Stress and How Bacteria Cope with Death and Survival

Enhanced photodynamic inactivation against Escherichia coli O157:H7 provided by chitosan/curcumin coating and its application in food contact surfaces

Sterilisation technologies are essential to eliminate foodborne pathogens from food contact surfaces. However, most of the current sterilisation methods involve high energy and chemical consumption. In this study, a photodynamic inactivation coating featuring excellent antibacterial activity was prepared by dispersing curcumin as a plant-based photosensitiser in a chitosan solution. The coating generated abundant reactive oxygen species (ROS) after light irradiation at 420 nm, which eradicated ≥99.999 % of Escherichia coli O157:H7. It was also found that ROS damaged the cell membrane, leading to the leakage of cell contents and cell shrinkage on the basis of chitosan. In addition, the production of ROS first excited the bacterial antioxidant defence system resulting in the increase of peroxidase (POD) and superoxide dismutase (SOD). ROS levels exceed its capacity, causing damage to the defence system and further oxidative decomposition of large molecules, such as DNA and proteins, eventually leading to the death of E. coli O157:H7. We also found the curcumin/chitosan coating could effectively remove E. coli O157:H7 biofilms by oxidative of extracellular polysaccharides and proteins. All the contributors made the chitosan/curcumin coating an efficient detergent comparable with HClO.

Dual roles of the conditional extracellular vesicles derived from Pseudomonas aeruginosa biofilms: Promoting and inhibiting bacterial biofilm growth

Antibiotic-resistant biofilm infections have emerged as public health concerns because of their enhanced tolerance to high-dose antibiotic treatments. The biofilm life cycle involves multiple developmental stages, which are tightly regulated by active cell-cell communication via specific extracellular signal messengers such as extracellular vesicles. This study was aimed at exploring the roles of extracellular vesicles secreted by Pseudomonas aeruginosa at different developmental stages in controlling biofilm growth. Our results show that extracellular vesicles secreted by P. aeruginosa biofilms during their exponential growth phase (G-EVs) enhance biofilm growth. In contrast, extracellular vesicles secreted by P. aeruginosa biofilms during their death/survival phase (D-EVs) can effectively inhibit/eliminate P. aeruginosa PAO1 biofilms up to 4.8-log10 CFU/cm2. The inhibition effectiveness of D-EVs against P. aeruginosa biofilms grown for 96 h improved further in the presence of 10-50 μM Fe3+ ions. Proteomic analysis suggests the inhibition involves an iron-dependent ferroptosis mechanism. This study is the first to report the functional role of bacterial extracellular vesicles in bacterial growth, which depends on the developmental stage of the parent bacteria. The finding of D-EV-activated ferroptosis-based bacterial death may have significant implications for preventing antibiotic resistance in biofilms.

Mycobacterial FtsEX-RipC interaction is required for normal growth and cell morphology in rifampicin and low ionic strength conditions

Tuberculosis, a lung disease caused by Mycobacterium tuberculosis (Mtb), remains a major global health problem ranking as the second leading cause of death from a single infectious agent. One of the major factors contributing toward Mtb's success as a pathogen is its unique cell wall and its ability to counteract various arms of the host's immune response. A recent genome-scale study profiled a list of candidate genes that are predicted to be essential for Mtb survival of host-mediated responses. One candidate was FtsEX, a protein complex composed of an ATP-binding domain, FtsE, and a transmembrane domain, FtsX. FtsEX functions through interaction with a periplasmic hydrolase, RipC. Homologs of FtsEX exist in other bacteria and have been linked with playing a key role in regulating peptidoglycan hydrolysis during cell elongation and division. Here, we report on Mycobacterium smegmatis, FtsE, FtsX, and RipC and their protective roles in stressful conditions. We demonstrate that the individual genes of FtsEX complex and RipC are not essential for survival in normal growth conditions but conditionally essential in low-salt media and antibiotic-treated media. Growth defects in these conditions were characterized by short and bulgy cells as well as elongated filamentous cells. Our results suggest that FtsE, FtsX, and RipC are required for both normal cell elongation and division and ultimately for survival in stressful conditions.

IMPORTANCE

Mycobacterial cell growth and division are coordinated with regulated peptidoglycan hydrolysis. Understanding cell wall gene complexes that govern normal cell division and elongation will aid in the development of tools to disarm the ability of mycobacteria to survive immune-like and antibiotic stresses. We combined genetic analyses and scanning electron microscopy to analyze morphological changes of mycobacterial FtsEX and RipC mutants in stressful conditions. We demonstrate that FtsE, FtsX, FtsEX, and RipC are conditionally required for the survival of Mycobacterium smegmatis during rifampicin treatment and in low-salt conditions. Growth defects in these conditions were characterized by short and bulgy cells as well as elongated filamentous cells. We also show that the FtsEX-RipC interaction is essential for the survival of M. smegmatis in rifampicin. Our results suggest that FtsE, FtsX, and RipC are required for normal cell wall regulation and ultimately for survival in stressful conditions.

Evolution of pH-sensitive transcription termination during adaptation to repeated long-term starvation

Fluctuating environments that consist of regular cycles of co-occurring stress are a common challenge faced by cellular populations. For a population to thrive in constantly changing conditions, an ability to coordinate a rapid cellular response is essential. Here, we identify a mutation conferring an arginine-to-histidine (Arg to His) substitution in the transcription terminator Rho. The rho R109H mutation frequently arose in E. coli populations experimentally evolved under repeated long-term starvation conditions, during which feast and famine result in drastic environmental pH fluctuations. Metagenomic sequencing revealed that populations containing the rho mutation also possess putative loss-of-function mutations in ydcI, which encodes a recently characterized transcription factor associated with pH homeostasis. Genetic reconstructions of these mutations show that the rho allele confers a plastic alkaline-induced reduction of Rho function that, when found in tandem with a ΔydcI allele, leads to intracellular alkalinization and genetic assimilation of Rho mutant function. We further identify Arg to His substitutions at analogous sites in rho alleles from species originating from fluctuating alkaline environments. Our results suggest that Arg to His substitutions in global regulators of gene expression can serve to rapidly coordinate complex responses through pH sensing and shed light on how cellular populations across the tree of life use environmental cues to coordinate rapid responses to complex, fluctuating environments.

Chlamydospore dormancy and predatory activity of nematophagous fungus Duddingtonia flagrans

The chlamydospores of Duddingtonia flagrans are an essential survival and reproductive structure and also an effective ingredient for the biocontrol of parasitic nematodes in livestock. In this study, entering and exiting dormancy conditions and predatory activity of the fungal chlamydospores were conducted. During this fungal growth process, the cultivation time is negatively correlated with spore germination rates. After the spores were processed by vacuum drying for 168 h, their germination rate dropped to 0.94%. In contrast, the percentage of living spores remained 54.82%, suggesting that the spores entered structural dormancy in the arid environment. Meanwhile, the efficacies of the spore against Haemonchus contortus larvae were 93.05% (0 h), 92.19% (16 h), 92.77% (96 h), and 86.45% (168 h), respectively. After dormant spores were stored at 4°C, -20°C, and 28°C (RH90 ~ 95%) for 7 days, their germination rate began to increase significantly (p < 0.05). For in vitro predation assay under the condition of 28°C (RH90 ~ 95%), the predation rate was significantly higher on the 7th day after incubation than that on the 3rd day (p < 0.05). During the period when spores were stored at room temperature for 8 months, their germination rate decreased in the first 5 months and then increased slowly to reach a peak in the 7th month. However, the reduction rate of H. contortus L3 in feces captured by spores remained above 71% for the first 7 months. These results will help us increase the end products yield and the quality of biological control of parasitic nematodes in livestock.

High-throughput screening of the effects of 90 xenobiotics on the simplified human gut microbiota model (SIHUMIx): a metaproteomic and metabolomic study

The human gut microbiota is a complex microbial community with critical functions for the host, including the transformation of various chemicals. While effects on microorganisms has been evaluated using single-species models, their functional effects within more complex microbial communities remain unclear. In this study, we investigated the response of a simplified human gut microbiota model (SIHUMIx) cultivated in an in vitro bioreactor system in combination with 96 deep-well plates after exposure to 90 different xenobiotics, comprising 54 plant protection products and 36 food additives and dyes, at environmentally relevant concentrations. We employed metaproteomics and metabolomics to evaluate changes in bacterial abundances, the production of Short Chain Fatty Acids (SCFAs), and the regulation of metabolic pathways. Our findings unveiled significant changes induced by 23 out of 54 plant protection products and 28 out of 36 food additives across all three categories assessed. Notable highlights include azoxystrobin, fluroxypyr, and ethoxyquin causing a substantial reduction (log2FC < -0.5) in the concentrations of the primary SCFAs: acetate, butyrate, and propionate. Several food additives had significant effects on the relative abundances of bacterial species; for example, acid orange 7 and saccharin led to a 75% decrease in Clostridium butyricum, with saccharin causing an additional 2.5-fold increase in E. coli compared to the control. Furthermore, both groups exhibited up- and down-regulation of various pathways, including those related to the metabolism of amino acids such as histidine, valine, leucine, and isoleucine, as well as bacterial secretion systems and energy pathways like starch, sucrose, butanoate, and pyruvate metabolism. This research introduces an efficient in vitro technique that enables high-throughput screening of the structure and function of a simplified and well-defined human gut microbiota model against 90 chemicals using metaproteomics and metabolomics. We believe this approach will be instrumental in characterizing chemical-microbiota interactions especially important for regulatory chemical risk assessments.

A heritable iron memory enables decision-making in Escherichia coli

The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered when Escherichia coli encounters a new surface, improving its future swarming efficiency. We conducted >10,000 single-cell swarm assays to discover that cells store memory in the form of cellular iron levels. This "iron" memory preexists in planktonic cells, but the act of swarming reinforces it. A cell with low iron initiates swarming early and is a better swarmer, while the opposite is true for a cell with high iron. The swarming potential of a mother cell, which tracks with its iron memory, is passed down to its fourth-generation daughter cells. This memory is naturally lost by the seventh generation, but artificially manipulating iron levels allows it to persist much longer. A mathematical model with a time-delay component faithfully recreates the observed dynamic interconversions between different swarming potentials. We demonstrate that cellular iron levels also track with biofilm formation and antibiotic tolerance, suggesting that iron memory may impact other physiologies.

Prior exposure of microbial communities to seawater reduces resilience but increases compositional and functional resistance to flooding events

Storm surges, flooding, and the encroachment of seawater onto agricultural land are predicted to increase with climate change. These flooding events fundamentally alter many soil properties and have knock-on effects on the microbial community composition and its functioning. The hypotheses tested in this study were (1) that the extent of change (resistance) of microbial community functioning and structure during seawater flooding is a factor of pre-adaptation to the stress, and (2) if structure and function are altered, the pre-adaptation will result in communities returning to previous state prior to flooding (resilience) faster than unexposed communities. We chose a naturally occurring saltmarsh-terrestrial pasture gradient from which three elevations were selected to create mesocosms. By selecting these sites, we were able to incorporate the legacy of differing levels of seawater ingress and exposure. Mesocosms were submerged in seawater for 0, 1, 96- and 192-h, with half of the mesocosms sacrificed immediately after flooding, and the other half taken after a 14 day "recovery" period. The following parameters were monitored: 1) changes in soil environmental parameters, 2) prokaryotic community composition, and 3) microbial functioning. Our results indicated that any length of seawater inundation significantly altered the physicochemical properties of all the soils, although a greater change is observed in the pasture site compared to the saltmarsh sites. These changes remained following a recovery period. Interestingly, our results indicated that for community composition, there was a high degree of resistance for the Saltmarsh mesocosms, with the Pasture mesocosm displaying higher resilience. Further, we observed a functional shift in the enzyme activities with labile hemicellulose being preferentially utilised over cellulose, with the effect increasing with longer floods. These results suggest that changing bacterial physiology is more critical to understanding the impact of storm surges on agricultural systems than bulk community change.

Analysis of Antibacterial Efficacy and Cellular Alignment Regulation on Plasma Nanotextured Chitosan Surfaces

To address implant-related infections, antibacterial solutions specific to biomaterials are required to prevent bacterial proliferation. Traditional antibiotic usage has been found insufficient, motivating researchers to investigate alternative strategies such as surface modification and the application of antifouling or infection-resistant properties. A developing interest lies in designing surfaces that mimic natural antibacterial nanotopographies. In this study, we conducted a quantitative analysis of the outcomes from plasma nanotexturing, with particular emphasis on how the organization of topography influences antibacterial efficacy and the regulation of cell alignment. Plasma nanotexturing was applied to chitosan surfaces, which gradually transformed from nanopores to pillars and eventually into tilted pillars, as the plasma parameters (fluence and angle) increased. We used directed plasma nanosynthesis, a plasma-based technique that primarily induces topographical alterations on the surfaces. The surfaces were systematically characterized, incorporating methods such as scanning electron microscopy (SEM), atomic force microscopy (AFM), and X-ray photoelectron spectroscopy (XPS). A comprehensive comparison of the nanotextures was executed by utilizing a trapezoidal method to calculate aspect ratios and assess texture orientation by examining the gaps in the nanostructures. We evaluated antibacterial properties against E. coli and S. aureus strains and assessed the survival and alignment of human bone marrow mesenchymal stem cells. Our findings reveal a significant reduction in bacterial adhesion (>80%) and growth on nanotextured surfaces, underscoring their potential for clinical applications. Moreover, we measured cell alignment, presenting the results in both a color-coded and numerical format to demonstrate the preferential alignment orientation induced specially by the tilted nanotexture. These insights highlight the profound impacts of plasma nanotexturing, indicating its potential for innovative biomedical applications such as advanced wound healing and tissue engineering.

How Bacterial Pathogens Coordinate Appetite with Virulence

Cells adjust growth and metabolism to nutrient availability. Having access to a variety of carbon sources during infection of their animal hosts, facultative intracellular pathogens must efficiently prioritize carbon utilization. Here, we discuss how carbon source controls bacterial virulence, with an emphasis on Salmonella enterica serovar Typhimurium, which causes gastroenteritis in immunocompetent humans and a typhoid-like disease in mice, and propose that virulence factors can regulate carbon source prioritization by modifying cellular physiology. On the one hand, bacterial regulators of carbon metabolism control virulence programs, indicating that pathogenic traits appear in response to carbon source availability. On the other hand, signals controlling virulence regulators may impact carbon source utilization, suggesting that stimuli that bacterial pathogens experience within the host can directly impinge on carbon source prioritization. In addition, pathogen-triggered intestinal inflammation can disrupt the gut microbiota and thus the availability of carbon sources. By coordinating virulence factors with carbon utilization determinants, pathogens adopt metabolic pathways that may not be the most energy efficient because such pathways promote resistance to antimicrobial agents and also because host-imposed deprivation of specific nutrients may hinder the operation of certain pathways. We propose that metabolic prioritization by bacteria underlies the pathogenic outcome of an infection.

A three-colour stress biosensor reveals multimodal response in single cells and spatiotemporal dynamics of biofilms

The plethora of stress factors that can damage microbial cells has evolved sophisticated stress response mechanisms. While existing bioreporters can monitor individual responses, sensors for detecting multimodal stress responses in living microorganisms are still lacking. Orthogonally detectable red, green, and blue fluorescent proteins combined in a single plasmid, dubbed RGB-S reporter, enable simultaneous, independent, and real-time analysis of the transcriptional response of Escherichia coli using three promoters which report physiological stress (PosmY for RpoS), genotoxicity (PsulA for SOS), and cytotoxicity (PgrpE for RpoH). The bioreporter is compatible with standard analysis and Fluorescent Activated Cell Sorting (FACS) combined with subsequent transcriptome analysis. Various stressors, including the biotechnologically relevant 2-propanol, activate one, two, or all three stress responses, which can significantly impact non-stress-related metabolic pathways. Implemented in microfluidic cultivation with confocal fluorescence microscopy imaging, the RGB-S reporter enabled spatiotemporal analysis of live biofilms revealing stratified subpopulations of bacteria with heterogeneous stress responses.

Iron Memory in E. coli

The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered when E. coli encounters a new surface, improving its future swarming efficiency. We conducted >10,000 single-cell swarm assays to discover that cells store memory in the form of cellular iron levels. This memory pre-exists in planktonic cells, but the act of swarming reinforces it. A cell with low iron initiates swarming early and is a better swarmer, while the opposite is true for a cell with high iron. The swarming potential of a mother cell, whether low or high, is passed down to its fourth-generation daughter cells. This memory is naturally lost by the seventh generation, but artificially manipulating iron levels allows it to persist much longer. A mathematical model with a time-delay component faithfully recreates the observed dynamic interconversions between different swarming potentials. We also demonstrate that iron memory can integrate multiple stimuli, impacting other bacterial behaviors such as biofilm formation and antibiotic tolerance.

Extracellular DNA includes an important fraction of high-risk antibiotic resistance genes in treated wastewaters

Wastewater treatment plants are among the main hotspots for the release of antibiotic resistance genes (ARGs) into the environment. ARGs in treated wastewater can be found in the intracellular DNA (iDNA) and in the extracellular DNA (eDNA). In this study, we investigated the fate and the distribution (either in eDNA or in iDNA) of ARGs in the treated wastewaters pre and post-disinfection by shotgun metagenomics. The richness of the intracellular resistome was found to be higher than the extracellular one. However, the latter included different high risk ARGs. About 11% of the recovered metagenome assembled genomes (MAGs) from the extracted DNA was positive for at least one ARG and, among them, several were positive for more ARGs. The high-risk ARG bacA was the most frequently detected gene among the MAGs. The disinfection demonstrated to be an important driver of the composition of the antibiotic resistomes. Our results demonstrated that eDNA represents an important fraction of the overall ARGs, including a number of high-risk ARGs, which reach the environment with treated wastewater effluents. The studied disinfections only marginally affect the whole antibiotic resistome but cause important shifts from intracellular to extracellular DNA, potentially threating human health.

The genetic response of Salmonella Typhimurium during trans-cinnamaldehyde assisted heat treatment and its correlation with bacterial resistance in different low moisture food components

Our previous study found that water activity (a_w)- and matrix-dependent bacterial resistance wasdeveloped in Salmonella Typhimurium during antimicrobial-assisted heat treatment in low moisture foods (LMFs) matrices. To better understand the molecular mechanism behind the observed bacterial resistance, gene expression analysis was conducted on S. Typhimurium adapted to different conditions with or without the trans-cinnamaldehyde (CA)-assisted heat treatment via quantitative polymerase chain reaction (qPCR). Expression profiles of nine stress-related genes were analyzed. The upregulation of rpoH and dnaK and downregulation of ompC were observed during bacterial adaptation in LMF matrices and the combined heat treatment, which likely contributed to the bacterial resistance during the combined treatment. Their expression profiles were partially consistent with the previously-observed effect of a_w or matrix on bacterial resistance. The upregulation of rpoE, otsB, proV, and fadA was also observed during adaptation in LMF matrices and might contribute to desiccation resistance, but likely did not contribute to bacterial resistance during the combined heat treatment. The observed upregulation of fabA and downregulation of ibpA could not be directly linked to bacterial resistance to either desiccation or the combined heat treatment. The results may assist the development of more efficient processing methods against S. Typhimurium in LMFs.

Intrabacterial Regulation of a Cytotoxic Effector by Its Cognate Metaeffector Promotes Legionella pneumophila Virulence

Legionella pneumophila is a natural pathogen of unicellular protozoa that can opportunistically infect macrophages and cause Legionnaires' Disease. Intracellular replication is driven by hundreds of bacterial effector proteins that are translocated into infected host cells by a Dot/Icm type IV secretion system. L. pneumophila effectors are temporally regulated in part by a unique family of translocated regulatory effectors, termed metaeffectors, which bind and modulate the function of a cognate effector in host cells. Regulation of the cytotoxic effector SidI by its cognate metaeffector, MesI, is critical for L. pneumophila virulence in natural and opportunistic hosts. MesI binds and negatively regulates SidI activity in vitro, but how impaired regulation of SidI impairs L. pneumophila intracellular replication is unclear. Using a chromosomally encoded inducible expression system, we found that SidI was toxic to L. pneumophila when uncoupled from MesI. SidI enzymatic activity was required for intrabacterial toxicity since L. pneumophila growth was unaffected by induced expression of a catalytically inactive sidI allele. We also found that MesI translocation into host cells was dispensable for intracellular replication and that MesI-deficient bacteria were rapidly degraded within host cells. These data suggest that MesI promotes L. pneumophila intracellular replication by regulating SidI within the bacterium and reveal a unique role for intrabacterial effector regulation by a translocated metaeffector in L. pneumophila virulence. IMPORTANCE Legionella pneumophila replicates within phagocytic host cells using hundreds of effector protein virulence factors, which canonically subvert the function of host proteins and pathways. L. pneumophila encodes a unique family of translocated effectors called metaeffectors, which bind and regulate the function of a cognate effector in host cells. The metaeffector MesI promotes L. pneumophila virulence by regulating the cytotoxic effector SidI; however, the MesI regulatory mechanism is poorly understood. We discovered a unique intrabacterial role for MesI in L. pneumophila virulence. When uncoupled from MesI, SidI was toxic to L. pneumophila in vitro and triggered robust bacterial degradation in host cells. Furthermore, translocation of MesI was dispensable for intracellular replication, demonstrating that intrabacterial regulation of SidI contributes to L. pneumophila virulence. These data show a novel and important role for translocated effector activity within the bacterium, which challenges the dogma that L. pneumophila effectors function exclusively within host cells.

Autotoxin-mediated latecomer killing in yeast communities

Cellular adaptation to stressful environments such as starvation is essential to the survival of microbial communities, but the uniform response of the cell community may lead to entire cell death or severe damage to their fitness. Here, we demonstrate an elaborate response of the yeast community against glucose depletion, in which the first adapted cells kill the latecomer cells. During glucose depletion, yeast cells release autotoxins, such as leucic acid and L-2keto-3methylvalerate, which can even kill the clonal cells of the ones producing them. Although these autotoxins were likely to induce mass suicide, some cells differentiated to adapt to the autotoxins without genetic changes. If nondifferentiated latecomers tried to invade the habitat, autotoxins damaged or killed the latecomers, but the differentiated cells could selectively survive. Phylogenetically distant fission and budding yeast shared this behavior using the same autotoxins, suggesting that latecomer killing may be the universal system of intercellular communication, which may be relevant to the evolutional transition from unicellular to multicellular organisms.

A Plasma-Based Decontamination Process Reveals Potential for an in-Process Surface-Sanitation Method

Methods, which use an indirect plasma treatment for the inactivation of microorganisms in foods, claim a vastly growing field of research. This paper presents a method that uses plasma-processed air (PPA) as a sanitizer. In addition to a sanitation concept for the decontamination of produce in the value chain, the presented method offers a possible application as an “in-process” surface sanitation. PPA provides antimicrobial-potent species, which are predominantly reactive nitrogen species (RNS); this has an outstanding groove penetration property. In an experimental approach, surfaces, made from materials, which are frequently used for the construction of food-processing plants, were inoculated with different microorganisms. Listeria monocytogenes (ATCC 15313), Staphylococcus aureus (ATCC 6538), Escherichia coli (ATCC 10538), Salmonella enterica subsp. enterica serovar Typhimurium (ATCC 43971), and Salmonella enterica subsp. enterica serovar Enteritidis (ATCC 13076) are all microorganisms that frequently appear in foods and possess the risk for cross-contamination from the plant to the produce or vice versa. The contaminated samples were treated for various treatment times (1–5 min) with PPA of different antimicrobial potencies. Subsequently, the microbial load on the specimens was determined and compared with the load of untreated samples. As a result, reduction factors (RF) up to several log10-steps were obtained. Although surface and the bacterial strain showed an influence on the RF, the major influence was seen by a prolongation of the treatment time and an increase in the potency of the PPA.

Effects of Phenotypic Variation on Biological Properties of Endophytic Bacteria Bacillus mojavensis PS17

Simple Summary

Microorganisms play an important role in agriculture by protecting and stimulating the growth of plants. The phenotypic activities of microbial biological agents (MBA) can change under different environmental conditions. However, to adapt to these harsh conditions, genetic mutations take place in bacteria that are seen phenotypically, which might not be beneficial or less beneficial to the plants. Some adaptative mechanisms used by microorganisms, especially bacteria, to face these environmental factors lead to the appearance of subpopulations with different morphotypes that may be more adapted to survive in stressful conditions. Moreover, in favorable conditions, these subpopulations may become dominant among the overall bacterial population. In this study, Bacillus mojavensis undergoes phase variation when grown in a minimal medium, in which two colonies, opaque (morphotype I) and translucent (morphotype II), were generated. The characteristics of the generated morphotypes were determined and compared with those of their original strain. Overall, the results obtained showed that the phenotypic characteristics of morphotype I statistically differed from morphotype II. This phenomenon may be one of the factors behind the dissimilarities in the results between the laboratory and field data on the application of MBA.

Abstract

The use of microorganism-based products in agricultural practices is gaining more interest as an alternative to chemical methods due to their non-toxic bactericidal and fungicidal properties. Various factors influence the efficacy of the microorganisms used as biological control agents in infield conditions as compared to laboratory conditions due to ecological and physiological aspects. Abiotic factors have been shown to trigger phase variations in bacterial microorganisms as a mechanism for adapting to hostile environments. In this study, we investigated the stability of the morphotype and the effects of phenotypic variation on the biological properties of Bacillus mojavensis strain PS17. B. mojavensis PS17 generated two variants (opaque and translucent) that were given the names morphotype I and II, respectively. The partial sequence of the 16S rRNA gene revealed that both morphotypes belonged to B. mojavensis. BOX and ERIC fingerprinting PCR also showed the same DNA profiles in both morphotypes. The characteristics of morphotype I did not differ from the original strain, while morphotype II showed a lower hydrolytic enzyme activity, phytohormone production, and antagonistic ability against phytopathogenic fungi. Both morphotypes demonstrated endophytic ability in tomato plants. A low growth rate of the strain PS17(II) in a minimal medium was observed in comparison to the PS17(I) strain. Furthermore, the capacity for biocontrol of B. mojavensis PS17(II) was not effective in the suppression of root rot disease in the tomato plants caused by Fusarium oxysporum f. sp. radices-lycopersici stain ZUM2407, compared to B. mojavensis PS17(I), whose inhibition was almost 47.9 ± 1.03% effective.

Role of Promising Secondary Metabolites to Confer Resistance Against Environmental Stresses in Crop Plants: Current Scenario and Future Perspectives

Plants often face incompatible growing environments like drought, salinity, cold, frost, and elevated temperatures that affect plant growth and development leading to low yield and, in worse circumstances, plant death. The arsenal of versatile compounds for plant consumption and structure is called metabolites, which allows them to develop strategies to stop enemies, fight pathogens, replace their competitors and go beyond environmental restraints. These elements are formed under particular abiotic stresses like flooding, heat, drought, cold, etc., and biotic stress such as a pathogenic attack, thus associated with survival strategy of plants. Stress responses of plants are vigorous and include multifaceted crosstalk between different levels of regulation, including regulation of metabolism and expression of genes for morphological and physiological adaptation. To date, many of these compounds and their biosynthetic pathways have been found in the plant kingdom. Metabolites like amino acids, phenolics, hormones, polyamines, compatible solutes, antioxidants, pathogen related proteins (PR proteins), etc. are crucial for growth, stress tolerance, and plant defense. This review focuses on promising metabolites involved in stress tolerance under severe conditions and events signaling the mediation of stress-induced metabolic changes are presented.

Proteomic Signatures of Microbial Adaptation to the Highest Ultraviolet-Irradiation on Earth: Lessons From a Soil Actinobacterium

In the Central Andean region in South America, high-altitude ecosystems (3500-6000 masl) are distributed across Argentina, Chile, Bolivia, and Peru, in which poly-extremophilic microbes thrive under extreme environmental conditions. In particular, in the Puna region, total solar irradiation and UV incidence are the highest on Earth, thus, restraining the physiology of individual microorganisms and the composition of microbial communities. UV-resistance of microbial strains thriving in High-Altitude Andean Lakes was demonstrated and their mechanisms were partially characterized by genomic analysis, biochemical and physiological assays. Then, the existence of a network of physiological and molecular mechanisms triggered by ultraviolet light exposure was hypothesized and called "UV-resistome". It includes some or all of the following subsystems: (i) UV sensing and effective response regulators, (ii) UV-avoidance and shielding strategies, (iii) damage tolerance and oxidative stress response, (iv) energy management and metabolic resetting, and (v) DNA damage repair. Genes involved in the described UV-resistome were recently described in the genome of Nesterenkonia sp. Act20, an actinobacterium which showed survival to high UV-B doses as well as efficient photorepairing capability. The aim of this work was to use a proteomic approach together with photoproduct measurements to help dissecting the molecular events involved in the adaptive response of a model High-Altitude Andean Lakes (HAAL) extremophilic actinobacterium, Nesterenkonia sp. Act20, under artificial UV-B radiation. Our results demonstrate that UV-B exposure induced over-abundance of a well-defined set of proteins while recovery treatments restored the proteomic profiles present before the UV-challenge. The proteins involved in this complex molecular network were categorized within the UV-resistome subsystems: damage tolerance and oxidative stress response, energy management and metabolic resetting, and DNA damage repair.

pH Stress Mediated Alteration in Protein Composition and Reduction in Cytotoxic Potential of Gardnerella vaginalis Membrane Vesicles

The vagina of healthy women is predominantly colonized by lactobacilli but it also harbors a limited proportion of certain anaerobes such as Gardnerella vaginalis. An increase in G. vaginalis along with other anaerobes on account of perturbation in the vaginal microbiota is associated with bacterial vaginosis (BV). Although strategies adopted by G. vaginalis for survival and pathogenesis in a conducive environment (i.e., high vaginal pH, characteristic of BV) have been previously studied, the approaches potentially employed for adaptation to the low pH of the healthy vagina are unknown. In the present study, we investigated the effect of acidic stress on the modulation of the production and function of membrane vesicles (MVs) of G. vaginalis. pH stress led to a distortion of the bacterial cell morphology as well as an altered biogenesis of MVs, as revealed by transmission electron microscopy (TEM). Both qualitative and quantitative differences in protein content of MVs produced in response to pH stress were observed by flow cytometry. A significant change in the protein composition characterized by presence of chaperones despite a reduction in number of proteins was also noted in the stress induced MVs. Further, these changes were also reflected in the reduced cytotoxic potential toward vaginal epithelial cells. Although, these findings need to be validated in the in vivo settings, the modulation of G. vaginalis MV biogenesis, composition and function appears to reflect the exposure to acidic conditions prevailing in the host vaginal mileu in the absence of vaginal infection.

Effect of two thermoresistant non-starter lactic acid bacteria strains on volatilome profile during Cheddar ripening simulation

Dairy farm management practices can modify milk microbiota and therefore modulate non-starter lactic acid bacteria (NSLAB) found in cheese. These NSLAB can cause organoleptic defects. This study aimed to investigate the impact of two potential NSLAB in Cheddar cheesemaking: Lactiplantibacillus plantarum RKG 2-212 a strain isolated both in corn silage and raw milk, and Lactobacillus delbrueckii RKG R10, a strain isolated after pasteurisation of milk from a farm using grass and legume silage, and corn silage. The whole genome of these two lactobacilli was first sequenced. Then, the thermoresistance was evaluated after treatment at 60 °C for 5 min and compared to reference strains. Both lactobacilli were highly thermoresistant compared to other three lactic acid bacteria which are Lactococcus lactis subsp. cremoris ATCC 19257 and SK11, and L. plantarum ATCC 14917 (P < 0.0001). They lost less than 1 log cfu/mL (Δlog) and their genome contained a great number of copy number of genes coding for heat shock protein. During a Pearce test activity simulating Cheddar cheesemaking, the two lactobacilli did not show interaction with the starter Lcc. lactis subsp. cremoris SK11, and their population remained stable. During a ripening simulation, L. delbrueckii RKG R10 had a slight loss in viability in cheese slurry samples incubated at 30 °C for 12 d. However, L. plantarum RKG 2-212 had considerable growth, from 6.51 to 8.3 log cfu/g. This growth was associated with the acidification of the slurries (P < 0.0001). The presence of the lactobacilli modified the profile of volatile compounds evaluated by gas chromatography-mass spectrometry, accounting for 10.7% of the variation. The strain L. plantarum RKG 2-212 produced volatile compounds in greater quantity that could be associated with organoleptic defects such as acetic acid and 2-methylbutyraldehyde. Therefore, silage can be a vector of thermoresistant lactic acid bacteria for milk which can lead to flavor defects in cheese.

Membrane Depolarization and Apoptosis-Like Cell Death in an Alkaline Environment in the Rice Pathogen Burkholderia glumae

The rice pathogen Burkholderia glumae uses amino acids as a principal carbon source and thus produces ammonia in amino acid-rich culture medium such as Luria-Bertani (LB) broth. To counteract ammonia-mediated environmental alkaline toxicity, the bacterium produces a public good, oxalate, in a quorum sensing (QS)-dependent manner. QS mutants of B. glumae experience alkaline toxicity and may undergo cell death at the stationary phase when grown in LB medium. Here, we show that the cell-death processes of QS mutants due to alkaline environmental conditions are similar to the apoptosis-like cell death reported in other bacteria. Staining QS mutants with bis-(1,3-dibutylbarbituric acid)-trimethine oxonol revealed membrane depolarization. CellROX™ staining showed excessive generation of reactive oxygen species (ROS) in QS mutants. The expression of genes encoding HNH endonuclease (BGLU_1G15690), oligoribonuclease (BGLU_1G09120), ribonuclease E (BGLU_1G09400), and Hu-beta (BGLU_1G13530) was significantly elevated in QS mutants compared to that in wild-type BGR1, consistent with the degradation of cellular materials as observed under transmission electron microscopy (TEM). A homeostatic neutral pH was not attainable by QS mutants grown in LB broth or by wild-type BGR1 grown in an artificially amended alkaline environment. At an artificially adjusted alkaline pH, wild-type BGR1 underwent apoptosis-like cell death similar to that observed in QS mutants. These results show that environmental alkaline stress interferes with homeostatic neutral cellular pH, induces membrane depolarization, and causes apoptosis-like cell death in B. glumae.

Biodegradation of used polyethylene bags by a new marine strain of Alcaligenes faecalis LNDR-1

Disposable plastic bags of two different chemical compositions and colors were remediated by the application of novel mesophilic group of bacteria isolated from the banks of sea water, using a 10 week soil burial method. The new strain, LNDR-1, was identified as Alcaligens faecalis by its morphological features and 16S rRNA sequencing. LNDR-1 was able to produce extracellular enzymes such as lipase, CMCase, xylanase, and protease, having PET surface degrading activity. It was found that LNDR-1 had a better decay rate of 15.25 ± 1% and 21.72 ± 2.1% for black and white plastic bags respectively in 10 weeks without prior oxidation as compared to S. marcescens. Polyethylene degradation was confirmed by substantial weight loss, alterations in surface topology, and hydrophobicity index and was found to be directly proportional to the ability to form biofilm on the plastic surface. FTIR results suggest presence of different metabolites in the bags treated with bacterial biofilm in comparison to the control setup inferring various types of metabolic pathways. Present study also reveals the ability of the strain to utilize the used polyethylene bag as the carbon source, without any prior treatment, and as per the literature survey, the working strain is with the capacity to biodegrade plastic at a considerably appreciable rate. This study suggests effectual method for the mechanism of biodegradation of plastic mediated by extracellular enzymes and formation of biofilm.

The two Pseudomonas aeruginosa DksA stringent response proteins are largely interchangeable at the whole transcriptome level and in the control of virulence-related traits

The stringent response regulator DksA plays a key role in Gram negative bacteria adaptation to challenging environments. Intriguingly, the plant and human pathogen Pseudomonas aeruginosa is unique as it expresses two functional DksA paralogs: DksA1 and DksA2. However, the role of DksA2 in P. aeruginosa adaptive strategies has been poorly investigated so far. Here, RNA-Seq analysis and phenotypic assays showed that P. aeruginosa DksA1 and DksA2 proteins are largely interchangeable. Relative to wild type P. aeruginosa, transcription of 1779 genes was altered in a dksA1 dksA2 double mutant, and the wild type expression level of ≥90% of these genes was restored by in trans complementation with either dksA1 or dksA2. Interestingly, the expression of a small sub-set of genes seems to be preferentially or exclusively complemented by either dksA1 or dksA2. In addition, evidence has been provided that the DksA-dependent regulation of virulence genes expression is independent and hierarchically dominant over two major P. aeruginosa regulatory circuits, i.e., quorum sensing and cyclic-di-GMP signalling systems. Our findings support the prominent role of both DksA paralogs in P. aeruginosa environmental adaptation.

The role of carotenoids in proton-pumping rhodopsin as a primitive solar energy conversion system

Rhodopsin and carotenoids are two molecules that certain bacteria use to absorb and utilize light. Type I rhodopsin, the simplest active proton transporter, converts light energy into an electrochemical potential. Light produces a proton gradient, which is known as the proton motive force across the cell membrane. Some carotenoids are involved in light absorbance and transfer of absorbed energy to chlorophyll during photosynthesis. A previous study in Salinibacter ruber has shown that carotenoids act as antennae to harvest light and transfer energy to retinal in xanthorhodopsin (XR). Here, we describe the role of canthaxanthin (CAN), a carotenoid, as an antenna for Gloeobacter rhodopsin (GR). The non-covalent complex formed by the interaction between CAN and GR doubled the proton pumping speed and improved the pumping capacity by 1.5-fold. The complex also tripled the proton pumping speed and improved the pumping capacity by 5-fold in the presence of strong and weak light, respectively. Interestingly, when canthaxanthin was bound to Gloeobacter rhodopsin, it showed a 126-fold increase in heat resistance, and it survived better under drought conditions than Gloeobacter rhodopsin. The results suggest direct complementation of Gloeobacter rhodopsin with a carotenoid for primitive solar energy harvesting in cyanobacteria.

High temperatures enhance the microbial genetic potential to recycle C and N from necromass in high-mountain soils

Climate change is strongly affecting high-mountain soils and warming in particular is associated with pronounced changes in microbe-mediated C and N cycling, affecting plant-soil interactions and greenhouse gas balances and therefore feedbacks to global warming. We used shotgun metagenomics to assess changes in microbial community structures, as well as changes in microbial C- and N-cycling potential and stress response genes and we linked these data with changes in soil C and N pools and temperature-dependent measurements of bacterial growth rates. We did so by incubating high-elevation soil from the Swiss Alps at 4°C, 15°C, 25°C, or 35°C for 1 month. We found no shift with increasing temperature in the C-substrate-degrader community towards taxa more capable of degrading recalcitrant organic matter. Conversely, at 35°C, we found an increase in genes associated with the degradation and modification of microbial cell walls, together with high bacterial growth rates. Together, these findings suggest that the rapidly growing high-temperature community is fueled by necromass from heat-sensitive taxa. This interpretation was further supported by a shift in the microbial N-cycling potential towards N mineralization and assimilation under higher temperatures, along with reduced potential for conversions among inorganic N forms. Microbial stress-response genes reacted inconsistently to increasing temperature, suggesting that the high-temperature community was not severely stressed by these conditions. Rather, soil microbes were able to acclimate by changing the thermal properties of membranes and cell walls as indicated by an increase in genes involved in membrane and cell wall modifications as well as a shift in the optimum temperature for bacterial growth towards the treatment temperature. Overall, our results suggest that high temperatures, as they may occur with heat waves under global warming, promote a highly active microbial community capable of rapid mineralization of microbial necromass, which may transiently amplify warming effects.

The study of the molecular mechanism of Lactobacillus paracasei clumping via divalent metal ions by electrophoretic separation

In this work, the molecular mechanism of Lactobacillus paracasei bio-colloid clumping under divalent metal ions treatment such as zinc, copper and magnesium at constant concentrations was studied. The work involved experimental (electrophoretic - capillary electrophoresis in pseudo-isotachophoresis mode, spectroscopic and spectrometric - FT-IR and MALDI-TOF-MS, microscopic - fluorescent microscopy, and flow cytometry) and theoretical (DFT calculations of model complex systems) characterization. Electrophoretic results have pointed out the formation of aggregates under the Zn²⁺ and Cu²⁺ modification, whereas the use of the Mg²⁺ allowed focusing the zone of L. paracasei biocolloid. According to the FT-IR analysis, the major functional groups involved in the aggregation are deprotonated carboxyl and amide groups derived from the bacterial surface structure. Nature of the divalent metal ions was shown to be one of the key factors influencing the bacterial aggregation process. Proteomic analysis showed that surface modification had a considerable impact on bacteria molecular profiles and protein expression, mainly linked to the activation of carbohydrate and nucleotides metabolism as well with the transcription regulation and membrane transport. Density-functional theory (DFT) calculations of modeled Cu²⁺, Mg²⁺ and Zn²⁺ coordination complexes support the interaction between the divalent metal ions and bacterial proteins. Consequently, the possible mechanism of the aggregation phenomenon was proposed. Therefore, this comprehensive study could be further applied in evaluation of biocolloid aggregation under different types of metal ions.

Global transcriptome analysis of Rhizobium favelukesii LPU83 in response to acid stress

Acidic environments naturally occur worldwide and inappropriate agricultural management may also cause acidification of soils. Low soil pH values are an important barrier in the plant-rhizobia interaction. Acidic conditions disturb the establishment of the efficient rhizobia usually used as biofertilizer. This negative effect on the rhizobia-legume symbiosis is mainly due to the low acid tolerance of the bacteria. Here, we describe the identification of relevant factors in the acid tolerance of Rhizobium favelukesii using transcriptome sequencing. A total of 1924 genes were differentially expressed under acidic conditions, with ∼60% underexpressed. Rhizobium favelukesii acid response mainly includes changes in the energy metabolism and protein turnover, as well as a combination of mechanisms that may contribute to this phenotype, including GABA and histidine metabolism, cell envelope modifications and reverse proton efflux. We confirmed the acid-sensitive phenotype of a mutant in the braD gene, which showed higher expression under acid stress. Remarkably, 60% of the coding sequences encoded in the symbiotic plasmid were underexpressed and we evidenced that a strain cured for this plasmid featured an improved performance under acidic conditions. Hence, this work provides relevant information in the characterization of genes associated with tolerance or adaptation to acidic stress of R. favelukesii.

The impact of cell structure, metabolism and group behavior for the survival of bacteria under stress conditions

Microbes from diverse types of habitats are continuously exposed to external challenges, which may include acidic, alkaline, and toxic metabolites stress as well as nutrient deficiencies. To promote their own survival, bacteria have to rapidly adapt to external perturbations by inducing particular stress responses that typically involve genetic and/or cellular changes. In addition, pathogenic bacteria need to sense and withstand these environmental stresses within a host to establish and maintain infection. These responses can be, in principle, induced by changes in bacterial cell structure, metabolism and group behavior. Bacterial nucleic acids may serve as the core part of the stress response, and the cell envelope and ribosomes protect genetic structures from damage. Cellular metabolism and group behavior, such as quorum sensing system, can play a more important role in resisting stress than we have now found. Since bacteria survival can be only appreciated if we better understand the mechanisms behind bacterial stress response, here we review how morphological and physiological features may lead to bacterial resistance upon exposure to particular stress-inducing factors.

Heat stress as an innovative approach to enhance the antioxidant production in Pseudooceanicola and Bacillus isolates

It is well known that the quality and quantity of bioactive metabolites in plants and microorganisms are affected by environmental factors. We applied heat stress as a promising approach to stimulate the production of antioxidants in four heat-tolerant bacterial strains (HT1 to HT4) isolated from Aushazia Lake, Qassim Region, Saudi Arabia. The phylogenetic analysis of the 16S rRNA sequences indicated that HT1, HT3 and HT4 belong to genus Bacillus. While HT2 is closely related to Pseudooceanicola marinus with 96.78% similarity. Heat stress differentially induced oxidative damage i.e., high lipid peroxidation, lipoxygenase and xanthine oxidase levels in HT strains. Subsequently, heat stress induced the levels of flavonoids and polyphenols in all strains and glutathione (GSH) in HT2. Heat stress also improved the antioxidant enzyme activities, namely, CAT, SOD and POX in all strains and thioredoxin activity in HT3 and HT4. While GSH cycle (GSH level and GPX, GR, Grx and GST activities) was only detectable and enhanced by heat stress in HT2. The hierarchical cluster analysis of the antioxidants also supported the strain-specific responses. In conclusion, heat stress is a promising approach to enhance antioxidant production in bacteria with potential applications in food quality improvement and health promotion.

Salinity Stress Enhances the Antioxidant Capacity of Bacillus and Planococcus Species Isolated From Saline Lake Environment

This study aims at exploiting salinity stress as an innovative, simple, and cheap method to enhance the production of antioxidant metabolites and enzymes from bacteria for potential application as functional additives to foods and pharmaceuticals. We investigated the physiological and biochemical responses of four bacterial isolates, which exhibited high tolerance to 20% NaCl (wt/vol), out of 27 bacterial strains isolated from Aushazia Lake, Qassim region, Saudi Arabia. The phylogenetic analysis of the 16S rRNA genes of these four isolates indicated that strains ST1 and ST2 belong to genus Bacillus, whereas strains ST3 and ST4 belong to genus Planococcus. Salinity stress differentially induced oxidative damage, where strains ST3 and ST4 showed increased lipid peroxidation, lipoxygenase, and xanthine oxidase levels. Consequently, high antioxidant contents were produced to control oxidative stress, particularly in ST3 and ST4. These two Planococcus strains showed increased glutathione cycle, phenols, flavonoids, antioxidant capacity, catalase, and/or superoxide dismutase (SOD). Interestingly, the production of glutathione by Planococcus strains was some thousand folds greater than by higher plants. On the other hand, the induction of antioxidants in ST1 and ST2 was restricted to phenols, flavonoids, peroxidase, glutaredoxin, and/or SOD. The hierarchical analysis also supported strain-specific responses. This is the first report that exploited salinity stress for promoting the production of antioxidants from bacterial isolates, which can be utilized as postbiotics for promising applications in foods and pharmaceuticals.

The Stringent Stress Response Controls Proteases and Global Regulators under Optimal Growth Conditions in Pseudomonas aeruginosa

Microorganisms need to adapt rapidly to survive harsh environmental changes. Here, we showed the broad influence of the highly studied bacterial stringent stress response under nonstressful conditions that indicate its general physiological importance and might reflect the readiness of bacteria to respond to and activate acute stress responses. Using RNA-Seq to investigate the transcriptional network of Pseudomonas aeruginosa cells revealed that >30% of all genes changed expression in a stringent response mutant under optimal growth conditions. This included genes regulated by global transcriptional regulators and novel downstream effectors. Our results help to understand the importance of this stress regulator in bacterial lifestyle under relatively unstressed conditions. As such, it draws attention to the consequences of targeting this ubiquitous bacterial signaling molecule.

The bacterial stringent stress response, mediated by the signaling molecule guanosine tetraphosphate, ppGpp, has recently gained attention as being important during normal cellular growth and as a potential new therapeutic target, which warrants detailed mechanistic understanding. Here, we used intracellular protein tracking in Pseudomonas aeruginosa PAO1, which indicated that RelA was bound to the ribosome, while SpoT localized at the cell poles. Transcriptome sequencing (RNA-Seq) was used to investigate the transcriptome of a ppGpp-deficient strain under nonstressful, nutrient-rich broth conditions where the mutant grew at the same rate as the parent strain. In the exponential growth phase, the lack of ppGpp led to >1,600 transcriptional changes (fold change cutoff of ±1.5), providing further novel insights into the normal physiological role of ppGpp. The stringent response was linked to gene expression of various proteases and secretion systems, including aprA, PA0277, impA, and clpP2. The previously observed reduction in cytotoxicity toward red blood cells in a stringent response mutant appeared to be due to aprA. Investigation of an aprA mutant in a murine skin infection model showed increased survival rates of mice infected with the aprA mutant, consistent with previous observations that stringent response mutants have reduced virulence. In addition, the overexpression of relA, but not induction of ppGpp with serine hydroxamate, dysregulated global transcriptional regulators as well as >30% of the regulatory networks controlled by AlgR, OxyR, LasR, and AmrZ. Together, these data expand our knowledge about ppGpp and its regulatory network and role in environmental adaptation. It also confirms its important role throughout the normal growth cycle of bacteria.

IMPORTANCE Microorganisms need to adapt rapidly to survive harsh environmental changes. Here, we showed the broad influence of the highly studied bacterial stringent stress response under nonstressful conditions that indicate its general physiological importance and might reflect the readiness of bacteria to respond to and activate acute stress responses. Using RNA-Seq to investigate the transcriptional network of Pseudomonas aeruginosa cells revealed that >30% of all genes changed expression in a stringent response mutant under optimal growth conditions. This included genes regulated by global transcriptional regulators and novel downstream effectors. Our results help to understand the importance of this stress regulator in bacterial lifestyle under relatively unstressed conditions. As such, it draws attention to the consequences of targeting this ubiquitous bacterial signaling molecule.

Overview of biochar production from preservative-treated wood with detailed analysis of biochar characteristics, heavy metals behaviors, and their ecotoxicity

Concerns over the disposal of preservative-treated wood waste and its related environmental problems are the main driving forces of research into the recycling of preservative-treated wood. Preservative-treated wood waste composed of cellulose, hemicellulose, and lignin with several types of heavy metals can be recycled in various ways, such as wood-based composites, heavy metal extraction, energy recovery, etc. In particular, thermochemical conversion has attracted considerable attention recently because energy can be recovered from biomass as liquid fuel and bio-oil, as well as produce bio-char with a high carbon content, which can be applied to valuable products, such as soil amendment, adsorbents, solid fuels, and catalyst supports. On the other hand, environmental issues, such as heavy metal volatilization and heavy metal leaching, are still a challenge. This review reports the state-of-the-art knowledge of biochar production from preservative-treated wood with the main focus on the feedstock, process technology, biochar characteristics, application, and environmental issues. This review provides important information for future studies into the recycling of preservative-treated woods into biochar.

Recent advances of pH homeostasis mechanisms in Corynebacterium glutamicum

Corynebacterium glutamicum is generally regarded as a safe microorganism, and widely used in the large-scale production of various amino acids and organic acids, such as L-glutamate, L-lysine and succinic acid. During the process of industrial fermentation, C. glutamicum is usually exposed to varying environmental stresses, such as variations in pH, salinity, temperature, and osmolality. Among them, pH fluctuations are regarded as one of the most frequent environmental stresses in microbial fermentation. In this review, we summarize the current knowledge of pH homeostasis mechanisms adopted by C. glutamicum for coping with low acidic pH and high alkaline pH stresses. Facing with low pH environments, C. glutamicum develops a variety of strategies to maintain intracellular pH homeostasis, such as lowering intracellular reactive oxygen species, the improvement of potassium transport, the regulation of mycothiol-related pathways, as well as the repression of sulfur assimilation. While during alkaline pH stresses, the Mrp-type Na⁺/H⁺ antiporters are shown to play a dominant role in conferring C. glutamicum cells resistance to alkaline pH. Furthermore, we also discuss the general strategies and prospects on metabolic engineering of C. glutamicum to improve alkaline or acid resistance.

Temperature as competitive strategy determining factor in pulse-fed aerobic bioreactors

Exposing a microbial community to alternating absence and presence of carbon substrate in aerobic conditions is an effective strategy for enrichment of storage polymers (polyhydroxybutyrate, PHB) producing microorganisms. In this work we investigate to which extent intermediate storage polymer production is a temperature independent microbial competition determining factor. Eight parallel bioreactors were operated in the temperature range of 20-40 °C, but intermediate storage polymer production was only obtained at 25-35 °C. Besides PHB production and consumption, cell decay and subsequent cryptic growth on lysis products was found to determine process properties and the microbial community structure at all operational temperatures. At 40 °C decay processes cannot be overcome with additional energy from storage polymers, and fast-growing microorganisms dominate the system. At 20 °C, highly competitive communities with ambiguous storage properties were enriched. The results described here demonstrate that a rigorous experimental approach could aid in the understanding of competitive strategies in microbial communities.

Nutrition Related Stress Factors Reduce the Transfer of Extended-Spectrum Beta-Lactamase Resistance Genes between an Escherichia coli Donor and a Salmonella Typhimurium Recipient In Vitro

The transfer of extended spectrum β-lactamase (ESBL)-genes occurs frequently between different bacteria species. The aim of this study was to investigate the impact of nutrition related stress factors on this transfer. Thus, an Escherichia coli donor and a Salmonella Typhimurium recipient were co-incubated for 4 h in media containing different levels of the stress factors' pH, osmolality, copper, zinc and acetic, propionic, lactic, and n-butyric acid, as well as subtherapeutic levels of cefotaxime, sulfamethoxazole/trimethoprim, and nitrofurantoin. Conjugation frequencies were calculated as transconjugants per donor, recipient, and total bacterial count. A correction factor for the stress impact on bacterial growth was used. Acetic, lactic, and n-butyric, acid, as well as pH, showed no significant impact. In contrast, increasing concentrations of propionate, zinc, copper, and nitrofurantoin, as well as increased osmolality reduced conjugation frequencies. Sulfamethoxazole/trimethoprim and cefotaxime showed increased transconjugants per donor, which decreased after correction for stress. This study showed, for the model mating pair, that conjugation frequencies decreased under different physiological stress conditions, and, thus, the hypothesis that stress factors may enhance conjugation should be viewed with caution. Furthermore, for studies on in vitro gene transfer, it is vital to consider the impact of studied stressors on bacterial growth.

Plausible role of bacterial toxin-antitoxin system in persister cell formation and elimination

Although, a large proportion of pathogenic bacteria gets eliminated from hosts after antibiotic treatment, a fraction of population confronts against such effects and undergoes growth arrest to form persisters. Persistence in bacteria is a dormant physiological state where cells escape the effects of antimicrobials as well as other host immune defences without any genetic mutations. The state of dormancy is achieved through various complex phenomena and it is known that a gene pair named as toxin-antitoxin (TA) acts as a key player of persister cell formation where the toxin is activated either stochastically or after an environmental insult, thereby silencing the physiological processes. However, the controversial role of TA modules in persister cell formation has also been documented with reasonable clarity. Persisters may revert back from state of quiescence and regrow when conditions become favourable for their propagation. Therefore, the elimination of dormant bacteria is crucial, and currently, research interest is highly focussed on developing several antipersister strategies that may kill persister bacteria by targeting different molecules. It is worth examining these targets to develop appropriate therapeutic interventions against bacterial infections and it is believed that earmarking TA system can be a novel approach for resuscitation of persisters. In this review, we discussed the role of TA modules in mediating persistence with highlighting on the debatable issues regarding contribution of these modules in dormant bacteria formation. Furthermore, we discussed if these modules in bacteria can be targeted for successful elimination of dormant persister cells.

Nasal colonization with methicillin-resistant Staphylococcus aureus associated with elevated homocysteine levels in the general US adults

Given the emergence of community-acquired methicillin-resistant Staphylococcus aureus (MRSA) as a global health threat, understanding the risk factors for MRSA infection in the community may be a reasonable strategy to prevent it. We investigated the associations between serum homocysteine levels and prevalence of nasal colonization with S aureus and MRSA among United States adults. We conducted a cross-sectional analysis of a nationally representative sample of 7832 adults (20 years or older). The main outcome variables were nasal colonization with S aureus and MRSA. Percentages of colonization with S aureus and MRSA were calculated by the quartiles of serum homocysteine. A total of 7832 of 2051 subjects (26.2%) were culture positive for S aureus, 98 (4.8%) of whom had nasal colonization with MRSA. In comparison with subjects having the lowest serum homocysteine, the odds of nasal colonization with MRSA were significantly higher in those with the highest homocysteine (odds ratio, 3.09; 95% confidence interval, 1.11-8.61) in multivariate analysis, adjusted for all confounding variables. By contrast, homocysteine elevation was not significantly associated with S aureus colonization. Nasal colonization with MRSA in the general community was significantly associated with increases in serum homocysteine levels.

Comparative stress response to food preservation conditions of ST19 and ST213 genotypes of Salmonella enterica serotype Typhimurium

The replacement of the most prevalent Salmonella enterica genotypes has been documented worldwide. Here we tested the hypothesis that the current prevalent sequence type ST213 of serotype Typhimurium in Mexico has a higher resistance to stressful food preservation conditions than the displaced sequence ST19. ST19 showed higher cell viability percentages than ST213 in osmotic (685 mM NaCl) and acidic (pH 3.5) stress conditions and in combination with refrigeration (4 °C) and ambient (≈22 °C) temperatures. Both genotypes showed the same poststress recovery growth. ST213 formed biofilm and filamentous cells (FCs) under stress, whereas ST19 did not. ST213 cells also showed higher motility. The capacity of ST213 to form FCs may explain its lower viability percentages when compared with ST19, i.e., ST213 cells divided less under stress conditions, but FCs had the same recovery capacity of ST19 cells. ST213 presented a higher unsaturated/saturated fatty acids ratio (0.5-0.6) than ST19 (0.2-0.5), which indicates higher membrane fluidity. The transcript levels of the rpoS gene were similar between genotypes under the experimental conditions employed. Biofilm formation, the generation of FCs, cell motility and membrane modification seem to make ST213 more resistant than ST19 to food preservation environments.

Plasma-Treated Air and Water-Assessment of Synergistic Antimicrobial Effects for Sanitation of Food Processing Surfaces and Environment

The synergistic antimicrobial effects of plasma-processed air (PPA) and plasma-treated water (PTW), which are indirectly generated by a microwave-induced non-atmospheric pressure plasma, were investigated with the aid of proliferation assays. For this purpose, microorganisms (Listeria monocytogenes, Escherichia coli, Pectobacterium carotovorum, sporulated Bacillus atrophaeus) were cultivated as monocultures on specimens with polymeric surface structures. Both the distinct and synergistic antimicrobial potential of PPA and PTW were governed by the plasma-on time (5⁻50 s) and the treatment time of the specimens with PPA/PTW (1⁻5 min). In single PTW treatment of the bacteria, an elevation of the reduction factor with increasing treatment time could be observed (e.g., reduction factor of 2.4 to 3.0 for P. carotovorum). In comparison, the combination of PTW and subsequent PPA treatment leads to synergistic effects that are clearly not induced by longer treatment times. These findings have been valid for all bacteria (L. monocytogenes > P. carotovorum = E. coli). Controversially, the effect is reversed for endospores of B. atrophaeus. With pure PPA treatment, a strong inactivation at 50 s plasma-on time is detectable, whereas single PTW treatment shows no effect even with increasing treatment parameters. The use of synergistic effects of PTW for cleaning and PPA for drying shows a clear alternative for currently used sanitation methods in production plants. Highlights: Non-thermal atmospheric pressure microwave plasma source used indirect in two different modes-gaseous and liquid; Measurement of short and long-living nitrite and nitrate in corrosive gas PPA (plasma-processed air) and complex liquid PTW (plasma-treated water); Application of PTW and PPA in single and combined use for biological decontamination of different microorganisms.

Causes and Consequences of a Variant Strain of Phaeobacter inhibens With Reduced Competition

Phaeobacter inhibens 2.10 is an effective biofilm former and colonizer of marine surfaces and has the ability to outcompete other microbiota. During biofilm dispersal P. inhibens 2.10 produces heritable phenotypic variants, including those that have a reduced ability to inhibit the co-occurring bacterium Pseudoalteromonas tunicata. However, the genetic changes that underpin the phenotypic variation and what the ecological consequences are for variants within the population are unclear. To answer these questions we sequenced the genomes of strain NCV12a1, a biofilm variant of P. inhibens 2.10 with reduced inhibitory activity and the P. inhibens 2.10 WT parental strain. Genome wide analysis revealed point mutations in genes involved in synthesis of the antibacterial compound tropodithietic acid (TDA) and indirectly in extracellular polymeric substances (EPS) production. However, confocal laser scanning microscopy analyses found little differences in biofilm growth between P. inhibens 2.10 WT (parental) and NCV12a1. P. inhibens NCV12a1 was also not outcompeted in co-cultured biofilms with P. tunicata, despite its reduced inhibitory activity, rather these biofilms were thicker than those produced when the WT strain was co-cultured with P. tunicata. Notably, dispersal populations from biofilms of P. inhibens NCV12a1 had a higher proportion of WT-like morphotypes when co-cultured with P. tunicata. These observations may explain why the otherwise non-inhibiting variant persists in the presence of a natural competitor, adding to our understanding of the relative importance of genetic diversification in microbial biofilms.