Turn on the Mtr pathway genes under pLacI promoter in Shewanella oneidensis MR-1

Underrated risk of antibiotic resistance genes dissemination mediated by bioaerosols released from anaerobic biological wastewater treatment system

Antibiotic resistance has been recognized as one of the most prevalent public health problems. The bioaerosol-mediated spread of antibiotic resistance genes (ARGs) is an important but underrated pathway. Therefore, this work investigated the comprehensive resistome and pathogen-induced risk in bioaerosols released from anaerobic ammonium oxidation (anammox) process under antibiotic stress. The results showed that the bioaerosol oxidation potential increased by 2.7 times after the addition of sulfamethoxazole (SMX) into the anammox system. Based on the metagenomic analyses, abundant ARGs were enriched in bioaerosols, especially novA, olec, msbA and patA. There were many antibiotic resistance contigs carrying at least two mobile genetic elements (MGEs) in bioaerosols. Compared to the control, SMX caused the significant increase in ARGs proportion in plasmids from 11.4 % to 19.4 %. Similarly, the abundance of the type IV secretion system protein encoding genes (mtrA and mtrB) increased by 30.2 % and 31.5 %, respectively, which was conducive to gene transfer between bacteria. In addition, SMX stress induced the reactive oxygen species (ROS) production and the upregulation of genes related to membrane protein and DNA replication, further facilitating ARGs transfer. The co-occurrence networks showed that Aquamicrobium and Microbacterium probably were the hosts of most ARGs. Notably, four abundant human pathogens were detected in bioaerosols from the anammox system, which raised concerns on the health risk of resistant bioaerosol diffusion. These findings reveal the potential of horizontal gene transfer through bioaerosols and provide a guidance for systematically assessing the risk of environmental antibiotic resistance and relevant pathogens.

Shewanella oneidensis: Biotechnological Application of Metal-Reducing Bacteria

What is an unconventional organism in biotechnology? The γ-proteobacterium Shewanella oneidensis might fall into this category as it was initially established as a laboratory model organism for a process that was not seen as potentially interesting for biotechnology. The reduction of solid-state extracellular electron acceptors such as iron and manganese oxides is highly relevant for many biogeochemical cycles, although it turned out in recent years to be quite relevant for many potential biotechnological applications as well. Applications started with the production of nanoparticles and dramatically increased after understanding that electrodes in bioelectrochemical systems can also be used by these organisms. From the potential production of current and hydrogen in these systems and the development of biosensors, the field expanded to anode-assisted fermentations enabling fermentation reactions that were - so far - dependent on oxygen as an electron acceptor. Now the field expands further to cathode-dependent production routines. As a side product to all these application endeavors, S. oneidensis was understood more and more, and our understanding and genetic repertoire is at eye level to E. coli. Corresponding to this line of thought, this chapter will first summarize the available arsenal of tools in molecular biology that was established for working with the organism and thereafter describe so far established directions of application. Last but not least, we will highlight potential future directions of work with the unconventional model organism S. oneidensis.

Optimizing the Metal Bioreduction Process in Recombinant Shewanella azerbaijanica Bacteria: A Novel Approach via mtrC Gene Cloning and Nitrate-Reducing Pathway Destruction

Environmental pollution is growing every day in terms of the increase in population, industrialization, and urbanization. Shewanella azerbaijanica is introduced as a highly potent bacterium in metal bioremediation. The mtrC gene was selected as a cloning target to improve electron flux chains in the EET (extracellular electron transfer) pathway. Using the SDM (site-directed mutagenesis) technique, the unique gene assembly featured the mtrC gene sandwiched between two napD/B genes to disrupt the nitrate reduction pathway, which serves as the primary metal reduction competitor. Shew-mtrC gene construction was transferred to expression plasmid pET28a (+) in the expression host bacteria (E. coli BL21 and S. azerbaijanica), in pUC57, cloning plasmid, which was transferred to the cloning host bacteria E. coli Top10 and S. azerbaijanica. All cloning procedures (i.e., synthesis, insertion, transformation, cloning, and protein expression) were verified and confirmed by precise tests. ATR-FTIR analysis, CD, western blotting, affinity chromatography, SDS-PAGE, and other techniques were used to confirm the expression and structure of the MtrC protein. The genome sequence and primers were designed according to the submitted Shewanella oneidensis MR-1 genome, the most similar bacteria to this native species. The performance of recombinant S. azerbaijanica bacterium in metal bioremediation, as sustainable strategy, has to be verified by more research.

Modular Engineering Strategy to Redirect Electron Flux into the Electron-Transfer Chain for Enhancing Extracellular Electron Transfer in Shewanella oneidensis

Efficient extracellular electron transfer (EET) of exoelectrogens is critical for practical applications of various bioelectrochemical systems. However, the low efficiency of electron transfer remains a major bottleneck. In this study, a modular engineering strategy, including broadening the sources of the intracellular electron pool, enhancing intracellular nicotinamide adenine dinucleotide (NADH) regeneration, and promoting electron release from electron pools, was developed to redirect electron flux into the electron transfer chain in Shewanella oneidensis MR-1. Among them, four genes include gene SO1522 encoding a lactate transporter for broadening the sources of the intracellular electron pool, gene gapA encoding a glyceraldehyde-3-phosphate dehydrogenase and gene mdh encoding a malate dehydrogenase in the central carbon metabolism for enhancing intracellular NADH regeneration, and gene ndh encoding NADH dehydrogenase on the inner membrane for releasing electrons from intracellular electron pools into the electron-transport chain. Upon assembly of the four genes, electron flux was directly redirected from the electron donor to the electron-transfer chain, achieving 62% increase in intracellular NADH levels, which resulted in a 3.5-fold enhancement in the power density from 59.5 ± 3.2 mW/m² (wild type) to 270.0 ± 12.7 mW/m² (recombinant strain). This study confirmed that redirecting electron flux from the electron donor to the electron-transfer chain is a viable approach to enhance the EET rate of S. oneidensis.

Growth and genome-based insights of Fe(III) reduction of the high-temperature and NaCl-tolerant Shewanella xiamenensis from Changqing oilfield of China

Introduction

A facultative anaerobe bacterium Shewanella xiamenensis CQ-Y1 was isolated from the wastewater of Changqing oilfield in Shaanxi Province of China. Shewanella is the important dissimilatory metal-reducing bacteria. It exhibited a well potential application in biodegradation and bioremediation.

Methods

Genome sequencing, assembling and functional annotation were conducted to explore the genome information of CQ-Y1. The effect of temperatures and NaCl concentrations on the CQ-Y1 growth and Fe(III) reduction were investigated by UV visible spectrophotometry, SEM and XRD.

Results

Genomic analysis revealed its complete genome was a circular chromosome of 4,710,887 bp with a GC content of 46.50% and 4,110 CDSs genes, 86 tRNAs and 26 rRNAs. It contains genes encoding for Na⁺/H⁺ antiporter, K⁺/Cl^- transporter, heat shock protein associated with NaCl and high-temperature resistance. The presence of genes related to flavin, Cytochrome c, siderophore, and other related proteins supported Fe(III) reduction. In addition, CQ-Y1 could survive at 10% NaCl (w/v) and 45°C, and temperature showed more pronounced effects than NaCl concentration on the bacterial growth. The maximum Fe(III) reduction ratio of CQ-Y1 reached 70.1% at 30°C without NaCl, and the reduction reaction remained active at 40°C with 3% NaCl (w/v). NaCl concentration was more effective than temperature on microbial Fe(III) reduction. And the reduction products under high temperature and high NaCl conditions were characterized as Fe₃(PO₄)₂, FeCl₂ and Fe(OH)₂.

Discussion

Accordingly, a Fe(III) reduction mechanism of CQ-Y1 mediated by Cytochrome c and flavin was hypothesised. These findings could provide information for a better understanding of the origin and evolution of genomic and metabolic diversity of S. xiamenensis.

Pathogenic strains of Shewanella putrefaciens contain plasmids that are absent in the probiotic strain Pdp11

Shewanella putrefaciens Pdp11 is a strain described as a probiotic for use in aquaculture. However, S. putrefaciens includes strains reported to be pathogenic or saprophytic to fish. Although the probiotic trait has been related to the presence of a group of genes in its genome, the existence of plasmids that could determine the probiotic or pathogenic character of this bacterium is unknown. In the present work, we searched for plasmids in several strains of S. putrefaciens that differ in their pathogenic and probiotic character. Under the different conditions tested, plasmids were only found in two of the five pathogenic strains, but not in the probiotic strain nor in the two saprophytic strains tested. Using a workflow integrating Sanger and Illumina reads, the complete consensus sequences of the plasmids were obtained. Plasmids differed in one ORF and encoded a putative replication initiator protein of the repB family, as well as proteins related to plasmid stability and a toxin-antitoxin system. Phylogenetic analysis showed some similarity to functional repB proteins of other Shewanella species. The implication of these plasmids in the probiotic or pathogenic nature of S. putrefaciens is discussed.

Redirection of metabolic flux in Shewanella oneidensis MR-1 by CRISPRi and modular design for 5-aminolevulinic acid production

Programming non-canonical organisms is more attractive due to the prospect of high-value chemical production. Among all, Shewanella oneidensis MR-1 possesses outstanding heme synthesis ability and is well-known for electron transfer, thus has high potential in microbial fuel cell and bioremediation. However, heme, as the final product of C4 and C5 pathways, is regulated by heme cluster for the high-value 5-aminolevulinic acid (ALA) for cancer photodynamic therapy, which has never been explored in MR-1. Herein, the heme metabolism in MR-1 was firstly optimized for ALA production. We applied CRISPR interference (CRISPRi) targeted on the genes to fine-tune carbon flux in TCA cycle and redirected the carbon out-flux from heme, leading to a significant change in the amino acid profiles, while downregulation of the essential hemB showed a 2-fold increasing ALA production via the C5 pathway. In contrast, the modular design including of glucokinase, GroELS chaperone, and ALA synthase from Rhodobacter capsulatus enhanced ALA production markedly in the C4 pathway. By integrating gene cluster under dual T7 promoters, we obtained a new strain M::TRG, which significantly improved ALA production by 145-fold. We rewired the metabolic flux of MR-1 through this modular design and successfully produced the high-value ALA compound at the first time.

Engineering S. oneidensis for Performance Improvement of Microbial Fuel Cell-a Mini Review

Microbial fuel cell (MFC) is a promising technology that utilizes exoelectrogens cultivated in the form of biofilm to generate power from various types of sources supplied. A metal-reducing pathway is utilized by these organisms to transfer electrons obtained from the metabolism of substrate from anaerobic respiration extracellularly. A widely established model organism that is capable of extracellular electron transfer (EET) is Shewanella oneidensis. This review highlights the strategies used in the transformation of S. oneidensis and the recent development of MFC in terms of intervention through genetic modifications. S. oneidensis was genetically engineered for several aims including the study on the underlying mechanisms of EET, and the enhancement of power generation and wastewater treating potential when used in an MFC. Through engineering S. oneidensis, genes responsible for EET are identified and strategies on enhancing the EET efficiency are studied. Overexpressing genes related to EET to enhance biofilm formation, mediator biosynthesis, and respiration appears as one of the common approaches.

Mechanism study of photo-induced gold nanoparticles formation by Shewanella oneidensis MR-1

Shewanella oneidensis MR-1, a bioelectricity generating bacterium, is broadly used in bioremediation, microbial fuel cell and dissimilatory reduction and recovery of precious metals. Herein, we report for the first time that photo induction as a trigger to stimulate gold nanoparticles (Au@NPs) formation by MR-1, with wavelength and light intensity as two key variables. Results indicated that sigmoidal model is the best fit for Au@NPs formation at various wavelengths (with R² > 0.97). Light intensity in terms of photosynthetic photon flux density (PPFD) critically influences the rate constant in the low-light intensity region (PPFD < 20), while wavelength controls the maximum rate constant in the high-light region (PPFD > 20). By deletion of Mtr pathway genes in MR-1, we proposed the mechanism for light induced Au@NP formation is the excitation effect of light on certain active groups and extracellular polymeric substances (EPS) on the cell surface. Also, the release of electrons from proteins and co-enzyme complexes enhance electron generation. To the best of our knowledge, this is the first-attempt to explore the effect of photo-induction on Au@NPs production by MR-1, which provides an alternative cost-effective and eco-friendly process in green chemical industry.