Chemotaxis In Bacteria Research Articles

Comparative transcriptome analysis explored the molecular mechanisms of a luxR-type regulator regulating intracellular survival of Aeromonas hydrophila.

Aeromonas hydrophila is not a traditional intracellular bacterium. However, previous studies revealed that pathogenic A. hydrophila B11 could temporarily survive for at least 24 h in fish phagocytes, and the regulation of intracellular survival in bacteria was associated with regulators of the LuxR-type. The mechanisms of luxR08110 on the A. hydrophila's survival in macrophages were investigated using comprehensive transcriptome analysis and biological phenotype analysis in this study. The results showed that after luxR08110 was silenced, the intracellular survival ability of bacteria was significantly diminished. Comparative transcriptome analysis revealed that luxR08110 was a critical regulator of A. hydrophila, which regulated the expression of over 1200 genes, involving in bacterial flagellar assembly and chemotaxis, ribosome, sulphur metabolism, glycerolipid metabolism, and other mechanisms. Further studies confirmed that after the inhibition of expression of luxR08110, the motility, chemotaxis and adhesion of A. hydrophila significantly decreased. Moreover, compared with the wild-type strain, the survival rates of silencing strain were all considerably reduced under both H2O2 and low pH stress conditions. According to both transcriptome analysis and phenotypic tests, the luxR08110 of A. hydrophila could act as global regulator in bacteria intracellular survival. This regulator regulated intracellular survival of A. hydrophila mainly through two ways. One way is to regulate bacterial flagellar synthesis and further affects the motility, chemotaxis and adhesion of bacteria. The other way is to regulate sulphur and glycerolipid metabolisms, thus affecting bacterial energy production and the ability to resist environmental stress.

Defensive alteration of root exudate composition by grafting Prunus sp. onto resistant rootstock contributes to reducing crown gall disease.

Grafting is a traditional and significant strategy to suppress soil-borne diseases, such as the crown gall disease caused by tumorigenic Agrobacterium and Rhizobium. Root exudates and the rhizosphere microbiome play critical roles in controlling crown gall disease, but their roles in suppressing crown gall disease in grafted plants remain unclear. Here, disease-susceptible cherry rootstock 'Gisela 6' and disease-resistant cherry rootstock 'Haiying 1' were grafted onto each other or self-grafted. The effect of their root exudates on the soil microbiome composition and the abundance of pathogenic Agrobacterium were studied. Grafting onto the disease-resistant rootstock helped to reduce the abundance of pathogenic Agrobacterium, accompanied by altering root exudation, enriching potential beneficial bacteria, and changing soil function. Then, the composition of the root exudates from grafted plants was analyzed and the potential compounds responsible for decreasing pathogenic Agrobacterium abundance were identified. Based on quantitative measurement of the concentrations of the compounds and testing the impacts of supplied pure chemicals on abundance and chemotaxis of pathogenic Agrobacterium and potential beneficial bacteria, the decreased valine in root exudates of the plant grafted onto resistant rootstock was found to contribute to decreasing Agrobacterium abundance, enriching some potential beneficial bacteria and suppressing crown gall disease. This study provides insights into the mechanism whereby grafted plants suppress soil-borne disease.

Systematic mapping of chemoreceptor specificities for Pseudomonas aeruginosa.

Chemotaxis of motile bacteria has multiple physiological functions. It enables bacteria to locate optimal ecological niches, mediates collective behaviors, and can play an important role in infection. These multiple functions largely depend on ligand specificities of chemoreceptors, and the number and identities of chemoreceptors show high diversity between organisms. Similar diversity is observed for the spectra of chemoeffectors, which include not only chemicals of high metabolic value but also bacterial, plant, and animal signaling molecules. However, the systematic identification of chemoeffectors and their mapping to specific chemoreceptors remains a challenge. Here, we combined several in vivo and in vitro approaches to establish a systematic screening strategy for the identification of receptor ligands and we applied it to identify a number of new physiologically relevant chemoeffectors for the important opportunistic human pathogen P. aeruginosa. This strategy can be equally applicable to map specificities of sensory domains from a wide variety of receptor types and bacteria.

Azospirillum brasilense AerC and Tlp4b Cytoplasmic Chemoreceptors Are Promiscuous and Interact with the Two Membrane-Bound Chemotaxis Signaling Clusters Mediating Chemotaxis Responses.

Chemotaxis in Bacteria and Archaea depends on the presence of hexagonal polar arrays composed of membrane-bound chemoreceptors that interact with rings of baseplate signaling proteins. In the alphaproteobacterium Azospirillum brasilense, chemotaxis is controlled by two chemotaxis signaling systems (Che1 and Che4) that mix at the baseplates of two spatially distinct membrane-bound chemoreceptor arrays. The subcellular localization and organization of transmembrane chemoreceptors in chemotaxis signaling clusters have been well characterized but those of soluble chemoreceptors remain relatively underexplored. By combining mutagenesis, microscopy, and biochemical assays, we show that the cytoplasmic chemoreceptors AerC and Tlp4b function in chemotaxis and localize to and interact with membrane-bound chemoreceptors and chemotaxis signaling proteins from both polar arrays, indicating that soluble chemoreceptors are promiscuous. The interactions of AerC and Tlp4b with polar chemotaxis signaling clusters are not equivalent and suggest distinct functions. Tlp4b, but not AerC, modulates the abundance of chemoreceptors within the signaling clusters through an unknown mechanism. The AerC chemoreceptor, but not Tlp4b, is able to traffic in and out of chemotaxis signaling clusters depending on its level of expression. We also identify a role of the chemoreceptor composition of chemotaxis signaling clusters in regulating their polar subcellular organization. The organization of chemotaxis signaling proteins as large membrane-bound arrays underlies chemotaxis sensitivity. Our findings suggest that the composition of chemoreceptors may fine-tune chemotaxis signaling not only through their chemosensory specificity but also through their role in the organization of polar chemotaxis signaling clusters. IMPORTANCE Cytoplasmic chemoreceptors represent about 14% of all chemoreceptors encoded in bacterial and archaeal genomes, but little is known about how they interact with and function in large polar assemblies of membrane-bound chemotaxis signaling clusters. Here, we show that two soluble chemoreceptors with a role in chemotaxis are promiscuous and interact with two distinct membrane-bound chemotaxis signaling clusters that control all chemotaxis responses in Azospirillum brasilense. We also found that any change in the chemoreceptor composition of chemotaxis signaling clusters alters their polar organization, suggesting a dynamic interplay between the sensory specificity of chemotaxis signaling clusters and their polar membrane organization.

The application of the photo-electro-Fenton process in the treatment of wastewater reduces the abundance of genes associated with pathogenicity factors, antibiotic resistance, and metabolism: A metagenomic analysis.

The objective of this work was to determine the effect of advanced oxidation systems on the taxonomic and functional diversity of pathogenic microorganisms in the effluent of the wastewater treatment plant in Bogotá - Colombia (“El Salitre” WWTP) by metagenomics analysis. The taxonomic and functional diversity of the microorganisms, before and after oxidation treatment, was determined by Illumina mass sequencing, detecting human pathogenic genera as Pseudomonas (28.0%), Arcobacter (10.0%), Aeromonas (4.0%), Sulfurospirillum (4.0%), Salmonella (3.0%), and Clostridiales (3.0%). Likewise, pathogenicity factors such as antimicrobial resistance genes (ARGs) also were detected in high abundances (∼5% of metagenome reads). In the effluent treated with the photoelectro-Fenton system (for 5, 30, and 60 min), a significant reduction of pathogenicity factors was observed in all cases. ARGs, chemotaxis, quorum sensing, secretion systems, and toxins of pathogenic bacteria (such as Arcobacter, Pseudomonas, Serratia, and Salmonella) were reduced at near-zero log2 values, demonstrating that the photoelectro-Fenton process is a promising alternative to reduce the biological risk associated with this pathogenicity factors.

Rate thresholds in cell signaling have functional and phenotypic consequences in non-linear time-dependent environments.

All cells employ signal transduction pathways to respond to physiologically relevant extracellular cytokines, stressors, nutrient levels, hormones, morphogens, and other stimuli that vary in concentration and rate in healthy and diseased states. A central unsolved fundamental question in cell signaling is whether and how cells sense and integrate information conveyed by changes in the rate of extracellular stimuli concentrations, in addition to the absolute difference in concentration. We propose that different environmental changes over time influence cell behavior in addition to different signaling molecules or different genetic backgrounds. However, most current biomedical research focuses on acute environmental changes and does not consider how cells respond to environments that change slowly over time. As an example of such environmental change, we review cell sensitivity to environmental rate changes, including the novel mechanism of rate threshold. A rate threshold is defined as a threshold in the rate of change in the environment in which a rate value below the threshold does not activate signaling and a rate value above the threshold leads to signal activation. We reviewed p38/Hog1 osmotic stress signaling in yeast, chemotaxis and stress response in bacteria, cyclic adenosine monophosphate signaling in Amoebae, growth factors signaling in mammalian cells, morphogen dynamics during development, temporal dynamics of glucose and insulin signaling, and spatio-temproral stressors in the kidney. These reviewed examples from the literature indicate that rate thresholds are widespread and an underappreciated fundamental property of cell signaling. Finally, by studying cells in non-linear environments, we outline future directions to understand cell physiology better in normal and pathophysiological conditions.

Investigation of self-assembly and topological changes in the sessile droplets of Klebsiella oxytoca by Chronological study

The infectious droplet from the patient self-assembles into a novel pattern depending on bacterial interaction with substrate and liquid. The spatial location of bacteria inside the droplet fluctuates depending on the non-covalent forces. The deformation and dehydration induced stress on bacteria in evaporating contagious-fluid droplets alters the viability and infectivity. The self-assembly of Klebsiella oxytoca (KO) in contagious sessile droplets was studied by natural evaporation. KO forms novel patterns as the droplets exsiccate, thus revealing the unexplored topological changes that govern its survival and infection strategies. The droplets of both bacterial suspension in Milli-Q and SRF of volume 0.95 ± 0.1 μl were placed on the glass material for assessment of the self-assembly. The bacterial suspension was stained before allowing them to desicate. The bacterial chemotaxis and deposition near the end of evaporation are recorded using the bright and dark field optical method. The random time interval is also measured to track the bacterial movement. The investigation shows that the majority of the bacterial population moves toward the rim of the droplet because of edge closely packing, leading to enhanced viability and pathogenesis on the famously known “coffee ring” and few bacteria are present at the centre of the droplet which represents chemotaxis of bacteria. The mechanistic insight gained via our study can have far-reaching implications for bacterial infection through droplets e.g., through open wounds.

Performance Analysis of Chemotaxis-Inspired Stochastic Controllers for Multi-Agent Coverage

In this study, we analyze the performance of stochastic coverage controllers inspired by the chemotaxis of bacteria. The control algorithm of bacteria to generate the chemotaxis switches between forward movement and random rotation based on the difference between the current and previous concentration of a chemical. The considered coverage controllers mimic this algorithm, where bacteria and the chemical concentration are regarded as agents and the achieved degree of coverage, respectively. Because the coverage controllers operate similar to the control algorithm of bacteria, they are potentially suitable for molecular robots. Molecular robots, which consist of biomolecules, are recognized as a key component in the development of future medical systems based on micro-robots working inside the human body. However, the performance of the controllers has not yet been analyzed, and no theoretical guarantee of coverage completion has been provided. We address this problem by determining whether a performance index that quantifies the achieved degree of coverage increases over time for the feedback system. We first show that the performance index is characterized by the distance between agents under certain conditions. Using this result, we prove that the performance index increases with probability 1 under some conditions although the controllers are stochastic. This provides partial evidence for coverage completion, which makes the controllers more reliable. The analysis result is validated by numerical experiments.

Rhizobial Chemotaxis and Motility Systems at Work in the Soil.

Bacteria navigate their way often as individual cells through their chemical and biological environment in aqueous medium or across solid surfaces. They swim when starved or in response to physical and chemical stimuli. Flagella-driven chemotaxis in bacteria has emerged as a paradigm for both signal transduction and cellular decision-making. By altering motility, bacteria swim toward nutrient-rich environments, movement modulated by their chemotaxis systems with the addition of pili for surface movement. The numbers and types of chemoreceptors reflect the bacterial niche and lifestyle, with those adapted to complex environments having diverse metabolic capabilities, encoding far more chemoreceptors in their genomes. The Alpha-proteobacteria typify the latter case, with soil bacteria such as rhizobia, endosymbionts of legume plants, where motility and chemotaxis are essential for competitive symbiosis initiation, among other processes. This review describes the current knowledge of motility and chemotaxis in six model soil bacteria: Sinorhizobium meliloti, Agrobacterium fabacearum, Rhizobium leguminosarum, Azorhizobium caulinodans, Azospirillum brasilense, and Bradyrhizobium diazoefficiens. Although motility and chemotaxis systems have a conserved core, rhizobia possess several modifications that optimize their movements in soil and root surface environments. The soil provides a unique challenge for microbial mobility, since water pathways through particles are not always continuous, especially in drier conditions. The effectiveness of symbiont inoculants in a field context relies on their mobility and dispersal through the soil, often assisted by water percolation or macroorganism movement or networks. Thus, this review summarizes the factors that make it essential to consider and test rhizobial motility and chemotaxis for any potential inoculant.

Biased reorientation in the chemotaxis of peritrichous bacteria Salmonella enterica serovar Typhimurium

Many kinds of peritrichous bacteria that repeat runs and tumbles by using multiple flagella exhibit chemotaxis by sensing a difference in the concentration of the attractant or repellent between two adjacent time points. If a cell senses that the concentration of an attractant has increased, their flagellar motors decrease the switching frequency from counterclockwise to clockwise direction of rotation, which causes a longer run in swimming up the concentration gradient than swimming down. We investigated the turn angle in tumbles of peritrichous bacteria swimming across the concentration gradient of a chemoattractant because the change in the switching frequency in the rotational direction may affect the way tumbles. We tracked several hundreds of runs and tumbles of single cells of Salmonella enterica serovar Typhimurium in the concentration gradient of L-serine and found that the turn angle depends on the concentration gradient that the cell senses just before the tumble. The turn angle is biased toward a smaller value when the cells swim up the concentration gradient, whereas the distribution of the angle is almost uniform (random direction) when the cells swim down the gradient. The effect of the observed bias in the turn angle on the degree of chemotaxis was investigated by random walk simulation. In the concentration field where attractants diffuse concentrically from the point source, we found that this angular distribution clearly affects the reduction of the mean-square displacement of the cell that has started at the attractant source, that is, the bias in the turn angle distribution contributes to chemotaxis in peritrichous bacteria.

State of the art of bacterial chemotaxis.

Bacterial chemotaxis is a biased movement of bacteria toward the beneficial chemical gradient or away from a toxic chemical gradient. This movement is achieved by sensing a chemical gradient by chemoreceptors. In most of the chemotaxis studies, Escherichia coli has been used as a model organism. E. colihave about 4-6 flagella on their surfaces, and the motility is achieved by rotating the flagella. Each flagellum has reversible flagellar motors at its base,which rotate the flagella in counterclockwise and clockwise directions to achieve "run" and "tumble." The chemotaxis of bacteria is regulated by a network of interacting proteins. The sensory signal is processed and transmitted to the flagellar motor by cytoplasmic proteins. Bacterial chemotaxis plays an important role in many biological processes such as biofilm formation, quorum sensing, bacterial pathogenesis, and host infection. Bacterial chemotaxis can be applied for bioremediation, horizontal gene transfer, drug delivery, or maybe some other industry in near future. This review contains an overview of bacterial chemotaxis, recent findings of the physiological importance of bacterial chemotaxis in other biological processes, and the application of bacterial chemotaxis.

Neutrophil specific granule and NETosis defects in gray platelet syndrome

AbstractGray platelet syndrome (GPS) is an autosomal recessive bleeding disorder characterized by a lack of α-granules in platelets and progressive myelofibrosis. Rare loss-of-function variants in neurobeachin-like 2 (NBEAL2), a member of the family of beige and Chédiak-Higashi (BEACH) genes, are causal of GPS. It is suggested that BEACH domain containing proteins are involved in fusion, fission, and trafficking of vesicles and granules. Studies in knockout mice suggest that NBEAL2 may control the formation and retention of granules in neutrophils. We found that neutrophils obtained from the peripheral blood from 13 patients with GPS have a normal distribution of azurophilic granules but show a deficiency of specific granules (SGs), as confirmed by immunoelectron microscopy and mass spectrometry proteomics analyses. CD34+ hematopoietic stem cells (HSCs) from patients with GPS differentiated into mature neutrophils also lacked NBEAL2 expression but showed similar SG protein expression as control cells. This is indicative of normal granulopoiesis in GPS and identifies NBEAL2 as a potentially important regulator of granule release. Patient neutrophil functions, including production of reactive oxygen species, chemotaxis, and killing of bacteria and fungi, were intact. NETosis was absent in circulating GPS neutrophils. Lack of NETosis is suggested to be independent of NBEAL2 expression but associated with SG defects instead, as indicated by comparison with HSC-derived neutrophils. Since patients with GPS do not excessively suffer from infections, the consequence of the reduced SG content and lack of NETosis for innate immunity remains to be explored.

Chemotaxis-selective colonization of mangrove rhizosphere microbes on nine different microplastics

Microplastics pollution poses a new threat to the environment of intertidal zone. The sea forest, mangrove, has been polluted by a large number of plastic debris worldwide. To fill the gaps in knowledge of mangrove rhizosphere microbes connected with the ‘plasticsphere’, a semi-controlled in situ exposure experiment for nine different types of microplastics were conducted in mangrove ecosystem. A sign of biodegrading was observed on polyethylene, polyamide 6 and polyvinyl chloride microplastics surface after 3 months exposure. We discovered that the metabolic activities of the dominant bacteria on certain microplastics were related to the specific groups on polymers molecule. The selective colonization may be driven by the chemotaxis of bacteria. Specially, microplastics biofilms of polyethylene, polyamide 6, polyvinyl chloride and expanded polystyrene possess distinctive dominant bacteria assemblages which have great significance in ecosystem processes involving carbon cycle or sulfur cycle. Community of mangrove soil microorganism and microplastic biofilm varies as the seasons changes. As a new niche, microplastics has higher inclusivity to bacteria than surrounding soil. Additionally, pathogens for human beings (Vibrio parahaemolyticus and Escherichia-Shigella) were detected both in microplastics and soil. We stress that the interaction between microplastics and rhizosphere microorganisms may affect the growth and health of mangrove plants. Besides, we point out that mangrove rhizosphere microorganism can be an ideal candidate for plastics-degradation.

Multi-Robot Control Inspired by Bacterial Chemotaxis: Coverage and Rendezvous via Networking of Chemotaxis Controllers

This paper presents networked controllers for the coordination of multi-robot systems, inspired by the chemotaxis of bacteria. Chemotaxis is a biological phenomenon wherein each organism senses the concentration of a chemical in its environment and moves to the highest (or lowest) concentration point. The problem studied herein is a coverage problem, specifically, the problem of finding networked controllers to deploy robots so that they are located uniformly on a given space. To solve this problem, we decompose a global performance index quantifying the achieved degree of coverage into local indices that can be calculated in a distributed manner over the network of robots. By combining this with a controller causing chemotaxis, we present a solution to the coverage problem wherein each robot performs either a forward movement or random rotation based on the local performance index at each time step. Moreover, we extend this solution to rendezvous at an unspecified point. Simulation and experimental results demonstrate that our solution achieves coverage and rendezvous only via the above two types of robot movements and can handle different tasks simply by changing the global performance index, through the appropriate use of the chemotaxis controller.

Simulation of chemotaxis in monotrichous and peritrichous bacteria by a biased random walk model based on observation

Simulation of chemotaxis in monotrichous and peritrichous bacteria by a biased random walk model based on observation

A path-integral characterization of run and tumble motion and chemotaxis of bacteria

Bacteria such as Escherichia coli move about in a series of runs and tumbles: while a run state (straight motion) entails all the flagellar motors spinning in counterclockwise (CCW) mode, a tumble is caused by a shift in the state of one or more motors to clockwise (CW) spinning mode. In the presence of an attractant gradient in the environment, runs in the favourable direction are extended, and this results in a net drift of the organism in the direction of the gradient. Existing theoretical predictions for the drift velocity are limited to exponentially distributed run durations. However, recent experimental observations strongly suggest that the CCW and CW intervals have gamma, rather than exponential distributions. We present a path-integral method which can be used to compute various quantities of interest for the run and tumble walk, with and without chemotaxis, for arbitrary distributions of run and tumble intervals, as power series expansions in the gradient. The effectiveness of the method is demonstrated by deriving a number of existing results for the mean-squared displacement (including motion with directional persistence and algebraically distributed run times) and also chemotactic drift (with exponentially distributed run intervals) in a systematic way, starting from a set of general formulae. New results for chemotactic drift velocity for gamma-distributed run and tumble intervals are then derived, in the limit of weak gradients. Finally, by making use of available experimental data, we make testable predictions for the dependence of the drift velocity on the clockwise bias of the flagellar motor.

Restrictive water condition modifies the root exudates composition during peanut-PGPR interaction and conditions early events, reversing the negative effects on plant growth

Water deficit is one of the most serious environmental factors that affect the productivity of crops in the world. Arachis hypogaea is a legume with a high nutritional value and 70% is cultivated in semi-arid regions. This research aimed to study the effect of water deficit on peanut root exudates composition, analyzing the importance of exudates on peanut-PGPR interaction under restrictive water condition.Peanut seedlings were subjected to six treatments: 0 and 15 mM PEG, in combination with non-inoculated, Bradyrhizobium sp. and Bradyrhizobium-Azospirillum brasilense inoculated treatments. We analyzed the 7-day peanut root exudate in response to a water restrictive condition and the presence of bacterial inocula. Molecular analysis was performed by HPLC, UPLC and GC. Bacteria motility, chemotaxis, bacterial adhesion to peanut roots and peanut growth parameters were analyzed.Restrictive water condition modified the pattern of molecules exuded by roots, increasing the exudation of Naringenin, oleic FA, citric and lactic acid, and stimulation the release of terpenes of known antioxidant and antimicrobial activity. The presence of microorganisms modified the composition of root exudates. Water deficit affected the first events of peanut-PGPR interaction and the root exudates favored bacterial mobility, the chemotaxis and attachment of bacteria to peanut roots.Changes in the profile of molecules exuded by roots allowed A. hypogaea-Bradyrhizobium and A.hypogaea–Bradyrhizobium-Azospirillum interaction thus reversing the negative effects of restrictive water condition on peanut growth. These findings have a future potential application to improve plant-PGPR interactions under water deficit by formulating inoculants containing key molecules exuded during stress.

Interplay between the bacterial protein deacetylase CobB and the second messenger c-di-GMP.

As a ubiquitous bacterial secondary messenger, c-di-GMP plays key regulatory roles in processes such as bacterial motility and transcription regulation. CobB is the Sir2 family protein deacetylase that controls energy metabolism, chemotaxis, and DNA supercoiling in many bacteria. Using an Escherichia coli proteome microarray, we found that c-di-GMP strongly binds to CobB. Further, protein deacetylation assays showed that c-di-GMP inhibits the activity of CobB and thereby modulates the biogenesis of acetyl-CoA. Interestingly, we also found that one of the key enzymes directly involved in c-di-GMP production, DgcZ, is a substrate of CobB. Deacetylation of DgcZ by CobB enhances its activity and thus the production of c-di-GMP. Our work establishes a novel negative feedback loop linking c-di-GMP biogenesis and CobB-mediated protein deacetylation.

Effect of <italic>hfq2</italic> gene in <italic>Aeromonas hydrophila</italic> on biofilm formation

The RNA-binding protein Hfq is an evolutionarily conserved sRNA chaperone protein that can regulate the RNA translation at the post-transcription level and is involved in the regulation of important physiological functions in bacteria. The Aeromonas hydrophila ATCC 7966 genome contains two copies of the hfq gene ( AHA_0924 and AHA_3797 ). AHA_0924 has been found to share pronounced homology with many popular bacterial species and its biological functions was well documented. However, only few bacterial species carry the second hfq gene copy and its role remains largely unknown. To better understand the physiological function of AHA_3797 ( hfq2 ), we first successfully knocked out hfq2 using homologous recombination technology and found that its biofilm formation capability was significantly reduced in this study ( P ∆hfq2 in biofilm status. Our results showed a total of 1538 proteins, including 131 proteins that were up-regulated and 140 proteins that were down-regulated. Selected altered proteins were validated by Western blot analysis, which indicated the proteomics results were reliable. The following Gene Ontology (GO) annotation enrichment analysis in molecular functional clustering showed that up-regulated proteins were mainly involved in receptor activity, transaminase activity, and metal ion binding function, while down-regulated proteins were mainly involved in oxidoreductase activity. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, the most plentiful up-regulated proteins tended to be involved in the biosynthesis of antibiotics, while the down-regulated proteins mainly involved chemotaxis of bacteria. We also found ∆hfq2 caused much of the up-regulation of bacterial iron transport-related proteins, such as colicin I receptor and TonB-dependent copper receptor, and down-regulation of chemotaxis-associated proteins, such as CheY, in the biofilm. The deletion of hfq2 did not result in a significant change in the expression of homologous Hfq protein, suggesting that the roles of both Hfq in the biofilm formation process of A. hydrophila are different. To verify the role of iron homeostasis during hfq2 -mediated biofilm formation, we compared the biofilm formation between ∆hfq2 and the wide-type strain under iron limitation conditions. The results showed that the biofilm formation of the control strain decreased, whereas that of ∆hfq2 i ncreased significantly after the addition of 200 μmol/L ferrous iron chelating 2,2′-dipyridyl (DIP), suggesting that Hfq2 protein negatively regulates intracellular iron homeostasis and affects biofilm formation. In general, this is the first work to confirm that the deletion of the hfq2 gene of A. hydrophila affects the formation of biofilm, suggesting that this gene is not a pseudogene, but rather it plays an important regulatory role in the formation of bacterial biofilm. Establishing the mechanism by which Hfq2 protein regulates bacterial biofilm formation would be of considerable scientific significance and may be helpful in the prevention and control of pathogenic bacteria and the development of new antibacterial strategies in the future.

PID Control as a Process of Active Inference with Linear Generative Models.

In the past few decades, probabilistic interpretations of brain functions have become widespread in cognitive science and neuroscience. In particular, the free energy principle and active inference are increasingly popular theories of cognitive functions that claim to offer a unified understanding of life and cognition within a general mathematical framework derived from information and control theory, and statistical mechanics. However, we argue that if the active inference proposal is to be taken as a general process theory for biological systems, it is necessary to understand how it relates to existing control theoretical approaches routinely used to study and explain biological systems. For example, recently, PID (Proportional-Integral-Derivative) control has been shown to be implemented in simple molecular systems and is becoming a popular mechanistic explanation of behaviours such as chemotaxis in bacteria and amoebae, and robust adaptation in biochemical networks. In this work, we will show how PID controllers can fit a more general theory of life and cognition under the principle of (variational) free energy minimisation when using approximate linear generative models of the world. This more general interpretation also provides a new perspective on traditional problems of PID controllers such as parameter tuning as well as the need to balance performances and robustness conditions of a controller. Specifically, we then show how these problems can be understood in terms of the optimisation of the precisions (inverse variances) modulating different prediction errors in the free energy functional.