Energy Taxis toward Redox-Active Surfaces Decreases the Transport of Electroactive Bacteria in Saturated Porous Media

Altered Cell Viability, Morphology, and Motility under Ciprofloxacin Stress Influence the Transport and Resistance of Bacteria in Saturated Porous Media

The ubiquitous occurrence of antibiotics in the environment induces various stress responses of microbes and increases the risk of the emergence and spread of antimicrobial resistance (AMR). In this study, the transport and retention of Shewanella oneidensis cells in saturated porous media was investigated under different levels of ciprofloxacin (CIP) stress. Exposing to lethal CIP stress caused significant viability loss and stimulated cell transport due to increasing hydrophilicity and decreasing surface roughness. While exposure to sublethal CIP stress did not affect MR-1's viability, elongation of cells promoted their retention in sand columns via straining and orientation effects. The elongated cells likely adopted an end-on configuration to minimize repulsive interaction energy when approaching sand surfaces and deposited in a side-on position due to local surface roughness and charge heterogeneity of sands. The more diminished breakthrough of MR-1 cells in redox-active media was ascribed to their improving extracellular electron transfer and energy taxis activities under sublethal CIP stress. Moreover, the retention of elongated cells in porous media facilitated the de novo emergence of a resistant gyrase mutant, whose remobilization might exacerbate the AMR dissemination.

Light-regulated dentification and dissimilatory nitrate reduction by nano-bio electric syntrophic consortium

Microbial-oriented nitrogen recycling is a vital strategy for nitrogen pollution control in the treatment of low C/N wastewater. However, the deficient electron donors in water body limits the reactive nitrogen recovery. Herein, we design a nano-bio electric syntrophic consortium for light-regulated dentification and dissimilatory nitrate reduction to ammonium (DNRA) without organic carbon sources input. Using Fe0 coupons as the sole electron donor, the extracellular electron uptake rate of a model denitrifier (Pseudomonas aeruginosa PAO1) is enhanced by coculturing it with an electroactive bioregulator, Shewanella oneidensis MR-1 (MR-1), thereby achieving an average nitrate removal rate of 63.8 ± 0.1 mg N/d/L with ammonium recovery efficiency of 27.1 ± 0.2 % under illumination. Notably, in situ self-assembled FeS nanoparticles via a bottom-up Fe0 biocorrosion approach are observed on the outer membrane and periplasmic space of MR-1. Under illumination, native MtrCOmcA-CymA protein complex and FeS nanoparticles act in electron conduits to facilitate transmembrane photoelectron uptake of MR-1 for microbial DNRA process. Biochemical and transcriptomic analyses reveal that the NADH generation, chemotaxis moving and energy-taxis of MR-1 hybrids strength the driving force for microbial DNRA process. Overall, we demonstrate that the constructed FeS-assisted coculture, as an emerging model of electric syntrophy, could support the solar-triggered nitrogen metabolism from non-phototrophic microbes. Given that Fe0 biocorrosion is a facile route to MR-1 growth, this nano-bio system also affords a promising pathway for low C/N wastewater treatment and reactive nitrogen recovery via DNRA process.

The role of interface interaction between iron/sulfate-reducing bacteria (ISRB) and goethite in sulfur (S) redox cycling couple with Cd immobilization

Microbial sulfate reduction leads to the formation of various chalcophile trace metal sulfides, thereby immobilizing chalcophile trace metals in sediments. Iron/sulfate-reducing bacteria (ISRB) are ubiquitous in soils and sediments, its ability to reduce Fe(III) (oxyhydr)oxides and biogeochemical significance have attracted much attention. This research investigated the effect of the goethite and ISRB induced S cycle on cadmium mobility. The experiment demonstrated that the removal of Cd(II) in coexistence of ISRB19 and goethite was more efficiently than their individual components. Combined with X-ray absorption spectroscopy (XAS), transmission electron microscopy (TEM), Raman spectra and X-ray photoelectron spectroscopy (XPS), conclusions can be drawn that goethite enhanced Cd(II) retention by ISRB, which was attributed to the formation of metabolism product during interaction between ISRB19 (Enterobacter chengduensis) and goethite. Our results revealed the interaction of goethite and ISRB in S cycling under anaerobic conditions with its implications for Cd(II) remediation.

Biogenic amorphous FeOOH activated additional intracellular electron flow pathways for accelerating reductive dechlorination of tetrachloroethylene

Dissimilatory iron-reducing bacteria (DIRB) with extracellular electron transfer (EET) capabilities have shown significant potential for bioremediating halogenated hydrocarbon contaminated sites rich in iron and humic substances. However, the role and microbial molecular mechanisms of iron-humic acid (Fe-HA) complexes in the reductive dehalogenation process of DIRB remains inadequately elucidated. In this study, we developed a sustainable carbon cycling approach using Fe-HA complexes to modulate the electron flux from sawdust (SD), enabling almost complete reductive dechlorination by most DIRB (e.g., Shewanella oneidensis MR-1) that lack complex iron-sulfur molybdo enzymes. The SD-Fe-HA/MR-1 system achieved a 96.52% removal efficiency of tetrachloroethylene (PCE) at concentrations up to 250 μmol/L within 60 days. Material characterization revealed that DIRB facilitated the hydrolysis of macromolecular carbon sources by inducing the formation of amorphous ferrihydrite (FeOOH) in Fe-HA complexes. More importantly, the bioavailable FeOOH activated additional intracellular electron flow pathways, increasing the activity of potential dehalogenases. Transcriptome further highlight the innovative role of biogenic amorphous FeOOH in integrating intracellular redox metabolism with extracellular charge exchange to facilitate reductive dechlorination in DIRB. These findings provide novel insights into accelerating reductive dechlorination in-situ contaminated sites lacking obligate dehalogenating bacteria.

Cr(VI) bioreduction enhanced by the electron transfer between flavin reductase and persistent free radicals

Persistent free radicals (PFRs) in biochar are an important electron shuttle for mediating electron transfer, which has significant impact on the biogeochemical redox reactions. Although the influence of biochar on the extracellular electron transfer (EET) for redox cycle has been extensively studied, the molecular mechanism for promoting the EET with PFRs remains poorly understood. This study investigated the oxygen-centered PFRs-mediated Cr(VI) reduction by Shewanella oneidensis MR-1 (MR-1) and exhibited the molecular mechanism of electron transfer between flavin substances and PFRs. Results showed that the Cr(VI) bioreduction rate by MR-1 increased from 31% to 70% with the addition of biochar. Electrochemical results illustrated that biochar increased biocurrent generation in the Cr(VI) bioreduction process. 3D-EEM and LC/MS spectra indicated that MR-1 secreted the flavin mononucleotide (FMN) reductase that relied on the [H] to provide the electrons. Electron paramagnetic resonance spectra illustrated that PFRs in biochar accepted the electrons from FMN reductase and stored those bioelectrons. Because of the oxidation of FMN, the electron transfer from FMN reductase to PFRs would increase the intracellular reactive oxygen species, which further produced the extracellular ·O2-. The reduced PFRs released the bioelectrons, accelerating the Cr(VI) reduction by ·O2-. Together with the results of the mutant strains experiment, it was found that the EET by c-cytochrome and free radicals contributed to the Cr(VI) bioreduction by 7.1% and 92.9%, respectively. These findings revealed that the PFRs could participate in the EET process and promote the redox reactions, providing a new approach for enhancing the remediation of heavy metal pollution by microorganisms and suggesting the important role of PFRs in the electron transfer process.

Effects of mono- and multicomponent nonaqueous-phase liquid on the migration and retention of pollutant-degrading bacteria in porous media

The successful implementation of in-situ bioremediation of nonaqueous-phase liquid (NAPL) contamination in soil-groundwater systems is greatly influenced by the migration performance of NAPL-degrading bacteria. However, the impact and mechanisms of NAPL on the migration/retention of pollutant-degrading bacteria remain unclear. This study investigated the migration/retention performance of A. lwoffii U1091, a strain capable of degrading diesel while producing surfactants, in porous media without and with the presence of mono- and multicomponent NAPL (n-dodecane and diesel) under environmentally relevant conditions. The results showed that under all examined conditions (5 and 50 mM NaCl solution at flow rates of 4 and 8 m/d), the presence of n-dodecane/diesel in porous media could reduce the migration and enhance retention of A. lwoffii in quartz sand columns. Moreover, comparing with mutlicomponent NAPLs of n-dodecane, the monocomponent NAPLs (diesel) exhibited a greater reduction effect on the retention of A. lwoffii in porous media. Through systemically investigating the potential mechanisms via tracer experiment, visible chamber experiment, and theoretical calculation, we found that the reduction in porosity, repulsive forces and movement speeds, the presence of stagnant flow zones in porous media, particularly the biosurfactants generated by A. lwoffii contributed to the enhanced retention of bacteria in NAPL-contaminated porous media. Moreover, owing to presence of the greater amount of hydrophilic components in diesel than in n-dodecane, the available binding sites for the adsorption of bacteria were lower in diesel, resulting in the slightly decreased retention of A. lwoffii in porous media containing diesel than n-dodecane. This study demonstrated that comparing with porous media without NAPL contamination, the retention of strain capable of degrading NAPL in porous media with NAPL contamination was enhanced, beneficial for the subsequent biodegradation of NAPL.

Enhancement of waterborne pathogen removal by functionalized biochar with ε-polylysine ″dynamic arms″: Potential application in ultrafiltration system

Widespread outbreaks of threatening infections caused by unknown pathogens and water transmission have spawned the development of adsorption methods for pathogen elimination. We proposed a biochar functionalization strategy involving ε-polylysine (PLL), a bio-macromolecular poly(amino acid)s with variable folding conformations, as a "pathogen gripper" on biochar. PLL was successfully bridged onto biochar via polydopamine (PDA) crosslinking. The extension of electropositive side chains within PLL enables the capture of both nanoscale viruses and micrometer-scale bacteria in water, achieving excellent removal performances. This functionalized biochar was tentatively incorporated into ultrafiltration (UF) system, to achieve effective and controllable adsorption and retention of pathogens, and to realize the transfer of pathogens from membrane surface/pore to biochar surface as well as flushing water. The biochar-amended UF systems presents complete retention (∼7 LRV) and hydraulic elution of pathogens into membrane flushing water. Improvements in removal of organics and anti-fouling capability were observed, indicating the broken trade-off in UF pathogen removal dependent on irreversible fouling. Chemical characterizations revealed adsorption mechanisms encompassing electrostatic/hydrophobic interactions, pore filling, electron transfer, chemical bonding and secondary structure transitions. Microscopic and mechanical analyses validated the mechanisms for rapid adsorption and pathogen lysis. Low-concentration alkaline solution for used biochar regeneration, facilitated the deprotonation and transformation of PLL side chain to folded structures (α-helix/β-sheet). Biochar regeneration process also promoted the effective detachment/inactivation of pathogens and protection of functional groups on biochar, corroborated by physicochemical inspection and molecular dynamics simulation. The foldability of poly(amino acid)s acting like dynamic arms, significantly contributed to pathogen capture/desorption/inactivation and biochar regeneration. This study also inspires future investigation for performances of UF systems amended by poly(amino acid)s-functionalized biochar under diverse pressure, temperature, reactive oxygen species of feeds and chemical cleaning solutions, with far-reaching implications for public health, environmental applications of biochar, and UF process improvement.

Insight into Impact of Phosphate on the Cotransport and Corelease of Eu(III) with Bentonite Colloids in Saturated Quartz Columns

Understanding the fate and transport of radionuclides in porous media reduces the risk of contaminating soils and groundwater systems. While the cotransport of bentonite colloids (BC) with radionuclides in saturated media is well documented, the role of phosphate (P) in the colloid-driven transport of radionuclides in saturated porous media is still unaddressed; in particular, phosphate increases the mobilities of radionuclides in porous media, which should be subjected to an environmental risk assessment and model construction. In this work, the effects of phosphate on the transport and release of Eu(III) in different colloid systems (P-Eu(III), P-BC, P-BC-Eu(III)) was investigated with a fundamental colloid chemistry approach and a range of characterization techniques. The results showed that intrinsic europium colloids with size of 685 nm were formed by precipitation with phosphate, which affected the mobility of Eu(III) due to colloid stability and physical straining. Phosphate enhanced BC and BC-Eu(III) transport, and a high phosphate concentration promoted BC transport by eliminating physical straining and enhancing the electrostatic repulsions. The crystal structure of EuPO4 was not destroyed by the subsequent introduction of BC, which carried EuPO4 for further migration. However, when phosphate, bentonite and Eu(III) coexisted in a colloid suspension, the phosphate promoted Eu(III) transport by preferentially interacting with the BC to form ternary BC-P-Eu(III) pseudo-colloids rather than forming the intrinsic EuPO4 colloids. The synergetic role of P and BC on Eu(III) transport involved a relatively complex process and was not a simply additive effect. The findings in this work highlight the significance of phosphate in controlling the fate and transport of Ln(III)/Am(III) radionuclides in the presence of intrinsic colloids and pseudo-colloids in P-rich colloid-bearing environments.

Chemodiversity of soil organic matters determines biodegradation of polychlorinated biphenyls by a graphene oxide-assisted bacterial agent

A promising strategy for degrading persistent organic pollutants (POPs) in soil is amendment with nanomaterial-assisted functional bacteria. However, the influence of soil organic matter chemodiversity on the performance of nanomaterial-assisted bacterial agents remains unclear. Herein, different types of soil (Mollisol soil, MS; Ultisol soil, US; and Inceptisol soil, IS) were inoculated with a graphene oxide (GO)-assisted bacterial agent (Bradyrhizobium diazoefficiens USDA 110, B. diazoefficiens USDA 110) to investigate the association between soil organic matter chemodiversity and stimulation of polychlorinated biphenyl (PCB) degradation. Results indicated that the high-aromatic solid organic matter (SOM) inhibited PCB bioavailability, and lignin-dominant dissolved organic matter (DOM) with high biotransformation potential was a favored substrate for all PCB degraders, which led to no stimulation of PCB degradation in MS. Differently, high-aliphatic SOM in US and IS promoted PCB bioavailability. The high/low biotransformation potential of multiple DOM components (e.g., lignin, condensed hydrocarbon, unsaturated hydrocarbon, etc.) in US/IS further resulted to the enhanced PCB degradation by B. diazoefficiens USDA 110 (up to 30.34%) /all PCB degraders (up to 17.65%), respectively. Overall, the category and biotransformation potential of DOM components and the aromaticity of SOM collaboratively determine the stimulation of GO-assisted bacterial agent on PCB degradation.

Phosphate-solubilizing microorganisms regulate the release and transformation of phosphorus in biochar-based slow-release fertilizer

Coupling phosphate-solubilizing microorganisms (PSM) can improve the availability of phosphorous (P) in biochar-based slow-release P fertilizers (BPF). However, the mechanism in release and transformation of P in BPF regulated by PSM is still unclear. Herein, the biocompatibility and the adhesion behaviors of BPF and PSM (Enterobacter hormaechei Rs-198) in soil were firstly studied, and a 90 days' laboratory-scale soil incubation experiment of BPF and Rs-198 was performed to study the transformation of P of BPF. The results show that BPF has a good biocompatibility for Rs-198 due to its low aromaticity, graphitization and free radicals' content (0.084 mg/g). Rs-198 are adhered to the surface of BPF in soil due to the high negative secondary energy minimum and low total interaction energy between Rs-198 and BPF. Available P in the incubation of BPF and Rs-198 (BR treatment) is significantly higher than that of the incubation of BPF (BF treatment) at initial 60 days. However, the content of available P in BR treatment is much lower compared with that in BF treatment on day 90, which is attributed to the entrapment of released P from BPF by Rs-198 and the formation of polyphosphate (polyP) rather than bound with soil mineral. Overall, this study presents new insights into the transformation of P in BPF regulated by PSM.

Transport of plastic particles in natural porous media under freeze-thaw treatment: Effects of porous media property

Freeze-thaw (FT) cycles would alter physical and chemical properties of soil and thus influence the transport of plastic particles (one type of emerging contaminant with great concerns). This study was designed to investigate the effects of FT treatment on the mobility of plastic particles (nanoplastics as representative) in columns packed with natural soils (i.e. loamy sand and sandy soil, quartz sand employed as comparison). We found that FT treatment of different types of porous media would induce different transport behaviors of plastic particles. Specifically, FT treatment of quartz sand did not affect plastic particles mobility. While FT treatment of loamy sand and sandy soil increased plastic particles transport. The increased pore sizes and disintegration of small soil particles from soils (the detached soil would serve as mobile vehicle for the transport of plastic particle) led to the facilitated mobility of plastic particles in two types of soils after FT treatment. The presence of preferential flow paths induced by FT treatment also drove to the enhanced mobility of plastic particles in sandy soil with FT treatment. This study clearly showed that the mobility of model plastic particles in two types of natural soils was greatly enhanced by FT treatment.

The roles of Fe oxyhydroxide coating and chemical aging in pyrogenic carbon nanoparticle transport in unsaturated porous media

Pyrogenic carbon (PyC) nanoparticles are widespread in the environment, which is important to global carbon cycle. PyC can exist for millions of years and undergo various environmental aging processes. To better understand the roles of Fe oxyhydroxides and water content on the pristine and aged PyC transport, adsorption and column experiments were conducted under three saturations (100%, 70%, and 40%) and three pH (5, 7, and 9) in both clean and Fe oxyhydroxide-coated sand. At high water saturations (100% and 70%), the mobility of both the pristine and aged PyC was enhanced at high pH due to strong electrostatic repulsion, and the aged PyC showed higher mobility than the pristine PyC because of its more negative charge and hydrophilic surface. The coating of Fe oxyhydroxides on sand decreased the mobility of both the pristine and aged PyC due to weak electrostatic repulsion, large specific surface area, and high roughness. At low saturation (40%), solution pH showed little effect on both the pristine and aged PyC mobility, and water saturation became the main factor affecting PyC mobility. Almost no pristine or aged PyC transported out from the Fe oxyhydroxide-coated sand column because Fe oxide increased the roughness of the sand surface, which led to a sharp increase in the air-water-solid interface and retention sites. This study demonstrates that water content, environmental aging, and Fe oxyhydroxides are significant in the fate and transport of PyC nanoparticles in environments, which provides a good fundamental understanding for the assessment of pyrogenic carbon application in environmental protection and carbon sequestration.

Enhanced Cr(VI) bioreduction by biochar: Insight into the persistent free radicals mediated extracellular electron transfer

Biochar can act as a shuttle to accelerate the extracellular electron transfer (EET) by exoelectrogens. However, it is poorly understood how the persistent free radicals (PFRs) in biochar affected EET and the redox reaction. Herein, the effects of the biochar and chitosan modified biochar (CBC) on the Cr(VI) bioreduction by Shewanella oneidensis MR-1 (MR-1) was investigated. Kinetic study indicated that the Cr(VI) bioreduction rate constant by MR-1 was increased by 1.8-33.7 folds in the presence of biochar, and by 2.7-60.2 folds in the presence of CBC, respectively. Moreover, Cr(VI) bioreduction rates increased with the decreasing pH. Results suggested that the electrostatic attraction between Cr(VI) and redox-active particles could accelerate the EET by c-cytochrome due to the promotion of the Cr(VI) migration from aqueous phase to biochar or CBC. Electron paramagnetic resonance analysis suggested that the PFRs affected the electron transfer from the ·O₂^- generated by MR-1 to Cr(VI) and accelerate the Cr(VI) bioreduction. Remarkably, in the presence of PFRs, this electron shuttling process was dependent on the non-metal-reducing respiratory pathway. Our results offer new insights that free radicals may be widely involved in the EET and strongly impact on the redox reaction in the environment.

Versatile mechanisms and enhanced strategies of pollutants removal mediated by Shewanella oneidensis: A review

The removal of environmental pollutants is important for a sustainable ecosystem and human health. Shewanella oneidensis (S. oneidensis) has diverse electron transfer pathways and can use a variety of contaminants as electron acceptors or electron donors. This paper reviews S. oneidensis's function in removing environmental pollutants, including heavy metals, inorganic non-metallic ions (INMIs), and toxic organic pollutants. S. oneidensis can mineralize o-xylene (OX), phenanthrene (PHE), and pyridine (Py) as electron donors, and also reduce azo dyes, nitro aromatic compounds (NACs), heavy metals, and iodate by extracellular electron transfer (EET). For azo dyes, NACs, Cr(VI), nitrite, nitrate, thiosulfate, and sulfite that can cross the membrane, S. oneidensis transfers electrons to intracellular reductases to catalyze their reduction. However, most organic pollutants cannot be directly degraded by S. oneidensis, but S. oneidensis can remove these pollutants by self-synthesizing catalysts or photocatalysts, constructing bio-photocatalytic systems, driving Fenton reactions, forming microbial consortia, and genetic engineering. However, the industrial-scale application of S. oneidensis is insufficient. Future research on the metabolism of S. oneidensis and interfacial reactions with other materials needs to be deepened, and large-scale reactors should be developed that can be used for practical engineering applications.

Freeze-thaw cycles induce diverse bacteria release behaviors from quartz sand columns with different water saturations

Bacteria present in natural environment especially those in cold regions would experience freeze-thaw (FT) process during day-night and season turns. However, knowledge about the influence of FT on bacteria release behaviors in porous media was limited. In present study, the bacteria release behaviors from quartz sand columns without and with 1 and 3 FT treatment cycles under three water saturations (θ=100%, 90%, and 60%) were investigated. We found that for all three water saturated columns without FT treatment, negligible bacteria released from columns via background salt solution elution, while the subsequent release of bacteria from sand columns via low ionic strength (IS) solution elution decreased with decreasing column water saturations. More importantly, we found unlike the negligible bacteria release in columns without FT treatment, for columns with high saturations (θ=100% and 90%), FT treatment could promote bacteria release with background salt solution elution. Moreover, for high saturated columns, FT treatment would decrease subsequent bacteria release with low IS solution elution. This phenomenon was more obvious with increasing FT treatment cycles. In contrast, FT treatment had negligible influence on bacteria release from columns with lower saturation (θ=60%). The decreased bacterial sizes, the loss of bacterial flagella, as well as the change of local configuration of porous media (via changing water into ice and ice back into water) during the FT processes contributed to increased bacteria release via background salt solution elution from high saturated sand columns. While, the reduced amount of bacteria being retained at secondary energy minima drove to the subsequently decreased bacteria release via low IS solution elution. The results of this study clearly showed that for porous media with high saturations, FT cycles would increase the risk of bacteria detaching from porous media with flushing by the background solution.

Perspectives on Microbial Electron Transfer Networks for Environmental Biotechnology

The overlap of microbiology and electrochemistry provides plenty of opportunities for a deeper understanding of the redox biogeochemical cycle of natural-abundant elements (like iron, nitrogen, and sulfur) on Earth. The electroactive microorganisms (EAMs) mediate electron flows outward the cytomembrane via diverse pathways like multiheme cytochromes, bridging an electronic connection between abiotic and biotic reactions. On an environmental level, decades of research on EAMs and the derived subject termed “electromicrobiology” provide a rich collection of multidisciplinary knowledge and establish various bioelectrochemical designs for the development of environmental biotechnology. Recent advances suggest that EAMs actually make greater differences on a larger scale, and the metabolism of microbial community and ecological interactions between microbes play a great role in bioremediation processes. In this perspective, we propose the concept of microbial electron transfer network (METN) that demonstrates the “species-to-species” interactions further and discuss several key questions ranging from cellular modification to microbiome construction. Future research directions including metabolic flux regulation and microbes–materials interactions are also highlighted to advance understanding of METN for the development of next-generation environmental biotechnology.

Comparative Genomics Unveils the Habitat Adaptation and Metabolic Profiles of Clostridium in an Artificial Ecosystem for Liquor Production

Pit mud is a typical artificial ecosystem for Chinese liquor production. Clostridium inhabiting pit mud plays essential roles in the flavor formation of strong-flavor baijiu. The relative abundance of Clostridium increased with pit mud quality, further influencing the quality of baijiu.

Anaerobic bacterial responses to carbonaceous materials and implications for contaminant transformation: Cellular, metabolic, and community level findings

Carbonaceous materials (CM) enhance the abundance and activity of bacteria capable of persistent organic (micro)pollutant (POP) degradation. This review synthesizes anaerobic bacterial responses to minimally modified CM in non-fuel cell bioremediation applications at three stages: attachment, metabolism, and biofilm genetic composition. Established relationships between biological behavior and CM surface properties are identified, but temporal relationships are not well understood, making it difficult to connect substratum properties and "pioneer" bacteria with mature microorganism-CM systems. Stark differences in laboratory methodology at each temporal stage results in observational, but not causative, linkages as system complexity increases. This review is the first to critically examine relationships between material and cellular properties with respect to time. The work highlights critical knowledge gaps that must be addressed to accurately predict microorganism-CM behavior and to tailor CM properties for optimized microbial activity, critical frontiers in establishing this approach as an effective bioremediation strategy.

Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3

Because of the ability to metabolize a large number of electron acceptors such as nitrate, nitrite, fumarate, and metal oxides, Shewanella species have attracted much attention in recent years. Generally, the use of these electron acceptors is mainly achieved through electron transfer proteins and their interactions which will dynamically change across different environmental conditions in cells. Therefore, functional analysis of condition-specific molecular networks can reveal biological information on electron transfer processes. By integrating expression data and molecular networks, we constructed condition-specific molecular networks for Shewanella piezotolerans WP3. We then identified condition-specific key genes and studied their potential functions with an emphasis on their roles in electron transfer processes. Functional module analysis showed that different flagellar assembly modules appeared under these conditions and suggested that flagellar proteins are important for these conditions. We also identified the electron transfer modules underlying these various environmental conditions. The present results could help with screening electron transfer genes and understanding electron transfer processes under various environmental conditions for the Shewanella species.