Repair of UV damage in bacteria

Repair of genomic interstrand crosslinks

Genomic interstrand crosslinks (ICLs) are formed by reactive species generated during normal cellular metabolism, produced by the microbiome, and employed in cancer chemotherapy. While there are multiple options for replication dependent and independent ICL repair, the crucial step for each is unhooking one DNA strand from the other. Much of our insight into mechanisms of unhooking comes from powerful model systems based on plasmids with defined ICLs introduced into cells or cell free extracts. Here we describe the properties of exogenous and endogenous ICL forming compounds and provide an historical perspective on early work on ICL repair. We discuss the modes of unhooking elucidated in the model systems, the concordance or lack thereof in drug resistant tumors, and the evolving view of DNA adducts, including ICLs, formed by metabolic aldehydes.

The use of droplet-based microfluidic technologies for accelerated selection of Yarrowia lipolytica and Phaffia rhodozyma yeast mutants

Microorganisms are widely used for the industrial production of various valuable products, such as pharmaceuticals, food and beverages, biofuels, enzymes, amino acids, vaccines, etc. Research is constantly carried out to improve their properties, mainly to increase their productivity and efficiency and reduce the cost of the processes. The selection of microorganisms with improved qualities takes a lot of time and resources (both human and material); therefore, this process itself needs optimization. In the last two decades, microfluidics technology appeared in bioengineering, which allows for manipulating small particles (from tens of microns to nanometre scale) in the flow of liquid in microchannels. The technology is based on small-volume objects (microdroplets from nano to femtolitres), which are manipulated using a microchip. The chip is made of an optically transparent inert to liquid medium material and contains a series of channels of small size (<1 mm) of certain geometry. Based on the physical and chemical properties of microparticles (like size, weight, optical density, dielectric constant, etc.), they are separated using microsensors. The idea of accelerated selection of microorganisms is the application of microfluidic technologies to separate mutants with improved qualities after mutagenesis. This article discusses the possible application and practical implementation of microfluidic separation of mutants, including yeasts like Yarrowia lipolytica and Phaffia rhodozyma after chemical mutagenesis will be discussed.

UV damage induces production of mitochondrial DNA fragments with specific length profiles

UV light is a potent mutagen that induces bulky DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). Photodamage and other bulky lesions occurring in nuclear genomes can be repaired through nucleotide excision repair (NER), where incisions on both sides of a damaged site precede the removal of a single-stranded oligonucleotide containing the damage. Mitochondrial genomes (mtDNAs) are also susceptible to damage from UV light, but current evidence suggests that the only way to eliminate bulky mtDNA damage is through mtDNA degradation. Damage-containing oligonucleotides excised during NER can be captured with antidamage antibodies and sequenced (XR-seq) to produce high-resolution maps of active repair locations following UV exposure. We analyzed previously published datasets from Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster to identify reads originating from the mtDNA (and plastid genome in A. thaliana). In A. thaliana and S. cerevisiae, the mtDNA-mapping reads have unique length distributions compared to the nuclear-mapping reads. The dominant fragment size was 26 nt in S. cerevisiae and 28 nt in A. thaliana with distinct secondary peaks occurring in regular intervals. These reads also show a nonrandom distribution of di-pyrimidines (the substrate for CPD formation) with TT enrichment at positions 7-8 of the reads. Therefore, UV damage to mtDNA appears to result in production of DNA fragments of characteristic lengths and positions relative to the damaged location. The mechanisms producing these fragments are unclear, but we hypothesize that they result from a previously uncharacterized DNA degradation pathway or repair mechanism in mitochondria.

Exploring Non-Thermal Plasma and UV Radiation as Biofilm Control Strategies against Foodborne Filamentous Fungal Contaminants

In recent years, non-thermal plasma (NTP) has emerged as a promising tool for decontamination and disinfection within the food industry. Given the increasing resistance of microbial biofilms to conventional disinfectants and their adverse environmental effects, this method has significant potential for eliminating biofilm formation or mitigating the metabolic activity of grown biofilms. A comparative study was conducted evaluating the efficacy of UV radiation and NTP in eradicating mature biofilms of four common foodborne filamentous fungal contaminants: Alternaria alternata, Aspergillus niger, Fusarium culmorum, and Fusarium graminearum. The findings reveal that while UV radiation exhibits variable efficacy depending on the duration of exposure and fungal species, NTP induces substantial morphological alterations in biofilms, disrupting hyphae, and reducing extracellular polymeric substance production, particularly in A. alternata and F. culmorum. Notably, scanning electron microscopy analysis demonstrates significant disruption of the hyphae in NTP-treated biofilms, indicating its ability to penetrate the biofilm matrix, which is a promising outcome for biofilm eradication strategies. The use of NTP could offer a more environmentally friendly and potentially more effective alternative to traditional disinfection methods.

Draft genome sequences of three rhodopsin possessing Croceitalea sp. strains, isolated from the sea surface microlayer in Japan

Here, we present the draft genome sequences of three Croceitalea sp. strains containing microbial rhodopsins, isolated from the Japanese coastal sea surface microlayer, which is exposed to intense sunlight. This study will contribute to the understanding of the genus Croceitalea and the diversity of microbial rhodopsins.

Research progress in photodynamic therapy for Helicobacter pylori infection

Helicobacter pylori (H. pylori) is a pathogenic microorganism that colonizes the human gastric mucosa and can lead to various gastric disorders, including gastritis, gastric ulcers, and gastric cancer. However, the increasing prevalence of antibiotic resistance in H. pylori has prompted the search for alternative treatment options. Photodynamic therapy has emerged as a potential alternative therapy, thus offering the advantage of avoiding some of the side effects associated with antibiotics and effectively targeting drug-resistant strains. In the postantibiotic era, photodynamic therapy (PDT) has shown promise as a novel treatment for H. pylori infection. This review focused on elucidating the mechanism of photodynamic therapy in the treatment of H. pylori. Additionally, we present an overview of the current research on photodynamic therapy by examining both standalone photodynamic therapy and combination therapies for H. pylori infection treatment. Furthermore, the safety profile of photodynamic therapy was also evaluated. Finally, we discuss the challenges and prospects associated with this innovative technology, with an aim to provide new insights and methodologies for the treatment of H. pylori infection.

Oxidative stress-induced DNA damage and DNA repair mechanisms in mangrove bacteria exposed to climatic and heavy metal stressors

Bacteria thriving in the mangrove ecosystem are major drivers of elemental cycles. Climate change and environmental stressors (heavy metals) influence the performance of these microorganisms, thereby affecting the biogeochemical cycle. The present study reports the genotoxic effect of climatic and heavy metal stressors on mangrove bacteria and their adaptation strategies. Comparative analysis between two bacterial strains, Bacillus stercoris GST-03 and Pseudomonas balearica DST-02 isolated from the Bhitarkanika mangrove ecosystem, Odisha, India, showed cellular injuries in response to various stressors as evident by declined growth, elevated levels of reactive oxygen species (ROS) and resulted DNA damage. B. stercoris GST-03 showed more tolerance towards acidic pH, whereas P. balearica DST-02 showed higher tolerance towards UV exposure and heavy metals (Lead and Cadmium). The adaptation strategies of the strains revealed a significant role of GST in ROS scavenging activity and the involvement of Nucleotide excision repair or SOS response pathways. However, irreparable DNA damage was observed at pH 9 and 200 ppm Cd in B. stercoris GST-03, and at pH 4, 1000 ppm of Pb and 200 ppm of Cd in P. balearica DST-02. The current findings provide a broad overview of bacterial response and adaptability concerning future climate and environmental changes.

Exploring the impact of oral bacteria remnants on stem cells from the Apical papilla: mineralization potential and inflammatory response

Introduction

Bacterial persistence is considered one of the main causal factors for regenerative endodontic treatment (RET) failure in immature permanent teeth. This interference is claimed to be caused by the interaction of bacteria that reside in the root canal with the stem cells that are one of the essentials for RET. The aim of the study was to investigate whether prolonged exposure of stem cells from the apical papilla (SCAP) to bacterial remnants of Fusobacterium nucleatum, Actinomyces gerensceriae, Slackia exigua, Enterococcus faecalis, Peptostreptococcaceae yurii, commonly found in infected traumatized root canals, and the probiotic bacteria Lactobacillus gasseri and Limosilactobacillus reuteri, can alter SCAP's inflammatory response and mineralization potential.

Methods

To assess the effect of bacterial remnants on SCAP, we used UV-C-inactivated bacteria (as cell wall-associated virulence factors) and bacterial DNA. Histochemical staining using Osteoimage Mineralization Assay and Alizarin Red analysis was performed to study SCAP mineralization, while inflammatory and osteo/odontogenic-related responses of SCAPs were assessed with Multiplex ELISA.

Results

We showed that mineralization promotion was greater with UV C-inactivated bacteria compared to bacterial DNA. Immunofluorescence analysis detected that the early mineralization marker alkaline phosphatase (ALP) was increased by the level of E. coli lipopolysaccharide (LPS) positive control in the case of UV-C-inactivated bacteria; meanwhile, DNA treatment decreased the level of ALP compared to the positive control. SCAP's secretome assessed with Multiplex ELISA showed the upregulation of pro-inflammatory factors IL-6, IL-8, GM-CSF, IL-1b, neurotrophic factor BDNF, and angiogenic factor VEGF, induced by UV-C-killed bacteria.

Discussion

The results suggest that long term stimulation (for 21 days) of SCAP with UV-C-inactivated bacteria stimulate their mineralization and inflammatory response, while DNA influence has no such effect, which opens up new ideas about the nature of RET failure.

UV damage induces production of mitochondrial DNA fragments with specific length profiles

UV light is a potent mutagen that induces bulky DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). In eukaryotic cells, photodamage and other bulky lesions occurring in nuclear genomes (nucDNAs) can be repaired through nucleotide excision repair (NER), where dual incisions on both sides of a damaged site precede the removal of a single-stranded oligonucleotide containing the damage. Mitochondrial genomes (mtDNAs) are also susceptible to damage from UV light, but current views hold that the only way to eliminate bulky DNA damage in mtDNAs is through mtDNA degradation. Damage-containing oligonucleotides excised during NER can be captured with anti-damage antibodies and sequenced (XR-seq) to produce high resolution maps of active repair locations following UV exposure. We analyzed previously published datasets from Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster to identify reads originating from the mtDNA (and plastid genome in A. thaliana). In A. thaliana and S. cerevisiae, the mtDNA-mapping reads have unique length distributions compared to the nuclear-mapping reads. The dominant fragment size was 26 nt in S. cerevisiae and 28 nt in A. thaliana with distinct secondary peaks occurring in 2-nt (S. cerevisiae) or 4-nt (A. thaliana) intervals. These reads also show a nonrandom distribution of di-pyrimidines (the substrate for CPD formation) with TT enrichment at positions 7-8 of the reads. Therefore, UV damage to mtDNA appears to result in production of DNA fragments of characteristic lengths and positions relative to the damaged location. We hypothesize that these fragments may reflect the outcome of a previously uncharacterized mechanism of NER-like repair in mitochondria or a programmed mtDNA degradation pathway.

Genomic Instability Evolutionary Footprints on Human Health: Driving Forces or Side Effects?

In this work, we propose a comprehensive perspective on genomic instability comprising not only the accumulation of mutations but also telomeric shortening, epigenetic alterations and other mechanisms that could contribute to genomic information conservation or corruption. First, we present mechanisms playing a role in genomic instability across the kingdoms of life. Then, we explore the impact of genomic instability on the human being across its evolutionary history and on present-day human health, with a particular focus on aging and complex disorders. Finally, we discuss the role of non-coding RNAs, highlighting future approaches for a better living and an expanded healthy lifespan.

Susceptibility of Diaphorina citri to Irradiation with UV-A and UV-B and the Applicability of the Bunsen-Roscoe Reciprocity Law

Populations of Diaphorina citri decline with elevation and, in a study in Bhutan, were rarely found above 1200 m ASL. The impact of ultraviolet (UV) radiation, particularly UV-B, on immature stages of the psyllid was proposed as limiting factor. As no studies have been undertaken on the influences of UV radiation on the development of D. citri, we examined the effects of UV-A and UV-B on different stadia of the psyllid. In addition, compliance with the Bunsen-Roscoe reciprocity law was examined. Irradiation with UV-A marginally reduced egg hatch and the survival times of emerging nymphs. Early instar nymphs were little affected by this waveband, but the survival of adults was reduced at the higher doses used. With UV-B, egg hatch and the survival times of early and late instar nymphs declined in proportion to UV-B dose. A dose of 57.6 kJ m^-2 d^-1 reduced the survival time of only adult females. Female fecundity was reduced at high UV-A and UV-B doses but increased at low doses. The Bunsen-Roscoe law held true for eggs and early instar nymphs for different durations and irradiances of UV-B. Eggs and nymphs had ED₅₀ values for UV-B lower than the daily fluxes of this wavelength experienced worldwide. Thus, UV-B could be a factor causing the psyllid to be scarce at high elevations.

Memory Effect on the Survival of Deinococcus radiodurans after Exposure in Near Space

Near space (20 to 100 km in altitude) is an extreme environment with high radiation and extreme cold, making it difficult for organisms to survive. However, many studies had shown that there were still microbes living in this extremely harsh environment. It was particularly important to study which factors affected the survival of microorganisms living in near space after exposure to irradiation, as this was related to many studies, such as studies of radioresistance mechanisms, panspermia hypothesis, long-distance microbial transfer, and developing extraterrestrial habitats. Survival after radiation was probably influenced by the growth condition before radiation, which is called the memory effect. In this research, we used different growth conditions to affect the growth of Deinococcus radiodurans and lyophilized bacteria in exponential phase to maintain the physiological state at this stage. Then high-altitude scientific balloon exposure experiments were carried out by using the Chinese Academy of Sciences Balloon-Borne Astrobiology Platform (CAS-BAP) at Dachaidan, Qinghai, China (37°44'N, 95°21'E). The aim was to investigate which factors influence survival after near-space exposure. The results suggested that there was a memory effect on the survival of D. radiodurans after exposure. If the differences in growth rate were caused by differences in nutrition, the survival rate and growth rate were positively correlated. Moreover, the addition of paraquat and Mn2+ during the growth phase can also increase survival. This finding may help to deepen the understanding of the mechanics of radiation protection and provide relevant evidence for many studies, such as of long-distance transfer of microorganisms in near space. IMPORTANCE Earth's near space is an extreme environment with high radiation and extreme cold. Which factors affect the survival of microbes in near space is related to many studies, such as studies of radioresistance mechanisms, panspermia hypothesis, long-distance microbial transfer, and developing extraterrestrial habitats. We performed several exposure experiments with Deinococcus radiodurans in near space to investigate which factors influence the survival rate after near-space exposure; that is, there was a relationship between survival after radiation and the growth condition before radiation. The results suggested that there was a memory effect on the survival of D. radiodurans after exposure. This finding may help to deepen the understanding of the mechanism of radiation protection and provide relevant evidence for many studies, such as of long-distance transfer of microorganisms in near space.

Bacterial filaments recover by successive and accelerated asymmetric divisions that allow rapid post-stress cell proliferation

Filamentation is a reversible morphological change triggered in response to various stresses that bacteria might encounter in the environment, during host infection or antibiotic treatments. Here we re-visit the dynamics of filament formation and recovery using a consistent framework based on live-cells microscopy. We compare the fate of filamentous Escherichia coli induced by cephalexin that inhibits cell division or by UV-induced DNA-damage that additionally perturbs chromosome segregation. We show that both filament types recover by successive and accelerated rounds of divisions that preferentially occur at the filaments' tip, thus resulting in the rapid production of multiple daughter cells with tightly regulated size. The DNA content, viability and further division of the daughter cells essentially depends on the coordination between chromosome segregation and division within the mother filament. Septum positioning at the filaments' tip depends on the Min system, while the nucleoid occlusion protein SlmA regulates the timing of division to prevent septum closure on unsegregated chromosomes. Our results not only recapitulate earlier conclusions but provide a higher level of detail regarding filaments division and the fate of the daughter cells. Together with previous reports, this work uncovers how filamentation recovery allows for a rapid cell proliferation after stress treatment.

DNA repair enzymes of the Antarctic Dry Valley metagenome

Microbiota inhabiting the Dry Valleys of Antarctica are subjected to multiple stressors that can damage deoxyribonucleic acid (DNA) such as desiccation, high ultraviolet light (UV) and multiple freeze-thaw cycles. To identify novel or highly-divergent DNA-processing enzymes that may enable effective DNA repair, we have sequenced metagenomes from 30 sample-sites which are part of the most extensive Antarctic biodiversity survey undertaken to date. We then used these to construct wide-ranging sequence similarity networks from protein-coding sequences and identified candidate genes involved in specialized repair processes including unique nucleases as well as a diverse range of adenosine triphosphate (ATP) -dependent DNA ligases implicated in stationary-phase DNA repair processes. In one of the first direct investigations of enzyme function from these unique samples, we have heterologously expressed and assayed a number of these enzymes, providing insight into the mechanisms that may enable resident microbes to survive these threats to their genomic integrity.

Macrophage activation highlight an important role for NER proteins in the survival, latency and multiplication of Mycobacterium tuberculosis

Nucleotide excision repair (NER) is one of the most extensively studied DNA repair processes in both prokaryotes and eukaryotes. The NER pathway is a highly conserved, ATP-dependent multi-step process involving several proteins/enzymes that function in a concerted manner to recognize and excise a wide spectrum of helix-distorting DNA lesions and bulky adducts by nuclease cleavage on either side of the damaged bases. As such, the NER pathway of Mycobacterium tuberculosis (Mtb) is essential for its survival within the hostile environment of macrophages and disease progression. This review focuses on present published knowledge about the crucial roles of Mtb NER proteins in the survival and multiplication of the pathogen within the macrophages and as potential targets for drug discovery.

Protection and Damage Repair Mechanisms Contributed To the Survival of Chroococcidiopsis sp. Exposed To a Mars-Like Near Space Environment

Chroococcidiopsis spp. can withstand extremely harsh environments, including a Mars-like environment. However, studies are lacking on the molecular mechanisms of Chroococcidiopsis sp. surviving in Mars-like environments. In the HH-21-5 mission, the desert cyanobacterium Chroococcidiopsis sp. was exposed to a Mars-like environment (near space; 35 km altitude) for 4 h, and a single-factor environment of near space was simulated on the ground. We investigated the survival and endurance mechanisms of Chroococcidiopsis sp. ASB-02 after exposing it to near space by studying its physiological and transcriptional properties. After the exposure, Chroococcidiopsis sp. ASB-02 exhibited high cell viability, although photosystem II activity decreased and the levels of reactive oxygen species increased. The single-factor simulation experiments revealed that for the survival of Chroococcidiopsis sp. ASB-02 in near space, UV radiation was the most important limiting factor, and it was followed by temperature. The near space environment triggered multiple metabolic pathway responses in Chroococcidiopsis sp. ASB-02. The upregulation of extracellular polysaccharides as well as carotenoid and scytonemin biosynthesis genes in response to UV radiation attenuated the extent of radiation reaching the cells. At the same time, genes related to protein synthesis were upregulated in response to the low temperature, overcoming the decrease in metabolic activity that was caused by the low temperature. In near space and after rehydration, the genes involved in various DNA and photosystem II repair pathways were upregulated. This reflected the damage to the DNA and photosystem II protein subunits in cells during the flight and suggested that repair mechanisms play an important role in the recovery of Chroococcidiopsis sp. ASB-02. IMPORTANCE This study reported that the protective and repair mechanisms of Chroococcidiopsis sp. ASB-02 contributed to its endurance ability in a Mars-like near space environment. In Chroococcidiopsis sp. ASB-02, a Mars-like near space environment activated the expression of genes involved in extracellular polysaccharides (EPS), carotenoid, scytonemin, and protein syntheses, which provided additional protection. Additionally, the cell damage repair process enhanced the recovery rate of Chroococcidiopsis sp. ASB-02 after the flight. This study will help to enhance the understanding of the tolerance mechanism of Chroococcidiopsis sp. and to provide important guidance as to the survival requirements for microbial life in a Mars-like environment.

Single-molecule fluorescence imaging techniques reveal molecular mechanisms underlying deoxyribonucleic acid damage repair

Advances in single-molecule techniques have uncovered numerous biological secrets that cannot be disclosed by traditional methods. Among a variety of single-molecule methods, single-molecule fluorescence imaging techniques enable real-time visualization of biomolecular interactions and have allowed the accumulation of convincing evidence. These techniques have been broadly utilized for studying DNA metabolic events such as replication, transcription, and DNA repair, which are fundamental biological reactions. In particular, DNA repair has received much attention because it maintains genomic integrity and is associated with diverse human diseases. In this review, we introduce representative single-molecule fluorescence imaging techniques and survey how each technique has been employed for investigating the detailed mechanisms underlying DNA repair pathways. In addition, we briefly show how live-cell imaging at the single-molecule level contributes to understanding DNA repair processes inside cells.

Interrogating the substrate specificity landscape of UvrC reveals novel insights into its non-canonical function

Although it is relatively unexplored, accumulating data highlight the importance of tripartite crosstalk between nucleotide excision repair (NER), DNA replication, and recombination in the maintenance of genome stability; however, elucidating the underlying mechanisms remains challenging. While Escherichia coli uvrA and uvrB can fully complement polAΔ cells in DNA replication, uvrC attenuates this alternative DNA replication pathway, but the exact mechanism by which uvrC suppresses DNA replication is unknown. Furthermore, the identity of bona fide canonical and non-canonical substrates for UvrCs are undefined. Here, we reveal that Mycobacterium tuberculosis UvrC (MtUvrC) strongly binds to, and robustly cleaves, key intermediates of DNA replication/recombination as compared with the model NER substrates. Notably, inactivation of MtUvrC ATPase activity significantly attenuated its endonuclease activity, thus suggesting a causal link between these two functions. We built an in silico model of the interaction of MtUvrC with the Holliday junction (HJ), using a combination of homology modeling, molecular docking, and molecular dynamic simulations. The model predicted residues that were potentially involved in HJ binding. Six of these residues were mutated either singly or in pairs, and the resulting MtUvrC variants were purified and characterized. Among them, residues Glu595 and Arg597 in the helix-hairpin-helix motif were found to be crucial for the interaction between MtUvrC and HJ; consequently, mutations in these residues, or inhibition of ATP hydrolysis, strongly abrogated its DNA-binding and endonuclease activities. Viewed together, these findings expand the substrate specificity landscape of UvrCs and provide crucial mechanistic insights into the interplay between NER and DNA replication/recombination.

Multiple Photolyases Protect the Marine Cyanobacterium Synechococcus from Ultraviolet Radiation

Marine cyanobacteria depend on light for photosynthesis, restricting their growth to the photic zone. The upper part of this layer is exposed to strong UV radiation (UVR), a DNA mutagen that can harm these microorganisms. To thrive in UVR-rich waters, marine cyanobacteria employ photoprotection strategies that are still not well defined. Among these are photolyases, light-activated enzymes that repair DNA dimers generated by UVR. Our analysis of genomes of 81 strains of Synechococcus, Cyanobium, and Prochlorococcus isolated from the world’s oceans shows that they possess up to five genes encoding different members of the photolyase/cryptochrome family, including a photolyase with a novel domain arrangement encoded by either one or two separate genes. We disrupted the putative photolyase-encoding genes in Synechococcus sp. strain RS9916 and discovered that each gene contributes to the overall capacity of this organism to survive UVR. Additionally, each conferred increased survival after UVR exposure when transformed into Escherichia coli lacking its photolyase and SOS response. Our results provide the first evidence that this large set of photolyases endows Synechococcus with UVR resistance that is far superior to that of E. coli, but that, unlike for E. coli, these photolyases provide Synechococcus with the vast majority of its UVR tolerance.

Retention and Inactivation of Quality Indicator Bacteria Using a Photocatalytic Membrane Reactor

The development of effective disinfection treatment processes is crucial to help the water industry cope with the inevitable challenges resulting from the increase in human population and climate change. Climate change leads to heavy rainfall, flooding and hot weather events that are associated with waterborne diseases. Developing effective treatment technologies will improve our resilience to cope with these events and our capacity to safeguard public health. A submerged hybrid reactor was used to test the efficiency of membrane filtration, direct photolysis (using ultraviolet-C low-pressure mercury lamps, as well as ultraviolet-C and ultraviolet-A light-emitting diodes panels) and the combination of both treatment processes (membrane filtration and photolysis) to retain and inactivate water quality indicator bacteria. The developed photocatalytic membranes effectively retained the target microorganisms that were then successfully inactivated by photolysis and advanced oxidation processes. The new hybrid reactor could be a promising approach to treat drinking water, recreational water and wastewater produced by different industries in small-scale systems. Furthermore, the results obtained with membranes coated with titanium dioxide and copper combined with ultraviolet-A light sources show that the process may be a promising approach to guarantee water disinfection using natural sunlight.

Does light-based tertiary treatment prevent the spread of antibiotic resistance genes? Performance, regrowth and future direction

The common occurrence of antibiotic-resistance genes (ARGs) originating from pathogenic and facultative pathogenic bacteria pose a high risk to aquatic environments. Low removal of ARGs in conventional wastewater treatment processes and horizontal dissemination of resistance genes between environmental bacteria and human pathogens have made antibiotic resistance evolution a complex global health issue. The phenomenon of regrowth of bacteria after disinfection raised some concerns regarding the long-lasting safety of treated waters. Despite the inactivation of living antibiotic-resistant bacteria (ARB), the possibility of transferring intact and liberated DNA containing ARGs remains. A step in this direction would be to apply new types of disinfection methods addressing this issue in detail, such as light-based advanced oxidation, that potentially enhance the effect of direct light interaction with DNA. This study is devoted to comprehensively and critically review the current state-of-art for light-driven disinfection. The main focus of the article is to provide an insight into the different photochemical disinfection methods currently being studied worldwide with respect to ARGs removal as an alternative to conventional methods. The systematic comparison of UV/chlorination, UV/H₂O₂, sulfate radical based-AOPs, photocatalytic processes and photoFenton considering their mode of action on molecular level, operational parameters of the processes, and overall efficiency of removal of ARGs is presented. An in-depth discussion of different light-dependent inactivation pathways, influence of DBP and DOM on ARG removal and the potential bacterial regrowth after treatment is presented. Based on presented revision the risk of ARG transfer from reactivated bacteria has been evaluated, leading to a future direction for research addressing the challenges of light-based disinfection technologies.

Effective ultraviolet C light disinfection of respirators demonstrated in challenges with Geobacillus stearothermophilus spores and SARS-CoV-2 virus

BACKGROUND

The global COVID-19 pandemic, accompanied by spikes in the number of patients in hospitals, required substantial amounts of respiratory protective devices (respirators), thereby causing shortages. Disinfection of used respirators by applying ultraviolet C (UVC) light may enable safe reuse, reducing shortages.

AIM

To determine whether UVC disinfection is applicable to enable repeated safe reuse of respirators.

METHODS

The UVC chamber, equipped with low-pressure mercury discharge lamps emitting at 254 nm, was used to determine the sporicidal and virucidal effects. Respirators challenged with spores and viruses were exposed to various UVC energy levels. Deactivation of the biological agents was studied as well as UVC effects on particle filtration properties and respirator fit.

FINDINGS

A 5 log10 reduction of G. thermophilus spore viability by a UVC dose of 1.1 J/cm2 was observed. By simulating spores present in the middle of the respirators, a 5 log10 reduction was achieved at a UVC dose of 10 J/cm2. SARS-CoV-2 viruses were inactivated by 4 log10 upon exposure to 19.5 mJ/cm2 UVC. In case UVC must be transmitted through all layers of the respirators to reach the spores and virus, a reduction of >5 log10 was achieved using a UVC dose of 10 J/cm2. Exposure to a six-times higher UVC dose did not significantly affect the integrity of the fit nor aerosol filtering capacity of the respirator.

CONCLUSION

UVC was shown to be a mild and effective way of respirator disinfection allowing for reuse of the UVC-treated respirators.

Application of 233 nm far-UVC LEDs for eradication of MRSA and MSSA and risk assessment on skin models

A newly developed UVC LED source with an emission wavelength of 233 nm was proved on bactericidal efficacy and skin tolerability. The bactericidal efficacy was qualitatively analysed using blood agar test. Subsequently, quantitative analyses were performed on germ carrier tests using the MRSA strain DSM11822, the MSSA strain DSM799, S. epidermidis DSM1798 with various soil loads. Additionally, the compatibility of the germicidal radiation doses on excised human skin and reconstructed human epidermis was proved. Cell viability, DNA damage and production of radicals were assessed in comparison to typical UVC radiation from discharge lamps (222 nm, 254 nm) and UVB (280–380 nm) radiation for clinical assessment. At a dose of 40 mJ/cm², the 233 nm light source reduced the viable microorganisms by a log₁₀ reduction (LR) of 5 log₁₀ levels if no soil load was present. Mucin and protein containing soil loads diminished the effect to an LR of 1.5–3.3. A salt solution representing artificial sweat (pH 8.4) had only minor effects on the reduction. The viability of the skin models was not reduced and the DNA damage was far below the damage evoked by 0.1 UVB minimal erythema dose, which can be regarded as safe. Furthermore, the induced damage vanished after 24 h. Irradiation on four consecutive days also did not evoke DNA damage. The radical formation was far lower than 20 min outdoor visible light would cause, which is classified as low radical load and can be compensated by the antioxidant defence system.

uvrY deletion and acetate reduce gut colonization of Crohn's disease-associated adherent-invasive Escherichia coli by decreasing expression of type 1 fimbriae

Adherent-invasive Escherichia coli (AIEC) is involved in onset and/or exacerbation of Crohn's disease. AIEC adapts to the gut environment by altering gene-expression programs, leading to successful gut-lumen colonization. However, the underlying mechanism of gut colonization is still far from clarified. Here, we show the role of UvrY, a response regulator of bacterial two-component signal transduction systems, in AIEC gut colonization. An AIEC mutant lacking the uvrY gene exhibited impairment of competitive colonization in the murine intestinal tract. UvrY contributes to functional expression of type 1 fimbriae by activating expression of small RNA CsrB, which confers adherence and invasion into epithelial cells on AIEC. In contrast, acetate suppresses the UvrY-dependent expression of type 1 fimbriae, resulting in less efficient cell invasion and attenuated gut colonization. Our findings might lead to therapeutic interventions for CD, in which inhibitions of UvrY activation and acetate supplementation reduce the colonization levels of AIEC by decreasing type-1 fimbriae expression.

Bridging the gap between microbial limits and extremes in space: space microbial biotechnology in the next 15 years

The establishment of a permanent human settlement in space is one of humanity's ambitions. To achieve this, microorganisms will be used to carry out many functions such as recycling, food and pharmaceutical production, mining and other processes. However, the physical and chemical extremes in all locations beyond Earth exceed known growth limits of microbial life. Making microbes more tolerant of a greater range of extraterrestrial extremes will not produce organisms that can grow in unmodified extraterrestrial environments since in many of them not even liquid water can exist. However, by narrowing the gap, the engineering demands on bioindustrial processes can be reduced and greater robustness can be incorporated into the biological component. I identify and describe these required microbial biotechnological modifications and speculate on long-term possibilities such as microbial biotechnology on Saturn's moon Titan to support a human presence in the outer Solar System and bioprocessing of asteroids. A challenge for space microbial biotechnology in the coming decades is to narrow the microbial gap by systemically identifying the genes required to do this and incorporating them into microbial systems that can be used to carry out bioindustrial processes of interest.

Flow Cytometric Analysis of Bacterial Protein Synthesis: Monitoring Vitality After Water Treatment

Bacterial vitality after water disinfection treatment was investigated using bio-orthogonal non-canonical amino acid tagging (BONCAT) and flow cytometry (FCM). Protein synthesis activity and DNA integrity (BONCAT–SYBR Green) was monitored in Escherichia coli monocultures and in natural marine samples after UV irradiation (from 25 to 200 mJ/cm²) and heat treatment (from 15 to 45 min at 55°C). UV irradiation of E. coli caused DNA degradation followed by the decrease in protein synthesis within a period of 24 h. Heat treatment affected both DNA integrity and protein synthesis immediately, with an increased effect over time. Results from the BONCAT method were compared with results from well-known methods such as plate counts (focusing on growth) and LIVE/DEAD™ BacLight™ (focusing on membrane permeability). The methods differed somewhat with respect to vitality levels detected in bacteria after the treatments, but the results were complementary and revealed that cells maintained metabolic activity and membrane integrity despite loss of cell division. Similarly, analysis of protein synthesis in marine bacteria with BONCAT displayed residual activity despite inability to grow or reproduce. Background controls (time zero blanks) prepared using different fixatives (formaldehyde, isopropanol, and acetic acid) and several different bacterial strains revealed that the BONCAT protocol still resulted in labeled, i.e., apparently active, cells. The reason for this is unclear and needs further investigation to be understood. Our results show that BONCAT and FCM can detect, enumerate, and differentiate bacterial cells after physical water treatments such as UV irradiation and heating. The method is reliable to enumerate and explore vitality of single cells, and a great advantage with BONCAT is that all proteins synthesized within cells are analyzed, compared to assays targeting specific elements such as enzyme activity.

UV and bacteriophages as a chemical-free approach for cleaning membranes from anaerobic bioreactors

Anaerobic membrane bioreactor (AnMBR) for wastewater treatment has attracted much interest due to its efficacy in providing high-quality effluent with minimal energy costs. However, membrane biofouling represents the main bottleneck for AnMBR because it diminishes flux and necessitates frequent replacement of membranes. In this study, we assessed the feasibility of combining bacteriophages and UV-C irradiation to provide a chemical-free approach to remove biofoulants on the membrane. The combination of bacteriophage and UV-C resulted in better log cells removal and ca. 2× higher extracellular polymeric substance (EPS) concentration reduction in mature biofoulants compared to either UV-C or bacteriophage alone. The cleaning mechanism behind this combined approach is by 1) reducing the relative abundance of Acinetobacter spp. and selected bacteria (e.g., Paludibacter, Pseudomonas, Cloacibacterium, and gram-positive Firmicutes) associated with the membrane biofilm and 2) forming cavities in the biofilm to maintain water flux through the membrane. When the combined treatment was further compared with the common chemical cleaning procedure, a similar reduction on the cell numbers was observed (1.4 log). However, the combined treatment was less effective in removing EPS compared with chemical cleaning. These results suggest that the combination of UV-C and bacteriophage have an additive effect in biofouling reduction, representing a potential chemical-free method to remove reversible biofoulants on membrane fitted to an AnMBR.

Antimicrobial photodynamic therapy (aPDT) for biofilm treatments. Possible synergy between aPDT and pulsed electric fields

Currently, microbial biofilms have been the cause of a wide variety of infections in the human body, reaching 80% of all bacterial and fungal infections. The biofilms present specific properties that increase the resistance to antimicrobial treatments. Thus, the development of new approaches is urgent, and antimicrobial photodynamic therapy (aPDT) has been shown as a promising candidate. aPDT involves a synergic association of a photosensitizer (PS), molecular oxygen and visible light, producing highly reactive oxygen species (ROS) that cause the oxidation of several cellular components. This therapy attacks many components of the biofilm, including proteins, lipids, and nucleic acids present within the biofilm matrix; causing inhibition even in the cells that are inside the extracellular polymeric substance (EPS). Recent advances in designing new PSs to increase the production of ROS and the combination of aPDT with other therapies, especially pulsed electric fields (PEF), have contributed to enhanced biofilm inhibition. The PEF has proven to have antimicrobial effect once it is known that extensive chemical reactions occur when electric fields are applied. This type of treatment kills microorganisms not only due to membrane rupture but also due to the formation of reactive compounds including free oxygen, hydrogen, hydroxyl and hydroperoxyl radicals. So, this review aims to show the progress of aPDT and PEF against the biofilms, suggesting that the association of both methods can potentiate their effects and overcome biofilm infections.

The c-di-AMP signaling system influences stress tolerance and biofilm formation of Streptococcus mitis

Streptococcus mitis is a commensal bacterial species of the oral cavity, with the potential for opportunistic pathogenesis. For successful colonization, S. mitis must be able to adhere to surfaces of the oral cavity and survive and adapt to frequently changing environmental conditions. Cyclic-di-AMP (c-di-AMP) is a nucleotide second messenger, involved in the regulation of stress responses and biofilm formation in several bacterial species. Cyclic-di-AMP is produced by diadenylate cyclases and degraded by phosphodiesterases. We have previously shown that in S. mitis, one diadenylate cyclase (CdaA) and at least two phosphodiesterases (Pde1 and Pde2) regulate the intracellular concentration of c-di-AMP. In this study, we utilized S. mitis deletion mutants of cdaA, pde1, and pde2 to analyze the role of c-di-AMP signaling in various stress responses, biofilm formation, and adhesion to eukaryotic cells. Here, we demonstrate that the Δpde1 mutant displayed a tendency toward increased susceptibility to acetic acid at pH 4.0. Deletion of cdaA increases auto-aggregation of S. mitis but reduces biofilm formation on an abiotic surface. These phenotypes are more pronounced under acidic extracellular conditions. Inactivation of pde1 or pde2 reduced the tolerance to ciprofloxacin, and UV radiation and the Δpde1 mutant was more susceptible to Triton X-100, indicating a role for c-di-AMP signaling in responses to DNA damage and cell membrane perturbation. Finally, the Δpde2 mutant displayed a tendency toward a reduced ability to adhere to oral keratinocytes. Taken together, our results indicate an important role for c-di-AMP signaling in cellular processes important for colonization of the mouth.

Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases

It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field and alkylating metabolic radicals added to these threats. Here, we propose that ancient forms of life had only two distinct repair mechanisms: versatile apurinic/apyrimidinic (AP) endonucleases to cope with both AP sites and deaminated residues, and enzymes catalyzing the direct reversal of UV and alkylation damage. The absence of uracil–DNA N-glycosylases in some Archaea, together with the presence of an AP endonuclease, which can cleave uracil-containing DNA, suggests that the AP endonuclease-initiated nucleotide incision repair (NIR) pathway evolved independently from DNA glycosylase-mediated base excision repair. NIR may be a relic that appeared in an early thermophilic ancestor to counteract spontaneous DNA damage. We hypothesize that a rise in the oxygen level in the Earth’s atmosphere ~2 Ga triggered the narrow specialization of AP endonucleases and DNA glycosylases to cope efficiently with a widened array of oxidative base damage and complex DNA lesions.

Revival of Anhydrobiotic Cyanobacterium Biofilms Exposed to Space Vacuum and Prolonged Dryness: Implications for Future Missions beyond Low Earth Orbit

Dried biofilms of Chroococcidiopsis sp. CCMEE 029 were revived after a 672-day exposure to space vacuum outside the International Space Station during the EXPOSE-R2 space mission. After retrieval, they were air-dried stored for 3.5 years. Space vacuum reduced cell viability and increased DNA damage compared to air-dried storage for 6 years under laboratory conditions. Long exposure times to space vacuum and extreme dryness decrease the changes of survival that ultimately depend on DNA damage repair upon rehydration, and hence, an in silico analysis of Chroococcidiopsis sp. CCMEE 029's genome was performed with a focus on DNA repair pathways. The analysis identified a high number of genes that encode proteins of the homologous recombination RecF pathway and base excision repair that were over-expressed during 1 and 6 h rehydration of space-vacuum exposed biofilms. This suggests that Chroococcidiopsis developed a survival strategy against desiccation, with DNA repair playing a key role, which allowed the revival of biofilms exposed to space vacuum. Unravelling how long anhydrobiotic cyanobacteria can persist under space vacuum followed by prolonged air-dried storage is relevant to future astrobiological experiments that use space platforms and might require prolonged air-dried storage of the exposed samples before retrieval to Earth.

Development of Antimicrobial Phototreatment Tolerance: Why the Methodology Matters

Due to rapidly growing antimicrobial resistance, there is an urgent need to develop alternative, non-antibiotic strategies. Recently, numerous light-based approaches, demonstrating killing efficacy regardless of microbial drug resistance, have gained wide attention and are considered some of the most promising antimicrobial modalities. These light-based therapies include five treatments for which high bactericidal activity was demonstrated using numerous in vitro and in vivo studies: antimicrobial blue light (aBL), antimicrobial photodynamic inactivation (aPDI), pulsed light (PL), cold atmospheric plasma (CAP), and ultraviolet (UV) light. Based on their multitarget activity leading to deleterious effects to numerous cell structures-i.e., cell envelopes, proteins, lipids, and genetic material-light-based treatments are considered to have a low risk for the development of tolerance and/or resistance. Nevertheless, the most recent studies indicate that repetitive sublethal phototreatment may provoke tolerance development, but there is no standard methodology for the proper evaluation of this phenomenon. The statement concerning the lack of development of resistance to these modalities seem to be justified; however, the most significant motivation for this review paper was to critically discuss existing dogma concerning the lack of tolerance development, indicating that its assessment is more complex and requires better terminology and methodology.

Bacterial and abiogenic carbonates formed in caves-no vital effect on clumped isotope compositions

Speleothems (dominated by cave-hosted carbonate deposits) are valuable archives of paleoclimate conditions. As such, they are potential targets of clumped isotope analyses that may yield quantified data about past temperature variations. Clumped isotope analyses of stalagmites, however, seldom provide useful temperature values due to various isotope fractionation processes. This study focuses on the determination of the microbially induced vital effect, i.e., the isotope fractionation processes related to bacterial carbonate production. A cave site with biologically mediated amorphous calcium carbonate precitation was selected as a natural laboratory. Calcite deposits were farmed under a UV lamp to prevent bacterial activity, as well as under control conditions. Microbiological analyses and morphological investigations using scanning electron microscopy showed that the UV lamp treatment effectively reduced the number of bacterial cells, and that bacterial carbonate production strongly influenced the carbonate’s morphology. Stable oxygen isotope analyses of calcite and drip waters, as well as clumped isotope measurements revealed that, although most of the studied carbonates formed close to oxygen isotope equilibrium, clumped isotope Δ₄₇ values varied widely from equilibrium to strongly fractionated data. Site-specific kinetic fractionations played a dominant role in the distribution of Δ₄₇ values, whereas bacterial carbonate production did not result in a detectable clumped isotope effect.

Phosphoproteomic Analysis Reveals Rio1-Related Protein Phosphorylation Changes in Response to UV Irradiation in Sulfolobus islandicus REY15A

DNA damage response (DDR) in eukaryotes is largely regulated by protein phosphorylation. In archaea, many proteins are phosphorylated, however, it is unclear how the cells respond to DNA damage through global protein phosphorylation. We previously found that Δrio1, a Rio1 kinase homolog deletion strain of Sulfolobus islandicus REY15A, was sensitive to UV irradiation. In this study, we showed that Δrio1 grew faster than the wild type. Quantitative phosphoproteomic analysis of the wild type and Δrio1, untreated and irradiated with UV irradiation, revealed 562 phosphorylated sites (with a Ser/Thr/Tyr ratio of 65.3%/23.8%/10.9%) of 333 proteins in total. The phosphorylation levels of 35 sites of 30 proteins changed with >1.3-fold in the wild type strain upon UV irradiation. Interestingly, more than half of the UV-induced changes in the wild type did not occur in the Δrio1 strain, which were mainly associated with proteins synthesis and turnover. In addition, a protein kinase and several transcriptional regulators were differentially phosphorylated after UV treatment, and some of the changes were dependent on Rio1. Finally, many proteins involved in various cellular metabolisms exhibited Riol-related and UV-independent phosphorylation changes. Our results suggest that Rio1 is involved in the regulation of protein recycling and signal transduction in response to UV irradiation, and plays regulatory roles in multiple cellular processes in S. islandicus.

Mycobacteria excise DNA damage in 12- or 13-nucleotide-long oligomers by prokaryotic-type dual incisions and performs transcription-coupled repair

In nucleotide excision repair, bulky DNA lesions such as UV-induced cyclobutane pyrimidine dimers are removed from the genome by concerted dual incisions bracketing the lesion, followed by gap filling and ligation. So far, two dual-incision patterns have been discovered: the prokaryotic type, which removes the damage in 11-13-nucleotide-long oligomers, and the eukaryotic type, which removes the damage in 24-32-nucleotide-long oligomers. However, a recent study reported that the UvrC protein of Mycobacterium tuberculosis removes damage in a manner analogous to yeast and humans in a 25-mer oligonucleotide arising from incisions at 15 nt from the 3´ end and 9 nt from the 5´ end flanking the damage. To test this model, we used the in vivo excision assay and the excision repair sequencing genome-wide repair mapping method developed in our laboratory to determine the repair pattern and genome-wide repair map of Mycobacterium smegmatis We find that M. smegmatis, which possesses homologs of the Escherichia coli uvrA, uvrB, and uvrC genes, removes cyclobutane pyrimidine dimers from the genome in a manner identical to the prokaryotic pattern by incising 7 nt 5´ and 3 or 4 nt 3´ to the photoproduct, and performs transcription-coupled repair in a manner similar to E. coli.

The mechanisms underlying antigenic variation and maintenance of genomic integrity in Mycoplasma pneumoniae and Mycoplasma genitalium

Mycoplasma pneumoniae and Mycoplasma genitalium are important causative agents of infections in humans. Like all other mycoplasmas, these species possess genomes that are significantly smaller than that of other prokaryotes. Moreover, both organisms possess an exceptionally compact set of DNA recombination and repair-associated genes. These genes, however, are sufficient to generate antigenic variation by means of homologous recombination between specific repetitive genomic elements. At the same time, these mycoplasmas have likely evolved strategies to maintain the stability and integrity of their 'minimal' genomes. Previous studies have indicated that there are considerable differences between mycoplasmas and other bacteria in the composition of their DNA recombination and repair machinery. However, the complete repertoire of activities executed by the putative recombination and repair enzymes encoded by Mycoplasma species is not yet fully understood. In this paper, we review the current knowledge on the proteins that likely form part of the DNA repair and recombination pathways of two of the most clinically relevant Mycoplasma species, M. pneumoniae and M. genitalium. The characterization of these proteins will help to define the minimal enzymatic requirements for creating bacterial genetic diversity (antigenic variation) on the one hand, while maintaining genomic integrity on the other.

The intrinsic ATPase activity of Mycobacterium tuberculosis UvrC is crucial for its damage-specific DNA incision function

To ensure genome stability, bacteria have evolved a network of DNA repair mechanisms; among them, the UvrABC-dependent nucleotide excision repair (NER) pathway is essential for the incision of a variety of bulky adducts generated by exogenous chemicals, UV radiation and by-products of cellular metabolism. However, very little is known about the enzymatic properties of Mycobacterium tuberculosis UvrABC excinuclease complex. Furthermore, the biochemical properties of Escherichia coli UvrC (EcUvrC) are not well understood (compared to UvrA and UvrB), perhaps due to its limited availability and/or activity instability in vitro. In addition, homology modelling of M. tuberculosis UvrC (MtUvrC) revealed the presence of a putative ATP-binding pocket, although its function remains unknown. To elucidate the biochemical properties of UvrC, we constructed and purified wild-type MtUvrC and its eight variants harbouring mutations within the ATP-binding pocket. The data from DNA-binding studies suggest that MtUvrC exhibits high-affinity for duplex DNA containing a bubble or fluorescein-dT moiety, over fluorescein-adducted single-stranded DNA. Most notably, MtUvrC has an intrinsic UvrB-independent ATPase activity, which drives dual incision of the damaged DNA strand. In contrast, EcUvrC is devoid of ATPase activity; however, it retains the ability to bind ATP at levels comparable to that of MtUvrC. The ATPase-deficient variants map to residues lining the MtUvrC ATP-binding pocket. Further analysis of these variants revealed separation of function between ATPase and DNA-binding activities in MtUvrC. Altogether, these findings reveal functional diversity of the bacterial NER machinery and a paradigm for the evolution of a catalytic scaffold in UvrC.

Validating biochemical features at the genome level in the Antarctic bacterium Hymenobacter sp. strain UV11

We present experimental data that complement and validate some biochemical features at the genome level in the UVC-resistant Antarctic bacterium Hymenobacter sp. UV11 strain. The genome was sequenced, assembled and annotated. It has 6 096 246 bp, a GC content of 60.6% and 5155 predicted genes. The secretome analysis, by combining in silico predictions with shotgun proteomics data, showed that UV11 strain produces extracellular proteases and carbohydrases with potential biotechnological uses. We observed the formation of outer membrane vesicles, mesosomes and carbon-storage compounds by using transmission electron microscopy. The in silico analysis of the genome revealed the presence of genes involved in the metabolism of glycogen-like molecules and starch. By HPLC-UV-Vis analysis and 1H-NMR spectra, we verified that strain UV11 produces xanthophyll-like carotenoids such as 2'-hydroxyflexixanthin, and the in silico analysis showed that this bacterium has genes involved in the biosynthesis of cathaxanthin, zeaxanthin and astaxanthin. We also found genes involved in the repair of UV-damaged DNA such as a photolyase, the nucleotide excision repair system and the production of ATP-dependent proteases that are important cellular components involved in the endurance to physiological stresses. This information will help us to better understand the ecological role played by Hymenobacter strains in the extreme Antarctic environment.

Blue light emitting diodes enhance the antivirulence effects of Curcumin against Helicobacter pylori

Introduction. Growing concern about the increasing frequency of resistance of Helicobacter pylori to the available antimicrobial agents worldwide has encouraged the search for new strategies in treating and eradicating H. pylori infections. Endoscopic blue-light therapy has been used in patients with H. pylori gastritis with limited success due to subsequent repopulation with H. pylori. Clinical trials using Curcumin could not eradicate infection either.Aim. We studied the effect of blue light emitting diodes (LEDs) in conjunction with Curcumin on H. pylori, since this has not been previously reported.Methodology. We examined the effect of Curcumin with and without irradiation with blue LEDs on the viability of H. pylori and four key factors important for colonization and establishment of H. pylori infection, namely urease production, motility, adhesion and biofilm formation.Results. We found that a combination of Curcumin and blue LEDs caused significant reductions in viability, urease production, motility, haemagglutination activity, as well as increased disruption of mature preformed biofilms of H. pylori, in comparison to Curcumin alone (P<0.0001), at sublethal concentrations of Curcumin.Conclusion. Targeting the virulence factors of H. pylori with blue LED photoactivated Curcumin would theoretically cripple this pathogen from colonizing and causing tissue damage and perhaps overcome the problem of repopulation with H. pylori that often occurs following endoscopic blue-light therapy.

UV-C Irradiation of Rolled Fillets of Ham Inoculated with Yersinia enterocolitica and Brochothrix thermosphacta

Bacteria on ready-to-eat meat may cause diseases and lead to faster deterioration of the product. In this study, ready-to-eat sliced ham samples were inoculated with Yersinia enterocolitica or Brochothrix thermosphacta and treated with ultraviolet (UV) light. The initial effect of a UV-C irradiation was investigated with doses of 408, 2040, 4080, and 6120 mJ/cm² and the effect after 0, 7, and 14 days of refrigerated storage with doses of 408 and 4080 mJ/cm². Furthermore, inoculated ham samples were stored under light and dark conditions after the UV-C treatment to investigate the effect of photoreactivation. To assess the ham quality the parameters color and antioxidant capacity were analyzed during storage. UV-C light reduced Yersinia enterocolitica and Brochothrix thermosphacta counts by up to 1.11 log₁₀ and 0.79 log₁₀ colony forming units/g, respectively, during storage. No photoreactivation of the bacteria was observed. Furthermore, significantly lower a* and higher b* values after 7 and 14 days of storage and a significantly higher antioxidant capacity on day 0 after treatment with 4080 mJ/cm² were detected. However, there were no other significant differences between treated and untreated samples. Hence, a UV-C treatment can reduce microbial surface contamination of ready-to-eat sliced ham without causing considerable quality changes.

Adaptative transcriptional response of Dietzia cinnamea P4 strain to sunlight simulator

Responses to sunlight exposure of the oil-degrading Dietzia cinnamea P4 strain were evaluated by transcriptional levels of SOS genes, photoreactivation and genes involved in tolerance to high levels of reactive oxygen species. The P4 strain was exposed for 1 and 2 h and the magnitude of level changes in the mRNA was evaluated by qPCR. The results described the activation of the SOS system, with the decline of the repressor lexA gene levels and the concomitant increase of recA and uvrAD genes levels. The genes that participate in the photoreactivation process were also responsive to sunlight. The phrB gene encoding deoxyribodipyrimidine photo-lyase had its expression increased after 1-h exposure, while the phytAB genes showed a progressive increase over the studied period. The protective genes against reactive oxygen species, catalases, superoxides, peroxidases, and thioredoxins, had their expression rates detected under the conditions validated in this study. These results show a fast and coordinated response of genes from different DNA repair and tolerance mechanisms employed by strain P4, suggesting a complex concerted protective action against environmental stressors.

Efficacy of UVC-LED in water disinfection on Bacillus species with consideration of antibiotic resistance issue

Ultraviolet light emitting diode (UV-LED) has attracted extensive attention as a new technology to replace traditional mercury lamp for water disinfection. This study reported for the first time the application of UVC-LEDs in range of 200-280 nm for the treatment of two Gram-positive tetracycline resistant bacteria (TRB) from Bacillus species and their tetracycline resistant gene (TRG). The results showed that UVC-LEDs can inactivate TRB up to 5.7-log and inhibit TRG expression, especially at 268 nm. The required fluence was approximate to that of the referential non-resistant bacteria using the same UVC-LED, but far less than that of TRB using mercury lamp. After UVC-LED irradiation, photoreactivation was the dominant mechanism to repair TRB, just like non-resistant bacteria. But contrary to non-resistant bacteria, the regrowth ratio of TRB was remarkably high at 24 h since the end of the irradition, nevertheless the number of the regrown bacteria in the irradiated water was still less than that in the non-irradiated water. Whereas TRB restored resistance after repair even applying 268 nm at a fluence up to 46.08 mJ/cm² (maximum in this study). This study highlights the merits of UVC-LED to effectively inactivate TRB in a prompt, energy-efficient and resistance-reducing way, while future study on TRB regrowth and resistance resilience is needed.

Inactivation by helium cold atmospheric pressure plasma for Escherichia coli and Staphylococcus aureus

A helium cold atmospheric pressure plasma jet (HCAPPJ) driven by a commercial neon power supply was designed and utilized for inactivation bacteria. The generated reactive spices by HCAPPJ were investigated by optical emission spectroscopy. The reactive species of OH, OI, OI, N21+, N21+ and He were identified in the UV–Vis wavelength region. The reactive species was not detected between 200 nm and 300 nm, as the flow rate of helium gas increased that led to the plasma temperature reducing to a value near to the room temperature. In this work, we studied the impact of HCAPPJ on Gram-positive and Gram-negative bacteria. The survival amounts of the two types of bacteria were decreased vastly when the rate flow rate was equal to 10 L/min.

Over-Expression of UV-Damage DNA Repair Genes and Ribonucleic Acid Persistence Contribute to the Resilience of Dried Biofilms of the Desert Cyanobacetrium Chroococcidiopsis Exposed to Mars-Like UV Flux and Long-Term Desiccation

The survival limits of the desert cyanobacterium Chroococcidiopsis were challenged by rewetting dried biofilms and dried biofilms exposed to 1.5 × 10³ kJ/m² of a Mars-like UV, after 7 years of air-dried storage. PCR-stop assays revealed the presence of DNA lesions in dried biofilms and an increased accumulation in dried-UV-irradiated biofilms. Different types and/or amounts of DNA lesions were highlighted by a different expression of uvrA, uvrB, uvrC, phrA, and uvsE genes in dried-rewetted biofilms and dried-UV-irradiated-rewetted biofilms, after rehydration for 30 and 60 min. The up-regulation in dried-rewetted biofilms of uvsE gene encoding an UV damage endonuclease, suggested that UV-damage DNA repair contributed to the repair of desiccation-induced damage. While the phrA gene encoding a photolyase was up-regulated only in dried-UV-irradiated-rewetted biofilms. Nucleotide excision repair genes were over-expressed in dried-rewetted biofilms and dried-UV-irradiated-rewetted biofilms, with uvrC gene showing the highest increase in dried-UV-irradiated-rewetted biofilms. Dried biofilms preserved intact mRNAs (at least of the investigated genes) and 16S ribosomal RNA that the persistence of the ribosome machinery and mRNAs might have played a key role in the early phase recovery. Results have implications for the search of extra-terrestrial life by contributing to the definition of habitability of astrobiologically relevant targets such as Mars or planets orbiting around other stars.

Persistence and Decay of Fecal Microbiota in Aquatic Habitats

Fecal microorganisms can enter water bodies in diverse ways, including runoff, sewage discharge, and direct fecal deposition. Once in water, the microorganisms experience conditions that are very different from intestinal habitats. The transition from host to aquatic environment may lead to rapid inactivation, some degree of persistence, or growth. Microorganisms may remain planktonic, be deposited in sediment, wash up on beaches, or attach to aquatic vegetation. Each of these habitats offers a panoply of different stressors or advantages, including UV light exposure, temperature fluctuations, salinity, nutrient availability, and biotic interactions with the indigenous microbiota (e.g., predation and/or competition). The host sources of fecal microorganisms are likewise numerous, including wildlife, pets, livestock, and humans. Most of these microorganisms are unlikely to affect human health, but certain taxa can cause waterborne disease. Others signal increased probability of pathogen presence, e.g., the fecal indicator bacteria Escherichia coli and enterococci and bacteriophages, or act as fecal source identifiers (microbial source tracking markers). The effects of environmental factors on decay are frequently inconsistent across microbial species, fecal sources, and measurement strategies (e.g., culture versus molecular). Therefore, broad generalizations about the fate of fecal microorganisms in aquatic environments are problematic, compromising efforts to predict microbial decay and health risk from contamination events. This review summarizes the recent literature on decay of fecal microorganisms in aquatic environments, recognizes defensible generalizations, and identifies knowledge gaps that may provide particularly fruitful avenues for obtaining a better understanding of the fates of these organisms in aquatic environments.

Variation of Microbial Communities in Aquatic Sediments under Long-Term Exposure to Decabromodiphenyl Ether and UVA Irradiation

Abiotic components create different types of environmental stress on bacterial communities in aquatic ecosystems. In this study, the long-term exposure to various abiotic factors, namely a high-dose of the toxic chemical decabromodiphenyl ether (BDE-209), continuous UVA irradiation, and different types of sediment, were evaluated in order to assess their influence on the bacterial community. The dominant bacterial community in a single stress situation, i.e., exposure to BDE-209 include members of Comamonadaceae, members of Xanthomonadaceae, a Pseudomonas sp. and a Hydrogenophaga sp. Such bacteria are capable of biodegrading polybrominated diphenyl ethers (PBDEs). When multiple environmental stresses were present, Acidobacteria bacterium and a Terrimonas sp. were predominant, which equipped the population with multiple physiological characteristics that made it capable of both PBDE biodegradation and resistance to UVA irradiation. Methloversatilis sp. and Flavisolibacter sp. were identified as representative genera in this population that were radioresistant. In addition to the above, sediment heterogeneity is also able to alter bacterial community diversity. In total, seventeen species of bacteria were identified in the microcosms containing more clay particles and higher levels of soil organic matter (SOM). This means that these communities are more diverse than in microcosms that contained more sand particles and a lower SOM, which were found to have only twelve identifiable bacterial species. This is the first report to evaluate how changes in bacterial communities in aquatic sediment are affected by the presence of multiple variable environmental factors at the same time.

Antarctic heterotrophic bacterium Hymenobacter nivis P3T displays light-enhanced growth and expresses putative photoactive proteins

Hymenobacter nivis P3^T is a heterotrophic bacterium isolated from Antarctic red snow generated by algal blooms. Despite being non-photosynthetic, H. nivis was dominantly found in the red snow environment that is exposed to high light and UV irradiation, suggesting that this species can flourish under such harsh conditions. In order to further understand the adaptive strategies on the snow surface environment of Antarctica, the genome of H. nivis P3^T was sequenced and analyzed, which identified genes putatively encoding for light-reactive proteins such as proteorhodopsin, phytochrome, photolyase and several copies of cryptochromes. Culture-based experiments revealed that H. nivis P3^T growth was significantly enhanced under light conditions, while dark conditions had increased extracellular polymeric substances. Furthermore, the expression of several putative light-reactive proteins was determined by proteomic analysis. These results indicate that H. nivis P3^T is able to potentially utilize light, which may explain its dominance on the red snow surface environment of Antarctica. ORIGINALITY-SIGNIFICANCE STATEMENT: The role of proteorhodopsin in heterotrophic bacteria is not well-characterized, as only a handful of proteorhodopsin-harbouring isolates were shown to have a light-enhanced phenotype through culture-based experiments to date. This is the first study that demonstrates light-stimulated growth and protein expression evidence of photoactive proteins for a non-marine psychrophile and for a member of the genus Hymenobacter. It is also the first study that provides comprehensive proteome information for this genus. This study presents significant results in understanding the adaptive mechanism of a heterotrophic non-photosynthetic bacterium thriving on the snow surface environment of Antarctica as well as demonstrating the role of light-utilization in promoting growth, possibly through proteorhodopsin.

Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil

The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32T, LB39T and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32T and LB39T were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.