and nitrate or oxygen as an electron acceptor may play an important role in initiating disaggregation of bedrock.     

Direct and Mn-Controlled Indirect Iron Oxidation by Leptothrix discophora SS-1 and Leptothrix cholodnii

Direct biotic and homogeneous abiotic Fe(II) oxidation rates as well as oxidation rates of Fe(II) with MnO_X were determined in laboratory experiments and compared with biotic Mn(II) oxidation rates. In groundwaters and thermal installation waters, parameters for both Fe(II) oxidation steps were studied and products of biotic and abiotic Fe(II) and Mn(II) oxidation were analyzed. Direct Fe(II) oxidation of active Leptothrix cholodnii cultures can reach first-order rates of up to 1.17 ± 0.90 h^?1. Second-order rates of Fe(II) oxidation with biogenic, Leptothrix-cholodnii- and Leptothrix-discophora-SS-1-originating MnO_X lead to rates comparable with those as obtained with abiotic H⁺-birnessite.     

Iron cycling at corroding carbon steel surfaces

Surfaces of carbon steel (CS) exposed to mixed cultures of iron-oxidizing bacteria (FeOB) and dissimilatory iron-reducing bacteria (FeRB) in seawater media under aerobic conditions were rougher than surfaces of CS exposed to pure cultures of either type of microorganism. The roughened surface, demonstrated by profilometry, is an indication of loss of metal from the surface. In the presence of CS, aerobically grown FeOB produced tight, twisted helical stalks encrusted with iron oxides. When CS was exposed anaerobically in the presence of FeRB, some surface oxides were removed. However, when the same FeOB and FeRB were grown together in an aerobic medium, FeOB stalks were less encrusted with iron oxides and appeared less tightly coiled. These observations suggest that iron oxides on the stalks were reduced and solubilized by the FeRB. Roughened surfaces of CS and denuded stalks were replicated with culture combinations of different species of FeOB and FeRB under three experimental conditions. Measurements of electrochemical polarization resistance established different rates of corrosion of CS in aerobic and anaerobic media, but could not differentiate rate differences between sterile controls and inoculated exposures for a given bulk concentration of dissolved oxygen. Similarly, total iron in the electrolyte could not be used to differentiate treatments. The experiments demonstrate the potential for iron cycling (oxidation and reduction) on corroding CS in aerobic seawater media.     

Bioleaching of Heavy Metals from Textile Sludge by Indigenous Sulfur-and-Iron-Oxidizing Microorganisms Using Elemental Sulfur and Ferrous Sulfate as Energy Sources: A Comparative Study

The present study was undertaken to investigate the potential of enriched indigenous sulfur-and-iron-oxidizing microorganisms in the bioleaching of Cu, Ni, Zn and Fe from textile sludges by using elemental sulfur and ferrous sulfate (FS), respectively, as an energy source under batch conditions. The experiments were performed with three different textile sludges (S1, S2 and S3) at initial neutral pH of the sludges procured from different parts of the country i.e., UP, Haryana and Punjab. The three sludges used were not only procured from different parts of the country but also differ in physiochemical characteristics. The extent of heavy metals solubilization in each sludge was found to be different using sulfur- and iron-oxidizing microorganisms. The results of the study indicate that sulfur-oxidizing microorganisms were found more efficient in the bioleaching process, irrespective of any sludge. The use of sulfur-oxidizing microorganisms led to higher solubilization of heavy metals and after 7 days of bioleaching about 84–96% Cu, 64–78% Ni, 81–92% Zn and 74–88% Fe were removed compared to 62–73% Cu, 62–66% Ni, 74–78% Zn and 70–78% Fe using iron-oxidizing microorganisms. This study had shown the feasibility of applying the bioleaching process to textile sludge contaminated with heavy metals. The results of the present study indicate that the bioleached sludge would be safer for land application.     

Interdependencies between Biotic and Abiotic Ferrous Iron Oxidation and Influence of pH,Oxygen and Ferric Iron Deposits

The effect of pH, oxygen and ferrous iron on growth and oxidation rates of iron-oxidizing bacteria (Gallionella spp and Leptothrix spp) as well as indirect effects, the most prominent being catalytic activity of the produced ferric iron deposits, were investigated. Deposits of biotic origin exhibit slightly lower surface oxidation rates compared to abiotically produced ferric iron. It was shown that the required habitat conditions of the studied species hardly overlap, but increase the pH/oxygen range of potential Fe(II) oxidation conditions. The study highlights the combined effect of microbial iron oxidation and catalytic properties of the Mn and Fe oxidation products.