Neutrophilic Fe-oxidizing Bacteria Research Articles

Assessing Marine Microbial Induced Corrosion at Santa Catalina Island, California.

High iron and eutrophic conditions are reported as environmental factors leading to accelerated low-water corrosion, an enhanced form of near-shore microbial induced corrosion. To explore this hypothesis, we deployed flow-through colonization systems in laboratory-based aquarium tanks under a continuous flow of surface seawater from Santa Catalina Island, CA, USA, for periods of 2 and 6 months. Substrates consisted of mild steel – a major constituent of maritime infrastructure – and the naturally occurring iron sulfide mineral pyrite. Four conditions were tested: free-venting “high-flux” conditions; a “stagnant” condition; an “active” flow-through condition with seawater slowly pumped over the substrates; and an “enrichment” condition where the slow pumping of seawater was supplemented with nutrient rich medium. Electron microscopy analyses of the 2-month high flux incubations document coating of substrates with “twisted stalks,” resembling iron oxyhydroxide bioprecipitates made by marine neutrophilic Fe-oxidizing bacteria (FeOB). Six-month incubations exhibit increased biofilm and substrate corrosion in the active flow and nutrient enriched conditions relative to the stagnant condition. A scarcity of twisted stalks was observed for all 6 month slow-flow conditions compared to the high-flux condition, which may be attributable to oxygen concentrations in the slow-flux conditions being prohibitively low for sustained growth of stalk-producing bacteria. All substrates developed microbial communities reflective of the original seawater input, as based on 16S rRNA gene sequencing. Deltaproteobacteria sequences increased in relative abundance in the active flow and nutrient enrichment conditions, whereas Gammaproteobacteria sequences were relatively more abundant in the stagnant condition. These results indicate that (i) high-flux incubations with higher oxygen availability favor the development of biofilms with twisted stalks resembling those of marine neutrophilic FeOB and (ii) long-term nutrient stimulation results in substrate corrosion and biofilms with different bacterial community composition and structure relative to stagnant and non-nutritionally enhanced incubations. Similar microbial succession scenarios, involving increases in nutritional input leading to the proliferation of anaerobic iron and sulfur-cycling guilds, may occur at the nearby Port of Los Angeles and cause potential damage to maritime port infrastructure.

Restrictions on the Production of Multi-Wall Carbon Nanotubes and Nanofibers by Gallionella sp.

ABSTRACTThe enzymatic oxidization of dissolved Fe(II) to Fe(III) by neutrophilic Fe-oxidizing bacteria plays a significant role in biological cycling of iron by inducing the precipitation of Fe(III) oxyhydroxide in aqueous environments. Among the diverse neutrophilic Fe-oxidizing bacteria, the genus Gallionella has received wide attention for its production of unique twisted extracellular stalks. Hallberg and Tai (2014) recently reported the detection of multi-wall carbon nanotubes on the twisted-stalks, and they viewed those carbon nanotubes as being biologically produced by Gallionella. We scrutinized Gallionella-produced biofilms collected from natural environments by scanning electron microscopy and high-resolution transmission electron microscopy. Ferrihydrite and lepidocrocite were the only nano-scaled minerals observed on the stalk, while there were nanometer-sized sheet-like graphitic contaminants on the grid in the vicinity of the sample which showed the same morphology as Hallberg and Tai (2014) observed. Moreover, similar materials on an empty grid and a grid loaded with randomly selected synthesized materials were also observed. Based on the current knowledge of carbon nanotube syntheses, none of the three known synthesizing methods including root-growth, rolling-up and bottom-up could be biochemically produced by any life because of the significant kinetic and energy obstacles. The carbon nanomaterials reported by Hallberg and Tai (2014) were clearly contaminations from amorphous carbon film on the grids for holding samples for transmission electron microscopic observations.

Mineralogical characterization and formation of Fe-Si oxyhydroxide deposits from modern seafloor hydrothermal vents

We have studied mineralogical characteristics of Fe-Si oxide precipitates from hydrothermal fields of the Valu Fa Ridge, Lau Basin, especially the role that the neutrophilic Fe-oxidizing bacteria played in their formation, using various analytical techniques (XRD, SEM, EPMA, TG/DTA, and FTIR). According to this examination, the Fe-Si oxide formation can be divided into two stages. At the initial stage, the Fe-oxidizing bacteria bound and oxidized Fe2+ into Fe3+ to fix CO2, triggering precipitation of Fe-oxyhydroxide (ferrihydrite) and construction of a loose network of Fe-rich filaments. Subsequently, the decreased porosity of the network resulting from the gradual growth of the filaments led to a decline in the mixing between seawater and the hydrothermal fluids. Then the conductive cooling of the network resulted in saturation of the dissolved Si with respect to amorphous silica. As a result, significant precipitation of opal-A occurred through inorganic polymerization. However, part of the silica was immobilized by bonding to Fe-OH functional groups and yielded unpolymerized silica, which is characterized by Fe-O-Si bond. Owing to the incorporation of Si into the ferrihydrite structure and its adsorption on the ferrihydrite surface, the modern hydrothermal Fe-Si oxides are thermally stable. DSC measurements indicate the full segregation of cristobalite from hematite at about 800 °C in an O2 atmosphere. These observations indicate that primary alternating Si- and Fe-rich layers may be absent in the Archean ocean and that alternating bands in BIFs represent a diagenetic process; our work thus provides a potential clue that can be used to unravel the precipitation and diagenetic mechanisms of Precambrian banded iron formations (BIF).

Growth model of a hydrothermal low-temperature Si-rich chimney: Example from the CDE hydrothermal field, Lau Basin

The CDE hydrothermal field was first discovered during a Chinese cruise to the East Lau Basin Spreading Centre in 2007. Apart from significant amounts of loose Fe-Si-Mn (oxyhydr) oxide (referred to as oxide below) precipitates, a small Si-rich oxide chimney was also recovered on this cruise. In this study, we report on the mineralogical and geochemical analyses of this chimney and a model for its growth that has been developed. Based on the mineralogy and O isotope results, the chimney walls can be divided into four growth generations (layers) from the inner to the outer layers: amorphous opal and barite layer (precipitation temperature 68.5°C based on oxygen isotope determinations), a rod-like amorphous layer (precipitation temperature 39.6°C), a filamentous Fe-Si oxide layer, and an outer Fe-Mn oxide layer. Investigations based on SEM and EDS showed that neutrophilic Fe-oxidizing bacteria play an important role in the formation of this chimney, particularly in the outer two generations. In the first stage, the metabolic activity of the microbes results in the pervasive precipitation of the filamentous Fe-rich oxides inside a ring formed by some amorphous opal and barite; therefore, a loose porous layer forms. In the second stage, amorphous opal then precipitates inside this wall as a result of conductive cooling and gradually controls the mixing between the hydrothermal fluids and ambient seawaters. In the third stage, barite and some amorphous opal form from the higher temperature fluids at the summit of the chimney growth history. In the last stage, the chimney wall becomes thicker and denser and the exchange of hydrothermal fluids and seawater ceases. As a result, a Fe-Mn oxide layer precipitates onto the outer surface of the chimney wall as neutrophilic Fe-oxidizing bacteria reoccupy the surface of the chimney. This mineral sequence and the resultant growth generations are confirmed by the chemical characteristics of the chimney wall. Sr isotopes extracted from the Fe oxides of the four-generation wall generally show a decreasing trend of the 87Sr/86Sr ratios from the second layer to the inner layer (from 0.707008 to 0.705877) except for the outer layer (0.706502). The Sr isotope and chondrite normalized REE patterns of the corresponding bulk samples from the chimney wall also display a similar trend. Our study shows that the biogenic filament network plays a key role in the formation of the chimney in contrast to previous growth models of higher temperature chimneys, which often ignore the influence of biogenic factors.

Formation of Fe–Mn–Si oxide and nontronite deposits in hydrothermal fields on the Valu Fa Ridge, Lau Basin

Hydrothermal Fe–Mn–Si oxides and nontronite are pervasive in the Hine Hina, Vai Lili and Mariner hydrothermal fields along the central Valu Fa Ridge, Lau Basin. Morphometric and mineralogical analyses reveal that the iron-rich filaments are the most important constituents of these Fe–Mn–Si oxide deposits. Both the morphologies and chemical composition of the filaments indicate that neutrophilic Fe-oxidizing bacteria have played a key role in the formation of these deposits. A key process of the formation of these deposits is the creation of a complicated filamentous network in which a series of metabolic activities and passive sorption and nucleation processes occur. The precipitation of dissolved Si in unsaturated and saturated states leads to a “two-generation” growth model in the hydrothermal vents. The precipitation of amorphous opal occurs in a relatively narrow temperature range (41.1–42.9 °C) based on oxygen isotope analyses, indicating a fast precipitation rate of opal-A when conductive cooling of the hydrothermal fluid occurrs. Patchy nontronite in the Mariner fields is a product of the direct precipitation from hydrothermal fluids at a temperature of ∼87.9 °C, whereas the scattered nontronite at the Hine Hina field is the product of the replacement of hydrothermal Fe–Si oxides at a temperature of ∼46.2 °C.

High‐resolution 2D and 3D cryo‐TEM reveals structural adaptations of two stalk‐forming bacteria to an Fe‐oxidizing lifestyle

Aerobic neutrophilic Fe-oxidizing bacteria (FeOB) thrive where oxic and iron-rich anoxic waters meet. Here, iron microbial mats are commonly developed by stalk-forming Fe-oxidizers adapted to these iron-rich gradient environments, somehow avoiding iron encrustation. Few details are known about FeOB physiology; thus, the bases of these adaptations, notably the mechanisms of interactions with iron, are poorly understood. We examined two stalked FeOB: the marine Zetaproteobacterium Mariprofundus ferrooxydans and a terrestrial Betaproteobacterium Gallionella-like organism. We used cryo-transmission electron microscopy and cryo-electron tomography to provide unprecedented ultrastructural data on intact cell-mineral systems. Both FeOB localize iron mineral formation at stalk extrusion sites, while avoiding surface and periplasmic mineralization. The M. ferrooxydans cell surface is densely covered in fibrils while the terrestrial FeOB surface is smooth, suggesting a difference in surface chemistry. Only the terrestrial FeOB exhibited a putative chemotaxis apparatus, which may be due to differences in chemotaxis mechanisms. Both FeOB have a single flagellum, which alone is insufficient to account for cell motion during iron oxidation, suggesting that stalk extrusion is a mechanism for motility. Our results delineate the physical framework of iron transformations and characterize possible structural adaptations to the iron-oxidizing lifestyle. This study shows ultrastructural similarities and differences between two distinct FeOB, setting the stage for further (e.g. genomic) comparisons that will help us understand functional differences and evolutionary history.

Lithotrophic iron-oxidizing bacteria produce organic stalks to control mineral growth: implications for biosignature formation

Neutrophilic Fe-oxidizing bacteria (FeOB) are often identified by their distinctive morphologies, such as the extracellular twisted ribbon-like stalks formed by Gallionella ferruginea or Mariprofundus ferrooxydans. Similar filaments preserved in silica are often identified as FeOB fossils in rocks. Although it is assumed that twisted iron stalks are indicative of FeOB, the stalk's metabolic role has not been established. To this end, we studied the marine FeOB M. ferrooxydans by light, X-ray and electron microscopy. Using time-lapse light microscopy, we observed cells excreting stalks during growth (averaging 2.2 μm h(-1)). Scanning transmission X-ray microscopy and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy show that stalks are Fe(III)-rich, whereas cells are low in Fe. Transmission electron microscopy reveals that stalks are composed of several fibrils, which contain few-nanometer-sized iron oxyhydroxide crystals. Lepidocrocite crystals that nucleated on the fibril surface are much larger (∼100 nm), suggesting that mineral growth within fibrils is retarded, relative to sites surrounding fibrils. C and N 1s NEXAFS spectroscopy and fluorescence probing show that stalks primarily contain carboxyl-rich polysaccharides. On the basis of these results, we suggest a physiological model for Fe oxidation in which cells excrete oxidized Fe bound to organic polymers. These organic molecules retard mineral growth, preventing cell encrustation. This model describes an essential role for stalk formation in FeOB growth. We suggest that stalk-like morphologies observed in modern and ancient samples may be correlated confidently with the Fe-oxidizing metabolism as a robust biosignature.

A novel lineage of proteobacteria involved in formation of marine Fe-oxidizing microbial mat communities.

BackgroundFor decades it has been recognized that neutrophilic Fe-oxidizing bacteria (FeOB) are associated with hydrothermal venting of Fe(II)-rich fluids associated with seamounts in the world's oceans. The evidence was based almost entirely on the mineralogical remains of the microbes, which themselves had neither been brought into culture or been assigned to a specific phylogenetic clade. We have used both cultivation and cultivation-independent techniques to study Fe-rich microbial mats associated with hydrothermal venting at Loihi Seamount, a submarine volcano.Methodology/Principle FindingsUsing gradient enrichment techniques, two iron-oxidizing bacteria, strains PV-1 and JV-1, were isolated. Chemolithotrophic growth was observed under microaerobic conditions; Fe(II) and Fe0 were the only energy sources that supported growth. Both strains produced filamentous stalk-like structures composed of multiple nanometer sized fibrils of Fe-oxyhydroxide. These were consistent with mineralogical structures found in the iron mats. Phylogenetic analysis of the small subunit (SSU) rRNA gene demonstrated that strains PV-1 and JV-1 were identical and formed a monophyletic group deeply rooted within the Proteobacteria. The most similar sequence (85.3% similarity) from a cultivated isolate came from Methylophaga marina. Phylogenetic analysis of the RecA and GyrB protein sequences confirmed that these strains are distantly related to other members of the Proteobacteria. A cultivation-independent analysis of the SSU rRNA gene by terminal-restriction fragment (T-RF) profiling showed that this phylotype was most common in a variety of microbial mats collected at different times and locations at Loihi.ConclusionsOn the basis of phylogenetic and physiological data, it is proposed that isolate PV-1T ( = ATCC BAA-1019: JCM 14766) represents the type strain of a novel species in a new genus, Mariprofundus ferrooxydans gen. nov., sp. nov. Furthermore, the strain is the first cultured representative of a new candidatus class of the Proteobacteria that is widely distributed in deep-sea environments, Candidatus ζ (zeta)-Proteobacteria cl. nov.

Neutrophilic Iron-Oxidizing Bacteria in the Ocean: Their Habitats, Diversity, and Roles in Mineral Deposition, Rock Alteration, and Biomass Production in the Deep-Sea

The importance of metals to life has long been appreciated. Iron (Fe) is the fourth most abundant element overall, and the second most abundant element that is redox-active in near-surface aqueous habitats, rendering it the most important environmental metal. While it has long been recognized that microorganisms participate in the global iron cycle, appreciation for the pivotal role that redox cycling of iron plays in energy conservation among diverse prokaryotes has grown substantially in the past decade. In addition, redox reactions involving Fe are linked to several other biogeochemical cycles (e.g., carbon), with significant ecological ramifications. The increasing appreciation for the role of microbes in redox transformations of Fe is reflected in a recent surge in biological and environmental studies of microorganisms that conserve energy for growth from redox cycling of Fe compounds, particularly in the deep ocean. Here we highlight some of the key habitats where microbial Fe-oxidation plays significant ecological and biogeochemical roles in the oceanic regime, and provide a synthesis of recent studies concerning this important physiological group. We also provide the first evidence that microbial Fe-oxidizing bacteria are a critical factor in the kinetics of mineral dissolution at the seafloor, by accelerating dissolution by 6–8 times over abiotic rates. We assert that these recent studies, which indicate that microbial Fe-oxidation is widespread in the deep-sea, combined with the apparent role that this group play in promoting rock and mineral weathering, indicate that a great deal more attention to these microorganisms is warranted in order to elucidate the full physiological and phylogenetic diversity and activity of the neutrophilic Fe-oxidizing bacteria in the oceans.

Glycine betaine as a cryoprotectant for prokaryotes

Osmoprotectants are low molecular weight, hydrophilic, nontoxic molecules that assist a cell under osmotic stress to stabilize its concentration of internal solutes. These properties are similar to compounds used as cryoprotectants for the preservation of prokaryotic cells during freezing. This study tested the ability of a common compatible solute, glycine betaine (GB), to act as a cryoprotectant. In a series of freeze-drying studies using a variety of prokaryotes, GB performed as well, or better than, two commonly used cryoprotectants, sucrose/bovine serum albumin (S/BSA) and trehalose/dextran (T/D). GB did especially well maintaining cell viability after long-term storage (simulated equivalent of 20 years) for microorganisms like Neisseria gonorrhoeae and Streptococcus pneumoniae. GB was tested for its ability to preserve members of the genus Acidothiobacillus, a difficult genus to preserve. For two strains of Acidithiobacillus ferrooxidans that were preserved using liquid drying, GB performed as well as S/BSA. Results were more mixed for two strains of Acidithiobacillus thiooxidans; one strain could be preserved with S/BSA but not GB, the other strain gave low recoveries with both cryoprotectants. GB also proved to be a useful cryoprotectant for liquid nitrogen preservation yielding equivalent results to the cryopreservative, glycerol for halophilic archaea, and neutrophilic Fe-oxidizing bacteria. These results indicate that GB is a simple and useful cryoprotectant that works for a wide range of prokaryotic organisms under different cryopreservation regimens.

Seafloor bioalteration of sulfide minerals: results from in situ incubation studies

We present results of incubation studies conducted at low temperatures (∼4°C) in the vicinity of a seafloor hydrothermal vent system. We reacted Fe-, S-, Cu-, and Zn-bearing minerals including pyrite, marcasite, chalcopyrite, sphalerite, elemental sulfur, and a portion of a natural chimney sulfide structure for 2 months at the Main Endeavour Segment of the Juan de Fuca Ridge in the Pacific Ocean. Our study utilizes Fluorescent In Situ Hybridizations (FISH), Scanning and Transmission Electron Microscopy (SEM, TEM), and light microscopic analysis. The surfaces of these minerals are solely colonized by Bacteria and not by Archaea. Colonization densities vary over an order of magnitude with the following sequence: elemental sulfur > chimney sulfide > marcasite > pyrite > sphalerite > chalcopyrite, and correspond well with the abiotic oxidation kinetics of these materials, excepting elemental sulfur, which is both the least reactive to oxidizing species and the most heavily colonized. Colonization densities also correspond with apparent degree of reaction (dissolution pitting + accumulation of secondary alteration products). Heavy accumulations of secondary Fe oxides on Fe-bearing minerals, most notably on the chimney sulfide, form in situ as the result of mineral dissolution and the activity of neutrophilic Fe-oxidizing bacteria. Results suggest that mineral-oxidizing bacteria play a prominent role in weathering of seafloor sulfide deposits, and that microbial utilization of mineral substrates contributes to biomass production in seafloor hydrothermal environments.

Neutrophilic Fe-oxidizing bacteria are abundant at the Loihi Seamount hydrothermal vents and play a major role in Fe oxide deposition.

A number of hydrothermal vent sites exist on the summit of the Loihi Seamount, a shield volcano that is part of the Hawaiian archipelago. The vents are 1,100 to 1,325 m below the surface and range in temperature from slightly above ambient (10 degrees C) to high temperature (167 degrees C). The vent fluid is characterized by high concentrations of CO2 (up to 17 mM) and Fe(II) (up to 268 microM), but there is a general paucity of H2S. Most of the vents are surrounded by microbial mats that have a gelatinous texture and are heavily encrusted with rust-colored Fe oxides. Visually, the Fe oxides appeared homogeneous. However, light microscopy revealed that the oxides had different morphologies, which fell into three classes: (i) sheaths, (ii) twisted or irregular filaments, and (iii) amorphous oxides. A morphological analysis of eight different samples indicated that the amorphous oxides were overall the most abundant; however, five sites had >50% sheaths and filamentous oxides. These latter morphologies are most likely the direct result of microbial deposition. Direct cell counts revealed that all of the oxides had abundant microbial populations associated with them, from 6.9 x 10(7) to 5.3 x 10(8) cells per ml of mat material. At most sites, end point dilution series for lithotrophic Fe oxidizers were successful out to dilutions of 10(-6) and 10(-7). A pure culture was obtained from a 10(-7) dilution tube; this strain, JV-1, was an obligate, microaerophilic Fe oxidizer that grew at 25 to 30 degrees C. A non-cultivation-based molecular approach with terminal-restriction fragment length polymorphism also indicated the common presence of Fe-oxidizing bacteria at Loihi. Together, these results indicate that Fe-oxidizing bacteria are common at the Loihi Seamount and probably play a major role in Fe oxidation. A review of the literature suggests that microbially mediated Fe oxidation at hydrothermal vents may be important globally.