Biomolecular Insights into Extracellular Pollutant Reduction Pathways of Geobacter sulfurreducens Using a Base Editor System

Multienergy Codriven Electron Transfer Across the Nano-Bio Interface for Efficient Photobiocatalysis

Integrating biocatalysis with nanophotocatalysis provides a promising pathway to address the knotty environmental and energy problems. However, energy loss during the transfer of extracellular electrons across the nano-bio interface seriously limits the efficiency of whole-cell-based photobiocatalytic systems. Herein, we demonstrate an integrated multienergy codriven reaction platform containing BaTiO3 nanoparticles (BTO) for harvesting mechanical energy from flowing water to elevate the interfacial electric field, BiVO4 quantum dots (BQD) for harvesting light energy to generate photocarriers, and Geobacter sulfurreducens (GS) for accepting photoelectrons to accomplish the biocatalytic reactions. The synergism between the piezoelectric and photoelectric fields significantly promotes the cross-membrane transport of photoelectrons, contributing to enhanced acetate metabolism, electron transfer, and energy synthesis of GS microbes. Such well-designed BQD/BTO-GS hybrids result in the simultaneous degradation of organic contaminants and detoxification of heavy metals in water with approximately 100% treatment efficiency. The rates of tetracycline (TC) oxidation and Cr(VI) reduction are determined to be 32.8 and 9.58 times higher than that of GS biocatalysis, respectively. Our photobiocatalytic platform exhibits an exceptional apparent quantum yield of 15.54% at 400 nm, exceeding those of most reported abiotic-biotic photobiocatalytic systems. Further investigation verifies the extensibility of our multienergy codriven strategy to the other nano-bio hybrids for enhancing the biocatalytic efficiencies (such as methanogenesis, CO2 fixation, and denitrification), thus offering an inspiring platform for energy and environmental applications. This work not only presents crucial insights into the mechanism of the water-energy nexus but also provides a paradigm for the construction of sustainable reaction systems via multienergy harnessing.

Extracellular electron transfer-dependent bioremediation of uranium-contaminated groundwater: Advancements and challenges

Efficient and sustainable remediation of uranium-contaminated groundwater is critical for groundwater safety and the sustainable development of nuclear energy, particularly in the context of global carbon neutrality goals. This review explores the potential of microbial reduction processes that utilize extracellular electron transfer (EET) to convert soluble uranium (U(VI)) into its insoluble form (U(IV)), presenting a promising approach to groundwater remediation. The review first outlines the key processes and factors influencing the effectiveness of dissimilatory metal-reducing bacteria (DMRB), such as Geobacter and Shewanella, during uranium bioremediation and recovery. The cutting-edge progress on the molecular mechanism of EET-driven U(VI) reduction mediated by c-type cytochromes, conductive pili, and electron mediators, is critically reviewed. Additionally, advanced strategies such as optimizing electron transfer, leveraging synthetic biology approach, and integration with machine learning are discussed to enhance the efficiency of EET-driven processes. The review also considers the integration of EET processes into practical engineering applications, highlighting the need for optimization and innovation in bioremediation technologies. By providing a comprehensive overview of current progress and challenges, this review aims to inspire novel research and practical advancements in the field of uranium-contaminated groundwater remediation.

A universal and wide-range cytosine base editor via domain-inlaid and fidelity-optimized CRISPR-FrCas9

CRISPR-based base editor (BE) offer diverse editing options for genetic engineering of microorganisms, but its application is limited by protospacer adjacent motif (PAM) sequences, context preference, editing window, and off-target effects. Here, a series of iteratively improved cytosine base editors (CBEs) are constructed using the FrCas9 nickase (FrCas9n) with the unique PAM palindromic structure (NNTA) to alleviate these challenges. The deaminase domain-inlaid FrCas9n exhibits an editing range covering 38 nucleotides upstream and downstream of the palindromic PAM, without context preference, which is 6.3 times larger than that of traditional CBEs. Additionally, lower off-target editing is achieved when incorporating high-fidelity mutations at R61A and Q964A in FrCas9n, while maintaining high editing efficiency. The final CBE, HF-ID824-evoCDA-FrCas9n demonstrates broad applicability across different microbes such as Escherichia coli MG1655, Shewanella oneidensis MR-1, and Pseudomonas aeruginosa PAO1. Collectively, this tool offers robust gene editing for facilitating mechanistic studies, functional exploration, and protein evolution in microbes.

CO₂-enhanced methane production by integration of bamboo biochar during anaerobic co-digestion

This study investigates the enhancement of methane production in anaerobic co-digestion (AcoD) through the introduction of exogenous CO₂ and the application of bamboo biochar. Exogenous CO₂ boosts biogas yield by providing an additional carbon source, which requires optimized solubility and pH buffering to ensure effective methanation. Biochar serves as an electron shuttle and pH stabilizer, facilitating CO2 solubility and syntrophic interactions that enhance microbial stability. When combined, biochar and CO₂ (R2) achieved a significant synergistic effect, increasing specific methane production (SMP) by 42.56% compared to the control (R0). Independent additions of biochar (R1) and CO₂ (R3) also improved SMP, with increases of 35.50% and 28.01%, respectively. This enhancement is likely due to the elevated activity of homoacetogenic bacteria and hydrogenotrophic methanogens, with increased acsB gene expression 2.4-fold with biochar + CO₂ and 1.5-fold with CO₂ alone compared to the control. Additionally, biochar facilitated syntrophic metabolism mediated by Cytochrome-C, promoting electron transfer. The study also demonstrated that biochar and CO2 could enhance enzyme activity, including acetyl-CoA synthase, mhpF, and mhpE. Such improvements bolster AcoD efficiency and promote resource recycling within the circular economy framework.

Multi-dimensional perspectives into the pervasive role of microbial extracellular polymeric substances in electron transport processes

During the process of biological treatment, most microorganisms are encapsulated in extracellular polymeric substances (EPS), which protect the cell from adverse environments and aid in microbial attachment. Microorganisms utilize extracellular electron transfer (EET) for energy and information interchange with other cells and the outside environment. Understanding the role of steric EPS in EET is critical for studying microbiology and utilizing microorganisms in biogeochemical processes, pollutant transformation, and bioenergy generation. However, the current study shows that understanding the roles of EPS in the EET processes still needs a great deal of research. In view of recent research, this work aims to systematically summarize the production and functional group composition of microbial EPS. Additionally, EET pathways and the role of EPS in EET processes are detailed. Then factors impacting EET processes in EPS are then discussed, with a focus on the spatial structure and composition of EPS, conductive materials and environmental pollution, including antibiotics, pH and minerals. Finally, strategies to enhance EET, as well as current challenges and future prospects are outlined in detail. This review offers novel insights into the roles of EPS in biological electron transport and the application of microorganisms in pollutant transformation.

Hemicyanine-Based Highly Water-Soluble Probe for Extracellular Nitroreductase

Nitroreductase (NTR) has long been a target of interest for its important role involved in the nitro compounds metabolism. Various probes have been reported for NTR analysis, but rarely able to distinguish the extracellular NTR from intracellular ones. Herein we reported a new NTR sensor, HCyS-NO2, which was a hemicyanine molecule with one nitro and two sulfo groups attached. The nitro group acted as the reporting group to respond NTR reduction. Direct linkage of nitro group into the hemicyanine π conjugate system facilitated the intramolecular electron transfer (IET) process and thus quenched the fluorescence of hemicyanine core. Upon reduction with NTR, the nitro group was rapidly converted into the hydroxylamino and then the amino group, eliminating IET process and thus restoring the fluorescence. The sulfo groups installed significantly increased the hydrophilicity of the molecule, and introduced negative charges at physiological pH, preventing the diffusion into bacteria. Both gram-negative and gram-positive bacteria were able to turn on the fluorescence of HCyS-NO2, without detectable diffusion into cells, providing a useful tool to probe the extracellular reduction process.

Plant growth promotion and biocontrol properties of a synthetic community in the control of apple disease

BACKGROUND

Apple Replant Disease (ARD) is common in major apple-growing regions worldwide, but the role of rhizosphere microbiota in conferring ARD resistance and promoting plant growth remains unclear.

RESULTS

In this study, a synthetic microbial community (SynCom) was developed to enhance apple plant growth and combat apple pathogens. Eight unique bacteria selected via microbial culture were used to construct the antagonistic synthetic community, which was then inoculated into apple seedlings in greenhouse experiments. Changes in the rhizomicroflora and the growth of aboveground plants were monitored. The eight strains, belonging to the genera Bacillus and Streptomyces, have the ability to antagonize pathogens such as Fusarium oxysporum, Rhizoctonia solani, Botryosphaeria ribis, and Physalospora piricola. Additionally, these eight strains can stably colonize in apple rhizosphere and some of them can produce siderophores, ACC deaminase, and IAA. Greenhouse experiments with Malus hupehensis Rehd indicated that SynCom promotes plant growth (5.23%) and increases the nutrient content of the soil, including soil organic matter (9.25%) and available K (1.99%), P (7.89%), and N (0.19%), and increases bacterial richness and the relative abundance of potentially beneficial bacteria. SynCom also increased the stability of the rhizosphere microbial community, the assembly of which was dominated by deterministic processes (|β NTI| > 2).

CONCLUSIONS

Our results provide insights into the contribution of the microbiome to pathogen inhibition and host growth. The formulation and manipulation of similar SynComs may be a beneficial strategy for promoting plant growth and controlling soil-borne disease.

Phthalates Boost Natural Transformation of Extracellular Antibiotic Resistance Genes through Enhancing Bacterial Motility and DNA Environmental Persistence

The environmental dissemination of extracellular antibiotic resistance genes (eARGs) in wastewater and natural water bodies has aroused growing ecological concerns. The coexisting chemical pollutants in water are known to markedly affect the eARGs transfer behaviors of the environmental microbial community, but the detailed interactions and specific impacts remain elusive so far. Here, we revealed a concentration-dependent impact of dimethyl phthalate (DMP) and several other types of phthalate esters (common water pollutants released from plastics) on the natural transformation of eARGs. The DMP exposure at an environmentally relevant concentration (10 μg/L) resulted in a 4.8-times raised transformation frequency of Acinetobacter baylyi but severely suppressed the transformation at a high concentration (1000 μg/L). The promotion by low-concentration DMP was attributed to multiple mechanisms, including increased bacterial mobility and membrane permeability to facilitate eARGs uptake and improved resistance of the DMP-bounded eARGs (via noncovalent interaction) to enzymatic degradation (with suppressed DNase activity). Similar promoting effects of DMP on the eARGs transformation were also found in real wastewater and biofilm systems. In contrast, higher-concentration DMP suppressed the eARGs transformation by disrupting the DNA structure. Our findings highlight a potentially underestimated eARGs spreading in aquatic environments due to the impacts of coexisting chemical pollutants and deepen our understanding of the risks of biological-chemical combined pollution in wastewater and environmental water bodies.

Bibliometric insights into the evolution of uranium contamination reduction research topics: Focus on microbial reduction of uranium

Confronting the threat of environment uranium pollution, decades of research have yielded advanced and significant findings in uranium bioremediation, resulting in the accumulation of tremendous amount of high-quality literature. In this study, we analyzed over 10,000 uranium reduction-related papers published from 1990 to the present in the Web of Science based on bibliometrics, and revealed some critical information on knowledge structure, thematic evolution and additional attention. Methods including contribution comparison, co-occurrence and temporal evolution analysis are applied. The results of the distribution and impact analysis of authors, sources, and journals indicated that the United States is a leader in this field of research and China is on the rise. The top keywords remained stable, primarily focused on chemicals (uranium, iron, plutonium, nitrat, carbon), characters (divers, surfac, speciat), and microbiology (microbial commun, cytochrome, extracellular polymeric subst). Keywords related to new strains, reduction mechanisms and product characteristics demonstrated the strongest uptrend, while some keywords related to mechanism and performance were clearly emerging in the past 5 years. Furthermore, the evolution of the thematic progression can be categorized into three stages, commencing with the discovery of the enzymatic reduction of hexavalent uranium to tetravalent uranium, developing in the groundwater remediation process at uranium-contaminated sites, and delving into the research on microbial reduction mechanisms of uranium. For future research, enhancing the understanding of mechanisms, improving uranium removal performance, and exploring practical applications can be considered. This study provides unique insights into microbial uranium reduction research, providing valuable references for related studies in this field.

Ultrafast removal of toxic Cr(VI) by the marine bacterium Vibrio natriegens

The fastest-growing microbe Vibrio natriegens is an excellent platform for bioproduction processes. Until now, this marine bacterium has not been examined for bioremediation applications, where the production of substantial amounts of biomass would be beneficial. V. natriegens can perform extracellular electron transfer (EET) to Fe(III) via a single porin-cytochrome circuit conserved in Vibrionaceae. Electroactive microbes capable of EET to Fe(III) usually also reduce toxic metals such as carcinogenic Cr(VI), which is converted to Cr(III), thus decreasing its toxicity and mobility. Here, the performance of V. natriegens was explored for the bioremediation of Cr(VI). At a density of 100 mg/mL, V. natriegens removed 5-20 mg/L Cr(VI) within 30 s and 100 mg/L Cr(VI) within 10 min. In comparison, the model bacterium Escherichia coli grown to a comparable cell density removed Cr(VI) 36 times slower. To eliminate Cr(VI), V. natriegens had to be metabolically active, and functional outer-membrane c-type cytochromes were required. At the end of the Cr(VI) removal process, V. natriegens had reduced all of it into Cr(III) while adsorbing more than half of the metallic ions. These results demonstrate that V. natriegens, with its fast metabolism, is a viable option for the rapid treatment of aqueous pollution with Cr.

Nonsterilized Fermentation of Crude Glycerol for Polyhydroxybutyrate Production by Metabolically Engineered Vibrio natriegens

Polyhydroxybutyrate (PHB) is an attractive biodegradable polymer that can be produced through the microbial fermentation of organic wastes or wastewater. However, its mass production has been restricted by the poor utilization of organic wastes due to the presence of inhibitory substances, slow microbial growth, and high energy input required for feedstock sterilization. Here, Vibrio natriegens, a fast-growing bacterium with a broad substrate spectrum and high tolerance to salt and toxic substances, was genetically engineered to enable efficient PHB production from nonsterilized fermentation of organic wastes. The key genes encoding the PHB biosynthesis pathway of V. natriegens were identified through base editing and overexpressed. The metabolically engineered strain showed 166-fold higher PHB content (34.95 wt %) than the wide type when using glycerol as a substrate. Enhanced PHB production was also achieved when other sugars were used as feedstock. Importantly, it outperformed the engineered Escherichia coli MG1655 in PHB productivity (0.053 g/L/h) and tolerance to toxic substances in crude glycerol, without obvious activity decline under nonsterilized fermentation conditions. Our work demonstrates the great potential of engineered V. natriegens for low-cost PHB bioproduction and lays a foundation for exploiting this strain as a next-generation model chassis microorganism in synthetic biology.

Efficient and precise control of gene expression in Geobacter sulfurreducens through new genetic elements and tools for pollutant conversion

Geobacter species, exhibiting exceptional extracellular electron transfer aptitude, hold great potential for applications in pollution remediation, bioenergy production, and natural elemental cycles. Nonetheless, a scarcity of well-characterized genetic elements and gene expression tools constrains the effective and precise fine-tuning of gene expression in Geobacter species, thereby limiting their applications. Here, we examined a suite of genetic elements and developed a new genetic editing tool in Geobacter sulfurreducens to enhance their pollutant conversion capacity. First, the performances of the widely used inducible promoters, constitutive promoters, and ribosomal binding sites (RBSs) elements in G. sulfurreducens were quantitatively evaluated. Also, six native promoters with superior expression levels than constitutive promoters were identified on the genome of G. sulfurreducens. Employing the characterized genetic elements, the clustered regularly interspaced short palindromic repeats interference (CRISPRi) system was constructed in G. sulfurreducens to achieve the repression of an essential gene-aroK and morphogenic genes-ftsZ and mreB. Finally, applying the engineered strain to the reduction of tungsten trioxide (WO3 ), methyl orange (MO), and Cr(VI), We found that morphological elongation through ftsZ repression amplified the extracellular electron transfer proficiency of G. sulfurreducens and facilitated its contaminant transformation efficiency. These new systems provide rapid, versatile, and scalable tools poised to expedite advancements in Geobacter genomic engineering to favor environmental and other biotechnological applications.

Developing a Base Editing System for Marine Roseobacter Clade Bacteria

The Roseobacter clade bacteria are of great significance in marine ecology and biogeochemical cycles, and they are potential microbial chassis for marine synthetic biology due to their versatile metabolic capabilities. Here, we adapted a CRISPR-Cas-based system, base editing, with the combination of nuclease-deactivated Cas9 and deaminase for Roseobacter clade bacteria. Taking the model roseobacter Roseovarius nubinhibens as an example, we achieved precise and efficient genome editing at single-nucleotide resolution without generating double-strand breaks or requesting donor DNAs. Since R. nubinhibens can metabolize aromatic compounds, we interrogated the key genes in the β-ketoadipate pathway with our base editing system via the introduction of premature STOP codons. The essentiality of these genes was demonstrated, and for the first time, we determined PcaQ as a transcription activator experimentally. This is the first report of CRISPR-Cas-based genome editing in the entire clade of Roseobacter bacteria. We believe that our work provides a paradigm for interrogating marine ecology and biogeochemistry with direct genotype-and-phenotype linkages and potentially opens a new avenue for the synthetic biology of marine Roseobacter bacteria.