[Show abstract][Hide abstract] ABSTRACT: Yellowstone Lake (Yellowstone National Park, WY, USA) is a large high-altitude (2200 m), fresh-water lake, which straddles an extensive caldera and is the center of significant geothermal activity. The primary goal of this interdisciplinary study was to evaluate the microbial populations inhabiting thermal vent communities in Yellowstone Lake using 16S rRNA gene and random metagenome sequencing, and to determine how geochemical attributes of vent waters influence the distribution of specific microorganisms and their metabolic potential. Thermal vent waters and associated microbial biomass were sampled during two field seasons (2007-2008) using a remotely operated vehicle (ROV). Sublacustrine thermal vent waters (circa 50-90°C) contained elevated concentrations of numerous constituents associated with geothermal activity including dissolved hydrogen, sulfide, methane and carbon dioxide. Microorganisms associated with sulfur-rich filamentous "streamer" communities of Inflated Plain and West Thumb (pH range 5-6) were dominated by bacteria from the Aquificales, but also contained thermophilic archaea from the Crenarchaeota and Euryarchaeota. Novel groups of methanogens and members of the Korarchaeota were observed in vents from West Thumb and Elliot's Crater (pH 5-6). Conversely, metagenome sequence from Mary Bay vent sediments did not yield large assemblies, and contained diverse thermophilic and nonthermophilic bacterial relatives. Analysis of functional genes associated with the major vent populations indicated a direct linkage to high concentrations of carbon dioxide, reduced sulfur (sulfide and/or elemental S), hydrogen and methane in the deep thermal ecosystems. Our observations show that sublacustrine thermal vents in Yellowstone Lake support novel thermophilic communities, which contain microorganisms with functional attributes not found to date in terrestrial geothermal systems of YNP.
Full-text · Article · Oct 2015 · Frontiers in Microbiology
[Show abstract][Hide abstract] ABSTRACT: Bacterial nanowires offer an extracellular electron transport (EET) pathway for linking the respiratory chain of bacteria to external surfaces, including oxidized metals in the environment and engineered electrodes in renewable energy devices. Despite the global, environmental, and technological consequences of this biotic-abiotic interaction, the composition, physiological relevance, and electron transport mechanisms of bacterial nanowires remain unclear. We report, to our knowledge, the first in vivo observations of the formation and respiratory impact of nanowires in the model metal-reducing microbe Shewanella oneidensis MR-1. Live fluorescence measurements, immunolabeling, and quantitative gene expression analysis point to S. oneidensis MR-1 nanowires as extensions of the outer membrane and periplasm that include the multiheme cytochromes responsible for EET, rather than pilin-based structures as previously thought. These membrane extensions are associated with outer membrane vesicles, structures ubiquitous in Gram-negative bacteria, and are consistent with bacterial nanowires that mediate long-range EET by the previously proposed multistep redox hopping mechanism. Redox-functionalized membrane and vesicular extensions may represent a general microbial strategy for electron transport and energy distribution.
Preview · Article · Aug 2014 · Proceedings of the National Academy of Sciences
[Show abstract][Hide abstract] ABSTRACT: Microbial extracellular electron transfer (EET) to solid surfaces is an important reaction for metal reduction occurring in various anoxic environments. However, it is challenging to accurately characterize EET-active microbial communities and each member's contribution to EET reactions because of changes in composition and concentrations of electron donors and solid-phase acceptors. Here, we used bioelectrochemical systems to systematically evaluate the synergistic effects of carbon source and surface redox potential on EET-active microbial community development, metabolic networks and overall electron transfer rates. The results indicate that faster biocatalytic rates were observed under electropositive electrode surface potential conditions, and under fatty acid-fed conditions. Temporal 16S rRNA-based microbial community analyses showed that Geobacter phylotypes were highly diverse and apparently dependent on surface potentials. The well-known electrogenic microbes affiliated with the Geobacter metallireducens clade were associated with lower surface potentials and less current generation, whereas Geobacter subsurface clades 1 and 2 were associated with higher surface potentials and greater current generation. An association was also observed between specific fermentative phylotypes and Geobacter phylotypes at specific surface potentials. When sugars were present, Tolumonas and Aeromonas phylotypes were preferentially associated with lower surface potentials, whereas Lactococcus phylotypes were found to be closely associated with Geobacter subsurface clades 1 and 2 phylotypes under higher surface potential conditions. Collectively, these results suggest that surface potentials provide a strong selective pressure, at the species and strain level, for both solid surface respirators and fermentative microbes throughout the EET-active community development.The ISME Journal advance online publication, 19 December 2013; doi:10.1038/ismej.2013.217.
[Show abstract][Hide abstract] ABSTRACT: Cathode reaction is one of the most serious limiting factors in a microbial fuel cell (MFC). The critical dissolved oxygen (DO) concentration of platinum loaded graphite electrode was reported as 2.2 mg/1 that is about 10-fold higher than an aerobic bacteria. A series of MFCs were run with cathode compartment inoculated with activated sludge (biotic), and not (abiotic) on the platinum loaded or bare graphite electrodes. At the beginning of the operation, current values from MFCs with bio-cathode and abiotic-cathode were 2.3±0.1 and 2.6±0.2 mA, respectively at air saturated water supply in the cathode. The current from MFCs with abiotic cathode didn't change, but that of MFCs with biotic cathode increased to 3.0 mA after 8 weeks. The Coulomb efficiency was 59.6% in the MFCs with biotic cathode that was much higher than the values was 15.6% of abiotic cathode. When the DO supply was reduced, the current from MFCs with abiotic cathode decreased more sharply than those with biotic cathode. When azide as using the respiratory inhibitor was added to the catholyte the current decreased in MFCs with biotic cathode, but didn't change in MFCs with abiotic cathode. The power density was higher in the MFCs with biotic cathode (430 W/m(3) cathode compartment) than the abiotic-cathode MFC (257 W/m(3) cathode compartment). Electron microscopic observation revealed nanowire structures both in biofilm developed on the anode and on the bio- cathode. These results show that electron consuming bacterial consortium can be used as a cathode catalyst to improve cathode reaction.
Full-text · Article · Nov 2013 · Journal of Microbiology and Biotechnology
[Show abstract][Hide abstract] ABSTRACT: The study of electrical transport in biomolecular materials is critical to our fundamental understanding of physiology and to the development of practical bioelectronics applications. In this study, we investigated the electronic transport characteristics of Shewanella oneidensis MR-1 nanowires by conducting-probe atomic force microscopy (CP-AFM) and by constructing field-effect transistors (FETs) based on individual Shewanella nanowires. Here we show that Shewanella nanowires exhibit p-type, tunable electronic behaviour with a field-effect mobility on the order of 10(-1) cm(2)/Vs, comparable to devices based on synthetic organic semiconductors. This study opens up opportunities to use such bacterial nanowires as a new semiconducting biomaterial for making bioelectronics, and to enhance the power output of microbial fuel cells through engineering the interfaces between metallic electrodes and bacterial nanowires.
[Show abstract][Hide abstract] ABSTRACT: Microorganisms play key roles in biogeochemical and nutrient cycling in all ecosystems on Earth, yet little is known about the processes controlling their biogeographic distributions. Here we report an investigation of magnetotactic bacteria (MTB) designed to evaluate the roles of niche-based process and spatial process in explaining variation in bacterial communities across large spatial scales. Our results show that both environmental heterogeneity and geographic distance play significant roles in shaping dominant populations of MTB community composition. At the spatial scale in this study, the biogeography of MTB is relatively more influenced by environmental factors than geographic distance, suggesting that local conditions override the effects of dispersal history on structuring MTB community. Of note, we found that the strength of geomagnetic field may influence the biogeography of MTB. We argue that MTB have the potential to serve as a model group to uncover the underlying processes that influence microbial biogeography.
[Show abstract][Hide abstract] ABSTRACT: Objective:
Bacterial biofilms play a role in the pathogenesis of bisphosphonate-related osteonecrosis of the jaw (BRONJ). The purpose of this preliminary study was to test the hypothesis that the extracellular filaments observed in biofilms associated with BRONJ contain electrically conductive nanowires.
Bone samples of patients affected by BRONJ were evaluated for conductive nanowires by scanning electron microscopy (SEM) and conductive probe atomic force microscopy (CP-AFM). We created nanofabricated electrodes to measure electrical transport along putative nanowires.
SEM revealed large-scale multispecies biofilms containing numerous filamentous structures throughout necrotic bone. CP-AFM analysis revealed that these structures were electrically conductive nanowires with resistivities on the order of 20 Ω·cm. Nanofabricated electrodes spaced along the nanowires confirmed their ability to transfer electrons over micron-scale lengths.
Electrically conductive bacterial nanowires to date have been described only in environmental isolates. This study shows for the first time that these nanowires can also be found in clinically relevant biofilm-mediated diseases, such as BRONJ, and may represent an important target for therapy.
[Show abstract][Hide abstract] ABSTRACT: Oxygen consumption in marine sediments is often coupled to the oxidation of sulphide generated by degradation of organic matter in deeper, oxygen-free layers. Geochemical observations have shown that this coupling can be mediated by electric currents carried by unidentified electron transporters across centimetre-wide zones. Here we present evidence that the native conductors are long, filamentous bacteria. They abounded in sediment zones with electric currents and along their length they contained strings with distinct properties in accordance with a function as electron transporters. Living, electrical cables add a new dimension to the understanding of interactions in nature and may find use in technology development.
[Show abstract][Hide abstract] ABSTRACT: Mediated electron transfer has been implicated as a primary mechanism of extracellular electron transfer to insoluble electron acceptors in anaerobic cultures of the facultative anaerobe Shewanella oneidensis. In this work, planktonic and biofilm cultures of S. oneidensis exposed to carbon-limited environments trigger an electrochemical response thought to be the signature of an electrochemically active metabolite. This metabolite was detected via cyclic voltammetry for S. oneidensis MR-1 biofilms. The observed electrochemical potentials correspond to redox potentials of flavin-containing molecules. Chromatographic techniques were then used to quantify concentrations of riboflavin by the carbon-limited environmental response of planktonic S. oneidensis. Further evidence of flavin redox chemistry was associated with biofilm formation on multi-walled carbon nanotube-modified Toray paper under carbon-starved environments. By encapsulating one such electrode in silica, the encapsulated biofilm exhibits riboflavin redox activity earlier than a non-encapsulated system after media replacement. This work explores the electrochemical nature of riboflavin interaction with an electrode after secretion from S. oneidensis and in comparison to abiotic systems.
[Show abstract][Hide abstract] ABSTRACT: Microbial fuel cells (MFCs) are devices that exploit microorganisms as biocatalysts to recover energy from organic matter in the form of electricity. One of the goals of MFC research is to develop the technology for cost-effective wastewater treatment. However, before practical MFC applications are implemented it is important to gain fundamental knowledge about long-term system performance, reproducibility, and the formation and maintenance of functionally-stable microbial communities. Here we report findings from a MFC operated for over 300 days using only primary clarifier effluent collected from a municipal wastewater treatment plant as the microbial resource and substrate. The system was operated in a repeat-batch mode, where the reactor solution was replaced once every two weeks with new primary effluent that consisted of different microbial and chemical compositions with every batch exchange. The turbidity of the primary clarifier effluent solution notably decreased, and 97% of biological oxygen demand (BOD) was removed after an 8-13 day residence time for each batch cycle. On average, the limiting current density was 1000 mA/m(2), the maximum power density was 13 mW/m(2), and coulombic efficiency was 25%. Interestingly, the electrochemical performance and BOD removal rates were very reproducible throughout MFC operation regardless of the sample variability associated with each wastewater exchange. While MFC performance was very reproducible, the phylogenetic analyses of anode-associated electricity-generating biofilms showed that the microbial populations temporally fluctuated and maintained a high biodiversity throughout the year-long experiment. These results suggest that MFC communities are both self-selecting and self-optimizing, thereby able to develop and maintain functional stability regardless of fluctuations in carbon source(s) and regular introduction of microbial competitors. These results contribute significantly toward the practical application of MFC systems for long-term wastewater treatment as well as demonstrating MFC technology as a useful device to enrich for functionally stable microbial populations.
[Show abstract][Hide abstract] ABSTRACT: Electrochemical gradients established in redox transition zones, such as
those that form at sediment-water interfaces or within the near
subsurface, are active sites of microbial activity. Many of the
processes catalyzed by microorganisms, including sulfate and iron
reduction, transform minerals either by direct enzymatic redox reactions
or by indirect chemical reactions involving metabolic byproducts, such
as Fe(II) or sulfide. Recent results suggest that electrically
conductive protein filaments called bacterial nanowires may contribute
to electron transfer within these transition zones at rates that far
exceed diffusion. We have developed a series of correlated microscopic,
spectroscopic and microsensor techniques to investigate coupled
'electrobiogeochemical' processes within redox transition zones. The
approaches are designed to spatially resolve the distribution of
microbes, biogenic minerals, dissolved aqueous chemistry, and conductive
nanowires that contribute to electrobiogeochemical processes that form
across these electrochemical gradients. Results gleaned from this
research are expected to provide a better understanding of the
fundamental mechanisms that contribute to a variety of biogeophysical
phenomena, many of which can be detected remotely.
[Show abstract][Hide abstract] ABSTRACT: It was recently discovered that Shewanella oneidensis MR-1, a dissimilatory metal-reducing bacterium, can grow electrically conductive extracellular appendages. Such bacterial nanowires, as they are termed, function as electron-transfer conduits to far-field electron acceptors or among neighbouring cells. A recent advance in the field was the characterization of bacterial nanowires' resistivity along their length, which is on the order of 1 Ω cm. This finding has motivated the exploration of their potential use in biofuel cells, bionanoelectronics and other bionanodevices. Along with conductivity measurements, it is also important to characterize the nature of these nanowires and their mechanical properties. In this work, we have confirmed the nature of these nanowires is protein. In addition, we have investigated the elasticity of bacterial nanowires using two independent atomic force microscopy techniques: (i) real-time elastic modulus mapping by AFM HarmoniX using T-shaped cantilevers with an offset tip and (ii) conventional AFM nanoindentation by force–distance curve fitting based on Hertz model. Results from both techniques demonstrated that the Young's modulus of bacterial nanowires is on the order of 1 GPa. This work inspires us with new applications of bacterial nanowires: with electrical conductivity comparable to that of moderately doped inorganic semiconductors and elasticity similar to polymeric materials, bacterial nanowires can function as electron-transfer conduits for biofuel cells and building blocks for bionanoelectronics and flexible nanoelectronics.
[Show abstract][Hide abstract] ABSTRACT: The Yellowstone geothermal complex has yielded foundational discoveries that have significantly enhanced our understanding of the Archaea. This study continues on this theme, examining Yellowstone Lake and its lake floor hydrothermal vents. Significant Archaea novelty and diversity were found associated with two near-surface photic zone environments and two vents that varied in their depth, temperature and geochemical profile. Phylogenetic diversity was assessed using 454-FLX sequencing (~51,000 pyrosequencing reads; V1 and V2 regions) and Sanger sequencing of 200 near-full-length polymerase chain reaction (PCR) clones. Automated classifiers (Ribosomal Database Project (RDP) and Greengenes) were problematic for the 454-FLX reads (wrong domain or phylum), although BLAST analysis of the 454-FLX reads against the phylogenetically placed full-length Sanger sequenced PCR clones proved reliable. Most of the archaeal diversity was associated with vents, and as expected there were differences between the vents and the near-surface photic zone samples. Thaumarchaeota dominated all samples: vent-associated organisms corresponded to the largely uncharacterized Marine Group I, and in surface waters, ~69-84% of the 454-FLX reads matched archaeal clones representing organisms that are Nitrosopumilus maritimus-like (96-97% identity). Importance of the lake nitrogen cycling was also suggested by >5% of the alkaline vent phylotypes being closely related to the nitrifier Candidatus Nitrosocaldus yellowstonii. The Euryarchaeota were primarily related to the uncharacterized environmental clones that make up the Deep Sea Euryarchaeal Group or Deep Sea Hydrothermal Vent Group-6. The phylogenetic parallels of Yellowstone Lake archaea to marine microorganisms provide opportunities to examine interesting evolutionary tracks between freshwater and marine lineages.
[Show abstract][Hide abstract] ABSTRACT: Yellowstone Lake is central to the balanced functioning of the Yellowstone ecosystem, yet little is known about the microbial component of its food chain. A remotely operated vehicle provided video documentation (http://www.tbi.montana.edu/media/videos/) and allowed sampling of dilute surface zone waters and enriched lake floor hydrothermal vent fluids. Vent emissions contained substantial H(2)S, CH(4), CO(2) and H(2), although CH(4) and H(2) levels were also significant throughout the lake. Pyrosequencing and near full-length sequencing of Bacteria 16S rRNA gene diversity associated with two vents and two surface water environments demonstrated that this lake contains significant bacterial diversity. Biomass was size-fractionated by sequentially filtering through 20-µm-, 3.0-µm-, 0.8-µm- and 0.1-µm-pore-size filters, with the >0.1 to <0.8 µm size class being the focus of this study. Major phyla included Acidobacteria, Actinobacteria, Bacteroidetes, α- and β-Proteobacteria and Cyanobacteria, with 21 other phyla represented at varying levels. Surface waters were dominated by two phylotypes: the Actinobacteria freshwater acI group and an α-Proteobacteria clade tightly linked with freshwater SAR11-like organisms. We also obtained evidence of novel thermophiles and recovered Prochlorococcus phylotypes (97-100% identity) in one near surface photic zone region of the lake. The combined geochemical and microbial analyses suggest that the foundation of this lake's food chain is not simple. Phototrophy presumably is an important driver of primary productivity in photic zone waters; however, chemosynthetic hydrogenotrophy and methanotrophy are likely important components of the lake's food chain.
Full-text · Article · Mar 2011 · Environmental Microbiology
[Show abstract][Hide abstract] ABSTRACT: Yellowstone Lake (Yellowstone National Park, WY, USA) is a large, high-altitude, fresh-water lake that straddles the most recent Yellowstone caldera, and is situated on top of significant hydrothermal activity. An interdisciplinary study is underway to evaluate the geochemical and geomicrobiological characteristics of several hydrothermal vent environments sampled using a remotely operated vehicle, and to determine the degree to which these vents may influence the biology of this young freshwater ecosystem. Approximately six different vent systems (locations) were sampled during 2007 and 2008, and included water obtained directly from the hydrothermal vents as well as biomass and sediment associated with these high-temperature environments. Thorough geochemical analysis of these hydrothermal environments reveals variation in pH, sulfide, hydrogen and other potential electron donors that may drive primary productivity. The concentrations of dissolved hydrogen and sulfide were extremely high in numerous vents sampled, especially the deeper (30-50 m) vents located in the Inflated Plain, West Thumb, and Mary Bay. Significant dilution of hydrothermal fluids occurs due to mixing with surrounding lake water. Despite this, the temperatures observed in many of these hydrothermal vents range from 50-90 C, and elevated concentrations of constituents typically associated with geothermal activity in Yellowstone are observed in waters sampled directly from vent discharge. Microorganisms associated with elemental sulfur mats and filamentous `streamer' communities of Inflated Plain and West Thumb (pH range 5-6) were dominated by members of the deeply-rooted bacterial Order Aquificales, but also contain thermophilic members of the domain Archaea. Assembly of metagenome sequence from the Inflated Plain vent biomass and to a lesser extent, West Thumb vent biomass reveal the importance of Sulfurihydrogenibium-like organisms, also important in numerous terrestrial geothermal outflow channels of YNP. Analysis of functional genes present in the consensus metagenome sequence representing these populations indicate metabolic potential for oxidation of reduced sulfur and hydrogen, both of which are present at high concentrations in these vent ecosystems. Metagenome sequence of biomass associated with sediments from hydrothermal vents at Mary Bay (50 m depth) suggest greater archaeal and bacterial diversity in this environment, which may be due to higher concentrations of hydrogen, iron, and manganese measured in these environments. Results from metagenome sequence and modest 16S rRNA gene surveys from hydrothermal vent biomass indicate that several groups of novel thermophilic archaea inhabit these sites, and in many cases, are represented by organisms not found in YNP terrestrial geothermal environments that have been characterized to date. The hydrothermal vents from Inflated Plain and West Thumb indicate a linkage between various geochemical attributes (sulfide, hydrogen) and the metabolic potential associated with dominant Aquificales populations present in these communities.
[Show abstract][Hide abstract] ABSTRACT: The spectral induced polarization (SIP) technique is a promising biogeophysical technique for sensing microbially-induced changes in the petrophysical properties of porous media. Recent studies by Schmutz et al. for samples freshly contaminated with oil show a well defined relaxation peak in the 0.001-0.1 Hz frequency rangewith the magnitude of the phase and resistivity increasing with increase in the relative saturation of the oil. In this study, we extend work of Abdel Aal et al. by acquiring SIP measurements in the frequency range between 0.001 and 1000 Hz on sediment cores retrieved from a hydrocarbon contaminated site where intrinsic bioremediation is occurring. Our results show the following: (1) in general for both the saturated and unsaturated zone samples, the real and imaginary conductivity for samples from within the plume are higher than those for background samples; (2) the imaginary conductivity results show a well defined peak in the frequency range between 0.001 - 0.01 Hz for contaminated samples with the magnitude higher for samples from the smear zone (contaminated with residual-phase hydrocarbon), exceeding values obtained for samples contaminated with dissolved-phase hydrocarbons; (3) a secondary peak not observed in uncontaminated samples is also observed around 100 Hz for the contaminated samples. Our results are consistent with the Abel Aal et al. study suggesting that biodegradation increases the magnitude of the imaginary conductivity response. The peak at the lower frequency may be due to the polarization of the Stern layer as suggested by Schmutz et al. Our laboratory SIP measurements from core samples are consistent with downhole time domain induced polarization measurements that also how that the contaminated borehole is more chargeable than the background borehole.
[Show abstract][Hide abstract] ABSTRACT: Recent biogeophysical research suggests that microbial processes and resulting redox conditions at mature, hydrocarbon-contaminated sites undergoing biodegradation generate distinct electrical geophysical signatures. Improved understanding of these geophysical signatures could permit the development of geophysical imaging technologies for long-term, minimally invasive, and sustainable monitoring of natural biodegradation at such sites. The National Crude Oil Spill Fate and Natural Attenuation Research Site, Bemidji, Minnesota, is a unique field laboratory for investigating the geophysical signatures of a mature oil-spill where natural attenuation is well documented at the field-scale. Our attention focused on identifying two proposed source mechanisms for generating biogeophysical signatures: (1) self potential (SP) signals due to current sources (geobatteries) generated at the sharp redox front presented by the water table if/when long-range electron transport between reduced and oxidized zones occurs; and (2) complex resistivity (CR) signals due to enhanced electrochemical storage of charge accompanying microbial growth and biofilm development. We performed SP, CR, and time-domain induced polarization (IP) measurements from the surface, down boreholes, and in the laboratory on cores extracted from the site. Two-dimensional (2D) CR imaging was performed on a transect that intercepted a pool of oil where free product at the water table is ~0.4 m thick (South Pool). Surface SP profiles and 2D IP imaging were conducted on multiple transects, including lines that intercepted the most extensive pool (North Pool) where free product is up to 1 m thick. Self-potential and IP measurements were recorded down a borehole drilled in the North Pool where free product is thickest as well as down a near-identical well at a known uncontaminated site. Surface SP measurements at the North Pool were excessively contaminated by AC power lines that service the facility. However SP measurements at the South Pool, and down boreholes in the North Pool did not exhibit the large (+100 mV) anomalies indicative of a geobattery source current mechanism. It is instead likely that the ~20 mV anomalies observed at this site are driven by electro-diffusion potentials associated with the gradients in the chemical potential of the charge carriers, locally enhanced by reducing conditions driven by biodegradation. Preliminary analysis of the CR measurements conducted on cores extracted from the boreholes show evidence of low frequency polarization enhancement associated with the zone of contamination and the smear zone around the water table.