Quantification of electron transfer rates to a solid phase electron acceptor through the stages of biofilm formation from single cells to multicellular communities

Microbial fuel cell (MFC) technology has enabled new insights into the mechanisms of electron transfer from dissimilatory metal reducing bacteria to a solid phase electron acceptor. Using solid electrodes as electron acceptors enables quantitative real-time measurements of electron transfer rates to these surfaces. We describe here an optically accessible, dual anode, continuous flow MFC that enables real-time microscopic imaging of anode populations as they develop from single attached cells to a mature biofilms. We used this system to characterize how differences in external resistance affect cellular electron transfer rates on a per cell basis and overall biofilm development in Shewanella oneidensis strain MR-1. When a low external resistance (100 Omega) was used, estimates of current per cell reached a maximum of 204 fA/cell (1.3 x 10(6) e(-) cell(-1) sec(-1)), while when a higher (1 MOmega) resistance was used, only 75 fA/cell (0.4 x 10(6) e(-) cell(-1) sec(-1)) was produced. The 1 MOmega anode biomass consistently developed into a mature thick biofilm with tower morphology (>50 microm thick), whereas only a thin biofilm (<5 microm thick) was observed on the 100 Omega anode. These data suggest a link between the ability of a surface to accept electrons and biofilm structure development.

The Impact of Bacterial Strain on the Products of Dissimilatory Iron Reduction

Three bacterial strains from the genus Shewanella were used to examine the influence of specific bacteria on the products of dissimilatory iron reduction. Strains CN32, MR-4 and W3-18-1 were incubated with HFO (hydrous ferric oxide) as the terminal electron acceptor and lactate as the organic carbon and energy source. Mineral products of iron reduction were analyzed using X-ray powder diffraction, electron microscopy, coulometry and susceptometry. Under identical nutrient loadings, iron reduction rates for strains CN32 and W3-18-1 were similar, and about twice as fast as MR-4. Qualitative and quantitative assessment of mineralized end products (secondary minerals) indicated that different products were formed during experiments with similar reduction rates but different strains (CN32 and W3-18-1), and similar products were formed during experiments with different iron reduction rates and different strains (CN32 and MR-4). The major product of iron reduction by strains CN32 and MR-4 was magnetite, while for W3-18-1 it was a mixture of magnetite and iron carbonate hydroxide hydrate (green rust), a precursor to fougerite. Another notable difference was that strains CN32 and MR-4 converted all of the starting ferric iron material into magnetite, while W3-18-1 did not convert most of the Fe(3+) into a recognizable crystalline material. Biofilm formation is more robust in W3-18-1 than in the other two strains used in this study. The differences in mineralization may be an indicator that EPS (or another cellular product from W3-18-1) may interfere with the crystallization of magnetite or facilitate formation of green rust. These results suggest that the relative abundance of mineral end products and the relative distribution of these products are strongly dependent on the bacterial species or strain catalyzing iron reduction.

Conserved synteny at the protein family level reveals genes underlying Shewanella species' cold tolerance and predicts their novel phenotypes

Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na⁺/H⁺ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.

Electricity production coupled to ammonium in a microbial fuel cell

The production of electricity from ammonium was examined using a rotating-cathode microbial fuel cell (MFC). The addition of ammonium chloride, ammonium sulfate, or ammonium phosphate (monobasic) resulted in electricity generation, while adding sodium chloride, nitrate, or nitrite did not cause any increase in current production. The peak current increased with increasing amount of ammonium addition up to 62.3 mM of ammonium chloride, suggesting that ammonium was involved in electricity generation either directly as the anodic fuel or indirectly as substrates for nitrifiers to produce organic compounds for heterotrophs. Adding nitrate or nitrite with ammonium increased current production compared to solely ammonium addition. Using 16S rRNA-linked molecular analyses, we found ammonium-oxidizing bacteria and denitrifying bacteria on both the anode and cathode electrodes, whereas no anammox bacteria were detected. The dominant ammonium-oxidizing bacteria were closely related to Nitrosomonas europaea. The present MFC achieved an ammonium removal efficiency of 49.2 +/- 5.9 or 69.7 +/- 3.6%, depending on hydraulic retention time, but exhibited a very low Coulombic efficiency.

Self-sustained phototrophic microbial fuel cells based on the synergistic cooperation between photosynthetic microorganisms and heterotrophic bacteria

A sediment-type self-sustained phototrophic microbial fuel cell (MFC) was developed to generate electricity through the synergistic interaction between photosynthetic microorganisms and heterotrophic bacteria. Under illumination, the MFC continuously produced electricity without the external input of exogenous organics or nutrients. The current increased in the dark and decreased with the light on, possibly because of the negative effect of the oxygen produced via photosynthesis. Continuous illumination inhibited the current production while the continuous dark period stimulated the current production. Extended darkness resulted in a decrease of current, probably because of the consumption of the organics accumulated during the light phase. Using color filters or increasing the thickness of the sediment resulted in a reduction of the oxygen-induced inhibition. Molecular taxonomic analysis revealed that photosynthetic microorganisms including cyanobacteria and microalgae predominated in the water phase, adjacent to the cathode and on the surface of the sediment. In contrast, the sediments were dominated by heterotrophic bacteria, becoming less diverse with increasing depth. In addition, results from the air-cathode phototrophic MFC confirmed the light-induced current production while the test with the two-chamber MFC (in the dark) indicated the presence of electricigenic bacteria in the sediment.

Effect of oxidative stress on the growth of magnetic particles in Magnetospirillum magneticum

Individual magnetosome-containing magnetic mineral particles (MMP) from magnetotactic bacteria grow rapidly such that only a small fraction (5%) of all magnetosomes contain dwarf (< or =20 nm) MMP. Studies of the developmental stages in the growth of MMP are difficult due to the absence of techniques to separate dwarf from mature particles and because the former are sensitive to extraction procedures. Here, O2 stress was used to inhibit MMP expression in Magnetospirillum magneticum strain AMB-1. In addition, defined growth conditions not requiring chemical monitoring or manipulation of the gas composition during growth resulted in the production of cells containing high numbers of dwarf MMP. Cells exposed to different incubation treatments and cells with dwarf MMP were compared to cells with normal MMP with respect to growth, respiration, iron content, and relative magnetite load (RML). The cells were examined by electron microscopy, low temperature magnetometry, X-ray diffraction (XRD), and Mössbauer spectroscopy. In the 0-110 microM O2(aq) range, growth was positively correlated with [O2] and negatively correlated with RML. Most MMP formed during exponential growth of the cells. At 50-100 microM O2(aq) with stirring (150 rpm) and 30% O2 loss during incubation, MMP expression was strongly inhibited whereas MMP nucleation was not. Cells highly enriched (~95%) in dwarf MMP were obtained at the end of the exponential phase in stirred (150 rpm) cultures containing 45 microM O2(aq). Only one dwarf MMP formed in each MMP vesicle and the chain arrangement was largely preserved. O2-stress-induced dwarf MMP consisted of non-euhedral spheroids (~25 nm) that were similar in shape and size to immature MMP from normal cells. They consisted solely of magnetite, with a single domain signature, no superparamagnetic behavior, and magnetic signatures, Fe(II)/Fe(III) ratios, and XRD patterns very similar to those of mature MMP. These results show that O2 stress in liquid cultures amended with an inorganic redox buffer (S2O3 2-/S0) can be used to produce abundant dwarf MMP that are good proxies for studying MMP development.

Simultaneous interferometric measurement of corrosive or demineralizing bacteria and their mineral interfaces

Here, we report simultaneous surface profile measurements of several bacterial species involved in microbially influenced corrosion and their solid-surface interfaces by using vertical scanning interferometry. The capacity to nondestructively quantify microscale topographic changes beneath a single bacterium without its removal offers a unique opportunity to examine in vivo microbe-surface interactions.

Early detection of oxidized surfaces using Shewanella oneidensis MR-1 as a tool

Corrosion is a natural global problem of immense importance. Oxidation of iron and steel not only compromises the structural stability of a widely used and versatile material but it also creates an abrasive compound (iron oxide) that can score the surfaces of metals, rendering them useless for the purpose for which they were designed. Clearly, the identification of corrosion in its nascent stages is a high priority for reasons that range from aesthetics to economics. Many bacteria in the facultatively aerobic genus Shewanella have the capacity to respire some metal oxides, such as iron oxide, by way of a variety of oxide-binding proteins lodged in their outer membrane. In this study, a rapid, cost-effective system for the specific early detection of a variety of oxidized steel surfaces is described, taking advantage of bacteria with natural affinities for iron oxides, to identify the sites of nascent corrosion.

DNA perseverance of microorganisms exposed to silica: an experimental study

The persistence of DNA from microorganisms exposed to various concentrations of SiO2 (ranging from 0 to 3000 p.p.m.) was monitored over time. The impact of silica mineralization or silicification on the longevity of 16S rRNA and 16 s rDNA genes from whole cells of Bacillus subtilis and Escherichia coli K12 was quantified using real-time polymerase chain reaction (RT-PCR), and cells were visualized using optical microscopy. For B. subtilis, DNA longevity decreased in experiments with higher levels of SiO2 (1000 and 3000 p.p.m.), in comparison to zero or low (100 p.p.m.) levels. For B. subtilis, cell viability was greatest in the absence of silica, and markedly decreased in the presence of any concentration of silica. Survival of Escherichia coli cells, on the other hand, was not sensitive to silica in the solution. All cells died at similar rates over the 180 days they were monitored, decreasing to about 1% survival. DNA longevity for E. coli did appear to be enhanced to some degree by the presence of 1000 p.p.m. silica, but higher or lower concentrations showed no increased longevity in comparison to the no-silica control. Overall, findings of this study do not support the hypothesis that siliceous environments provide enhanced protection and preservation of DNA over time. However, results of this study do provide guidelines on the persistence of DNA that might be expected in modern silica-rich environments, which may be an important factor for proper characterization of present-day microbial communities.

Classification of organic and biological materials with deep ultraviolet excitation

We show that native fluorescence can be used to differentiate classes or groups of organic molecules and biological materials when excitation occurs at specific excitation wavelengths in the deep ultraviolet (UV) region. Native fluorescence excitation-emission maps (EEMs) of pure organic materials, microbiological samples, and environmental background materials were compared using excitation wavelengths between 200-400 nm with emission wavelengths from 270 to 500 nm. These samples included polycyclic aromatic hydrocarbons (PAHs), nitrogen- and sulfur-bearing organic heterocycles, bacterial spores, and bacterial vegetative whole cells (both Gram positive and Gram negative). Each sample was categorized into ten distinct groups based on fluorescence properties. Emission spectra at each of 40 excitation wavelengths were analyzed using principal component analysis (PCA). Optimum excitation wavelengths for differentiating groups were determined using two metrics. We show that deep UV excitation at 235 (+/-2) nm optimally separates all organic and biological groups within our dataset with >90% confidence. For the specific case of separation of bacterial spores from all other samples in the database, excitation at wavelengths less than 250 nm provides maximum separation with >6sigma confidence.

Towards environmental systems biology of Shewanella

Bacteria of the genus Shewanella are known for their versatile electron-accepting capacities, which allow them to couple the decomposition of organic matter to the reduction of the various terminal electron acceptors that they encounter in their stratified environments. Owing to their diverse metabolic capabilities, shewanellae are important for carbon cycling and have considerable potential for the remediation of contaminated environments and use in microbial fuel cells. Systems-level analysis of the model species Shewanella oneidensis MR-1 and other members of this genus has provided new insights into the signal-transduction proteins, regulators, and metabolic and respiratory subsystems that govern the remarkable versatility of the shewanellae.

In search of the microbe/mineral interface: quantitative analysis of bacteria on metal surfaces using vertical scanning interferometry

To understand the development of biofilms on metal surfaces, analysis of initial bacterial attachment to surfaces is crucial. Here we present the results of a study, using Shewanella oneidensis MR-1 as a model organism, in which vertical scanning interferometry (VSI) was used to investigate the initial stages of cell attachment to glass, steel and aluminium surfaces. It was found that while VSI gave unambiguous results with opaque surfaces, when reflective surfaces were used, an artifact sometimes appeared, with the bacteria appearing as rod-shaped pits rather than as cells on the surface. When the bacteria were altered to increase opacity, this artifact disappeared, and upon further investigation, it was found that the observational artifact was the result of a conflict between light reflected from the bacteria and the light reflected from the bacteria-metal interface. These results suggest that not only can bacteria be measured on surfaces using VSI, but with some modifications to the analytical software, there may be a unique window for studying the bacterial/substrate interface that can be used for quantitative observations. Imaging and characterization of the bacteria-substrate interface in vivo (previously invisible) will provide new insights into the interactions that occur at this important juncture.

The use of electrochemical impedance spectroscopy (EIS) in the evaluation of the electrochemical properties of a microbial fuel cell

Electrochemical impedance spectroscopy (EIS) has been used to determine several electrochemical properties of the anode and cathode of a mediator-less microbial fuel cell (MFC) under different operational conditions. These operational conditions included a system with and without the bacterial catalyst and EIS measurements at the open-circuit potential of the anode and the cathode or at an applied cell voltage. In all cases the impedance spectra followed a simple one-time-constant model (OTCM) in which the solution resistance is in series with a parallel combination of the polarization resistance and the electrode capacitance. Analysis of the impedance spectra showed that addition of Shewanella oneidensis MR-1 to a solution of buffer and lactate greatly increased the rate of the lactate oxidation at the anode under open-circuit conditions. The large decrease of open-circuit potential of the anode increased the cell voltage of the MFC and its power output. Measurements of impedance spectra for the MFC at different cell voltages resulted in determining the internal resistance (R(int)) of the MFC and it was found that R(int) is a function of cell voltage. Additionally, R(int) was equal to R(ext) at the cell voltage corresponding to maximum power, where R(ext) is the external resistance that must be applied across the circuit to obtain the maximum power output.

Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants

Shewanella oneidensis MR-1 is a gram-negative facultative anaerobe capable of utilizing a broad range of electron acceptors, including several solid substrates. S. oneidensis MR-1 can reduce Mn(IV) and Fe(III) oxides and can produce current in microbial fuel cells. The mechanisms that are employed by S. oneidensis MR-1 to execute these processes have not yet been fully elucidated. Several different S. oneidensis MR-1 deletion mutants were generated and tested for current production and metal oxide reduction. The results showed that a few key cytochromes play a role in all of the processes but that their degrees of participation in each process are very different. Overall, these data suggest a very complex picture of electron transfer to solid and soluble substrates by S. oneidensis MR-1.

Cellular and Subcellular Structure of Neoproterozoic Animal Embryos

Stereoblastic embryos from the Doushantuo Formation of China exhibit occasional asynchronous cell division, with diminishing blastomere volume as cleavage proceeded. Asynchronous cell division is common in modern embryos, implying that sophisticated mechanisms for differential cell division timing and embryonic cell lineage differentiation evolved before 551 million years ago. Subcellular structures akin to organelles, coated yolk granules, or lipid vesicles occur in these embryos. Paired reniform structures within embryo cells may represent fossil evidence of cells about to undergo division. Embryos exhibit no evidence of epithelial organization, even in embryos composed of approximately 1000 cells. Many of these features are compatible with metazoans, but the absence of epithelialization is consistent only with a stem-metazoan affinity for Doushantuo embryos.

Shewanella loihica sp. nov., isolated from iron-rich microbial mats in the Pacific Ocean

A novel marine bacterial strain, PV-4(T), isolated from a microbial mat located at a hydrothermal vent of Loihi Seamount in the Pacific Ocean, has been characterized. This micro-organism is orangey in colour, Gram-negative, polarly flagellated, facultatively anaerobic and psychrotolerant (temperature range, 0-42 degrees C). No growth was observed with nitrate, nitrite, DMSO or thiosulfate as the electron acceptor and lactate as the electron donor. The major fatty acid detected in strain PV-4(T) was iso-C(15 : 0). Strain PV-4(T) had ubiquinones consisting mainly of Q-7 and Q-8, and possessed menaquinone MK-7. The DNA G+C content of the strain was 53.8 mol% and the genome size was about 4.5 Mbp. Phylogenetic analyses based on 16S rRNA gene sequences placed PV-4(T) within the genus Shewanella. PV-4(T) exhibited 16S rRNA gene sequence similarity levels of 99.6 and 97.5 %, respectively, with respect to the type strains of Shewanella aquimarina and Shewanella marisflavi. DNA from strain PV-4(T) showed low mean levels of relatedness to the DNAs of S. aquimarina (50.5 %) and S. marisflavi (8.5 %). On the basis of phylogenetic and phenotypic characteristics, the bacterium was classified in the genus Shewanella within a distinct novel species, for which the name Shewanella loihica sp. nov. is proposed. The type strain is PV-4(T) (=ATCC BAA-1088(T)=DSM 17748(T)).

Comparative Genomics and Experimental Characterization of N-Acetylglucosamine Utilization Pathway of Shewanella oneidensis

We used a comparative genomics approach implemented in the SEED annotation environment to reconstruct the chitin and GlcNAc utilization subsystem and regulatory network in most proteobacteria, including 11 species of Shewanella with completely sequenced genomes. Comparative analysis of candidate regulatory sites allowed us to characterize three different GlcNAc-specific regulons, NagC, NagR, and NagQ, in various proteobacteria and to tentatively assign a number of novel genes with specific functional roles, in particular new GlcNAc-related transport systems, to this subsystem. Genes SO3506 and SO3507, originally annotated as hypothetical in Shewanella oneidensis MR-1, were suggested to encode novel variants of GlcN-6-P deaminase and GlcNAc kinase, respectively. Reconstitution of the GlcNAc catabolic pathway in vitro using these purified recombinant proteins and GlcNAc-6-P deacetylase (SO3505) validated the entire pathway. Kinetic characterization of GlcN-6-P deaminase demonstrated that it is the subject of allosteric activation by GlcNAc-6-P. Consistent with genomic data, all tested Shewanella strains except S. frigidimarina, which lacked representative genes for the GlcNAc metabolism, were capable of utilizing GlcNAc as the sole source of carbon and energy. This study expands the range of carbon substrates utilized by Shewanella spp., unambiguously identifies several genes involved in chitin metabolism, and describes a novel variant of the classical three-step biochemical conversion of GlcNAc to fructose 6-phosphate first described in Escherichia coli.

Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms

Shewanella oneidensis MR-1 produced electrically conductive pilus-like appendages called bacterial nanowires in direct response to electron-acceptor limitation. Mutants deficient in genes for c-type decaheme cytochromes MtrC and OmcA, and those that lacked a functional Type II secretion pathway displayed nanowires that were poorly conductive. These mutants were also deficient in their ability to reduce hydrous ferric oxide and in their ability to generate current in a microbial fuel cell. Nanowires produced by the oxygenic phototrophic cyanobacterium Synechocystis PCC6803 and the thermophilic, fermentative bacterium Pelotomaculum thermopropionicum reveal that electrically conductive appendages are not exclusive to dissimilatory metal-reducing bacteria and may, in fact, represent a common bacterial strategy for efficient electron transfer and energy distribution.