Shewanella oneidensis in a lactate-fed pure-culture and a glucose-fed co-culture with Lactococcus lactis with an electrode as electron acceptor

Engineered cytochrome fused extracellular matrix enabled efficient extracellular electron transfer and improved performance of microbial fuel cell

Microbial fuel cell (MFC) was a promising technology for energy harvesting from wastewater. However, inefficient bacterial extracellular electron transfer (EET) limited the performance as well as the applications of MFC. Here, a new strategy to reinforce the EET by engineering synthetic extracellular matrix (ECM) with cytochrome fused curli was developed. By genetically fusing a minimal cytochrome domain (MCD) with the curli protein CsgA and heterogeneously expressing in model exoelectrogen of Shewanella oneidensis MR-1, the cytochrome fused electroactive curli network was successfully constructed and assembled. Interestingly, the strain with the MCD fused synthetic ECM delivered about 2.4 times and 2.0 times higher voltage and power density output than these of wild type MR-1 in MFC. More impressively, electrochemical analysis suggested that this synthetic ECM not only introduced cytochrome of MCD, but also attracted more self-secreted electrochemically active substances, which might facilitate the EET and improve the MFC performance. This work demonstrated the possibility to manipulation the EET with ECM engineering, which opened up new path for exoelectrogen design and engineering.

Biological removal of sulfamethoxazole enhanced by S. oneidensis MR-1 via promoting NADH generation and electron transfer and consumption

The bio-removal efficiency of sulfamethoxazole (SMX) from wastewater is usually very poor. In this paper a new efficient method to biodegrade SMX was reported. The SMX biodegradation efficiency by Paracoccus denitrificans was observed to be remarkably enhanced from 48.9% to 94.2% after Shewanella oneidensis MR-1 addition. The mechanisms investigation revealed that P. denitrificans was the dominant microbe for SMX biodegradation. Although SMX biodegradation by S. oneidensis MR-1 alone was negligible, its presence advanced NADH generation. The proteomics assay revealed that the expression of key proteins relevant with complex I and III and cytochrome c in electron transfer chain were increased due to P. denitrificans acquiring iron from periplasm to cytoplasm being improved. In addition, the extracellular electron transfer capability was enhanced as S. oneidensis MR-1 not only produced flavin, but caused P. denitrificans to secret more extracellular polymeric substances. Further investigation indicated that the expression of key enzymes related to electron consumption in SMX biodegradation was up-regulated. Based on these findings, the pathways of S. oneidensis MR-1 promoting SMX biodegradation were proposed. As all nitrate could be removed with almost no nitrite accumulation, this study would also provide an attractive way for simultaneous bio-removal of multiple pollutants from wastewater.

Electrochemical Microwell Plate to Study Electroactive Microorganisms in Parallel and Real-Time

Microbial resource mining of electroactive microorganism (EAM) is currently methodically hampered due to unavailable electrochemical screening tools. Here, we introduce an electrochemical microwell plate (ec-MP) composed of a 96 electrochemical deepwell plate and a recently developed 96-channel multipotentiostat. Using the ec-MP we investigated the electrochemical and metabolic properties of the EAM models Shewanella oneidensis and Geobacter sulfurreducens with acetate and lactate as electron donor combined with an individual genetic analysis of each well. Electrochemical cultivation of pure cultures achieved maximum current densities (j_max) and coulombic efficiencies (CE) that were well in line with literature data. The co-cultivation of S. oneidensis and G. sulfurreducens led to an increased current density of j_max of 88.57 ± 14.04 µA cm⁻² (lactate) and j_max of 99.36 ± 19.12 µA cm⁻² (lactate and acetate). Further, a decreased time period of reaching j_max and biphasic current production was revealed and the microbial electrochemical performance could be linked to the shift in the relative abundance.

Microorganisms in sediment microbial fuel cells: Ecological niche, microbial response, and environmental function

A sediment microbial fuel cell (SMFC) is a device that harvests electrical energy from sediments rich in organic matter. SMFCs have been attracting increasing amounts of interest in environmental remediation, since they are capable of providing a clean and inexhaustible source of electron donors or acceptors and can be easily controlled by adjusting the electrochemical parameters. The microorganisms inhabiting sediments and the overlying water play a pivotal role in SMFCs. Since the SMFC is applied in an open environment rather than in an enclosed chamber, the effects of the environment on the microbes should be intense and the microbial community succession should be extremely complex. Thus, this review aims to provide an overview of the microorganisms in SMFCs, which few previous review papers have reported. In this study, the anodic and cathodic niches for the microorganisms in SMFCs are summarized, how the microbial population and community interact with the SMFC environment is discussed, a new microbial succession strategy called the electrode stimulation succession is proposed, and recent developments in the environmental functions of SMFCs are discussed from the perspective of microorganisms. Future studies are needed to investigate the electrode stimulation succession, the environmental function and the electron transfer mechanism in order to boost the application of SMFCs for power generation and environmental remediation.

Inhibition of Tumor Progression through the Coupling of Bacterial Respiration with Tumor Metabolism

By leveraging the ability of Shewanella oneidensis MR-1 (S. oneidensis MR-1) to anaerobically catabolize lactate through the transfer of electrons to metal minerals for respiration, a lactate-fueled biohybrid (Bac@MnO₂ ) was constructed by modifying manganese dioxide (MnO₂ ) nanoflowers on the S. oneidensis MR-1 surface. The biohybrid Bac@MnO₂ uses decorated MnO₂ nanoflowers as electron receptor and the tumor metabolite lactate as electron donor to make a complete bacterial respiration pathway at the tumor sites, which results in the continuous catabolism of intercellular lactate. Additionally, decorated MnO₂ nanoflowers can also catalyze the conversion of endogenous hydrogen peroxide (H₂ O₂ ) into generate oxygen (O₂ ), which could prevent lactate production by downregulating hypoxia-inducible factor-1α (HIF-1α) expression. As lactate plays a critical role in tumor development, the biohybrid Bac@MnO₂ could significantly inhibit tumor progression by coupling bacteria respiration with tumor metabolism.

Development of a RP-HPLC method for determination of glucose in Shewanella oneidensis cultures utilizing 1-phenyl-3-methyl-5-pyrazolone derivatization

A method was developed and validated for low-level detection of glucose. The method involves quantitation of glucose though derivitization with 1-phenyl-3-methyl-5-pyrazolone (PMP) and HPLC-DAD analysis. The developed method was found to be accurate and robust achieving detection limits as low as 0.09 nM. The applicability of the method was tested against microbial samples with glucose acting as a carbon fuel source. The method was shown to be able to accurately discriminate and quantify PMP-glucose derivatives within Shewanella oneidensis MR-1 samples. The method proved capable at examining glucose usage during the early hours of microbial growth, with detectable usage occurring as early as two hours. S. oneidensis cultures were found to grow more effectively in the presence of oxygen which coincided with more efficient glucose usage. Glucose usage further increased in the presence of competing electron acceptors. The rate at which S. oneidensis reached exponential growth was affected by the presence of ferric iron under microaerobic conditions. Such samples reached exponential growth approximately two hours sooner than aerobic samples.

Strategies for improving the electroactivity and specific metabolic functionality of microorganisms for various microbial electrochemical technologies

Electroactive microorganisms, which possess extracellular electron transfer (EET) capabilities, are the basis of microbial electrochemical technologies (METs) such as microbial fuel and electrolysis cells. These are considered for several applications ranging from the energy-efficient treatment of waste streams to the production of value-added chemicals and fuels, bioremediation, and biosensing. Various aspects related to the microorganisms, electrodes, separators, reactor design, and operational or process parameters influence the overall functioning of METs. The most fundamental and critical performance-determining factor is, however, the microorganism-electrode interactions. Modification of the electrode surfaces and microorganisms for optimizing their interactions has therefore been the major MET research focus area over the last decade. In the case of microorganisms, primarily their EET mechanisms and efficiencies along with the biofilm formation capabilities, collectively considered as microbial electroactivity, affect their interactions with the electrodes. In addition to electroactivity, the specific metabolic or biochemical functionality of microorganisms is equally crucial to the target MET application. In this article, we present the major strategies that are used to enhance the electroactivity and specific functionality of microorganisms pertaining to both anodic and cathodic processes of METs. These include simple physical methods based on the use of heat and magnetic field along with chemical, electrochemical, and growth media amendment approaches to the complex procedure-based microbial bioaugmentation, co-culture, and cell immobilization or entrapment, and advanced toolkit-based biofilm engineering, genetic modifications, and synthetic biology strategies. We further discuss the applicability and limitations of these strategies and possible future research directions for advancing the highly promising microbial electrochemistry-driven biotechnology.

Photoferrotrophs Produce a PioAB Electron Conduit for Extracellular Electron Uptake

Photoferrotrophy is a form of anoxygenic photosynthesis whereby bacteria utilize soluble or insoluble forms of ferrous iron as an electron donor to fix carbon dioxide using light energy. They can also use poised electrodes as their electron donor via phototrophic extracellular electron uptake (phototrophic EEU). The electron uptake mechanisms underlying these processes are not well understood. Using Rhodopseudomonas palustris TIE-1 as a model, we show that a single periplasmic decaheme cytochrome c, PioA, and an outer membrane porin, PioB, form a complex allowing extracellular electron uptake across the outer membrane from both soluble iron and poised electrodes. We observe that PioA undergoes postsecretory proteolysis of its N terminus to produce a shorter heme-attached PioA (holo-PioAC, where PioAC represents the C terminus of PioA), which can exist both freely in the periplasm and in a complex with PioB. The extended N-terminal peptide controls heme attachment, and its processing is required to produce wild-type levels of holo-PioAC and holo-PioACB complex. It is also conserved in PioA homologs from other phototrophs. The presence of PioAB in these organisms correlate with their ability to perform photoferrotrophy and phototrophic EEU.IMPORTANCE Some anoxygenic phototrophs use soluble iron, insoluble iron minerals (such as rust), or their proxies (poised electrodes) as electron donors for photosynthesis. However, the underlying electron uptake mechanisms are not well established. Here, we show that these phototrophs use a protein complex made of an outer membrane porin and a periplasmic decaheme cytochrome (electron transfer protein) to harvest electrons from both soluble iron and poised electrodes. This complex has two unique characteristics: (i) it lacks an extracellular cytochrome c, and (ii) the periplasmic decaheme cytochrome c undergoes proteolytic cleavage to produce a functional electron transfer protein. These characteristics are conserved in phototrophs harboring homologous proteins.

Long-Term Behavior of Defined Mixed Cultures of Geobacter sulfurreducens and Shewanella oneidensis in Bioelectrochemical Systems

This work aims to investigate the long-term behavior of interactions of electrochemically active bacteria in bioelectrochemical systems. The electrochemical performance and biofilm characteristics of pure cultures of Geobacter sulfurreducens and Shewanella oneidensis are being compared to a defined mixed culture of both organisms. While S. oneidensis pure cultures did not form cohesive and stable biofilms on graphite anodes and only yielded 0.034 ± 0.011 mA/cm² as maximum current density by feeding of each 5 mM lactate and acetate, G. sulfurreducens pure cultures formed 69 μm thick, area-wide biofilms with 10 mM acetate as initial substrate concentration and yielded a current of 0.39 ± 0.09 mA/cm². Compared to the latter, a defined mixed culture of both species was able to yield 38% higher maximum current densities of 0.54 ± 0.07 mA/cm² with each 5 mM lactate and acetate. This increase in current density was associated with a likewise increased thickness of the anodic biofilm to approximately 93 μm. It was further investigated whether a sessile incorporation of S. oneidensis into the mixed culture biofilm, which has been reported previously for short-term experiments, is long-term stable. The results demonstrate that S. oneidensis was not stably incorporated into the biofilm; rather, the planktonic presence of S. oneidensis has a positive effect on the biofilm growth of G. sulfurreducens and thus on current production.

Engineering rheology of electrolytes using agar for improving the performance of bioelectrochemical systems

The present study is focused on enhancing the rheological properties of the electrolyte and eliminating sedimentation of microorganisms/flocs without affecting the electron transfer kinetics for improved bioelectricity generation. Agar derived from polysaccharide agarose (0.05-0.2%, w/v) was chosen as a rheology modifying agent. Electroanalytical investigations showed that electrolytes modified with 0.15% agar display a nine-fold increase in current density (1.2 mA/cm²) by a thermophilic strain (Geobacillus sp. 44C, 60 °C) when compared with the control. Sodium phosphate buffer (0.1 M, pH 7) electrolyte with riboflavin (0.1 mM) was used as the control. Electrolytes modified with 0.15% agar significantly improved chemical oxygen demand removal rates. This developed electrolyte will aid in improving bioelectricity generation in Bioelectrochemical Systems (BES). The developed strategy avoids the use of peristaltic pumps and magnetic stirrers, thereby improving the energy efficiency of the process.

Effects of wastewater constituents and operational conditions on the composition and dynamics of anodic microbial communities in bioelectrochemical systems

Over the last decade, there has been an ever-growing interest in bioelectrochemical systems (BES) as a sustainable technology enabling simultaneous wastewater treatment and biological production of, e.g. electricity, hydrogen, and further commodities. A key component of any BES degrading organic matter is the anode where electric current is biologically generated from the oxidation of organic compounds. The performance of BES depends on the interactions of the anodic microbial communities. To optimize the operational parameters and process design of BES a better comprehension of the microbial community dynamics and interactions at the anode is required. This paper reviews the abundance of different microorganisms in anodic biofilms and discusses their roles and possible side reactions with respect to their implications on the performance of BES utilizing wastewaters. The most important operational parameters affecting anodic microbial communities grown with wastewaters are highlighted and guidelines for controlling the composition of microbial communities are given.

Shewanella oneidensis MR-1 Utilizes both Sodium- and Proton-Pumping NADH Dehydrogenases during Aerobic Growth

Shewanella oneidensis MR-1 is a metal-reducing bacterium with the ability to utilize many different terminal electron acceptors, including oxygen and solid-metal oxides. Both metal oxide reduction and aerobic respiration have been studied extensively in this organism. However, electron transport chain processes upstream of the terminal oxidoreductases have been relatively understudied in this organism, especially electron transfer from NADH to respiratory quinones. Genome annotation indicates that S. oneidensis MR-1 encodes four NADH dehydrogenases, a proton-translocating dehydrogenase (Nuo), two sodium ion-translocating dehydrogenases (Nqr1 and Nqr2), and an “uncoupling” dehydrogenase (Ndh), but none of these complexes have been studied. Therefore, we conducted a study specifically focused on the effects of individual NADH dehydrogenase knockouts in S. oneidensis MR-1. We observed that two of the single-mutant strains, the ΔnuoN and ΔnqrF1 mutants, exhibited significant growth defects compared with the wild type. However, the defects were minor and only apparent under certain growth conditions. Further testing of the ΔnuoN ΔnqrF1 double-mutant strain yielded no growth in minimal medium under oxic conditions, indicating that Nuo and Nqr1 have overlapping functions, but at least one is necessary for aerobic growth. Coutilization of proton- and sodium ion-dependent energetics has important implications for the growth of this organism in environments with varied pH and salinity, including microbial electrochemical systems.

IMPORTANCE Bacteria utilize a wide variety of metabolic pathways that allow them to take advantage of different energy sources, and to do so with varied efficiency. The efficiency of a metabolic process determines the growth yield of an organism, or the amount of biomass it produces per amount of substrate consumed. This parameter has important implications in biotechnology and wastewater treatment, where low growth yields are often preferred to minimize the production of microbial biomass. In this study, we investigated respiratory pathways containing NADH dehydrogenases with varied efficiency (i.e., the number of ions translocated per NADH oxidized) in the metal-reducing bacterium Shewanella oneidensis MR-1. We observed that two different respiratory pathways are used concurrently, and at least one pathway must be functional for growth under oxic conditions.

Diversity-Function Relationships in Natural, Applied, and Engineered Microbial Ecosystems

The connection between ecosystem function and taxonomic diversity has been of interest and relevance to macroecologists for decades. After many years of lagging behind due to the difficulty of assigning both taxonomy and function to poorly distinguishable microscopic cells, microbial ecology now has access to a suite of powerful molecular tools which allow its practitioners to generate data relating to diversity and function of a microbial community on an unprecedented scale. Instead, the problem facing today's microbial ecologists is coupling the ease of generation of these datasets with the formulation and testing of workable hypotheses relating the diversity and function of environmental, host-associated, and engineered microbial communities. Here, we review the current state of knowledge regarding the links between taxonomic alpha- and beta-diversity and ecosystem function, comparing our knowledge in this area to that obtained by macroecologists who use more traditional techniques. We consider the methodologies that can be applied to study these properties and how successful they are at linking function to diversity, using examples from the study of model microbial ecosystems, methanogenic bioreactors (anaerobic digesters), and host-associated microbiota. Finally, we assess ways in which our newly acquired understanding might be used to manipulate diversity in ecosystems of interest in order to improve function for the benefit of us or the environment in general through the provision of ecosystem services.

Composition and role of the attached and planktonic microbial communities in mesophilic and thermophilic xylose-fed microbial fuel cells

A mesophilic (37 °C) and a thermophilic (55 °C) two-chamber microbial fuel cell (MFC) were studied and compared for their power production from xylose and the anode-attached, membrane-attached and planktonic microbial communities involved.

Resilience, Dynamics, and Interactions within a Model Multispecies Exoelectrogenic-Biofilm Community

Anode-associated multispecies exoelectrogenic biofilms are essential for the function of bioelectrochemical systems (BESs). The individual activities of anode-associated organisms and physiological responses resulting from coculturing are often hard to assess due to the high microbial diversity in these systems. Therefore, we developed a model multispecies biofilm comprising three exoelectrogenic proteobacteria, Shewanella oneidensis, Geobacter sulfurreducens, and Geobacter metallireducens, with the aim to study in detail the biofilm formation dynamics, the interactions between the organisms, and the overall activity of an exoelectrogenic biofilm as a consequence of the applied anode potential. The experiments revealed that the organisms build a stable biofilm on an electrode surface that is rather resilient to changes in the redox potential of the anode. The community operated at maximum electron transfer rates at electrode potentials that were higher than 0.04 V versus a normal hydrogen electrode. Current densities decreased gradually with lower potentials and reached half-maximal values at -0.08 V. Transcriptomic results point toward a positive interaction among the individual strains. S. oneidensis and G. sulfurreducens upregulated their central metabolisms as a response to cultivation under mixed-species conditions. G. sulfurreducens was detected in the planktonic phase of the bioelectrochemical reactors in mixed-culture experiments but not when it was grown in the absence of the other two organisms.IMPORTANCE In many cases, multispecies communities can convert organic substrates into electric power more efficiently than axenic cultures, a phenomenon that remains unresolved. In this study, we aimed to elucidate the potential mutual effects of multispecies communities in bioelectrochemical systems to understand how microbes interact in the coculture anodic network and to improve the community's conversion efficiency for organic substrates into electrical energy. The results reveal positive interactions that might lead to accelerated electron transfer in mixed-species anode communities. The observations made within this model biofilm might be applicable to a variety of nonaxenic systems in the field.

Comparative analysis of L-sorbose dehydrogenase by docking strategy for 2-keto-L-gulonic acid production in Ketogulonicigenium vulgare and Bacillus endophyticus consortium

Improving the yield of 2-keto-L-gulonic acid (2-KGA), the direct precursor of vitamin C, draws more and more attention in industrial production. In this study, we try to increase the 2-KGA productivity by computer-aided selection of genes encoding L-sorbose dehydrogenases (SDH) of Ketogulonicigenium vulgare. First, six SDHs were modeled by docking strategy to predict the binding mode with co-factor PQQ. The binding energy between SSDA1-H/SSDA1-L and PQQ was the highest, followed by SSDA3/SSDA2. The binding energy between SSDA1-P/SSDB and PQQ was the lowest. Then, these genes were overexpressed, respectively, in an industrial strain K. vulgare HKv604. Overexpression of ssda1-l and ssda1-h enhanced the 2-KGA production by 7.89 and 12.56 % in mono-cultured K. vulgare, and by 13.21 and 16.86 % when K. vulgare was co-cultured with Bacillus endophyticus. When the engineered K. vulgare SyBE_Kv000116013 (overexpression of ssda1-p) or SyBE_Kv000116016 (overexpression of ssdb) was co-cultured with B. endophyticus, the 2-KGA production decreased significantly. The docking results were in accordance with the experimental data, which indicated that computer-aided modeling is an efficient strategy for screening more efficient enzymes.

Glycerol-fed microbial fuel cell with a co-culture of Shewanella oneidensis MR-1 and Klebsiella pneumonae J2B

Glycerol is an attractive feedstock for bioenergy and bioconversion processes but its use in microbial fuel cells (MFCs) for electrical energy recovery has not been investigated extensively. This study compared the glycerol uptake and electricity generation of a co-culture of Shewanella oneidensis MR-1 and Klebsiella pneumonia J2B in a MFC with that of a single species inoculated counterpart. Glycerol was metabolized successfully in the co-culture MFC (MFC-J&M) with simultaneous electricity production but it was not utilized in the MR-1 only MFC (MFC-M). A current density of 10 mA/m(2) was obtained while acidic byproducts (lactate and acetate) were consumed in the co-culture MFC, whereas they are accumulated in the J2B-only MFC (MFC-J). MR-1 was distributed mainly on the electrode in MFC-J&M, whereas most of the J2B was observed in the suspension in the MFC-J reactor, indicating that the co-culture of both strains provides an ecological driving force for glycerol utilization using the electrode as an electron acceptor. This suggests that a co-culture MFC can be applied to electrical energy recovery from glycerol, which was previously known as a refractory substrate in a bioelectrochemical system.

Design, analysis and application of synthetic microbial consortia

The rapid development of synthetic biology has conferred almost perfect modification on single cells, and provided methodological support for synthesizing microbial consortia, which have a much wider application potential than synthetic single cells. Co-cultivating multiple cell populations with rational strategies based on interacting relationships within natural microbial consortia provides theoretical as well as experimental support for the successful obtaining of synthetic microbial consortia, promoting it into extensive research on both industrial applications in plenty of areas and also better understanding of natural microbial consortia. According to their composition complexity, synthetic microbial consortia are summarized in three aspects in this review and are discussed in principles of design and construction, insights and methods for analysis, and applications in energy, healthcare, etc.

Enhanced anaerobic dechlorination of polychlorinated biphenyl in sediments by bioanode stimulation

The application of a low-voltage electric field as an electron donor or acceptor to promote the bioremediation of chlorinated organic compounds represents a promising technology meeting the demand of developing an efficient and cost-effective strategy for in situ treatment of PCB-contaminated sediments. Here, we reported that bioanode stimulation with an anodic potential markedly enhanced dechlorination of 2,3,4,5-tetrachlorobiphenyl (PCB 61) contained in the sediment at an electronic waste recycling site of Qingyuan, Guangdong, China. The 110-day incubation of the bioanode with a potential poised at 0.2 V relative to saturated calomel electrode enabled 58% transformation of the total PCB 61 at the initial concentration of 100 μmol kg(-1), while only 23% was reduced in the open-circuit reference experiment. The introduction of acetate to the bioelectrochemical reactor (BER) further improved PCB 61 transformation to 82%. Analysis of the bacterial composition showed significant community shifts in response to variations in treatment. At phylum level, the bioanode stimulation resulted in substantially increased abundance of Actinobacteria, Bacteroidetes, and Chloroflexi either capable of PCB dechlorination, or detected in the PCB-contaminated environment. At genus level, the BER contained two types of microorganisms: electrochemically active bacteria (EAB) represented by Geobacter, Ignavibacterium, and Dysgonomonas, and dechlorinating bacteria including Hydrogenophaga, Alcanivorax, Sedimentibacter, Dehalogenimonas, Comamonas and Vibrio. These results suggest that the presence of EAB can promote the population of dechlorinating bacteria which are responsible for PCB 61 transformation.

Reorganization of a synthetic microbial consortium for one-step vitamin C fermentation

Background

In the industry, the conventional two-step fermentation method was used to produce 2-keto-l-gulonic acid (2-KGA), the precursor of vitamin C, by three strains, namely, Gluconobacter oxydans, Bacillus spp. and Ketogulonicigenium vulgare. Despite its high production efficiency, the long incubation period and an additional second sterilization process inhibit the further development. Therefore, we aimed to reorganize a synthetic consortium of G. oxydans and K. vulgare for one-step fermentation of 2-KGA and enhance the symbiotic interaction between microorganisms to perform better.

Results

During the fermentation, competition for sorbose of G. oxydans arose when co-cultured with K. vulgare. In this study, the competition between the two microbes was alleviated and their mutualism was enhanced by deleting genes involved in sorbose metabolism of G. oxydans. In the engineered synthetic consortium (H₆ + Kv), the yield of 2-KGA (mol/mol) against d-sorbitol reached 89.7 % within 36 h, increased by 29.6 %. Furthermore, metabolomic analysis was used to verify the enhancement of the symbiotic relationship and to provide us potential strategies for improving the synthetic consortium. Additionally, a significant redistribution of metabolism occurred by co-culturing the K. vulgare with the engineered G. oxydans, mainly reflected in the increased TCA cycle, purine, and fatty acid metabolism.

Conclusions

We reorganized and optimized a synthetic consortium of G. oxydans and K. vulgare to produce 2-KGA directly from d-sorbitol. The yield of 2-KGA was comparable to that of the conventional two-step fermentation. The metabolic interaction between the strains was further investigated by metabolomics, which verified the enhancement of the mutualism between the microbes and gave us a better understanding of the synthetic consortium.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0418-6) contains supplementary material, which is available to authorized users.

Methane Emission in a Specific Riparian-Zone Sediment Decreased with Bioelectrochemical Manipulation and Corresponded to the Microbial Community Dynamics

Dissimilatory metal-reducing bacteria are widespread in terrestrial ecosystems, especially in anaerobic soils and sediments. Thermodynamically, dissimilatory metal reduction is more favorable than sulfate reduction and methanogenesis but less favorable than denitrification and aerobic respiration. It is critical to understand the complex relationships, including the absence or presence of terminal electron acceptors, that govern microbial competition and coexistence in anaerobic soils and sediments, because subsurface microbial processes can effect greenhouse gas emissions from soils, possibly resulting in impacts at the global scale. Here, we elucidated the effect of an inexhaustible, ferrous-iron and humic-substance mimicking terminal electron acceptor by deploying potentiostatically poised electrodes in the sediment of a very specific stream riparian zone in Upstate New York state. At two sites within the same stream riparian zone during the course of 6 weeks in the spring of 2013, we measured CH4 and N2/N2O emissions from soil chambers containing either poised or unpoised electrodes, and we harvested biofilms from the electrodes to quantify microbial community dynamics. At the upstream site, which had a lower vegetation cover and highest soil temperatures, the poised electrodes inhibited CH4 emissions by ∼45% (when normalized to remove temporal effects). CH4 emissions were not significantly impacted at the downstream site. N2/N2O emissions were generally low at both sites and were not impacted by poised electrodes. We did not find a direct link between bioelectrochemical treatment and microbial community membership; however, we did find a correspondence between environment/function and microbial community dynamics.

Synthetic Ecology of Microbes: Mathematical Models and Applications

As the indispensable role of natural microbial communities in many aspects of life on Earth is uncovered, the bottom-up engineering of synthetic microbial consortia with novel functions is becoming an attractive alternative to engineering single-species systems. Here, we summarize recent work on synthetic microbial communities with a particular emphasis on open challenges and opportunities in environmental sustainability and human health. We next provide a critical overview of mathematical approaches, ranging from phenomenological to mechanistic, to decipher the principles that govern the function, dynamics and evolution of microbial ecosystems. Finally, we present our outlook on key aspects of microbial ecosystems and synthetic ecology that require further developments, including the need for more efficient computational algorithms, a better integration of empirical methods and model-driven analysis, the importance of improving gene function annotation, and the value of a standardized library of well-characterized organisms to be used as building blocks of synthetic communities.

Three-dimensional graphene/Pt nanoparticle composites as freestanding anode for enhancing performance of microbial fuel cells

Microbial fuel cells (MFCs) are able to directly convert about 50 to 90% of energy from oxidation of organic matters in waste to electricity and have great potential application in broad fields such as wastewater treatment. Unfortunately, the power density of the MFCs at present is significantly lower than the theoretical value because of technical limitations including low bacteria loading capacity and difficult electron transfer between the bacteria and the electrode. We reported a three-dimensional (3D) graphene aerogel (GA) decorated with platinum nanoparticles (Pt NPs) as an efficient freestanding anode for MFCs. The 3D GA/Pt-based anode has a continuous 3D macroporous structure that is favorable for microorganism immobilization and efficient electrolyte transport. Moreover, GA scaffold is homogenously decorated with Pt NPs to further enhance extracellular charge transfer between the bacteria and the anode. The MFCs constructed with 3D GA/Pt-based anode generate a remarkable maximum power density of 1460 mW/m(2), 5.3 times higher than that based on carbon cloth (273 mW/m(2)). It deserves to be stressed that 1460 mW/m(2) obtained from the GA/Pt anode shows the superior performance among all the reported MFCs inoculated with Shewanella oneidensis MR-1. Moreover, as a demonstration of the real application, the MFC equipped with the freestanding GA/Pt anode has been successfully applied in driving timer for the first time, which opens the avenue toward the real application of the MFCs.

Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism--case study of Faecalibacterium prausnitzii

Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 10(4) to 5 × 10(7) cells.mL(-1)). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM; kcat = 5.3 × 10(5) s(-1), at 37 °C) and glucose (KM = 6 μM; kcat = 2.4 × 10(5) s(-1)). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.

Metabolite-enabled mutualistic interaction between Shewanella oneidensis and Escherichia coli in a co-culture using an electrode as electron acceptor

Mutualistic interactions in planktonic microbial communities have been extensively studied. However, our understanding on mutualistic communities consisting of co-existing planktonic cells and biofilms is limited. Here, we report a planktonic cells-biofilm mutualistic system established by the fermentative bacterium Escherichia coli and the dissimilatory metal-reducing bacterium Shewanella oneidensis in a bioelectrochemical device, where planktonic cells in the anode media interact with the biofilms on the electrode. Our results show that the transfer of formate is the key mechanism in this mutualistic system. More importantly, we demonstrate that the relative distribution of E. coli and S. oneidensis in the liquid media and biofilm is likely driven by their metabolic functions towards an optimum communal metabolism in the bioelectrochemical device. RNA sequencing-based transcriptomic analyses of the interacting organisms in the mutualistic system potentially reveal differential expression of genes involved in extracellular electron transfer pathways in both species in the planktonic cultures and biofilms.

Improving mediated electron transport in anodic bioelectrocatalysis

A microbial fuel cell loaded with bio-cocatalyst beads immobilized with recombinant riboflavin-secreting Escherichia coli shows significantly enhanced performance.

Coupling electric energy and biogas production in anaerobic digesters – impacts on the microbiome

Microbiome based anaerobic digestion combined with microbial electrochemical technologies exploits biomass efficiently and flexibly by concurrent conversion to methane and electrons.

Combining microbial cultures for efficient production of electricity from butyrate in a microbial electrochemical cell

Butyrate is an important product of anaerobic fermentation; however, it is not directly used by characterized strains of the highly efficient anode respiring bacteria (ARB) Geobacter sulfurreducens in microbial electrochemical cells. By combining a butyrate-oxidizing community with a Geobacter rich culture, we generated a microbial community which outperformed many naturally derived communities found in the literature for current production from butyrate and rivaled the highest performing natural cultures in terms of current density (∼ 11A/m(2)) and Coulombic efficiency (∼ 70%). Microbial community analyses support the shift in the microbial community from one lacking efficient ARB in the marine hydrothermal vent community to a community consisting of ∼ 80% Geobacter in the anode biofilm. This demonstrates the successful production and adaptation of a novel microbial culture for generating electrical current from butyrate with high current density and high Coulombic efficiency, by combining two mixed microbial cultures containing complementing biochemical pathways.

The effect of salinity, redox mediators and temperature on anaerobic biodegradation of petroleum hydrocarbons in microbial fuel cells

Microbial fuel cells (MFCs) need to be robust if they are to be applied in the field for bioremediation. This study investigated the effect of temperature (20-50°C), salinity (0.5-2.5% (w/v) as sodium chloride), the use of redox mediators (riboflavin and anthraquinone-2-sulphonate, AQS) and prolonged fed-batch operation (60 days) on biodegradation of a petroleum hydrocarbon mix (i.e. phenanthrene and benzene) in MFCs. The performance criteria were degradation efficiency, % COD removal and electrochemical performance. Good electrochemical and degradation performance were maintained up to a salinity of 1.5% (w/v) but deteriorated by 35-fold and 4-fold respectively as salinity was raised to 2.5%w/v. Degradation rates and maximum power density were both improved by approximately 2-fold at 40°C compared to MFC performance at 30°C but decreased sharply by 4-fold when operating temperature was raised to 50°C. The optimum reactor performance obtained at 40°C was 1.15 mW/m(2) maximum power density, 89.1% COD removal and a degradation efficiency of 97.10%; at moderately saline (1% w/v) conditions the maximum power density was 1.06 mW/m(2), 79.1% COD removal and 91.6% degradation efficiency. This work suggests the possible application of MFC technology in the effective treatment of petroleum hydrocarbons contaminated site and refinery effluents.

Synthetic microbial consortia: from systematic analysis to construction and applications

Synthetic biology is an emerging research field that focuses on using rational engineering strategies to program biological systems, conferring on them new functions and behaviours. By developing genetic parts and devices based on transcriptional, translational, post-translational modules, many genetic circuits and metabolic pathways had been programmed in single cells. Extending engineering capabilities from single-cell behaviours to multicellular microbial consortia represents a new frontier of synthetic biology. Herein, we first reviewed binary interaction modes of microorganisms in microbial consortia and their underlying molecular mechanisms, which lay the foundation of programming cell-cell interactions in synthetic microbial consortia. Systems biology studies on cellular systems enable systematic understanding of diverse physiological processes of cells and their interactions, which in turn offer insights into the optimal design of synthetic consortia. Based on such fundamental understanding, a comprehensive array of synthetic microbial consortia constructed in the last decade were reviewed, including isogenic microbial communities programmed by quorum sensing-based cell-cell communications, sender-receiver microbial communities with one-way communications, and microbial ecosystems wired by two-way (bi-directional) communications. Furthermore, many applications including using synthetic microbial consortia for distributed bio-computations, chemicals and bioenergy production, medicine and human health, and environments were reviewed. Synergistic development of systems and synthetic biology will provide both a thorough understanding of naturally occurring microbial consortia and rational engineering of these complicated consortia for novel applications.

Electroanalysis of microbial anodes for bioelectrochemical systems: basics, progress and perspectives

Over about the last ten years, microbial anodes have been the subject of a huge number of fundamental studies dealing with an increasing variety of possible application domains.

Bio-current as an indicator for biogenic Fe(II) generation driven by dissimilatory iron reducing bacteria

Microbial reduction of insoluble iron minerals by dissimilatory iron reducing bacteria (DIRB) is an important environment process in the iron biogeochemical cycle. We reported that the bio-current generated from oxidation of organic matter by these bacteria in the presence of iron oxides can be used as an indicator for microbial dissolution of insoluble iron oxides. Bioelectrochemical experiments were conducted to investigate the effects of the specific bacteria and the phase identity of iron oxides on bio-current generation by recording the current response as a result of a poised constant potential. Experimental results indicated that the bio-current generation can be greatly enhanced by iron oxide addition under all the conditions varying in the type of pure culture or iron oxide. The increase in the bio-current was linearly correlated with the increased concentration of biogenic Fe(II) detected either by chemical analysis or cyclic voltammetry (CV) tests. This can be understood based on the proposed mechanism that the Fe(II)/Fe(III) couple functions as the electron mediator shuttling electrons from the microbes to the electrodes.

Detection of transcriptional triggers in the dynamics of microbial growth: application to the respiratorily versatile bacterium Shewanella oneidensis

The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making regulatory circuits. Here, we seek to understand the interplay between these two processes by combining high-throughput measurement of time-dependent mRNA profiles with a novel computational approach that searches for key genetic triggers of transcriptional changes. Our approach helped us understand the regulatory strategies of a respiratorily versatile bacterium with promising bioenergy and bioremediation applications, Shewanella oneidensis, in minimal and rich media. By comparing expression profiles across these two conditions, we unveiled components of the transcriptional program that depend mainly on the growth phase. Conversely, by integrating our time-dependent data with a previously available large compendium of static perturbation responses, we identified transcriptional changes that cannot be explained solely by internal network dynamics, but are rather triggered by specific genes acting as key mediators of an environment-dependent response. These transcriptional triggers include known and novel regulators that respond to carbon, nitrogen and oxygen limitation. Our analysis suggests a sequence of physiological responses, including a coupling between nitrogen depletion and glycogen storage, partially recapitulated through dynamic flux balance analysis, and experimentally confirmed by metabolite measurements. Our approach is broadly applicable to other systems.

Transcriptional analysis of Shewanella oneidensis MR-1 with an electrode compared to Fe(III)citrate or oxygen as terminal electron acceptor

Shewanella oneidensis is a target of extensive research in the fields of bioelectrochemical systems and bioremediation because of its versatile metabolic capabilities, especially with regard to respiration with extracellular electron acceptors. The physiological activity of S. oneidensis to respire at electrodes is of great interest, but the growth conditions in thin-layer biofilms make physiological analyses experimentally challenging. Here, we took a global approach to evaluate physiological activity with an electrode as terminal electron acceptor for the generation of electric current. We performed expression analysis with DNA microarrays to compare the overall gene expression with an electrode to that with soluble iron(III) or oxygen as the electron acceptor and applied new hierarchical model-based statistics for the differential expression analysis. We confirmed the differential expression of many genes that have previously been reported to be involved in electrode respiration, such as the entire mtr operon. We also formulate hypotheses on other possible gene involvements in electrode respiration, for example, a role of ScyA in inter-protein electron transfer and a regulatory role of the cbb3-type cytochrome c oxidase under anaerobic conditions. Further, we hypothesize that electrode respiration imposes a significant stress on S. oneidensis, resulting in higher energetic costs for electrode respiration than for soluble iron(III) respiration, which fosters a higher metabolic turnover to cover energy needs. Our hypotheses now require experimental verification, but this expression analysis provides a fundamental platform for further studies into the molecular mechanisms of S. oneidensis electron transfer and the physiologically special situation of growth on a poised-potential surface.