Discover insights from thousands of peer-reviewed papers on microbial electrochemical systems
Linxia Liu, Jinlong Li, Yuanming Gai et al.
Nature Communications · 2023
Vitamin B6 is an essential nutrient with extensive applications in the medicine, food, animal feed, and cosmetics industries. Pyridoxine (PN), the most common commercial form of vitamin B6, is currently chemically synthesized using expensive and toxic chemicals. However, the low catalytic efficiencies of natural enzymes and the tight regulation of the metabolic pathway have hindered PN production by the microbial fermentation process. Here, we report an engineered Escherichia coli strain for PN production. Parallel pathway engineering is performed to decouple PN production and cell growth. Further, protein engineering is rationally designed including the inefficient enzymes PdxA, PdxJ, and the initial enzymes Epd and Dxs. By the iterative multimodule optimization strategy, the final strain produces 1.4 g/L of PN with productivity of 29.16 mg/L/h by fed-batch fermentation. The strategies reported here will be useful for developing microbial strains for the production of vitamins and other bioproducts having inherently low metabolic fluxes.
Melodie M. Machovina, S.J.B. Mallinson, B. Knott et al.
Proceedings of the National Academy of Sciences · 2019
Significance Lignin is an abundant but underutilized heterogeneous polymer found in terrestrial plants. In current lignocellulosic biorefinery paradigms, lignin is primarily slated for incineration, but for a nonfood plant-based bioeconomy to be successful, lignin valorization is critical. An emerging concept to valorize lignin uses aromatic–catabolic pathways and microbes to funnel heterogeneous lignin-derived aromatic compounds to single high-value products. For this approach to be viable, the discovery and engineering of enzymes to conduct key reactions is critical. In this work, we have engineered a two-component cytochrome P450 enzyme system to conduct one of the most important reactions in biological lignin conversion: aromatic O-demethylation of syringol, the base aromatic unit of S-lignin, which is highly abundant in hardwoods and grasses. Microbial conversion of aromatic compounds is an emerging and promising strategy for valorization of the plant biopolymer lignin. A critical and often rate-limiting reaction in aromatic catabolism is O-aryl-demethylation of the abundant aromatic methoxy groups in lignin to form diols, which enables subsequent oxidative aromatic ring-opening. Recently, a cytochrome P450 system, GcoAB, was discovered to demethylate guaiacol (2-methoxyphenol), which can be produced from coniferyl alcohol-derived lignin, to form catechol. However, native GcoAB has minimal ability to demethylate syringol (2,6-dimethoxyphenol), the analogous compound that can be produced from sinapyl alcohol-derived lignin. Despite the abundance of sinapyl alcohol-based lignin in plants, no pathway for syringol catabolism has been reported to date. Here we used structure-guided protein engineering to enable microbial syringol utilization with GcoAB. Specifically, a phenylalanine residue (GcoA-F169) interferes with the binding of syringol in the active site, and on mutation to smaller amino acids, efficient syringol O-demethylation is achieved. Crystallography indicates that syringol adopts a productive binding pose in the variant, which molecular dynamics simulations trace to the elimination of steric clash between the highly flexible side chain of GcoA-F169 and the additional methoxy group of syringol. Finally, we demonstrate in vivo syringol turnover in Pseudomonas putida KT2440 with the GcoA-F169A variant. Taken together, our findings highlight the significant potential and plasticity of cytochrome P450 aromatic O-demethylases in the biological conversion of lignin-derived aromatic compounds.
Giles Obinna Ndochinwa, Qing-Yan Wang, N. O. Okoro et al.
Open Life Sciences · 2024
Abstract Recent advancements in protein/enzyme engineering have enabled the production of a diverse array of high-value compounds in microbial systems with the potential for industrial applications. The goal of this review is to articulate some of the most recent protein engineering advances in bacteria, yeast, and other microbial systems to produce valuable substances. These high-value substances include α-farnesene, vitamin B12, fumaric acid, linalool, glucaric acid, carminic acid, mycosporine-like amino acids, patchoulol, orcinol glucoside, d-lactic acid, keratinase, α-glucanotransferases, β-glucosidase, seleno-methylselenocysteine, fatty acids, high-efficiency β-glucosidase enzymes, cellulase, β-carotene, physcion, and glucoamylase. Additionally, recent advances in enzyme engineering for enhancing thermostability will be discussed. These findings have the potential to revolutionize various industries, including biotechnology, food, pharmaceuticals, and biofuels.
Kristof Verbeeck, Jo De Vrieze, Ilje Pikaar et al.
Microbial Biotechnology · 2021
Summary Anaerobic digesters produce biogas, a mixture of predominantly CH 4 and CO 2 , which is typically incinerated to recover electrical and/or thermal energy. In a context of circular economy, the CH 4 and CO 2 could be used as chemical feedstock in combination with ammonium from the digestate. Their combination into protein‐rich bacterial, used as animal feed additive, could contribute to the ever growing global demand for nutritive protein sources and improve the overall nitrogen efficiency of the current agro‐ feed/food chain. In this concept, renewable CH 4 and H 2 can serve as carbon‐neutral energy sources for the production of protein‐rich cellular biomass, while assimilating and upgrading recovered ammonia from the digestate. This study evaluated the potential of producing sustainable high‐quality protein additives in a decentralized way through coupling anaerobic digestion and microbial protein production using methanotrophic and hydrogenotrophic bacteria in an on‐farm bioreactor. We show that a practical case digester handling liquid piggery manure, of which the energy content is supplemented for 30% with co‐substrates, provides sufficient biogas to allow the subsequent microbial protein as feed production for about 37% of the number of pigs from which the manure was derived. Overall, producing microbial protein on the farm from available methane and ammonia liberated by anaerobic digesters treating manure appears economically and technically feasible within the current range of market prices existing for high‐quality protein. The case of producing biomethane for grid injection and upgrading the CO 2 with electrolytic hydrogen to microbial protein by means of hydrogen‐oxidizing bacteria was also examined but found less attractive at the current production prices of renewable hydrogen. Our calculations show that this route is only of commercial interest if the protein value equals the value of high‐value protein additives like fishmeal and if the avoided costs for nutrient removal from the digestate are taken into consideration.
Hongyu Zhao, Zhenyu Yao, Xiangbin Chen et al.
Microbial Biotechnology · 2017
Summary Phasins are unusual amphiphilic proteins that bind to microbial polyhydroxyalkanoate ( PHA ) granules in nature and show great potential for various applications in biotechnology and medicine. Despite their remarkable diversity, only the crystal structure of Pha P A h from Aeromonas hydrophila has been solved to date. Based on the structure of Pha P A h , homology models of Pha P A z from Azotobacter sp . FA ‐8 and Pha P TD from Halomonas bluephagenesis TD were successfully established, allowing rational mutagenesis to be conducted to enhance the stability and surfactant properties of these proteins. Pha P A z mutants, including Pha P A z Q38L and Pha P A z Q78L, as well as Pha P TD mutants, including Pha P TD Q 38M and Pha P TD Q 72M, showed better emulsification properties and improved thermostability (6‐10°C higher melting temperatures) compared with their wild‐type homologues under the same conditions. Importantly, the established PhaP homology‐modelling approach, based on the high‐resolution structure of Pha P A h , can be generalized to facilitate the study of other PhaP members.
Jitendra Kumar
Advances in Poultry Nutrition Research · 2021
Feathers are hard waste products, mainly composed of hard β-keratin, and are produced in large quantities in commercial poultry processing plants. Therefore, their industrial utilization is important economically as well as environmentally. Feathers degradation through keratinolytic microorganisms has been considered as an important method for efficient bioconversion, nutritional enhancement and eco-friendliness. The use of crude keratinase significantly increased the amino acid digestibility of raw feathers and commercial feather meal. This enzyme increased the digestibility of commercial feather meal and could replace as much as 7% of the dietary protein for growing chicks. However, feathers are currently utilized on a limited basis as a dietary protein supplement for animal feed because feather meal production is an expensive process, requiring significant amounts of energy. This review paper explains the nutritive value of feathers which makes suitable and inexpensive animal and poultry feed.
Jackson Z. Lee, Andrew Logan, Seth Terry et al.
Microbial Biotechnology · 2015
Summary As global fisheries decline, microbial single‐cell protein ( SCP ) produced from brewery process water has been highlighted as a potential source of protein for sustainable animal feed. However, biotechnological investigation of SCP is difficult because of the natural variation and complexity of microbial ecology in wastewater bioreactors. In this study, we investigate microbial response across a full‐scale brewery wastewater treatment plant and a parallel pilot bioreactor modified to produce an SCP product. A pyrosequencing survey of the brewery treatment plant showed that each unit process selected for a unique microbial community. Notably, flow equalization basins were dominated by P revotella , methanogenesis effluent had the highest levels of diversity, and clarifier wet‐well samples were sources of sequences for the candidate bacterial phyla of TM 7 and BD 1‐5. Next, the microbial response of a pilot bioreactor producing SCP was tracked over 1 year, showing that two different production trials produced two different communities originating from the same starting influent. However, SCP production resulted generally in enrichment of several clades of rhizospheric diazotrophs of A lphaproteobacteria and B etaproteobacteria in the bioreactor and even more so in the final product. These diazotrophs are potentially useful as the basis of a SCP product for commercial feed production.
Joseph A. Gredell, Christopher S. Frei, Patrick C. Cirino
Biotechnology Journal · 2012
Abstract Nature takes advantage of the malleability of protein and RNA sequence and structure to employ these macromolecules as molecular reporters whose conformation and functional roles depend on the presence of a specific ligand (an “effector” molecule). By following nature's example, ligand‐responsive proteins and RNA molecules are now routinely engineered and incorporated into customized molecular reporting systems (biosensors). Microbial small‐molecule biosensors and endogenous molecular reporters based on these sensing components find a variety of applications that include high‐throughput screening of biosynthesis libraries, environmental monitoring, and novel gene regulation in synthetic biology. Here, we review recent advances in engineering small‐molecule recognition by proteins and RNA and in coupling in vivo ligand binding to reporter‐gene expression or to allosteric activation of a protein conferring a detectable phenotype. Emphasis is placed on microbial screening systems that serve as molecular reporters and facilitate engineering the ligand‐binding component to recognize new molecules.
Silvio Matassa, Nico Boon, Ilje Pikaar et al.
Microbial Biotechnology · 2016
Summary Microbial biotechnology has a long history of producing feeds and foods. The key feature of today's market economy is that protein production by conventional agriculture based food supply chains is becoming a major issue in terms of global environmental pollution such as diffuse nutrient and greenhouse gas emissions, land use and water footprint. Time has come to re‐assess the current potentials of producing protein‐rich feed or food additives in the form of algae, yeasts, fungi and plain bacterial cellular biomass, producible with a lower environmental footprint compared with other plant or animal‐based alternatives. A major driver is the need to no longer disintegrate but rather upgrade a variety of low‐value organic and inorganic side streams in our current non‐cyclic economy. In this context, microbial bioconversions of such valuable matters to nutritive microbial cells and cell components are a powerful asset. The worldwide market of animal protein is of the order of several hundred million tons per year, that of plant protein several billion tons of protein per year; hence, the expansion of the production of microbial protein does not pose disruptive challenges towards the process of the latter. Besides protein as nutritive compounds, also other cellular components such as lipids (single cell oil), polyhydroxybuthyrate, exopolymeric saccharides, carotenoids, ectorines, (pro)vitamins and essential amino acids can be of value for the growing domain of novel nutrition. In order for microbial protein as feed or food to become a major and sustainable alternative, addressing the challenges of creating awareness and achieving public and broader regulatory acceptance are real and need to be addressed with care and expedience.
Anping Su, Qijun Yu, Ying Luo et al.
Microbial Biotechnology · 2021
Summary Gamma‐aminobutyric acid (GABA) and delta‐aminolevulinic acid (ALA), playing important roles in agriculture, medicine and other fields, are multifunctional non‐protein amino acids with similar and comparable properties and biosynthesis pathways. Recently, microbial synthesis has become an inevitable trend to produce GABA and ALA due to its green and sustainable characteristics. In addition, the development of metabolic engineering and synthetic biology has continuously accelerated and increased the GABA and ALA yield in microorganisms. Here, focusing on the current trends in metabolic engineering strategies for microbial synthesis of GABA and ALA, we analysed and compared the efficiency of various metabolic strategies in detail. Moreover, we provide the insights to meet challenges of realizing industrially competitive strains and highlight the future perspectives of GABA and ALA production.
Meirong Zhao, Jianfan Ma, Lei Zhang et al.
Microbial Cell Factories · 2024
Abstract Microbial proteins are promising substitutes for animal- and plant-based proteins. S. cerevisiae , a generally recognized as safe (GRAS) microorganism, has been frequently employed to generate heterologous proteins. However, constructing a universal yeast chassis for efficient protein production is still a challenge due to the varying properties of different proteins. With progress in synthetic biology, a multitude of molecular biology tools and metabolic engineering strategies have been employed to alleviate these issues. This review first analyses the advantages of protein production by S. cerevisiae . The most recent advances in improving heterologous protein yield are summarized and discussed in terms of protein hyperexpression systems, protein secretion engineering, glycosylation pathway engineering and systems metabolic engineering. Furthermore, the prospects for efficient and sustainable heterologous protein production by S. cerevisiae are also provided.
Marianna Villano, Federico Aulenta, Mauro Majone
Asia-Pacific Journal of Chemical Engineering · 2012
ABSTRACT Bioelectrochemical systems (BESs) are an emerging technology that uses solid‐state electrodes to stimulate microbial metabolism (either for substrate degradation or for products formation). Because of their versatility and unmatched level of control over the biological reactions, BESs hold a great potential for application in industrial and environmental bioprocesses. Among them, the bioelectrochemical production of renewable and carbon‐neutral energy carriers, such as hydrogen and methane, at the cathode of bioelectrochemical systems is recently attracting considerable attention. While exciting as a concept, the performance of the process seems to be still primarily limited by the low kinetics and efficiencies of the cathodic reactions. In this review, key opportunities for gaseous biofuels production with bioelectrochemical systems are addressed and compared with existing biotechnological approaches such as anaerobic digestion and dark fermentation. The major bottlenecks and challenges that still need to be faced to make this novel technology practical are presented and critically discussed. © 2012 Curtin University of Technology and John Wiley & Sons, Ltd.
Alice Boo, Harman Mehta, Rodrigo Ledesma Amaro et al.
bioRxiv (Cold Spring Harbor Laboratory) · 2023
Abstract Microbial consortia have been utilised for centuries to produce fermented foods and have great potential in applications such as therapeutics, biomaterials, fertilisers, and biobased production. Working together, microbes become specialized and perform complex tasks more efficiently, strengthening both cooperation and stability of the microbial community. However, imbalanced proportions of microbial community members can lead to unoptimized and diminished yields in biotechnology. To address this, we developed a burden-aware RNA-based multicellular feedback control system that stabilises and tunes coculture compositions. The system consists of three modules: a quorum sensing-based communication module to provide information about the densities of cocultured strains, an RNA-based comparator module to compare the ratio of densities of both strains to a pre-set desired ratio, and a customisable growth module that relies either on heterologous gene expression or on CRISPRi knockdowns to tune growth rates. We demonstrated that heterologous expression burden could be used to stabilise composition in a two-member E. coli coculture. This is the first coculture composition controller that does not rely on toxins or syntrophy for growth regulation and uses RNA sequestration to stabilise and control coculture composition. This work provides a fundamental basis to explore burden-aware multicellular feedback control strategies for robust stabilisation of synthetic community compositions.
Jong-Won Lee, Cong T. Trinh
bioRxiv (Cold Spring Harbor Laboratory) · 2018
ABSTRACT Background Green organic solvents such as lactate esters have broad industrial applications and favorable environmental profiles. Thus, manufacturing and use of these biodegradable solvents from renewable feedstocks help benefit the environment. However, to date, the direct microbial biosynthesis of lactate esters from fermentable sugars has not yet been demonstrated. Results In this study, we present a microbial conversion platform for direct biosynthesis of lactate esters from fermentable sugars. First, we designed a pyruvate-to-lactate ester module, consisting of a lactate dehydrogenase ( ldhA ) to convert pyruvate to lactate, a propionate CoA-transferase ( pct ) to convert lactate to lactyl-CoA, and an alcohol acyltransferase ( AAT ) to condense lactyl-CoA and alcohol(s) to make lactate ester(s). By generating a library of five pyruvate-to-lactate ester modules with divergent AATs, we screened for the best module(s) capable of producing a wide range of linear, branched, and aromatic lactate esters with an external alcohol supply. By co-introducing a pyruvate-to-lactate ester module and an alcohol (i.e., ethanol, isobutanol) module into a modular Escherichia coli (chassis) cell, we demonstrated for the first time the microbial biosynthesis of ethyl and isobutyl lactate esters directly from glucose. In an attempt to enhance ethyl lactate production as a proof-of-study, we re-modularized the pathway into 1) the upstream module to generate the ethanol and lactate precursors and 2) the downstream module to generate lactyl-CoA and condense it with ethanol to produce the target ethyl lactate. By manipulating the metabolic fluxes of the upstream and downstream modules through plasmid copy numbers, promoters, ribosome binding sites, and environmental perturbation, we were able to probe and alleviate the metabolic bottlenecks by improving ethyl lactate production by 4.96-fold. We found that AAT is the most rate limiting step in biosynthesis of lactate esters likely due to its low activity and specificity towards the non-natural substrate lactyl-CoA and alcohols. Conclusions We have successfully established the biosynthesis pathway of lactate esters from fermentable sugars and demonstrated for the first time the direct fermentative production of lactate esters from glucose using an E. coli modular cell. This study defines a cornerstone for the microbial production of lactate esters as green solvents from renewable resources with novel industrial applications.
Kenneth T. Walker, Ivy S Li, Jennifer Keane et al.
Nature Biotechnology · 2024
Environmental concerns are driving interest in postpetroleum synthetic textiles produced from microbial and fungal sources. Bacterial cellulose (BC) is a promising sustainable leather alternative, on account of its material properties, low infrastructure needs and biodegradability. However, for alternative textiles like BC to be fully sustainable, alternative ways to dye textiles need to be developed alongside alternative production methods. To address this, we genetically engineer Komagataeibacter rhaeticus to create a bacterial strain that grows self-pigmenting BC. Melanin biosynthesis in the bacteria from recombinant tyrosinase expression achieves dark black coloration robust to material use. Melanated BC production can be scaled up for the construction of prototype fashion products, and we illustrate the potential of combining engineered self-pigmentation with tools from synthetic biology, through the optogenetic patterning of gene expression in cellulose-producing bacteria. With this study, we demonstrate that combining genetic engineering with current and future methods of textile biofabrication has the potential to create a new class of textiles.
Ying-Ying Chen, Jia-Cong Huang, Cai-Yun Wu et al.
Critical Reviews in Biotechnology · 2024
Abstract 5-Aminolevulinic acid (5-ALA) is a non-proteinogenic amino acid essential for synthesizing tetrapyrrole compounds, including heme, chlorophyll, cytochrome, and vitamin B12. As a plant growth regulator, 5-ALA is extensively used in agriculture to enhance crop yield and quality. The complexity and low yield of chemical synthesis methods have led to significant interest in the microbial synthesis of 5-ALA. Advanced strategies, including the: enhancement of precursor and cofactor supply, compartmentalization of key enzymes, product transporters engineering, by-product formation reduction, and biosensor-based dynamic regulation, have been implemented in bacteria for 5-ALA production, significantly advancing its industrialization. This article offers a comprehensive review of recent developments in 5-ALA production using engineered bacteria and presents new insights to propel the field forward. Graphical Abstract
Yaofeng Zhou, Qianying Li, Yuhao Wu et al.
Advanced Materials · 2024
Engineered bacteria are widely used in cancer treatment because live facultative/obligate anaerobes can selectively proliferate at tumor sites and reach hypoxic regions, thereby causing nutritional competition, enhancing immune responses, and producing anticancer microbial agents in situ to suppress tumor growth. Despite the unique advantages of bacteria‐based cancer biotherapy, the insufficient treatment efficiency limits its application in the complete ablation of malignant tumors. The combination of nanomedicine and engineered bacteria has attracted increasing attention owing to their striking synergistic effects in cancer treatment. Engineered bacteria that function as natural vehicles can effectively deliver nanomedicines to tumor sites. Moreover, bacteria provide an opportunity to enhance nanomedicines by modulating the TME and producing substrates to support nanomedicine‐mediated anticancer reactions. Nanomedicine exhibits excellent optical, magnetic, acoustic, and catalytic properties, and plays an important role in promoting bacteria‐mediated biotherapies. The synergistic anticancer effects of engineered bacteria and nanomedicines in cancer therapy are comprehensively summarized in this review. Attention is paid not only to the fabrication of nanobiohybrid composites, but also to the interpromotion mechanism between engineered bacteria and nanomedicine in cancer therapy. Additionally, recent advances in engineered bacteria‐synergized multimodal cancer therapies are highlighted.
Laure Lapinsonnière, Matthieu Picot, F. Barrière
ChemSusChem · 2012
Catalyses of electrode reactions by oxidoreductases or living electroactive bacteria are compared and recent advances reviewed. The relation between the biological and nevertheless inert nature of enzymes and the living machinery of electroactive microbes is discussed. The way these biocatalysts may be electrically contacted to anodes or cathodes is considered with a focus on their immobilization at electrodes and on the issue of time stability of these assemblies. Recent improvements in power output of biofuel cells are reviewed together with applications that have appeared in the literature. This account also reviews new approaches for combining enzymes and living microbes in bioelectrochemical systems such as reproducing microbial metabolisms with enzyme cascades and expressing oxidoreductases on genetically engineered microbes. Finally, the use of surface chemistry for studying the microbe-electrode interface and bioelectrodes with cell organelles, such as mitochondria, or with higher organisms, such as yeasts, are discussed. Some perspectives for future research to extend this field are offered as conclusions.
N. Sekar, Jian Wang, Yan Zhou et al.
Biotechnology and Bioengineering · 2018
Cyanobacteria are used as anode catalysts in photo-bioelectrochemical cells to generate electricity in a sustainable, economic, and environmental friendly manner using only water and sunlight. Though cyanobacteria (CB) possess unique advantage for solar energy conversion by virtue of its robust photosynthesis, they cannot efficiently perform extracellular electron transfer (EET). The reasons being, unlike dissimilatory metal reducing bacteria (that are usually exploited in microbial fuel cells to generate electricity), (1) CB do not possess any special features on their outer membrane to carry out EET and, (2) the electrons generated in photosynthetic electron transport chain are channeled into competing respiratory pathways rather than to the anode. CB, genetically engineered to express outer membrane cytochrome S (OmcS), was found to generate ∼nine-fold higher photocurrent compared to that of wild-type cyanobacterium in our previous work. In this study, each of the three respiratory terminal oxidases in Synechococcus elongatus PCC7942 namely bd-type quinol oxidase, aa3 -type cytochrome oxidase, and cbb3 -type cytochrome oxidase was knocked-out one at a time (cyd- , cox- , and cco- respectively) and its contribution for extracellular ferricyanide reduction and photocurrent generation was investigated. The knock-out mutant lacking functional bd-type quinol oxidase (cyd- ) exhibited greater EET by reducing more ferricyanide compared to other single knock-out mutants as well as the wild type. Further, cyd- omcs (the cyd- mutant expressing OmcS) was found to generate more photocurrent than the corresponding single knock out controls and the wild-type. This study clearly demonstrates that the bd-quinol oxidase diverted more electrons from the photosynthetic electron transport chain towards respiratory oxygen reduction and knocking it out had certainly enhanced the cyanobacterial EET.
Gen Nakagawa, A. Kouzuma, Atsumi Hirose et al.
PLOS ONE · 2015
In bioelectrochemical systems, the electrode potential is an important parameter affecting the electron flow between electrodes and microbes and microbial metabolic activities. Here, we investigated the metabolic characteristics of a glucose-utilizing strain of engineered Shewanella oneidensis under electrode-respiring conditions in electrochemical reactors for gaining insight into how metabolic pathways in electrochemically active bacteria are affected by the electrode potential. When an electrochemical reactor was operated with its working electrode poised at +0.4 V (vs. an Ag/AgCl reference electrode), the engineered S. oneidensis strain, carrying a plasmid encoding a sugar permease and glucose kinase of Escherichia coli, generated current by oxidizing glucose to acetate and produced D-lactate as an intermediate metabolite. However, D-lactate accumulation was not observed when the engineered strain was grown with a working electrode poised at 0 V. We also found that transcription of genes involved in pyruvate and D-lactate metabolisms was upregulated at a high electrode potential compared with their transcription at a low electrode potential. These results suggest that the carbon catabolic pathway of S. oneidensis can be modified by controlling the potential of a working electrode in an electrochemical bioreactor.
Lei Cheng, Di Min, Ru-Li He et al.
Biotechnology and Bioengineering · 2020
Shewanella oneidensis MR‐1, a model strain of exoelectrogenic bacteria (EEB), plays a key role in environmental bioremediation and bioelectrochemical systems because of its unique respiration capacity. However, only a narrow range of substrates can be utilized by S. oneidensis MR‐1 as carbon sources, resulting in its limited applications. In this study, a rapid, highly efficient, and easily manipulated base‐editing system pCBEso was developed by fusing a Cas9 nickase (Cas9n (D10A)) with the cytidine deaminase rAPOBEC1 in S. oneidensis MR‐1. The C‐to‐T conversion of suitable C within the base‐editing window could be readily and efficiently achieved by the pCBEso system without requiring double‐strand break or repair templates. Moreover, double‐locus simultaneous editing was successfully accomplished with an efficiency of 87.5%. With this tool, the key genes involving in N‐acetylglucosamine (GlcNAc) or glucose metabolism in S. oneidensis MR‐1 were identified. Furthermore, an engineered strain with expanded carbon source utilization spectra was constructed and exhibited a higher degradation rate for multiple organic pollutants (i.e., azo dyes and organoarsenic compounds) than the wild‐type when glucose or GlcNAc was used as the sole carbon source. Such a base‐editing system could be readily applied to other EEB. This study not only enhances the substrate utilization and pollutant degradation capacities of S. oneidensis MR‐1 but also accelerates the robust construction of engineered strains for environmental bioremediation.
Sandipan Banerjee, Nitu Gupta, Krishnendu Pramanik et al.
Environmental Science and Pollution Research · 2023
Degradation, detoxification, or removal of the omnipresent polycyclic aromatic hydrocarbons (PAHs) from the ecosphere as well as their prevention from entering into food chain has never appeared simple. In this context, cost-effective, eco-friendly, and sustainable solutions like microbe-mediated strategies have been adopted worldwide. With this connection, measures have been taken by multifarious modes of microbial remedial strategies, i.e., enzymatic degradation, biofilm and biosurfactant production, application of biochar-immobilized microbes, lactic acid bacteria, rhizospheric-phyllospheric-endophytic microorganisms, genetically engineered microorganisms, and bioelectrochemical techniques like microbial fuel cell. In this review, a nine-way directional approach which is based on the microbial resources reported over the last couple of decades has been described. Fungi were found to be the most dominant taxa among the CPAH-degrading microbial community constituting 52.2%, while bacteria, algae, and yeasts occupied 37.4%, 9.1%, and 1.3%, respectively. In addition to these, category-wise CPAH degrading efficiencies of each microbial taxon, consortium-based applications, CPAH degradation–related molecular tools, and factors affecting CPAH degradation are the other important aspects of this review in light of their appropriate selection and application in the PAH-contaminated environment for better human-health management in order to achieve a sustainable ecosystem. Graphical Abstract
Sara Díaz-Rullo Edreira, I. Vasiliadou, Amanda Prado et al.
Communications Biology · 2024
Reducing greenhouse gas emissions is critical for humanity nowadays, but it can be beneficial by developing engineered systems that valorize CO2 into commodities, thus mimicking nature’s wisdom. Purple phototrophic bacteria (PPB) naturally accept CO2 into their metabolism as a primary redox sink system in photo-heterotrophy. Dedicated use of this feature for developing sustainable processes (e.g., through negative-emissions photo-bioelectrosynthesis) requires a deep knowledge of the inherent metabolic mechanisms. This work provides evidence of tuning the PPB metabolic mechanisms upon redox stressing through negative polarization (−0.4 and −0.8 V vs. Ag/AgCl) in photo-bioelectrochemical devices. A mixed PPB-culture upregulates its ability to capture CO2 from organics oxidation through the Calvin-Besson-Bassam cycle and anaplerotic pathways, and the redox imbalance is promoted to polyhydroxyalkanoates production. The ecological relationship of PPB with mutualist bacteria stabilizes the system and opens the door for future development of photo-bioelectrochemical devices focused on CO up-cycling.
Yu‐Jing Jiang, Su Hui, Liping Jiang et al.
Chemistry – A European Journal · 2022
Microbial fuel cell (MFC) is a promising approach that could utilize microorganisms to oxidize biodegradable pollutants in wastewater and generate electrical power simultaneously. Introducing advanced anode nanomaterials is generally considered as an effective way to enhance MFC performance by increasing bacterial adhesion and facilitating bacteria extracellular electron transfer (EET). This review focuses on the key advances of recent anode modification materials, as well as the current understanding of the microbial EET process occurring at the bacteria-electrode interface. Based on the difference in combination mode of the exoelectrogens and nanomaterials, anode surface modification, hybrid biofilm construction and single-bacterial surface modification strategies are elucidated exhaustively. The inherent mechanisms may help to break through the performance output bottleneck of MFCs by rational design of EET-related nanomaterials, and lead to the widespread application of microbial electrochemical systems.
J. D'aes, Marie-Alice Fraiture, Bert Bogaerts et al.
Life · 2022
Genetically modified microorganisms (GMM) are frequently employed for manufacturing microbial fermentation products such as food enzymes or vitamins. Although the fermentation product is required to be pure, GMM contaminations have repeatedly been reported in numerous commercial microbial fermentation produce types, leading to several rapid alerts at the European level. The aim of this study was to investigate the added value of shotgun metagenomic high-throughput sequencing to confirm and extend the results of classical analysis methods for the genomic characterization of unauthorized GMM. By combining short- and long-read metagenomic sequencing, two transgenic constructs were characterized, with insertions of alpha-amylase genes originating from B. amyloliquefaciens and B. licheniformis, respectively, and a transgenic construct with a protease gene insertion originating from B. velezensis, which were all present in all four investigated samples. Additionally, the samples were contaminated with up to three unculturable Bacillus strains, carrying genetic modifications that may hamper their ability to sporulate. Moreover, several samples contained viable Bacillus strains. Altogether these contaminations constitute a considerable load of antimicrobial resistance genes, that may represent a potential public health risk. In conclusion, our study showcases the added value of metagenomics to investigate the quality and safety of complex commercial microbial fermentation products.
D. Nosek, O. Samsel, T. Pokój et al.
International Journal of Environmental Science and Technology · 2023
The commercialization of microbial fuel cell technology is limited by high operating costs and low electricity production due to poor electron transfer to the anode. Operational costs can be lowered by utilizing waste materials, and cell performance can be improved by anode modification. This study investigated how anode modification with iron compounds changed the efficiency of energy generation and the microbiome of microbial fuel cells fueled with waste volatile fatty acids from a full-scale anaerobic digestion. Anode modification with 2.5 g Fe_2O_3/m^2 increased the power density, current density, and voltage by 3.6-fold, 1.8-fold, and 1.4-fold, respectively. In the microbial fuel cell influent, propionic, enanthic, and iso-caproic acids predominated (60, 15, and 13% of all volatile fatty acids, respectively); in the outflow, propionic (71%) and valeric acids (17%) predominated. In anodic biofilms, Acidovorax sp. were most abundant; they have a great capacity for volatile fatty acids decomposition, and their abundance doubled in the microbial fuel cell with an iron-modified anode. The presence of iron significantly increased the abundance of the genera Pseudomonas and Geothrix , which were mainly responsible for electricity production. These results indicate that anode modification with iron changes the anode microbiome, favoring efficient volatile fatty acids metabolism and a greater abundance of electrogens in the biofilm, which ensures better electricity generation.
Yangkai Duan, Zhi Zhu, Ke Cai et al.
PLoS ONE · 2011
Biodiesel is a renewable alternative to petroleum diesel fuel that can contribute to carbon dioxide emission reduction and energy supply. Biodiesel is composed of fatty acid alkyl esters, including fatty acid methyl esters (FAMEs) and fatty acid ethyl esters (FAEEs), and is currently produced through the transesterification reaction of methanol (or ethanol) and triacylglycerols (TAGs). TAGs are mainly obtained from oilseed plants and microalgae. A sustainable supply of TAGs is a major bottleneck for current biodiesel production. Here we report the de novo biosynthesis of FAEEs from glucose, which can be derived from lignocellulosic biomass, in genetically engineered Escherichia coli by introduction of the ethanol-producing pathway from Zymomonas mobilis, genetic manipulation to increase the pool of fatty acyl-CoA, and heterologous expression of acyl-coenzyme A: diacylglycerol acyltransferase from Acinetobacter baylyi. An optimized fed-batch microbial fermentation of the modified E. coli strain yielded a titer of 922 mg L−1 FAEEs that consisted primarily of ethyl palmitate, -oleate, -myristate and -palmitoleate.
S. A. Hussain, Alexis García, Md Ahsanul Kabir Khan et al.
Genes · 2020
Concerns about global warming, fossil-fuel depletion, food security, and human health have promoted metabolic engineers to develop tools/strategies to overproduce microbial functional oils directly from renewable resources. Medium-chain fatty acids (MCFAs, C8–C12) have been shown to be important sources due to their diverse biotechnological importance, providing benefits ranging from functional lipids to uses in bio-fuel production. However, oleaginous microbes do not carry native pathways for the production of MCFAs, and therefore, diverse approaches have been adapted to compensate for the requirements of industrial demand. Mucor circinelloides is a promising organism for lipid production (15–36% cell dry weight; CDW) and the investigation of mechanisms of lipid accumulation; however, it mostly produces long-chain fatty acids (LCFAs). To address this challenge, we genetically modified strain M. circinelloides MU758, first by integrating heterologous acyl-ACP thioesterase (TE) into fatty acid synthase (FAS) complex and subsequently by modifying the β-oxidation pathway by disrupting the acyl-CoA oxidase (ACOX) and/or acyl-CoA thioesterase (ACOT) genes with a preference for medium-chain acyl-CoAs, to elevate the yield of MCFAs. The resultant mutant strains (M-1, M-2, and M-3, respectively) showed a significant increase in lipid production in comparison to the wild-type strain (WT). MCFAs in M-1 (47.45%) was sharply increased compared to the wild type strain (2.25%), and it was further increased in M-2 (60.09%) suggesting a negative role of ACOX in MCFAs production. However, MCFAs in M-3 were much decreased compared to M-1,suggesting a positive role of ACOT in MCFAs production. The M-2 strain showed maximum lipid productivity (~1800 milligram per liter per day or mg/L.d) and MCFAs productivity (~1100 mg/L.d). Taken together, this study elaborates on how the combination of two multidimensional approaches, TE gene over-expression and modification of the β-oxidation pathway via substantial knockout of specific ACOX gene, significantly increased the production of MCFAs. This synergistic approach ultimately offers a novel opportunity for synthetic/industrial biologists to increase the content of MCFAs.
C. K. Ng, Samuel L Putra, Joseph Kennerley et al.
Microbial Biotechnology · 2021
The ability to directly modify native and established biofilms has enormous potential in understanding microbial ecology and application of biofilm in 'real‐world' systems. However, efficient genetic transformation of established biofilms at any scale remains challenging. In this study, we applied an ultrasound‐mediated DNA delivery (UDD) technique to introduce plasmid to established non‐competent biofilms in situ. Two different plasmids containing genes coding for superfolder green fluorescent protein (sfGFP) and the flavin synthesis pathway were introduced into established bacterial biofilms in microfluidic flow (transformation efficiency of 3.9 ± 0.3 × 10‐7 cells in biofilm) and microbial fuel cells (MFCs), respectively, both employing UDD. Gene expression and functional effects of genetically modified bacterial biofilms were observed, where some cells in UDD‐treated Pseudomonas putida UWC1 biofilms expressed sfGFP in flow cells and UDD‐treated Shewanella oneidensis MR‐1 biofilms generated significantly (P < 0.05) greater (61%) bioelectricity production (21.9 ± 1.2 µA cm−2) in MFC than a wild‐type control group (~ 13.6 ± 1.6 µA cm−2). The effects of UDD were amplified in subsequent growth under selection pressure due to antibiotic resistance and metabolism enhancement. UDD‐induced gene transfer on biofilms grown in both microbial flow cells and MFC systems was successfully demonstrated, with working volumes of 0.16 cm3 and 300 cm3, respectively, demonstrating a significant scale‐up in operating volume. This is the first study to report on a potentially scalable direct genetic engineering method for established non‐competent biofilms, which can be exploited in enhancing their capability towards environmental, industrial and medical applications.
Hye Jin Lim, Dong-Myung Kim
Methods and Protocols · 2019
Due to the ongoing crises of fossil fuel depletion, climate change, and environmental pollution, microbial processes are increasingly considered as a potential alternative for cleaner and more efficient production of the diverse chemicals required for modern civilization. However, many issues, including low efficiency of raw material conversion and unintended release of genetically modified microorganisms into the environment, have limited the use of bioprocesses that rely on recombinant microorganisms. Cell-free metabolic engineering is emerging as a new approach that overcomes the limitations of existing cell-based systems. Instead of relying on metabolic processes carried out by living cells, cell-free metabolic engineering harnesses the metabolic activities of cell lysates in vitro. Such approaches offer several potential benefits, including operational simplicity, high conversion yield and productivity, and prevention of environmental release of microorganisms. In this article, we review the recent progress in this field and discuss the prospects of this technique as a next-generation bioconversion platform for the chemical industry.
Yan Qiao, Shu-juan Bao, C. Li
Energy & Environmental Science · 2010
Microbial fuel cells (MFCs) are promising clean energy sources for simultaneous recycling of organic waste while harvesting electricity. The electrocatalysis of the anode is crucial for improvement of the energy conversion efficiency, power density and energy density of MFCs, which is significantly related to the microbes, electrode and electron transfer scheme between the microbes and electrode. This paper reviews and discusses electrocatalysis in MFCs, particularly addressing the recent advances in anodic electrocatalysis with direct electrochemistry of genetically modified bacteria and novel electrode materials for performance improvement, and some remaining challenges to be overcome.
M. Rashid, S. Andleeb
2018 International Conference on Power Generation Systems and Renewable Energy Technologies (PGSRET) · 2018
Pseudomonas aeruginosa produces Pyocyanin which serves as a good electron transport shuttle in Microbial Fuel Cells. Studies have implicated higher Microbial Fuel Cell energy yield with higher PCN production by P. aeruginosa thus improving energy output. For obtaining high pyocyanin producing strain of P. aeruginosa, sewage water samples were taken from various sites in Islamabad and were cultured in LB media at 37°C. Characterization was performed by both biochemically as well as genetically. For pyocyanin yield assessment Rf value and λmax were determined. Pyocyanin was isolated via repeated chloroform and acidified water extraction and quantified. Physiochemical and nutritional conditions for pyocyanin production were optimized in the form of designed modified semisynthetic media. Optimized production was achieved and pyocyanin yield was increased to 3 folds than normal and control conditions. The designed pyocyanin yield media can be used to improve energy output in microbial fuel cells.
Lucila Díaz-Orozco, Mario Moscosa Santillán, Rosa Elena Delgado Portales et al.
Polymers · 2025
Lactic acid is a vital organic acid with a wide range of industrial applications, particularly in the food, pharmaceutical, cosmetic, and biomedical sectors. The conventional production of lactic acid from refined sugars poses high costs and significant environmental impacts, leading to the exploration of alternative raw materials and more sustainable processes. Lignocellulosic biomass, particularly agro-industrial residues such as agave bagasse, represents a promising substrate for lactic acid production. Agave bagasse, a by-product of the tequila and mezcal industries, is rich in fermentable carbohydrates, making it an ideal raw material for biotechnological processes. The use of lactic acid bacteria (LAB), particularly genetically modified microorganisms (GMMs), has been shown to enhance fermentation efficiency and lactic acid yield. This review explores the potential of lignocellulosic biomass as a substrate for microbial fermentation to produce lactic acid and other high-value products. It covers the composition and pretreatment of some agricultural residues, the selection of suitable microorganisms, and the optimization of fermentation conditions. The paper highlights the promising future of agro-industrial residue valorization through biotechnological processes and the sustainable production of lactic acid as an alternative to conventional methods.
Jing Sun, Wenbin Wu, Huajun Tang et al.
Scientific Reports · 2015
Abstract Despite heated debates over the safety of genetically modified (GM) food, GM crops have been expanding rapidly. Much research has focused on the expansion of GM crops. However, the spatiotemporal dynamics of non-genetically modified (non-GM) crops are not clear, although they may have significant environmental and agronomic impacts and important policy implications. To understand the dynamics of non-GM crops and to inform the debates among relevant stakeholders, we conducted spatiotemporal analyses of China’s major non-GM soybean production region, the Heilongjiang Province. Even though the total soybean planting area decreased from 2005 to 2010, surprisingly, there were hotspots of increase. The results also showed hotspots of loss as well as a large decline in the number and continuity of soybean plots. Since China is the largest non-GM soybean producer in the world, the decline of its major production region may signal the continual decline of global non-GM soybeans.
Andreas S. Petsas, Maria C. Vagi
Current Pharmaceutical Biotechnology · 2019
Nowadays, numerous synthetic and semisynthetic chemicals are extensively produced and consequently used worldwide for many different purposes, such as pharmaceuticals, pesticides, hydrocarbons with aromatic rings (known as polycyclic aromatic hydrocarbons, PAHs), multi-substituted biphenyls with halogens (such as polychlorinated biphenyls, PCBs), and many other toxic and persistent chemical species. The presence of the aforementioned xenobiotic substances not only in various environmental matrices (water, air, and soil), but also in biological tissues (organisms) as well as in several compartments of raw or processed food (of fruit, vegetal, and animal origin), has raised global scientific concerns regarding their potential toxicity towards non target organisms including humans. Additionally, the ability of those persistent organic pollutants to be magnified via food consumption (food chain) has become a crucial threat to human health. Microbial degradation is considered an important route influencing the fate of those toxicants in each matrix. The technique of bioremediation, either with microorganisms (native or genetically modified) which are applied directly (in a reactor or in situ), or with cell extracts or purified enzymes preparations, is reported as a low cost and potential detoxification technology for the removal of toxic chemicals. The sources and toxic impacts of target groups of chemicals are briefly presented in the present study, whereas the bioremediation applications for the removal of pharmaceuticals and other organic contaminants using microbial strains are critically reviewed. All the recently published data concerning the genes encoding the relevant enzymes that catalyze the degradation reactions, the mechanisms of reactions and parameters that influence the bioremediation process are discussed. Finally, research needs and future trends in the direction of decontamination are high-lightened.
Eduardo C. Oliveira-Filho, Cesar K. Grisolia
International Journal of Environmental Research and Public Health · 2022
The use of microbial insecticides and their toxins in biological control and transgenic plants has increased their presence in the environment. Although they are natural products, the main concerns are related to the potential impacts on the environment and human health. Several assays have been performed worldwide to investigate the toxicity or adverse effects of these microbial products or their individual toxins. This overview examines the published data concerning the knowledge obtained about the ecotoxicity and environmental risks of these natural pesticides. The data presented show that many results are difficult to compare due to the diversity of measurement units used in the different research data. Even so, the products and toxins tested present low toxicity and low risk when compared to the concentrations used for pesticide purposes. Complementary studies should be carried out to assess possible effects on human health.
Radhika Velankar, Gauri Nerkar, Mukta Nagpurkar et al.
Genetics · 2024
Transgenic technology has significantly contributed to the genetic improvement of crop plants by improving important agronomic traits like insect/pest resistance, disease resistance, herbicide tolerance, abiotic stress tolerance, and quality improvement. Conventional breeding programs are time consuming and laborious involving screening thousands of progenies for the development of a new hybrid variety. Genetic engineering is a precise tool to develop a new variety in a short duration. Genetically Modified Crops have been used for expression of recombinant proteins of high therapeutic value, monoclonal antibodies, nutraceuticals, edible vaccines, and improved saccharification efficiency of biofuel crops for bioethanol production. The agricultural productivity is limited by global climate changes and unfavorable abiotic and biotic factors posing challenges for crop scientists to meet the rising demand for global food supply. Developing climate-resilient crops will bring more land under agriculture and more vegetation for carbon sequestration thereby annulling global warming. This chapter provides an insight into the principles, advantages, and limitations of the methods used in genetic transformation and the advancements in genome editing, agronomic traits improved in Genetically Modified Crops, potential applications of transgenic technology in biopharming and bioethanol production, biosafety and regulation of transgenic crops, and the challenges in the development of Genetically Modified Crops.
Ashutosh Kumar, Banshidhar, Priyanka Jaiswal et al.
Genetically Modified Plants and Beyond · 2022
With the advancement in the field of agricultural biotechnology, many genetically modified crops like Bt- cotton, Bt- brinjal have been developed and commercialised to fulfil the need of the world population. Several biosafety concerns viz., risk to human health, risk to environment, ecological concern o has been raised after the rapid commercialization of GM crops every year across the world. As per Convention on biodiversity (CBD), Biosafety is a term used to describe efforts to reduce and eliminate the potential risk resulting from biotechnology and its product. Though many concerns being raised time to time, strict biosafety guideline must be followed before introducing a GM crop in public domain especially in resource poor developing countries.
Lital Alfonta
Electroanalysis · 2010
Abstract This article reviews the advances that were made towards the understanding and the improvement of electron transfer and communication between living cells and electrodes with a specific emphasis on microbial fuel cells and bioelectrical systems. It summarizes the efforts that were made thus far to improve electron transfer between microorganisms and electrodes using the genetically based understanding of electron transfer in such organisms and the manipulations that can be performed to improve the transfer and subsequently control over power output. Future directions in the field are also reviewed and suggested in this article.
Yu Cheng, Liyan Zhang, Qihong Chen et al.
2022 12th International Conference on Power, Energy and Electrical Engineering (CPEEE) · 2022
Due to the noise of diesel engine backup power systems, serious environmental pollution, and the inability to provide uninterrupted power supply, the backup power system of proton exchange membrane fuel cells has gradually attracted the attention of the industry. This article mainly focuses on a backup power system consisting of two fuel cells and lithium-ion batteries as the research object and proposes an energy management strategy based on model predictive control (MPC). MPC, under the constraints of fuel cell output power and output power increment, takes system hydrogen consumption as the objective function to solve the optimal power distribution between fuel cell and lithium-ion battery. Finally, MPC is compared with state machine energy management strategy by simulation. The results show that the energy management strategy based on MPC reduces hydrogen consumption by 18.83% and improves the overall efficiency of the fuel cell by 3.05%.