Biology subjects

Adamatzky, A.

Publications and source records attributed to Adamatzky, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Freshwater Blackworms Solving a Maze

We investigated the behaviour of freshwater blackworms (\emph{Lumbriculus variegatus}) in a circular maze containing food in its central chamber. Analysis of 11 time-lapse recordings showed that all tested worms entered the central chamber, although first-arrival times and spatial exploration patterns varied substantially. Registered occupancy maps revealed non-uniform use of corridors and chambers. Because the study did not include a no-food control, the observations demonstrate central-chamber entry and spatial exploration but do not by themselves establish food localisation or chemotaxis. The assay provides a reproducible framework for studying annelid exploration and for future controlled comparisons of sensory cues and maze complexity.

biophysics↗

bioRxiv2026

Propagation of electrical spike trains in substrates colonised by oyster fungi

We investigate electrical signalling in substrates colonised by oyster fungi using long-term, multi-channel electrophysiological recordings. Electrical ac-tivity was recorded continuously for approximately fifteen days using a linear array of eight differential electrode channels sampled at 1 Hz. Slow electrical spikes with durations from tens of seconds to tens of minutes and millivolt-scale amplitudes were identified, and spike trains exhibited highly variable inter-spike intervals on time scales of minutes to hours. Analysis of temporal relationships between channels reveals directional propagation of electrical activity along the electrode array, with delay distributions between adjacent channels showing pronounced positive peaks and a monotonic lead-lag order-ing across channels. Median delays of approximately 180 s between channels separated by approximately 2 cm correspond to an estimated propagation speed of about 0.7 cm/min (approximately 40 cm/h). Control analyses us-ing temporally shuffled spike trains indicated its biological origin. These re-sults demonstrate that electrical activity in oyster fungi propagates through the mycelial network as slow travelling signals consistent with ionic wave dynamics.

biophysics↗

bioRxiv2025

Extracellular electrophysiological effects on MEA recordings of living mycelium following in-vivo polydopamine polymerisation

Fungi produce multiple melanins found in nature, including the eumelanins (black or dark brown), pheomelanins (yellow or red) and the highly diverse group of allomelanins. The fungal melanins provide protection against UV radiation, oxidative stress, desiccation, host immune evasion and antifungal drug resistance. As a result, research on melanin in fungi is wide ranging including development of anti-fungals and surface interfacing bioelectronics. In-vivo polymerisation of compounds with electrical or ionic conductivity can provide a useful method to interface with the electrophysiology of biological organisms. However, the impact of such interventions is unknown where anti-fungal activity is present and interferes with the target signaling in the organism. Melanin compounds are promising for achieving bioelectronic interfaces with mycelium. However, the identification of the role of melanin in blocking calcium flux in airway epithelial cells and phagosomes underscores the significance of investigating its effects in more detail. Additionally, synthetic analogs such as polydopamine are thought to exhibit similar metal ion chelation properties, supporting the biochemical parallels between natural and artificial melanins. In this paper, we investigate the polymerisation of synthetic melanins in mycelium from the intracellular environment and onto microelectrodes in terms of extracellular electrophysiology. At concentrations of 5 mM and 10 mM extracellular electrophysiological activity is significantly inhibited suggesting a putative link to reduction in Ca2+ efflux and antifungal properties. The dispersed mycelial cultures were estimated to comprise of a total of 200 spiking units across triplicates (T1= 117, T2=40, T3=43). The triplicates had a combined mean trough-to-peak time of 1.72 {+/-} 0.07 ms. Selection of electrophysiology interfacing polymers should be carefully orchestrated to avoid impacting baseline physiology of fungi.

microbiology↗

bioRxiv2025

Millisecond spiking units in dispersed mycelial liquid culture MEA recordings absent in dehydrated and fungicidal assays

The extracellular electrophysiology of dispersed mycelial liquid cultures has not previously been investigated in terms of wide bandwidth frequency components and presence of putative spiking units. Here, we identify stereotypical discrete unit mycelial spikes in 150-3000 Hz filtered extracellular electrophysiological recordings of liquid dispersed mycelial cultures. Hard gold coated and custom designed microelectrode arrays with individual electrode radius of 100 {micro}m were used to identify spikes with frequency components between 150-3000 Hz. The dispersed mycelial cultures were estimated to comprise of a total of 177 spiking units across triplicates (T1= 83, T2=44, T3=50). The triplicates had a combined mean trough-to-peak time of 1.58 {+/-} 0.14 ms. Dehydration and H2O2 based fungicidal assays showed reduction of the spiking units to zero. Differences in power spectral density (PSD) and Fourier transform analysis of the respective traces suggest that physical structures in the dehydration assay were preserved but that the interface between the mycelium and the electrodes was removed. Biofilm formation was not, therefore, required to detect extracellular spikes using the methods described here. The fungicidal assays removed the discrete unit electrophysiological spike resulting in zero spiking units detected, confirming the physiological origin of the extracellular signals. Extracellular electrophysiology can be studied directly in dispersed liquid cultures of mycelium using suitable microelectrode interfaces without complex media or synthetic interventions such as conductive polymers or nanoparticles.

bioengineering↗

bioRxiv2025

Effects of nystatin on discrete unit 150-3000 Hz extracellular spikes in biofilm forming Hericium erinaceus liquid cultures recorded using custommicroelectrode arrays

Extracellular electrical potentials have been observed in a number of filamentous mycelial species with incommensurable and non-stereotypic features. In Basidiomycetes, detecting these signals reliably is dependent on the properties of the cell wall and plasma membrane and requires implementation of microelectrode array hardware, filtering and spike sorting methods. In this paper, we present recording methods for detection of discrete unit extracellular spikes in biofilm forming liquid cultures of Hericium erinaceus. We utilised custom designed microelectrode arrays (MEAs) with passive planar hard gold microelectrodes and individual radius of 100 {micro}m in recordings at a sample rate of 30 kHz. Triplicate recordings of mycelial samples in a double shielded electromagnetic and RF shield box were conducted for wild-type, ionophore assays and fungicidal assays. The recordings were analysed offline using the Kilosort4 sorting algorithm resulting in detection of discrete unit spikes with milliseconds durations. The clustered spike waveforms for the wild-type triplicates were estimated to have a mean trough-to-peak-time of 2.68 {+/-} 0.087 ms and width at half maximum of 0.8 {+/-} 0.031 ms across a combined total of 418 spiking units. Ionophore assays using nystatin solution (10,000 units/ml) exhibited significant statistical differences including a reduction of total units to 97. A decrease in the trough-to-peak time of the mean waveform (1.97 {+/-} 0.32 ms) and an increase in the width at half maximum (2.7 {+/-} 2.45 ms) were also observed. Nystatin was found reduce the mean extracellular spike amplitude from 173.06 {micro}V in the wild-type to 25.76 {micro}V in the assay. Physiological disruption of the cell wall and plasma membrane was confirmed by environmental scanning microscopy comparison of triplicates at 90 % humidity. In comparison, a fungicidal assay utilising 12% w/v H2O2 solution resulted in zero spiking units and absence of discrete unit activity across all channels in triplicate recordings.

bioengineering↗

bioRxiv2025

Scanning Electron Microscopy Study of Bacterial Growth in Mycelial Extracellular Matrices

Fungi and bacteria are found living in a wide variety of environments and their interactions are important in many processes including soil health, human and animal physiology and in biotechnological applications. The specificity of interaction between these microorganisms in co-culture is difficult to establish. For example, differentiation between trivial processes as a result of stochastic mixing compared with mutualistic or antagonistic interactions. Here, we investigate a single morphological feature of co-cultures of planktonic bacterial growth within biofilm-forming liquid cultures of mycelium. Namely, the attachment of bacterial co-habitants of species Bacillus subtilis to fungal hyphae of species Hericium erinaceus. The bacteria-in-mycelial-biofilm method was developed and utilised to allow for attachment of bacteria to hyphae via containment within extracellular polymeric substances (EPS) and the overall extracellular matrix (ECM) of the mycelium. Attachment structures appear to result from the hyphal surface as a result of production of EPS. The mean biofilm area across T1-3 was 3.90 ({micro}m2) {+/-} 0.72 ({micro}m2) and the mean percentage coverage was 18.33 (%) {+/-} 5.52 (%). The bacterial biofilm components could not be ruled out as co-contributing to formation of attachment structures due to the structures being present connecting individual bacterium as well as to hyphae.

microbiology↗

bioRxiv2024

Towards intelligent living facades: On electrical activity of ordinary moss Brachythecium rutabulum

Mosses display resilience and ecological importance, significantly shaping their environments. With their strong attachment to challenging substrates, mosses can serve as viable options for green living facades. In our initial steps towards developing sensing and computing living facades using moss, we analysed the endogenous electrical activity of mosses to establish foun-dational knowledge for future information processing devices. Employing macro-electrode recording techniques, we identified three patterns of electrical activity in ordinary moss: high-frequency oscillations at 1.2 Hz, medium-frequency oscillations at 2 {middle dot} 10-4 Hz, and low-frequency oscillations at approximately 4 {middle dot} 10-4. Additionally, we observed indications of coordinated electrical activity in moss cushions.

biophysics↗

bioRxiv2024

Functionalising the electrical properties of Kombucha zoogleal mats for biosensing applications

Kombucha is a type of tea that is fermented using yeast and bacteria. During this process, a film made of cellulose is produced. This film has unique properties such as biodegradability, flexibility, shape conformability, and ability to self-grow, as well as be produced across customised scales. In our previous studies, we demonstrated that Kombucha mats exhibit electrical activity represented by spikes of electrical potential. We propose using microbial fermentation as a method for in situ functionalisation to modulate the electroactive nature of Kombucha cellulose mats, where graphene and zeolite were used for the functionalisation. We subjected the pure and functionalised Kombucha mats to mechanical stimulation by applying different weights and geometries. Our experiments demonstrated that Kombucha mats functionalised with graphene and zeolite exhibit memfractive properties and respond to load by producing distinctive spiking patterns. Our findings present incredible opportunities for the in situ development of functionalised hybrid materials with sensing, computing, and memory capabilities. These materials can self-assemble and self-grow after fusing their living and synthetic components. This study contributes to an emergent area of research on bioelectronic sensing and hybrid living materials, opening up exciting opportunities for use in smart wearables, diagnostics, health monitoring and energy harvesting applications.

bioengineering↗

bioRxiv2023

On effect of chloroform on electrical activity of proteinoids

Proteinoids, or thermal proteins, produce hollow microspheres in aqueous solution. Ensembles of the microspheres produce endogenous spikes of electrical activity, similar to that of neurons. To make a first step towards evaluation of the mechanisms of such electrical behaviour we decided to expose proteinoids to chloroform. We found that while chloroform does not inhibit the electrical oscillations of proteinoids it causes substantial changes in the patterns of electrical activity. Namely, incremental chloroform exposure strongly affect proteinoid microsphere electrical activity across multiple metrics. As chloroform levels rise, the spike potential drops from 0.9 mV under control conditions to 0.1 mV at 25 mg/mL. This progressive spike potential decrease suggests chloroform suppresses proteinoid electrical activity. The time between spikes, the interspike period, follows a similar pattern. Minimal chloroform exposure does not change the average inter-spike period, while higher exposures do. It drops from 23.2 min under control experiments to 3.8 min at 25 mg/mL chloroform, indicating increased frequency of the electrical activity. These findings might leads to deeper understanding of the electrical activity of proteinoids and their potential application in the domain of bioelectronics.

biophysics↗

bioRxiv2023

On interaction of proteinoids with simulated neural networks

Proteinoids are thermal proteins which swell into microspheres in solution. The proteinoid microspheres show spiking of electrical potential similar to that to that of living neurons. Rich spectrum of proteinoids spiking responses to optical and electrical stimulation makes them promising candidates for neuromorphic unconventional computing devices. We decided to evaluate neuron-like activity of proteinoids in the experimental setups of their interaction with simulate neuronal network of Izhikevich neurons. The simulated neural networks stimulate and modulate electrical activity of proteinoid ensembles by interacting with them via arbitrary form programmable function generator. Different amino-acid compositions of proteinoids responded uniquely to input spiking from simulated neurons. We demonstrated that patterns of electrical spiking activity of proteinoids and complexity of the activity can be tuned by patterns of spikes generated by simulated neurons. The research opens novel venues to establishing interacting between nanobrains - brain-like organoids made from molecules, not animal cells -- and real nervous systems.

biophysics↗

bioRxiv2023

Exploring Discrete Space-Time Models for Information Transfer: Analogies from Mycelial Networks to the Cosmic Web

Fungal mycelium networks are large scale biological networks along which nutrients, metabolites flow. Recently, we discovered a rich spectrum of electrical activity in mycelium networks, including action-potential spikes and trains of spikes. Reasoning by analogy with animals and plants, where travelling patterns of electrical activity perform integrative and communicative mechanisms, we speculated that waves of electrical activity transfer information in mycelium networks. Using a new discrete space-time model with emergent radial spanning-tree topology, hypothetically comparable mycelial morphology and physically comparable information transfer, we provide physical arguments for the use of such a model, and by considering growing mycelium network by analogy with growing network of matter in the cosmic web, we develop mathematical models and theoretical concepts to characterise the parameters of the information transfer.

bioinformatics↗

bioRxiv2023

Bioelectrical Synchronisation of Spruce Trees during aSolar Eclipse

Regular light-dark cycles greatly affect organisms, and events like eclipses induce distinctive physiological and behavioural shifts. While well-documented in animals, plant behaviour during eclipses remains largely unexplored. Here we monitored multiple spruce trees to assess their individual and collective bioelectrical responses to a solar eclipse. Trees anticipated the eclipse, synchronising their individual bioelectrical behaviour hours in advance. Older trees displayed greater anticipatory behaviour with early time-asymmetry and entropy increases, characteristic of memory dynamics in open dissipative systems such as trees. These results reveal a complex relationship between individual and collective tree behaviour, shaped by individual age and physiology as well as collective history and memory. This highlights the adaptive significance of synchrony and collective memory in plants, offering new insights on coordinated behaviours in nature. One Sentence SummaryTrees anticipate and respond collectively to a solar eclipse.

plant biology↗

bioRxiv2023

Tuning electrical spiking of Schizophyllum commune with light

When studying the split-gill fungus Schizophyllum commune, we observed that the growing colonies displayed endogenous spikes of electrical potential similar to the action potentials of neurons. In order to investigate the impact of light on the electrical activities of these colonies, we exposed them to intermittent stimulation with cold light (5800k) and later with blue (c. 470nm), red (c. 642nm) and green (c. 538nm) light. Our findings revealed spiking activity can be influenced using this input including observable responses with patterns of spiking at relatively high average amplitudes (>1mV) appearing consistently upon illumination of the sample. The response is likely related to the activity of fungal photoreceptors, including potential sensitisation to blue light in the cellular signalling pathways facilitated by white collar proteins (WC-1, WC-2) in S. commune. Based on these findings, we suggest that fungal photosensors and photonic computing substrates have the potential to enable applications beyond the scope of conventional electronics via relatively fast spiking responses to light tuned by external input stimulation. Further work should focus on identifying the signal transduction pathway for responses to different wavelengths of light and its role in translation into engineered ELMs to extend existing studies in fungal photobiology.

bioengineering↗

bioRxiv2023

Logical gates in ensembles of proteinoid microspheres

Proteinoid are thermal proteins which swell into microspheres in aqueous solution. Ensembles of proteinoids produce electrical spiking activity similar to that of neurons. We introduce a novel method for implementing logical gates in the ensembles of proteinoid microspheres using chronoamperometry. Chronoamperometry is a technique that involves applying a voltage pulse to proteinoid microspheres and measuring their current response. We have observed that proteinoids exhibit distinct current patterns that align with various logical outputs. We identify four types of logical gates: AND, OR, XOR, and NAND. These gates are determined by the current response of proteinoid microspheres. Additionally, we demonstrate that proteinoid microspheres have the ability to modify their current response over time, which is influenced by their previous exposure to voltage. This indicates that they possess a capacity for learning and are capable of adapting to their environment. Our research showcases the ability of proteinoid microspheres to perform logical operations and computations through their inherent electrical properties.

bioengineering↗

bioRxiv2023

Recognition of sounds by ensembles of proteinoids

Proteinoids are artificial polymers that imitate certain characteristics of natural proteins, including self-organization, catalytic activity, and responsiveness to external stimuli. This paper investigates the potential of proteinoids as organic audio signal processors. We convert sounds of English alphabet into waveforms of electrical potential, feed the waveforms into proteinoid solutions and record electrical responses of the proteinoids. We also undertake a detailed comparison of proteinoids electrical responses (frequencies, periods, and amplitudes) with original input signals. We found that responses of proteinoids are less regular, lower dominant frequency, wider distribution of proteinoids and less skewed distribution of amplitudes compared with input signals. We found that letter of English alphabet uniquely maps onto a pattern of electrical activity of a proteinoid ensemble, that is the proteinoid ensembles recognise spoken letters of English alphabet. The finding will be used in further designs of organic electronic devices, based on ensembles of proteinoids, for sound processing and speech recognition.

biophysics↗

bioRxiv2023

Electrical spiking activity of proteinoids-ZnO colloids

We are studying the remarkable electrical properties of Proteinoids-ZnO micro-spheres with the aim of exploring their potential for a new form of computing. Our research has revealed that these microspheres exhibit behavior similar to neurons, generating electrical spikes that resemble action potentials. Through our investigations, we have studied the underlying mechanism behind this electrical activity and proposed that the spikes arise from oscillations between the degradation and reorganization of proteinoid molecules on the surface of ZnO. These findings offer valuable insights into the potential use of Proteinoids-ZnO colloids in unconventional computing and the development of novel neuromorphic liquid circuits.

biophysics↗

bioRxiv2023

Are fungi capacitors?

The emerging field of living technologies aims to create new functional hybrid materials in which living systems interface and interact with inanimate ones. Combining research into living technologies with emerging developments in computing architecture has enabled the generation of organic electronics from plants and slime mould. Here, we expand on this work by studying capacitive properties of a substrate colonised by mycelium of grey oyster fungi, Pleurotus ostreatus. Capacitors play a fundamental role in traditional analogue and digital electronic systems and have a range of uses including sensing, energy storage and filter circuits. Mycelium has the potential to be used as an organic replacement for traditional capacitor technology. Here, were show that the capacitance of mycelium is in the order of hundreds of picofarads and at the same time a voltage-dependent pseudocapacitance of the order of hundreds of microfarads. We also demonstrate that the charge density of the mycelium dielectric decays rapidly with increasing distance from the source probes. This is important as it indicates that small cells of mycelium could be used as a charge carrier or storage medium, when employed as part of an array with reasonable density.

biophysics↗

bioRxiv2023

Multiscalar electrical spiking in Schizophyllum commune

Growing colonies of the split-gill fungus Schizophyllum commune show action potential-like spikes of extracellular electrical potential. We analysed several days of electrical activity recording of the fungus and discovered three families of oscillatory patterns. Very slow activity at a scale of hours, slow activity at a scale of tens minutes and very fast activity at scale of half-minute. We simulated the spiking behaviour using FitzHugh-Nagume model, uncovered mechanisms of spike shaping. We speculated that spikes of electrical potential might be associated with transportation of nutrients and metabolites.

biophysics↗