Light helps bacteria make important lifestyle decisions

Signaling by a bacterial phytochrome histidine kinase involves a conformational cascade reorganizing the dimeric photoreceptor

Phytochromes (Phys) are a divergent cohort of bili-proteins that detect light through reversible interconversion between dark-adapted Pr and photoactivated Pfr states. While our understandings of downstream events are emerging, it remains unclear how Phys translate light into an interpretable conformational signal. Here, we present models of both states for a dimeric Phy with histidine kinase (HK) activity from the proteobacterium Pseudomonas syringae, which were built from high-resolution cryo-EM maps (2.8-3.4-Å) of the photosensory module (PSM) and its following signaling (S) helix together with lower resolution maps for the downstream output region augmented by RoseTTAFold and AlphaFold structural predictions. The head-to-head models reveal the PSM and its photointerconversion mechanism with strong clarity, while the HK region is interpretable but relatively mobile. Pr/Pfr comparisons show that bilin phototransformation alters PSM architecture culminating in a scissoring motion of the paired S-helices linking the PSMs to the HK bidomains that ends in reorientation of the paired catalytic ATPase modules relative to the phosphoacceptor histidines. This action apparently primes autophosphorylation enroute to phosphotransfer to the cognate DNA-binding response regulator AlgB which drives quorum-sensing behavior through transient association with the photoreceptor. Collectively, these models illustrate how light absorption conformationally translates into accelerated signaling by Phy-type kinases.

The phototrophic metabolic behaviour of Candidatus accumulibacter

The phototrophic capability of Candidatus Accumulibacter (Accumulibacter), a common polyphosphate accumulating organism (PAO) in enhanced biological phosphorus removal (EBPR) systems, was investigated in this study. Accumulibacter is phylogenetically related to the purple bacteria Rhodocyclus from the family Rhodocyclaceae, which belongs to the class Betaproteobacteria. Rhodocyclus typically exhibits both chemoheterotrophic and phototrophic growth, however, limited studies have evaluated the phototrophic potential of Accumulibacter. To address this gap, short and extended light cycle tests were conducted using a highly enriched Accumulibacter culture (95%) to evaluate its responses to illumination. Results showed that, after an initial period of adaptation to light conditions (approximately 4-5 h), Accumulibacter exhibited complete phosphorus (P) uptake by utilising polyhydroxyalkanoates (PHA), and additionally by consuming glycogen, which contrasted with its typical aerobic metabolism. Mass, energy, and redox balance analyses demonstrated that Accumulibacter needed to employ phototrophic metabolism to meet its energy requirements. Calculations revealed that the light reactions contributed to the generation of, at least more than 67% of the ATP necessary for P uptake and growth. Extended light tests, spanning 21 days with dark/light cycles, suggested that Accumulibacter generated ATP through light during initial operation, however, it likely reverted to conventional anaerobic/aerobic metabolism under dark/light conditions due to microalgal growth in the mixed culture, contributing to oxygen production. In contrast, extended light tests with an enriched Tetrasphaera culture, lacking phototrophic genes in its genome, clearly demonstrated that phototrophic P uptake did not occur. These findings highlight the adaptive metabolic capabilities of Accumulibacter, enabling it to utilise phototrophic pathways for energy generation during oxygen deprivation, which holds the potential to advance phototrophic-EBPR technology development.

LOV1 protein of Pseudomonas cichorii JBC1 modulates its virulence and lifestyles in response to blue light

Bacteria perceive light signals via photoreceptors and modulate many physiological and genetic processes. The impacts played by light, oxygen, or voltage (LOV) and blue light (BL) photosensory proteins on the virulence-related traits of plant bacterial pathogens are diverse and complex. In this study, we identified LOV protein (Pc-LOV1) from Pseudomonas cichorii JBC1 (PcJBC1) and characterized its function using LOV1-deficient mutant (JBC1Δlov1). In the dark state, the recombinant Pc-LOV1 protein showed an absorption band in UV-A region with a double peak at 340 nm and 365 nm, and within the blue-region, it exhibited a main absorption at 448 nm along with two shoulder peaks at 425 nm and 475 nm, which is a typical feature of oxidized flavin within LOV domain. The adduct-state lifetime (τrec) of Pc-LOV1 was 67.03 ± 4.34 min at 25 °C. BL negatively influenced the virulence of PcJBC1 and the virulence of JBC1Δlov1 increased irrespective of BL, indicating that Pc-LOV1 negatively regulates PcJBC1 virulence. Pc-LOV1 and BL positively regulated traits relevant to colonization on plant surface, such as adhesion to the plant tissue and biofilm formation. In contrast, swarming motility, exopolysaccharide production, and siderophore synthesis were negatively controlled. Gene expression supported the modulation of bacterial features by Pc-LOV1. Overall, our results suggest that the LOV photosensory system plays crucial roles in the adaptive responses and virulence of the bacterial pathogen PcJBC1. The roles of other photoreceptors, sensing of other wavelengths, and signal networking require further investigation.

Comprehensive analysis of diel rhythmic expression of the medaka toll-like receptor gene family

Several immune-related genes, including Toll-like receptors (TLR), are associated with circadian rhythms in mammals. However, information on the circadian rhythmic expression of TLRs in fish is limited. In this study, we aimed to analyze the regulation of diel oscillations in the expression of TLR genes in Japanese medaka (Oryzias latipes). The expression analysis revealed diel expression patterns of tlr1, tlr5m, tlr21, and clock genes (bmal1 and clock1) under a 12 h light:12 h dark cycle. The clock gene response element (E-box) was identified in the transcriptional regulatory regions of tlr1, tlr5m, and tlr21. Moreover, overexpressed bmal1 and clock1 enhanced expression levels of tlr1, tlr5m, and tlr21 in medaka embryo (OLHdrR-e3) cells. The expression of tlr1, tlr5m, and tlr21 was significantly decreased in OLHdrR-e3 after generating a bmal1 knockdown using a morpholino oligo. These results indicate the regulation of the diel rhythmic expression of several fish TLRs by clock genes.

Blue-light irradiation induced partial nitrification

The role of ray radiation from the sunlight acting on organisms has long-term been investigated. However, how the light with different wavelengths affects nitrification and the involved nitrifiers are still elusive. Here, we found more than 60 % of differentially expressed genes (DEGs) in nitrifiers were observed under irradiation of blue light with wavelengths of 440-480 nm, which were 13.4 % and 20.3 % under red light and white light irradiation respectively. Blue light was more helpful to achieve partial nitrification rather than white light or red light, where ammonium oxidization by ammonia-oxidizing archaea (AOA) with the increased relative abundance from 8.6 % to 14.2 % played a vital role. This was further evidenced by the enhanced TCA cycle, reactive oxygen species (ROS) scavenge and DNA repair capacity in AOA under blue-light irradiation. In contrast, nitrite-oxidizing bacteria (NOB) was inhibited severely to achieve partial nitrification, and the newly discovered encoded blue light photoreceptor proteins made them more sensitive to blue light and hindered cell activity. Ammonia-oxidizing bacteria (AOB) expressed genes for DNA repair capacity under blue-light irradiation, which ensured their tiny impact by light irradiation. This study provided valuable insights into the photosensitivity mechanism of nitrifiers and shed light on the diverse regulatory by light with different radiation wavelengths in artificial systems, broadening our comprehension of the nitrogen cycle on earth.

Effects of different light wavelengths on Bacillus subtilis and Bacillus velezensis, two biocontrol agents isolated from the maize phyllosphere

In previous studies, two strains isolated from the maize phyllosphere were identified as Bacillus subtilis (EM-A7) and Bacillus velezensis (EM-A8) and selected as potential biocontrol agents against Exserohilum turcicum. This study aimed to assess the ability of EM-A7 and EM-A8 to form biofilm and have antagonistic activity under varying light conditions. LED sources were custom-designed so that each corresponded to a given spectrum at a specific photosynthetically active photon flux density. Significant differences were observed in growth parameters (generation time and constant growth rate) under different LED sources. Blue light inhibited the growth of both strains. Red increased k rate in EM-A8, while the g values increased in EM-A7. Red and white light generally increased biofilm formation, and blue light inhibited it. EM-A7 and EM-A8 significantly reduced their ability to swim under blue LED, but it was not affected by red, green, or white light. The ability to swarm was negatively affected. Fungal growth decreased significantly compared to the control when the bacterium growing on the same plate had been previously incubated under red and white light or in the dark. These results indicate that different light wavelengths clearly influenced the aspects assessed in B. subtilis and B. velezensis, with the effects of blue light being overall negative and those of red and white overall positive. Given that, all these factors can be important for the establishment and survival of Bacillus strains on leaves, as well as for their effectiveness against pathogens, light could be a significant factor to consider in the design of biocontrol strategies.

The blue light-dependent LOV-protein LdaP of Dinoroseobacter shibae acts as antirepressor of the PpsR repressor, regulating photosynthetic gene cluster expression

In the marine α-proteobacterium Dinoroseobacter shibae more than 40 genes of the aerobic anoxygenic photosynthesis are regulated in a light-dependent manner. A genome-wide screen of 5,605 clones from a D. shibae transposon library for loss of pigmentation and changes in bacteriochlorophyll absorbance identified 179 mutant clones. The gene encoding the LOV-domain containing protein Dshi_1135 was identified by its colorless phenotype. The mutant phenotype was complemented by the expression of a Dshi_1135-strep fusion protein in trans. The recombinantly produced and chromatographically purified Dshi_1135 protein was able to undergo a blue light-induced photocycle mediated by bound FMN. Transcriptome analyses revealed an essential role for Dshi_1135 in the light-dependent expression of the photosynthetic gene cluster. Interactomic studies identified the repressor protein PpsR as an interaction partner of Dshi_1135. The physical contact between PpsR and the Dshi_1135 protein was verified in vivo using the bacterial adenylate cyclase-based two-hybrid system. In addition, the antirepressor function of the Dshi_1135 protein was demonstrated in vivo testing of a bchF-lacZ reporter gene fusion in a heterologous Escherichia coli-based host system. We therefore propose to rename the Dshi_1135 protein to LdaP (light-dependent antirepressor of PpsR). Using the bacterial two-hybrid system, it was also shown that cobalamin (B12) is essential for the interaction of the antirepressor PpaA with PpsR. A regulatory model for the photosynthetic gene cluster in D. shibae was derived, including the repressor PpsR, the light-dependent antirepressor LdaP and the B12-dependent antirepressor PpaA.

Diurnal cycles drive rhythmic physiology and promote survival in facultative phototrophic bacteria

Bacteria have evolved many strategies to spare energy when nutrients become scarce. One widespread such strategy is facultative phototrophy, which helps heterotrophs supplement their energy supply using light. Our knowledge of the impact that such behaviors have on bacterial fitness and physiology is, however, still limited. Here, we study how a representative of the genus Porphyrobacter, in which aerobic anoxygenic phototrophy is ancestral, responds to different light regimes under nutrient limitation. We show that bacterial survival in stationary phase relies on functional reaction centers and varies depending on the light regime. Under dark-light alternance, our bacterial model presents a diphasic life history dependent on phototrophy: during dark phases, the cells inhibit DNA replication and part of the population lyses and releases nutrients, while subsequent light phases allow for the recovery and renewed growth of the surviving cells. We correlate these cyclic variations with a pervasive pattern of rhythmic transcription which reflects global changes in diurnal metabolic activity. Finally, we demonstrate that, compared to either a phototrophy mutant or a bacteriochlorophyll a overproducer, the wild type strain is better adapted to natural environments, where regular dark-light cycles are interspersed with additional accidental dark episodes. Overall, our results highlight the importance of light-induced biological rhythms in a new model of aerobic anoxygenic phototroph representative of an ecologically important group of environmental bacteria.

Current Trends of Bacterial and Fungal Optoproteins for Novel Optical Applications

Photoproteins, luminescent proteins or optoproteins are a kind of light-response protein responsible for the conversion of light into biochemical energy that is used by some bacteria or fungi to regulate specific biological processes. Within these specific proteins, there are groups such as the photoreceptors that respond to a given light wavelength and generate reactions susceptible to being used for the development of high-novel applications, such as the optocontrol of metabolic pathways. Photoswitchable proteins play important roles during the development of new materials due to their capacity to change their conformational structure by providing/eliminating a specific light stimulus. Additionally, there are bioluminescent proteins that produce light during a heatless chemical reaction and are useful to be employed as biomarkers in several fields such as imaging, cell biology, disease tracking and pollutant detection. The classification of these optoproteins from bacteria and fungi as photoreceptors or photoresponse elements according to the excitation-emission spectrum (UV-Vis-IR), as well as their potential use in novel applications, is addressed in this article by providing a structured scheme for this broad area of knowledge.

Raman Optical Activity of Retinal Chromophore in Sensory Rhodopsin II

Raman optical activity (ROA) spectroscopy was used to study the conformation of the retinal chromophore in sensory rhodopsin II (SRII), which is a blue-green light sensor of microbes. The ROA spectrum consisted of the negative vibrational bands of the chromophore, whose relative intensities are similar to those of the parent Raman spectrum. This spectral feature was explained by the left-handed helical twist of the retinal chromophore on the basis of quantum chemical calculations. On the other hand, we found that the chromophore conformation based on the crystal structures of SRII has a right-handed helical twist, which does not agree with the observation. This specific result suggests that the consistency with chiro-optical properties can be a key criterion for the accurate prediction and/or evaluation of chromophore conformation in retinal-binding proteins.

A novel BLUF photoreceptor modulates the Xanthomonas citri subsp. citri-host plant interaction

Plant-pathogen interaction is influenced by multiple environmental factors, including temperature and light. Recent works have shown that light modulates not only the defense response of plants but also the pathogens virulence. Xanthomonas citri subsp. citri (Xcc) is the bacterium responsible for citrus canker, an important plant disease worldwide. The Xcc genome presents four genes encoding putative photoreceptors: one bacteriophytochrome and three blue light photoreceptors, one LOV and two BLUFs (bluf1: XAC2120 and bluf2: XAC3278). The presence of two BLUFs proteins is an outstanding feature of Xcc. In this work we show that the bluf2 gene is functional. The mutant strain, XccΔbluf2, was constructed demonstrating that BLUF2 regulates swimming-type motility, adhesion to leaves, exopolysaccharide production and biofilm formation, features involved in the Xcc virulence processes. An important aspect during the plant-pathogen interaction is the oxidative response of the host and the consequent reaction of the pathogen. We observed that ROS detoxification is regulated by Xcc bluf2 gene. The phenotypes of disease in orange plants produced by WT and XccΔbluf2 strains were evaluated, observing different phenotypes. Altogether, these results show that BLUF2 negatively regulates virulence during citrus canker. This work constitutes the first report on BLUF-like receptors in plant pathogenic bacteria.

Gas and light: triggers of c-di-GMP-mediated regulation

The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to sensory domains, their activities are likely controlled by environmental signals, thereby altering cellular c-di-GMP levels and regulating bacterial adaptive behaviors. Previous studies on c-di-GMP-mediated regulation mainly focused on downstream signaling pathways, including the identification of CMEs, cellular c-di-GMP receptors, and c-di-GMP-regulated processes. The mechanisms of CME regulation by upstream signaling modules received less attention, resulting in a limited understanding of the c-di-GMP regulatory networks. We review here the diversity of sensory domains related to bacterial CME regulation. We specifically discuss those domains that are capable of sensing gaseous or light signals and the mechanisms they use for regulating cellular c-di-GMP levels. It is hoped that this review would help refine the complete c-di-GMP regulatory networks and improve our understanding of bacterial behaviors in changing environments. In practical terms, this may eventually provide a way to control c-di-GMP-mediated bacterial biofilm formation and pathogenesis in general.

Blue light promotes zero-valent sulfur production in a deep-sea bacterium

Increasing evidence has shown that light exists in a diverse range of deep-sea environments. We unexpectedly found that blue light is necessary to produce excess zero-valent sulfur (ZVS) in Erythrobacter flavus 21-3, a bacterium that has been recently isolated from a deep-sea cold seep. E. flavus 21-3 is able to convert thiosulfate to ZVS using a novel thiosulfate oxidation pathway comprising a thiosulfate dehydrogenase (TsdA) and a thiosulfohydrolase (SoxB). Using proteomic, bacterial two-hybrid and heterologous expression assays, we found that the light-oxygen-voltage histidine kinase LOV-1477 responds to blue light and activates the diguanylate cyclase DGC-2902 to produce c-di-GMP. Subsequently, the PilZ domain-containing protein mPilZ-1753 binds to c-di-GMP and activates TsdA through direct interaction. Finally, Raman spectroscopy and gene knockout results verified that TsdA and two SoxB homologs cooperate to regulate ZVS production. As ZVS is an energy source for E. flavus 21-3, we propose that deep-sea blue light provides E. flavus 21-3 with a selective advantage in the cold seep, suggesting a previously unappreciated relationship between light-sensing pathways and sulfur metabolism in a deep-sea microorganism.

Anammox bacteria adapt to long-term light irradiation in photogranules

Photogranules composed of algae, nitrifiers, and anammox bacteria are promising for nitrogen removal from wastewater with reduced aeration and carbon emissions. However, it is difficult to be achieved as the potential inhibition of anammox bacteria by light. In this study, a syntrophic algal-partial nitrification/anammox granular sludge process was developed, with a nitrogen removal rate of 294.5 mg N/(L·d). We found the symbiosis in the community promoted the adaptation of anammox bacteria under light, and cross-feeding played an important role. Microalgae in the outer layers of photogranules sheltered most of the light and supplied cofactors and amino acids to promote nitrogen removal. In particular, Myxococcota MYX1 degraded the extracellular proteins produced by microalgae, providing amino acids to the entire bacterial community, which helped anammox bacteria save metabolic energy and adapt to light. Notably, the anammox bacteria Candidatus Brocadia exhibited unique light-sensing potential and adaptations to light irradiation compared with Candidatus Jettenia, including diverse DNA repair, scavenging of reactive oxygen species, cell movement. The phytochrome-like proteins encoded by Candidatus Brocadia further facilitated their spatial positioning and niche partitioning in photogranules. This study provides insights into the response of anammox bacteria in the algae-bacteria symbiosis system and suggests its potential application for carbon-negative nitrogen removal.

Control of light-dependent behaviour in cyanobacteria by the second messenger cyclic di-GMP

Nucleotide-derived signalling molecules control a wide range of cellular processes in all organisms. The bacteria-specific cyclic dinucleotide c-di-GMP plays a crucial role in regulating motility-to-sessility transitions, cell cycle progression, and virulence. Cyanobacteria are phototrophic prokaryotes that perform oxygenic photosynthesis and are widespread microorganisms that colonize almost all habitats on Earth. In contrast to photosynthetic processes that are well understood, the behavioural responses of cyanobacteria have rarely been studied in detail. Analyses of cyanobacterial genomes have revealed that they encode a large number of proteins that are potentially involved in the synthesis and degradation of c-di-GMP. Recent studies have demonstrated that c-di-GMP coordinates many different aspects of the cyanobacterial lifestyle, mostly in a light-dependent manner. In this review, we focus on the current knowledge of light-regulated c-di-GMP signalling systems in cyanobacteria. Specifically, we highlight the progress made in understanding the most prominent behavioural responses of the model cyanobacterial strains Thermosynechococcus vulcanus and Synechocystis sp. PCC 6803. We discuss why and how cyanobacteria extract crucial information from their light environment to regulate ecophysiologically important cellular responses. Finally, we emphasize the questions that remain to be addressed.

Decrypting the multi-functional biological activators and inducers of defense responses against biotic stresses in plants

Plant diseases are still the main problem for the reduction in crop yield and a threat to global food security. Additionally, excessive usage of chemical inputs such as pesticides and fungicides to control plant diseases have created another serious problem for human and environmental health. In view of this, the application of plant growth-promoting rhizobacteria (PGPR) for controlling plant disease incidences has been identified as an eco-friendly approach for coping with the food security issue. In this review, we have identified different ways by which PGPRs are capable of reducing phytopathogenic infestations and enhancing crop yield. PGPR suppresses plant diseases, both directly and indirectly, mediated by microbial metabolites and signaling components. Microbial synthesized anti-pathogenic metabolites such as siderophores, antibiotics, lytic enzymes, hydrogen cyanide, and several others act directly on phytopathogens. The indirect mechanisms of reducing plant disease infestation are caused by the stimulation of plant immune responses known as initiation of systemic resistance (ISR) which is mediated by triggering plant immune responses elicited through pathogen-associated molecular patterns (PAMPs). The ISR triggered in the infected region of the plant leads to the development of systemic acquired resistance (SAR) throughout the plant making the plant resistant to a wide range of pathogens. A number of PGPRs including Pseudomonas and Bacillus genera have proven their ability to stimulate ISR. However, there are still some challenges in the large-scale application and acceptance of PGPR for pest and disease management. Further, we discuss the newly formulated PGPR inoculants possessing both plant growth-promoting activities and plant disease suppression ability for a holistic approach to sustaining plant health and enhancing crop productivity.

Multiomics and optobiotechnological approaches for the development of microalgal strain for production of aviation biofuel and biorefinery

Demand and consumption of fossil fuels is increasing daily, and oil reserves are depleting. Technological developments are required towards developing sustainable renewable energy sources and microalgae are emerging as a potential candidate for various application-driven research. Molecular understanding attained through omics and system biology approach empowering researchers to modify various metabolic pathways of microalgal system for efficient extraction of biofuel and important biomolecules. This review furnish insight into different "advanced approaches" like optogenetics, systems biology and multi-omics for enhanced production of FAS (Fatty Acid Synthesis) and lipids in microalgae and their associated challenges. These new approaches would be helpful in the path of developing microalgae inspired technological platforms for optobiorefinery, which could be explored as source material to produce biofuels and other valuable bio-compounds on a large scale.

Red and Blue Light Differently Influence Actinidia chinensis Performance and Its Interaction with Pseudomonas syringae pv. Actinidiae

Light composition modulates plant growth and defenses, thus influencing plant-pathogen interactions. We investigated the effects of different light-emitting diode (LED) red (R) (665 nm) and blue (B) (470 nm) light combinations on Actinidia chinensis performance by evaluating biometric parameters, chlorophyll a fluorescence, gas exchange and photosynthesis-related gene expression. Moreover, the influence of light on the infection by Pseudomonas syringae pv. actinidiae (Psa), the etiological agent of bacterial canker of kiwifruit, was investigated. Our study shows that 50%R-50%B (50R) and 25%R-75%B (25R) lead to the highest PSII efficiency and photosynthetic rate, but are the least effective in controlling the endophytic colonization of the host by Psa. Monochromatic red light severely reduced ΦPSII, ETR, Pn, TSS and photosynthesis-related genes expression, and both monochromatic lights lead to a reduction of DW and pigments content. Monochromatic blue light was the only treatment significantly reducing disease symptoms but did not reduce bacterial endophytic population. Our results suggest that monochromatic blue light reduces infection primarily by modulating Psa virulence more than host plant defenses.

Blue Light Signaling Regulates Escherichia coli W1688 Biofilm Formation and l-Threonine Production

Escherichia coli biofilm may form naturally on biotic and abiotic surfaces; this represents a promising approach for efficient biochemical production in industrial fermentation. Recently, industrial exploitation of the advantages of optogenetics, such as simple operation, high spatiotemporal control, and programmability, for regulation of biofilm formation has garnered considerable attention. In this study, we used the blue light signaling-induced optogenetic system Magnet in an E. coli biofilm-based immobilized fermentation system to produce l-threonine in sufficient quantity. Blue light signaling significantly affected the phenotype of E. coli W1688. A series of biofilm-related experiments confirmed the inhibitory effect of blue light signaling on E. coli W1688 biofilm. Subsequently, a strain lacking a blue light-sensing protein (YcgF) was constructed via genetic engineering, which substantially reduced the inhibitory effect of blue light signaling on biofilm. A high-efficiency biofilm-forming system, Magnet, was constructed, which enhanced bacterial aggregation and biofilm formation. Furthermore, l-threonine production was increased from 10.12 to 16.57 g/L during immobilized fermentation, and the fermentation period was shortened by 6 h. IMPORTANCE We confirmed the mechanism underlying the inhibitory effects of blue light signaling on E. coli biofilm formation and constructed a strain lacking a blue light-sensing protein; this mitigated the aforementioned effects of blue light signaling and ensured normal fermentation performance. Furthermore, this study elucidated that the blue light signaling-induced optogenetic system Magnet effectively regulates E. coli biofilm formation and contributes to l-threonine production. This study not only enriches the mechanism of blue light signaling to regulate E. coli biofilm formation but also provides a theoretical basis and feasibility reference for the application of optogenetics technology in biofilm-based immobilized fermentation systems.

Genetic, physiological, and cellular heterogeneities of bacterial pathogens in food matrices: Consequences for food safety

In complex food systems, bacteria live in heterogeneous microstructures, and the population displays phenotypic heterogeneities at the single-cell level. This review provides an overview of spatiotemporal drivers of phenotypic heterogeneity of bacterial pathogens in food matrices at three levels. The first level is the genotypic heterogeneity due to the possibility for various strains of a given species to contaminate food, each of them having specific genetic features. Then, physiological heterogeneities are induced within the same strain, due to specific microenvironments and heterogeneous adaptative responses to the food microstructure. The third level of phenotypic heterogeneity is related to cellular heterogeneity of the same strain in a specific microenvironment. Finally, we consider how these phenotypic heterogeneities at the single-cell level could be implemented in mathematical models to predict bacterial behavior and help ensure microbiological food safety.

Exploiting Violet-Blue Light to Kill Campylobacter jejuni: Analysis of Global Responses, Modeling of Transcription Factor Activities, and Identification of Protein Targets

Campylobacter jejuni is a microaerophilic foodborne zoonotic pathogen of worldwide concern as the leading cause of bacterial gastroenteritis. Many strains are increasingly antibiotic resistant and new methods of control are required to reduce food-chain contamination. One possibility is photodynamic inactivation (PDI) using violet-blue (VB) light, to which C. jejuni is highly susceptible. Here, we show that flavin and protoporphyrin IX are major endogenous photosensitizers and that exposure of cells to VB light increases intracellular reactive oxygen species (ROS) to high levels, as indicated by a dichlorodihydrofluorescein reporter. Unusually for an oxygen-respiring bacterium, C. jejuni employs several ROS-sensitive iron-sulfur cluster enzymes in central metabolic pathways; we show that VB light causes rapid inactivation of both pyruvate and 2-oxoglutarate oxidoreductases, thus interrupting the citric acid cycle. Cells exposed to VB light also lose heme from c-type cytochromes, restricting electron transport, likely due to irreversible oxidation of heme-ligating cysteine residues. Evaluation of global gene expression changes by RNAseq and probabilistic modeling showed a two-stage protein damage/oxidative stress response to VB light, driven by specific regulators, including HspR, PerR, Fur, and RacR. Deletion mutant analysis showed that superoxide dismutase and the cytochrome CccA were particularly important for VB light survival and that abolishing repression of chaperones and oxidative stress resistance genes by HcrA, HspR, or PerR increased tolerance to VB light. Our results explain the high innate sensitivity of C. jejuni to VB light and provide new insights that may be helpful in exploiting PDI for novel food-chain interventions to control this pathogen. IMPORTANCE Campylobacteriosis caused by C. jejuni is one of the most widespread zoonotic enteric diseases worldwide and represents an enormous human health and economic burden, compounded by the emergence of antibiotic-resistant strains. New interventions are urgently needed to reduce food-chain contamination. Although UV light is well known to be bactericidal, it is highly mutagenic and problematic for continuous exposure in food production facilities; in contrast, narrow spectrum violet-blue (VB) light is much safer. We confirmed that C. jejuni is highly susceptible to VB light and then identified some of the global regulatory networks involved in responding to photo-oxidative damage. The identification of damaged cellular components underpins efforts to develop commercial applications of VB light-based technologies.

Light/Dark and Temperature Cycling Modulate Metabolic Electron Flow in Pseudomonas aeruginosa Biofilms

Sunlight drives phototrophic metabolism, which affects redox conditions and produces substrates for nonphototrophs. These environmental parameters fluctuate daily due to Earth’s rotation, and nonphototrophic organisms can therefore benefit from the ability to respond to, or even anticipate, such changes. Circadian rhythms, such as daily changes in body temperature, in host organisms can also affect local conditions for colonizing bacteria. Here, we investigated the effects of light/dark and temperature cycling on biofilms of the opportunistic pathogen Pseudomonas aeruginosa PA14. We grew biofilms in the presence of a respiratory indicator dye and found that enhanced dye reduction occurred in biofilm zones that formed during dark intervals and at lower temperatures. This pattern formation occurred with cycling of blue, red, or far-red light, and a screen of mutants representing potential sensory proteins identified two with defects in pattern formation, specifically under red light cycling. We also found that the physiological states of biofilm subzones formed under specific light and temperature conditions were retained during subsequent condition cycling. Light/dark and temperature cycling affected expression of genes involved in primary metabolic pathways and redox homeostasis, including those encoding electron transport chain components. Consistent with this, we found that cbb₃-type oxidases contribute to dye reduction under light/dark cycling conditions. Together, our results indicate that cyclic changes in light exposure and temperature have lasting effects on redox metabolism in biofilms formed by a nonphototrophic, pathogenic bacterium.

Light alters microbiota and electron transport: Evidence for enhanced mesophilic digestion of municipal sludge

Light as an environmental factor can affect the process of anaerobic digestion, but there is no systematic study in municipal wastewater sludge mesophilic digestion. In this study, the effects of light on the performance of the anaerobic digestion system and photo-anaerobic microbiota (PAM) were evaluated in lighted anaerobic batch digesters (LABRs). The methane yield from the reactor under the dark condition (LABR0) was 179.2 mL CH₄/g COD, which was lower than 305.4 mL CH₄/g COD and 223.0 mL CH₄/g COD (n = 3, p < 0.05) from reactors under the light intensity of 3600 lm (LABR1) and 7200 lm (LABR2), respectively. The dominant genera in the bacterial and archaeal communities were Bacillus and Methanosarcina under light conditions, Enterococcus and Methanobacterium under dark conditions. And these two bacteria acted as electroactive bacterial genera, indicating that light changes the combination of direct interspecies electron transfer (DIET) microbial partners and activates the DIET pathway for methane production. The electron conduction pathways analysis further suggests that biological DIET (bDIET) between microbial biomass, rather than DIET via conductive material (cDIET) between microbes and conductive materials, is promoted and behaves as the dominant factor enhancing methane production under light conditions. The morphology of microorganisms and the amount and properties of EPS corroborate these views. Our findings are guided to anaerobic digester constructions under the outdoor environment with light exposure.

Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering

Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light-absorbing (Pr)-to-far-red light-absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa. Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an "II"-framed close form of the Pfr state to an "O"-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.

Light Regulates Acinetobacter baumannii Chromosomal and pAB3 Plasmid Genes at 37°C

The opportunistic pathogen A. baumannii has a remarkable capacity to persist in the hospital environment and cause devastating human infections. This capacity can be attributed partly to the sensing and regulatory systems that enable this pathogen to modify its physiology based on environmental cues. One of the signals that A. baumannii senses and responds to is light through the sensing and regulatory roles of the BlsA photoreceptor protein in cells cultured at temperatures below 30°C. This report presents evidence that a light stimulon is operational at 37°C, a condition at which the BlsA production and activity are drastically impaired. Global transcriptional analysis showed that the 37°C light stimulon includes the differential expression of chromosomal genes encoding a wide range of functions that are known to be involved in the adaptation to different metabolic conditions, as well as virulence and persistence in the host and the medical environment. Unexpectedly, the 37°C light stimulon also includes the differential expression of conjugation functions encoded by pAB3 plasmid genes. Our work further demonstrates that the TetR1 and H-NS regulators encoded by this conjugative plasmid control the expression of H₂O₂ resistance and surface motility, respectively. Furthermore, our data showed that pAB3 has an overall negative effect on the expression of these phenotypes and plays no significant virulence role. Although the nature of the bacterial factors and the mechanisms by which the regulation is attained at 37°C remain unknown, taken together, our work expands the current knowledge about light sensing and gene regulation in A. baumannii. IMPORTANCE As a facultative pathogen, Acinetobacter baumannii persists in various environments by sensing different environmental cues, including light. This report provides evidence of light-dependent regulation at 37°C of the expression of genes coding for a wide range of functions, including those involved in the conjugation of the pAB3 plasmid. Although this plasmid affects the expression of virulence traits when tested under laboratory conditions, it does not have a significant impact when tested using ex vivo and in vivo experimental models. These findings provide a better understanding of the interplay between light regulation and plasmid persistence in the pathobiology of A. baumannii.

A Deep-Sea Bacterium Senses Blue Light via a BLUF-Dependent Pathway

Light is a ubiquitous energy source and environmental signal that broadly impacts the lifestyle of a large number of photosynthetic/nonphotosynthetic microorganisms living in the euphotic layer. However, the responses of deep-sea microbes to light are largely unknown, even though blue light is proposed to be distributed in the deep ocean. Here, we successfully cultured a novel bacterial species, named Spongiibacter nanhainus CSC3.9, from deep-sea cold seep samples by a blue light induction approach. The growth of strain CSC3.9 was obviously promoted by the illumination of blue light. We next determined BLUF (a typical blue light photoreceptor) was the most essential factor directing light sensing of strain CSC3.9 through a combined proteomic and genetic method. The function of light sensing mediated by BLUF was further confirmed by the in vitro-synthesized protein. Notably, homologs of BLUF widely existed across the marine microorganisms (containing Spongiibacter species) derived from different environments, including cold seeps. This strongly indicates that the distribution of light utilization by the nonphototrophic bacteria living in the ocean is broad and has been substantially underestimated.

IMPORTANCE Extensive studies have been conducted to explore the mechanisms of light sensing and utilization by microorganisms that live in the photic zone. Strikingly, accumulated evidence shows that light is distributed in the deep biosphere. However, the existence and process of light sensing and utilization by microbes inhabiting the deep ocean have been seldom reported. In the present study, a novel bacterial strain, Spongiibacter nanhainus CSC3.9, was enriched and purified from a deep-sea cold seep sample through a blue light induction method. Combined with genomic, proteomic, genetic, and biochemical approaches, the mechanism of this novel strain sensing blue light through a BLUF-dependent pathway was detailed. Our study provides a good model to study the mechanisms of light sensing mediated by deep-sea nonphototrophic bacteria.

Dining in Blue Light Impairs the Appetite of Some Leaf Epiphytes

Background: The phyllosphere is subjected to fluctuating abiotic conditions. This study examined the phenotypic plasticity (PP) of four selected non-phototrophic phyllosphere bacteria [control strain: Pseudomonas sp. DR 5-09; Pseudomonas agarici, Bacillus thuringiensis serovar israeliensis (Bti), and Streptomyces griseoviridis (SG)] regarding their respiration patterns and surfactant activity as affected by light spectrum and nutrient supply.

Methods: The PP of the strains was examined under four light regimes [darkness (control); monochromatic light-emitting diodes (LED) at 460 nm (blue) and 660 nm (red); continuously polychromatic white LEDs], in the presence of 379 substrates and conditions.

Results: Light treatment affected the studied bacterial strains regarding substrate utilization (Pseudomonas strains > SG > Bti). Blue LEDs provoked the most pronounced impact on the phenotypic reaction norms of the Pseudomonas strains and Bti. The two Gram-positive strains Bti and SG, respectively, revealed inconsistent biosurfactant formation in all cases. Biosurfactant formation by both Pseudomonas strains was supported by most substrates incubated in darkness, and blue LED exposure altered the surface activity profoundly. Blue and white LEDs enhanced biofilm formation in PA in highly utilized C-sources. Putative blue light receptor proteins were found in both Pseudomonas strains, showing 91% similarity with the sequence from NCBI accession number WP_064119393.

Conclusion: Light quality–nutrient interactions affect biosurfactant activity and biofilm formation of some non-phototrophic phyllosphere bacteria and are, thus, crucial for dynamics of the phyllosphere microbiome.

Natural diversity provides a broad spectrum of cyanobacteriochrome-based diguanylate cyclases

Cyanobacteriochromes (CBCRs) are spectrally diverse photosensors from cyanobacteria distantly related to phytochromes that exploit photoisomerization of linear tetrapyrrole (bilin) chromophores to regulate associated signaling output domains. Unlike phytochromes, a single CBCR domain is sufficient for photoperception. CBCR domains that regulate the production or degradation of cyclic nucleotide second messengers are becoming increasingly well characterized. Cyclic di-guanosine monophosphate (c-di-GMP) is a widespread small-molecule regulator of bacterial motility, developmental transitions, and biofilm formation whose biosynthesis is regulated by CBCRs coupled to GGDEF (diguanylate cyclase) output domains. In this study, we compare the properties of diverse CBCR-GGDEF proteins with those of synthetic CBCR-GGDEF chimeras. Our investigation shows that natural diversity generates promising candidates for robust, broad spectrum optogenetic applications in live cells. Since light quality is constantly changing during plant development as upper leaves begin to shade lower leaves-affecting elongation growth, initiation of flowering, and responses to pathogens, these studies presage application of CBCR-GGDEF sensors to regulate orthogonal, c-di-GMP-regulated circuits in agronomically important plants for robust mitigation of such deleterious responses under natural growing conditions in the field.

Photo-biodegradation of imidacloprid under blue light-emitting diodes with bacteria and co-metabolic regulation

Imidacloprid (IMI) is existence in the soil environment with a half-life habitually more than hundred days. This study targets to determine, identify and characterize photo-biodegradation bacteria from neonicotinoids (NEOs) contaminated agricultural field soils. The sub-surface soil had a higher level contamination of NEOs, in specifically greater concentration of IMI (3445.2 ± 0.09 μg/g) and thiacloprid (4084.4 ± 0.09 μg/g) has been found. Three bacteria Ralstonia pickettii (PBMS-2), Bacillus cereus (PBMS-3) and Shinella zoogloeoides (PBMS-4) was identified from soil-free stable enrichment cultures. The biodegradability of IMI (50 mg L^-1) by three bacteria under different colors of light-emitting diodes (LEDs) with a constant 12 V power supply was tested and found that the blue-LEDs had greatest efficiency in supporting biodegradation of IMI which is called photo-biodegradation. In specific, the rate of photo-biodegradation of IMI by Ralstonia pickettii (87%), Bacillus cereus (80%) and Shinella zoogloeoides (80%) was measured. Besides this study also tested the effect of aeration (rpm), pH, and temperature on photo-biodegradation of IMI. There were seven intermediate metabolites were measured as biodegradation products of IMI under photo-biodegradation conditions and they are; IMI-urea, IMI-desnitro, 6-chloronicotinic acid, 6-hydroxy nicotinic acid, IMI- aminoguanidine, IMI-nitrosoguanidine and 4,5-hydroxy IMI, these metabolites are may non-toxic to the environment.

Genetic Factors Affect the Survival and Behaviors of Selected Bacteria during Antimicrobial Blue Light Treatment

Antimicrobial resistance is a global, mounting and dynamic issue that poses an immediate threat to human, animal, and environmental health. Among the alternative antimicrobial treatments proposed to reduce the external use of antibiotics is electromagnetic radiation, such as blue light. The prevailing mechanistic model is that blue light can be absorbed by endogenous porphyrins within the bacterial cell, inducing the production of reactive oxygen species, which subsequently inflict oxidative damages upon different cellular components. Nevertheless, it is unclear whether other mechanisms are involved, particularly those that can affect the efficacy of antimicrobial blue light treatments. In this review, we summarize evidence of inherent factors that may confer protection to a selected group of bacteria against blue light-induced oxidative damages or modulate the physiological characteristics of the treated bacteria, such as virulence and motility. These include descriptions of three major photoreceptors in bacteria, chemoreceptors, SOS-dependent DNA repair and non-SOS protective mechanisms. Future directions are also provided to assist with research efforts to increase the efficacy of antimicrobial blue light and to minimize the development of blue light-tolerant phenotypes.

Antibiofilm and cytotoxic effect of 3,3'-dihydroxycurcumin (DHC) as photosensitizer agent in antimicrobial photodynamic therapy for endodontic purposes

BACKGROUND

Curcuminoids have been designed not only to improve chemical and metabolic stability of curcumin (CUR), but also to increase its antimicrobial activity, without effecting its ability as photosensitizer agent in antimicrobial photodynamic therapy (aPDT) with light emitting diode (LED). This study evaluated the antimicrobial and antibiofilm action of curcumin analog DHC (or 3,3'-dihydroxycurcumin), submitted or not to LED irradiation, on microorganisms of endodontic importance and its influence on fibroblasts viability.

METHODS

DHC was synthetized by modified Pablon's methodology and the experiments were conducted under irradiation or not with indium gallium nitride-based LED (440-480nm, 100 mW/cm², 0.78 cm²,60 s). The antimicrobial activity of CUR and DHC were determined by the Minimum Inhibitory and Bactericidal Concentration assays against Gram-positive and Gram-negative bacteria and the effect of both compounds on fibroblast viability was tested using colorimetric assays. They were also evaluated on 72h and 7days single-species biofilms and on 14 days multispecies biofilms formed inside dentin tubules by bacterial colonies counts and confocal microscopy, respectively. Data were analyzed statistically considering p<0.05.

RESULTS

DHC had bactericidal effect against all bacteria tested higher than CUR, in planktonic conditions. CUR and DHC (at 39 and 19 μg/mL, respectively) were cytocompatible and LED irradiation reduced fibroblast viability, regardless of compound. CUR and DHC reduced the growth of single-species biofilms and the effect of aPDT was bacteria dependent. DHC reduced more than 70% of microorganisms from multispecies biofilms, superior to CUR effect.

CONCLUSIONS

DHC showed low cytotoxicity and antibiofilm effect similar to curcumin, when submitted or not to aPDT, and could be further explored as a bioactive compound for endodontic purposes.

Absence of Light Exposure Increases Pathogenicity of Pseudomonas aeruginosa Pneumonia-Associated Clinical Isolates

Pseudomonas aeruginosa can alter its lifestyle in response to changes in environmental conditions. The switch to a pathogenic host-associated lifestyle can be triggered by the luminosity settings, resorting to at least one photoreceptor which senses light and regulates cellular processes. This study aimed to address how light exposure affects the dynamic and adaptability of two P. aeruginosa pneumonia-associated isolates, HB13 and HB15. A phenotypic characterization of two opposing growth conditions, constant illumination and intensity of full-spectrum light and total absence of light, was performed. Given the nature of P. aeruginosa pathogenicity, distinct fractions were characterized, and its inherent pathogenic potential screened by comparing induced morphological alterations and cytotoxicity against human pulmonary epithelial cells (A549 cell line). Growth in the dark promoted some virulence-associated traits (e.g., pigment production, LasA proteolytic activity), which, together with higher cytotoxicity of secreted fractions, supported an increased pathogenic potential in conditions that better mimic the lung microenvironment of P. aeruginosa. These preliminary findings evidenced that light exposure settings may influence the P. aeruginosa pathogenic potential, likely owing to differential production of virulence factors. Thus, this study raised awareness towards the importance in controlling light conditions during bacterial pathogenicity evaluation approaches, to more accurately interpret bacterial responses.

Molecular and structural facets of c-di-GMP signalling associated with biofilm formation in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic human pathogen and is the primary cause of nosocomial infections. Biofilm formation by this organism results in chronic and hard to eradicate infections. The intracellular signalling molecule bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is a secondary messenger in bacterial cells crucial for motile to sessile transition. The signalling pathway components encompass two classes of enzymes with antagonistic activities, the diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) that regulate the cellular levels of c-di-GMP at distinct stages of biofilm initiation, maturation and dispersion. This review summarizes the structural analysis and functional studies of the DGCs and PDEs involved in biofilm regulation in P. aeruginosa. In addition, we also describe the effector proteins that sense the perturbations in c-di-GMP levels to elicit a functional output. Finally, we discuss possible mechanisms that allow the dynamic levels of c-di-GMP to regulate cognate cellular response. Uncovering the details of the regulation of the c-di-GMP signalling pathway is vital for understanding the behaviour of the pathogen and characterization of novel targets for anti-biofilm interventions.

Light modulates important physiological features of Ralstonia pseudosolanacearum during the colonization of tomato plants

Ralstonia pseudosolanacearum GMI1000 (Rpso GMI1000) is a soil-borne vascular phytopathogen that infects host plants through the root system causing wilting disease in a wide range of agro-economic interest crops, producing economical losses. Several features contribute to the full bacterial virulence. In this work we study the participation of light, an important environmental factor, in the regulation of the physiological attributes and infectivity of Rpso GMI1000. In silico analysis of the Rpso genome revealed the presence of a Rsp0254 gene, which encodes a putative blue light LOV-type photoreceptor. We constructed a mutant strain of Rpso lacking the LOV protein and found that the loss of this protein and light, influenced characteristics involved in the pathogenicity process such as motility, adhesion and the biofilms development, which allows the successful host plant colonization, rendering bacterial wilt. This protein could be involved in the adaptive responses to environmental changes. We demonstrated that light sensing and the LOV protein, would be used as a location signal in the host plant, to regulate the expression of several virulence factors, in a time and tissue dependent way. Consequently, bacteria could use an external signal and Rpsolov gene to know their location within plant tissue during the colonization process.

Light-Triggered Carotenogenesis in Myxococcus xanthus: New Paradigms in Photosensory Signaling, Transduction and Gene Regulation

Myxobacteria are Gram-negative δ-proteobacteria found predominantly in terrestrial habitats and often brightly colored due to the biosynthesis of carotenoids. Carotenoids are lipophilic isoprenoid pigments that protect cells from damage and death by quenching highly reactive and toxic oxidative species, like singlet oxygen, generated upon growth under light. The model myxobacterium Myxococcus xanthus turns from yellow in the dark to red upon exposure to light because of the photoinduction of carotenoid biosynthesis. How light is sensed and transduced to bring about regulated carotenogenesis in order to combat photooxidative stress has been extensively investigated in M. xanthus using genetic, biochemical and high-resolution structural methods. These studies have unearthed new paradigms in bacterial light sensing, signal transduction and gene regulation, and have led to the discovery of prototypical members of widely distributed protein families with novel functions. Major advances have been made over the last decade in elucidating the molecular mechanisms underlying the light-dependent signaling and regulation of the transcriptional response leading to carotenogenesis in M. xanthus. This review aims to provide an up-to-date overview of these findings and their significance.

Blue and red light photoemitters as approach to inhibit Staphylococcus aureus and Pseudomonas aeruginosa growth

The ability of pathogenic bacteria acquire resistance to the existing antibiotics has long been considered a dangerous health risk threat. Currently, the use of visible light has been considered a new approach to treat bacterial infections as an alternative to antibiotics. Herein, we investigated the antimicrobial effect of two range of visible light, blue and red, on Staphylococcus aureus and Pseudomonas aeruginosa, two pathogenic bacterial commonly found in healthcare settings-acquired infections and responsible for high rate of morbidity and mortality. Bacterial cultures were exposed to blue or red light (470 nm and 660 nm) provided by light-emitting diodes - LED. The fluencies and irradiance used for blue and red light were 284.90 J/cm2, 13.19 mW/cm2 and 603.44 J/cm2, 27.93 mW/cm2 respectively. Different experimental approaches were used to determine the optimal conditions of light application. Only exposure to blue light for 6 hours was able to inhibit about 75% in vitro growth of both bacterial species after 24 hours. The surviving exposed bacteria formed colonies significantly smaller than controls, however, these bacteria were able to resume growth after 48 hours. Blue light was able to inhibit bacterial growth upon inoculation in both saline solution and BHI culture medium. We can conclude that blue light, but not red light, is capable of temporarily retarding the growth of gram negative and gram positive bacteria.

Resolving Structural Changes of Photoreceptors in Living Escherichia coli via In-cell Infrared Difference Spectroscopy

Several in-cell spectroscopic techniques have been developed recently to investigate the structure and mechanism of proteins in their native environment. Conditions in vivo differ dramatically from those selected for in vitro experiments. Accordingly, the cellular environment can affect the protein mechanism for example by molecular crowding or binding of small molecules. Fourier transform infrared (FTIR) difference spectroscopy is a well-suited method to study the light-induced structural responses of photoreceptors including changes in cofactor, side chains and secondary structure. Here, we describe a protocol to study the response of cofactor and protein in living E. coli cells via in-cell infrared difference (ICIRD) spectroscopy using the attenuated total reflection (ATR) configuration. Proteins are overexpressed in E. coli, the cells are transferred into saline solution and the copy number per cell is determined using fluorescence spectroscopy. The suspension is centrifuged and the concentrated cells transferred onto the ATR cell inside the FTIR spectrometer. The thermostatted cell is sealed and illuminated from the top with an LED. Intensity spectra are recorded before and after illumination to generate the difference spectrum of the receptor inside the living cell. With ICIRD spectroscopy, structural changes of soluble photoreceptors are resolved in a near-native environment. The approach works in H₂O at ambient conditions, is label free, without any limitations in protein size and does not require any purification step. Graphic abstract: In-cell infrared difference spectroscopy on photoreceptors in living E. coli using attenuated total reflection.

Light exposure interferes with electroactive biofilm enrichment and reduces extracellular electron transfer efficiency

Light plays a vital role in shaping the structure of natural biofilms, but the effect of light on electroactive biofilm (EAB) has not been systematically studied. Herein, the influence of light on the formation of EAB was investigated. The EAB grown in darkness was more electroactive (EAB-0) with a peak current of ∼4.5 A/m², which was 196 and 5556 times higher than EABs formed under light intensities of 600 (EAB-600) and 1200 lux (EAB-1200). A thin EAB (30 μm) with spherical pink aggregates was obtained after 13 days in the darkness, comparing to a dense and flat biofilm grown under light conditions. Although the biomass in EAB-1200 (38.5 ± 1.6 mg/L) was 3 times larger than that in EAB-0 (11.4 ± 1.8 mg/L), the degradation of substrate was not sufficient. EAB-0 contained 85% Geobacter species, while the Rhodopseudomonas species made up 66% and 75% of EAB-600 and EAB-1200, respectively. The polysaccharides produced by EAB-1200 was 4801 ± 253 mg/m², which were 2.3 times higher than 2073 ± 160 mg/m² of EAB-0, resulting in lower electro-conductivity of the extracellular polymeric substances (EPS) under light conditions. Our findings confirmed that the light exposure affected EAB performance by altering the microbial components, electron transfer capacity, and biofilm morphology, which can be used in predictions of the formation and properties of engineered EAB in outdoor environments.

Antimicrobial Blue Light versus Pathogenic Bacteria: Mechanism, Application in the Food Industry, Hurdle Technologies and Potential Resistance

Blue light primarily exhibits antimicrobial activity through the activation of endogenous photosensitizers, which leads to the formation of reactive oxygen species that attack components of bacterial cells. Current data show that blue light is innocuous on the skin, but may inflict photo-damage to the eyes. Laboratory measurements indicate that antimicrobial blue light has minimal effects on the sensorial and nutritional properties of foods, although future research using human panels is required to ascertain these findings. Food properties also affect the efficacy of antimicrobial blue light, with attenuation or enhancement of the bactericidal activity observed in the presence of absorptive materials (for example, proteins on meats) or photosensitizers (for example, riboflavin in milk), respectively. Blue light can also be coupled with other treatments, such as polyphenols, essential oils and organic acids. While complete resistance to blue light has not been reported, isolated evidence suggests that bacterial tolerance to blue light may occur over time, especially through gene mutations, although at a slower rate than antibiotic resistance. Future studies can aim at characterizing the amount and type of intracellular photosensitizers across bacterial species and at assessing the oxygen-independent mechanism of blue light-for example, the inactivation of spoilage bacteria in vacuum-packed meats.

The adherence-associated Fdp fasciclin I domain protein of the biohydrogen producer Rhodobacter sphaeroides is regulated by the global Prr pathway

Expression of fdp, encoding a fasciclin I domain protein important for adherence in the hydrogen-producing bacterium Rhodobacter sphaeroides, was investigated under a range of conditions to gain insights into optimization of adherence for immobilization strategies suitable for H₂ production. The fdp promoter was linked to a lacZ reporter and expressed in wild type and in PRRB and PRRA mutant strains of the Prr regulatory pathway. Expression was significantly negatively regulated by Prr under all conditions of aerobiosis tested including anaerobic conditions (required for H₂ production), and aerobically regardless of growth phase, growth medium complexity or composition, carbon source, heat and cold shock and dark/light conditions. Negative fdp regulation by Prr was reflected in cellular levels of translated Fdp protein. Since Prr is required directly for nitrogenase expression, we propose optimization of Fdp-based adherence in R. sphaeroides for immobilized biohydrogen production by inactivation of the PrrA binding site(s) upstream of fdp.

Light Response of Pseudomonas putida KT2440 Mediated by Class II LitR, a Photosensor Homolog

Pseudomonas putida KT2440 retains three homologs (PplR1 to PplR3) of the LitR/CarH family, an adenosyl B₁₂-dependent light-sensitive MerR family transcriptional regulator. Transcriptome analysis revealed the existence of a number of photoinducible genes, including pplR1, phrB (encoding DNA photolyase), ufaM (furan-containing fatty acid synthase), folE (GTP cyclohydrolase I), cryB (cryptochrome-like protein), and multiple genes without annotated/known function. Transcriptional analysis by quantitative reverse transcription-PCR with knockout mutants of pplR1 to pplR3 showed that a triple knockout completely abolished the light-inducible transcription in P. putida, which indicates the occurrence of ternary regulation of PplR proteins. A DNase I footprint assay showed that PplR1 protein specifically binds to the promoter regions of light-inducible genes, suggesting a consensus PplR1-binding direct repeat, 5'-T(G/A)TACAN₁₂TGTA(C/T)A-3'. The disruption of B₁₂ biosynthesis cluster did not affect the light-inducible transcription; however, disruption of ppSB1-LOV (where LOV indicates "light, oxygen, or voltage") and ppSB2-LOV, encoding blue light photoreceptors adjacently located to pplR3 and pplR2, respectively, led to the complete loss of light-inducible transcription. Overall, the results suggest that the three PplRs and two PpSB-LOVs cooperatively regulate the light-inducible gene expression. The wide distribution of the pplR/ppSB-LOV cognate pair homologs in Pseudomonas spp. and related bacteria suggests that the response and adaptation to light are similarly regulated in the group of nonphototrophic bacteria.IMPORTANCE The LitR/CarH family is a new group of photosensor homologous to MerR-type transcriptional regulators. Proteins of this family are distributed to various nonphototrophic bacteria and grouped into at least five classes (I to V). Pseudomonas putida retaining three class II LitR proteins exhibited a genome-wide response to light. All three paralogs were functional and mediated photodependent activation of promoters directing the transcription of light-induced genes or operons. Two LOV (light, oxygen, or voltage) domain proteins, adjacently encoded by two litR genes, were also essential for the photodependent transcriptional control. Despite the difference in light-sensing mechanisms, the DNA binding consensus of class II LitR [T(G/A)TA(C/T)A] was the same as that of class I. This is the first study showing the actual involvement of class II LitR in light-induced transcription.

Bacteriophytochrome from Magnetospirillum magneticum affects phototactic behavior in response to light

Phytochromes are a class of photoreceptors found in plants and in some fungi, cyanobacteria, and photoautotrophic and heterotrophic bacteria. Although phytochromes have been structurally characterized in some bacteria, their biological and ecological roles in magnetotactic bacteria remain unexplored. Here, we describe the biochemical characterization of recombinant bacteriophytochrome (BphP) from magnetotactic bacteria Magnetospirillum magneticum AMB-1 (MmBphP). The recombinant MmBphP displays all the characteristic features, including the property of binding to biliverdin (BV), of a genuine phytochrome. Site-directed mutagenesis identified that cysteine-14 is important for chromophore covalent binding and photoreversibility. Arginine-240 and histidine-246 play key roles in binding to BV. The N-terminal photosensory core domain of MmBphP lacking the C-terminus found in other phytochromes is sufficient to exhibit the characteristic red/far-red-light-induced fast photoreversibility of phytochromes. Moreover, our results showed MmBphP is involved in the phototactic response, suggesting its conservative role as a stress protectant. This finding provided us a better understanding of the physiological function of this group of photoreceptors and photoresponse of magnetotactic bacteria.

Light-Mediated Decreases in Cyclic di-GMP Levels Inhibit Structure Formation in Pseudomonas aeruginosa Biofilms

Light is known to trigger regulatory responses in diverse organisms, including slime molds, animals, plants, and phototrophic bacteria. However, light-dependent processes in nonphototrophic bacteria, and those of pathogens in particular, have received comparatively little research attention. In this study, we examined the impact of light on multicellular development in Pseudomonas aeruginosa, a leading cause of biofilm-based bacterial infections. We grew P. aeruginosa strain PA14 in a colony morphology assay and found that growth under prolonged exposure to low-intensity blue light inhibited biofilm matrix production and thereby the formation of vertical biofilm structures (i.e., "wrinkles"). Light-dependent inhibition of biofilm wrinkling was correlated with low levels of cyclic di-GMP (c-di-GMP), consistent with the role of this signal in stimulating matrix production. A screen of enzymes with the potential to catalyze c-di-GMP synthesis or degradation identified c-di-GMP phosphodiesterases that contribute to light-dependent inhibition of biofilm wrinkling. One of these, RmcA, was previously characterized by our group for its role in mediating the effect of redox-active P. aeruginosa metabolites called phenazines on biofilm wrinkle formation. Our results suggest that an RmcA sensory domain that is predicted to bind a flavin cofactor is involved in light-dependent inhibition of wrinkling. Together, these findings indicate that P. aeruginosa integrates information about light exposure and redox state in its regulation of biofilm development.IMPORTANCE Light exposure tunes circadian rhythms, which modulate the immune response and affect susceptibility to infection in plants and animals. Though molecular responses to light are defined for model plant and animal hosts, analogous pathways that function in bacterial pathogens are understudied. We examined the response to light exposure in biofilms (matrix-encased multicellular assemblages) of the nonphotosynthetic bacterium Pseudomonas aeruginosa We found that light at intensities that are not harmful to human cells inhibited biofilm maturation via effects on cellular signals. Because biofilm formation is a critical factor in many types of P. aeruginosa infections, including burn wound infections that may be exposed to light, these effects could be relevant for pathogenicity.

Flagella and Swimming Behavior of Marine Magnetotactic Bacteria

Marine environments are generally characterized by low bulk concentrations of nutrients that are susceptible to steady or intermittent motion driven by currents and local turbulence. Marine bacteria have therefore developed strategies, such as very fast-swimming and the exploitation of multiple directional sensing–response systems in order to efficiently migrate towards favorable places in nutrient gradients. The magnetotactic bacteria (MTB) even utilize Earth’s magnetic field to facilitate downward swimming into the oxic–anoxic interface, which is the most favorable place for their persistence and proliferation, in chemically stratified sediments or water columns. To ensure the desired flagella-propelled motility, marine MTBs have evolved an exquisite flagellar apparatus, and an extremely high number (tens of thousands) of flagella can be found on a single entity, displaying a complex polar, axial, bounce, and photosensitive magnetotactic behavior. In this review, we describe gene clusters, the flagellar apparatus architecture, and the swimming behavior of marine unicellular and multicellular magnetotactic bacteria. The physiological significance and mechanisms that govern these motions are discussed.

Photosensing and quorum sensing are integrated to control Pseudomonas aeruginosa collective behaviors

Bacteria convert changes in sensory inputs into alterations in gene expression, behavior, and lifestyles. A common lifestyle choice that bacteria make is whether to exhibit individual behavior and exist in the free-living planktonic state or to engage in collective behavior and form sessile communities called biofilms. Transitions between individual and collective behaviors are controlled by the chemical cell-to-cell communication process called quorum sensing. Here, we show that quorum sensing represses Pseudomonas aeruginosa biofilm formation and virulence by activating expression of genes encoding the KinB–AlgB two-component system (TCS). Phospho-AlgB represses biofilm and virulence genes, while KinB dephosphorylates and thereby inactivates AlgB. We discover that the photoreceptor BphP is the kinase that, in response to light, phosphorylates and activates AlgB. Indeed, exposing P. aeruginosa to light represses biofilm formation and virulence gene expression. To our knowledge, P. aeruginosa was not previously known to detect and respond to light. The KinB–AlgB–BphP module is present in all pseudomonads, and we demonstrate that AlgB is the partner response regulator for BphP in diverse bacterial phyla. We propose that in the KinB–AlgB–BphP system, AlgB functions as the node at which varied sensory information is integrated. This network architecture provides a mechanism enabling bacteria to integrate at least two different sensory inputs, quorum sensing (via RhlR-driven activation of algB) and light (via BphP–AlgB), into the control of collective behaviors. This study sets the stage for light-mediated control of P. aeruginosa infectivity.

Photosensing and quorum sensing are integrated to control collective behaviors of the pathogenic bacterium Pseudomonas aeruginosa; the information is transduced via a phosphorylation–dephosphorylation sensory system. The study has implications for light-mediated control of P. aeruginosa infectivity.

Exposure to Broad-Spectrum Visible Light Causes Major Transcriptomic Changes in Listeria monocytogenes EGDe

Listeria monocytogenes, the causative agent of the serious foodborne disease listeriosis, can rapidly adapt to a wide range of environmental stresses, including visible light. This study shows that exposure of the L. monocytogenes EGDe strain to low-intensity, broad-spectrum visible light inhibited bacterial growth and caused altered multicellular behavior during growth on semisolid agar compared to when the bacteria were grown in complete darkness. These light-dependent changes were observed regardless of the presence of the blue light receptor (Lmo0799) and the stressosome regulator sigma B (SigB), which have been suggested to be important for the ability of L. monocytogenes to respond to blue light. A genome-wide transcriptional analysis revealed that exposure of L. monocytogenes EGDe to broad-spectrum visible light caused altered expression of 2,409 genes belonging to 18 metabolic pathways compared to bacteria grown in darkness. The light-dependent differentially expressed genes are involved in functions such as glycan metabolism, cell wall synthesis, chemotaxis, flagellar synthesis, and resistance to oxidative stress. Exposure to light conferred reduced bacterial motility in semisolid agar, which correlates well with the light-dependent reduction in transcript levels of flagellar and chemotaxis genes. Similar light-induced reduction in growth and motility was also observed in two different L. monocytogenes food isolates, suggesting that these responses are typical for L. monocytogenes Together, the results show that even relatively small doses of broad-spectrum visible light cause genome-wide transcriptional changes, reduced growth, and motility in L. monocytogenesIMPORTANCE Despite major efforts to control L. monocytogenes, this pathogen remains a major problem for the food industry, where it poses a continuous risk of food contamination. The ability of L. monocytogenes to sense and adapt to different stressors in the environment enables it to persist in many different niches, including food production facilities and in food products. The present study shows that exposure of L. monocytogenes to low-intensity broad-spectrum visible light reduces its growth and motility and alters its multicellular behavior. Light exposure also caused genome-wide changes in transcript levels, affecting multiple metabolic pathways, which are likely to influence the bacterial physiology and lifestyle. In practical terms, the data presented in this study suggest that broad-spectrum visible light is an important environmental variable to consider as a strategy to improve food safety by reducing L. monocytogenes contamination in food production environments.

Light on the cell cycle of the non-photosynthetic bacterium Ramlibacter tataouinensis

Ramlibacter tataouinensis TTB310, a non-photosynthetic betaproteobacterium isolated from a semi-arid region of southern Tunisia, forms both rods and cysts. Cysts are resistant to desiccation and divide when water and nutrients are available. Rods are motile and capable of dissemination. Due to the strong correlation between sunlight and desiccation, light is probably an important external signal for anticipating desiccating conditions. Six genes encoding potential light sensors were identified in strain TTB310. Two genes encode for bacteriophytochromes, while the four remaining genes encode for putative blue light receptors. We determined the spectral and photochemical properties of the two recombinant bacteriophytochromes RtBphP1 and RtBphP2. In both cases, they act as sensitive red light detectors. Cyst divisions and a complete cyst-rod-cyst cycle are the main processes in darkness, whereas rod divisions predominate in red or far-red light. Mutant phenotypes caused by the inactivation of genes encoding bacteriophytochromes or heme oxygenase clearly show that both bacteriophytochromes are involved in regulating the rod-rod division. This process could favor rapid rod divisions at sunrise, after dew formation but before the progressive onset of desiccation. Our study provides the first evidence of a light-based strategy evolved in a non-photosynthetic bacterium to exploit scarse water in a desert environment.