Efficient long-range conduction in cable bacteria through nickel protein wires

Analysis of biofilm assembly by large area automated AFM

Biofilms are complex microbial communities critical in medical, industrial, and environmental contexts. Understanding their assembly, structure, genetic regulation, interspecies interactions, and environmental responses is key to developing effective control and mitigation strategies. While atomic force microscopy (AFM) offers critically important high-resolution insights on structural and functional properties at the cellular and even sub-cellular level, its limited scan range and labor-intensive nature restricts the ability to link these smaller scale features to the functional macroscale organization of the films. We begin to address this limitation by introducing an automated large area AFM approach capable of capturing high-resolution images over millimeter-scale areas, aided by machine learning for seamless image stitching, cell detection, and classification. Large area AFM is shown to provide a very detailed view of spatial heterogeneity and cellular morphology during the early stages of biofilm formation which were previously obscured. Using this approach, we examined the organization of Pantoea sp. YR343 on PFOTS-treated glass surfaces. Our findings reveal a preferred cellular orientation among surface-attached cells, forming a distinctive honeycomb pattern. Detailed mapping of flagella interactions suggests that flagellar coordination plays a role in biofilm assembly beyond initial attachment. Additionally, we use large-area AFM to characterize surface modifications on silicon substrates, observing a significant reduction in bacterial density. This highlights the potential of this method for studying surface modifications to better understand and control bacterial adhesion and biofilm formation.

A novel cable bacteria species with a distinct morphology and genomic potential

Cable bacteria form a group of multicellular prokaryotes that enable electron transfer over centimeter-scale distances within marine and freshwater sediments. To this end, the periplasm of these filamentous bacteria contains specialized conductive fibers, which extend along the full length of each filament and incorporate a novel Ni-containing NiBiD cofactor. Currently, the cable bacteria include two recognized genera, Candidatus Electrothrix and Candidatus Electronema, but the genetic and morphological diversity within the clade remains underexplored. Here, we report the isolation and characterization of a novel cable bacteria species from an intertidal estuarine mudflat within Yaquina Bay (Oregon, USA). A clonal enrichment culture of a single strain (designated YB6) was generated, and filaments were subjected to genomic, morphological, spectroscopic, and electrical characterization. Strain YB6 shares key physiological traits with other cable bacteria, such as long-distance electron conduction and the presence of the nickel bis(dithiolene) cofactor. At the same time, YB6 exhibits distinctive morphological features, including pronounced surface ridges that are up to three times wider than in other cable bacteria. Additionally, filaments are extensively enveloped by extracellular sheaths. Genomic analysis reveals that strain YB6 harbors metabolic pathways and genes found in both the Ca. Electrothrix and Ca. Electronema genera. Phylogenetic and phylogenomic analyses indicate that strain YB6 represents a novel species (average nucleotide identity <95%) that forms an early branch within the Ca. Electrothrix clade. The proposed name is Ca. Electrothrix yaqonensis sp. nov., honoring the Yako'n tribe of Native Americans whose ancestral lands encompassed Yaquina Bay.IMPORTANCEThis study expands our understanding of the genetic and morphological diversity of cable bacteria, a group of prokaryotes with a unique metabolism based on long-range conduction. We present the detailed morphological and genomic characterization of a novel species: Ca. Electrothrix yaqonensis, strain YB6, isolated from an intertidal estuarine mudflat. Importantly, the strain exhibits a distinctive ridge morphology (harboring the conductive fibers) and abundant formation of extracellular sheaths. Genomic analysis reveals that YB6 shares metabolic features with both Ca. Electrothrix and Ca. Electronema genera.

Comparison of cable bacteria genera reveals details of their conduction machinery

Cable bacteria are centimeter-long multicellular bacteria conducting electricity through periplasmic conductive fibers (PCFs). Using single-strain enrichments of the genera Electrothrix and Electronema we systematically investigate variations and similarities in morphology and electrical properties across both genera. Electrical conductivity of different PCFs spans three orders of magnitude warranting further investigations of the plasticity of their conduction machinery. Using electron microscopy and elemental analyses, we show that the two cable bacteria genera have similar cell envelopes and cell-cell junction ultrastructures. Iron, sulfur, and nickel signals are co-localized with the PCFs, indicating key functional roles of these elements. The PCFs are organized as stranded rope-like structures composed of multiple strands. Furthermore, we report lamellae-like structures formed at the cell-cell junctions with a core layer connecting to the PCFs, and intriguing vesicle-like inner membrane invaginations below the PCFs. Finally, using bioinformatic tools, we identify a cytochrome family with predicted structural homology to known multi-heme nanowire proteins from other electroactive microorganisms and suggest that these cytochromes can play a role in the extra- or intercellular electron conduction of cable bacteria.

Nickel-Dithiolene Cofactors as Electron Donors and Acceptors in Protein Hosts

Metal dithiolene compounds are attracting considerable attention in the field of molecular electronics, particularly as constituents of materials with high charge-carrier mobilities. Recent experiments on cable bacteria that perform centimeter-scale charge transport suggest that Ni-bis(dithiolene) cofactors are important components of the bacterial conductive network. Further, current-voltage experiments of cable-bacteria-conductive sheaths have measured high conductivity values as compared to other electron-transfer bacteria. An important question is how the Ni-bis(dithiolene) structures participating as electron donors/acceptors contribute to the high conductivity. Currently, the protein and cofactor structures of these bacterial networks are largely unknown. Given this limitation, in this work, we explore the more general question of how Ni-bis(dithiolene) molecules would perform as electron donor and acceptor centers in protein-mediated charge transfer. Our aim is to deduce order-of-magnitude higher bounds for charge-transfer rates in such systems as a function of donor-acceptor distance, protein-bridge (amino acid) sequence, cofactor size, and redox state. These bounds are useful for predicting charge-transfer mechanisms and estimating rates in the absence of detailed structural information on protein wires that may use Ni-bis(dithiolene) redox cofactors. Our analysis is also relevant to the design of artificial Ni-bis(dithiolene) protein wires.

Cable Bacteria and Their Biotechnological Application

Cable bacteria grow as multicellular filaments several centimetres deep into the sediment of freshwaters and oceans. Hereby, cable bacteria show unique characteristics such as electrogenic sulphur oxidation, extremely high conductivity and ability for CO2 fixation. This offers several possibilities of future applications in biotechnology with an outlook to sustainable processes. So far, research on cable bacteria is mostly concerning metabolism, electron transfer and effect on the surrounding sediment. Cultures are always performed on sediment from the natural habitat and in simple, small-scale reaction tubes, requiring further development for reproducible cultivation with scale-up capabilities. However, based on the known properties of cable bacteria, possible areas of application can already be derived. The use of cable bacteria in bioremediation is a promising approach, as the degradation of hydrocarbons has already been proven. Co-cultivation with plants could open up a further field of application, such as the described reduction of methane emissions from rice fields. Due to the extremely high conductivity of the filaments, cable bacteria are also very promising for incorporation into biodegradable microelectronics. By integrating electrodes into a suitable reactor system, bioelectrochemical processes could be implemented, either with the goal of electron uptake and product formation or for electricity generation.

Electron transfer in multicentre redox proteins: from fundamentals to extracellular electron transfer

Multicentre redox proteins participate in diverse metabolic processes, such as redox shuttling, multielectron catalysis, or long-distance electron conduction. The detail in which these processes can be analysed depends on the capacity of experimental methods to discriminate the multiple microstates that can be populated while the protein changes from the fully reduced to the fully oxidized state. The population of each state depends on the redox potential of the individual centres and on the magnitude of the interactions between the individual redox centres and their neighbours. It also depends on the interactions with binding sites for other ligands, such as protons, giving origin to the redox-Bohr effect. Modelling strategies that match the capacity of experimental methods to discriminate the contributions of individual centres are presented. These models provide thermodynamic and kinetic characterization of multicentre redox proteins. The current state of the art in the characterization of multicentre redox proteins is illustrated using the case of multiheme cytochromes involved in the process of extracellular electron transfer. In this new frontier of biological electron transfer, which can extend over distances that exceed the size of the individual multicentre redox proteins by orders of magnitude, current experimental data are still unable, in most cases, to provide discrimination between incoherent conduction by heme orbitals and coherent band conduction.

A Microbial-Centric View of Mobile Phones: Enhancing the Technological Feasibility of Biotechnological Recovery of Critical Metals

End-of-life (EoL) mobile phones represent a valuable reservoir of critical raw materials at higher concentrations compared to primary ores. This review emphasizes the critical need to transition from single-material recovery approaches to comprehensive, holistic strategies for recycling EoL mobile phones. In response to the call for sustainable techniques with reduced energy consumption and pollutant emissions, biohydrometallurgy emerges as a promising solution. The present work intends to review the most relevant studies focusing on the exploitation of microbial consortia in bioleaching and biorecovery processes. All living organisms need macro- and micronutrients for their metabolic functionalities, including some of the elements contained in mobile phones. By exploring the interactions between microbial communities and the diverse elements found in mobile phones, this paper establishes a microbial-centric perspective by connecting each element of each layer to their role in the microbial cell system. A special focus is dedicated to the concepts of ecodesign and modularity as key requirements in electronics to potentially increase selectivity of microbial consortia in the bioleaching process. By bridging microbial science with sustainable design, this review proposes an innovative roadmap to optimize metal recovery, aligning with the principles of the circular economy and advancing scalable biotechnological solutions for electronic waste management.

Multidisciplinary methodologies used in the study of cable bacteria

Cable bacteria are a unique type of filamentous microorganism that can grow up to centimetres long and are capable of long-distance electron transport over their entire lengths. Due to their unique metabolism and conductive capacities, the study of cable bacteria has required technical innovations, both in adapting existing techniques and developing entirely new ones. This review discusses the existing methods used to study eight distinct aspects of cable bacteria research, including the challenges of culturing them in laboratory conditions, performing physical and biochemical extractions, and analysing the conductive mechanism. As cable bacteria research requires an interdisciplinary approach, methods from a range of fields are discussed, such as biogeochemistry, genomics, materials science, and electrochemistry. A critical analysis of the current state of each approach is presented, highlighting the advantages and drawbacks of both commonly used and emerging methods.

Electrical signaling in fungi: past and present challenges

Electrical signaling is a fundamental mechanism for integrating environmental stimuli and coordinating responses in living organisms. While extensively studied in animals and plants, the role of electrical signaling in fungi remains a largely underexplored field. Early studies suggested that filamentous fungi generate action potential-like signals and electrical currents at hyphal tips, yet their function in intracellular communication remained unclear. Renewed interest in fungal electrical activity has fueled developments such as the hypothesis that mycorrhizal networks facilitate electrical communication between plants and the emerging field of fungal-based electronic materials. Given their continuous plasma membrane, specialized septal pores, and insulating cell wall structures, filamentous fungi possess architectural features that could support electrical signaling over long distances. However, studying electrical phenomena in fungal networks presents unique challenges due to the microscopic dimensions of hyphae, the structural complexity of highly modular mycelial networks, and the limitations of traditional electrophysiological methods. This review synthesizes current evidence for electrical signaling in filamentous fungi, evaluates methodological approaches, and highlights experimental challenges. By addressing these challenges and identifying best practices, we aim to advance research in this field and provide a foundation for future studies exploring the role of electrical signaling in fungal biology.

Long-Distance Electron Transport in Unicellular Organisms and Biofilms

Electrical forces are widespread in single-celled organisms and underpin sophisticated communication systems. Bacterial biofilm colonies, for example, attract new members electrically. Bacteria also join together end to end and engage in long-distance electron transport along bacterial filaments over centimetres. This transport of electrons across around 10,000 cells separates life-essential redox reactions spatially and keeps "colleagues breathing" in otherwise challenging aquatic sediments.

Carbon-based nanomaterials enhance the growth of cable bacteria in brackish sediments

Cable bacteria are long, multicellular bacteria that conduct electrical currents over centimetre distances within sediment to support their metabolism. Recent studies have shown their potential for extracellular electron transport (EET), allowing the possibility to donate electrons to solid electrodes and potentially enabling electrical interactions with other microbes. However, the mechanisms and capabilities of their EET, and their potential to interact electronically with other materials in their environment has not been explored. As sediment can contain conductive minerals, this study aimed to investigate the effect of carbon-based colloidal nanomaterials such as graphene oxide (GO), sulfur-doped graphene oxide (S-GO), and carbon nanotubes on cable bacteria. When S-GO was added to sediment, cable bacteria grew with higher activity, and in higher density at depth, whilst GO had little initial effect but showed a delayed enhancement of cable activity. This is thought to be due the reduction of GO via iron oxidation within the sediment, allowing it to become more conjugated, resulting in more similar conductive properties to S-GO. We speculate that the enhancement of cable bacteria growth is due to the electron shuttling properties of S-GO and similar materials, allowing for more efficient transfer of electrons between cable bacteria and to electron acceptors.

Temperature-Dependent Characterization of Long-Range Conduction in Conductive Protein Fibers of Cable Bacteria

Multicellular cable bacteria display an exceptional form of biological conduction, channeling electric currents across centimeter distances through a regular network of protein fibers embedded in the cell envelope. The fiber conductivity is among the highest recorded for biomaterials, but the underlying mechanism of electron transport remains elusive. Here, we performed detailed characterization of the conductance from room temperature down to liquid helium temperature to attain insight into the mechanism of long-range conduction. A consistent behavior is seen within and across individual filaments. The conductance near room temperature reveals thermally activated behavior, yet with a low activation energy. At cryogenic temperatures, the conductance at moderate electric fields becomes virtually independent of temperature, suggesting that quantum vibrations couple to the charge transport through nuclear tunneling. Our data support an incoherent multistep hopping model within parallel conduction channels with a low activation energy and high transfer efficiency between hopping sites. This model explains the capacity of cable bacteria to transport electrons across centimeter-scale distances, thus illustrating how electric currents can be guided through extremely long supramolecular protein structures.

On the diversity, phylogeny and biogeography of cable bacteria

Cable bacteria have acquired a unique metabolism, which induces long-distance electron transport along their centimeter-long multicellular filaments. At present, cable bacteria are thought to form a monophyletic clade with two described genera. However, their diversity has not been systematically investigated. To investigate the phylogenetic relationships within the cable bacteria clade, 16S rRNA gene sequences were compiled from literature and public databases (SILVA 138 SSU and NCBI GenBank). These were complemented with novel sequences obtained from natural sediment enrichments across a wide range of salinities (2-34). To enable taxonomic resolution at the species level, we designed a procedure to attain full-length 16S rRNA gene sequences from individual cable bacterium filaments using an optimized nested PCR protocol and Sanger sequencing. The final database contained 1,876 long 16S rRNA gene sequences (≥800 bp) originating from 92 aquatic locations, ranging from polar to tropical regions and from intertidal to deep sea sediments. The resulting phylogenetic tree reveals 90 potential species-level clades (based on a delineation value of 98.7% 16S rRNA gene sequence identity) that reside within six genus-level clusters. Hence, the diversity of cable bacteria appears to be substantially larger than the two genera and 13 species that have been officially named up to now. Particularly brackish environments with strong salinity fluctuations, as well as sediments with low free sulfide concentrations and deep sea sediments harbor a large pool of novel and undescribed cable bacteria taxa.

Spatial distribution of cable bacteria in nationwide organic-matter-polluted urban rivers in China

An overload of labile organic matter triggers the water blackening and odorization in urban rivers, leading to a unique microbiome driving biogeochemical cycles in these anoxic habitats. Among the key players in these environments, cable bacteria interfere directly with C/N/S/O cycling, and are closely associated with phylogenetically diverse microorganisms in anoxic sediment as an electron conduit to mediate long-distance electron transport from deep-anoxic-layer sulfide to oxic-layer oxygen. Despite their hypothesized importance in black-odorous urban rivers, the spatial distribution patterns and roles of cable bacteria in large-scale polluted urban rivers remain inadequately understood. This study examined the diversity and spatial distribution pattern of cable bacteria in sediment samples from 186 black-odorous urban rivers across China. Results revealed the co-existence of two well-characterized cable bacteria (i.e., Candidatus Electrothrix and Candidatus Electronema), with Candidatus Electrothrix exhibiting a comparatively wider distribution in the polluted urban rivers. Concentrations of DOC, SS, sulfate, nitrate, and heavy metals (e.g., Ni and Cr) were correlated with the cable bacteria diversity, indicating their essential role in biogeochemical cycles. The activation energy of cable bacteria was 0.624 eV, close to the canonical 0.65 eV. Furthermore, cable bacteria were identified as key connectors and module hubs, closely associated with denitrifiers, sulfate-reducing bacteria, methanogens and alkane degraders, highlighting their role as keystone functional lineages in the contaminated urban rivers. Our study provided the first large-scale and comprehensive insight into the cable bacteria diversity, spatial distribution, and their essential function as keystone species in organic-matter-polluted urban rivers.

Long-distance electron transport in multicellular freshwater cable bacteria

Filamentous multicellular cable bacteria perform centimeter-scale electron transport in a process that couples oxidation of an electron donor (sulfide) in deeper sediment to the reduction of an electron acceptor (oxygen or nitrate) near the surface. While this electric metabolism is prevalent in both marine and freshwater sediments, detailed electronic measurements of the conductivity previously focused on the marine cable bacteria (Candidatus Electrothrix), rather than freshwater cable bacteria, which form a separate genus (Candidatus Electronema) and contribute essential geochemical roles in freshwater sediments. Here, we characterize the electron transport characteristics of Ca. Electronema cable bacteria from Southern California freshwater sediments. Current-voltage measurements of intact cable filaments bridging interdigitated electrodes confirmed their persistent conductivity under a controlled atmosphere and the variable sensitivity of this conduction to air exposure. Electrostatic and conductive atomic force microscopies mapped out the characteristics of the cell envelope's nanofiber network, implicating it as the conductive pathway in a manner consistent with previous findings in marine cable bacteria. Four-probe measurements of microelectrodes addressing intact cables demonstrated nanoampere currents up to 200 μm lengths at modest driving voltages, allowing us to quantify the nanofiber conductivity at 0.1 S/cm for freshwater cable bacteria filaments under our measurement conditions. Such a high conductivity can support the remarkable sulfide-to-oxygen electrical currents mediated by cable bacteria in sediments. These measurements expand the knowledgebase of long-distance electron transport to the freshwater niche while shedding light on the underlying conductive network of cable bacteria.

Comparative genomic analysis of nickel homeostasis in cable bacteria

BACKGROUND

Cable bacteria are filamentous members of the Desulfobulbaceae family that are capable of performing centimetre‑scale electron transport in marine and freshwater sediments. This long‑distance electron transport is mediated by a network of parallel conductive fibres embedded in the cell envelope. This fibre network efficiently transports electrical currents along the entire length of the centimetre‑long filament. Recent analyses show that these fibres consist of metalloproteins that harbour a novel nickel‑containing cofactor, which indicates that cable bacteria have evolved a unique form of biological electron transport. This nickel‑dependent conduction mechanism suggests that cable bacteria are strongly dependent on nickel as a biosynthetic resource. Here, we performed a comprehensive comparative genomic analysis of the genes linked to nickel homeostasis. We compared the genome‑encoded adaptation to nickel of cable bacteria to related members of the Desulfobulbaceae family and other members of the Desulfobulbales order.

RESULTS

Presently, four closed genomes are available for the monophyletic cable bacteria clade that consists of the genera Candidatus Electrothrix and Candidatus Electronema. To increase the phylogenomic coverage, we additionally generated two closed genomes of cable bacteria: Candidatus Electrothrix gigas strain HY10‑6 and Candidatus Electrothrix antwerpensis strain GW3‑4, which are the first closed genomes of their respective species. Nickel homeostasis genes were identified in a database of 38 cable bacteria genomes (including 6 closed genomes). Gene prevalence was compared to 19 genomes of related strains, residing within the Desulfobulbales order but outside of the cable bacteria clade, revealing several genome‑encoded adaptations to nickel homeostasis in cable bacteria. Phylogenetic analysis indicates that nickel importers, nickel‑binding enzymes and nickel chaperones of cable bacteria are affiliated to organisms outside the Desulfobulbaceae family, with several proteins showing affiliation to organisms outside of the Desulfobacterota phylum. Conspicuously, cable bacteria encode a unique periplasmic nickel export protein RcnA, which possesses a putative cytoplasmic histidine‑rich loop that has been largely expanded compared to RcnA homologs in other organisms.

CONCLUSION

Cable bacteria genomes show a clear genetic adaptation for nickel utilization when compared to closely related genera. This fully aligns with the nickel‑dependent conduction mechanism that is uniquely found in cable bacteria.

Cable bacteria: widespread filamentous electroactive microorganisms protecting environments

Cable bacteria have been identified and detected worldwide since their discovery in marine sediments in Aarhus Bay, Denmark. Their activity can account for the majority of oxygen consumption and sulfide depletion in sediments, and they induce sulfate accumulation, pH excursions, and the generation of electric fields. In addition, they can affect the fluxes of other elements such as calcium, iron, manganese, nitrogen, and phosphorous. Recent developments in our understanding of the impact of cable bacteria on element cycling have revealed their positive contributions to mitigating environmental problems, such as recovering self-purification capacity, enhancing petroleum hydrocarbon degradation, alleviating phosphorus eutrophication, delaying euxinia, and reducing methane emission. We highlight recent research outcomes on their distribution, state-of-the-art findings on their physiological characteristics, and ecological contributions.

Electrogenic sulfur oxidation mediated by cable bacteria and its ecological effects

At the sediment-water interfaces, filamentous cable bacteria transport electrons from sulfide oxidation along their filaments towards oxygen or nitrate as electron acceptors. These multicellular bacteria belonging to the family Desulfobulbaceae thus form a biogeobattery that mediates redox processes between multiple elements. Cable bacteria were first reported in 2012. In the past years, cable bacteria have been found to be widely distributed across the globe. Their potential in shaping the surface water environments has been extensively studied but is not fully elucidated. In this review, the biogeochemical characteristics, conduction mechanisms, and geographical distribution of cable bacteria, as well as their ecological effects, are systematically reviewed and discussed. Novel insights for understanding and applying the role of cable bacteria in aquatic ecology are summarized.

Towards bioprocess engineering of cable bacteria: Establishment of a synthetic sediment

Cable bacteria, characterized by their multicellular filamentous growth, are prevalent in both freshwater and marine sediments. They possess the unique ability to transport electrons over distances of centimeters. Coupled with their capacity to fix CO2 and their record-breaking conductivity for biological materials, these bacteria present promising prospects for bioprocess engineering, including potential electrochemical applications. However, the cultivation of cable bacteria has been limited to their natural sediment, constraining their utility in production processes. To address this, our study designs synthetic sediment, drawing on ion exchange chromatography data from natural sediments and existing literature on the requirements of cable bacteria. We examined the effects of varying bentonite concentrations on water retention and the impacts of different sands. For the first time, we cultivated cable bacteria on synthetic sediment, specifically the freshwater strain Electronema aureum GS. This cultivation was conducted over 10 weeks in a specially developed sediment bioreactor, resulting in an increased density of cable bacteria in the sediment and growth up to a depth of 5 cm. The creation of this synthetic sediment paves the way for the reproducible cultivation of cable bacteria. It also opens up possibilities for future process scale-up using readily available components. This advancement holds significant implications for the broader field of bioprocess engineering.

Electron Transfer in the Biogeochemical Sulfur Cycle

Microorganisms are key players in the global biogeochemical sulfur cycle. Among them, some have garnered particular attention due to their electrical activity and ability to perform extracellular electron transfer. A growing body of research has highlighted their extensive phylogenetic and metabolic diversity, revealing their crucial roles in ecological processes. In this review, we delve into the electron transfer process between sulfate-reducing bacteria and anaerobic alkane-oxidizing archaea, which facilitates growth within syntrophic communities. Furthermore, we review the phenomenon of long-distance electron transfer and potential extracellular electron transfer in multicellular filamentous sulfur-oxidizing bacteria. These bacteria, with their vast application prospects and ecological significance, play a pivotal role in various ecological processes. Subsequently, we discuss the important role of the pili/cytochrome for electron transfer and presented cutting-edge approaches for exploring and studying electroactive microorganisms. This review provides a comprehensive overview of electroactive microorganisms participating in the biogeochemical sulfur cycle. By examining their electron transfer mechanisms, and the potential ecological and applied implications, we offer novel insights into microbial sulfur metabolism, thereby advancing applications in the development of sustainable bioelectronics materials and bioremediation technologies.

Cable bacteria: Living electrical conduits for biogeochemical cycling and water environment restoration

Since the discovery of multicellular cable bacteria in marine sediments in 2012, they have attracted widespread attention and interest due to their unprecedented ability to generate and transport electrical currents over centimeter-scale long-range distances. The cosmopolitan distribution of cable bacteria in both marine and freshwater systems, along with their substantial impact on local biogeochemistry, has uncovered their important role in element cycling and ecosystem functioning of aquatic environments. Considerable research efforts have been devoted to the potential utilization of cable bacteria for various water management purposes during the past few years. However, there lacks a critical summary on the advances and contributions of cable bacteria to biogeochemical cycles and water environment restoration. This review aims to provide an up-to-date and comprehensive overview of the current research on cable bacteria, with a particular view on their participation in aquatic biogeochemical cycles and promising applications in water environment restoration. It systematically analyzes (i) the global distribution of cable bacteria in aquatic ecosystems and the major environmental factors affecting their survival, diversity, and composition, (ii) the interactive associations between cable bacteria and other microorganisms as well as aquatic plants and infauna, (iii) the underlying role of cable bacteria in sedimentary biogeochemical cycling of essential elements including but not limited to sulfur, iron, phosphorus, and nitrogen, (iv) the practical explorations of cable bacteria for water pollution control, greenhouse gas emission reduction, aquatic ecological environment restoration, as well as possible combinations with other water remediation technologies. It is believed to give a step-by-step introduction to progress on cable bacteria, highlight key findings, opportunities and challenges of using cable bacteria for water environment restoration, and propose directions for further exploration.

Multi-wavelength Raman microscopy of nickel-based electron transport in cable bacteria

Cable bacteria embed a network of conductive protein fibers in their cell envelope that efficiently guides electron transport over distances spanning up to several centimeters. This form of long-distance electron transport is unique in biology and is mediated by a metalloprotein with a sulfur-coordinated nickel (Ni) cofactor. However, the molecular structure of this cofactor remains presently unknown. Here, we applied multi-wavelength Raman microscopy to identify cell compounds linked to the unique cable bacterium physiology, combined with stable isotope labeling, and orientation-dependent and ultralow-frequency Raman microscopy to gain insight into the structure and organization of this novel Ni-cofactor. Raman spectra of native cable bacterium filaments reveal vibrational modes originating from cytochromes, polyphosphate granules, proteins, as well as the Ni-cofactor. After selective extraction of the conductive fiber network from the cell envelope, the Raman spectrum becomes simpler, and primarily retains vibrational modes associated with the Ni-cofactor. These Ni-cofactor modes exhibit intense Raman scattering as well as a strong orientation-dependent response. The signal intensity is particularly elevated when the polarization of incident laser light is parallel to the direction of the conductive fibers. This orientation dependence allows to selectively identify the modes that are associated with the Ni-cofactor. We identified 13 such modes, some of which display strong Raman signals across the entire range of applied wavelengths (405-1,064 nm). Assignment of vibrational modes, supported by stable isotope labeling, suggest that the structure of the Ni-cofactor shares a resemblance with that of nickel bis(1,2-dithiolene) complexes. Overall, our results indicate that cable bacteria have evolved a unique cofactor structure that does not resemble any of the known Ni-cofactors in biology.

Cable Bacteria Skeletons as Catalytically Active Electrodes

Cable bacteria are multicellular, filamentous bacteria that use internal conductive fibers to transfer electrons over centimeter distances from donors within anoxic sediment layers to oxygen at the surface. We extracted the fibers and used them as free-standing bio-based electrodes to investigate their electrocatalytic behavior. The fibers catalyzed the reversible interconversion of oxygen and water, and an electric current was running through the fibers even when the potential difference was generated solely by a gradient of oxygen concentration. Oxygen reduction as well as oxygen evolution were confirmed by optical measurements. Within living cable bacteria, oxygen reduction by direct electrocatalysis on the fibers and not by membrane-bound proteins readily explains exceptionally high cell-specific oxygen consumption rates observed in the oxic zone, while electrocatalytic water oxidation may provide oxygen to cells in the anoxic zone.

Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads

Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance electron transport, they exert a disproportionately large impact on the biogeochemistry of their environment. Current available genomes of marine cable bacteria are highly fragmented and incomplete, hampering the elucidation of their unique electrogenic physiology. Here, we present a metagenomic pipeline that combines Nanopore long-read and Illumina short-read shotgun sequencing. Starting from a clonal enrichment of a cable bacterium, we recovered a circular metagenome-assembled genome (5.09 Mbp in size), which represents a novel cable bacterium species with the proposed name Candidatus Electrothrix scaldis. The closed genome contains 1109 novel identified genes, including key metabolic enzymes not previously described in incomplete genomes of cable bacteria. We examined in detail the factors leading to genome closure. Foremost, native, non-amplified long reads are crucial to resolve the many repetitive regions within the genome of cable bacteria, and by analysing the whole metagenomic assembly, we found that low strain diversity is key for achieving genome closure. The insights and approaches presented here could help achieve genome closure for other keystone micro-organisms present in complex environmental samples at low abundance.

A model analysis of centimeter-long electron transport in cable bacteria

The recent discovery of cable bacteria has greatly expanded the known length scale of biological electron transport, as these multi-cellular bacteria are capable of mediating electrical currents across centimeter-scale distances. To enable such long-range conduction, cable bacteria embed a network of regularly spaced, parallel protein fibers in their cell envelope. These fibers exhibit extraordinary electrical properties for a biological material, including an electrical conductivity that can exceed 100 S cm-1. Traditionally, long-range electron transport through proteins is described as a multi-step hopping process, in which the individual hopping steps are described by Marcus electron transport theory. Here, we investigate to what extent such a classical hopping model can explain the conductance data recorded for individual cable bacterium filaments. To this end, the conductive fiber network in cable bacteria is modelled as a set of parallel one-dimensional hopping chains. Comparison of model simulated and experimental current(I)/voltage(V) curves, reveals that the charge transport is field-driven rather than concentration-driven, and there is no significant injection barrier between electrodes and filaments. However, the observed high conductivity levels (>100 S cm-1) can only be reproduced, if we include much longer hopping distances (a > 10 nm) and lower reorganisation energies (λ < 0.2 eV) than conventionally used in electron relay models of protein structures. Overall, our model analysis suggests that the conduction mechanism in cable bacteria is markedly distinct from other known forms of long-range biological electron transport, such as in multi-heme cytochromes.

Indications for a genetic basis for big bacteria and description of the giant cable bacterium Candidatus Electrothrix gigas sp. nov

Bacterial cells can vary greatly in size, from a few hundred nanometers to hundreds of micrometers in diameter. Filamentous cable bacteria also display substantial size differences, with filament diameters ranging from 0.4 to 8 µm. We analyzed the genomes of cable bacterium filaments from 11 coastal environments of which the resulting 23 new genomes represent 10 novel species-level clades of Candidatus Electrothrix and two clades that putatively represent novel genus-level diversity. Fluorescence in situ hybridization with a species-level probe showed that large-sized cable bacteria belong to a novel species with the proposed name Ca. Electrothrix gigas. Comparative genome analysis suggests genes that play a role in the construction or functioning of large cable bacteria cells: the genomes of Ca. Electrothrix gigas encode a novel actin-like protein as well as a species-specific gene cluster encoding four putative pilin proteins and a putative type II secretion platform protein, which are not present in other cable bacteria. The novel actin-like protein was also found in a number of other giant bacteria, suggesting there could be a genetic basis for large cell size. This actin-like protein (denoted big bacteria protein, Bbp) may have a function analogous to other actin proteins in cell structure or intracellular transport. We contend that Bbp may help overcome the challenges of diffusion limitation and/or morphological complexity presented by the large cells of Ca. Electrothrix gigas and other giant bacteria. IMPORTANCE In this study, we substantially expand the known diversity of marine cable bacteria and describe cable bacteria with a large diameter as a novel species with the proposed name Candidatus Electrothrix gigas. In the genomes of this species, we identified a gene that encodes a novel actin-like protein [denoted big bacteria protein (Bbp)]. The bbp gene was also found in a number of other giant bacteria, predominantly affiliated to Desulfobacterota and Gammaproteobacteria, indicating that there may be a genetic basis for large cell size. Thus far, mostly structural adaptations of giant bacteria, vacuoles, and other inclusions or organelles have been observed, which are employed to overcome nutrient diffusion limitation in their environment. In analogy to other actin proteins, Bbp could fulfill a structural role in the cell or potentially facilitate intracellular transport.

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Candidatus Electrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. Also, a closed, circular genome of cable bacteria has not been published yet. To address this, we performed Nanopore long-read and Illumina short-read shotgun sequencing of selected environmental samples and a single-strain enrichment of Ca. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to name Ca. Electronema halotolerans and Ca. Electrothrix laxa, respectively. The Ca. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the "saltwater" Ca. Electrothrix species, indicating how Ca. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.

Bubbleless Air Shapes Biofilms and Facilitates Natural Organic Matter Transformation in Biological Activated Carbon

The biodegradation in the middle and downstream of slow-rate biological activated carbon (BAC) is limited by insufficient dissolved oxygen (DO) concentrations. In this study, a bubbleless aerated BAC (termed ABAC) process was developed by installing a hollow fiber membrane (HFM) module within a BAC filter to continuously provide aeration throughout the BAC system. The BAC filter without an HFM was termed NBAC. The laboratory-scale ABAC and NBAC systems operated continuously for 426 days using secondary sewage effluent as an influent. The DO concentrations for NBAC and ABAC were 0.78 ± 0.27 and 4.31 ± 0.44 mg/L, respectively, with the latter providing the ABAC with greater electron acceptors for biodegradation and a microbial community with better biodegradation and metabolism capacity. The biofilms in ABAC secreted 47.3% less EPS and exhibited greater electron transfer capacity than those in NBAC, resulting in enhanced contaminant degradation efficiency and long-term stability. The extra organic matter removed by ABAC included refractory substances with a low elemental ratio of oxygen to carbon (O/C) and a high elemental ratio of hydrogen to carbon (H/C). The proposed ABAC filter provides a valuable, practical example of how to modify the BAC technology to shape the microbial community, and its activity, by optimizing the ambient atmosphere.

Living electronics: A catalogue of engineered living electronic components

Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.

Soft X-ray Fluorescence and Near-Edge Absorption Microscopy for Investigating Metabolic Features in Biological Systems: A Review

Scanning transmission X-ray microscopy (STXM) provides the imaging of biological specimens allowing the parallel collection of localized spectroscopic information by X-ray fluorescence (XRF) and/or X-ray Absorption Near Edge Spectroscopy (XANES). The complex metabolic mechanisms which can take place in biological systems can be explored by these techniques by tracing even small quantities of the chemical elements involved in the metabolic pathways. Here, we present a review of the most recent publications in the synchrotrons' scenario where soft X-ray spectro-microscopy has been employed in life science as well as in environmental research.

Microbial succession in a marine sediment: Inferring interspecific microbial interactions with marine cable bacteria

Cable bacteria are long, filamentous, multicellular bacteria that grow in marine sediments and couple sulfide oxidation to oxygen reduction over centimetre-scale distances via long-distance electron transport. Cable bacteria can strongly modify biogeochemical cycling and may affect microbial community networks. Here we examine interspecific interactions with marine cable bacteria (Ca. Electrothrix) by monitoring the succession of 16S rRNA amplicons (DNA and RNA) and cell abundance across depth and time, contrasting sediments with and without cable bacteria growth. In the oxic zone, cable bacteria activity was positively associated with abundant predatory bacteria (Bdellovibrionota, Myxococcota, Bradymonadales), indicating putative predation on cathodic cells. At suboxic depths, cable bacteria activity was positively associated with sulfate-reducing and magnetotactic bacteria, consistent with cable bacteria functioning as ecosystem engineers that modify their local biogeochemical environment, benefitting certain microbes. Cable bacteria activity was negatively associated with chemoautotrophic sulfur-oxidizing Gammaproteobacteria (Thiogranum, Sedimenticola) at oxic depths, suggesting competition, and positively correlated with these taxa at suboxic depths, suggesting syntrophy and/or facilitation. These observations are consistent with chemoautotrophic sulfur oxidizers benefitting from an oxidizing potential imparted by cable bacteria at suboxic depths, possibly by using cable bacteria as acceptors for electrons or electron equivalents, but by an as yet enigmatic mechanism.

Water quality drives the distribution of freshwater cable bacteria

Cable bacteria are a group of recently found filamentous sulfide-oxidizing Desulfobulbaceae that significantly impact biogeochemical cycling. However, the limited understanding of cable bacteria distribution patterns and the driving force hindered our abilities to evaluate and maximize their contribution to environmental health. We evaluated cable bacteria assemblages from ten river sediments in the Pearl River Delta, China. The results revealed a clear biogeographic distribution pattern of cable bacteria, and their communities were deterministically assembled through water quality-driven selection. Cable bacteria are diverse in the river sediments with a few generalists and many specialists, and the water quality IV and V environments are the "hot spot." We then provided evidence on their morphology, function, and genome to demonstrate how water quality might shape the cable bacteria assemblages. Reduced cell width, inhibited function, and water quality-related adaptive genomic traits were detected in sulfide-limited water quality III and contaminant-stressed water quality VI environments. Specifically, those genomic traits were contributed to carbon and sulfur metabolism in the water quality III environment and stress resistance in the water quality VI environment. Overall, these findings provided a helpful baseline in evaluating the contribution of cable bacteria in the freshwater ecosystem and suggested that their high diversity and flexibility in phylogeny, morphology, and genome allowed them to adapt and contribute to various environmental conditions.

Revealing Fast Cu-Ion Transport and Enhanced Conductivity at the CuInP2S6-In4/3P2S6 Heterointerface

Van der Waals layered ferroelectrics, such as CuInP₂S₆ (CIPS), offer a versatile platform for miniaturization of ferroelectric device technologies. Control of the targeted composition and kinetics of CIPS synthesis enables the formation of stable self-assembled heterostructures of ferroelectric CIPS and nonferroelectric In_4/3P₂S₆ (IPS). Here, we use quantitative scanning probe microscopy methods combined with density functional theory (DFT) to explore in detail the nanoscale variability in dynamic functional properties of the CIPS-IPS heterostructure. We report evidence of fast ionic transport which mediates an appreciable out-of-plane electromechanical response of the CIPS surface in the paraelectric phase. Further, we map the nanoscale dielectric and ionic conductivity properties as we thermally stimulate the ferroelectric-paraelectric phase transition, recovering the local dielectric behavior during this phase transition. Finally, aided by DFT, we reveal a substantial and tunable conductivity enhancement at the CIPS/IPS interface, indicating the possibility of engineering its interfacial properties for next generation device applications.

Protocol for using autoclaved intertidal sediment as a medium to enrich marine cable bacteria

Cable bacteria (CB) are non-isolated filamentous bacteria in the family of Desulfobulbaceae, known for fostering centimeter-long electron transfer in sediments with pronounced redox zonation. This protocol details steps to extract CB filaments from cultured natural sediment, inoculate autoclaved sediment with extracted filaments, and subsequently evaluate the growth and enrichment of CB. We also describe the approaches for collecting suitable sediment, preparing autoclaved sediment, and manufacturing glass needles and hooks for the extraction of CB.

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Prepare autoclaved sediment as an enrichment medium for cable bacteria

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Manufacture glass needles and hooks as tools to extract cable bacteria

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Video demonstration of cable bacteria extraction and autoclaved sediment inoculation

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Recover prolific cable bacteria biomass grown in autoclaved sediment

Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Biomaterials and Electroactive Bacteria for Biodegradable Electronics

The global production of unrecycled electronic waste is extensively growing each year, urging the search for alternatives in biodegradable electronic materials. Electroactive bacteria and their nanowires have emerged as a new route toward electronic biological materials (e-biologics). Recent studies on electron transport in cable bacteria—filamentous, multicellular electroactive bacteria—showed centimeter long electron transport in an organized conductive fiber structure with high conductivities and remarkable intrinsic electrical properties. In this work we give a brief overview of the recent advances in biodegradable electronics with a focus on the use of biomaterials and electroactive bacteria, and with special attention for cable bacteria. We investigate the potential of cable bacteria in this field, as we compare the intrinsic electrical properties of cable bacteria to organic and inorganic electronic materials. Based on their intrinsic electrical properties, we show cable bacteria filaments to have great potential as for instance interconnects and transistor channels in a new generation of bioelectronics. Together with other biomaterials and electroactive bacteria they open electrifying routes toward a new generation of biodegradable electronics.

Electronic Structure of de Novo Peptide ACC-Hex from First Principles

Proteins are promising components for bioelectronic devices due in part to their biocompatibility, flexibility, and chemical diversity, which enable tuning of material properties. Indeed, an increasingly broad range of conductive protein supramolecular materials have been reported. However, due to their structural and environmental complexity, the electronic structure, and hence conductivity, of protein assemblies is not well-understood. Here we perform an all-atom simulation of the physical and electronic structure of a recently synthesized self-assembled peptide antiparallel coiled-coil hexamer, ACC-Hex. Using classical molecular dynamics and first-principles density functional theory, we examine the interactions of each peptide, containing phenylalanine residues along a hydrophobic core, to form a hexamer structure. We find that while frontier electronic orbitals are composed of phenylalanine, the peptide backbone and remaining residues, including those influenced by solvent, also contribute to the electronic density. Additionally, by studying dimers extracted from the hexamer, we show that structural distortions due to atomic fluctuations significantly impact the electronic structure of the peptide bundle. These results indicate that it is necessary to consider the full atomistic picture when using the electronic structure of supramolecular protein complexes to predict electronic properties.

Microbial nanowires

In this Quick guide, Derek Lovley introduces microbial nanowires-conductive extracellular appendages made by some bacteria and archaea.

Electrical properties of outer membrane extensions from Shewanella oneidensis MR-1

Shewanella oneidensis MR-1 is a metal-reducing bacterium that is able to exchange electrons with solid-phase minerals outside the cell. These bacterial cells can produce outer membrane extensions (OMEs) that are tens of nanometers wide and several microns long. The capability of these OMEs to transport electrons is currently under investigation. Tubular chemically fixed OMEs from S. oneidensis have shown good dc conducting properties when measured in an air environment. However, no direct demonstration of the conductivity of the more common bubble-like OMEs has been provided yet, due to the inherent difficulties in measuring it. In the present work, we measured the electrical properties of bubble-like OMEs in a dry air environment by Scanning Dielectric Microscopy (SDM) in force detection mode. We found that at the frequency of the measurements (∼2 kHz), OMEs show an insulating behavior, with an equivalent homogeneous dielectric constant ε_OME = 3.7 ± 0.7 and no dephasing between the applied ac voltage and the measured ac electric force. The dielectric constant measured for the OMEs is comparable to that obtained for insulating supramolecular protein structures (ε_protein = 3-4), pointing towards a rich protein composition of the OMEs, probably coming from the periplasm. Based on the detection sensitivity of the measuring instrument, the upper limit for the ac longitudinal conductivity of bubble-like OMEs in a dry air environment has been set to σ_OME,ac < 10^-5 S m^-1, a value several orders of magnitude smaller than the dc conductivity measured in tubular chemically fixed OMEs. The lack of conductivity of bubble-like OMEs can be attributed to the relatively large separation between cytochromes in these larger OMEs and to the suppression of cytochrome mobility due to the dry environmental conditions.

Engineering Biological Electron Transfer and Redox Pathways for Nanoparticle Synthesis

Many species of bacteria are naturally capable of types of electron transport not observed in eukaryotic cells. Some species live in environments containing heavy metals not typically encountered by cells of multicellular organisms, such as arsenic, cadmium, and mercury, leading to the evolution of enzymes to deal with these environmental toxins. Bacteria also inhabit a variety of extreme environments, and are capable of respiration even in the absence of oxygen as a terminal electron acceptor. Over the years, several of these exotic redox and electron transport pathways have been discovered and characterized in molecular-level detail, and more recently synthetic biology has begun to utilize these pathways to engineer cells capable of detecting and processing a variety of metals and semimetals. One such application is the biologically controlled synthesis of nanoparticles. This review will introduce the basic concepts of bacterial metal reduction, summarize recent work in engineering bacteria for nanoparticle production, and highlight the most cutting-edge work in the characterization and application of bacterial electron transport pathways.