Hydrophobic substances induce water stress in microbial cells

Microbiological and toxicity analyses of the synthetic polymer polyhexamethylene guanidine hydrochloride against endodontic microorganisms

Failures in endodontic treatments are common due to microbial resistance in the pulp canal. The study evaluated the in vitro activity of polyhexamethylene guanidine hydrochloride (PHMGH) against endodontic strains, as well as in vivo toxicity. Using minimum inhibitory concentration and minimum bactericidal concentration techniques, PHMGH was effective against all microorganisms, even at low concentrations. At 50.0 µg/mL, it inhibited Enterococcus faecalis; furthermore, when compared to chlorhexidine (CLX), it demonstrated values 19 times lower against Candida albicans. The polymer's activity was also determined by agar diffusion, evaluating products A (calcium hydroxide - Ca(OH)2, as a reference), B (Ca(OH)2 combined with physiological solution, reference with a vehicle), C (PHMGH 6.25%), D (PHMGH 3.125%), E (PHMGH 1.5625%), F (PHMGH 0.78125%), G (PHMGH 6.25% and Ca(OH)2), H (PHMGH 3.125% and Ca(OH)2), I (PHMGH 1.5625% and Ca(OH)2), J (PHMGH 0.78125% and Ca(OH)2), and K (positive control, CLX 0.12%). Products containing PHMGH were more effective than the references against all strains, and C, D, and G were more effective than CLX against Peptostreptococcus anaerobius, Actinomyces naeslundii, and Actinomyces viscosus. According to the fractional inhibitory concentration index, the combination of PHMGH and CLX showed indifference for Peptostreptococcus anaerobius, Actinomyces naeslundii, Actinomyces viscosus and Escherichia coli, antagonism for Candida albicans, and synergy for Enterococcus faecalis. The toxicity of PHMGH at different concentrations was tested in Caenorhabditis elegans and did not show lethality in nematodes, with the LC50 observed only at the highest concentration (100 µg/mL) after two days of exposure. It is suggested that PHMGH exhibited antimicrobial activity against endodontic strains and low toxicity, raising expectations for new preventive and therapeutic products in endodontics.

Burning question: Rethinking organohalide degradation strategy for bioremediation applications

Organohalides are widespread pollutants that pose significant environmental hazards due to their high degree of halogenation and elevated redox potentials, making them resistant to natural attenuation. Traditional bioremediation approaches, primarily relying on bioaugmentation and biostimulation, often fall short of achieving complete detoxification. Furthermore, the emergence of complex halogenated pollutants, such as per- and polyfluoroalkyl substances (PFASs), further complicates remediation efforts. Therefore, there is a pressing need to reconsider novel approaches for more efficient remediation of these recalcitrant pollutants. This review proposes novel redox-potential-mediated hybrid bioprocesses, tailored to the physicochemical properties of pollutants and their environmental contexts, to achieve complete detoxification of organohalides. The possible scenarios for the proposed bioremediation approaches are further discussed. In anaerobic environments, such as sediment and groundwater, microbial reductive dehalogenation coupled with fermentation and methanogenesis can convert organohalides into carbon dioxide and methane. In environments with anaerobic-aerobic alternation, such as paddy soil and wetlands, a synergistic process involving reduction and oxidation can facilitate the complete mineralization of highly halogenated organic compounds. Future research should focus on in-depth exploration of microbial consortia, the application of ecological principles-guided strategies, and the development of bioinspired-designed techniques. This paper contributes to the academic discourse by proposing innovative remediation strategies tailored to the complexities of organohalide pollution.

Recent advances in understanding the fitness and survival mechanisms of Vibrio parahaemolyticus

The presence of Vibrio parahaemolyticus (Vp) in different production stages of seafood has generated negative impacts on both public health and the sustainability of the industry. To further better investigate the fitness of Vp at the phenotypical level, a great number of studies have been conducted in recent years using plate counting methods. In the meantime, with the increasing accessibility of the next generation sequencing and the advances in analytical chemistry techniques, omics-oriented biotechnologies have further advanced our knowledge in the survival and virulence mechanisms of Vp at various molecular levels. These observations provide insights to guide the development of novel prevention and control strategies and benefit the monitoring and mitigation of food safety risks associated with Vp contamination. To timely capture these recent advances, this review firstly summarizes the most recent phenotypical level studies and provide insights about the survival of Vp under important in vitro stresses and on aquatic products. After that, molecular survival mechanisms of Vp at transcriptomic and proteomic levels are summarized and discussed. Looking forward, other newer omics-biotechnology such as metabolomics and secretomics show great potential to be used for confirming the cellular responses of Vp. Powerful data mining tools from the field of machine learning and artificial intelligence, that can better utilize the omics data and solve complex problems in the processing, analysis, and interpretation of omics data, will further improve our mechanistic understanding of Vp.

Enhanced chaotrope tolerance and (S)-2-hydroxypropiophenone production by recombinant Pseudomonas putida engineered with Pprl from Deinococcus radiodurans

Pseudomonas putida is a soil bacterium with multiple uses in fermentation and biotransformation processes. P. putida ATCC 12633 can biotransform benzaldehyde and other aldehydes into valuable α-hydroxyketones, such as (S)-2-hydroxypropiophenone. However, poor tolerance of this strain toward chaotropic aldehydes hampers efficient biotransformation processes. To circumvent this problem, we expressed the gene encoding the global regulator PprI from Deinococcus radiodurans, an inducer of pleiotropic proteins promoting DNA repair, in P. putida. Fine-tuned gene expression was achieved using an expression plasmid under the control of the LacIQ /Ptrc system, and the cross-protective role of PprI was assessed against multiple stress treatments. Moreover, the stress-tolerant P. putida strain was tested for 2-hydroxypropiophenone production using whole resting cells in the presence of relevant aldehyde substrates. P. putida cells harbouring the global transcriptional regulator exhibited high tolerance toward benzaldehyde, acetaldehyde, ethanol, butanol, NaCl, H2 O2 and thermal stress, thereby reflecting the multistress protection profile conferred by PprI. Additionally, the engineered cells converted aldehydes to 2-hydroxypropiophenone more efficiently than the parental P. putida strain. 2-Hydroxypropiophenone concentration reached 1.6 g L-1 upon a 3-h incubation under optimized conditions, at a cell concentration of 0.033 g wet cell weight mL-1 in the presence of 20 mM benzaldehyde and 600 mM acetaldehyde. Product yield and productivity were 0.74 g 2-HPP g-1 benzaldehyde and 0.089 g 2-HPP g cell dry weight-1  h-1 , respectively, 35% higher than the control experiments. Taken together, these results demonstrate that introducing PprI from D. radiodurans enhances chaotrope tolerance and 2-HPP production in P. putida ATCC 12633.

The Pareto principle: To what extent does it apply to resource acquisition in stable microbial communities and thereby steer their geno-/ecotype compositions and interactions between their members?

The Pareto principle, or 20:80 rule, describes resource distribution in stable communities whereby 20% of community members acquire 80% of a key resource. In this Burning Question, we ask to what extent the Pareto principle applies to the acquisition of limiting resources in stable microbial communities; how it may contribute to our understanding of microbial interactions, microbial community exploration of evolutionary space, and microbial community dysbiosis; and whether it can serve as a benchmark of microbial community stability and functional optimality?

Scientific novelty beyond the experiment

Practical experiments drive important scientific discoveries in biology, but theory-based research studies also contribute novel-sometimes paradigm-changing-findings. Here, we appraise the roles of theory-based approaches focusing on the experiment-dominated wet-biology research areas of microbial growth and survival, cell physiology, host-pathogen interactions, and competitive or symbiotic interactions. Additional examples relate to analyses of genome-sequence data, climate change and planetary health, habitability, and astrobiology. We assess the importance of thought at each step of the research process; the roles of natural philosophy, and inconsistencies in logic and language, as drivers of scientific progress; the value of thought experiments; the use and limitations of artificial intelligence technologies, including their potential for interdisciplinary and transdisciplinary research; and other instances when theory is the most-direct and most-scientifically robust route to scientific novelty including the development of techniques for practical experimentation or fieldwork. We highlight the intrinsic need for human engagement in scientific innovation, an issue pertinent to the ongoing controversy over papers authored using/authored by artificial intelligence (such as the large language model/chatbot ChatGPT). Other issues discussed are the way in which aspects of language can bias thinking towards the spatial rather than the temporal (and how this biased thinking can lead to skewed scientific terminology); receptivity to research that is non-mainstream; and the importance of theory-based science in education and epistemology. Whereas we briefly highlight classic works (those by Oakes Ames, Francis H.C. Crick and James D. Watson, Charles R. Darwin, Albert Einstein, James E. Lovelock, Lynn Margulis, Gilbert Ryle, Erwin R.J.A. Schrödinger, Alan M. Turing, and others), the focus is on microbiology studies that are more-recent, discussing these in the context of the scientific process and the types of scientific novelty that they represent. These include several studies carried out during the 2020 to 2022 lockdowns of the COVID-19 pandemic when access to research laboratories was disallowed (or limited). We interviewed the authors of some of the featured microbiology-related papers and-although we ourselves are involved in laboratory experiments and practical fieldwork-also drew from our own research experiences showing that such studies can not only produce new scientific findings but can also transcend barriers between disciplines, act counter to scientific reductionism, integrate biological data across different timescales and levels of complexity, and circumvent constraints imposed by practical techniques. In relation to urgent research needs, we believe that climate change and other global challenges may require approaches beyond the experiment.

Modes-of-action of antifungal compounds: Stressors and (target-site-specific) toxins, toxicants, or Toxin-stressors

Fungi and antifungal compounds are relevant to the United Nation's Sustainable Development Goals. However, the modes-of-action of antifungals-whether they are naturally occurring substances or anthropogenic fungicides-are often unknown or are misallocated in terms of their mechanistic category. Here, we consider the most effective approaches to identifying whether antifungal substances are cellular stressors, toxins/toxicants (that are target-site-specific), or have a hybrid mode-of-action as Toxin-stressors (that induce cellular stress yet are target-site-specific). This newly described 'toxin-stressor' category includes some photosensitisers that target the cell membrane and, once activated by light or ultraviolet radiation, cause oxidative damage. We provide a glossary of terms and a diagrammatic representation of diverse types of stressors, toxic substances, and Toxin-stressors, a classification that is pertinent to inhibitory substances not only for fungi but for all types of cellular life. A decision-tree approach can also be used to help differentiate toxic substances from cellular stressors (Curr Opin Biotechnol 2015 33: 228-259). For compounds that target specific sites in the cell, we evaluate the relative merits of using metabolite analyses, chemical genetics, chemoproteomics, transcriptomics, and the target-based drug-discovery approach (based on that used in pharmaceutical research), focusing on both ascomycete models and the less-studied basidiomycete fungi. Chemical genetic methods to elucidate modes-of-action currently have limited application for fungi where molecular tools are not yet available; we discuss ways to circumvent this bottleneck. We also discuss ecologically commonplace scenarios in which multiple substances act to limit the functionality of the fungal cell and a number of as-yet-unresolved questions about the modes-of-action of antifungal compounds pertaining to the Sustainable Development Goals.

Photoantimicrobials in agriculture

Classical approaches for controlling plant pathogens may be impaired by the development of pathogen resistance to chemical pesticides and by limited availability of effective antimicrobial agents. Recent increases in consumer awareness of and/or legislation regarding environmental and human health, and the urgent need to improve food security, are driving increased demand for safer antimicrobial strategies. Therefore, there is a need for a step change in the approaches used for controlling pre- and post-harvest diseases and foodborne human pathogens. The use of light-activated antimicrobial substances for the so-called antimicrobial photodynamic treatment is known to be effective not only in a clinical context, but also for use in agriculture to control plant-pathogenic fungi and bacteria, and to eliminate foodborne human pathogens from seeds, sprouted seeds, fruits, and vegetables. Here, we take a holistic approach to review and re-evaluate recent findings on: (i) the ecology of naturally-occurring photoantimicrobials, (ii) photodynamic processes including the light-activated antimicrobial activities of some plant metabolites, and (iii) fungus-induced photosensitization of plants. The inhibitory mechanisms of both natural and synthetic light-activated substances, known as photosensitizers, are discussed in the contexts of microbial stress biology and agricultural biotechnology. Their modes-of-antimicrobial action make them neither stressors nor toxins/toxicants (with specific modes of poisonous activity), but a hybrid/combination of both. We highlight the use of photoantimicrobials for the control of plant-pathogenic fungi and quantify their potential contribution to global food security.

Perchlorate-Specific Proteomic Stress Responses of Debaryomyces hansenii Could Enable Microbial Survival in Martian Brines

If life exists on Mars, it would face several challenges including the presence of perchlorates, which destabilize biomacromolecules by inducing chaotropic stress. However, little is known about perchlorate toxicity for microorganism on the cellular level. Here we present the first proteomic investigation on the perchlorate-specific stress responses of the halotolerant yeast Debaryomyces hansenii and compare these to generally known salt stress adaptations. We found that the responses to NaCl and NaClO₄ -induced stresses share many common metabolic features, e.g., signaling pathways, elevated energy metabolism, or osmolyte biosynthesis. Nevertheless, several new perchlorate-specific stress responses could be identified, such as protein glycosylation and cell wall remodulations, presumably in order to stabilize protein structures and the cell envelope. These stress responses would also be relevant for life on Mars, which - given the environmental conditions - likely developed chaotropic defense strategies such as stabilized confirmations of biomacromolecules and the formation of cell clusters. This article is protected by copyright. All rights reserved.

Significance of both alkB and P450 alkane-degrading systems in Tsukamurella tyrosinosolvens: proteomic evidence

The Tsukamurella tyrosinosolvens PS2 strain was isolated from hydrocarbons-contaminated petrochemical sludge as a long chain alkane-utilizing bacteria. Complete genome analysis showed the presence of two alkane oxidation systems: alkane 1-monooxygenase (alkB) and cytochrome P450 monooxygenase (P450) genes with established high homology to the well-known alkane-degrading actinobacteria. According to the comparative genome analysis, both systems have a wide distribution among environmental and clinical isolates of the genus Tsukamurella and other members of Actinobacteria. We compared the expression of different proteins during the growth of Tsukamurella on sucrose and on hexadecane. Both alkane monooxygenases were upregulated on hexadecane: AlkB-up to 2.5 times, P450-up to 276 times. All proteins of the hexadecane oxidation pathway to acetyl-CoA were also upregulated. Accompanying proteins for alkane degradation involved in biosurfactant synthesis and transport of organic and inorganic molecules were increased. The change in the carbon source affected the pathways for the regulation of translation and transcription. The proteomic profile showed that hexadecane is an adverse factor causing activation of general and universal stress proteins as well as shock and resistance proteins. Differently expressed proteins of Tsukamurella tyrosinosolvens PS2 shed light on the alkane degradation in other members of Actinobacteria class. KEY POINTS: • alkB and P450 systems have a wide distribution among the genus Tsukamurella. • alkB and P450 systems have coexpression with the predominant role of P450 protein. • Hexadecane causes significant changes in bacterial proteome.

Water is a preservative of microbes

Water is the cellular milieu, drives all biochemistry within Earth's biosphere and facilitates microbe-mediated decay processes. Instead of reviewing these topics, the current article focuses on the activities of water as a preservative-its capacity to maintain the long-term integrity and viability of microbial cells-and identifies the mechanisms by which this occurs. Water provides for, and maintains, cellular structures; buffers against thermodynamic extremes, at various scales; can mitigate events that are traumatic to the cell membrane, such as desiccation-rehydration, freeze-thawing and thermal shock; prevents microbial dehydration that can otherwise exacerbate oxidative damage; mitigates against biocidal factors (in some circumstances reducing ultraviolet radiation and diluting solute stressors or toxic substances); and is effective at electrostatic screening so prevents damage to the cell by the intense electrostatic fields of some ions. In addition, the water retained in desiccated cells (historically referred to as 'bound' water) plays key roles in biomacromolecular structures and their interactions even for fully hydrated cells. Assuming that the components of the cell membrane are chemically stable or at least repairable, and the environment is fairly constant, water molecules can apparently maintain membrane geometries over very long periods provided these configurations represent thermodynamically stable states. The spores and vegetative cells of many microbes survive longer in the presence of vapour-phase water (at moderate-to-high relative humidities) than under more-arid conditions. There are several mechanisms by which large bodies of water, when cooled during subzero weather conditions remain in a liquid state thus preventing potentially dangerous (freeze-thaw) transitions for their microbiome. Microbial life can be preserved in pure water, freshwater systems, seawater, brines, ice/permafrost, sugar-rich aqueous milieux and vapour-phase water according to laboratory-based studies carried out over periods of years to decades and some natural environments that have yielded cells that are apparently thousands, or even (for hypersaline fluid inclusions of mineralized NaCl) hundreds of millions, of years old. The term preservative has often been restricted to those substances used to extend the shelf life of foods (e.g. sodium benzoate, nitrites and sulphites) or those used to conserve dead organisms, such as ethanol or formaldehyde. For living microorganisms however, the ultimate preservative may actually be water. Implications of this role are discussed with reference to the ecology of halophiles, human pathogens and other microbes; food science; biotechnology; biosignatures for life and other aspects of astrobiology; and the large-scale release/reactivation of preserved microbes caused by global climate change.

The physiology and metabolic properties of a novel, low-abundance Psychrilyobacter species isolated from the anoxic Black Sea shed light on its ecological role

Members of the Psychrilyobacter spp. of the phylum Fusobacteria have been recently suggested to be amongst the most significant primary degraders of the detrital organic matter in sulfidic marine habitats, despite representing only a small proportion (<0.1%) of the microbial community. In this study, we have isolated a previously uncultured Psychrilyobacter species (strains SD5^T and BL5; Psychrilyobacter piezotolerans sp. nov.) from the sulfidic waters (i.e., 2000 m depth) of the Black Sea and investigated its physiology and genomic capability in order to better understand potential ecological adaptation strategies. P. piezotolerans utilized a broad range of organic substituents (carbohydrates and proteins) and, remarkably, grew at sulfide concentrations up to 32 mM. These flexible physiological properties were supported by the presence of the respective metabolic pathways in the genomes of both strains. Growth at varying hydrostatic pressure (0.1-50 MPa) was sustained by modifying its membrane lipid composition. Thus, we have isolated a novel member of the 'rare biosphere', which endures the extreme conditions and may play a significant role in the degradation of detrital organic matter sinking into the sulfidic waters of the Black Sea.

Plant metabolite 5-pentadecyl resorcinol is produced by the Amazonian fungus Penicillium sclerotiorum LM 5679

Since the classic studies of Alexander Flemming, Penicillium strains have been known as a rich source of antimicrobial substances. Recent studies have identified novel metabolites produced by Penicillium sclerotiorum that have antibacterial, antifouling and pharmaceutical activities. Here, we report the isolation of a P. sclerotiorum (LM 5679) from Amazonian soil and carry out a culture-based study to determine whether it can produce any novel secondary metabolite(s) that are not thus-far reported for this genus. Using a submerged culture system, secondary metabolites were recovered by solvent extract followed by thin-layer chromatography, nuclear magnetic resonance, and mass spectroscopy. One novel secondary metabolite was isolated from P. sclerotiorum (LM 5679); the phenolic compound 5-pentadecyl resorcinol widely known as an antifungal, that is produced by diverse plant species. This metabolite was not reported previously in any Penicillium species and was only found once before in fungi (that time, in a Fusarium). Here, we discuss the known activities of 5-pentadecyl resorcinol in the context of its mode-of-action as a hydrophobic (chaotropicity-mediated) stressor.

Astrobiology of life on Earth

Astrobiology is mistakenly regarded by some as a field confined to studies of life beyond Earth. Here, we consider life on Earth through an astrobiological lens. Whereas classical studies of microbiology historically focused on various anthropocentric sub-fields (such as fermented foods or commensals and pathogens of crop plants, livestock and humans), addressing key biological questions via astrobiological approaches can further our understanding of all life on Earth. We highlight potential implications of this approach through the articles in this Environmental Microbiology special issue 'Ecophysiology of Extremophiles'. They report on the microbiology of places/processes including low-temperature environments and chemically diverse saline- and hypersaline habitats; aspects of sulphur metabolism in hypersaline lakes, dysoxic marine waters, and thermal acidic springs; biology of extremophile viruses; the survival of terrestrial extremophiles on the surface of Mars; biological soils crusts and rock-associated microbes of deserts; subsurface and deep biosphere, including a salticle formed within Triassic halite; and interactions of microbes with igneous and sedimentary rocks. These studies, some of which we highlight here, contribute to our understanding of the spatiotemporal reach of Earth'sfunctional biosphere, and the tenacity of terrestrial life. Their findings will help set the stage for future work focused on the constraints for life, and how organisms adapt and evolve to circumvent these constraints.

Subsurface and surface halophile communities of the chaotropic Salar de Uyuni

Salar de Uyuni (SdU) is the biggest athalosaline environment on Earth, holding a high percentage of the known world Li reserves. Due to its hypersalinity, temperature and humidity fluctuations, high exposure to UV radiation, and its elevated concentration of chaotropic agents like MgCl₂ , LiCl and NaBr, SdU is considered a polyextreme environment. Here, we report the prokaryotic abundance and diversity of 46 samples obtained in different seasons and geographical areas. The identified bacterial community was found to be more heterogeneous than the archaeal community, with both communities varying geographically. A seasonal difference has been detected for archaea. Salinibacter, Halonotius and Halorubrum were the most abundant genera in Salar de Uyuni. Different unclassified archaea were also detected. In addition, the diversity of two subsurface samples obtained at 20 and 80 m depth was evaluated and compared with the surface data, generating an evolutionary record of a multilayer hypersaline ecosystem.

Acarbose protects from central and peripheral metabolic imbalance induced by benzene exposure

Benzene is a well-known human carcinogen that is one of the major components of air pollution. Sources of benzene in ambient air include cigarette smoke, e-cigarettes vaping, and evaporation of benzene containing petrol processes. While the carcinogenic effects of benzene exposure have been well studied, less is known about the metabolic effects of benzene exposure. We show that chronic exposure to benzene at low levels induces a severe metabolic imbalance in a sex-specific manner, and is associated with hypothalamic inflammation and endoplasmic reticulum (ER) stress. Benzene exposure rapidly activates hypothalamic ER stress and neuroinflammatory responses in male mice, while pharmacological inhibition of ER stress response by inhibiting IRE1α-XBP1 pathway significantly alleviates benzene-induced glial inflammatory responses. Additionally, feeding mice with Acarbose, a clinically available anti-diabetes drug, protected against benzene induced central and peripheral metabolic imbalance. Acarbose imitates the slowing of dietary carbohydrate digestion, suggesting that choosing a diet with a low glycemic index might be a potential strategy for reducing the negative metabolic effect of chronic exposure to benzene for smokers or people living/working in urban environments with high concentrations of exposure to automobile exhausts.

The effect of polar head group of dodecyl surfactants on the growth of wheat and cucumber

The increasing application of various surfactants nowadays, may lead to the contamination of the natural environment and represent potential threat to terrestrial higher plants. In this article, the effect of 13 surfactants, with dodecyl alkyl chain and various aromatic (imidazolium, pyridinium, thiazolium) and aliphatic (guanidinium, ammonium, thiosemicarbazidium) polar heads, on germination, development and growth of wheat and cucumber was investigated. The study aimed to prove how changes in lipophilicity of surfactants and their various structural modifications (existence of the aliphatic or aromatic polar group, the introduction of oxygen and sulfur) influence toxicity towards investigated plants. The calculated lipophilic parameter (AlogP) is shown to be a useful parameter for predicting potential toxicity of the compound. The strategy of using surfactants with aliphatic polar heads instead of aromatic prove to be a promising strategy in reducing harmful effect, as well as the introduction of polar groups in the structure of cation. From all investigated compounds, surfactants with imidazolium polar head displayed the most harmful effect towards wheat and cucumber. The cucumber seeds were more sensitive to the addition of surfactants comparing to wheat. All obtained experimental results were additionally investigated using computational methods, simulating the transport of surfactants through a lipid bilayer. The influence of cation tendency to fit in lipid bilayer structure was correlated with toxicity. For the first time, it is concluded that cation ability to mimic the structure of bilayer have less harmful effect on plant development.

Destressing Yeast for Higher Biofuel Yields: Can Excess Chaotropicity Be Mitigated?

Biofuels have the capacity to contribute to carbon dioxide emission reduction and to energy security as oil reserves diminish and/or become concentrated in politically unstable regions. However, challenges exist in obtaining the maximum yield from industrial fermentations. One challenge arises from the nature of alcohols. These compounds are chaotropic (i.e. causes disorder in the system) which causes stress in the microbes producing the biofuel. Brewer's yeast (Saccharomyces cerevisiae) typically cannot grow at ethanol concentration much above 17% (v/v). Mitigation of these properties has the potential to increase yield. Previously, we have explored the effects of chaotropes on model enzyme systems and attempted (largely unsuccessfully) to offset these effects by kosmotropes (compounds which increase the order of the system, i.e. the "opposite" of chaotropes). Here we present some theoretical results which suggest that high molecular mass polyethylene glycols may be the most effective kosmotropic additives in terms of both efficacy and cost. The assumptions and limitations of these calculations are also presented. A deeper understanding of the effects of chaotropes on biofuel-producing microbes is likely to inform improvements in bioethanol yields and enable more rational approaches to the "neutralisation" of chaotropicity.

Microorganisms populating the water-related indoor biome

Modernisation of our households created novel opportunities for microbial growth and thus changed the array of microorganisms we come in contact with. While many studies have investigated microorganisms in the air and dust, tap water, another major input of microbial propagules, has received far less attention. The quality of drinking water in developed world is strictly regulated to prevent immediate danger to human health. However, fungi, algae, protists and bacteria of less immediate concern are usually not screened for. These organisms can thus use water as a vector of transmission into the households, especially if they are resistant to various water treatment procedures. Good tolerance of unfavourable abiotic conditions is also important for survival once microbes enter the household. Limitation of water availability, high or low temperatures, application of antimicrobial chemicals and other measures are taken to prevent indoor microbial overgrowth. These conditions, together with a large number of novel chemicals in our homes, shape the diversity and abundance of indoor microbiota through constant selection of the most resilient species, resulting in a substantial overlap in diversity of indoor and natural extreme environments. At least in fungi, extremotolerance has been linked to human pathogenicity, explaining why many species found in novel indoor habitats (such as dishwasher) are notable opportunistic pathogens. As a result, microorganisms that often enter our households with water and are then enriched in novel indoor habitats might have a hitherto underestimated impact on the well-being of the increasingly indoor-bound human population. KEY POINTS: Domestic environment harbours a large diversity of microorganisms. Microbiota of water-related indoor habitats mainly originates from tap water. Bathrooms, kitchens and household appliances select for polyextremotolerant species. Many household-related microorganisms are human opportunistic pathogens.

Protective Role of Bacterial Alkanesulfonate Monooxygenase under Oxidative Stress

Bacterial alkane metabolism is associated with a number of cellular stresses, including membrane stress and oxidative stress, and the limited uptake of charged ions such as sulfate. In the present study, the genes ssuD and tauD in Acinetobacter oleivorans DR1 cells, which encode an alkanesulfonate monooxygenase and a taurine dioxygenase, respectively, were found to be responsible for hexadecanesulfonate (C₁₆SO₃H) and taurine metabolism, and Cbl was experimentally identified as a potential regulator of ssuD and tauD expression. The expression of ssuD and tauD occurred under sulfate-limited conditions generated during n-hexadecane degradation. Interestingly, expression analysis and knockout experiments suggested that both genes are required to protect cells against oxidative stress, including that generated by n-hexadecane degradation and H₂O₂ exposure. Measurable levels of intracellular hexadecanesulfonate were also produced during n-hexadecane degradation. Phylogenetic analysis suggested that ssuD and tauD are mainly present in soil-dwelling aerobes within the Betaproteobacteria and Gammaproteobacteria classes, which suggests that they function as controllers of the sulfur cycle and play a protective role against oxidative stress in sulfur-limited conditions.IMPORTANCE ssuD and tauD, which play a role in the degradation of organosulfonate, were expressed during n-hexadecane metabolism and oxidative stress conditions in A. oleivorans DR1. Our study confirmed that hexadecanesulfonate was accidentally generated during bacterial n-hexadecane degradation in sulfate-limited conditions. Removal of this by-product by SsuD and TauD must be necessary for bacterial survival under oxidative stress generated during n-hexadecane degradation.

Impact of high salinity and the compatible solute glycine betaine on gene expression of Bacillus subtilis

The Gram-positive bacterium Bacillus subtilis is frequently exposed to hyperosmotic conditions. In addition to the induction of genes involved in the accumulation of compatible solutes, high salinity exerts widespread effects on B. subtilis physiology, including changes in cell wall metabolism, induction of an iron limitation response, reduced motility and suppression of sporulation. We performed a combined whole-transcriptome and proteome analysis of B. subtilis 168 cells continuously cultivated at low or high (1.2 M NaCl) salinity. Our study revealed significant changes in the expression of more than one-fourth of the protein-coding genes and of numerous non-coding RNAs. New aspects in understanding the impact of high salinity on B. subtilis include a sustained low-level induction of the SigB-dependent general stress response and strong repression of biofilm formation under high-salinity conditions. The accumulation of compatible solutes such as glycine betaine aids the cells to cope with water stress by maintaining physiologically adequate levels of turgor and also affects multiple cellular processes through interactions with cellular components. Therefore, we additionally analysed the global effects of glycine betaine on the transcriptome and proteome of B. subtilis and revealed that it influences gene expression not only under high-salinity, but also under standard growth conditions.

Viridistratins A-C, Antimicrobial and Cytotoxic Benzo[j]fluoranthenes from Stromata of Annulohypoxylon viridistratum (Hypoxylaceae, Ascomycota)

During the course of our search for novel biologically active metabolites from tropical fungi, we are using chemotaxonomic and taxonomic methodology for the preselection of interesting materials. Recently, three previously undescribed benzo[j]fluoranthenes (1-3) together with the known derivatives truncatones A and C (4, 5) were isolated from the stromata of the recently described species Annulohypoxylon viridistratum collected in Thailand. Their chemical structures were elucidated by means of spectral methods, including nuclear magnetic resonance (NMR) spectroscopy and high-resolution mass spectrometry (HR-MS). The new compounds, for which we propose the trivial names viridistratins A-C, exhibited weak-to-moderate antimicrobial and cytotoxic activities in cell-based assays.

Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau

Little is known about life in the boron-rich hot springs of Trans-Himalayas. Here, we explore the geomicrobiology of a 4438-m-high spring which emanates ~70 °C-water from a boratic microbialite called Shivlinga. Due to low atmospheric pressure, the vent-water is close to boiling point so can entropically destabilize biomacromolecular systems. Starting from the vent, Shivlinga’s geomicrobiology was revealed along the thermal gradients of an outflow-channel and a progressively-drying mineral matrix that has no running water; ecosystem constraints were then considered in relation to those of entropically comparable environments. The spring-water chemistry and sinter mineralogy were dominated by borates, sodium, thiosulfate, sulfate, sulfite, sulfide, bicarbonate, and other macromolecule-stabilizing (kosmotropic) substances. Microbial diversity was high along both of the hydrothermal gradients. Bacteria, Eukarya and Archaea constituted >98%, ~1% and <1% of Shivlinga’s microbiome, respectively. Temperature constrained the biodiversity at ~50 °C and ~60 °C, but not below 46 °C. Along each thermal gradient, in the vent-to-apron trajectory, communities were dominated by Aquificae/Deinococcus-Thermus, then Chlorobi/Chloroflexi/Cyanobacteria, and finally Bacteroidetes/Proteobacteria/Firmicutes. Interestingly, sites of >45 °C were inhabited by phylogenetic relatives of taxa for which laboratory growth is not known at >45 °C. Shivlinga’s geomicrobiology highlights the possibility that the system’s kosmotrope-dominated chemistry mitigates against the biomacromolecule-disordering effects of its thermal water.

Evaluating cytotoxicity of methyl benzoate in vitro

Methyl benzoate (MB) is a small, hydrophobic organic compound that is isolated from the freshwater fern, Salvinia molesta. Because of its pleasant odor, it has been used as a fragrance and flavor enhancer. In addition, it is used to attract orchid bees for pollination in the farm and has been tested for its potential to be developed as a green pesticide targeting a diverse group of insects. In spite of its wide applications, the safety of MB to humans remains poorly understood. In this study, we tested the cytotoxicity of MB against cultured human cells, including kidney, colon, and neuronal cells. Furthermore, other natural and synthetic benzoic acids such as ethyl benzoate (EB) and vinyl benzoate (VB) were compared with MB for their similarity and broad commercial and industrial applications. We found that MB and VB have the least and most overall toxicity to the tested human cells, respectively. In addition, the expression of some genes involved in cell cycle, protein quality control, and neurotransmission such as cyclin D1, HSP70, and ACHE genes was differentially expressed in the presence of these chemicals, most noticeably in treatment of VB. Our study provided the LC₅₀ values of these benzoic acids for human cells in vitro and suggested their mild toxicity that should be considered in the industrial and agricultural applications to be within safe limits.

Osmotolerance as a determinant of microbial ecology: A study of phylogenetically diverse fungi

Osmotic stress induced by high solute concentration can prevent fungal metabolism and growth due to alterations in properties of the cytosol, changes in turgor, and the energy required to synthesize and retain compatible solutes. We used germination to quantify tolerance/sensitivity to the osmolyte KCl (0.1-4.5 M, in 0.1 M increments) for 71 strains (40 species) of ecologically diverse fungi. These include 11 saprotrophic species (17 strains, including two xerophilic species), five mycoparasitic species (five strains), six plant-pathogenic species (13 strains), and 19 entomopathogenic species (36 strains). A dendrogram obtained from cluster analyses, based on KCl inhibitory concentrations 50 % and 90 % calculated by Probit Analysis, revealed three groups of fungal isolates accordingly to their osmotolerance. The most-osmotolerant group (Group 3) contained the majority of saprotrophic fungi, and Aspergillus niger (F19) was the most tolerant. The highly xerophilic Aspergillus montevidense and Aspergillus pseudoglaucus were the second- and third-most tolerant species, respectively. All Aspergillus and Cladosporium species belonged to Group 3, followed by the entomopathogens Colletotrichum fioriniae, Simplicillium lanosoniveum, and Trichothecium roseum. Group 2 exhibited a moderate osmotolerance, and included plant-pathogens such as Colletotrichum and Fusarium, mycoparasites such as Clonostachys spp, some saprotrophs such as Mucor and Penicillium spp., and some entomopathogens such as Isaria, Lecanicillium, Mariannaea, Simplicillium, and Torrubiella. Group 1 contained the osmo-sensitive strains: the rest of the entomopathogens and the mycoparasitic Gliocladium and Trichoderma. Although stress tolerance did not correlate with their primary ecological niche, classification of these 71 fungal strains was more closely aligned with their ecology than with their phylogenetic relatedness. We discuss the implications for both microbial ecology and fungal taxonomy.

Four Challenges for Better Biocatalysts

Biocatalysis (the use of biological molecules or materials to catalyse chemical reactions) has considerable potential. The use of biological molecules as catalysts enables new and more specific syntheses. It also meets many of the core principles of “green chemistry”. While there have been some considerable successes in biocatalysis, the full potential has yet to be realised. This results, partly, from some key challenges in understanding the fundamental biochemistry of enzymes. This review summarises four of these challenges: the need to understand protein folding, the need for a qualitative understanding of the hydrophobic effect, the need to understand and quantify the effects of organic solvents on biomolecules and the need for a deep understanding of enzymatic catalysis. If these challenges were addressed, then the number of successful biocatalysis projects is likely to increase. It would enable accurate prediction of protein structures, and the effects of changes in sequence or solution conditions on these structures. We would be better able to predict how substrates bind and are transformed into products, again leading to better enzyme engineering. Most significantly, it may enable the de novo design of enzymes to catalyse specific reactions.

Selective extraction of lactoferrin from acidic whey using CTAB/n-heptanol reverse micellar system

A reverse micellar system comprising CTAB/n-heptanol, developed for extracting lactoferrin (LF) from a synthetic solution of LF, was investigated for the selective extraction of LF from synthetic whey protein solution, which was prepared by mixing the pure whey proteins. The process conditions obtained during the process was further extended to extract the LF from real acidic whey. The selective extraction of LF was improved by studying the effect of NaCl concentration (additive) and aqueous phase pH on the partitioning of LF into the micellar phase. The highest extraction of LF (98.7%) from acidic whey to micellar phase was achieved at the aqueous phase pH of 10.3 and NaCl concentration of 1.1 M. The LF was back extracted to the aqueous stripping phase with 94% extraction efficiency and 100% purity. The recycling capacity of the organic phase after the back extraction of LF was analyzed to make the process more economical.

DNA Adsorption Studies of Poly(4,4'-Cychlohexylidene Bisphenol Oxalate)/Silica Nanocomposites

The present study deals with the synthesis, characterization, and DNA extraction of poly(4,4′-cyclohexylidene bisphenol oxalate)/silica (Si) nanocomposites (NCs). The effects of varying the monomer/Si (3.7%, 7%, and 13%) ratio towards the size and morphology of the resulting NC and its DNA extraction capabilities have also been studied. For the NC synthesis, two different methods were followed, including the direct mixing of poly(4,4′-cyclohexylidene bisphenol oxalate) with fumed Si, and in situ polymerization of the 4,4′-cyclohexylidene bisphenol monomer in the presence of fumed silica (11 nm). The formed NCs were thoroughly investigated by using different techniques such as scanning electron microscopy (SEM), fourier transform infrared (FTIR) spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), powdered X-ray diffraction (XRD), and Brunauer–Emmett–Teller (BET) analysis where the results supported that there was the successful formation of poly(4,4′-cyclohexylidene bisphenol oxalate)/Si NC. Within the three different NC samples, the one with 13% Si was found to maintain a very high surface area of 12.237 m²/g, as compared to the other two samples consisting of 7% Si (3.362 m²/g) and 3.7% Si (1.788 m²/g). Further, the solid phase DNA extraction studies indicated that the efficiency is strongly influenced by the amount of polymer (0.2 g > 0.1 g > 0.02 g) and the type of binding buffer. Among the three binding buffers tested, the guanidine hydrochloride/EtOH buffer produced the most satisfactory results in terms of yield (1,348,000 ng) and extraction efficiency (3370 ng/mL) as compared to the other two buffers of NaCl (2 M) and phosphate buffered silane. Based on our results, it can be indicated that the developed poly(4,4′-cyclohexylidene bisphenol oxalate)/Si NC can serve as one of the suitable candidates for the extraction of DNA in high amounts as compared to other traditional solid phase approaches.

Synthesis, Characterization, and Application of Poly(4,4'-Cyclohexylidene Bisphenol Oxalate) for Solid-Phase Extraction of DNA

The present study has synthesized poly(4,4'-cyclohexylidene bisphenol oxalate) by the condensation of oxalyl chloride with 4,4'-cyclohexylidene bisphenol, where its efficacy was tested for the solid-phase extraction of DNA. The synthesized polymer in the form of a white powder was characterized by FTIR, TGA-DTG, SEM, and BET analysis. The study utilized solid-phase application of the resulting polymer to extract DNA. The analysis of results provided the information that the extraction efficiency is a strong dependent of polymer amount and binding buffer type. Among the three types of buffers tested, the GuHCl buffer produced the most satisfactory results in terms of yield and efficiency of extraction. Moreover, the absorbance ratio of A260/A280 in all of the samples varied from 1.682 to 1.491, thereby confirming the capability of poly(4,4'-cyclohexylidene bisphenol oxalate) to elute pure DNA. The results demonstrated an increased DNA binding capacity with respect to increased percentage of the polymer. The study has concluded that poly(bisphenol Z oxalate) can be applied as one of the potential candidates for the high efficiency extraction of DNA by means of a simple, cost-effective, and environmentally friendly approach compared to the other traditional solid-phase methods.

NaCl-saturated brines are thermodynamically moderate, rather than extreme, microbial habitats

NaCl-saturated brines such as saltern crystalliser ponds, inland salt lakes, deep-sea brines and liquids-of-deliquescence on halite are commonly regarded as a paradigm for the limit of life on Earth. There are, however, other habitats that are thermodynamically more extreme. Typically, NaCl-saturated environments contain all domains of life and perform complete biogeochemical cycling. Despite their reduced water activity, ∼0.755 at 5 M NaCl, some halophiles belonging to the Archaea and Bacteria exhibit optimum growth/metabolism in these brines. Furthermore, the recognised water-activity limit for microbial function, ∼0.585 for some strains of fungi, lies far below 0.755. Other biophysical constraints on the microbial biosphere (temperatures of >121°C; pH > 12; and high chaotropicity; e.g. ethanol at >18.9% w/v (24% v/v) and MgCl2 at >3.03 M) can prevent any cellular metabolism or ecosystem function. By contrast, NaCl-saturated environments contain biomass-dense, metabolically diverse, highly active and complex microbial ecosystems; and this underscores their moderate character. Here, we survey the evidence that NaCl-saturated brines are biologically permissive, fertile habitats that are thermodynamically mid-range rather than extreme. Indeed, were NaCl sufficiently soluble, some halophiles might grow at concentrations of up to 8 M. It may be that the finite solubility of NaCl has stabilised the genetic composition of halophile populations and limited the action of natural selection in driving halophile evolution towards greater xerophilicity. Further implications are considered for the origin(s) of life and other aspects of astrobiology.

Bacillus megaterium adapts to acid stress condition through a network of genes: Insight from a genome-wide transcriptome analysis

RNA-seq analysis of B. megaterium exposed to pH 7.0 and pH 4.5 showed differential expression of 207 genes related to several processes. Among the 207 genes, 11 genes displayed increased transcription exclusively in pH 4.5. Exposure to pH 4.5 induced the expression of genes related to maintenance of cell integrity, pH homeostasis, alternative energy generation and modification of metabolic processes. Metabolic processes like pentose phosphate pathway, fatty acid biosynthesis, cysteine and methionine metabolism and synthesis of arginine and proline were remodeled during acid stress. Genes associated with oxidative stress and osmotic stress were up-regulated at pH 4.5 indicating a link between acid stress and other stresses. Acid stress also induced expression of genes that encoded general stress-responsive proteins as well as several hypothetical proteins. Our study indicates that a network of genes aid B. megaterium G18 to adapt and survive in acid stress condition.

Stress-free microbes lack vitality

Stress is an inextricable aspect of life, and stress biology has been a field of intensive study over the last 200-300 years. In human psychology, we consider a stress-free condition to be one of relaxation or happiness, yet with respect to microbial cells we do not have a concept that describes being non-stressed. Stresses within, and stress tolerance of, microbial systems lie at the crux of critical global challenges, such as optimising soil- and plant-health and crop yields; reducing food spoilage; bioremediation of polluted environments; effective biological control and biofuel production; gaining insight into aging processes in humans; and understanding astrobiology. There is no consensus on how to measure cellular stress, or even how we define it. 'Stress' implies that physical forces act on the microbial system in such a way that impairs its ability to function. Ironically, however, a cell that exhibits optimal growth also has reduced energy generation, is less resilient to change, and can have poor competitive ability. Furthermore, rapid growth is associated with a high level of oxidative damage and compromised vitality of the system. Stresses induced by temperature, pH, water activity, chaotropicity, reactive oxygen species, dehydration-rehydration cycles, ionizing radiation, and changes in turgor or other mechanical forces are well-known. Our knowledge of cellular stress responses, such as signal-transduction pathways, compatible-solute metabolism, protein-stabilization proteins, and plasma-membrane adaptations, is also considerable. However, we have limited understanding of the complex and dynamic stresses that typically occur in microbial habitats or industrial systems, and how these impact the biophysics, cellular biology and evolutionary trajectories of microbes. There is also a paucity of information on why the cellular system ultimately fails under extremes of stress, and it is even debatable whether any microbe can ever be completely stress-free. However, cells that exhibit optimal rates of biotic activity are likely to exhibit low ecological fitness compared with those that are moderately stressed; in other words, stress can enhance microbial vitality, vigour and resilience. 'Stress' is sometimes applied mistakenly to describe the effects of toxic substances that have target site-specific modes-of-action (e.g. antibiotics) rather than and do not inhibit the cell via any type of stress-mediated mechanism. Whereas terms such as 'rapid-growth stress', 'nutrient stress' and 'biotic stress' span a range of logical categories, their modes-of-action do usually involve a biophysical component. Stress can impact all levels of biology (from biomacromolecules to ecosystems), is a potent driver for evolutionary processes and - it could be argued - is an inherent property of life itself. The published articles that follow include a number of unprecedented findings and were compiled for this special issue Biology of Fungal Systems under Stress. Collectively, they are testament to the breadth and importance of the stress-biology field.

The second International Symposium on Fungal Stress: ISFUS

The topic of 'fungal stress' is central to many important disciplines, including medical mycology, chronobiology, plant and insect pathology, industrial microbiology, material sciences, and astrobiology. The International Symposium on Fungal Stress (ISFUS) brought together researchers, who study fungal stress in a variety of fields. The second ISFUS was held in May 8-11 2017 in Goiania, Goiás, Brazil and hosted by the Instituto de Patologia Tropical e Saúde Pública at the Universidade Federal de Goiás. It was supported by grants from CAPES and FAPEG. Twenty-seven speakers from 15 countries presented their research related to fungal stress biology. The Symposium was divided into seven topics: 1. Fungal biology in extreme environments; 2. Stress mechanisms and responses in fungi: molecular biology, biochemistry, biophysics, and cellular biology; 3. Fungal photobiology in the context of stress; 4. Role of stress in fungal pathogenesis; 5. Fungal stress and bioremediation; 6. Fungal stress in agriculture and forestry; and 7. Fungal stress in industrial applications. This article provides an overview of the science presented and discussed at ISFUS-2017.

Metabolic and stress responses of Acinetobacter oleivorans DR1 during long-chain alkane degradation

Acinetobacter oleivorans DR1 can utilize C₁₂–C₃₀ alkanes as a sole carbon source but not short‐chain alkanes (C₆, C₁₀). Two copies of each alkB‐, almA‐ and ladA‐type alkane hydroxylase (AH) are present in the genome of DR1 cells. Expression and mutational analyses of AHs showed that alkB1 and alkB2 are the major AH‐encoding genes under C₁₂–C₃₀, and the roles of other almA‐ and ladA genes are negligible. Our data suggested that AlkB1 is responsible for long‐chain alkane utilization (C₂₄–C₂₆), and AlkB2 is important for medium‐chain alkane (C₁₂–C₁₆) metabolism. Phylogenetic analyses revealed large incongruities between phylogenies of 16S rRNA and each AH gene, which implies that A. oleivorans DR1 has acquired multiple alkane hydroxylases through horizontal gene transfer. Transcriptomic and qRT‐PCR analyses suggested that genes participating in the synthesis of siderophore, trehalose and poly 3‐hydroxybutyrate (PHB) were expressed at much higher levels when cells used C₃₀ than when used succinate as a carbon source. The following biochemical assays supported our gene expression analyses: (i) quantification of siderophore, (ii) measurement of trehalose and (iii) observation of PHB storage. Interestingly, highly induced both ackA gene encoding an acetate kinase A and pta gene encoding a phosphotransacetylase suggested unusual ATP synthesis during C₃₀ alkane degradation, which was demonstrated by ATP measurement using the ΔackA mutant. Impaired growth of the ΔaceA mutant indicated that the glyoxylate shunt pathway is important when C₃₀ alkane is utilized. Our data provide insight into long‐chain alkane degradation in soil microorganisms.

Biosynthesis of the antimicrobial cyclic lipopeptides nunamycin and nunapeptin by Pseudomonas fluorescens strain In5 is regulated by the LuxR-type transcriptional regulator NunF

Nunamycin and nunapeptin are two antimicrobial cyclic lipopeptides (CLPs) produced by Pseudomonas fluorescens In5 and synthesized by nonribosomal synthetases (NRPS) located on two gene clusters designated the nun–nup regulon. Organization of the regulon is similar to clusters found in other CLP‐producing pseudomonads except for the border regions where putative LuxR‐type regulators are located. This study focuses on understanding the regulatory role of the LuxR‐type‐encoding gene nunF in CLP production of P. fluorescens In5. Functional analysis of nunF coupled with liquid chromatography–high‐resolution mass spectrometry (LC‐HRMS) showed that CLP biosynthesis is regulated by nunF. Quantitative real‐time PCR analysis indicated that transcription of the NRPS genes catalyzing CLP production is strongly reduced when nunF is mutated indicating that nunF is part of the nun–nup regulon. Swarming and biofilm formation was reduced in a nunF knockout mutant suggesting that these CLPs may also play a role in these phenomena as observed in other pseudomonads. Fusion of the nunF promoter region to mCherry showed that nunF is strongly upregulated in response to carbon sources indicating the presence of a fungus suggesting that environmental elicitors may also influence nunF expression which upon activation regulates nunamycin and nunapeptin production required for the growth inhibition of phytopathogens.

The significance of proline and glutamate on butanol chaotropic stress in Bacillus subtilis 168

BACKGROUND

Butanol is an intensively used industrial solvent and an attractive alternative biofuel, but the bioproduction suffers from its high toxicity. Among the native butanol producers and heterologous butanol-producing hosts, Bacillus subtilis 168 exhibited relatively higher butanol tolerance. Nevertheless, organic solvent tolerance mechanisms in Bacilli and Gram-positive bacteria have relatively less information. Thus, this study aimed to elucidate butanol stress responses that may involve in unique tolerance of B. subtilis 168 to butanol and other alcohol biocommodities.

RESULTS

Using comparative proteomics approach and molecular analysis of butanol-challenged B. subtilis 168, 108 butanol-responsive proteins were revealed, and classified into seven groups according to their biological functions. While parts of them may be similar to the proteins reportedly involved in solvent stress response in other Gram-positive bacteria, significant role of proline in the proline-glutamate-arginine metabolism was substantiated. Detection of intracellular proline and glutamate accumulation, as well as glutamate transient conversion during butanol exposure confirmed their necessity, especially proline, for cellular butanol tolerance. Disruption of the particular genes in proline biosynthesis pathways clarified the essential role of the anabolic ProB-ProA-ProI system over the osmoadaptive ProH-ProA-ProJ system for cellular protection in response to butanol exposure. Molecular modifications to increase gene dosage for proline biosynthesis as well as for glutamate acquisition enhanced butanol tolerance of B. subtilis 168 up to 1.8% (vol/vol) under the conditions tested.

CONCLUSION

This work revealed the important role of proline as an effective compatible solute that is required to protect cells against butanol chaotropic effect and to maintain cellular functions in B. subtilis 168 during butanol exposure. Nevertheless, the accumulation of intracellular proline against butanol stress required a metabolic conversion of glutamate through the specific biosynthetic ProB-ProA-ProI route. Thus, exogenous addition of glutamate, but not proline, enhanced butanol tolerance. These findings serve as a practical knowledge to enhance B. subtilis 168 butanol tolerance, and demonstrate means to engineer the bacterial host to promote higher butanol/alcohol tolerance of B. subtilis 168 for the production of butanol and other alcohol biocommodities.

Comparison of Three Different DNA Extraction Methods for Linguatula serrata as a Food Born Pathogen

BACKGROUND

One of the most important items in molecular characterization of food-borne pathogens is high quality genomic DNA. In this study, we investigated three protocols and compared their simplicity, duration and costs for extracting genomic DNA from Linguatula serrata.

METHODS

The larvae were collected from the sheep's visceral organs from the Yazd Slaughterhouse during May 2013. DNA extraction was done in three different methods, including commercial DNA extraction kit, Phenol Chloroform Isoamylalcohol (PCI), and salting out. Extracted DNA in each method was assessed for quantity and quality using spectrophotometery and agarose gel electrophoresis, respectively.

RESULTS

The less duration was regarding to commercial DNA extraction kit and then salting out protocol. The cost benefit one was salting out and then PCI method. The best quantity was regarding to PCI with 72.20±29.20 ng/μl, and purity of OD260/OD280 in 1.76±0.947. Agarose gel electrophoresis for assessing the quality found all the same.

CONCLUSION

Salting out is introduced as the best method for DNA extraction from L. seratta as a food-borne pathogen with the least costand appropriate purity. Although, the best purity was regarding to PCI but PCI is not safe as salting out. In addition, the duration of salting out was less than PCI. The least duration was seen in commercial DNA extraction kit, but it is expensive and therefore is not recommended for developing countries where consumption of offal is common.

Glycerol enhances fungal germination at the water-activity limit for life

For the most-extreme fungal xerophiles, metabolic activity and cell division typically halts between 0.700 and 0.640 water activity (approximately 70.0-64.0% relative humidity). Here, we investigate whether glycerol can enhance xerophile germination under acute water-activity regimes, using an experimental system which represents the biophysical limit of Earth's biosphere. Spores from a variety of species, including Aspergillus penicillioides, Eurotium halophilicum, Xerochrysium xerophilum (formerly Chrysosporium xerophilum) and Xeromyces bisporus, were produced by cultures growing on media supplemented with glycerol (and contained up to 189 mg glycerol g dry spores-1 ). The ability of these spores to germinate, and the kinetics of germination, were then determined on a range of media designed to recreate stresses experienced in microbial habitats or anthropogenic systems (with water-activities from 0.765 to 0.575). For A. penicillioides, Eurotium amstelodami, E. halophilicum, X. xerophilum and X. bisporus, germination occurred at lower water-activities than previously recorded (0.640, 0.685, 0.651, 0.664 and 0.637 respectively). In addition, the kinetics of germination at low water-activities were substantially faster than those reported previously. Extrapolations indicated theoretical water-activity minima below these values; as low as 0.570 for A. penicillioides and X. bisporus. Glycerol is present at high concentrations (up to molar levels) in many types of microbial habitat. We discuss the likely role of glycerol in expanding the water-activity limit for microbial cell function in relation to temporal constraints and location of the microbial cell or habitat. The findings reported here have also critical implications for understanding the extremes of Earth's biosphere; for understanding the potency of disease-causing microorganisms; and in biotechnologies that operate at the limits of microbial function.