Use of SWATH mass spectrometry for quantitative proteomic investigation of Shewanella oneidensis MR-1 biofilms grown on graphite cloth electrodes

Quantitative proteomics from low biomass, biofilm samples is not well documented. In this study we show successful use of SWATH-MS for quantitative proteomic analysis of a microbial electrochemically active biofilm. Shewanella oneidensis MR-1 was grown on carbon cloth electrodes under continuous anodic electrochemical polarizations in a bioelectrochemical system (BES). Using lactate as the electron donor, anodes serving as terminal microbial electron acceptors were operated at three different electrode potentials (+0.71 V, +0.21 V & -0.19V vs. SHE) and the development of catalytic activity was monitored by measuring the current traces over time. Once maximum current was reached (usually within 21-29 h) the electrochemical systems were shut off and biofilm proteins were extracted from the electrodes for proteomic assessment. SWATH-MS analysis identified 704 proteins, and quantitative comparison was made of those associated with tricarboxcylic acid (TCA) cycle. Metabolic differences detected between the biofilms suggested a branching of the S. oneidensis TCA cycle when grown at the different electrode potentials. In addition, the higher abundance of enzymes involved in the TCA cycle at higher potential indicates an increase in metabolic activity, which is expected given the assumed higher energy gains. This study demonstrates high numbers of identifications on BES biofilm samples can be achieved in comparison to what is currently reported. This is most likely due to the minimal preparation steps required for SWATH-MS. (C) 2014 Elsevier GmbH. All rights reserved

Evaluating the potential impact of proton carriers on syntrophic propionate oxidation

Anaerobic propionic acid degradation relies on interspecies electron transfer (IET) between propionate oxidisers and electron acceptor microorganisms, via either molecular hydrogen, formate or direct transfers. We evaluated the possibility of stimulating direct IET, hence enhancing propionate oxidation, by increasing availability of proton carriers to decrease solution resistance and reduce pH gradients. Phosphate was used as a proton carrying anion, and chloride as control ion together with potassium as counter ion. Propionic acid consumption in anaerobic granules was assessed in a square factorial design with ratios (1:0, 2:1, 1:1, 1:2 and 0:1) of total phosphate (TP) to Cl-, at 1X, 10X, and 30X native conductivity (1.5 mS.cm(-1)). Maximum specific uptake rate, half saturation, and time delay were estimated using model-based analysis. Community profiles were analysed by fluorescent in situ hybridisation and 16S rRNA gene pyrosequencing. The strongest performance was at balanced (1:1) ratios at 10X conductivity where presumptive propionate oxidisers namely Syntrophobacter and Candidatus Cloacamonas were more abundant. There was a shift from Methanobacteriales at high phosphate, to Methanosaeta at low TP:Cl ratios and low conductivity. A lack of response to TP, and low percentage of presumptive electroactive organisms suggested that DIET was not favoured under the current experimental conditions

Biomimetic Peptide Nanowires Designed for Conductivity

The filamentous peptide-based nanowires produced by some dissimilatory metal-reducing bacteria, such as Geobacter sulfurreducens, display excellent natural conductivity. Their mechanism of conduction is assumed to be a combination of delocalized electrons through closely aligned aromatic amino acids and hopping/charge transfer. The proteins that form these microbial nanowires are structured from a coiled-coil, for which the design rules have been reported in the literature. Furthermore, at least one biomimetic system using related synthetic peptides has shown that the incorporation of aromatic residues can be used to enhance conductivity of peptide fibers. Herein, the de novo design of peptide sequences is used to enhance the conductivity of peptide gels, as inspired by microbial nanowires. A critical factor hampering investigations in both microbiology and materials development is inconsistent reporting of biomaterial conductivity measurements, with consistent methodologies needed for such investigations. We have reported a method herein to analyze non-Ohmic behavior using existing parameters, which is a statistically insightful approach for detecting small changes in biologically based samples. Aromatic residues were found to contribute to peptide gel conductivity, with the importance of the peptide confirmation and fibril assembly demonstrated both experimentally and computationally. This is a small step (in combination with parallel research under way by other researchers) toward developing effective peptide-based conducting nanowires, opening the door to the use of electronics in water and physiological environments for bioelectronic and bioenergy applications

Nitrogen Removal in Bioelectrochemical Systems

Bioelectrochemical systems couple the oxidation of an electron donor at the anode with the reduction of an electron acceptor at the cathode, using microorganisms to catalyse one or both reactions. When the overall reaction is exergonic, a power output is generated and the system is referred to as microbial fuel cell (MFC); when power is added to the system and hydrogen is produced at the cathode through electrolysis of water, the system is referred to as microbial electrolysis cell (MEC). This PhD thesis is principally focused on the microbial fuel cells technology. Microbial fuel cells are regarded as a sustainable technology for electric energy generation from the oxidation of organic substrates contained in wastewater. The rising need for renewable energy sources and sanitation has encouraged intense research in this novel technology. Nevertheless, up untill now the interest has been primarily focused on the anodic oxidation of organic matter contained in wastewater. However, in addition to organics, wastewater also contains other pollutants, such as soluble nitrogen compounds, for which specific treatment is required. In conventional wastewater treatment systems, the organics available in the wastewater are typically used as electron donor during denitrification. However, a considerable fraction (>50%) of the chemical oxygen demand (COD) is still oxidized aerobically due to the large recirculation flows from the nitrification to the denitrification stages required in anoxic/aerobic configurations to allow for low nitrate levels in the final effluent. This increased COD demand is normally fulfilled by supplementary COD addition, with consequent increase of treatment costs. Alternatively, microorganisms can use inorganic carbon substrates and inorganic electron donors such as hydrogen for denitrification. However, the use of compressed hydrogen is hampered by its low solubility. As a solution, electrochemical hydrogen production permits in situ delivery of the electron donor and is advantaged by simplified control and dissolution of H2. The energy requirements to provide reducing power for denitrification can be decreased if bacteria use the electrode directly as electron donor without intermediate hydrogen production in bioelectrochemical systems. However, fundamental knowledge on bioelectrochemical denitrification is still lacking, therefore, this PhD thesis aims to fill some of these knowledge gaps and to solve some of the bottlenecks of the use of biocathodes. In particular, the goals of this work are: (i) to produce a suitable microbial community able to use the cathode as the sole electron donor during denitrification; (ii) to engineer a bioelectrochemical system able to couple the cathodic denitrification with the oxidation of organics at the anode; (iii) to characterize and quantify the electron losses during anodic and cathodic processes; (iv) to develop a bioelectrochemical system that maximises the nitrogen removal by integrating the nitrification stage into the cathode; finally, (v) to provide an insight into the structural properties of the biofilm performing nitrogen removal at the cathode. The results reveal that microbes can effectively utilize the electrode as electron donor for nitrate reduction to gaseous nitrogen at a redox potential that excludes intermediate production of hydrogen. Measurements revealed that acetoclastic methanogenesis and bacterial growth were responsible for causing the major electron losses at the anode. Adjusting the anodic potential did not achieve a significant overall reduction of the electron losses. At the cathode, the charge transfer efficiencies were instead very high, with the losses only due to the generation of nitrous oxide. Moreover, adjustments of the cathode potential resulted in higher efficiency. High carbon and nitrogen removal was obtained with a COD demand for denitrification as low as 2.4 g per g nitrogen denitrified, which is much lower than typically observed in heterotrophic–based nitrogen removal technologies (>7 g g 1). Nitrogen was removed at rates up to 0.256 kg N m-3 d-1, which is comparable to other autotrophic denitrification processes. Simultaneous nitrification and denitrification was observed in a combined system with cathodic aeration, at bulk dissolved oxygen (DO) levels up to 5 mg L-1, which is considerably higher than normally considered feasible for the process. Confocal laser scanning microscope analysis revealed the existence of a structured biofilm where putative nitrifying organisms occupied the outer layers in contact with the aerated bulk liquid, and putative denitrifying organisms occupy the layers closer to the electrode. These findings are significant in the field of bioelectrochemical systems as they help to unravel some of the complex questions relating to biocathodes. Additionally, the system provides an attractive option to achieve a very high level of nitrogen removal from wastewater with low COD/N ratios due to the selective utilisation of the COD for the denitrification reaction via the electrical transfer of reducing equivalents from the anode to the cathode. However, this research creates new questions, particularly regarding the mechanisms of electron transfer at the cathode. Also a number of practical design and optimisation challenges need to be overcome before wider applications can be considered

The nanostructure of microbially-reduced graphene oxide fosters thick and highly-performing electrochemically-active biofilms

Biofilms of electrochemically-active organisms are used in microbial electrochemical technologies (METs) to catalyze bioreactions otherwise not possible at bare electrodes. At present, however, achievable current outputs are still below levels considered sufficient for economic viability of large-scale METs implementations. Here, we report three-dimensional, self-aggregating biofilm composites comprising of microbial cells embedded with microbially-reduced graphene oxide (rGO) nanoparticles to form a thick macro-porous network with superior electrochemical properties. In the presence of metabolic substrate, these hybrid biofilms are capable of producing up to five times more catalytic current than the control biofilms. Cyclic voltammetry, linear sweep voltammetry, and electrochemical impedance spectroscopy, show that in spite of the increased thickness, the biofilms amended with GO display lower polarization/charge transfer resistance compared to the controls, which we ascribe to the incorporation of rGO into the biofilms, which (1) promotes fast electron transfer, yet conserving a macroporous structure that allows free diffusion of reactants and products, and (2) enhances the interfacial dynamics by allowing a higher load of microbial cells per electrode surface area. These results suggest an easy-to-apply and cost-effective method to produce high-performing electrochemically-active biofilms in situ

Biofuels

Increasing pressure to move towards energy sustainability and reduce society's dependence on fossil fuels has led to much research and development in the area of biofuels. First-generation biofuel production (e.g., ethanol from corn) is a mature technology, but competition with food crops raises questions about sustainability. Second-generation biofuels are produced from waste biomass and thus are perceived as more viable, but technology is not ready for large-scale implementation particularly due to the hydrolysis challenge. The third generation of biofuels captures sunlight directly as fuels or fuel precursors via photosynthesis. Prokaryotic organisms play a crucial role in the majority of the processes involved in biofuel production. Pure culture bioproduction includes ethanol from Zymomonas mobilis, modified Escherichia coli, and Clostridia. However, pure cultures are only efficient at the conversion of sugary biomass, not lignocellulosic biomass. They have thus limited applicability towards second-generation biofuel production. Pure culture prokaryotic biodiesel production is also being investigated (mostly using cyanobacteria). However, similarly to eukaryotic biodiesel production, energy efficiencies are still poor. Mixed culture production is thus far the most successful process at converting complex waste biomass to usable fuels, mainly methane through anaerobic digestion, which is perceived by many as the biofuel technology with highest potential