Melanin production and use as a soluble electron shuttle for Fe(III) oxide reduction and as a terminal electron acceptor by Shewanella algae BrY

Dissimilatory metal-reducing bacteria (DMRB) utilize numerous compounds as terminal electron acceptors, including insoluble iron oxides. The mechanism(s) of insoluble-mineral reduction by DMRB is not well understood. Here we report that extracellular melanin is produced by Shewanella algae BrY. The extracted melanin served as the sole terminal electron acceptor. Upon reduction the reduced, soluble melanin reduced insoluble hydrous ferric oxide in the absence of bacteria, thus demonstrating that melanin produced by S. algae BrY is a soluble Fe(III)-reducing compound. In the presence of bacteria, melanin acted as an electron conduit to Fe(III) minerals and increased Fe(III) mineral reduction rates. Growth of S. algae BrY occurred in anaerobic minimal medium supplemented with melanin extracted from previously grown aerobic cultures of S. algae BrY. Melanin produced by S. algae BrY imparts increased versatility to this organism as a soluble Fe(III) reductant, an electron conduit for iron mineral reduction, and a sole terminal electron acceptor that supports growth.

Transcriptional regulation under pressure conditions by RNA polymerase sigma54 factor with a two-component regulatory system in Shewanella violacea

Deep-sea bacteria have unique systems for gene and protein expression controlled by hydrostatic pressure. One of the sigma factors, sigma54, was found to play an important role in pressure-regulated transcription in a deep-sea piezophilic bacterium, Shewanella violacea. A glutamine synthetase gene (glnA) has been targeted as a model for the pressure-regulated promoter to investigate transcriptional regulation by the sigma54 factor. Recognition sites for sigma54 and sigma70 factors were observed at an upstream region of the glnA, and NtrC-binding sites were also identified at the same region. Primer extension analyses revealed that the transcription initiation sites of both promoters were determined and that transcription from the sigma54 site was regulated by elevated pressure. The sigma54 promoter is known to be activated by a two-component signal transduction system, the NtrB-NtrC phosphorylation relay. Our results suggested that this system might be regulated by deep-sea conditions and that the gene expression controlled by the sigma54 promoter was actually regulated by pressure. We propose a possible model of the molecular mechanisms for pressure-regulated transcription.

Microbial iron respiration can protect steel from corrosion

Microbiologically influenced corrosion (MC) of steel has been attributed to the activity of biofilms that include anaerobic microorganisms such as iron-respiring bacteria, yet the mechanisms by which these organisms influence corrosion have been unclear. To study this process, we generated mutants of the iron-respiring bacterium Shewanella oneidensis strain MR-1 that were defective in biofilm formation and/or iron reduction. Electrochemical impedance spectroscopy was used to determine changes in the corrosion rate and corrosion potential as a function of time for these mutants in comparison to the wild type. Counter to prevailing theories of MC, our results indicate that biofilms comprising iron-respiring bacteria may reduce rather than accelerate the corrosion rate of steel. Corrosion inhibition appears to be due to reduction of ferric ions to ferrous ions and increased consumption of oxygen, both of which are direct consequences of microbial respiration.

Protective role of tolC in efflux of the electron shuttle anthraquinone-2,6-disulfonate

Extracellular electron transfer can play an important role in microbial respiration on insoluble minerals. The humic acid analog anthraquinone-2,6-disulfonate (AQDS) is commonly used as an electron shuttle during studies of extracellular electron transfer. Here we provide genetic evidence that AQDS enters Shewanella oneidensis strain MR-1 and causes cell death if it accumulates past a critical concentration. A tolC homolog protects the cell from toxicity by mediating the efflux of AQDS. Electron transfer to AQDS appears to be independent of the tolC pathway, however, and requires the outer membrane protein encoded by mtrB. We suggest that there may be structural and functional relationships between quinone-containing electron shuttles and antibiotics.

Chromate reduction in Shewanella oneidensis MR-1 is an inducible process associated with anaerobic growth

Cr(VI) reduction was observed during tests with Shewanella oneidensis MR-1 (previously named S. putrefaciens MR-1) while being grown with nitrate or fumarate as electron acceptor and lactate as electron donor. From the onset of anoxic growth on fumarate, we measured a gradual and progressive increase in the specific Cr(VI) reduction rate with incubation time until a maximum was reached at late exponential/early stationary phase. Under denitrifying conditions, the specific Cr(VI) reduction rate was inhibited by nitrite, which is produced during nitrate reduction. However, once nitrite was consumed, the specific reduction rate increased until a maximum was reached, again during the late exponential/early stationary phase. Thus, under both fumarate- and nitrate-reducing conditions, an increase in the specific Cr(VI) reduction rate was observed as the microorganisms transition from oxic to anoxic growth conditions, presumably as a result of induction of enzyme systems capable of reducing Cr(VI). Although Cr(VI) reduction has been studied in MR-1 and in other facultative bacteria under both oxic and anoxic conditions, a transition in specific reduction rates based on physiological conditions during growth is a novel finding. Such physiological responses provide information required for optimizing the operation of in situ systems for remediating groundwater contaminated with heavy metals and radionuclides, especially those that are characterized by temporal variations in oxygen content. Moreover, such information may point the way to a better understanding of the cellular processes used by soil bacteria to accomplish Cr(VI) reduction.

Transcriptional and proteomic analysis of a ferric uptake regulator (fur) mutant of Shewanella oneidensis: possible involvement of fur in energy metabolism, transcriptional regulation, and oxidative stress

The iron-directed, coordinate regulation of genes depends on the fur (ferric uptake regulator) gene product, which acts as an iron-responsive, transcriptional repressor protein. To investigate the biological function of a fur homolog in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1, a fur knockout strain (FUR1) was generated by suicide plasmid integration into this gene and characterized using phenotype assays, DNA microarrays containing 691 arrayed genes, and two-dimensional polyacrylamide gel electrophoresis. Physiological studies indicated that FUR1 was similar to the wild-type strain when they were compared for anaerobic growth and reduction of various electron acceptors. Transcription profiling, however, revealed that genes with predicted functions in electron transport, energy metabolism, transcriptional regulation, and oxidative stress protection were either repressed (ccoNQ, etrA, cytochrome b and c maturation-encoding genes, qor, yiaY, sodB, rpoH, phoB, and chvI) or induced (yggW, pdhC, prpC, aceE, fdhD, and ppc) in the fur mutant. Disruption of fur also resulted in derepression of genes (hxuC, alcC, fhuA, hemR, irgA, and ompW) putatively involved in iron uptake. This agreed with the finding that the fur mutant produced threefold-higher levels of siderophore than the wild-type strain under conditions of sufficient iron. Analysis of a subset of the FUR1 proteome (i.e., primarily soluble cytoplasmic and periplasmic proteins) indicated that 11 major protein species reproducibly showed significant (P < 0.05) differences in abundance relative to the wild type. Protein identification using mass spectrometry indicated that the expression of two of these proteins (SodB and AlcC) correlated with the microarray data. These results suggest a possible regulatory role of S. oneidensis MR-1 Fur in energy metabolism that extends the traditional model of Fur as a negative regulator of iron acquisition systems.

Measurement of iron(III) bioavailability in pure iron oxide minerals and soils using anthraquinone-2,6-disulfonate oxidation

The quinol form (AHDS) of 9,10-anthraquinone-2,6-disulfonate (AQDS) was used as a titrant to determine bioavailability of Fe(III) in pure iron minerals and several soils. AHDS oxidation to AQDS was coupled to Fe(III) reduction to Fe(ll) in biological media consisting of trace salts and vitamins, providing estimates of bioavailability consistentwith the biogeochemical mechanisms and conditions that control Fe(III) availability to iron-reducing bacteria. Iron(III) oxide sources were synthetic oxides (amorphous and crystalline) and three soils separated into two size fractions each (0-500 and 500-1000 microm). This titration gave a measurement of the amount of Fe(III) available to dissimilatory iron-reducing bacteria and was compared to hydroxylamine reduction, oxalate extraction, and biological reduction by Shewanella alga BrY. The advantage of AHDS titration over existing chemical techniques is that it can be performed at normal soil pH and ionic strength, and it allows for distinction of iron(III) oxides rendered unavailable by sorption of Fe(II) or by other pH-dependent geochemical processes. This approach also allows distinction of Fe(III) present in micropores that is not directly available to bacteria but bioavailable in the presence of an electron shuttle capable of transporting electrons into the micropores.

Influence of acetate and CO2 on the TMAO-reduction reaction by Shewanella baltica

In this work, the TMAO-reduction by Shewanella baltica, one of the representative spoilage organisms in modified atmosphere packaged marine fish fillets, and the effect of acetate and CO2 on this reduction were studied in vitro. The growth of S. baltica and the corresponding evolution of some compounds (acetate, lactate, pyruvate, glucose and trimethylamine (TMA)) were followed during storage at 4 degrees C in two types of broths. The first medium was a defined medium (pH = 6.8) to which lactate or pyruvate was added as hydrogen donor. Pyruvate showed to be more efficient as H-donor for S. baltica than lactate, as growth was much faster when equimolar amounts of pyruvate instead of lactate were present. Although the growth of S. baltica, when pyruvate is used as H-donor and no acetate is added, was not much inhibited by the CO2-atmosphere, CO2 had a pronounced effect on the studied reactions as it partly inhibited the reduction of pyruvate to acetate. The effect of acetate on this reaction was, on the other hand, not significant. To simulate the reactions occurring in situ, a buffered fish extract (pH = 6.8) was used. In spite of the neutral pH, the growth of S. baltica in this medium was highly inhibited by relatively small concentrations of acetate (< 0.3%). When 0.1% of acetate was added to the fish extract, less acetate was formed and lactate was more slowly consumed in comparison to the experiments without the addition of acetate. The consumption of lactate and the production of acetate were almost completely inhibited when the fish extract contained 0.25% of acetate. Apparently, the addition of acetate inhibited the use of lactate as H-donor. After extended storage times (17 days at 4 degrees C) TMA production started. Most probably, alternative H-donors were used by S. baltica, from which the pathway seems to be less energy efficient. This can be deduced from the exceptional growth inhibition of S. baltica by small amounts of acetate. However, when practical storage times for fish (e.g. 6 days at 4 degrees C after packaging) are considered, growth and TMAO-reduction by S. baltica was completely inhibited during this period by 0.25% of acetate.

Production of polyunsaturated fatty acids by polyketide synthases in both prokaryotes and eukaryotes

Polyunsaturated fatty acids (PUFAs) are essential membrane components in higher eukaryotes and are the precursors of many lipid-derived signaling molecules. Here, pathways for PUFA synthesis are described that do not require desaturation and elongation of saturated fatty acids. These pathways are catalyzed by polyketide synthases (PKSs) that are distinct from previously recognized PKSs in both structure and mechanism. Generation of cis double bonds probably involves position-specific isomerases; such enzymes might be useful in the production of new families of antibiotics. It is likely that PUFA synthesis in cold marine ecosystems is accomplished in part by these PKS enzymes.

Isolation and characterization of psychotrophic bacteria from oil-reservoir water and oil sands

Four psychrotrophic strains, which grew at 4 degrees C but not at 37 degrees C, were isolated from Japanese oil-reservoir water (strains SIB1, SIC1, SIS1) and Canadian oil sands (strain CAB1). Strains SIB1, SIS1, and CAB1 had a maximum growth rate at 20 degrees C and grew to the highest cell densities at the cultivation temperature of 0-4 degrees C. Strain SIS1 was capable of growing even at -5 degrees C. The growth profile of strain SIC1 was rather similar to that of a mesophilic bacterium. Strains SIB1, SIC1, and SIS1 were identified as members of the genus Shewanella, and strain CAB1 was a member of the genus Arthrobacter. All these strains exhibited weak degradation ability against catechol, a hydroxylated aromatic hydrocarbon, and tributyrin. These strains are expected to be of potential use in the in situ bioremediation technology of hazardous hydrocarbons and esters under low-temperature conditions.

Bacterial recognition of mineral surfaces: nanoscale interactions between Shewanella and alpha-FeOOH

Force microscopy has been used to quantitatively measure the infinitesimal forces that characterize interactions between Shewanella oneidensis (a dissimilatory metal-reducing bacterium) and goethite (alpha-FeOOH), both commonly found in Earth near-surface environments. Force measurements with subnanonewton resolution were made in real time with living cells under aerobic and anaerobic solutions as a function of the distance, in nanometers, between a cell and the mineral surface. Energy values [in attojoules (10(-18) joules)] derived from these measurements show that the affinity between S. oneidensis and goethite rapidly increases by two to five times under anaerobic conditions in which electron transfer from bacterium to mineral is expected. Specific signatures in the force curves suggest that a 150-kilodalton putative iron reductase is mobilized within the outer membrane of S. oneidensis and specifically interacts with the goethite surface to facilitate the electron transfer process.

Microbially catalyzed nitrate-dependent oxidation of biogenic solid-phase Fe(II) compounds

The potential for microbially catalyzed NO3(-)-dependent oxidation of solid-phase Fe(II) compounds was examined using a previously described autotrophic, denitrifying, Fe(II)-oxidizing enrichment culture. The following solid-phase Fe(II)-bearing minerals were considered: microbially reduced synthetic goethite, two different end products of microbially hydrous ferric oxide (HFO) reduction (biogenic Fe3O4 and biogenic FeCO3), chemically precipitated FeCO3, and two microbially reduced iron(III) oxide-rich subsoils. The microbially reduced goethite, subsoils, and chemically precipitated FeCO3 were subject to rapid NO3(-)-dependent Fe(II) oxidation. Significant oxidation of biogenic Fe3O4 was observed. Very little biogenic FeCO3 was oxidized. No reduction of NO3- or oxidation of Fe(II) occurred in pasteurized cultures. The molar ratio of NO3- reduced to Fe(II) oxidized in cultures containing chemically precipitated FeCO3, and one of the microbially reduced subsoils approximated the theoretical stoichiometry of 0.2:1. However, molar ratios obtained for oxidation of microbially reduced goethite, the other subsoil, and the HFO reduction end products did not agree with this theoretical value. These discrepancies may be related to heterotrophic NO3- reduction coupled to oxidation of dead Fe(III)-reducing bacterial biomass. Our findings demonstrate that microbally catalyzed NO3(-)-dependent Fe(II) oxidation has the potential to significantly accelerate the oxidation of solid-phase Fe(II) compounds by oxidized N species. This process could have an important influence on the migration of contaminant metals and radionuclides in subsurface environments.

The biotechnological potential of piezophiles

Microorganisms that prefer high-pressure conditions are termed piezophiles (previously termed barophiles). The molecular basis of piezophily is now being investigated extensively focusing on aspects of gene regulation and the function of certain proteins in deep-sea isolates. Little attention has been paid, however, to the potential biotechnological applications of piezophiles compared with other extremophiles. Based on the fundamental knowledge available, we will try to answer the following questions: How can we exploit the biotechnological potential of piezophiles? What can be understood by the application of high-pressure in biological systems?

Kinetics of chromium (VI) reduction by a type strain Shewanella alga under different growth conditions

We conducted kinetic batch experiments to determine the reduction of Chromium(VI) by a type strain of Shewanella alga (BrY-MT) ATCC 55627. Chromium(VI) was reduced to Chromium(III) by BrY-MT grown in three different substrates: BHIB (brain heart infusion broth), TSB (tryptic soy broth), and M9 (minimum broth). Four different Cr(VI) concentrations 4.836, 10.00, 37.125, and 260.00 mg l-1 were reduced at different rates by BrY-MT in both aerobic and anaerobic conditions. BrY-MT grown in BHIB reduced the maximum amount of Cr(VI) followed by TSB and M9. Carbondioxide produced from bacterial respiration varied with and without Cr(VI) under both aerobic and anaerobic conditions. The Cr(VI) reduction data under anaerobic condition was fitted by a monod model to determine the bacterial kinetic parameters. The kinetic parameters determined by fitting the anaerobic experimental data were used to run a forward simulation for experiments conducted under aerobic conditions. The monod model was modified to account for an inhibition parameter for the Cr(VI) experiment at 260 mg l-1. All the parameters varied within a narrow range, and were distinct for different substrates. Our studies show that, successful in situ bioremediation of Cr(VI) is depended on the type of substrates (electron donors) and the concentration of Cr(VI) in geologic medium.

Expression of a tetraheme protein, Desulfovibrio vulgaris Miyazaki F cytochrome c(3), in Shewanella oneidensis MR-1

Cytochrome c(3) from Desulfovibrio vulgaris Miyazaki F was successfully expressed in the facultative aerobe Shewanella oneidensis MR-1 under anaerobic, microaerophilic, and aerobic conditions, with yields of 0.3 to 0.5 mg of cytochrome/g of cells. A derivative of the broad-host-range plasmid pRK415 containing the cytochrome c(3) gene from D. vulgaris Miyazaki F was used for transformation of S. oneidensis MR-1, resulting in the production of protein product that was indistinguishable from that produced by D. vulgaris Miyazaki F, except for the presence of one extra alanine residue at the N terminus.

Pressure regulation of soluble cytochromes c in a deep-Sea piezophilic bacterium, Shewanella violacea

Two c-type cytochromes from the soluble fraction of a deep-sea moderately piezophilic bacterium, Shewanella violacea, were purified and characterized, and the genes coding for these cytochromes were cloned and sequenced. One of the cytochromes, designated cytochrome c(A), was found to have a molecular mass of approximately 8.3 kDa, and it contained one heme c per molecule. The other, designated cytochrome c(B), was found to have a molecular mass of approximately 23 kDa, and it contained two heme c molecules per protein molecule. The amount of cytochrome c(B) expressed in cells grown at high hydrostatic pressure (50 MPa) was less than that in cells grown at atmospheric pressure, whereas cytochrome c(A) was constitutively expressed under all pressure conditions examined. The results of Northern blotting analysis were consistent with the above-mentioned observations and suggested that the pressure regulation of cytochrome c(B) gene expression occurred at the transcriptional level. These results suggest that the components of the respiratory chain of moderately piezophilic S. violacea could be exchanged according to the growth pressure conditions.

Dissimilatory Fe(III) oxide reduction by Shewanella alga BrY requires adhesion

The Derjaguin-Landau-Verwey-Overbeek (DLVO) theory was used to examine the relationship between adhesion and dissimilatory Fe(III) oxide reduction. Adhesion of Shewanella alga BrY to hydrous ferric oxide (HFO) was correlated with ionic strength and thus was accurately described by the DLVO theory. Reduction of insoluble HFO was also correlated with KCl concentration. In contrast, there was no correlation between soluble Fe(III) reduction and ionic strength. A correlation between HFO reduction rate and adhesion to HFO was observed. These results provide direct evidence that adhesion is requisite for Fe(III) oxide reduction in the absence of soluble electron shuttles.

Bacterial reduction of copper-contaminated ferric oxide: copper toxicity and the interaction between fermentative and iron-reducing bacteria

Fe(III) oxide is an important heavy-metal sink, and bacteria are responsible for much of the Fe(III) reduced in nonsulfidogenic aquatic environments, yet factors governing the bacterial reduction of heavy metal-contaminated iron oxide are largely unknown. In this study with a stabilized bacterial consortium enriched from metal-contaminated sediments, we demonstrate that Cu toxicity impedes anaerobic carbon oxidation and bacterial reduction of hydrous ferric oxide (HFO). In the enrichment culture, a Clostridium sp. fermented lactate to propionate and acetate and Fe(III) reducers coupled acetate oxidation to HFO reduction. Increasing the amount of Cu in the culture medium significantly extended the time before Fe(III) reduction occurred and decreased the reduction rate, but did not affect the extent of HFO reduction. The Clostridium had a higher Cu-complexation capacity than the Fe(III) reducer Shewanella alga. Iron reduction was inhibited until almost all of the dissolved Cu was removed from solution and occurred two to seven times faster if the sediment enrichment culture was fed lactate instead of acetate. Our findings suggest that fermentative bacteria play a role in ameliorating heavy metal toxicity to iron-reducing bacteria. Fermenters may therefore enhance metal release in sediments by facilitating the bacterial reductive dissolution of heavy metal-contaminated HFO.

Characterization of a flavocytochrome that is induced during the anaerobic respiration of Fe3+ by Shewanella frigidimarina NCIMB400

A 63.9 kDa periplasmic tetrahaem flavocytochrome c(3), designated Ifc(3), was found to be expressed in Shewanella frigidimarina NCIMB400 grown anaerobically with ferric citrate or ferric pyrophosphate as the sole terminal electron acceptor, but not in anaerobic cultures of the bacterium with other respiratory substrates. Ifc(3) was purified to homogeneity and revealed by biochemical, spectroscopic and primary structure analyses to contain four low-spin bis-His-ligated c(3)-haems, with midpoint reduction potentials of -73, -141, -174 and -259 mV. A low-potential flavin was present in the form of non-covalently bound FAD; the protein possessed a unidirectional fumarate reductase activity. Disruption of the chromosomal gene encoding Ifc(3), ifcA, did not lead to a significant change in the rate of Fe(3+) reduction in batch culture. However, during such growth the Ifc(3)-deficient mutant produced both a 35 kDa periplasmic c-type cytochrome and a 45 kDa membrane-associated c-type cytochrome at markedly higher levels than did the parent strain. Nucleotide sequencing data from directly upstream of ifcA indicated the presence of an open reading frame encoding a putative outer-membrane beta-barrel protein of 324 amino acid residues.