Voltage-gated calcium flux mediates Escherichia coli mechanosensation

Nitazoxanide synergizes polymyxin B against Escherichia coli by depleting cellular energy

The rapid expansion of antibiotic-resistant bacterial diseases is a global burden on public health. It makes sense to repurpose and reposition already-approved medications for use as supplementary agents in synergistic combinations with existing antibiotics. Here, we demonstrate that the anthelmintic drug nitazoxanide (NTZ) synergistically enhances the effectiveness of the lipopeptide antibiotic polymyxin B in inhibiting gram-negative bacteria, including those resistant to polymyxin B. Mechanistic investigations revealed that nitazoxanide inhibited calcium influx and cell membrane depolarization, enhanced the affinity between polymyxin B and the extracellular membrane, and promoted intracellular ATP depletion and an increase in reactive oxygen species (ROS), thus enhancing the penetration and disruption of the Escherichia coli cell membrane by polymyxin B. The transcriptomic analysis revealed that the combination resulted in energy depletion by inhibiting both aerobic and anaerobic respiration patterns in bacterial cells. The increased bactericidal effect of polymyxin B on the E. coli ∆nuoC strain further indicates that NuoC could be a promising target for nitazoxanide. Furthermore, the combination of nitazoxanide and polymyxin B showed promising therapeutic effects in a mouse infection model infected with E. coli. Taken together, these results demonstrate the potential of nitazoxanide as a novel adjuvant to polymyxin B, to overcome antibiotic resistance and improve therapeutic outcomes in refractory infections.IMPORTANCEThe rapid spread of antibiotic-resistant bacteria poses a serious threat to public health. The search for potential compounds that can increase the antibacterial activity of existing antibiotics is a promising strategy for addressing this issue. Here, the synergistic activity of the FDA-approved agent nitazoxanide (NTZ) combined with polymyxin B was investigated in vitro using checkerboard assays and time-kill curves. The synergistic mechanisms of the combination of nitazoxanide and polymyxin B were explored by fluorescent dye, transmission electron microscopy (TEM), and transcriptomic analysis. The synergistic efficacy was evaluated in vivo by the Escherichia coli and mouse sepsis models. These results suggested that nitazoxanide, as a promising antibiotic adjuvant, can effectively enhance polymyxin B activity, providing a potential strategy for treating multidrug-resistant bacteria.

Mechanobiology of bacterial biofilms: Implications for orthopedic infection

Postoperative bacterial infections are prevalent complications in both human and veterinary orthopedic surgery, particularly when a biofilm develops. These infections often result in delayed healing, early revision, permanent functional loss, and, in severe cases, amputation. The diagnosis and treatment pose significant challenges, and bacterial biofilm further amplifies the therapeutic difficulty as it confers protection against the host immune system and against antibiotics which are usually administered as a first-line therapeutic option. However, the inappropriate use of antibiotics has led to the emergence of numerous multidrug-resistant organisms, which largely compromise the already imperfect treatment efficiency. In this context, the study of bacterial biofilm formation allows to better target antibiotic use and to evaluate alternative therapeutic strategies. Exploration of the roles played by mechanical factors on biofilm development is of particular interest, especially because cartilage and bone tissues are reactive environments that are subjected to mechanical load. This review delves into the current landscape of biofilm mechanobiology, exploring the role of mechanical factors on biofilm development through a multiscale prism starting from bacterial microscopic scale to reach biofilm mesoscopic size and finally the macroscopic scale of the fracture site or bone-implant interface.

Pyrgos[n]cages: Redefining antibacterial strategy against drug resistance

Amid rising antibiotic resistance, the quest for advanced antibacterial agents to surpass microbial adaptation is paramount. This study introduces Pyrgos[n]cages (n = 1 to 4), pioneering multidecker cationic covalent organic cages engineered to combat drug-resistant bacteria via a dual-targeting approach. Synthesized through successive photocatalytic bromination and cage-forming reactions, these architectures stand out for their dense positive charge distribution, exceptional stability, and substantial rigidity. Pyrgos[n]cages exhibit potent bactericidal activity by disrupting bacterial membrane potential and binding to DNA. Notably, these structures show unparalleled success in eradicating both extracellular and intracellular drug-resistant pathogens in diverse infection scenarios, with antibacterial efficiency markedly increasing over 100-fold as the decker number rises from 1 to 3. This study provides an advance in antibacterial tactics and underscores the transformative potential of covalent organic cages in devising enduring countermeasures against antibiotic-resistant microbial threats.

Ion Signaling in Cell Motility and Development in Dictyostelium discoideum

Cell-to-cell communication is fundamental to the organization and functionality of multicellular organisms. Intercellular signals orchestrate a variety of cellular responses, including gene expression and protein function changes, and contribute to the integrated functions of individual tissues. Dictyostelium discoideum is a model organism for cell-to-cell interactions mediated by chemical signals and multicellular formation mechanisms. Upon starvation, D. discoideum cells exhibit coordinated cell aggregation via cyclic adenosine 3',5'-monophosphate (cAMP) gradients and chemotaxis, which facilitates the unicellular-to-multicellular transition. During this process, the calcium signaling synchronizes with the cAMP signaling. The resulting multicellular body exhibits organized collective migration and ultimately forms a fruiting body. Various signaling molecules, such as ion signals, regulate the spatiotemporal differentiation patterns within multicellular bodies. Understanding cell-to-cell and ion signaling in Dictyostelium provides insight into general multicellular formation and differentiation processes. Exploring cell-to-cell and ion signaling enhances our understanding of the fundamental biological processes related to cell communication, coordination, and differentiation, with wide-ranging implications for developmental biology, evolutionary biology, biomedical research, and synthetic biology. In this review, I discuss the role of ion signaling in cell motility and development in D. discoideum.

Bacterial Electrophysiology

Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology.

Towards optical measurements of membrane potential values in Bacillus subtilis using fluorescence lifetime

Membrane potential (MP) changes can provide a simple readout of bacterial functional and metabolic state or stress levels. While several optical methods exist for measuring fast changes in MP in excitable cells, there is a dearth of such methods for absolute and precise measurements of steady-state membrane potentials (MPs) in bacterial cells. Conventional electrode-based methods for the measurement of MP are not suitable for calibrating optical methods in small bacterial cells. While optical measurement based on Nernstian indicators have been successfully used, they do not provide absolute or precise quantification of MP or its changes. We present a novel, calibrated MP recording approach to address this gap. Our method is based on (i) a unique VoltageFluor (VF) optical transducer, whose fluorescence lifetime varies as a function of MP via photoinduced electron transfer (PeT) and (ii) a quantitative phasor-FLIM analysis for high-throughput readout. This method allows MP changes to be easily recorded, quantified and visualized. Using our preliminary Bacillus subtilis-specific MP versus VF lifetime calibration, we estimated the MP for unperturbed B. subtilis cells to be -65 mV and that for chemically depolarized cells as -14 mV. Our work paves the way for deeper insights into bacterial electrophysiology and bioelectricity research.

From the Microbiome to the Electrome: Implications for the Microbiota-Gut-Brain Axis

The gut microbiome plays a fundamental role in metabolism, as well as the immune and nervous systems. Microbial imbalance (dysbiosis) can contribute to subsequent physical and mental pathologies. As such, interest has been growing in the microbiota-gut-brain brain axis and the bioelectrical communication that could exist between bacterial and nervous cells. The aim of this study was to investigate the bioelectrical profile (electrome) of two bacterial species characteristic of the gut microbiome: a Proteobacteria Gram-negative bacillus Escherichia coli (E. coli), and a Firmicutes Gram-positive coccus Enterococcus faecalis (E. faecalis). We analyzed both bacterial strains to (i) validate the fluorescent probe bis-(1,3-dibutylbarbituric acid) trimethine oxonol, DiBAC4(3), as a reliable reporter of the changes in membrane potential (Vmem) for both bacteria; (ii) assess the evolution of the bioelectric profile throughout the growth of both strains; (iii) investigate the effects of two neural-type stimuli on Vmem changes: the excitatory neurotransmitter glutamate (Glu) and the inhibitory neurotransmitter γ-aminobutyric acid (GABA); (iv) examine the impact of the bioelectrical changes induced by neurotransmitters on bacterial growth, viability, and cultivability using absorbance, live/dead fluorescent probes, and viable counts, respectively. Our findings reveal distinct bioelectrical profiles characteristic of each bacterial species and growth phase. Importantly, neural-type stimuli induce Vmem changes without affecting bacterial growth, viability, or cultivability, suggesting a specific bioelectrical response in bacterial cells to neurotransmitter cues. These results contribute to understanding the bacterial response to external stimuli, with potential implications for modulating bacterial bioelectricity as a novel therapeutic target.

Determination of cinnamaldehyde, thymol and eugenol in essential oils by LC-MS/MS and antibacterial activity of them against bacteria

Plant essential oils contain many secondary metabolites, some of which can effectively inhibit the growth of pathogenic microorganisms, so it is a very promising antibacterial agent. In this study, a qualitative and quantitative method based on high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was developed for the simultaneous determination of three bioactive substances, cinnamaldehyde (CNM), thymol (THY), and eugenol (EUG), in the essential oils of plants. Necessary tests for linearity, limit of quantification, recovery, carryover contamination and precision of the method were carried out. Then, the antibacterial activity of 3 bioactive compounds against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) was evaluated by minimal inhibitory concentration and the synergistic antimicrobial effect. The results indicated that CNM, THY and EUG had good antibacterial activity. According to the results of fractional inhibitory concentration index (FICI), it is considered that CNM + THY and CNM + THY + EUG has obvious synergistic inhibitory effect on E. coli, and CNM + THY and CNM + EUG has obvious synergistic inhibitory effect on S. aureus. Finally, we analyzed the effect of the bioactive compounds on trace elements in bacteria and found significant changes in magnesium, calcium, copper and iron.

Spatiotemporal dynamics of the proton motive force on single bacterial cells

Electrochemical gradients across biological membranes are vital for cellular bioenergetics. In bacteria, the proton motive force (PMF) drives essential processes like adenosine triphosphate production and motility. Traditionally viewed as temporally and spatially stable, recent research reveals a dynamic PMF behavior at both single-cell and community levels. Moreover, the observed lateral segregation of respiratory complexes could suggest a spatial heterogeneity of the PMF. Using a light-activated proton pump and detecting the activity of the bacterial flagellar motor, we perturb and probe the PMF of single cells. Spatially homogeneous PMF perturbations reveal millisecond-scale temporal dynamics and an asymmetrical capacitive response. Localized perturbations show a rapid lateral PMF homogenization, faster than proton diffusion, akin to the electrotonic potential spread observed in passive neurons, explained by cable theory. These observations imply a global coupling between PMF sources and consumers along the membrane, precluding sustained PMF spatial heterogeneity but allowing for rapid temporal changes.

Fluorescent Protein-Based Sensors for Detecting Essential Metal Ions across the Tree of Life

Genetically encoded fluorescent metal ion sensors are powerful tools for elucidating metal dynamics in living systems. Over the last 25 years since the first examples of genetically encoded fluorescent protein-based calcium indicators, this toolbox of probes has expanded to include other essential and non-essential metal ions. Collectively, these tools have illuminated fundamental aspects of metal homeostasis and trafficking that are crucial to fields ranging from neurobiology to human nutrition. Despite these advances, much of the application of metal ion sensors remains limited to mammalian cells and tissues and a limited number of essential metals. Applications beyond mammalian systems and in vivo applications in living organisms have primarily used genetically encoded calcium ion sensors. The aim of this Perspective is to provide, with the support of historical and recent literature, an updated and critical view of the design and use of fluorescent protein-based sensors for detecting essential metal ions in various organisms. We highlight the historical progress and achievements with calcium sensors and discuss more recent advances and opportunities for the detection of other essential metal ions. We also discuss outstanding challenges in the field and directions for future studies, including detecting a wider variety of metal ions, developing and implementing a broader spectral range of sensors for multiplexing experiments, and applying sensors to a wider range of single- and multi-species biological systems.

Intermittent proton bursts of single lactic acid bacteria

Lactic acid bacteria are a kind of probiotic microorganisms that efficiently convert carbohydrates to lactic acids, thus playing essential roles in fermentation and food industry. While conventional wisdom often suggests continuous release of protons from bacteria during acidification, here we developed a methodology to measure the dynamics of proton release at the single bacteria level, and report on the discovery of a proton burst phenomenon, i.e., the intermittent efflux of protons, of single Lactobacillus plantarum bacteria. When placing an individual bacterium in an oil-sealed microwell, efflux and accumulation of protons consequently reduced the pH in the confined extracellular medium, which was monitored with fluorescent pH indicators in a high-throughput and real-time manner. In addition to the slow and continuous proton release behavior (as expected), stochastic and intermittent proton burst events were surprisingly observed with a typical timescale of several seconds. It was attributed to the regulatory response of bacteria by activating H+-ATPase to compensate the stochastic and transient depolarizations of membrane potential. These findings not only revealed an unprecedented proton burst phenomenon in lactic acid bacteria, but also shed new lights on the intrinsic roles of H+-ATPase in membrane potential homeostasis, with implications for both fermentation industry and bacterial electrophysiology.

Klebsiella pneumoniae DedA family proteins have redundant roles in divalent cation homeostasis and resistance to phagocytosis

The DedA superfamily is a highly conserved family of membrane proteins. Deletion of Escherichia coli yqjA and yghB, encoding related DedA family proteins, results in sensitivity to elevated temperature, antibiotics, and alkaline pH. The human pathogen Klebsiella pneumoniae possesses genes encoding DedA family proteins with >90% amino acid identity to E. coli YqjA and YghB. We hypothesized that the deletion of K. pneumoniae yqjA and yghB will impact its physiology and may reduce its virulence. The K. pneumoniae ΔyqjA ΔyghB mutant (strain VT101) displayed a growth defect at 42°C and alkaline pH sensitivity, not unlike its E. coli counterpart. However, VT101 retained mostly wild-type resistance to antibiotics. We found VT101 was sensitive to the chelating agent EDTA, the anionic detergent SDS, and agents capable of alkalizing the bacterial cytoplasm such as bicarbonate or chloroquine. We could restore growth at alkaline pH and at elevated temperature by addition of 0.5-2 mM Ca2+ or Mg2+ to the culture media. VT101 displayed a slower uptake of calcium, which was dependent upon calcium channel activity. VT201, with similar deletions as VT101 but derived from a virulent K. pneumoniae strain, was highly susceptible to phagocytosis by alveolar macrophages and displayed a defect in the production of capsule. These findings suggest divalent cation homeostasis and virulence are interlinked by common functions of the DedA family.IMPORTANCEKlebsiella pneumoniae is a dangerous human pathogen. The DedA protein family is found in all bacteria and is a membrane transporter often required for virulence and antibiotic resistance. K. pneumoniae possesses homologs of E. coli YqjA and YghB, with 60% amino acid identity and redundant functions, which we have previously shown to be required for tolerance to biocides and alkaline pH. A K. pneumoniae strain lacking yqjA and yghB was found to be sensitive to alkaline pH, elevated temperature, and EDTA/SDS and displayed a defect in calcium uptake. Sensitivity to these conditions was reversed by addition of calcium or magnesium to the growth medium. Introduction of ΔyqjA and ΔyghB mutations into virulent K. pneumoniae resulted in the loss of capsule, increased phagocytosis by macrophages, and a partial loss of virulence. These results show that targeting the Klebsiella DedA family results in impaired divalent cation transport and, in turn, loss of virulence.

Excite the unexcitable: engineering cells and redox signaling for targeted bioelectronic control

The ever-growing influence of technology in our lives has led to an increasing interest in the development of smart electronic devices to interrogate and control biological systems. Recently, redox-mediated electrogenetics introduced a novel avenue that enables direct bioelectronic control at the genetic level. In this review, we discuss recent advances in methodologies for bioelectronic control, ranging from electrical stimulation to engineering efforts that allow traditionally unexcitable cells to be electrically 'programmable.' Alongside ion-transport signaling, we suggest redox as a route for rational engineering because it is a native form of electronic communication in biology. Using redox as a common language allows the interfacing of electronics and biology. This newfound connection opens a gateway of possibilities for next-generation bioelectronic tools.

Mechanosensation induces persistent bacterial growth during bacteriophage predation

IMPORTANCE

Bacteria and bacteriophage form one of the most important predator-prey relationships on earth, yet how the long-term stability of this ecological interaction is achieved is unclear. Here, we demonstrate that Escherichia coli can rapidly grow during bacteriophage predation if they are doing so in spatially confined environments. This discovery revises our understanding of bacteria-bacteriophage population dynamics in many real-world environments where bacteria grow in confinement, such as the gut and the soil. Additionally, this result has clear implications for the potential of bacteriophage therapy and the role of mechanosensation during bacterial pathogenesis.

A high-throughput and low-waste viability assay for microbes

Counting viable cells is a universal practice in microbiology. The colony-forming unit (CFU) assay has remained the gold standard to measure viability across disciplines, but it is time-intensive and resource-consuming. Here we describe the geometric viability assay (GVA) that replicates CFU measurements over 6 orders of magnitude while reducing over 10-fold the time and consumables required. GVA computes a sample's viable cell count on the basis of the distribution of embedded colonies growing inside a pipette tip. GVA is compatible with Gram-positive and Gram-negative planktonic bacteria (Escherichia coli, Pseudomonas aeruginosa and Bacillus subtilis), biofilms and fungi (Saccharomyces cerevisiae). Laborious CFU experiments such as checkerboard assays, treatment time-courses and drug screens against slow-growing cells are simplified by GVA. The ease and low cost of GVA evinces that it can replace existing viability assays and enable viability measurements at previously impractical scales.

Smart and Multifunctional Materials Based on Electroactive Poly(vinylidene fluoride): Recent Advances and Opportunities in Sensors, Actuators, Energy, Environmental, and Biomedical Applications

From scientific and technological points of view, poly(vinylidene fluoride), PVDF, is one of the most exciting polymers due to its overall physicochemical characteristics. This polymer can crystalize into five crystalline phases and can be processed in the form of films, fibers, membranes, and specific microstructures, being the physical properties controllable over a wide range through appropriate chemical modifications. Moreover, PVDF-based materials are characterized by excellent chemical, mechanical, thermal, and radiation resistance, and for their outstanding electroactive properties, including high dielectric, piezoelectric, pyroelectric, and ferroelectric response, being the best among polymer systems and thus noteworthy for an increasing number of technologies. This review summarizes and critically discusses the latest advances in PVDF and its copolymers, composites, and blends, including their main characteristics and processability, together with their tailorability and implementation in areas including sensors, actuators, energy harvesting and storage devices, environmental membranes, microfluidic, tissue engineering, and antimicrobial applications. The main conclusions, challenges and future trends concerning materials and application areas are also presented.

[Anaesthesia, a process common to all living organisms]

Because of their interest in medicine, most studies of anaesthesia focus on the nervous system of metazoans, and the fact that any life form can be anaesthetised is often underlooked. If electrical signalling is an essential phenomenon for the success of animals, it appears to be widespread beyond metazoans. Indeed, anaesthesia targets Na+/Ca2+ voltage-gated channels that exist in a wide variety of species and originate from ancestral channels that predate eukaryotes in the course of evolution. The fact that the anaesthetic capacity that leads to loss of sensitivity is common to all phyla may lead to two hypotheses: to be investigated is the evolutionary maintenance of the ability to be anaesthetised due to an adaptive advantage or to a simple intrinsic defect in ion channels? The study of anaesthesia in organisms phylogenetically distant from animals opens up promising prospects for the discovery of new anaesthetic treatments. Moreover, it should also lead to a better understanding of a still poorly understood phenomenon that yet unifies all living organisms. We hope that this new understanding of the unity of life will help humans to assume their responsibilities towards all species, at a time when we are threatening biodiversity with mass extinction.

Bioelectrical State of Bacteria Is Linked to Growth Dynamics and Response to Neurotransmitters: Perspectives for the Investigation of the Microbiota-Brain Axis

Inter-cellular communication is mediated by a sum of biochemical, biophysical, and bioelectrical signals. This might occur not only between cells belonging to the same tissue and/or animal species but also between cells that are, from an evolutionary point of view, far away. The possibility that bioelectrical communication takes place between bacteria and nerve cells has opened exciting perspectives in the study of the gut microbiota-brain axis. The aim of this paper is (i) to establish a reliable method for the assessment of the bioelectrical state of two bacterial strains: Bacillus subtilis (B. subtilis) and Limosilactobacillus reuteri (L. reuteri); (ii) to monitor the bacterial bioelectrical profile throughout its growth dynamics; and (iii) to evaluate the effects of two neurotransmitters (glutamate and γ-aminobutyric acid-GABA) on the bioelectrical signature of bacteria. Our results show that membrane potential (Vmem) and the proliferative capacity of the population are functionally linked in B. subtilis in each phase of the cell cycle. Remarkably, we demonstrate that bacteria respond to neural signals by changing Vmem properties. Finally, we show that Vmem changes in response to neural stimuli are present also in a microbiota-related strain L. reuteri. Our proof-of-principle data reveal a new methodological approach for the better understanding of the relation between bacteria and the brain, with a special focus on gut microbiota. Likewise, this approach will open exciting perspectives in the study of the inter-cellular mechanisms which regulate the bi-directional communication between bacteria and neurons and, ultimately, for designing gut microbiota-brain axis-targeted treatments for neuropsychiatric diseases.

Cell-autonomous diversification in bacteria arises from calcium dynamics self-organizing at a critical point

How dynamic bacterial calcium is regulated, with kinetics faster than typical mechanisms of cellular adaptation, is unknown. We discover bacterial calcium fluctuations are temporal-fractals resulting from a property known as self-organized criticality (SOC). SOC processes are poised at a phase transition separating ordered and chaotic dynamical regimes and are observed in many natural and anthropogenic systems. SOC in bacterial calcium emerges due to calcium channel coupling mediated via membrane voltage. Environmental or genetic perturbations modify calcium dynamics and the critical exponent suggesting a continuum of critical attractors. Moving along this continuum alters the collective information capacity of bacterial populations. We find that the stochastic transition from motile to sessile lifestyle is partially mediated by SOC-governed calcium fluctuations through the regulation of c-di-GMP. In summary, bacteria co-opt the physics of phase transitions to maintain dynamic calcium equilibrium, and this enables cell-autonomous population diversification during surface colonization by leveraging the stochasticity inherent at a boundary between phases.

Unlocking chloride sensing in the red at physiological pH with a fluorescent rhodopsin-based host

Chloride is a vital ion for all forms of life. Protein-based fluorescent biosensors can enable researchers to visualize chloride in cells but remain underdeveloped. Here, we demonstrate how a single point mutation in an engineered microbial rhodopsin results in ChloRED-1-CFP. This membrane-bound host is a far-red emitting, ratiometric sensor that provides a reversible readout of chloride in live bacteria at physiological pH, setting the stage to investigate the roles of chloride in diverse biological contexts.

Membrane Targeted Azobenzene Drives Optical Modulation of Bacterial Membrane Potential

Recent studies have shown that bacterial membrane potential is dynamic and plays signaling roles. Yet, little is still known about the mechanisms of membrane potential dynamics regulation-owing to a scarcity of appropriate research tools. Optical modulation of bacterial membrane potential could fill this gap and provide a new approach for studying and controlling bacterial physiology and electrical signaling. Here, the authors show that a membrane-targeted azobenzene (Ziapin2) can be used to photo-modulate the membrane potential in cells of the Gram-positive bacterium Bacillus subtilis. It is found that upon exposure to blue-green light (λ = 470 nm), isomerization of Ziapin2 in the bacteria membrane induces hyperpolarization of the potential. To investigate the origin of this phenomenon, ion-channel-deletion strains and ion channel blockers are examined. The authors found that in presence of the chloride channel blocker idanyloxyacetic acid-94 (IAA-94) or in absence of KtrAB potassium transporter, the hyperpolarization response is attenuated. These results reveal that the Ziapin2 isomerization can induce ion channel opening in the bacterial membrane and suggest that Ziapin2 can be used for studying and controlling bacterial electrical signaling. This new optical tool could contribute to better understand various microbial phenomena, such as biofilm electric signaling and antimicrobial resistance.

Advances in pulsed electric stimuli as a physical method for treating liquid foods

There is a need for alternative technologies that can deliver safe and nutritious foods at lower costs as compared to conventional processes. Pulsed electric field (PEF) technology has been utilised for a plethora of different applications in the life and physical sciences, such as gene/drug delivery in medicine and extraction of bioactive compounds in food science and technology. PEF technology for treating liquid foods involves engineering principles to develop the equipment, and quantitative biochemistry and microbiology techniques to validate the process. There are numerous challenges to address for its application in liquid foods such as the 5-log pathogen reduction target in food safety, maintaining the food quality, and scale up of this physical approach for industrial integration. Here, we present the engineering principles associated with pulsed electric fields, related inactivation models of microorganisms, electroporation and electropermeabilization theory, to increase the quality and safety of liquid foods; including water, milk, beer, wine, fruit juices, cider, and liquid eggs. Ultimately, we discuss the outlook of the field and emphasise research gaps.

Distance measurements between 5 nanometer diamonds - single particle magnetic resonance or optical super-resolution imaging?

5 nanometer sized detonation nanodiamonds (DNDs) are studied as potential single-particle labels for distance measurements in biomolecules. Nitrogen-vacancy (NV) defects in the crystal lattice can be addressed through their fluorescence and optically-detected magnetic resonance (ODMR) of a single particle can be recorded. To achieve single-particle distance measurements, we propose two complementary approaches based on spin-spin coupling or optical super-resolution imaging. As a first approach, we try to measure the mutual magnetic dipole-dipole coupling between two NV centers in close DNDs using a pulse ODMR sequence (DEER). The electron spin coherence time, a key parameter to reach long distance DEER measurements, was prolonged using dynamical decoupling reaching T _2,DD ≈ 20 μs, extending the Hahn echo decay time T ₂ by one order of magnitude. Nevertheless, an inter-particle NV-NV dipole coupling could not be measured. As a second approach, we successfully localize the NV centers in DNDs using STORM super-resolution imaging, achieving a localization precision of down to 15 nm, enabling optical nanometer-scale single-particle distance measurements.

Versatile nanodiamond-based tools for therapeutics and bioimaging

Nanodiamonds (NDs) are a remarkable class of carbon-based nanoparticles in nanomedicine which have recently become a hot topic of research due to their unique features including functionalization versatility, tunable opto-magnetic properties, chemical stability, minimal cytotoxicity, high affinity to biomolecules and biocompatibility. These attractive features make NDs versatile tools for a wide range of biologically relevant applications. In this feature article, we discuss the opto-magnetic properties of negatively charged nitrogen vacancy (NV^-) centres in NDs as fluorescence probes. We further discuss the frequently used chemical methods for surface chemistry modification of NDs which are relevant for biomedical applications. The in vitro and in vivo biocompatibility of modified NDs is also highlighted. Subsequently, we give an overview of recent state-of-the-art biomedical applications of NDs as versatile tools for bioimaging and detection, and as targeting nanocarriers for chemotherapy, photodynamic therapy, gene therapy, antimicrobial and antiviral therapy, and bone tissue engineering. Finally, we pinpoint the main challenges for NDs in biomedical applications which lie ahead and discuss perspectives on future directions in advancing the field for practical applications and clinical translations.

The elements of life: A biocentric tour of the periodic table

Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.

Collective polarization dynamics in bacterial colonies signify the occurrence of distinct subpopulations

Membrane potential in bacterial systems has been shown to be dynamic and tightly related to survivability at the single-cell level. However, little is known about spatiotemporal patterns of membrane potential in bacterial colonies and biofilms. Here, we discovered a transition from uncorrelated to collective dynamics within colonies formed by the human pathogen Neisseria gonorrhoeae. In freshly assembled colonies, polarization is heterogeneous with instances of transient and uncorrelated hyper- or depolarization of individual cells. As colonies reach a critical size, the polarization behavior transitions to collective dynamics: A hyperpolarized shell forms at the center, travels radially outward, and halts several micrometers from the colony periphery. Once the shell has passed, we detect an influx of potassium correlated with depolarization. Transient hyperpolarization also demarks the transition from volume to surface growth. By combining simulations and the use of an alternative electron acceptor for the respiratory chain, we provide strong evidence that local oxygen gradients shape the collective polarization dynamics. Finally, we show that within the hyperpolarized shell, tolerance against aminoglycoside antibiotics increases. These findings highlight that the polarization pattern can signify the differentiation into distinct subpopulations with different growth rates and antibiotic tolerance.

Sensitive bacterial Vm sensors revealed the excitability of bacterial Vm and its role in antibiotic tolerance

As an important free energy source, the membrane voltage (V_m) regulates many essential physiological processes in bacteria. However, in comparison with eukaryotic cells, knowledge of bacterial electrophysiology is very limited. Here, we developed a set of novel genetically encoded bacterial V_m sensors which allow single-cell recording of bacterial V_m dynamics in live cells with high temporal resolution. Using these new sensors, we reveal the electrically "excitable" and "resting" states of bacterial cells dependent on their metabolic status. In the electrically excitable state, frequent hyperpolarization spikes in bacterial V_m are observed, which are regulated by Na⁺/K⁺ ratio of the medium and facilitate increased antibiotic tolerance. In the electrically resting state, bacterial V_m displays significant cell-to-cell heterogeneity and is linked to the cell fate after antibiotic treatment. Our findings demonstrate the potential of our newly developed voltage sensors to reveal the underpinning connections between bacterial V_m and antibiotic tolerance.

High Throughput Viability Assay for Microbiology

Counting viable cells is a universal practice in microbiology. The colony forming unit (CFU) assay has remained the gold standard to measure viability across disciplines; however, it is time-intensive and resource-consuming. Herein, we describe the Geometric Viability Assay (GVA) that replicates CFU measurements over 6-orders of magnitude while reducing over 10-fold the time and consumables. GVA computes a sample's viable cell count based on the distribution of embedded colonies growing inside a pipette tip. GVA is compatible with gram-positive and -negative planktonic bacteria, biofilms, and yeast. Laborious CFU experiments such as checkerboard assays, treatment time-courses, and drug screens against slow-growing cells are simplified by GVA. We therefore screened a drug library against exponential and stationary phase E. coli leading to the discovery of the ROS-mediated, bactericidal mechanism of diphenyliodonium. The ease and low cost of GVA evinces it can accelerate existing viability assays and enable measurements at previously impractical scales.

Functional Interrogation of Ca2+ Signals in Human Cancer Cells In Vitro and Ex Vivo by Fluorescent Microscopy and Molecular Tools

Genetically encoded calcium indicators (GECIs) and high-resolution confocal microscopy enable dynamic visualization of calcium signals in cells and tissues. Two-dimensional and 3D biocompatible materials mimic the mechanical microenvironments of tumor and healthy tissues in a programmable manner. Cancer xenograft models and ex vivo functional imaging of tumor slices reveal physiologically relevant functions of calcium dynamics in tumors at different progression stages. Integration of these powerful techniques allows us to quantify, diagnose, model, and understand cancer pathobiology. Here, we describe detailed materials and methods used to establish this integrated interrogation platform, from generating transduced cancer cell lines that stably express CaViar (GCaMP5G + QuasAr2) to in vitro and ex vivo calcium imaging of the cells in 2D/3D hydrogels and tumor tissues. These tools open the possibility for detailed explorations of mechano-electro-chemical network dynamics in living systems.

Calcium responses to external mechanical stimuli in the multicellular stage of Dictyostelium discoideum

Calcium acts as a second messenger to regulate many cellular functions, including cell motility. In Dictyostelium discoideum, the cytosolic calcium level oscillates synchronously, and calcium waves propagate through the cell population during the early stages of development, including aggregation. In the unicellular phase, the calcium response through Piezo channels also functions in mechanosensing. However, calcium dynamics during multicellular morphogenesis are still unclear. Here, live imaging of cytosolic calcium revealed that calcium wave propagation, depending on cAMP relay, disappeared at the onset of multicellular body (slug) formation. Later, other forms of occasional calcium bursts and their propagation were observed in both anterior and posterior regions of migrating slugs. This calcium signaling also occurred in response to mechanical stimuli. Two pathways—calcium release from the endoplasmic reticulum via IP3 receptor and calcium influx from outside the cell—were involved in calcium signals induced by mechanical stimuli. These data suggest that calcium signaling is involved in mechanosensing in both the unicellular and multicellular phases of Dictyostelium development using different molecular mechanisms.

Measurement of the low-frequency charge noise of bacteria

Bacteria meticulously regulate their intracellular ion concentrations and create ionic concentration gradients across the bacterial membrane. These ionic concentration gradients provide free energy for many cellular processes and are maintained by transmembrane transport. Given the physical dimensions of a bacterium and the stochasticity in transmembrane transport, intracellular ion concentrations and hence the charge state of a bacterium are bound to fluctuate. Here we investigate the charge noise of hundreds of nonmotile bacteria by combining electrical measurement techniques from condensed matter physics with microfluidics. In our experiments, bacteria in a microchannel generate charge density fluctuations in the embedding electrolyte due to random influx and efflux of ions. Detected as electrical resistance noise, these charge density fluctuations display a power spectral density proportional to 1/f^{2} for frequencies 0.05Hz≤f≤1Hz. Fits to a simple noise model suggest that the steady-state charge of a bacterium fluctuates by ±1.30×10^{6}e(e≈1.60×10^{-19}C), indicating that bacterial ion homeostasis is highly dynamic and dominated by strong charge noise. The rms charge noise can then be used to estimate the fluctuations in the membrane potential; however, the estimates are unreliable due to our limited understanding of the intracellular concentration gradients.

The Power of Touch: Type 4 Pili, the von Willebrand A Domain, and Surface Sensing by Pseudomonas aeruginosa

Most microbes in the biosphere are attached to surfaces, where they experience mechanical forces due to hydrodynamic flow and cell-to-substratum interactions. These forces likely serve as mechanical cues that influence bacterial physiology and eventually drive environmental adaptation and fitness. Mechanosensors are cellular components capable of sensing a mechanical input and serve as part of a larger system for sensing and transducing mechanical signals. Two cellular components in bacteria that have emerged as candidate mechanosensors are the type IV pili (TFP) and the flagellum. Current models posit that bacteria transmit and convert TFP- and/or flagellum-dependent mechanical force inputs into biochemical signals, including cAMP and c-di-GMP, to drive surface adaptation. Here, we discuss the impact of force-induced changes on the structure and function of two eukaryotic proteins, titin and the human von Willebrand factor (vWF), and these proteins’ relevance to bacteria. Given the wealth of understanding about these eukaryotic mechanosensors, we can use them as a framework to understand the effect of force on Pseudomonas aeruginosa during the early stages of biofilm formation, with a particular emphasis on TFP and the documented surface-sensing mechanosensors PilY1 and FimH. We also discuss the importance of disulfide bonds in mediating force-induced conformational changes, which may modulate mechanosensing and downstream biochemical signaling. We conclude by sharing our perspective on the state of the field and what we deem exciting frontiers in studying bacterial mechanosensing to better understand the mechanisms whereby bacteria transition from a planktonic to a biofilm lifestyle.

Pseudomonas aeruginosa distinguishes surfaces by stiffness using retraction of type IV pili

While many bacteria can sense the presence of a surface, the mechanical properties of different surfaces vary tremendously and can be as rigid as bone or as soft as mucus. We show that the pathogen Pseudomonas aeruginosa distinguishes surfaces by stiffness and transcriptionally tunes its virulence to surface rigidity. This connection between pathogenicity and mechanical properties of the infection site presents an interesting potential for clinical applications. The mechanism behind stiffness sensing relies on the retraction of external appendages called type IV pili that deform the surface. While this mechanism has interesting parallels to stiffness sensing in mammalian cells, our results suggest that stiffness sensing in much smaller bacterial cells relies on temporal sensing instead of spatial sensing strategies.

The ability of eukaryotic cells to differentiate surface stiffness is fundamental for many processes like stem cell development. Bacteria were previously known to sense the presence of surfaces, but the extent to which they could differentiate stiffnesses remained unclear. Here we establish that the human pathogen Pseudomonas aeruginosa actively measures surface stiffness using type IV pili (TFP). Stiffness sensing is nonlinear, as induction of the virulence factor regulator is peaked with stiffness in a physiologically important range between 0.1 kPa (similar to mucus) and 1,000 kPa (similar to cartilage). Experiments on surfaces with distinct material properties establish that stiffness is the specific biophysical parameter important for this sensing. Traction force measurements reveal that the retraction of TFP is capable of deforming even stiff substrates. We show how slow diffusion of the pilin PilA in the inner membrane yields local concentration changes at the base of TFP during extension and retraction that change with substrate stiffness. We develop a quantitative biomechanical model that explains the transcriptional response to stiffness. A competition between PilA diffusion in the inner membrane and a loss/gain of monomers during TFP extension/retraction produces substrate stiffness-dependent dynamics of the local PilA concentration. We validated this model by manipulating the ATPase activity of the TFP motors to change TFP extension and retraction velocities and PilA concentration dynamics, altering the stiffness response in a predictable manner. Our results highlight stiffness sensing as a shared behavior across biological kingdoms, revealing generalizable principles of environmental sensing across small and large cells.

A simple and soft chemical deaggregation method producing single-digit detonation nanodiamonds

Detonation nanodiamonds (DNDs) are a class of very small and spherical diamond nanocrystals. They are used in polymer reinforcement materials or as drug delivery systems in the field of nanomedicine. Synthesized by detonation, only the final deaggregation step down to the single-digit nanometer size (<10 nm) unfolds their full potential. Existing deaggregation methods mainly rely on mechanical forces, such as high-power sonication or bead milling. These techniques entail drawbacks such as contamination of the sample and the need for a specialized apparatus. In this paper, we report a purely chemical deaggregation method by simply combining oxidation in air followed by a boiling acid treatment, to produce highly stable single-digit DNDs in a suspension. The resulting DNDs are surface functionalized with carboxyl groups, the final boiling acid treatment removes primary metal contaminants such as magnesium, iron or copper and the nanoparticles remain dispersed over a wide pH range. Our method can be easily carried out in a standard chemistry laboratory with commonly available laboratory apparatus. This is a key step for many DND-based applications, ranging from materials science to biological or medical applications.

Localized electrical stimulation triggers cell-type-specific proliferation in biofilms

Biological systems ranging from bacteria to mammals utilize electrochemical signaling. Although artificial electrochemical signals have been utilized to characterize neural tissue responses, the effects of such stimuli on non-neural systems remain unclear. To pursue this question, we developed an experimental platform that combines a microfluidic chip with a multielectrode array (MiCMA) to enable localized electrochemical stimulation of bacterial biofilms. The device also allows for the simultaneous measurement of the physiological response within the biofilm with single-cell resolution. We find that the stimulation of an electrode locally changes the ratio of the two major cell types comprising Bacillus subtilis biofilms, namely motile and extracellular-matrix-producing cells. Specifically, stimulation promotes the proliferation of motile cells but not matrix cells, even though these two cell types are genetically identical and reside in the same microenvironment. Our work thus reveals that an electronic interface can selectively target bacterial cell types, enabling the control of biofilm composition and development.

Gelidiales Are Not Just Agar—Revealing the Antimicrobial Potential of Gelidium corneum for Skin Disorders

In recent decades, seaweeds have proven to be an excellent source of bioactive molecules. Presently, the seaweed Gelidium corneum is harvested in a small area of the Portuguese coast exclusively for agar extraction. The aim of this work was to fully disclosure Gelidium corneum as a sustainable source of antimicrobial ingredients for new dermatological formulations, highlighting its potential to be explored in a circular economy context. For this purpose, after a green sequential extraction, these seaweed fractions (F1–F5) were chemically characterized (¹H NMR) and evaluated for their antimicrobial potential against Staphylococcus aureus, Staphylococcus epidermidis and Cutibacterium acnes. The most active fractions were also evaluated for their effects on membrane potential, membrane integrity and DNA damage. Fractions F2 and F3 displayed the best results, with IC₅₀ values of 16.1 (7.27–23.02) μg/mL and 51.04 (43.36–59.74) μg/mL against C. acnes, respectively, and 53.29 (48.75–57.91) μg/mL and 102.80 (87.15–122.30) μg/mL against S. epidermidis, respectively. The antimicrobial effects of both fractions seem to be related to membrane hyperpolarization and DNA damage. This dual mechanism of action may provide therapeutic advantages for the treatment of skin dysbiosis-related diseases.

Bacterial Homologs of Progestin and AdipoQ Receptors (PAQRs) Affect Membrane Energetics Homeostasis but Not Fluidity

Membrane potential homeostasis is essential for cell survival. Defects in membrane potential lead to pleiotropic phenotypes, consistent with the central role of membrane energetics in cell physiology. Homologs of the progestin and AdipoQ receptors (PAQRs) are conserved in multiple phyla of Bacteria and Eukarya. In eukaryotes, PAQRs are proposed to modulate membrane fluidity and fatty acid (FA) metabolism. The role of bacterial homologs has not been elucidated. Here, we use Escherichia coli and Bacillus subtilis to show that bacterial PAQR homologs, which we name “TrhA,” have a role in membrane energetics homeostasis. Using transcriptional fusions, we show that E. coli TrhA (encoded by yqfA) is part of the unsaturated fatty acid biosynthesis regulon. Fatty acid analyses and physiological assays show that a lack of TrhA in both E. coli and B. subtilis (encoded by yplQ) provokes subtle but consistent changes in membrane fatty acid profiles that do not translate to control of membrane fluidity. Instead, membrane proteomics in E. coli suggested a disrupted energy metabolism and dysregulated membrane energetics in the mutant, though it grew similarly to its parent. These changes translated into a disturbed membrane potential in the mutant relative to its parent under various growth conditions. Similar dysregulation of membrane energetics was observed in a different E. coli strain and in the distantly related B. subtilis. Together, our findings are consistent with a role for TrhA in membrane energetics homeostasis, through a mechanism that remains to be elucidated.

IMPORTANCE Eukaryotic homologs of the progestin and AdipoQ receptor family (PAQR) have been shown to regulate membrane fluidity by affecting, through unknown mechanisms, unsaturated fatty acid (FA) metabolism. The bacterial homologs studied here mediate small and consistent changes in unsaturated FA metabolism that do not seem to impact membrane fluidity but, rather, alter membrane energetics homeostasis. Together, the findings here suggest that bacterial and eukaryotic PAQRs share functions in maintaining membrane homeostasis (fluidity in eukaryotes and energetics for bacteria with TrhA homologs).

Representing Stimulus Information in an Energy Metabolism Pathway

We explored a computational model of astrocytic energy metabolism and demonstrated the theoretical plausibility that this type of pathway might be capable of coding information about stimuli in addition to its known functions in cellular energy and carbon budgets. Simulation results indicate that glycogenolytic glycolysis triggered by activation of adrenergic receptors can capture the intensity and duration features of a neuromodulator waveform and can respond in a dose-dependent manner, including non-linear state changes that are analogous to action potentials. We show how this metabolic pathway can translate information about external stimuli to production profiles of energy-carrying molecules such as lactate with a precision beyond simple signal transduction or non-linear amplification. The results suggest the operation of a metabolic state-machine from the spatially discontiguous yet interdependent metabolite elements. Such metabolic pathways might be well-positioned to code an additional level of salient information about a cell's environmental demands to impact its function. Our hypothesis has implications for the computational power and energy efficiency of the brain.

Signaling events that occur when cells of Escherichia coli encounter a glass surface

Microbial cells organized on solid surfaces are the most ancient form of biological communities. Yet how single cells interact with surfaces and integrate a variety of signals to establish a sessile lifestyle is poorly understood. We developed and used sensitive biosensors to determine the kinetics of second messengers’ responses to surface attachment. This allowed us to examine cell-by-cell variability of the initial signaling events and establish that some of these events depend on flagellar motor function while others do not. Environmentally determined factors, like the energetic status of the cell, can modulate all signaling events. The complex interplay between the surface interaction inputs and external conditions can now be studied using our system.

Bacterial cells interact with solid surfaces and change their lifestyle from single free-swimming cells to sessile communal structures (biofilms). Cyclic di-guanosine monophosphate (c-di-GMP) is central to this process, yet we lack tools for direct dynamic visualization of c-di-GMP in single cells. Here, we developed a fluorescent protein–based c-di-GMP–sensing system for Escherichia coli that allowed us to visualize initial signaling events and assess the role played by the flagellar motor. The sensor was pH sensitive, and the events that appeared on a seconds’ timescale were alkaline spikes in the intracellular pH. These spikes were not apparent when signals from different cells were averaged. Instead, a signal appeared on a minutes’ timescale that proved to be due to an increase in intracellular c-di-GMP. This increase, but not the alkaline spikes, depended upon a functional flagellar motor. The kinetics and the amplitude of both the pH and c-di-GMP responses displayed cell-to-cell variability indicative of the distinct ways the cells approached and interacted with the surface. The energetic status of a cell can modulate these events. In particular, the alkaline spikes displayed an oscillatory behavior and the c-di-GMP increase was modest in the presence of glucose.

Exploring electroactive microenvironments in polymer-based nanocomposites to sensitize bacterial cells to low-dose embedded silver nanoparticles

The search for alternative antimicrobial strategies capable of avoiding resistance mechanisms in bacteria are highly needed due to the alarming emergence of antimicrobial resistance. The application of physical stimuli as a mean of sensitizing bacteria for the action of antimicrobials on otherwise resistant bacteria or by allowing the action of low quantity of antimicrobials may be seen as a breakthrough for such purpose. This work proposes the development of antibacterial nanocomposites using the synergy between the electrically active microenvironments, created by a piezoelectric polymer (poly(vinylidene fluoride-co-trifluoroethylene) (PVDF-TrFE)), with green-synthesized silver nanoparticles (AgNPs). The electrical microenvironment is generated via mechanical stimulation of piezoelectric PVDF-TrFE/AgNPs films using a lab-made mechanical bioreactor. The generated material's electrical response further translates to bacterial cells, namely Escherichia coli and Staphylococcus epidermidis which in combination with AgNPs and the specific morphological features of the material induce important antibacterial and antibiofilm activity. Both porous and non-porous PVDF composites have shown antibacterial characteristics when stimulated at a mechanical frequency of 4 Hz being the effect boosted when AgNPs were incorporated in the nanocomposite, reducing in more than 80% the S. epidermidis bacterial growth in planktonic and biofilm form. The electroactive environments sensitize the bacteria allowing the action of a low dose of AgNPs (1.69% (w/w)). Importantly, the material did not compromise the viability of mammalian cells, thus being considered biocompatible. The piezoelectric stimulation of PVDF-based polymeric films may represent a breakthrough in the development of antibacterial coatings for devices used at hospital setting, taking advantage on the use of mechanical stimuli (pressure/touch) to exert antibacterial and antibiofilm activity. STATEMENT OF SIGNIFICANCE: The application of physical methods in alternative to the common chemical ones is seen as a breakthrough for avoiding the emergence of antimicrobial resistance. Antimicrobial strategies that take advantage on the capability of bacteria to sense physical stimuli such as mechanical and electrical cues are scarce. Electroactive nanocomposites comprised of poly(vinylidene fluoride-co-trifluoroethylene (PVDF-TrFE) and green-synthesized silver nanoparticles (AgNPs) were developed to obtain material able to inhibit the colonization of microorganisms. By applying a mechanical stimuli to the nanocomposite, which ultimately mimics movements such as walking or touching, an antimicrobial effect is obtained, resulting from the synergy between the electroactive microenvironments created on the surface of the material and the AgNPs. Such environments sensitize the bacteria to low doses of antimicrobials.

Hybrid Matters: Art and Science as a New Epistemology

Why do art and science collaborations matter? Hybrid Matters outlines an epistemological mapping of art and science as an emerging method of interrogation. Through the prism of COVID-19, Warner proposes a paradigm shift driven by care and empathy. In opposition to the notion of art as a vehicle for communicating science, Warner suggests a model in which art and science become mutually reinforcing, discovering alternative pathways of understanding in our relationship with natural ecology and one another.

Our sisters the plants? notes from phylogenetics and botany on plant kinship blindness

Before the upheaval brought about by phylogenetic classification, classical taxonomy separated living beings into two distinct kingdoms, animals and plants. Rooted in 'naturalist' cosmology, Western science has built its theoretical apparatus on this dichotomy mostly based on ancient Aristotelian ideas. Nowadays, despite the adoption of the Darwinian paradigm that unifies living organisms as a kinship, the concept of the "scale of beings" continues to structure our analysis and understanding of living species. Our aim is to combine developments in phylogeny, recent advances in biology, and renewed interest in plant agency to craft an interdisciplinary stance on the living realm. The lines at the origin of plant or animal have a common evolutionary history dating back to about 3.9 Ga, separating only 1.6 Ga ago. From a phylogenetic perspective of living species history, plants and animals belong to sister groups. With recent data related to the field of Plant Neurobiology, our aim is to discuss some socio-cultural obstacles, mainly in Western naturalist epistemology, that have prevented the integration of living organisms as relatives, while suggesting a few avenues inspired by practices principally from other ontologies that could help overcome these obstacles and build bridges between different ways of connecting to life.

Towards the Idea of Molecular Brains

How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.

Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective

Bioluminescence, the emission of light catalysed by luciferases, has evolved in many taxa from bacteria to vertebrates and is predominant in the marine environment. It is now well established that in animals possessing a nervous system capable of integrating light stimuli, bioluminescence triggers various behavioural responses and plays a role in intra- or interspecific visual communication. The function of light emission in unicellular organisms is less clear and it is currently thought that it has evolved in an ecological framework, to be perceived by visual animals. For example, while it is thought that bioluminescence allows bacteria to be ingested by zooplankton or fish, providing them with favourable conditions for growth and dispersal, the luminous flashes emitted by dinoflagellates may have evolved as an anti-predation system against copepods. In this short review, we re-examine this paradigm in light of recent findings in microorganism photoreception, signal integration and complex behaviours. Numerous studies show that on the one hand, bacteria and protists, whether autotrophs or heterotrophs, possess a variety of photoreceptors capable of perceiving and integrating light stimuli of different wavelengths. Single-cell light-perception produces responses ranging from phototaxis to more complex behaviours. On the other hand, there is growing evidence that unicellular prokaryotes and eukaryotes can perform complex tasks ranging from habituation and decision-making to associative learning, despite lacking a nervous system. Here, we focus our analysis on two taxa, bacteria and dinoflagellates, whose bioluminescence is well studied. We propose the hypothesis that similar to visual animals, the interplay between light-emission and reception could play multiple roles in intra- and interspecific communication and participate in complex behaviour in the unicellular world.

Biomedical Implants with Charge-Transfer Monitoring and Regulating Abilities

Transmembrane charge (ion/electron) transfer is essential for maintaining cellular homeostasis and is involved in many biological processes, from protein synthesis to embryonic development in organisms. Designing implant devices that can detect or regulate cellular transmembrane charge transfer is expected to sense and modulate the behaviors of host cells and tissues. Thus, charge transfer can be regarded as a bridge connecting living systems and human-made implantable devices. This review describes the mode and mechanism of charge transfer between organisms and nonliving materials, and summarizes the strategies to endow implants with charge-transfer regulating or monitoring abilities. Furthermore, three major charge-transfer controlling systems, including wired, self-activated, and stimuli-responsive biomedical implants, as well as the design principles and pivotal materials are systematically elaborated. The clinical challenges and the prospects for future development of these implant devices are also discussed.

IonoBiology: The functional dynamics of the intracellular metallome, with lessons from bacteria

Metal ions are essential for life and represent the second most abundant constituent (after water) of any living cell. While the biological importance of inorganic ions has been appreciated for over a century, we are far from a comprehensive understanding of the functional roles that ions play in cells and organisms. In particular, recent advances are challenging the traditional view that cells maintain constant levels of ion concentrations (ion homeostasis). In fact, the ionic composition (metallome) of cells appears to be purposefully dynamic. The scientific journey that started over 60 years ago with the seminal work by Hodgkin and Huxley on action potentials in neurons is far from reaching its end. New evidence is uncovering how changes in ionic composition regulate unexpected cellular functions and physiology, especially in bacteria, thereby hinting at the evolutionary origins of the dynamic metallome. It is an exciting time for this field of biology, which we discuss and refer to here as IonoBiology.

Bringing Microbiology to Light: Toward All-Optical Electrophysiology in Bacteria

The observation of neuron-like behavior in bacteria, such as the occurrence of electric spiking and extended bioelectric signaling, points to the role of membrane dynamics in prokaryotes. Electrophysiology of bacteria, however, has been overlooked for long time, due to the difficulties in monitoring bacterial bioelectric phenomena with those probing techniques that are commonly used for eukaryotes. Optical technologies can allow a paradigm shift in the field of electrophysiology of bacteria, as they would permit to elicit and monitor signaling rapidly, remotely, and with high spatiotemporal precision. In this perspective, we discuss about the potentiality of light interrogation methods in microbiology, encouraging the development of all-optical electrophysiology of bacteria.

BacFlash signals acid-resistance gene expression in bacteria

Intracellular pH (pHi) homeostasis is crucial for cellular functions and signal transduction across all kingdoms of life. In particular, bacterial pHi homeostasis is important for physiology, ecology, and pathogenesis. Here we report an exquisite bacterial acid-resistance (AR) mechanism in which proton leak elicits a pre-emptive AR response. A single bacterial cell undergoes quantal electrochemical excitation, termed "BacFlash", which consists of membrane depolarization, transient pHi rise, and bursting production of reactive oxygen species. BacFlash ignition is dictated by acid stress in the form of proton leak across the plasma membrane and the rate of BacFlash occurrence is reversely correlated with the pHi buffering capacity. Through genome-wide screening, we further identify the ATP synthase Fo complex subunit a as the putative proton sensor for BacFlash biogenesis. Importantly, persistent BacFlash hyperactivity activates transcription of a panel of key AR genes and predisposes the cells to survive imminent extreme acid stress. These findings demonstrate a prototypical coupling between electrochemical excitation and nucleoid gene expression in prokaryotes.

Toward Bacterial Bioelectric Signal Transduction

Bacteria are electrically powered organisms; cells maintain an electrical potential across their plasma membrane as a source of free energy to drive essential processes. In recent years, however, bacterial membrane potential has been increasingly recognized as dynamic. Those dynamics have been implicated in diverse physiological functions and behaviors, including cell division and cell-to-cell signaling. In eukaryotic cells, such dynamics play major roles in coupling bioelectrical stimuli to changes in internal cell states. Neuroscientists and physiologists have established detailed molecular pathways that transduce eukaryotic membrane potential dynamics to physiological and gene expression responses. We are only just beginning to explore these intracellular responses to bioelectrical activity in bacteria. In this review, we summarize progress in this area, including evidence of gene expression responses to stimuli from electrodes and mechanically induced membrane potential spikes. We argue that the combination of provocative results, missing molecular detail, and emerging tools makes the investigation of bioelectrically induced long-term intracellular responses an important and rewarding effort in the future of microbiology.