Geobacter: the microbe electric's physiology, ecology, and practical applications

Efficiency and mechanism of a novel La-based hydrogel designed for controlling lake eutrophication: Insight from phosphorus release characteristics of sediment, sulfur-driven autotrophic denitrification and cyanobacterial bloom response

Reported nutrient passivators often target single-nutrient control and require complex, energy-intensive processes. In this study, we developed a mesoporous network-structured spherical La-based hydrogel for dual nitrogen and phosphorus control. The hydrogel framework, cross-linked by sodium alginate and lanthanum, encapsulates free La³⁺. The preparation process avoids high-energy techniques and produces no waste, with recyclable reagents. Through adsorption tests, cryo-electron microscopy, and surface area and pore size analysis, we found that the mesoporous structure shields internal free La³⁺, preventing rapid release and minimizing waste of La³⁺. The cross-linked La³⁺ in the spherical framework is released by microbial degradation of the polysaccharide skeleton, inducing anaerobic conditions in the sediment and passivating soluble reactive phosphorus (SRP) simultaneously. The G-units in sodium alginate act as a carbon source, enhancing sulfur-nitrogen cycle coupling, denitrification and reducing NO₃⁻ release. Three-month laboratory simulations and nine-month field in-situ experiments demonstrated significant nutrient control. In the field trials, one month after application, the SRP concentration in the water column decreased to 0.006 mg/L (a 75 % reduction), and the NO₃⁻ concentration decreased to 0.15 mg/L (an 87.5 % reduction), with greatly improved water transparency and no cyanobacterial blooms. This study provides a novel design concept for a nutrient passivator that involves clean production, balanced input-output, and full mobilization of microbial metabolism. The properties, mechanisms, and effects of the material were comprehensively explored and verified from various aspects. This material can provide a new option for controlling endogenous pollution in eutrophic lakes.

Amino Acid Sequence Controls Enhanced Electron Transport in Heme-Binding Peptide Monolayers

Metal-binding proteins have the exceptional ability to facilitate long-range electron transport in nature. Despite recent progress, the sequence-structure-function relationships governing electron transport in heme-binding peptides and protein assemblies are not yet fully understood. In this work, the electronic properties of a series of heme-binding peptides inspired by cytochrome bc 1 are studied using a combination of molecular electronics experiments, molecular modeling, and simulation. Self-assembled monolayers (SAMs) are prepared using sequence-defined heme-binding peptides capable of forming helical secondary structures. Following monolayer formation, the structural properties and chemical composition of assembled peptides are determined using atomic force microscopy and X-ray photoelectron spectroscopy, and the electronic properties (current density-voltage response) are characterized using a soft contact liquid metal electrode method based on eutectic gallium-indium alloys (EGaIn). Our results show a substantial 1000-fold increase in current density across SAM junctions upon addition of heme compared to identical peptide sequences in the absence of heme, while maintaining a constant junction thickness. These findings show that amino acid composition and sequence directly control enhancements in electron transport in heme-binding peptides. Overall, this study demonstrates the potential of using sequence-defined synthetic peptides inspired by nature as functional bioelectronic materials.

Extracellular electron transfer proteins contribute to reduction of ferric minerals by Geobacter biofilms

To investigate how the thickness and extracellular electron transfer (EET) capabilities of microbial biofilms influence the reduction of ferric iron [Fe(III)]-containing minerals, we utilized four strains of Geobacter sulfurreducens with varying biofilm thicknesses and EET capabilities. These strains were engineered by modulating intracellular levels of dinucleotide second messengers. We systematically investigated the capacity of biofilms formed by four strains to reduce different Fe(III)-containing minerals including ferrihydrite, goethite, and lepidocrocite. By growing the G. sulfurreducens biofilm on the Fe(III) mineral-coated slides, our results showed that the strains forming thin biofilms on surfaces of Fe(III) minerals exhibited faster Fe(III) reduction rates compared to those with thick biofilms. Transcriptomic analyses revealed the upregulation of the genes encoding bacterial EET-involved proteins in the thin biofilms, highlighting the significant role of these proteins in reducing Fe(III)-containing minerals by G. sulfurreducens biofilms. Furthermore, genetic characterization identified the participation of two novel c-type cytochromes (c-Cyts), GSU1996 and GSU2513, in the reduction of Fe(III)-containing minerals by G. sulfurreducens biofilms. The results from this study provide an improved understanding of mineral-microbe interaction.IMPORTANCEGeobacter is a predominant species within biofilm communities that facilitate iron reduction, a process essential for the biogeochemical cycling of iron and other elements. However, the specific properties of Geobacter biofilms crucial for iron reduction remain unclear. By manipulating intracellular levels of dinucleotide second messengers to generate strains with varying biofilm properties, this research reveals that thinner biofilms exhibit superior rates of ferric iron [Fe(III)] mineral reduction compared to thicker biofilms. This finding highlights the vital role of proteins involved in extracellular electron transfer (EET) in enhancing the reduction of Fe(III)-containing minerals. The study further identifies two novel c-type cytochromes, GSU1996 and GSU2513, as important contributors to this process. These discoveries not only advance our understanding of microbial iron reduction but also offer new perspectives on the interactions between biofilms and mineral surfaces, potentially informing future research and applications in biogeochemical cycling and bioenergy.

Iron oxides semiconductor minerals photocatalysis reduce methane fluxes in paddy soils

Dissimilatory iron reduction could reduce ecosystems methane (CH4) emissions. However, the role of iron oxides especially with photocatalysis in controlling CH4 emissions is still unclear. In this study, hematite, goethite, and ferrihydrite were added to paddy soil and a 30-day indoor incubation experiment was then carried out. Three distinct treatments of simulating full sunlight illumination with a xenon lamp light source, shielding light at a wavelength of 550 nm, and darkness were designed to comprehensively explore the impact of semiconductor minerals photocatalysis on CH4 emissions from paddy soil. Our results showed that hematite, goethite, and ferrihydrite have the highest photoelectric conversion efficiencies at wavelengths of 550 nm, 500 nm, and less than 400 nm, respectively. When iron oxide semiconductor minerals receive light wavelengths with high photoelectric conversion efficiencies, they can mediate Geobacter metallirducens to generate highly efficient photocurrent. CH4 emissions were significantly reduced by adding goethite. In contrast, CH4 emissions were increased by adding hematite, but when the 550 nm light wavelength was blocked after adding hematite, the CH4 emissions were effectively inhibited with a reduction rate of 25 %, indicating iron oxide semiconductor minerals photocatalysis is a controlling factor in reducing CH4 fluxes. In conclusion, this study revealed that hematite and goethite are the main regulatory factors of CH4 emissions in paddy fields, and CH4 emissions can be reduced by adding goethite and blocking the 550 nm light wavelength.

Enhancing tetramethylammonium hydroxide degradation in anaerobic digestion: Neglected role of iron-based conductive materials in regulating degradation pathway

The rapid expansion of TFT-LCD industry led to significant environmental challenges due to the highly corrosive and ecotoxic tetramethylammonium hydroxide (TMAH). This study explores a previously unrecognized role of iron-based conductive materials - nano magnetite (Fe₃O₄) and nano zero-valent iron (ZVI) - in enhancing TMAH degradation and regulating degradation pathways in anaerobic digestion systems. Results show these materials significantly enhance degradation efficiency as TMAH concentration increases. At the highest TMAH level (10 g/L), while the control group achieved only 78.41 % degradation efficiency, Fe₃O₄ and ZVI groups reached efficiencies of 97.36 % and 94.96 %, with methane yields increased by 89.00 % and 97.21 %. Mechanistic exploration revealed these materials promoted secretion of charged functional groups into extracellular polymeric substances that effectively shielded microbes from TMAH toxicity. Additionally, they stimulated flavin and riboflavin production, enhancing interspecies electron transfer rates by up to 46.14-fold for Fe₃O₄ and 9.00-fold for ZVI. Microbial and metagenomic analyses further uncovered these materials induced a shift in TMAH degradation from methylotrophic methanogenesis to syntrophic metabolism, facilitating a more efficient breakdown of TMAH through direct interspecies electron transfer. These findings unravel the effects of iron-based conductive materials in regulating degradation pathways, offering a promising approach to addressing environmental challenges posed by TFT-LCD industry.

Low-molecular weight organic acids can enhance the microbial reduction of iron oxide nanoparticles and pollutants by improving electrons transfer

The combined application of dissimilatory iron-reducing bacteria (DIRB) and Fe(III) nanoparticles has garnered widespread interest in the contaminants transformation and removal. The efficiency of this composite system relies on the extracellular electron transfer (EET) process between DIRB and Fe(III) nanoparticles. While modifications to Fe(III) nanoparticles have demonstrated improvements in EET, enhancing DIRB activity also shows potential for further EET enhancement, meriting further investigation. In this study, we demonstrated that the addition of low-molecular organic acids (LMWOAs) (oxalate, pyruvate, malate, citrate, or fumarate) can improve the reduction of Fe2O3 nanoparticles by Geobacter sulfurreducens PCA through three pathways: increasing intracellular electron production, enhancing the reductive activity of extracellular metabolites, and improving the electron-donating capacity of extracellular polymeric substances. The maximum reduction of Fe2O3 nanoparticles reached up to 72 %. Our results further showed that LMWOAs significantly boosted the removal rate and ratio of Cr(VI) and hexachlorobenzene (HCB) by accelerating the EET process. Following the introduction of LMWOAs, the maximum reduction ratio of Cr(VI) reached 98 ± 0.05 % within 24 h, while the degradation efficiency of HCB reached 92 ± 0.06 % within 9 h. Overall, our study provided a precise mechanism of the role of LMWOAs on the EET process and a new strategy for reductive bioremediation of pollutants.

The role of CsrA in controls the extracellular electron transfer and biofilm production in Geobacter sulfurreducens

CsrA is a post-transcriptional regulator that controls biofilm formation, virulence, carbon metabolism, and motility, among other phenotypes in bacteria. CsrA has been extensively studied in γ-proteobacteria and firmicutes, However the cellular processes controlled for regulation in δ-proteobacteria remain unknown. In this work, we constructed and characterized the ΔcsrA mutant strain in Geobacter sulfurreducens to determine the involvement of the CsrA protein in the regulation of biofilm and extracellular electron transfer. The ΔcsrA mutant strain shows higher rates of insoluble Fe(III) reduction than the wild type using acetate as electron donor and the growth with fumarate and soluble (Fe(III)) was similar to wild type. Biofilm quantification and characterization by confocal laser scanning microscopy, showed that the ΔcsrA mutant produces up to twice as much biofilm as the wild type strain and more than 95% viable cells. Transcriptome analysis by RNA-seq showed that in ΔcsrA biofilms developed on an inert support, differentially expressed 244 genes (103 upregulated and 141 downregulated), including those related to extracellular electron transfer, exopolysaccharide synthesis, c-di-GMP synthesis and degradation. To validate the transcriptome data, RT-qPCR confirmed the differential expression of several selected genes in the ΔcsrA strain. Also, current production in microbial fuel cells was performed and the ΔcsrA strain produced 45-50% more current than the wild type. To identify the genes that changed expression in the ΔcsrA strain in the graphite electrodes in an MFC, a transcriptome analysis was performed 181 genes changed their expression in the ΔcsrA biofilms, of which 113 genes were differentially expressed only in MFC and 68 genes changed their expression as well as the transcriptome of biofilms grown on glass. In silico analysis of the 5'-UTR regions revealed that 76 genes that changed expression in the RNA-seq analysis have a consensus sequence for CsrA binding. To our knowledge this is the first report describing the involvement of CsrA in the regulation of extracellular electron transfer and biofilm in a member of the δ-proteobacteria.

Reshaped local microbiology metabolism by raw tea according to pile fermentation in the dark tea

INTRODUCTION

Traditionally, the mechanism of dark tea quality formation has centered on microorganisms, with quality regulated by manipulating microorganisms and their fermentation environment. Nevertheless, raw teas, the natural selective medium of microbial community, was completely ignored in the formation of dark tea unique flavors.

OBJECTIVES

This study aims to uncover the previously unappreciated interactions between raw tea and microorganisms, demonstrating the significant role of raw tea in the formation of dark tea quality.

METHODS

Sun-dried raw tea (SDT), baked raw tea (BT), and pan-fried raw tea (PFT) were pile fermented. Chemical profiles, microbial communities, and sensory qualities were assessed by metabolomics, high-throughput sequencing, and sensory evaluation, with correlation and multiple factor analyses used to explore their relationships.

RESULTS

Compared to PFT and BT, SDT had 18 % lower flavonoid content and 26 % lower catechin content, which favored dominant Agathobacter and Wickerhamomyces. Wickerhamomyces contributed to flower aroma by producing alcohols, esters and terpenes, while Agathobacter amplified acid production. The distinctive dominant bacterium Acidovorax in BT was positively correlated with alcohols and hydrocarbons, with Pearson's r > 0.6, resulting in a 47 % increase in volatile alcohol level, enhancing the fresh and refreshing attributes. A 70-80 % increase in iron concentration in PFT compared to SDT and BT resulted in the predominance of Geobacter, which exhibited a negative correlation with aldehydes. The presence of distinctive bacteria, Streptococcus and Ligilactobacillus, in PFT led to a significant rise in volatile acid content, increasing from 5 % to 25 %.

CONCLUSION

The chemical profiles of raw tea could reshape local microbiota, which then drives unique qualities of dark tea. This indicates dark tea quality is not passively shaped by the environmental microorganisms, but actively screened by raw tea chemistry. This study paves the way for targeted manipulation of raw tea chemical profiles to achieve desired dark tea flavor characteristics.

Microbially mediated iron redox processes for carbon and nitrogen removal from wastewater: Recent advances

Iron is the most abundant redox-active metal on Earth. The microbially mediated iron redox processes, including dissimilatory iron reduction (DIR), ammonium oxidation coupled with Fe(III) reduction (Feammox), Fe(III) dependent anaerobic oxidation of methane (Fe(III)-AOM), nitrate-reducing Fe(II) oxidation (NDFO), and Fe(II) dependent dissimilatory nitrate reduction to ammonium (Fe(II)-DNRA), play important parts in carbon and nitrogen biogeochemical cycling globally. In this review, the reaction mechanisms, electron transfer pathways, functional microorganisms, and characteristics of these processes are summarized; the prospective applications for carbon and nitrogen removal from wastewater are reviewed and discussed; and the research gaps and future directions of these processes for the treatment of wastewater are also underlined. This review is expected to give new insights into the development of economic and environmentally friendly iron-based wastewater treatment procedures.

A widespread and ancient bacterial machinery assembles cytochrome OmcS nanowires essential for extracellular electron transfer

Microbial extracellular electron transfer (EET) drives various globally important environmental phenomena and has biotechnology applications. Diverse prokaryotes have been proposed to perform EET via surface-displayed "nanowires" composed of multi-heme cytochromes. However, the mechanism that enables only a few cytochromes to polymerize into nanowires is unclear. Here, we identify a highly conserved omcS-companion (osc) cluster that drives the formation of cytochrome OmcS nanowires in Geobacter sulfurreducens. Through a combination of genetic, biochemical, and biophysical methods, we establish that prolyl isomerase-containing chaperon OscH, channel-like OscEFG, and β-propeller-like OscD are involved in the folding, secretion, and morphology maintenance of OmcS nanowires, respectively. OscH and OscG can interact with OmcS. Furthermore, overexpression of oscG accelerates EET by overproducing nanowires in an ATP-dependent manner. Heme loading splits OscD; ΔoscD accelerates cell growth, bundles nanowires into cables. Our findings establish the mechanism and prevalence of a specialized and modular assembly system for nanowires across phylogenetically diverse species and environments.

Microbial manganese redox cycling drives co-removal of nitrate and ammonium

Manganese (Mn), abundant in the Earth's crust, can act as an oxidant or a reductant for diverse nitrogen biotransformation processes. However, the functional microorganisms and their metabolic pathways, as well as interactions, remain largely elusive. Here, a microbial consortium was enriched from a mixture of freshwater sediments and activated sludge by feeding ammonium, nitrate and Mn(II), which established manganese-driven co-removal of nitrate and ammonium with removal rates of 5.83 and 2.30 mg N L-1 d-1, respectively. The batch tests and metagenomic analyses revealed a nitrate-dependent anaerobic manganese oxidation (NDMO) process mediated by Anaerolineales and Phycisphaerales and a manganese reduction coupled to anaerobic ammonium oxidation (Mnammox) process mediated by Chthonomonadales. Based on identified key genes involved in the nitrogen and manganese metabolic pathways, nitrate was likely reduced to nitrite and nitrogen gas in the NDMO process while ammonium was oxidized to nitrite in the Mnammox process, which in turn fuelled the Anammox process carried out by Candidatus Brocadia. This revealed the microbial interactions of NDMO, Mnammox, and Anammox processes responsible for manganese-driven co-removal of ammonium and nitrate. These findings provide a potential solution for biological nitrogen removal and expand our understanding of the nitrogen and manganese biogeochemical cycles.

New insights in uranium bioremediation by cytochromes of the bacterium Geotalea uraniireducens

The bacterium Geotalea uraniireducens, commonly found in uranium-contaminated environments, plays a key role in bioremediation strategies by converting the soluble hexavalent form of uranium (U(VI)) into less soluble forms (e.g., U(IV)). While most of the reduction and concomitant precipitation of uranium occur outside the cells, there have been reports of important reduction processes taking place in the periplasm. In any case, the triheme periplasmic cytochromes are key players, either by ensuring an effective interface between the cell's interior and exterior or by directly participating in the reduction of the metal. Therefore, understanding the functional mechanism of the highly abundant triheme cytochromes in G. uraniireducens' is crucial for elucidating the respiratory pathways in this bacterium. In this work, a detailed functional characterization of the triheme cytochromes PpcA and PpcB from G. uraniireducens was conducted using NMR and visible spectroscopy techniques. Despite sharing high amino acid sequence identity and structural homology with their counterparts from Geobacter sulfurreducens, the results showed that the heme reduction potential values are less negative, the order of oxidation of the hemes is distinct, and the redox and redox-Bohr network of interactions revealed unprecedented functional mechanisms in the cytochromes of G. uraniireducens. In these cytochromes, the reduction potential values of the three heme groups are much more similar, resulting in a narrower range of values, that facilitates directional electron flow from the inner membrane, thereby optimizing the uranium reduction.

Unlocking anaerobic digestion potential via extracellular electron transfer by exogenous materials: Current status and perspectives

The efficiency of energy transfer among microorganisms presents a substantial hurdle for the widespread implementation of anaerobic digestion techniques. Nonetheless, recent studies have demonstrated that enhancing the extracellular electron transfer (EET) can markedly enhance this efficiency. This review highlights recent advancements in EET for anaerobic digestion and examines the contribution of external additives to fostering enhanced efficiency within this context. Diverse mechanisms through which additives are employed to improve EET in anaerobic environments are delineated. Furthermore, specific strategies for effectively regulating EET are proposed, aiming to augment methane production from anaerobic digestion. This review thus offers a perspective on future research directions aimed at optimizing waste resources, enhancing methane production efficiency, and improving process predictability in anaerobic digestion.

Unprecedented N2O production by nitrate-ammonifying Geobacteraceae with distinctive N2O isotopocule signatures

Dissimilatory nitrate reduction to ammonium (DNRA), driven by nitrate-ammonifying bacteria, is an increasingly appreciated nitrogen-cycling pathway in terrestrial ecosystems. This process reportedly generates nitrous oxide (N2O), a strong greenhouse gas with ozone-depleting effects. However, it remains poorly understood how N2O is produced by environmental nitrate-ammonifiers and how to identify DNRA-derived N2O. In this study, we characterize two novel enzymatic pathways responsible for N2O production in Geobacteraceae strains, which are predominant nitrate-ammonifying bacteria in paddy soils. The first pathway involves a membrane-bound nitrate reductase (Nar) and a hybrid cluster protein complex (Hcp-Hcr) that catalyzes the conversion of NO2- to NO and subsequently to N2O. The second pathway is observed in Nar-deficient bacteria, where the nitrite reductase (NrfA) generates NO, which is then reduced to N2O by Hcp-Hcr. These enzyme combinations are prevalent across the domain Bacteria. Moreover, we observe distinctive isotopocule signatures of DNRA-derived N2O from other established N2O production pathways, especially through the highest 15N-site preference (SP) values (43.0‰-49.9‰) reported so far, indicating a robust means for N2O source partitioning. Our findings demonstrate two novel N2O production pathways in DNRA that can be isotopically distinguished from other pathways.IMPORTANCEStimulation of DNRA is a promising strategy to improve fertilizer efficiency and reduce N2O emission in agriculture soils. This process converts water-leachable NO3- and NO2- into soil-adsorbable NH4+, thereby alleviating nitrogen loss and N2O emission resulting from denitrification. However, several studies have noted that DNRA can also be a source of N2O, contributing to global warming. This contribution is often masked by other N2O generation processes, leading to a limited understanding of DNRA as an N2O source. Our study reveals two widespread yet overlooked N2O production pathways in Geobacteraceae, the predominant DNRA bacteria in paddy soils, along with their distinctive isotopocule signatures. These findings offer novel insights into the role of the DNRA bacteria in N2O production and underscore the significance of N2O isotopocule signatures in microbial N2O source tracking.

A critical review of Mnammox coupled with the NDMO for innovative nitrogen removal

In the context of increasing global nitrogen pollution, traditional biological nitrogen removal technologies like nitrification and denitrification are hindered by high energy consumption. Additionally, the deployment of anaerobic ammonium oxidation (Anammox) technology is constrained due to the slow growth rate of Anammox bacteria and there is a bottleneck in nitrogen removal efficiency. To overcome these technical bottlenecks, researchers have discovered a revolutionary nitrogen removal technology that cleverly combines the redox cycling of manganese with nitrification and denitrification reactions. In this new process, manganese dependent anaerobic ammonium oxidation (Mnammox) bacteria can convert NH4+ to N2 under anaerobic conditions, while nitrate/nitrite dependent manganese oxidation (NDMO) bacteria use NO3-/NO2- as electron acceptors to oxidize Mn2+ to Mn4+. Mn4+ acts as an electron acceptor in Mnammox reaction, thereby realizing the autotrophic nitrogen removal process. This innovative method not only simplifies the steps of biological denitrification, but also significantly reduces the consumption of oxygen and organic carbon, providing a more efficient and environmentally friendly solution to the problem of nitrogen pollution. The article initially provides a concise overview of prevalent nitrogen removal technologies and the application of manganese in these processes, and discusses the role of manganese in biogeochemical cycles, including its discovery, mechanism of action, microbial communities involved, and its impact on these key factors in the process. Subsequently, metabolic principles, benefits, advantages, and environmental considerations of Mnammox coupled with the NDMO process are analyzed in detail. Finally, this article summarizes the shortcomings of current research and looks forward to future research directions. The goal of this article is to provide a valuable reference for researchers to fully understand the application of manganese in nitrogen removal processes.

Cascading sulfur cycling in simulated oil sands pit lake water cap mesocosms transitioning from oxic to euxinic conditions

Base Mine Lake (BML), the first full-scale demonstration of oil sands tailings pit lake reclamation technology, is experiencing expansive, episodic hypolimnetic euxinia resulting in greater sulfur biogeochemical cycling within the water cap. Here, Fluid Fine Tailings (FFT)-water mesocosm experiments simulating the in situ BML summer hypolimnetic oxic-euxinic transition determined sulfur biogeochemical processes and their controlling factors. While mesocosm water caps without FFT amendments experienced limited geochemical and microbial changes during the experimental period, FFT-amended mesocosm water caps evidenced three successive stages of S speciation in ∼30 days: (S1) rising expansion of water cap euxinia from FFT to water surface; enabling (S2) rapid sulfate (SO42-) reduction and sulfide production directly within the water column; fostering (S3) generation and subsequent consumption of sulfur oxidation intermediate compounds (SOI). Identified key SOI, elemental S and thiosulfate, support subsequent SOI oxidation, reduction, and/or disproportionation processes in the system. Dominant water cap microbes shifted from methanotrophs and denitrifying/iron-reducing bacteria to functionally versatile sulfur-reducing bacteria (SRB) comprising sulfate-reducing bacteria (Desulfovibrionales) and SOI-reducing/disproportionating bacteria (Campylobacterales and Desulfobulbales). The observed microbial shift is driven by decreasing [SO42-] and organic aromaticity, with putative hydrocarbon-degrading bacteria providing electron donors for SRB. Comparison between unsterile and sterile water treatments further underscores the biogeochemical readiness of the in situ water cap to enhance oxidant depletion, euxinia expansion and establishment of water cap SRB communities aided by FFT migration of anaerobes. Results here identify the collective influence of FFT and water cap microbial communities on water cap euxinia expansion associated with sequential S reactions that are controlled by concentrations of oxidants, labile organic substrates and S species. This emphasizes the necessity of understanding this complex S cycling in assessing BML water cap O2 persistence.

Advances in microbial community, mechanisms and stimulation effects of direct interspecies electron transfer in anaerobic digestion

Anaerobic digestion (AD) has been proven to be an effective green technology for producing biomethane while reducing environmental pollution. The interspecies electron transfer (IET) processes in AD are critical for acetogenesis and methanogenesis, and these IET processes are carried out via mediated interspecies electron transfer (MIET) and direct interspecies electron transfer (DIET). The latter has recently become a topic of significant interest, considering its potential to allow diffusion-free electron transfer during the AD process steps. To date, different multi-heme c-type cytochromes, electrically conductive pili (e-pili), and other relevant accessories during DIET between microorganisms of different natures have been reported. Additionally, several studies have been carried out on metagenomics and metatranscriptomics for better detection of DIET, the role of DIET's stimulation in alleviating stressed conditions, such as high organic loading rates (OLR) and low pH, and the stimulation mechanisms of DIET in mixed cultures and co-cultures by various conductive materials. Keeping in view this significant research progress, this study provides in-depth insights into the DIET-active microbial community, DIET mechanisms of different species, utilization of various approaches for stimulating DIET, characterization approaches for effectively detecting DIET, and potential future research directions. This study can help accelerate the field's research progress, enable a better understanding of DIET in complex microbial communities, and allow its utilization to alleviate various inhibitions in complex AD processes.

Enhanced removal of PPCPs and antibiotic resistance genes in saline wastewater using a bioelectrochemical-constructed wetland system

Pharmaceuticals and personal care products (PPCPs) are insufficiently degraded in saline wastewater treatment processes and are found at high concentrations and detection frequencies in aquatic environments. In this study, the wetland plant Thalia dealbata was selected using a screening plant experiment to ensure good salt tolerance and high efficiency in removing PPCPs. An electric integrated vertical-flow constructed wetland (E-VFCW) was developed to improve the removal of PPCPs and reduce the abundance of antibiotic resistance genes (ARGs). The removal efficiency of ofloxacin, enrofloxacin, and diclofenac in the system with anaerobic cathodic and aerobic anodic chambers is higher than that of the control system (41.84 ± 2.88%, 47.29 ± 3.01%, 53.29 ± 2.54%) by approximately 20.31%, 16.04%, and 35.25%. The removal efficiency of ibuprofen in the system with the aerobic anodic and anaerobic cathodic chamber was 28.51% higher than that of the control system (72.41 ± 3.06%) and promotes the reduction of ARGs. Electrical stimulation can increase the activity of plant enzymes, increasing their adaptability to stress caused by PPCPs, and PPCPs are transferred to plants. Species related to PPCPs biodegradation (Geobacter, Lactococcus, Hydrogenophaga, and Nitrospira) were enriched in the anodic and cathodic chambers of the system. This study provides an essential reference for the removal of PPCPs in saline-constructed wetlands.

Reductive dehalogenase of Dehalococcoides mccartyi strain CBDB1 reduces cobalt- containing metal complexes enabling anodic respiration

Microorganisms capable of direct or mediated extracellular electron transfer (EET) have garnered significant attention for their various biotechnological applications, such as bioremediation, metal recovery, wastewater treatment, energy generation in microbial fuel cells, and microbial or enzymatic electrosynthesis. One microorganism of particular interest is the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1, known for its ability to reductively dehalogenate toxic and persistent halogenated organic compounds through organohalide respiration (OHR), using halogenated organics as terminal electron acceptors. A membrane-bound OHR protein complex couples electron transfer to proton translocation across the membrane, generating a proton motive force, which enables metabolism and proliferation. In this study we show that the halogenated compounds can be replaced with redox mediators that can putatively shuttle electrons between the OHR complex and the anode, coupling D. mccartyi cells to an electrode via mediated EET. We identified cobalt-containing metal complexes, referred to as cobalt chelates, as promising mediators using a photometric high throughput methyl viologen-based enzyme activity assay. Through various biochemical approaches, we show that cobalt chelates are specifically reduced by CBDB1 cells, putatively by the reductive dehalogenase subunit (RdhA) of the OHR complex. Using cyclic voltammetry, we also demonstrate that cobalt chelates exchange electrons with a gold electrode, making them promising candidates for bioelectrochemical cultivation. Furthermore, using the AlphaFold 2-calculated RdhA structure and molecular docking, we found that one of the identified cobalt chelates exhibits favorable binding to RdhA, with a binding energy of approximately -28 kJ mol-1. Taken together, our results indicate that bioelectrochemical cultivation of D. mccartyi with cobalt chelates as anode mediators, instead of toxic halogenated compounds, is feasible, which opens new perspectives for bioremediation and other biotechnological applications of strain CBDB1.

Assessing the impact of soil microbial fuel cells on atrazine removal in soil

Widespread pesticide use in agriculture is a major source of soil pollution, driving biodiversity loss and posing serious threads to human health. The recalcitrant nature of most of these pesticides demands for effective remediation strategies. In this study, we assess the ability of soil microbial fuel cell (SMFC) technology to bioremediate soil polluted by the model pesticide atrazine. To elucidate the degradation mechanism and consequently define effective implementation strategies, we provide the first comprehensive investigation of the SMFC performance, in which the monitoring of the electrochemical performance of the system is combined with Quadrupole Time-of-Flight (QTOF) mass spectrometry and microbial analyses. Our results show that, while both SMFC and natural attenuation lead to a reduction on atrazine levels, the SMFC modulates the activity of different microbial pathways. As a result, atrazine degradation by natural attenuation leads to high levels of deisoproylatrazine (DIPA), a very toxic degradation metabolite, while DIPA levels in soil treated by SMFC remain comparatively low. The beta diversity and differential abundance analyses revealed how the microbial community evolves over time in the SMFCs degrading atrazine, demonstrating the enrichment of electroactive taxa on the anode, and the enrichment of a mixture of electroactive and atrazine-degrading taxa at the cathode. The detection and taxonomic classification of peripheral atrazine degrading genes, atzA, atzB and atzC, was carried out in combination with the differential abundance analysis. Results revealed that these genes are likely harboured by members of the order Rhizobiales enriched at the cathode, thus promoting atrazine degradation via the conversion of hydroxyatrazine (HA) into N-isopropylammelide (NIPA), as confirmed by mass spectrometry data. Overall, the comprehensive approach adopted in this work, provides fundamental insights into the degradation pathways of atrazine in soil by SMFC technology, which is critical for practical applications, thus suggesting an effective approach to advance research in the field.

Potential applications of microbial genomics in nuclear non-proliferation

As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.

Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils

Global sewage sludge production is rapidly increasing, and its safe disposal is becoming an increasingly serious issue. One of the main methods of municipal sewage sludge management is based on its agricultural use. The wastewater and sewage sludge contain numerous antibiotic resistance genes (ARGs), and its microbiome differs significantly from the soil microbial community. The aim of the study was to assess the changes occurring in the soil microbial community and resistome after the addition of sewage sludge from municipal wastewater treatment plant (WWTP) in central Poland, from which the sludge is used for fertilizing agricultural soils on a regular basis. This study used a high-throughput shotgun metagenomics approach to compare the microbial communities and ARGs present in two soils fertilized with sewage sludge. The two soils represented different land uses and different physicochemical and granulometric properties. Both soils were characterized by a similar taxonomic composition of the bacterial community, despite dissimilarities between soils properties. Five phyla predominated, viz. Planctomycetes, Actinobacteria, Proteobacteria, Chloroflexi and Firmicutes, and they were present in comparable proportions in both soils. Network analysis revealed that the application of sewage sludge resulted in substantial qualitative and quantitative changes in bacterial taxonomic profile, with most abundant phyla being considerably depleted and replaced by Proteobacteria and Spirochaetes. In addition, the ratio of oligotrophic to copiotrophic bacteria substantially decreased in both amended soils. Furthermore, fertilized soils demonstrated greater diversity and richness of ARGs compared to control soils. The increased abundance concerned mainly genes of resistance to antibiotics most commonly used in human and animal medicine. The level of heavy metals in sewage sludge was low and did not exceed the standards permitted in Poland for sludge used in agriculture, and their level in fertilized soils was still inconsiderable.

Novel Insights on Extracellular Electron Transfer Networks in the Desulfovibrionaceae Family: Unveiling the Potential Significance of Horizontal Gene Transfer

Some sulfate-reducing bacteria (SRB), mainly belonging to the Desulfovibrionaceae family, have evolved the capability to conserve energy through microbial extracellular electron transfer (EET), suggesting that this process may be more widespread than previously believed. While previous evidence has shown that mobile genetic elements drive the plasticity and evolution of SRB and iron-reducing bacteria (FeRB), few have investigated the shared molecular mechanisms related to EET. To address this, we analyzed the prevalence and abundance of EET elements and how they contributed to their differentiation among 42 members of the Desulfovibrionaceae family and 23 and 59 members of Geobacteraceae and Shewanellaceae, respectively. Proteins involved in EET, such as the cytochromes PpcA and CymA, the outer membrane protein OmpJ, and the iron-sulfur cluster-binding CbcT, exhibited widespread distribution within Desulfovibrionaceae. Some of these showed modular diversification. Additional evidence revealed that horizontal gene transfer was involved in the acquiring and losing of critical genes, increasing the diversification and plasticity between the three families. The results suggest that specific EET genes were widely disseminated through horizontal transfer, where some changes reflected environmental adaptations. These findings enhance our comprehension of the evolution and distribution of proteins involved in EET processes, shedding light on their role in iron and sulfur biogeochemical cycling.

Isolation of Electrochemically Active Bacteria from an Anaerobic Digester Treating Food Waste and Their Characterization

Studies have used anaerobic-digester sludge and/or effluent as inocula for bioelectrochemical systems (BESs), such as microbial fuel cells (MFCs), for power generation, while limited studies have isolated and characterized electrochemically active bacteria (EAB) that inhabit anaerobic digesters. In the present work, single-chamber MFCs were operated using the anaerobic-digester effluent as the sole source of organics and microbes, and attempts were made to isolate EAB from anode biofilms in MFCs by repeated anaerobic cultivations on agar plates. Red colonies were selected from those grown on the agar plates, resulting in the isolation of three phylogenetically diverse strains affiliated with the phyla Bacillota, Campylobacterota and Deferribacterota. All these strains are capable of current generation in pure-culture BESs, while they exhibit different electrochemical properties as assessed by cyclic voltammetry. The analyses of their cell-free extracts show that cytochromes are abundantly present in their cells, suggesting their involvement in current generation. The results suggest that anaerobic digesters harbor diverse EAB, and it would be of interest to examine their ecological niches in anaerobic digestion.

Bacterial and Archaeal Communities in Erhai Lake Sediments: Abundance and Metabolic Insight into a Plateau Lake at the Edge of Eutrophication

The littoral zones of lakes are potential hotspots for local algal blooms and biogeochemical cycles; however, the microbial communities within the littoral sediments of eutrophic plateau lakes remain poorly understood. Here, we investigated the taxonomic composition, co-occurrence networks, and potential functional roles of both abundant and rare taxa within bacterial and archaeal communities, as well as physicochemical parameters, in littoral sediments from Erhai Lake, a mesotrophic lake transitioning towards eutrophy located in the Yunnan-Guizhou Plateau. 16S rRNA gene sequencing revealed that bacterial communities were dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, while Euryarchaeota was the main archaeal phylum. Co-occurrence network analysis revealed that keystone taxa mainly belonged to rare species in the bacterial domain, but in the archaeal domain, over half of keystone taxa were abundant species, demonstrating their fundamental roles in network persistence. The rare bacterial taxa contributed substantially to the overall abundance (81.52%), whereas a smaller subset of abundant archaeal taxa accounted for up to 82.70% of the overall abundance. Functional predictions highlighted a divergence in metabolic potentials, with abundant bacterial sub-communities enriched in pathways for nitrogen cycling, sulfur cycling, and chlorate reduction, while rare bacterial sub-communities were linked to carbon cycling processes such as methanotrophy. Abundant archaeal sub-communities exhibited a high potential for methanogenesis, chemoheterotrophy, and dark hydrogen oxidation. Spearman correlation analysis showed that genera such as Candidatus competibacter, Geobacter, Syntrophobacter, Methanocella, and Methanosarcina may serve as potential indicators of eutrophication. Overall, this study provides insight into the distinct roles that rare and abundant taxa play in the littoral sediments of mesotrophic plateau lakes.

Adding carbon sources to the substrates enhances Cr and Ni removal and mitigates greenhouse gas emissions in constructed wetlands

Constructed wetlands for wastewater treatment pose challenges related to long-term operational efficiency and greenhouse gas emissions on a global scale. This study investigated the impact of adding peat, humic acid, and biochar into the substrates of constructed wetlands and focused on Cr, and Ni removal, greenhouse gas emissions, and microbial communities in constructed wetlands. Biochar addition treatment achieved the highest removal efficiencies for total Cr (99.96%), Cr (VI) (100%), and total Ni (91.04%). Humic acid and biochar addition both significantly increased the heavy metal content in wetland plant Leersia hexandra and substrates of constructed wetlands. Further analysis of microbial community proportions by high-throughput sequencing revealed that biochar and humic acid treatments enhanced Cr and Ni removal efficiency by increasing the abundance of Bacteroidetes, Geobacter and Ascomycota. Humic acid addition treatment reduced CO2 emissions by decreasing the abundance of Bacteroidetes and increasing that of Basidiomycota. Peat treatment decreased CH4 emissions by reducing the abundance of the Bacteroidetes. Biochar treatment increased the abundance of the Firmicutes, Bacteroidetes, Proteobacteria as well as Basidiomycota, resulting in reduced N2O emissions. Biochar and humic acid treatments efficiently removed heavy metals from wastewater and mitigated greenhouse gas emissions in constructed wetlands by modifying the microbial communities.

Periplasmic electron transfer network in Geobacter sulfurreducens revealed by biomolecular interaction studies

Multiheme cytochromes located in different compartments are crucial for extracellular electron transfer in the bacterium Geobacter sulfurreducens to drive important environmental processes and biotechnological applications. Recent studies have unveiled that for particular sets of electron terminal acceptors, discrete respiratory pathways selectively recruit specific cytochromes from both the inner and outer membranes. However, such specificity was not observed for the abundant periplasmic cytochromes, namely the triheme cytochrome family PpcA-E. In this work, the distinctive NMR spectroscopic signatures of these proteins in different redox states were explored to monitor pairwise interactions and electron transfer reactions between each pair of cytochromes. The results showed that the five proteins interact transiently and can exchange electrons between each other revealing intra-promiscuity within the members of this family. This discovery is discussed in the light of the establishment of an effective electron transfer network by this pool of cytochromes. This network is advantageous to the bacteria as it enables the maintenance of the functional working potential redox range within the cells.

Biochar derived from alkali-treated sludge residue regulates anaerobic digestion: Enhancement performance and potential mechanisms

Biochar produced from bio-wastes has been widely used to promote the performance of anaerobic digestion. Waste activated sludge (WAS) is considered as a kind of popular precursor for biochar preparation, but the abundant resources in WAS were neglected previously. In this study, the roles of biochar prepared from raw, pretreated, and fermented sludge on anaerobic digestion were investigated. That is, parts of carbon sources and nutrients like polysaccharides, proteins, and phosphorus were firstly recovered after sludge pretreatment or fermentation, and then the sludge residuals were used as raw material to prepare biochar. The methane yield improved by 22.1% with adding the biochar (AK-BC) prepared by sludge residual obtained from alkaline pretreatment. Mechanism study suggested that the characteristics of AK-BC like specific surface area and defect levels were updated. Then, the conversion performance of intermediate metabolites and electro-activities of extracellular polymeric substances were up-regulated. As a result, the activity of electron transfer was increased with the presence of AK-BC, with increase ratio of 21.4%. In addition, the electroactive microorganisms like Anaerolineaceae and Methanosaeta were enriched with the presence of AK-BC, and the potential direct interspecies electron transfer was possibly established. Moreover, both aceticlastic and CO2-reducing methanogenesis pathways were improved by up-regulating related enzymes. Therefore, the proposed strategy can not only obtain preferred biochar but also recover abundant resources like carbon source, nutrients, and bioenergy.

Degradation of Complex Carbon Sources in Organic Fertilizers Facilitates Nitrogen Fixation

Biological nitrogen fixation is crucial for agriculture and improving fertilizer efficiency, but organic fertilizers in enhancing this process remain debated. Here, we investigate the impact of organic fertilizers on biological nitrogen fixation through experiments and propose a new model where bacterial interactions with complex carbon sources enhance nitrogen fixation. Field experiments showed that adding organic fertilizers increased the nitrogenase activity by 57.85%. Subculture experiments revealed that organic fertilizer addition enriched genes corresponding to complex carbon and energy metabolism, as well as nifJ involved in electron transfer for nitrogenase. It also enhanced bacterial interactions and enhanced connectors associated with complex carbon degradation. Validation experiments demonstrated that combinations increased nitrogenase activity by 2.98 times compared to the single. Our findings suggest that organic fertilizers promoted nitrogen fixation by enhancing microbial cooperation, improved the degradation of complex carbon sources, and thereby provided utilizable carbon sources, energy, and electrons to N-fixers, thus increasing nitrogenase activity and nitrogen fixation.

On the fundamentals of quantum rate theory and the long-range electron transport in respiratory chains

It has been shown that both the electron-transfer rate constant of an electrochemical reaction and the conductance quantum are correlated with the concept of quantum capacitance. This simple association between the two separate concepts has an entirely quantum rate basis that encompasses the electron-transfer rate theory as originally proposed by Rudolph A. Marcus whether statistical mechanics is appropriately taken into account. I have prepared a concise review of the quantum mechanical rate theory principles focused on its quantum electrodynamics character to demonstrate that it can reconcile the conflicting views established on attempting to use the super-exchange (supported on electron transfer) or 'metallic-like' (supported on conductance quantum) mechanisms separately to explain the highly efficient long-range electron transport observed in the respiratory processes of living cells. The unresolved issues related to long-range electron transport are clarified in light of the quantum rate theory with a discussion focused on Geobacter sulfurreducens films as a reference standard of the respiration chain. Theoretical analyses supported by experimental data suggest that the efficiency of respiration within a long-range electron transport path is intrinsically a quantum mechanical event that follows relativistic quantum electrodynamics principles as addressed by quantum rate theory.

Expression of filaments of the Geobacter extracellular cytochrome OmcS in Shewanella oneidensis

The physiological role of Geobacter sulfurreducens extracellular cytochrome filaments is a matter of debate and the development of proposed electronic device applications of cytochrome filaments awaits methods for large-scale cytochrome nanowire production. Functional studies in G. sulfurreducens are stymied by the broad diversity of redox-active proteins on the outer cell surface and the redundancy and plasticity of extracellular electron transport routes. G. sulfurreducens is a poor chassis for producing cytochrome nanowires for electronics because of its slow, low-yield, anaerobic growth. Here we report that filaments of the G. sulfurreducens cytochrome OmcS can be heterologously expressed in Shewanella oneidensis. Multiple lines of evidence demonstrated that a strain of S. oneidensis, expressing the G. sulfurreducens OmcS gene on a plasmid, localized OmcS on the outer cell surface. Atomic force microscopy revealed filaments with the unique morphology of OmcS filaments emanating from cells. Electron transfer to OmcS appeared to require a functional outer-membrane porin-cytochrome conduit. The results suggest that S. oneidensis, which grows rapidly to high culture densities under aerobic conditions, may be suitable for the development of a chassis for producing cytochrome nanowires for electronics applications and may also be a good model microbe for elucidating cytochrome filament function in anaerobic extracellular electron transfer.

Feammox bacterial biofilm formation in HFMB

Nitrogen pollution has been increasing with the development of industrialization. Consequently, the excessive deposition of reactive nitrogen in the environment has generated the loss of biodiversity and eutrophication of different ecosystems. In 2005, a Feammox process was discovered that anaerobically metabolizes ammonium. Feammox with the use of hollow fiber membrane bioreactors (HFMB), based on the formation of biofilms of bacterial communities, has emerged as a possible efficient and sustainable method for ammonium removal in environments with high iron concentrations. This work sought to study the possibility of implementing, at laboratory scale, an efficient method by evaluating the use of HFMB. Samples from an internal circulation reactor (IC) incubated in culture media for Feammox bacteria. The cultures were enriched in a batch reactor to evaluate growth conditions. Next, HFMB assembly was performed, and Feammox parameters were monitored. Also, conventional PCR and scanning electron microscopy (SEM) analysis were performed to characterize the bacterial communities associated with biofilm formation. The use of sodium acetate presented the best performance for Feammox activity. The HFMB operation showed an ammonium (NH4+) removal of 50%. SEM analysis of the fibers illustrated the formation of biofilm networks formed by bacteria, which were identified as Albidiferax ferrireducens, Geobacter spp, Ferrovum myxofaciens, Shewanella spp., and Anammox. Functional genes Archaea/Bacteria ammonia monooxygenase, nrxA, hzsB, nirS and nosZ were also identified. The implementation of HFMB Feammox could be used as a sustainable tool for the removal of ammonium from wastewater produced because of anthropogenic activities.

Untapped rich microbiota of mangroves of Pakistan: diversity and community compositions

The mangrove ecosystem is the world's fourth most productive ecosystem in terms of service value and offering rich biological resources. Microorganisms play vital roles in these ecological processes, thus researching the mangroves-microbiota is crucial for a deeper comprehension of mangroves dynamics. Amplicon sequencing that targeted V4 region of 16S rRNA gene was employed to profile the microbial diversities and community compositions of 19 soil samples, which were collected from the rhizosphere of 3 plant species (i.e., Avicennia marina, Ceriops tagal, and Rhizophora mucronata) in the mangrove forests of Lasbela coast, Pakistan. A total of 67 bacterial phyla were observed from three mangroves species, and these taxa were classified into 188 classes, 453 orders, 759 families, and 1327 genera. We found that Proteobacteria (34.9-38.4%) and Desulfobacteria (7.6-10.0%) were the dominant phyla followed by Chloroflexi (6.6-7.3%), Gemmatimonadota (5.4-6.8%), Bacteroidota (4.3-5.5%), Planctomycetota (4.4-4.9%) and Acidobacteriota (2.7-3.4%), Actinobacteriota (2.5-3.3%), and Crenarchaeota (2.5-3.3%). After considering the distribution of taxonomic groups, we prescribe that the distinctions in bacterial community composition and diversity are ascribed to the changes in physicochemical attributes of the soil samples (i.e., electrical conductivity (ECe), pH, total organic matter (OM), total organic carbon (OC), available phosphorus (P), and extractable potassium (CaCO3). The findings of this study indicated a high-level species diversity in Pakistani mangroves. The outcomes may also aid in the development of effective conservation policies for mangrove ecosystems, which have been hotspots for anthropogenic impacts in Pakistan. To our knowledge, this is the first microbial research from a Pakistani mangrove forest.

Iron Plaque: A Shield against Soil Contamination and Key to Sustainable Agriculture

Soils play a dominant role in supporting the survival and growth of crops and they are also extremely important for human health and food safety. At present, the contamination of soil by heavy metals remains a globally concerning environmental issue that needs to be resolved. In the environment, iron plaque, naturally occurring on the root surface of wetland plants, is found to be equipped with an excellent ability at blocking the migration of heavy metals from soils to plants, which can be further developed as an environmentally friendly strategy for soil remediation to ensure food security. Because of its large surface-to-volume porous structure, iron plaque exhibits high binding affinity to heavy metals. Moreover, iron plaque can be seen as a reservoir to store nutrients to support the growth of plants. In this review, the formation process of iron plaque, the ecological role that iron plaque plays in the environment and the interaction between iron plaque, plants and microbes, are summarized.

Geogenic Phosphorus Enrichment in Groundwater due to Anaerobic Methane Oxidation-Coupled Fe(III) Oxide Reduction

Accumulation of geogenic phosphorus (P) in groundwater is an emerging environmental concern, which is closely linked to coupled processes involving FeOOH and organic matter under methanogenic conditions. However, it remains unclear how P enrichment is associated with methane cycling, particularly the anaerobic methane oxidation (AMO). This study conducted a comprehensive investigation of carbon isotopes in dissolved inorganic carbon (DIC), CO2, and CH4, alongside Fe isotopes, microbial communities, and functions in quaternary aquifers of the central Yangtze River plain. The study found that P concentrations tended to increase with Fe(II) concentrations, δ56Fe, and δ13C-DIC, suggesting P accumulation due to the reductive dissolution of FeOOH under methanogenic conditions. The positive correlations of pmoA gene abundance versus δ13C-CH4 and Fe concentrations versus δ13C-CH4, and the prevalent presence of Candidatus_Methanoperedens, jointly demonstrated the potential significance of Fe(III)-mediated AMO process (Fe-AMO) alongside traditional methanogenesis. The increase of P concentration with δ13C-CH4 value, pmoA gene abundance, and Fe concentration suggested that the Fe-AMO process facilitated P enrichment in groundwater. Redundancy analysis confirmed this assertion, identifying P concentration as the primary determinant and the cooperative influence of Fe-AMO microorganisms such as Candidatus_Methanoperedens and Geobacter on P enrichment. Our work provided new insights into P dynamics in subsurface environments.

Recent advances in phyto-combined remediation of heavy metal pollution in soil

The global industrialization and modernization have witnessed a rapid progress made in agricultural production, along with the issue of soil heavy metal (HM) pollution, which has posed severe threats to soil quality, crop yield, and human health. Phytoremediation, as an alternative to physical and chemical methods, offers a more cost-effective, eco-friendly, and aesthetically appealing means for in-situ remediation. Despite its advantages, traditional phytoremediation faces challenges, including variable soil physicochemical properties, the bioavailability of HMs, and the slow growth and limited biomass of plants used for remediation. This study presents a critical overview of the predominant plant-based HM remediation strategies. It expounds upon the mechanisms of plant absorption, translocation, accumulation, and detoxification of HMs. Moreover, the advancements and practical applications of phyto-combined remediation strategies, such as the addition of exogenous substances, genetic modification of plants, enhancement by rhizosphere microorganisms, and intensification of agricultural technologies, are synthesized. In addition, this paper also emphasizes the economic and practical feasibility of some strategies, proposing solutions to extant challenges in traditional phytoremediation. It advocates for the development of cost-effective, minimally polluting, and biocompatible exogenous substances, along with the careful selection and application of hyperaccumulating plants. We further delineate specific future research avenues, such as refining genetic engineering techniques to avoid adverse impacts on plant growth and the ecosystem, and tailoring phyto-combined strategies to diverse soil types and HM pollutants. These proposed directions aim to enhance the practical application of phytoremediation and its integration into a broader remediation framework, thereby addressing the urgent need for sustainable soil decontamination and protection of ecological and human health.

Influence of fumarate on interspecies electron transfer and the metabolic shift induced in Clostridium pasteurianum by Geobacter sulfurreducens

AIMS

In previous studies, it was demonstrated that co-culturing Clostridium pasteurianum and Geobacter sulfurreducens triggers a metabolic shift in the former during glycerol fermentation. This shift, attributed to interspecies electron transfer and the exchange of other molecules, enhances the production of 1,3-propanediol at the expense of the butanol pathway. The aim of this investigation is to examine the impact of fumarate, a soluble compound usually used as an electron acceptor for G. sulfurreducens, in the metabolic shift previously described in C. pasteurianum.

METHODS AND RESULTS

Experiments were conducted by adding along with glycerol, acetate, and different quantities of fumarate in co-cultures of G. sulfurreducens and C. pasteurianum. A metabolic shift was exhibited in all the co-culture conditions. This shift was more pronounced at higher fumarate concentrations. Additionally, we observed G. sulfurreducens growing even in the absence of fumarate and utilizing small amounts of this compound as an electron donor rather than an electron acceptor in the co-cultures with high fumarate addition.

CONCLUSIONS

This study provided evidence that interspecies electron transfer continues to occur in the presence of a soluble electron acceptor, and the metabolic shift can be enhanced by promoting the growth of G. sulfurreducens.

Effects of simulated microgravity on current generation of electrochemically active bacteria: Insights from case-control study using random positioning machine

Electrochemically active bacteria (EAB) exhibit promising prospects for space exploration and life support systems. However, the effects of the space environment on EAB are unclear. In this study, the effects of simulated microgravity on the current generation of mixed-culture EAB were illustrated, and the underlying mechanism was elucidated. The results demonstrated that the electrochemical activity of mixed-culture EAB was enhanced, which was mainly due to the enrichment of Geobacter and the increase in EAB biomass. Additionally, the genes and proteins of the biofilm changed obviously under simulated microgravity conditions, including: I) genes related to signal transfer, II) genes related to cell wall synthesis, and III) genes related to riboflavin synthesis. This study first revealed the enrichment in EAB abundance, the increase in EAB biomass, and the promotion of current generation under simulated microgravity.

Removal and reduction mechanism of Cr (VI) in Leersia hexandra Swartz constructed wetland-microbial fuel cell coupling system

Cr (VI) is extremely harmful to both the environment and human health, and it can linger in the environment for a very long period. In this research, the Leersia hexandra Swartz constructed wetland-microbial fuel cell (CW-MFC) system was constructed to purify Cr (VI) wastewater. By comparing with the constructed wetland (CW) system, the system electricity generation, pollutants removal, Cr enrichment, and morphological transformation of the system were discussed. The results demonstrated that the L. hexandra CW-MFC system promoted removal of pollutants and production of electricity of the system. The maximum voltage of the system was 499 mV, the COD and Cr (VI) removal efficiency was 93.73% and 97.00%. At the same time, it enhanced the substrate and L. hexandra ability to absorb Cr and change it morphologically transformation. Additionally, the results of XPS and XANES showed that the majority of the Cr in the L. hexandra and substrate was present as Cr (III). In the L. hexandra CW-MFC system, Geobacter also functioned as the primary metal catabolic reducing and electrogenic bacteria. As a result, L. hexandra CW-MFC system possesses the added benefit of removing Cr (VI) while producing energy compared to the traditional CW system.

Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

Soil Geobacteraceae are the key predictors of neurotoxic methylmercury bioaccumulation in rice

Contamination of rice by the potent neurotoxin methylmercury (MeHg) originates from microbe-mediated Hg methylation in soils. However, the high diversity of Hg methylating microorganisms in soils hinders the prediction of MeHg formation and challenges the mitigation of MeHg bioaccumulation via regulating soil microbiomes. Here we explored the roles of various cropland microbial communities in MeHg formation in the potentials leading to MeHg accumulation in rice and reveal that Geobacteraceae are the key predictors of MeHg bioaccumulation in paddy soil systems. We characterized Hg methylating microorganisms from 67 cropland ecosystems across 3,600 latitudinal kilometres. The simulations of a rice-paddy biogeochemical model show that MeHg accumulation in rice is 1.3-1.7-fold more sensitive to changes in the relative abundance of Geobacteraceae compared to Hg input, which is recognized as the primary parameter in controlling MeHg exposure. These findings open up a window to predict MeHg formation and accumulation in human food webs, enabling more efficient mitigation of risks to human health through regulations of key soil microbiomes.

Role of sulfide on DNRA distribution and the microbial community structure in a sulfide-driven nitrate reduction process

Microbial nitrate reduction processes involve two competing pathways: denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA). This study investigated the distribution of DNRA in a sole sulfur-driven nitrogen conversion process using a laboratory-scale sequencing biofilm batch reactor (SBBR) through a series of batch tests with varying sulfide/nitrate (S/N) ratios. The results showed that DNRA became more dominant in the sulfide-oxidizing autotrophic denitrification (SOAD) process as the S/N ratio increased to 1.5:1, 1.7:1, and 2:1, reaching a peak of 35.3% at the S/N ratio of 1.5:1. Oxidation-reduction potential (ORP) patterns demonstrated distinct inflection points for nitrate and nitrite consumption under the SOAD-only conditions, whereas these points overlapped when DNRA coexisted with SOAD. Analysis of 16S ribosomal RNA identified Ignavibacterium, Hydrogenophaga, and Geobacter as the dominant genera responsible for DNRA during autotrophic nitrate reduction. The findings of the DNRA divergence investigation provided valuable insights into enhancing biological nitrogen removal processes, particularly when coupled with the anammox.

Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE

Extracellular electron transfer (EET) via microbial nanowires drives globally-important environmental processes and biotechnological applications for bioenergy, bioremediation, and bioelectronics. Due to highly-redundant and complex EET pathways, it is unclear how microbes wire electrons rapidly (>106 s-1) from the inner-membrane through outer-surface nanowires directly to an external environment despite a crowded periplasm and slow (<105 s-1) electron diffusion among periplasmic cytochromes. Here, we show that Geobacter sulfurreducens periplasmic cytochromes PpcABCDE inject electrons directly into OmcS nanowires by binding transiently with differing efficiencies, with the least-abundant cytochrome (PpcC) showing the highest efficiency. Remarkably, this defined nanowire-charging pathway is evolutionarily conserved in phylogenetically-diverse bacteria capable of EET. OmcS heme reduction potentials are within 200 mV of each other, with a midpoint 82 mV-higher than reported previously. This could explain efficient EET over micrometres at ultrafast (<200 fs) rates with negligible energy loss. Engineering this minimal nanowire-charging pathway may yield microbial chassis with improved performance.

Tourmaline mediated enhanced autotrophic denitrification: The mechanisms of electron transfer and Paracoccus enrichment

Autotrophic denitrification (AD) without carbon source is an inevitable choice for denitrification of municipal wastewater under the carbon peaking and carbon neutrality goals. This study first employed sulfur-tourmaline-AD (STAD) as an innovative nitrate removal trial technique in wastewater. STAD demonstrated a 2.23-fold increase in nitrate‑nitrogen (NO3--N) removal rate with reduced nitrite‑nitrogen (NO2--N) accumulation, effectively removing 99 % of nitrogen pollutants compared to sulfur denitrification. Some denitrifiers microorganisms that could secrete tyrosine, tryptophan, and aromatic protein (extracellular polymeric substances (EPS)). Moreover, according to the EPS composition and characteristics analysis, the secretion of loosely bound extracellular polymeric substances (LB-EPS) that bound to the bacterial endogenous respiration and enriched microbial abundance, was produced more in the STAD system, further improving the system stability. Furthermore, the addition of tourmaline (Tm) facilitated the discovery of a new genus (Paracoccus) that enhanced nitrate decomposition. Applying optimal electron donors through metabolic pathways and the microbial community helps to strengthen the AD process and treat low carbon/nitrogen ratio wastewater efficiently.

Nanoscale zero-valent iron alleviate antibiotic resistance risk during managed aquifer recharge (MAR) by regulating denitrifying bacterial network

The frequent occurrence of antibiotics in reclaimed water is concerning, in the case of managed aquifer recharge (MAR), it inevitably hinders further water purification and accelerates the evolutionary resistance in indigenous bacteria. In this study, we constructed two column reactors and nanoscale zero-valent iron (nZVI) amendment was applied for its effects on water quality variation, microbial community succession, and antibiotic resistance genes (ARGs) dissemination, deciphered the underlying mechanism of resistance risk reduction. Results showed that nZVI was oxidized to iron oxides in the sediment column, and total effluent iron concentration was within permissible limits. nZVI enhanced NO3--N removal by 15.5% through enriching denitrifying bacteria and genes, whereas made no effects on oxacillin (OXA) removal. In addition, nZVI exhibited a pivotal impact on ARGs and plasmids decreasing. Network analysis elucidated that the diversity and richness of ARG host declined with nZVI amendment. Denitrifying bacteria play a key role in suppressing horizontal gene transfer (HGT). The underlying mechanisms of inhibited HGT included the downregulated SOS response, the inhibited Type-Ⅳ secretion system and the weakened driving force. This study afforded vital insights into ARG spread control, providing a reference for future applications of nZVI in MAR.

Removal of nonylphenol ethoxylate surfactant in batch reactors: emphasis on methanogenic potential and microbial community characterization under optimized conditions

ABSTRACTNonylphenol ethoxylate (NPE) is an endocrine-disrupting chemical that has bioaccumulative, persistent and toxic characteristics in different environmental matrices and is difficult to remove in sewage treatment plants. In this study, the effects of the initial concentration of NPE (0.2 ± 0.03 - 3.0 ± 0.02 mg. L-1) and ethanol (73.9 ± 5.0-218.6 ± 10.6 mg. L-1) were investigated using factorial design. Assays were carried out in anaerobic batch reactors, using the Zinder basal medium, yeast extract (200 mg. L-1), vitamin solution and sodium bicarbonate (10% v/v). The optimal conditions were 218.56 mg.L-1 of ethanol and 1596.51 µg.L-1 of NPE, with 92% and 88% of NPE and organic matter removal, respectively, and methane yield (1689.8 ± 59.6 mmol) after 450 h of operation. In this condition, bacteria potentially involved in the degradation of this surfactant were identified in greater relative abundance, such as Acetoanaerobium (1.68%), Smithella (1.52%), Aminivibrio (0.91%), Petrimonas (0.57%) and Enterobacter (0.47%), as well as archaea Methanobacterium and Methanoregula, mainly involved in hydrogenotrophic pathway.

Soil Humic Acid Stimulates Potentially Active Dissimilatory Arsenate-Reducing Bacteria in Flooded Paddy Soil as Revealed by Metagenomic Stable Isotope Probing

Dissimilatory arsenate reduction contributes a large proportion of arsenic flux from flooded paddy soil, which is closely linked to soil organic carbon input and efflux. Humic acid (HA) represents a natural ingredient in soil and is shown to enhance microbial arsenate respiration to promote arsenic mobility. However, the community and function profiles of metabolically active arsenate-respiring bacteria and their interactions with HA in paddy soil remain unclear. To probe this linkage, we performed a genome-centric comparison of potentially active arsenate-respiring bacteria in anaerobic microcosms amended with 13C-lactate and HA by combining stable-isotope probing with genome-resolved metagenomics. Indeed, HA greatly accelerated the microbial reduction of arsenate to arsenite. Enrichment of bacteria that harbor arsenate-respiring reductase genes (arrA) in HA-enriched 13C-DNA was confirmed by metagenomic binning, which are affiliated with Firmicutes (mainly Desulfitobacterium, Bacillus, Brevibacillus, and Clostridia) and Acidobacteria. Characterization of reference extracellular electron transfer (EET)-related genes in these arrA-harboring bacteria supports the presence of EET-like genes, with partial electron-transport chain genes identified. This suggests that Gram-positive Firmicutes- and Acidobacteria-related members may harbor unspecified EET-associated genes involved in metal reduction. Our findings highlight the link between soil HA and potentially active arsenate-respiring bacteria, which can be considered when using HA for arsenic removal.

Arsenic Contamination of Groundwater Is Determined by Complex Interactions between Various Chemical and Biological Processes

At a great many locations worldwide, the safety of drinking water is not assured due to pollution with arsenic. Arsenic toxicity is a matter of both systems chemistry and systems biology: it is determined by complex and intertwined networks of chemical reactions in the inanimate environment, in microbes in that environment, and in the human body. We here review what is known about these networks and their interconnections. We then discuss how consideration of the systems aspects of arsenic levels in groundwater may open up new avenues towards the realization of safer drinking water. Along such avenues, both geochemical and microbiological conditions can optimize groundwater microbial ecology vis-à-vis reduced arsenic toxicity.

Electrical current disrupts the electron transfer in defined consortia

Improving methane production through electrical current application to anaerobic digesters has garnered interest in optimizing such microbial electrochemical technologies, with claims suggesting direct interspecies electron transfer (DIET) at the cathode enhances methane yield. However, previous studies with mixed microbial communities only reported interspecies interactions based on species co-occurrence at the cathode, lacking insight into how a poised cathode influences well-defined DIET-based partnerships. To address this, we investigated the impact of continuous and discontinuous exposure to a poised cathode (-0.7 V vs. standard hydrogen electrode) on a defined consortium of Geobacter metallireducens and Methanosarcina barkeri, known for their DIET capabilities. The physiology of DIET consortia exposed to electrical current was compared to that of unexposed consortia. In current-exposed incubations, overall metabolic activity and cell numbers for both partners declined. The consortium, receiving electrons from the poised cathode, accumulated acetate and hydrogen, with only 32% of the recovered electrons allocated to methane production. Discontinuous exposure intensified these detrimental effects. Conversely, unexposed control reactors efficiently converted ethanol to methane, transiently accumulating acetate and recovering 88% of electrons in methane. Our results demonstrate the overall detrimental effect of electrochemical stimulation on a DIET consortium. Besides, the data indicate that the presence of an alternative electron donor (cathode) hinders efficient electron retrieval by the methanogen from Geobacter, and induces catabolic repression of oxidative metabolism in Geobacter. This study emphasizes understanding specific DIET-based interactions to enhance methane production during electrical stimulation, providing insights for optimizing tailored interspecies partnerships in microbial electrochemical technologies.