Diffusion in inhomogeneous fluids: Hard spheres to polymer coatings.

We investigate diffusion in fluids near surfaces that may be coated with polymer films. We first consider diffusion in hard sphere fluids near a planar hard wall. We specifically consider color diffusion, where hard spheres are labeled A or B but are otherwise identical in all respects. In this inhomogeneous fluid, we consider a surface reaction-diffusion problem. At the left wall, a particle of species A is converted to one of species B upon a wall collision. At the opposing wall, the reverse reaction takes place: B → A. Using molecular dynamics simulation, we study the steady state of this system. We demonstrate that in the homogeneous region, a diffusing particle is subject to an equilibrium oscillatory force, the solvation force, that arises from the interfacial structuring of the fluid at the wall. For the hard sphere/hard wall system, the solvation force can be determined in various ways. We use the solvation force [the potential of mean force (PMF)] to solve the continuum diffusion equation. This provides an adequate and accurate description of the reaction-diffusion problem. The analysis is then extended to consider both color diffusion in the presence of a slowly varying one-body field such as gravity and a more applied problem of diffusion of free species through a surface film consisting of tethered chains. In both cases, the PMF experienced by the free particles is affected, but the diffusion problem can be treated in the same way as for the simpler hard sphere color diffusion case.

Metagenomic and Metatranscriptomic Characterization of a Microbial Community That Catalyzes Both Energy-Generating and Energy-Storing Electrode Reactions.

Electroactive bacteria are living catalysts, mediating energy-generating reactions at anodes or energy storage reactions at cathodes via extracellular electron transfer (EET). The Cathode-ANode (CANode) biofilm community was recently shown to facilitate both reactions; however, the identities of the primary constituents and underlying molecular mechanisms remain unknown. Here, we used metagenomics and metatranscriptomics to characterize the CANode biofilm. We show that a previously uncharacterized member of the family Desulfobulbaceae, Desulfobulbaceae-2, which had <1% relative abundance, had the highest relative gene expression and accounted for over 60% of all differentially expressed genes. At the anode potential, differential expression of genes for a conserved flavin oxidoreductase (Flx) and heterodisulfide reductase (Hdr) known to be involved in ethanol oxidation suggests a source of electrons for the energy-generating reaction. Genes for sulfate and carbon dioxide reduction pathways were expressed by Desulfobulbaceae-2 at both potentials and are the proposed energy storage reactions. Reduction reactions may be mediated by direct electron uptake from the electrode or from hydrogen generated at the cathode potential. The Desulfobulbaceae-2 genome is predicted to encode at least 85 multiheme (≥3 hemes) c-type cytochromes, some with as many as 26 heme-binding domains, that could facilitate reversible electron transfer with the electrode. Gene expression in other CANode biofilm species was also affected by the electrode potential, although to a lesser extent, and we cannot rule out their contribution to observed current. Results provide evidence of gene expression linked to energy storage and energy-generating reactions and will enable development of the CANode biofilm as a microbially driven rechargeable battery. IMPORTANCE Microbial electrochemical technologies (METs) rely on electroactive bacteria to catalyze energy-generating and energy storage reactions at electrodes. Known electroactive bacteria are not equally capable of both reactions, and METs are typically configured to be unidirectional. Here, we report on genomic and transcriptomic characterization of a recently described microbial electrode community called the Cathode-ANode (CANode). The CANode community is able to generate or store electrical current based on the electrode potential. During periods where energy is not needed, electrons generated from a renewable source, such as solar power, could be converted into energy storage compounds to later be reversibly oxidized by the same microbial catalyst. Thus, the CANode system can be thought of as a living "rechargeable battery." Results show that a single organism may be responsible for both reactions demonstrating a new paradigm for electroactive bacteria.

Field Demonstration of a Distributed Microsensor Network for Chemical Detection.

We have developed the ABEAM-15, a custom-built multiplexed reflectance device for the detection of vapor phase and aerosolized chemical plumes. The instrument incorporates fifteen individual sensing elements, has wireless communications, offers support for a battery pack, and is capable of both live and fully autonomous operation. Two housing options have been fabricated: a compact open housing for indoor use and a larger weather-sealed housing for outdoor use. Previously developed six-plex analysis algorithms are extended to 15-plex format and implemented on a laptop computer. We report the results of recent outdoor field trials with this instrument in Denver, CO in a stadium security scenario. Through software, the wireless modules on each instrument were configured to form a six-instrument, star-point topology, distributed microsensor network with live reporting and real-time data analysis. The network was tested with aerosols of methyl salicylate.

Development of a Colorimetric Sensor for Autonomous, Networked, Real-Time Application.

This review describes an ongoing effort intended to develop wireless sensor networks for real-time monitoring of airborne targets across a broad area. The goal is to apply the spectrophotometric characteristics of porphyrins and metalloporphyrins in a colorimetric array for detection and discrimination of changes in the chemical composition of environmental air samples. The work includes hardware, software, and firmware design as well as development of algorithms for identification of event occurrence and discrimination of targets. Here, we describe the prototype devices and algorithms related to this effort as well as work directed at selection of indicator arrays for use with the system. Finally, we review the field trials completed with the prototype devices and discuss the outlook for further development.

Molecular Mechanisms Contributing to the Growth and Physiology of an Extremophile Cultured with Dielectric Heating.

The effect of microwave frequency electromagnetic fields on living microorganisms is an active and highly contested area of research. One of the major drawbacks to using mesophilic organisms to study microwave radiation effects is the unavoidable heating of the organism, which has limited the scale (<5 ml) and duration (<1 h) of experiments. However, the negative effects of heating a mesophile can be mitigated by employing thermophiles (organisms able to grow at temperatures of >60°C). This study identified changes in global gene expression profiles during the growth of Thermus scotoductus SA-01 at 65°C using dielectric (2.45 GHz, i.e., microwave) heating. RNA sequencing was performed on cultures at 8, 14, and 24 h after inoculation to determine the molecular mechanisms contributing to long-term cellular growth and survival under microwave heating conditions. Over the course of growth, genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. Genes involved in cell wall biogenesis and elongation were also upregulated, consistent with the distinct elongated cell morphology observed after 24 h using microwave heating. Analysis of the global differential gene expression data enabled the identification of molecular processes specific to the response of T. scotoductus SA-01 to dielectric heating during growth. IMPORTANCE: The residual heating of living organisms in the microwave region of the electromagnetic spectrum has complicated the identification of radiation-only effects using microorganisms for 50 years. A majority of the previous experiments used either mature cells or short exposure times with low-energy high-frequency radiation. Using global differential gene expression data, we identified molecular processes unique to dielectric heating using Thermus scotoductus SA-01 cultured over 30 h in a commercial microwave digestor. Genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. These findings serve as a platform for future studies with mesophiles in order to better understand the response of microorganisms to microwave radiation.

'Candidatus Tenderia electrophaga', an uncultivated electroautotroph from a biocathode enrichment.

Biocathode communities are of interest for a variety of applications, including electrosynthesis, bioremediation, and biosensors, yet much remains to be understood about the biological processes that occur to enable these communities to grow. One major difficulty in understanding these communities is that the critical autotrophic organisms are difficult to cultivate. An uncultivated, electroautotrophic bacterium previously identified as an uncultivated member of the family Chromatiaceae appears to be a key organism in an autotrophic biocathode microbial community. Metagenomic, metaproteomic and metatranscriptomic characterization of this community indicates that there is likely a single organism that utilizes electrons from the cathode to fix CO2, yet this organism has not been obtained in pure culture. Fluorescence in situ hybridization reveals that the organism grows as rod-shaped cells approximately 1.8 × 0.6 µm, and forms large clumps on the cathode. The genomic DNA G+C content was 59.2 mol%. Here we identify the key features of this organism and propose 'Candidatus Tenderia electrophaga', within the Gammaproteobacteria on the basis of low nucleotide and predicted protein sequence identity to known members of the orders Chromatiales and Thiotrichales.

Development of a Detection Algorithm for Use with Reflectance-Based, Real-Time Chemical Sensing.

Here, we describe our efforts focused on development of an algorithm for identification of detection events in a real-time sensing application relying on reporting of color values using commercially available color sensing chips. The effort focuses on the identification of event occurrence, rather than target identification, and utilizes approaches suitable to onboard device incorporation to facilitate portable and autonomous use. The described algorithm first excludes electronic noise generated by the sensor system and determines response thresholds. This automatic adjustment provides the potential for use with device variations as well as accommodating differing indicator behaviors. Multiple signal channels (RGB) as well as multiple indicator array elements are combined for reporting of an event with a minimum of false responses. While the method reported was developed for use with paper-supported porphyrin and metalloporphyrin indicators, it should be equally applicable to other colorimetric indicators. Depending on device configurations, receiver operating characteristic (ROC) sensitivities of 1 could be obtained with specificities of 0.87 (threshold 160 ppb, ethanol).

Metaproteomic evidence of changes in protein expression following a change in electrode potential in a robust biocathode microbiome.

Microorganisms that respire electrodes may be exploited for biotechnology applications if key pathways for extracellular electron transfer can be identified and manipulated through bioengineering. To determine whether expression of proposed Biocathode-MCL extracellular electron transfer proteins are changed by modulating electrode potential without disrupting the relative distribution of microbial constituents, metaproteomic and 16S rRNA gene expression analyses were performed after switching from an optimal to suboptimal potential based on an expected decrease in electrode respiration. Five hundred and seventy-nine unique proteins were identified across both potentials, the majority of which were assigned to three previously defined Biocathode-MCL metagenomic clusters: a Marinobacter sp., a member of the family Chromatiaceae, and a Labrenzia sp (abbreviated as MCL). Statistical analysis of spectral counts using the Fisher's exact test identified 16 proteins associated with the optimal potential, five of which are predicted electron transfer proteins. The majority of proteins associated with the suboptimal potential were involved in protein turnover/synthesis, motility, and membrane transport. Unipept and 16S rRNA gene expression analyses indicated that the taxonomic profile of the microbiome did not change after 52 h at the suboptimal potential. These findings show that protein expression is sensitive to the electrode potential without inducing shifts in community composition, a feature that may be exploited for engineering Biocathode-MCL. All MS data have been deposited in the ProteomeXchange with identifier PXD001590 (http://proteomecentral.proteomexchange.org/dataset/PXD001590).

A previously uncharacterized, nonphotosynthetic member of the Chromatiaceae is the primary CO2-fixing constituent in a self-regenerating biocathode.

Biocathode extracellular electron transfer (EET) may be exploited for biotechnology applications, including microbially mediated O2 reduction in microbial fuel cells and microbial electrosynthesis. However, biocathode mechanistic studies needed to improve or engineer functionality have been limited to a few select species that form sparse, homogeneous biofilms characterized by little or no growth. Attempts to cultivate isolates from biocathode environmental enrichments often fail due to a lack of some advantage provided by life in a consortium, highlighting the need to study and understand biocathode consortia in situ. Here, we present metagenomic and metaproteomic characterization of a previously described biocathode biofilm (+310 mV versus a standard hydrogen electrode [SHE]) enriched from seawater, reducing O2, and presumably fixing CO2 for biomass generation. Metagenomics identified 16 distinct cluster genomes, 15 of which could be assigned at the family or genus level and whose abundance was roughly divided between Alpha- and Gammaproteobacteria. A total of 644 proteins were identified from shotgun metaproteomics and have been deposited in the the ProteomeXchange with identifier PXD001045. Cluster genomes were used to assign the taxonomic identities of 599 proteins, with Marinobacter, Chromatiaceae, and Labrenzia the most represented. RubisCO and phosphoribulokinase, along with 9 other Calvin-Benson-Bassham cycle proteins, were identified from Chromatiaceae. In addition, proteins similar to those predicted for iron oxidation pathways of known iron-oxidizing bacteria were observed for Chromatiaceae. These findings represent the first description of putative EET and CO2 fixation mechanisms for a self-regenerating, self-sustaining multispecies biocathode, providing potential targets for functional engineering, as well as new insights into biocathode EET pathways using proteomics.

Controlling Anti-Penetration Performance by Post-Grafting of Fluorinated Alkyl Chains onto Polystyrene-block-poly(vinyl methyl siloxane).

Polydimethylsiloxane (PDMS) has been widely used as a surface coating material, which has been reported to possess dynamic omniphobicity to a wide range of both polar and nonpolar solvents due to its high segmental flexibility and mobility. However, such high flexibility and mobility also enable penetration of small molecules into PDMS coatings, which alter the chemical and physical properties of the coating layers. To improve the anti-penetration properties of PDMS, a series of fluorinated alkyl segments are grafted to a diblock copolymer of polystyrene-block-poly(vinyl methyl siloxane) (PS-b-PVMS) using thiol-ene click reactions. This article reports the chemical characterization of these model fluorosilicone block copolymers and uses fluorescence measurements to investigate the dye penetration characteristics of polymer thin films. The introduction of longer fluorinated alkyl chains can gradually increase the anti-penetration properties as the time to reach the maximum fluorescence intensity (tpeak) gradually increases from 11 s of PS-b-PVMS to more than 1000 s of PS-b-P(n-C6F13-VMS). The improvement of anti-penetration properties is attributed to stronger inter-/intrachain interactions, phase segregation of ordered fluorinated side chains, and enhanced hydrophobicity caused by the grafting of fluorinated alkyl chains.

Water quality associated public health risk in Bo, Sierra Leone.

Human health depends on reliable access to safe drinking water, but in many developing countries only a limited number of wells and boreholes are available. Many of these water resources are contaminated with biological or chemical pollutants. The goal of this study was to examine water access and quality in urban Bo, Sierra Leone. A health census and community mapping project in one neighborhood in Bo identified the 36 water sources used by the community. A water sample was taken from each water source and tested for a variety of microbiological and physicochemical substances. Only 38.9% of the water sources met World Health Organization (WHO) microbial safety requirements based on fecal coliform levels. Physiochemical analysis indicated that the majority (91.7%) of the water sources met the requirements set by the WHO. In combination, 25% of these water resources met safe drinking water criteria. No variables associated with wells were statistically significant predictors of contamination. This study indicated that fecal contamination is the greatest health risk associated with drinking water. There is a need to raise hygiene awareness and implement inexpensive methods to reduce fecal contamination and improve drinking water safety in Bo, Sierra Leone.

Promoter Identification and Optimization for the Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Molecule N-3-Oxododecanoyl Homoserine Lactone.

Quorum sensing (QS) in bacteria has been well studied as a cellular communication phenomenon for decades. In recent years, such systems have been repurposed for the use of biosensors in both cellular and cell-free contexts as well as for inducible protein expression in nontraditional chassis organisms. Such biosensors are particularly intriguing when considering the association between the pathogenesis of some bacteria and their signaling intermediates. Considering this relationship and considering the recent demonstration of the species Lactobacillus plantarum WCFS1 as both a synthetic biology chassis and an organism capable of detecting a pathogen-associated QS molecule, we wanted to develop this organism as a QS sentinel. We used an approach combining techniques from both systems and synthetic biology to identify a number of native QS-response genes and to alter associated promoter activity to tune the output of L. plantarum cultures exposed to N-3-oxododecanoyl homoserine lactone. The resulting engineered QS sentinel reinforces the potential of modified lactic acid bacteria (LAB) for use in human-health-promoting applications and also demonstrates a simple rational workflow to engineer sentinel organisms to respond to any environmental or chemical stimuli.

Multiplexed tracking of protease activity using a single color of quantum dot vector and a time-gated Förster resonance energy transfer relay.

Semiconductor quantum dots (QDs) are attractive probes for optical sensing and imaging due to their unique photophysical attributes and nanoscale size. In particular, the development of assays and biosensors based on QDs and Förster resonance energy transfer (FRET) continues to be a prominent focus of research. Here, we demonstrate the application of QDs as simultaneous donors and acceptors in a time-gated FRET relay for the multiplexed detection of protease activity. In contrast to the current state-of-the-art, which uses multiple colors of QDs, multiplexing was achieved using only a single color of QD. The other constituents of the FRET relay, a luminescent terbium complex and fluorescent dye, were assembled to QDs via peptides that were selected as substrates for the model proteases trypsin and chymotrypsin. Loss of prompt FRET between the QD and dye signaled the activity of chymotrypsin; loss of time-gated FRET between the terbium and QD signaled the activity of trypsin. We applied the FRET relay in a series of quantitative, real-time kinetic assays of increasing biochemical complexity, including multiplexed sensing, measuring inhibition in a multiplexed format, and tracking the proteolytic activation of an inactive pro-protease to its active form in a coupled, multienzyme system. These capabilities were derived from a ratiometric analysis of the two FRET pathways in the relay and permitted extraction of initial reaction rates, enzyme specificity constants, and apparent inhibition constants. This work adds to the growing body of research on multifunctional nanoparticles and introduces multiplexed sensing as a novel capability for a single nanoparticle vector. Furthermore, the ability to track both enzymes within a coupled biological system using one vector represents a significant advancement for nanoparticle-based biosensing. Prospective applications in biochemical research, applied diagnostics, and drug discovery are discussed.

Home birth and hospital birth trends in Bo, Sierra Leone.

As of April 2010, all maternity care at government healthcare facilities in Sierra Leone is provided at no cost to patients. In late 2010, we conducted a community health census of 18 sections of the city of Bo (selected via randomized cluster sampling from 68 total sections). Among the 3421 women with a history of pregnancy who participated in the study, older women most often reported having a history of both home and hospital deliveries, while younger women showed a preference for hospital births. The proportion of lastborn children delivered at a healthcare facility increased from 71.8% of offspring 10-14 years old to 81.1% of those one to nine years old and 87.3% of infants born after April 2010. These findings suggest that the new maternal healthcare initiative has accelerated an existing trend toward a preference for healthcare facility births, at least in some urban parts of Sierra Leone.

Leapfrog diagnostics: Demonstration of a broad spectrum pathogen identification platform in a resource-limited setting.

BACKGROUND: Resource-limited tropical countries are home to numerous infectious pathogens of both human and zoonotic origin. A capability for early detection to allow rapid outbreak containment and prevent spread to non-endemic regions is severely impaired by inadequate diagnostic laboratory capacity, the absence of a "cold chain" and the lack of highly trained personnel. Building up detection capacity in these countries by direct replication of the systems existing in developed countries is not a feasible approach and instead requires "leapfrogging" to the deployment of the newest diagnostic systems that do not have the infrastructure requirements of systems used in developed countries. METHODS: A laboratory for molecular diagnostics of infectious agents was established in Bo, Sierra Leone with a hybrid solar/diesel/battery system to ensure stable power supply and a satellite modem to enable efficient communication. An array of room temperature stabilization and refrigeration technologies for reliable transport and storage of reagents and biological samples were also tested to ensure sustainable laboratory supplies for diagnostic assays. RESULTS: The laboratory demonstrated its operational proficiency by conducting an investigation of a suspected avian influenza outbreak at a commercial poultry farm at Bo using broad range resequencing microarrays and real time RT-PCR. The results of the investigation excluded influenza viruses as a possible cause of the outbreak and indicated a link between the outbreak and the presence of Klebsiella pneumoniae. CONCLUSIONS: This study demonstrated that by application of a carefully selected set of technologies and sufficient personnel training, it is feasible to deploy and effectively use a broad-range infectious pathogen detection technology in a severely resource-limited setting.

Conservation of Energetic Pathways for Electroautotrophy in the Uncultivated Candidate Order Tenderiales.

Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.

Application of a broad-range resequencing array for detection of pathogens in desert dust samples from Kuwait and Iraq.

A significant percentage of the human population is exposed to high levels of naturally occurring airborne dusts. Although the link between airborne particulate inhalation and a variety of respiratory diseases has long been established, little is known about the pathogenic role of the microbial component of the dust. In this study, we applied highly multiplexed PCR and a high-density resequencing microarray (RPM-TEI version 1.0) to screen samples of fine topsoil particles and airborne dust collected in 19 locations in Iraq and Kuwait for the presence of a broad range of human pathogens. The results indicated the presence of potential human pathogens, including Mycobacterium, Brucella, Coxiella burnetii, Clostridium perfringens, and Bacillus. The presence of Coxiella burnetii, a highly infectious potential biowarfare agent, was confirmed and detected in additional samples by use of a more sensitive technique (real-time PCR), indicating a high prevalence of this organism in the analyzed samples. The detection of potentially viable pathogens in breathable dusts from arid regions of Iraq and Kuwait underscores the importance of further study of these environments.

Porphyrin-embedded silicate materials for detection of hydrocarbon solvents.

The development of porphyrin-embedded mesoporous organosilicate materials for application to the detection of volatile hydrocarbon solvents is described. Design of the receptor and optical indicator construct begins with parallel selection of the porphyrin indicator and design of the mesoporous sorbent. For the porphyrin indicator, high binding affinity and strong changes in spectrophotometric character upon target interaction are desired. The sorbent should provide high target binding capacity and rapid binding kinetics. A number of porphyrin/metalloporphyrin variants and organosilicate sorbents were evaluated to determine the characteristics of their interaction with the targets, benzene, toluene, and hexane. The selected porphyrin candidates were covalently immobilized within a benzene-bridged sorbent. This construct was applied to the detection of targets using both fluorescence- and reflectance-based protocols. The use of red, green, and blue (RGB) color values from the constructs in a highly simplified detection scheme is described.

PepVAE: Variational Autoencoder Framework for Antimicrobial Peptide Generation and Activity Prediction.

New methods for antimicrobial design are critical for combating pathogenic bacteria in the post-antibiotic era. Fortunately, competition within complex communities has led to the natural evolution of antimicrobial peptide (AMP) sequences that have promising bactericidal properties. Unfortunately, the identification, characterization, and production of AMPs can prove complex and time consuming. Here, we report a peptide generation framework, PepVAE, based around variational autoencoder (VAE) and antimicrobial activity prediction models for designing novel AMPs using only sequences and experimental minimum inhibitory concentration (MIC) data as input. Sampling from distinct regions of the learned latent space allows for controllable generation of new AMP sequences with minimal input parameters. Extensive analysis of the PepVAE-generated sequences paired with antimicrobial activity prediction models supports this modular design framework as a promising system for development of novel AMPs, demonstrating controlled production of AMPs with experimental validation of predicted antimicrobial activity.

Marinobacter atlanticus electrode biofilms differentially regulate gene expression depending on electrode potential and lifestyle.

Marinobacter spp. are opportunitrophs with a broad metabolic range including interactions with metals and electrodes. Marinobacter atlanticus strain CP1 was previously isolated from a cathode biofilm microbial community enriched from a sediment microbial fuel cell. Like other Marinobacter spp., M. atlanticus generates small amounts of electrical current when grown as a biofilm on an electrode, which is enhanced by the addition of redox mediators. However, the molecular mechanism resulting in extracellular electron transfer is unknown. Here, RNA-sequencing was used to determine changes in gene expression in electrode-attached and planktonic cells of M. atlanticus when grown at electrode potentials that enable current production (310 and 510 mV vs. SHE) compared to a potential that enables electron uptake (160 mV). Cells grown at current-producing potentials had increased expression of genes for molybdate transport, regardless of planktonic or attached lifestyle. Electrode-attached cells at current-producing potentials showed increased expression of the major export protein for the type VI secretion system. Growth at 160 mV resulted in an increase in expression of genes related to stress response and DNA repair including both RecBCD and the LexA/RecA regulatory network, as well as genes for copper homeostasis. Changes in expression of proteins with PEP C-terminal extracellular export motifs suggests that M. atlanticus is remodeling the biofilm matrix in response to electrode potential. These results improve our understanding of the physiological adaptations required for M. atlanticus growth on electrodes, and suggest a role for metal acquisition, either as a requirement for metal cofactors of redox proteins or as a possible electron shuttling mechanism.