Stress and How Bacteria Cope with Death and Survival

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.

The alternative sigma factor RpoQ regulates colony morphology, biofilm formation and motility in the fish pathogen Aliivibrio salmonicida

Background

Quorum sensing (QS) is a cell-to cell communication system that bacteria use to synchronize activities as a group. LitR, the master regulator of QS in Aliivibrio salmonicida, was recently shown to regulate activities such as motility, rugosity and biofilm formation in a temperature dependent manner. LitR was also found to be a positive regulator of rpoQ. RpoQ is an alternative sigma factor belonging to the sigma −70 family. Alternative sigma factors direct gene transcription in response to environmental signals. In this work we have studied the role of RpoQ in biofilm formation, colony morphology and motility of A. salmonicida LFI1238.

Results

The rpoQ gene in A. salmonicida LFI1238 was deleted using allelic exchange. We found that RpoQ is a strong repressor of rugose colony morphology and biofilm formation, and that it controls motility of the bacteria. We also show that overexpression of rpoQ in a ΔlitR mutant of A. salmonicida disrupts the biofilm produced by the ΔlitR mutant and decreases its motility, whereas rpoQ overexpression in the wild-type completely eliminates the motility.

Conclusion

The present work demonstrates that the RpoQ sigma factor is a novel regulatory component involved in modulating motility, colony morphology and biofilm formation in the fish pathogen A. salmonicida. The findings also confirm that RpoQ functions downstream of the QS master regulator LitR. However further studies are needed to elucidate how LitR and RpoQ work together in controlling phenotypes related to QS in A. salmonicida.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1258-9) contains supplementary material, which is available to authorized users.

Dynamics of gene regulatory networks with stochastic propensities

Gene regulatory networks (GRNs) control the production of proteins in cells. It is well-known that this process is not deterministic. Numerous studies employed a non-deterministic transition structure to model these networks. However, it is not realistic to expect state-to-state transition probabilities to remain constant throughout an organism’s lifetime. In this work, we focus on modeling GRN state transition (edge) variability using an ever-changing set of propensities. We suspect that the source of this variation is due to internal noise at the molecular level and can be modeled by introducing additional stochasticity into GRN models. We employ a beta distribution, whose parameters are estimated to capture the pattern inherent in edge behavior with minimum error. Additionally, we develop a method for obtaining propensities from a pre-determined network.

Using Raman spectroscopy and chemometrics to identify the growth phase of Lactobacillus casei Zhang during batch culture at the single-cell level

Background

As microbial cultures are comprised of heterogeneous cells that differ according to their size and intracellular concentrations of DNA, proteins, and other constituents, the detailed identification and discrimination of the growth phases of bacterial populations in batch culture is challenging. Cell analysis is indispensable for quality control and cell enrichment.

Methods

In this paper, we report the results of our investigation on the use of single-cell Raman spectrometry (SCRS) for real-time analysis and prediction of cells in different growth phases during batch culture of Lactobacillus (L.) casei Zhang. A targeted analysis of defined cell growth phases at the level of the single cell, including lag phase, log phase, and stationary phase, was facilitated by SCRS.

Results

Spectral shifts were identified in different states of cell growth that reflect biochemical changes specific to each cell growth phase. Raman peaks associated with DNA and RNA displayed a decrease in intensity over time, whereas protein-specific and lipid-specific Raman vibrations increased at different rates. Furthermore, a supervised classification model (Random Forest) was used to specify the lag phase, log phase, and stationary phase of cells based on SCRS, and a mean sensitivity of 90.7% and mean specificity of 90.8% were achieved. In addition, the correct cell type was predicted at an accuracy of approximately 91.2%.

Conclusions

To conclude, Raman spectroscopy allows label-free, continuous monitoring of cell growth, which may facilitate more accurate estimates of the growth states of lactic acid bacterial populations during fermented batch culture in industry.

Whole-Genome Sequence of the Soil Bacterium Micrococcus sp. KBS0714

We present here a draft genome assembly of Micrococcus sp. KBS0714, which was isolated from agricultural soil. The genome provides insight into the strategies that Micrococcus spp. use to contend with environmental stressors such as desiccation and starvation in environmental and host-associated ecosystems.

Isogenic mutations in the Moraxella catarrhalis CydDC system display pleiotropic phenotypes and reveal the role of a palindrome sequence in its transcriptional regulation

Moraxella catarrhalis is becoming an important human respiratory tract pathogen affecting significant proportions from the population. However, still little is known about its physiology and molecular regulation. To this end, the CydDC, which is a heterodimeric ATP binding cassette transporter that has been shown to contribute to the maintenance of the redox homeostasis across the periplasm in other Gram-negative bacteria, is studied here. Amino acids multiple sequence alignments indicated that M. catarrhalis CydC is different from the CydC proteins of the bacterial species in which this system has been previously studied. These findings prompted further interest in studying this system in M. catarrhalis. Isogenic mutant in the CydDC system showed suppression in growth rate, hypersensitivity to oxidative and reductive stress and increased accumulation of intracellular cysteine levels. In addition, the growth of cydC^- mutant exhibited hypersensitivity to exogenous cysteine; however, it did not display a significant difference from its wild-type counterpart in the murine pulmonary clearance model. Moreover, a palindrome was detected 94bp upstream of the cydD ORF suggesting it might act as a potential regulatory element. Real-time reverse transcription-PCR analysis showed that deletion/change in the palindrome resulted into alterations in the transcription levels of cydC. A better understanding of such system and its regulation helps in developing better ways to combat M. catarrhalis infections.

Survival strategies of Escherichia coli and Vibrio spp.: contribution of the viable but nonculturable phenotype to their stress-resistance and persistence in adverse environments

In their natural ecosystems, bacteria are continuously exposed to changing environmental factors including physicochemical parameters (e.g. temperature, pH, etc.), availability of nutrients as well as interaction(s) with other organisms. To increase their tolerance and survival under adverse conditions, bacteria trigger a number of adaptation mechanisms. One of the well-known adaptation responses of the non-spore-forming bacteria is the acquisition of the viable but non-culturable (VBNC) state. This phenotype is induced by different stress factors (e.g. low temperature) and is characterized by the temporal loss of culturability, which can potentially be restored. Moreover, this response can be combined with the bust and boom strategy, which implies the death of the main population of the stressed cells (or their entry into the VBNC state) upon stress, thus enabling the remaining cells (i.e. residual culturable population) to subsist at the expense of the dead or/and VBNC cells. In this review, we discuss the characteristics of the VBNC state, its biological significance and contribution to bacterial survival.

Structure and Function of the Stressosome Signalling Hub

The stressosome is a multi-protein signal integration and transduction hub found in a wide range of bacterial species. The role that the stressosome plays in regulating the transcription of genes involved in the general stress response has been studied most extensively in the Gram-positive model organism Bacillus subtilis. The stressosome receives and relays the signal(s) that initiate a complex phosphorylation-dependent partner switching cascade, resulting in the activation of the alternative sigma factor σ^B. This sigma factor controls transcription of more than 150 genes involved in the general stress response. X-ray crystal structures of individual components of the stressosome and single-particle cryo-EM reconstructions of stressosome complexes, coupled with biochemical and single cell analyses, have permitted a detailed understanding of the dynamic signalling behaviour that arises from this multi-protein complex. Furthermore, bioinformatics analyses indicate that genetic modules encoding key stressosome proteins are found in a wide range of bacterial species, indicating an evolutionary advantage afforded by stressosome complexes. Interestingly, the genetic modules are associated with a variety of signalling modules encoding secondary messenger regulation systems, as well as classical two-component signal transduction systems, suggesting a diversification in function. In this chapter we review the current research into stressosome systems and discuss the functional implications of the unique structure of these signalling complexes.

Discovery of the first small-molecule CsrA-RNA interaction inhibitors using biophysical screening technologies

AIM

CsrA is a global post-transcriptional regulator protein affecting mRNA translation and/or stability. Widespread among bacteria, it is essential for their full virulence and thus represents a promising anti-infective drug target. Therefore, we aimed at the discovery of CsrA-RNA interaction inhibitors. Results & methodology: We followed two strategies: a screening of small molecules (A) and an RNA ligand-based approach (B). Using surface plasmon resonance-based binding and fluorescence polarization-based competition assays, (A) yielded seven small-molecule inhibitors, among them MM14 (IC50 of 4 µM). (B) resulted in RNA-based inhibitor GGARNA (IC50 of 113 µM).

CONCLUSION

The first small-molecule inhibitors of the CsrA-RNA interaction were discovered exhibiting micromolar affinities. These hits represent tools to investigate the effects of CsrA-RNA interaction inhibition on bacterial virulence.

Isolation of a non-genomic origin fluoroquinolone responsive regulatory element using a combinatorial bioengineering approach

Advances in chemical biology have led to selection of synthetic functional nucleic acids for in vivo applications. Discovery of synthetic nucleic acid regulatory elements has been a long-standing goal of chemical biologists. Availability of vast genome level genetic resources has motivated efforts for discovery and understanding of inducible synthetic genetic regulatory elements. Such elements can lead to custom-design of switches and sensors, oscillators, digital logic evaluators and cell–cell communicators. Here, we describe a simple, robust and universally applicable module for discovery of inducible gene regulatory elements. The distinguishing feature is the use of a toxic peptide as a reporter to suppress the background of unwanted bacterial recombinants. Using this strategy, we show that it is possible to isolate genetic elements of non-genomic origin which specifically get activated in the presence of DNA gyrase A inhibitors belonging to fluoroquinolone (FQ) group of chemicals. Further, using a system level genetic resource, we prove that the genetic regulation is exerted through histone-like nucleoid structuring (H-NS) repressor protein. Till date, there are no reports of in vivo selection of non-genomic origin inducible regulatory promoter like elements. Our strategy opens an uncharted route to discover inducible synthetic regulatory elements from biologically-inspired nucleic acid sequences.

Surviving the acid barrier: responses of pathogenic Vibrio cholerae to simulated gastric fluid

When bacteria are subjected to low acidic pHs of the gastric environment, they may enter the viable but nonculturable (VBNC) state of survival. In this state, bacteria cannot be cultured on solid media, still exhibit signs of metabolic activity (viability). In this study, the response of pathogenic Vibrio cholerae O1 and O139 to low pH-simulated environments of the human stomach was evaluated for their survival by culturability (plate count) and viability (flow cytometry-FC) assays. Bacteria were acid challenged with simulated gastric fluid (SGF) at pH 1.5, 2.5, 3.5 and 4.5 over a period of 180 min. Exposure to SGF up to 120 min increased acid tolerance of the Vibrios up to pH 3.5 with acid challenge occurring at pH 4.5. Bacteria were culturable from pH 2.5 to 4.5 up to 60 min SGF exposure. The stationary-phase cultures of Vibrio were able to survive SGF at all pHs in an 'injured' state with FC. This could possibly mean that the bacteria have entered the VBNC stage of survival. This is a worrying public health concern due to the fact that once favourable conditions arise (intestines), these Vibrios can change back to an infectious state and cause disease.

Lysine acetylation is a common post-translational modification of key metabolic pathway enzymes of the anaerobe Porphyromonas gingivalis

Porphyromonas gingivalis is a Gram-negative anaerobe considered to be a keystone pathogen in the development of the bacterial-associated inflammatory oral disease chronic periodontitis. Although post-translational modifications (PTMs) of proteins are commonly found to modify protein function in eukaryotes and prokaryotes, PTMs such as lysine acetylation have not been examined in P. gingivalis. Lysine acetylation is the addition of an acetyl group to a lysine which removes this amino acid's positive charge and can induce changes in a protein's secondary structure and reactivity. A proteomics based approach combining immune-affinity enrichment with high sensitivity Orbitrap mass spectrometry identified 130 lysine acetylated peptides from 92 P. gingivalis proteins. The majority of these peptides (71) were attributed to 45 proteins with predicted metabolic activity; these proteins could be mapped to several P. gingivalis metabolic pathways where enzymes catalysing sequential reactions within the same pathway were often found acetylated. In particular, the catabolic pathways of complex anaerobic fermentation of amino acids to produce energy had 12 enzymes lysine acetylated. The results suggest that lysine acetylation may be an important mechanism in metabolic regulation in P. gingivalis, which is vital for P. gingivalis survival and adaptation of its metabolism throughout infection. Statement of significance. Porphyromonas gingivalis is a keystone pathogen in the development of chronic periodontitis, an inflammatory disease of the supporting tissues of the teeth. The ability of the pathogen to induce dysbiosis and disease is related to an array of specific virulence factors and metabolic regulation that enables the bacterium to proliferate in an inflamed periodontal pocket. The mechanisms P. gingivalis uses to adapt to a changing and hostile environment are poorly understood and here we show, for the first time, that enzymes of critical metabolic pathways for energy production in this bacterium were acetylated on certain lysine residues. These enzymes were often found catalysing sequential reactions within the same catabolic pathway. The results suggest that lysine acetylation is an important mechanism of metabolic regulation in P. gingivalis vital for its adaptation and proliferation to produce disease.

Adaptation of Pseudomonas sp. AKS2 in biofilm on low-density polyethylene surface: an effective strategy for efficient survival and polymer degradation

Background

Pseudomonas sp. AKS2 can efficiently degrade low-density polyethylene (LDPE). It has been shown that this degradation of LDPE by AKS2 is correlated to its ability to form biofilm on the polymer surface. However, the underlying mechanism of this biofilm-mediated degradation remains unclear. Since bioremediation potential of an organism is related to its adaptability in a given environment, we hypothesized that AKS2 cells undergo successful adaptation in biofilm on LDPE, which leads to higher level of LDPE degradation. To verify this, the current study investigated a number of parameters of AKS2 cells in biofilm that are known to be involved in adaptation process.

Results

Successful adaptation always develops a viable microbial population. So we examined the viability of AKS2 cells in biofilm. We observed the presence of viable population in the biofilm. To gain an insight, the growth of AKS2 cells in biofilm on LDPE at different time points was examined. Results showed a better reproductive competence and more colonization for AKS2 biofilm cells than planktonic cells, indicating the increased fitness of AKS2 biofilm cells than their planktonic counterpart. Towards understanding fitness, we determined the hydrolytic activity, different carbon source utilization potentials, functional diversity and homogeneity of AKS2 biofilm cells. Results showed increased hydrolytic activity (approximately 31%), higher metabolic potential, higher functional diversity (approximately 27%) and homogeneity for biofilm-harvested cells than planktonic cells. We also examined cellular surface hydrophobicity, which is important for cellular attachment to LDPE surface. Consistent with the above results, the cell surface hydrophobicity of biofilm-harvested AKS2 cells was found to be higher (approximately 26%) compared to that of their planktonic counterpart. All these results demonstrated the occurrence of physiological as well as structural adaptations of AKS2 cells in biofilm on LDPE surface that resulted in better attachment, better utilization of polymer and better growth of AKS2 cells, leading to the development of a stable colony on LDPE surface.

Conclusions

The present study shows that AKS2 cells in biofilm on LDPE surface undergo successful adaptation that leads to enhanced LDPE degradation, and thus, it helps us to understand the underlying mechanism of biofilm-mediated polymer degradation process by AKS2 cells.

Fluorescent ZnO for imaging and induction of DNA fragmentation and ROS-mediated apoptosis in cancer cells

Systemic diagram shows the cell death mechanism through the generation of reactive oxygen species.

Bioavailability and biological effect of engineered silver nanoparticles in a forest soil

The extensive use of silver nanoparticles (SNPs) as antimicrobial in food, clothing and medicine, leads inevitably to a loss of such nanomaterial in soil and water. Little is known about the effects of soil contamination, in particular, on microbial cells, which play a fundamental ecological role. In this work, the impact of SNPs on forest soil has been studied, investigating eco-physiological indicators of microbial biomass and microbial diversity with culture-dependent and independent techniques. Moreover, SNPs bioavailability and uptake were assessed. Soil samples were spiked with SNPs at two different concentrations (10 and 100 μg g(-1)dw) and incubated with the relative controls for 30, 60 and 90 days. The overall parameters showed a significant influence of the SNPs on the soil microbial community, revealing a marked shift after 60 days of incubation.

Bacterial sigma factors as targets for engineered or synthetic transcriptional control

Sigma (σ) factors are the predominant constituents of transcription regulation in bacteria. σ Factors recruit the core RNA polymerase to recognize promoters with specific DNA sequences. Recently, engineering of transcriptional regulators has become a significant tool for strain engineering. The present review summarizes the recent advances in σ factor based engineering or synthetic design. The manipulation of σ factors presents insights into the bacterial stress tolerance and metabolite productivity. We envision more synthetic design based on σ factors that can be used to tune the regulatory network of bacteria.

A DNA mimic: the structure and mechanism of action for the anti-repressor protein AbbA

Bacteria respond to adverse environmental conditions by switching on the expression of large numbers of genes that enable them to adapt to unfavorable circumstances. In Bacillus subtilis, many adaptive genes are under the negative control of the global transition state regulator, the repressor protein AbrB. Stressful conditions lead to the de-repression of genes under AbrB control. Contributing to this de-repression is AbbA, an anti-repressor that binds to and blocks AbrB from binding to DNA. Here, we have determined the NMR structure of the functional AbbA dimer, confirmed that it binds to the N-terminal DNA-binding domain of AbrB, and have provided an initial description for the interaction using computational docking procedures. Interestingly, we show that AbbA has structural and surface characteristics that closely mimic the DNA phosphate backbone, enabling it to readily carry out its physiological function.

Global genome response of Escherichia coli O157∶H7 Sakai during dynamic changes in growth kinetics induced by an abrupt downshift in water activity

The present study was undertaken to investigate growth kinetics and time-dependent change in global expression of Escherichia coli O157∶H7 Sakai upon an abrupt downshift in water activity (aw). Based on viable count data, shifting E. coli from aw 0.993 to aw 0.985 or less caused an apparent loss, then recovery, of culturability. Exponential growth then resumed at a rate characteristic for the aw imposed. To understand the responses of this pathogen to abrupt osmotic stress, we employed an integrated genomic and proteomic approach to characterize its cellular response during exposure to a rapid downshift but still within the growth range from aw 0.993 to aw 0.967. Of particular interest, genes and proteins with cell envelope-related functions were induced during the initial loss and subsequent recovery of culturability. This implies that cells undergo remodeling of their envelope composition, enabling them to adapt to osmotic stress. Growth at low aw, however, involved up-regulating additional genes and proteins, which are involved in the biosynthesis of specific amino acids, and carbohydrate catabolism and energy generation. This suggests their important role in facilitating growth under such stress. Finally, we highlighted the ability of E. coli to activate multiple stress responses by transiently inducing the RpoE and RpoH regulons to control protein misfolding, while simultaneously activating the master stress regulator RpoS to mediate long-term adaptation to hyperosmolality. This investigation extends our understanding of the potential mechanisms used by pathogenic E. coli to adapt, survive and grow under osmotic stress, which could potentially be exploited to aid the selection and/or development of novel strategies to inactivate this pathogen.

Horizontal gene transfer can rescue prokaryotes from Muller's ratchet: benefit of DNA from dead cells and population subdivision

Horizontal gene transfer (HGT) is a major factor in the evolution of prokaryotes. An intriguing question is whether HGT is maintained during evolution of prokaryotes owing to its adaptive value or is a byproduct of selection driven by other factors such as consumption of extracellular DNA (eDNA) as a nutrient. One hypothesis posits that HGT can restore genes inactivated by mutations and thereby prevent stochastic, irreversible deterioration of genomes in finite populations known as Muller’s ratchet. To examine this hypothesis, we developed a population genetic model of prokaryotes undergoing HGT via homologous recombination. Analysis of this model indicates that HGT can prevent the operation of Muller’s ratchet even when the source of transferred genes is eDNA that comes from dead cells and on average carries more deleterious mutations than the DNA of recipient live cells. Moreover, if HGT is sufficiently frequent and eDNA diffusion sufficiently rapid, a subdivided population is shown to be more resistant to Muller’s ratchet than an undivided population of an equal overall size. Thus, to maintain genomic information in the face of Muller’s ratchet, it is more advantageous to partition individuals into multiple subpopulations and let them “cross-reference” each other’s genetic information through HGT than to collect all individuals in one population and thereby maximize the efficacy of natural selection. Taken together, the results suggest that HGT could be an important condition for the long-term maintenance of genomic information in prokaryotes through the prevention of Muller’s ratchet.

Achromobacter denitrificans strain YD35 pyruvate dehydrogenase controls NADH production to allow tolerance to extremely high nitrite levels

We identified the extremely nitrite-tolerant bacterium Achromobacter denitrificans YD35 that can grow in complex medium containing 100 mM nitrite (NO2(-)) under aerobic conditions. Nitrite induced global proteomic changes and upregulated tricarboxylate (TCA) cycle enzymes as well as antioxidant proteins in YD35. Transposon mutagenesis generated NO2(-)-hypersensitive mutants of YD35 that had mutations at genes for aconitate hydratase and α-ketoglutarate dehydrogenase in the TCA cycle and a pyruvate dehydrogenase (Pdh) E1 component, indicating the importance of TCA cycle metabolism to NO2(-) tolerance. A mutant in which the pdh gene cluster was disrupted (Δpdh mutant) could not grow in the presence of 100 mM NO2(-). Nitrite decreased the cellular NADH/NAD(+) ratio and the cellular ATP level. These defects were more severe in the Δpdh mutant, indicating that Pdh contributes to upregulating cellular NADH and ATP and NO2(-)-tolerant growth. Exogenous acetate, which generates acetyl coenzyme A and then is metabolized by the TCA cycle, compensated for these defects caused by disruption of the pdh gene cluster and those caused by NO2(-). These findings demonstrate a link between NO2(-) tolerance and pyruvate/acetate metabolism through the TCA cycle. The TCA cycle mechanism in YD35 enhances NADH production, and we consider that this contributes to a novel NO2(-)-tolerating mechanism in this strain.

The role of variable DNA tandem repeats in bacterial adaptation

DNA tandem repeats (TRs), also designated as satellite DNA, are inter- or intragenic nucleotide sequences that are repeated two or more times in a head-to-tail manner. Because TR tracts are prone to strand-slippage replication and recombination events that cause the TR copy number to increase or decrease, loci containing TRs are hypermutable. An increasing number of examples illustrate that bacteria can exploit this instability of TRs to reversibly shut down or modulate the function of specific genes, allowing them to adapt to changing environments on short evolutionary time scales without an increased overall mutation rate. In this review, we discuss the prevalence and distribution of inter- and intragenic TRs in bacteria and the mechanisms of their instability. In addition, we review evidence demonstrating a role of TR variations in bacterial adaptation strategies, ranging from immune evasion and tissue tropism to the modulation of environmental stress tolerance. Nevertheless, while bioinformatic analysis reveals that most bacterial genomes contain a few up to several dozens of intra- and intergenic TRs, only a small fraction of these have been functionally studied to date.

Real-time monitoring of cell viability and cell density on the basis of a three dimensional optical reflectance method (3D-ORM): investigation of the effect of sub-lethal and lethal injuries

Cell density and cell viability have been followed on-line by using a three-dimensional optical reflectance method (3D-ORM) probe. This method has allowed to highlight the differences between a well-mixed and a scale-down bioreactor configured in order to reproduce mixing deficiencies during a fed-batch culture of Escherichia coli. These differences have been observed both for the obscuration factor (OBF) and the coincidence probability delivered by the probe. These parameters are correlated to flow cytometry measurement based on the PI-uptake test and cell density based on optical density measurement. This first set of results has pointed out the fact that the 3D-ORM probe is sensitive to sub-lethal injuries encountered by microbial cells in process-related conditions. The effect of lethal injuries has been further investigated on the basis of additional experiments involving heat stress and a sharp increase of the OBF has been observed indicating that cells are effectively injured by the increase of temperature. However, further improvement of the probe are needed in order to give access to single-cell measurements.

Molecular adaptation mechanisms employed by ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds

Current international interest in finding alternative sources of energy to the diminishing supplies of fossil fuels has encouraged research efforts in improving biofuel production technologies. In countries which lack sufficient food, the use of sustainable lignocellulosic feedstocks, for the production of bioethanol, is an attractive option. In the pre-treatment of lignocellulosic feedstocks for ethanol production, various chemicals and/or enzymatic processes are employed. These methods generally result in a range of fermentable sugars, which are subjected to microbial fermentation and distillation to produce bioethanol. However, these methods also produce compounds that are inhibitory to the microbial fermentation process. These compounds include products of sugar dehydration and lignin depolymerisation, such as organic acids, derivatised furaldehydes and phenolic acids. These compounds are known to have a severe negative impact on the ethanologenic microorganisms involved in the fermentation process by compromising the integrity of their cell membranes, inhibiting essential enzymes and negatively interact with their DNA/RNA. It is therefore important to understand the molecular mechanisms of these inhibitions, and the mechanisms by which these microorganisms show increased adaptation to such inhibitors. Presented here is a concise overview of the molecular adaptation mechanisms of ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. These include general stress response and tolerance mechanisms, which are typically those that maintain intracellular pH homeostasis and cell membrane integrity, activation/regulation of global stress responses and inhibitor substrate-specific degradation pathways. We anticipate that understanding these adaptation responses will be essential in the design of 'intelligent' metabolic engineering strategies for the generation of hyper-tolerant fermentation bacteria strains.

Oxygen consumption rates of bacteria under nutrient-limited conditions

Many environments on Earth experience nutrient limitation and as a result have nongrowing or very slowly growing bacterial populations. To better understand bacterial respiration under environmentally relevant conditions, the effect of nutrient limitation on respiration rates of heterotrophic bacteria was measured. The oxygen consumption and population density of batch cultures of Escherichia coli K-12, Shewanella oneidensis MR-1, and Marinobacter aquaeolei VT8 were tracked for up to 200 days. The oxygen consumption per CFU (QO2) declined by more than 2 orders of magnitude for all three strains as they transitioned from nutrient-abundant log-phase growth to the nutrient-limited early stationary phase. The large reduction in QO2 from growth to stationary phase suggests that nutrient availability is an important factor in considering environmental respiration rates. Following the death phase, during the long-term stationary phase (LTSP), QO2 values of the surviving population increased with time and more cells were respiring than formed colonies. Within the respiring population, a subpopulation of highly respiring cells increased in abundance with time. Apparently, as cells enter LTSP, there is a viable but not culturable population whose bulk community and per cell respiration rates are dynamic. This result has a bearing on how minimal energy requirements are met, especially in nutrient-limited environments. The minimal QO2 rates support the extension of Kleiber's law to the mass of a bacterium (100-fg range).

Cannibalism and predation as paths for horizontal passage of Wolbachia between terrestrial isopods

The alpha-proteobacteria Wolbachia are the most widespread endosymbionts in arthropods and nematodes. Mainly maternally inherited, these so-called sex parasites have selected several strategies that increase their vertical dispersion in host populations. However, the lack of congruence between the Wolbachia and their host phylogenies suggests frequent horizontal transfers. One way that could be used for horizontal Wolbachia transfers between individuals is predation. The aim of this study was to test whether horizontal passage of Wolbachia is possible when an uninfected terrestrial isopod eats an infected one. After having eaten Armadillidium vulgare harbouring Wolbachia, the predator-recipients (the two woodlice A. vulgare and Porcellio dilatatus dilatatus) that were initially Wolbachia-free were tested positive for the presence of Wolbachia both by quantitative PCR and Fluorescence in situ Hybridization (FISH). Even if the titers were low compared to vertically infected individuals, this constitutes the first demonstration of Wolbachia occurrence in various organs of an initially uninfected host after eating an infected one.

Global transcriptional analysis of dehydrated Salmonella enterica serovar Typhimurium

Despite the scientific and industrial importance of desiccation tolerance in Salmonella, knowledge regarding its genetic basis is still scarce. In the present study, we performed a transcriptomic analysis of dehydrated and water-suspended Salmonella enterica serovar Typhimurium using microarrays. Dehydration induced expression of 90 genes and downregulated that of 7 genes. Ribosomal structural genes represented the most abundant functional group with a relatively higher transcription during dehydration. Other main induced functional groups included genes involved in amino acid metabolism, energy production, ion transport, transcription, and stress response. The highest induction was observed in the kdpFABC operon, encoding a potassium transport channel. Knockout mutations were generated in nine upregulated genes. Five mutants displayed lower tolerance to desiccation, implying the involvement of the corresponding genes in the adaptation of Salmonella to desiccation. These included genes encoding the isocitrate-lyase AceA, the lipid A biosynthesis palmitoleoyl-acyltransferase Ddg, the modular iron-sulfur cluster scaffolding protein NifU, the global regulator Fnr, and the alternative sigma factor RpoE. Notably, these proteins were previously implicated in the response of Salmonella to oxidative stress, heat shock, and cold shock. A strain with a mutation in the structural gene kdpA had a tolerance to dehydration comparable to that of the parent strain, implying that potassium transport through this system is dispensable for early adaptation to the dry environment. Nevertheless, this mutant was significantly impaired in long-term persistence during cold storage. Our findings indicate the involvement of a relatively small fraction of the Salmonella genome in transcriptional adjustment from water to dehydration, with a high prevalence of genes belonging to the protein biosynthesis machinery.

Adaptation of the neutral bacterial comet assay to assess antimicrobial-mediated DNA double-strand breaks in Escherichia coli

This study aimed to determine the mechanism of action of a natural antibacterial clay mineral mixture, designated as CB, by investigating the induction of DNA double-strand breaks (DSBs) in Escherichia coli. To quantify DNA damage upon exposure to soluble antimicrobial compounds, we modified a bacterial neutral comet assay, which associates the general length of an electrophoresed chromosome, or comet, with the degree of DSB-associated DNA damage. To appropriately account for antimicrobial-mediated strand fragmentation, suitable control reactions consisting of exposures to water, ethanol, kanamycin, and bleomycin were developed and optimized for the assay. Bacterial exposure to the CB clay resulted in significantly longer comet lengths, compared to water and kanamycin exposures, suggesting that the induction of DNA DSBs contributes to the killing activity of this antibacterial clay mineral mixture. The comet assay protocol described herein provides a general technique for evaluating soluble antimicrobial-derived DNA damage and for comparing DNA fragmentation between experimental and control assays.

Integrated transcriptomic and proteomic analysis of the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions of cold and water activity stress

An integrated transcriptomic and proteomic analysis was undertaken to determine the physiological response of Escherichia coli O157:H7 Sakai to steady-state conditions relevant to low temperature and water activity conditions experienced during meat carcass chilling in cold air. The response of E. coli during exponential growth at 25 °C a(w) 0.985, 14 °C a(w) 0.985, 25 °C a(w) 0.967, and 14 °C a(w) 0.967 was compared with that of a reference culture (35 °C a(w) 0.993). Gene and protein expression profiles of E. coli were more strongly affected by low water activity (a(w) 0.967) than by low temperature (14 °C). Predefined group enrichment analysis revealed that a universal response of E. coli to all test conditions included activation of the master stress response regulator RpoS and the Rcs phosphorelay system involved in the biosynthesis of the exopolysaccharide colanic acid, as well as down-regulation of elements involved in chemotaxis and motility. However, colanic acid-deficient mutants were shown to achieve comparable growth rates to their wild-type parents under all conditions, indicating that colanic acid is not required for growth. In contrast to the transcriptomic data, the proteomic data revealed that several processes involved in protein synthesis were down-regulated in overall expression at 14 °C a(w) 0.985, 25 °C a(w) 0.967, and 14 °C a(w) 0.967. This result suggests that during growth under these conditions, E. coli, although able to transcribe the required mRNA, may lack the cellular resources required for translation. Elucidating the global adaptive response of E. coli O157:H7 during exposure to chilling and water activity stress has provided a baseline of knowledge of the physiology of this pathogen.

Role of general stress-response alternative sigma factors σ(S) (RpoS) and σ(B) (SigB) in bacterial heat resistance as a function of treatment medium pH

This investigation aimed to determine the role of general stress-response alternative sigma factors σ(S) (RpoS) and σ(B) (SigB) in heat resistance and the occurrence of sublethal injuries in cell envelopes of stationary-phase Escherichia coli BJ4 and Listeria monocytogenes EGD-e cells, respectively, as a function of treatment medium pH. Given that microbial death followed first-order inactivation kinetics (R(2)>0.95) the traditional D(T) and z values were used to describe the heat inactivation kinetics. Influence of rpoS deletion was constant at every treatment temperature and pH, making a ΔrpoS deletion mutant strain approximately 5.5 times more heat sensitive than its parental strain for every studied condition. Furthermore, the influence of the pH of the treatment medium on the reduction of the heat resistance of E. coli was also constant and independent of the treatment temperature (average z value=4.9°C) in both parental and mutant strains. L. monocytogenes EGD-e z values obtained at pH 7.0 and 5.5 were not significantly different (p>0.05) in either parental or the ∆sigB deletion mutant strains (average z value=4.8°C). Nevertheless, at pH 4.0 the z value was higher (z=8.4°C), indicating that heat resistance of both L. monocytogenes strains was less dependent on temperature at pH 4.0. At both pH 5.5 and 7.0 the influence of sigB deletion was constant and independent of the treatment temperature, decreasing L. monocytogenes heat resistance approximately 2.5 times. In contrast, the absence of sigB did not decrease the heat resistance of L. monocytogenes at pH 4.0. The role of RpoS in protecting cell envelopes was more important in E. coli (4 times) than SigB in L. monocytogenes (1.5 times). Moreover, the role of σ(S) in increasing heat resistance seems more relevant in enhancing the intrinsic resilience of the cytoplasmic membrane, and to a lesser extent, outer membrane resilience. Knowledge of environmental conditions related to the activation of alternative sigma factors σ(S) and σ(B) and their effects on heat resistance would help us to avoid and/or identify situations that increase bacterial stress resistance. Therefore, more efficient food preservation processes might be designed.

Population dynamics and identification of efficient strains of Azospirillum in maize ecosystems of Bihar (India)

Information on inoculum load and diversity of native microbial community is an important prerequisite for crop management of microbial origin. Azospirillum has a proven role in benefiting the maize (Zea mays) crop in terms of nutrient (nitrogen) supply as well as plant growth enhancement. Bihar state has highest average national maize productivity although fertilizer consumption is minimum, indicating richness of Azospirillum both in terms of population and diversity in soils. An experiment was planned to generate basic information on Azospirillum population variation in maize soils under different agricultural practices and soil types of Bihar, to identify suitable agricultural practices supporting the target microorganism and efficient Azospirillum strain(s). No tillage, growing traditional maize cultivar, land use history (diara soil having history of maize cultivation), soil organic carbon (>1%) and intercrop with oat supported prevalence of Azospirillum in maize rhizosphere. Native Azospirillum population varied from 1 million to 1 billion/g soil under diverse agricultural practices and soil types. Such richness, however, does not necessarily mean that artificial inoculation of Azospirillum is not required in Bihar soils as 92% of Azospirillum isolates (50 isolates) were poor in nitrogen-fixing ability and 88% were poor on IAA production. Efficient strains of Azospirillum based on growth (three), acetylene reduction assay (three), IAA production (three), broad range of pH (two) and temperature tolerance were identified. The findings suggested that maize crop in Bihar should be inoculated in universal mode rather than site-specific mode.

Flow cytometry to assess biochemical pathways in heat-stressed Cronobacter spp. (formerly Enterobacter sakazakii)

AIMS

Using a flow cytometry (FC)-based approach in combination with four selected fluorescent probes, the biochemical pathway activated following the adaptation of Cronobacter spp. to lethal heat stress was investigated. This approach assessed the physiological changes induced in four strains of Cronobacter spp.

METHODS AND RESULTS

Using the commercially available live/dead viability assessment fluorescence probes, live, injured or dead bacterial cells were studied. Cellular respiration and membrane potential were evaluated using the dye-labelled probe 3,3'-dihexylocarbocyanine iodide, metabolic activity was evaluated using a fluorescein diacetate (FDA) probe, intracellular pH changes were measured using a carboxy-fluorescein diacetate succinimidyl ester probe, and reactive oxygen species were measured using a hydroethidine fluorescent probe. Adaptation to lethal heat stress induced physiological changes that potentially improve the survival of Cronobacter spp.

CONCLUSIONS

These data showed that in situ assessment of physiological behaviour of lethally stressed cells using multiparameter FC is a useful, rapid and sensitive tool to study and assess the viability and physiological state of Cronobacter cells.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows that FC is a valuable tool in the study of physiological aspects of increased survival because of sublethal adaptation to heat.

The role of particle size of particulate nano-zinc oxide wood preservatives on termite mortality and leach resistance

Historically most residential wood preservatives were aqueous soluble metal formulations, but recently metals ground to submicron size and dispersed in water to give particulate formulations have gained importance. In this study, the specific role nano-zinc oxide (ZnO) particle size and leach resistance plays in termite mortality resulting from exposure to particulate ZnO-treated wood was investigated. Southern yellow pine (SYP) sapwood impregnated with three concentrations of two particle sizes (30 and 70 nm) of ZnO were compared to wood treated with soluble zinc sulphate (ZnSO4) preservative for leach resistance and termite resistance. Less than four percent leached from the particulate nano-ZnO-treated specimens, while 13 to 25% of the zinc sulphate leached from the soluble treated wood. Nano-ZnO was essentially non-leachable from wood treated with 5% formulation for the 30-nm particle size. In a no-choice laboratory test, eastern subterranean termites (Reticulitermes flavipes) consumed less than 10% of the leached nano-ZnO-treated wood with 93 to 100% mortality in all treatment concentrations. In contrast, termites consumed 10 to 12% of the leached ZnSO4-treated wood, but with lower mortality: 29% in the 1% treatment group and less than 10% (5 and 8%, respectively) in the group of wood blocks treated with 2.5 and 5.0% ZnSO4. We conclude that termites were repelled from consuming wood treated with nano-ZnO, but when consumed it was more toxic to eastern subterranean termites than wood treated with the soluble metal oxide formulation. There were no differences in leaching or termite mortality between the two particle sizes of nano-ZnO.

Contrasting effects of ultraviolet radiation on the growth efficiency of freshwater bacteria

In this study, we tested the hypothesis that the growth efficiency of freshwater bacteria is differentially affected by ultraviolet radiation (UVR, 280-400 nm) as mediated through changes in their production and respiration rates. Five bacterial strains affiliated to Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Actinobacteria were isolated from different freshwater habitats and exposed in the laboratory to photosynthetically active radiation (PAR) and PAR + UVR, or kept in the dark for 4 h. Afterward, bacterial carbon production and respiration were assessed by measuring leucine incorporation and oxygen consumption rates, respectively. Ultraviolet radiation decreased significantly the bacterial production of Acidovorax sp., Pseudomonas sp. and Actinobacterium MHWTa3, and the respiration rate of Acidovorax sp. and Acinetobacter lwoffii. Measurements of respiration of a natural bacterial community collected from the same lake where A. lwoffii was isolated resulted in significantly higher rates after exposure to PAR + UVR than in the dark. In the presence of UVR, bacterial growth efficiency significantly decreased in Acidovorax sp., Pseudomonas sp., and Actinobacterium MHWTa3, but it increased in A. lwoffii or it remained unchanged in Sphingomonas sp. Our results indicate that although the outcome was strain-specific, UVR has the potential to alter the efficiency by which dissolved organic matter is transformed into bacterial biomass and thus to affect the biogeochemical carbon cycle.

Microbial seed banks: the ecological and evolutionary implications of dormancy

Dormancy is a bet-hedging strategy used by a wide range of taxa, including microorganisms. It refers to an organism's ability to enter a reversible state of low metabolic activity when faced with unfavourable environmental conditions. Dormant microorganisms generate a seed bank, which comprises individuals that are capable of being resuscitated following environmental change. In this Review, we highlight mechanisms that have evolved in microorganisms to allow them to successfully enter and exit a dormant state, and discuss the implications of microbial seed banks for evolutionary dynamics, population persistence, maintenance of biodiversity, and the stability of ecosystem processes.

Expression of clpL1 and clpL2 genes in Lactobacillus rhamnosus VTT E-97800 after exposure to acid and heat stress treatments or to freeze-drying

The aim of the study was to evaluate the potential of utilising the information on expression levels of selected stress genes in assessing the quality of probiotic products. For this purpose RT-qPCR methods were developed to study the expression of clpL1 and clpL2 stress genes in Lactobacillus rhamnosus VTT E-97800 (E800) cells after exposure to processing-related stress conditions or to freeze-drying. Heat treatments in laboratory scale were performed with E800 cells incubated at 47 °C or 50 °C for 60 min. Acid treatments were performed both at laboratory and fermenter scale. At laboratory scale E800 cells were inoculated into General Edible Medium (GEM) adjusted to pH 4.0 and pH 3.5 and incubated at 37 °C for 180 min, whereas fermenter-grown cells were exposed to pH 4.0 for 60 min at the end of the fermentation. RNA from fresh cells and freeze-dried powders was reverse transcribed after isolation, quantification and standardisation. clpL1 and clpL2 transcripts were analysed by RT-qPCR with SYBR Green I. clpL1 was induced in L. rhamnosus E800 cells exposed to 50 °C and to a much lesser extent to 47 °C. No induction was observed for clpL2 in E800 cells during either acid or heat treatment, in any of the conditions applied. RNA isolation from freeze-dried powders was unsuccessful although several attempts were made with high quality products. In conclusion, our results suggest that developing quality indicators for probiotic products based on differences in the expression of stress genes is a challenging task for several reasons: at least with some genes (like in the present study with clpL) quite harsh conditions are needed to detect differences in the gene expression; mRNA isolation from freeze-dried powders was unsuccessful which hampers the quality analysis of large proportion of probiotic products; and furthermore RT-qPCR proved to be a too laborious procedure for routine use.

Escherichia coli population heterogeneity: subpopulation dynamics at super-optimal temperatures

In the past years, we explored the dynamics of Escherichia coli K12 at super-optimal temperatures under static and dynamic temperature conditions (Van Derlinden et al. (2008b, 2009, 2010). Disturbed sigmoid growth curves, i.e., a sequence of growth, inactivation and re-growth, were observed, especially close to the maximum growth temperature. Based on the limited set of experiments (i.e., 2 static temperatures and 2 dynamic temperature profiles), the irregular growth curves were explained by postulating the co-existence of two subpopulations: a more resistant, growing population and a temperature sensitive, inactivating population. In this study, the dynamics of the two subpopulations are studied rigorously at 11 constant temperature levels in the region between 45°C and 46°C, with at least five repetitions per temperature. At all temperatures, the total population follows a sequence of growth, inactivation and re-growth. The sequence of different stages in the growth curves can be explained by the two subpopulations. The first growth phase and the inactivation phase reflect the presence of the sensitive subpopulation. Hereafter, the population's dynamics are dominated by the growth of the resistant subpopulation. Generally, cell counts are characterized by a large variability. The dynamics of the two subpopulations are carefully analyzed using a heterogeneous subpopulation type model to study the relation between the kinetic parameters of the two subpopulations and temperature, and to evaluate if the fraction d of resistant cells varies with temperature. Results indicate that the growth rate of the sensitive subpopulation decreases with increasing temperature within the range of 45-46°C. Furthermore, results point in the direction that the duration of this initial growth phase is approximately constant, i.e., around 2h. Possibly, the stress resistance of the cells decreases after a certain period because the metabolism is fully adapted to exponential growth. Also, the growth rate of the resistant subpopulation decreases with increasing temperature. Due to the extreme variability in the cell density data, derivation of accurate relations was not possible. From the heterogeneous model implementations, given the experimental set-up, both a constant d value and a temperature dependent d value seem plausible.

Quantification of the relative effects of temperature, pH, and water activity on inactivation of Escherichia coli in fermented meat by meta-analysis

Outbreaks of Escherichia coli infections linked to fermented meats have prompted much research into the kinetics of E. coli inactivation during fermented meat manufacture. A meta-analysis of data from 44 independent studies was undertaken that allowed the relative influences of pH, water activity (a(w)), and temperature on E. coli survival during fermented meat processing to be investigated. Data were reevaluated to determine rates of inactivation, providing 484 rate data points with various pH (2.8 to 6.14), a(w) (0.75 to 0.986), and temperature (-20 to 66 degrees C) values, product formulations, and E. coli strains and serotypes. When the data were presented as an Arrhenius model, temperature (0 to 47 degrees C) accounted for 61% of the variance in the ln(inactivation rate) data. In contrast, the pH or a(w) measured accounted for less than 8% of variability in the data, and the effects of other pH- and a(w)-based variables (i.e., total decrease and rates of reduction of those factors) were largely dependent on the temperature of the process. These findings indicate that although temperatures typically used in fermented meat manufacture are not lethal to E. coli per se, when other factors prevent E. coli growth (e.g., low pH and a(w)), the rate of inactivation of E. coli is dominated by temperature. In contrast, inactivation rates at temperatures above approximately 50 degrees C were characterized by smaller z values than those at 0 to 47 degrees C, suggesting that the mechanisms of inactivation are different in these temperature ranges. The Arrhenius model developed can be used to improve product safety by quantifying the effects of changes in temperature and/or time on E. coli inactivation during fermented meat manufacture.

Nonculturable response of animal enteropathogens in the agricultural environment and implications for food safety

Concerns about animal enteropathogen contamination of fresh horticultural products have,increased worldwide and are mainly due to the ability of bacteria to survive under stress conditions in the agricultural environment and during raw-vegetable processing. This review challenges the idea that the viable but nonculturable phenomenon that has been proven to occur in plant-associated environments contributes to human pathogen survival and might be correlated with foodborne infection. Factors associated with the nonculturable response of bacteria in the field and during postharvest processing and distribution are discussed, specifically for the most common animal enteropathogens linked with the consumption of raw products: Escherichia coli O157:H7, Salmonella, Listeria monocytogenes, and Shigella spp. The accurate detection of live bacterial populations is essential for pathogen screening in food and environmental safety control and in epidemiological analysis and may have to be considered for identification of critical control points at the time of food inspection.

Bioreactor mixing efficiency modulates the activity of a prpoS::GFP reporter gene in E. coli

Background

Extensive studies have shown that up-scaling of bioprocesses has a significant impact on the physiology of the microorganisms. Among the factors associated with the fluid dynamics of the bioreactor, concentration gradients induced by loss of the global mixing efficiency associated with the increasing scale is the main phenomena leading to strong physiological modifications at the level of the microbial population. These changes are not fully understood since they involve complex physiological mechanisms. In this work, we intend to investigate, at the single cell level, the expression of the rpoS gene associated with the stress response of E. coli. The cultures of the reporter strain have been performed in a small scale reactor as well as in a series of scaled-down bioreactors able to induce extracellular perturbations with increasing level of magnitude.

Results

The rpoS level has been monitored by the aim of a transcriptional reporter gene based on the synthesis of the green fluorescent protein (GFP). It has been observed that the level of GFP increases during the transition from batch to fed-batch phase. After this initial increase, the GFP content of the cell drops, primarily due to the dilution by cell division. However, a significant drop of the GFP content has been observed if using a partitioned bioreactor, for which the mixing conditions are very bad, leading to the exposure of the cells to cyclic and stochastic extracellular fluctuations. If considering the flow cytometric profile of the cell to cell GFP content, this drop has to be attributed to the appearance of segregation at the level of the GFP content among the microbial population.

Conclusion

The generation of extracellular perturbations (in the present case, at the level of the sugar concentration and the dissolved oxygen level) has led to a drop at the level of the rpoS expression level. This drop has to be attributed to a segregation phenomenon in microbial population, with a major sub-population exhibiting a low expression level and a minor sub-population keeping its initial elevated expression level. The intensity of the segregation, as well as its time of appearance during the culture can be related to the bioreactor mixing efficiency.