Stationary phase in gram-negative bacteria

Periplasmic methionine sulfoxide reductase (MsrP)-a secondary factor in stress survival and virulence of Salmonella Typhimurium

Among others, methionine residues are highly susceptible to host-generated oxidants. Repair of oxidized methionine (Met-SO) residues to methionine (Met) by methionine sulfoxide reductases (Msrs) play a chief role in stress survival of bacterial pathogens, including Salmonella Typhimurium. Periplasmic proteins, involved in many important cellular functions, are highly susceptible to host-generated oxidants. According to location in cell, two types of Msrs, cytoplasmic and periplasmic are present in S. Typhimurium. Owing to its localization, periplasmic Msr (MsrP) might play a crucial role in defending the host-generated oxidants. Here, we have assessed the role of MsrP in combating oxidative stress and colonization of S. Typhimurium. ΔmsrP (mutant strain) grew normally in in-vitro media. In comparison to S. Typhimurium (wild type), mutant strain showed mild hypersensitivity to HOCl and chloramine-T (ChT). Following exposure to HOCl, mutant strain showed almost similar protein carbonyl levels (a marker of protein oxidation) as compared to S. Typhimurium strain. Additionally, ΔmsrP strain showed higher susceptibility to neutrophils than the parent strain. Further, the mutant strain showed very mild defects in survival in mice spleen and liver as compared to wild-type strain. In a nutshell, our results indicate that MsrP plays only a secondary role in combating oxidative stress and colonization of S. Typhimurium.

Significant Changes in Cytoplasmic Amino Acid Composition Occur in the Transition between Mid-Exponential and Stationary Phases of Growth of Staphylococcus aureus: An Example of Adaptive Homeostasis in Response to Nutrient Limitations

The bacterial pathogen Staphylococcus aureus causes a wide range of infections that result in high morbidity and mortality rates worldwide. S. aureus is known for its capacity to survive harsh environments between hosts and certain strains are very efficient as opportunistic pathogens. It is important to understand their capacities for metabolic adaptation in response to changing environmental conditions. This investigation aimed to explore the alterations in the amino acid compositions of the cytoplasm as nutrients became limiting during the growth of S. aureus. Cells were grown under optimal growth conditions and harvested at the mid-exponential and stationary phases of growth and then extracted for the analyses of amino acids in the cytoplasm. The analyses revealed that the stationary phase cells had a significantly higher concentration of total cytoplasmic amino acids compared with cells at the mid-exponential phase and displayed substantial alterations in amino acid composition. Aspartic acid was the major amino acid in the stationary phase cells, whereas glutamic acid was the most abundant in the mid-exponential cells. The glutamic acid was reduced by 47% of its original value when the growth was extended to the stationary phase. Interestingly, certain amino acids were either absent or present depending on the phase of growth. These outcomes are in line with the premise that bacterial cells of S. aureus transition into a different form of metabolic homeostasis in the shift between the exponential and stationary phases of growth, as nutrients become depleted and waste products accumulate in the external medium. The ability of S. aureus to continually and promptly adapt to differences within growth phases may represent an essential strategy assisting its virulence as a successful opportunistic pathogen to establish infections. An understanding of the switch mechanisms controlling these obvious alterations in amino acids through the growth/life cycle of this virulent pathogen may provide novel clinical strategies to battle infection.

NtrC Increases Fitness of Salmonella enterica Serovar Typhimurium under Low and Fluctuating Nutrient Conditions

Enteric pathogens cycle between nutrient-rich host and nutrient-poor external environment. These pathogens compete for nutrients while cycling between host and external environment, and often experience starvation. In this context, we have studied the role of a global regulator (NtrC) of Salmonella Typhimurium. The ntrC knockout mutation caused extended lag phase (8 h) and slow growth in the minimal medium. In lag phase, the wild-type cells showed ~60-fold more expression of ntrC gene. Gene expression studies and biochemical assays showed that the extended lag phase and slow growth is due to slow metabolism, instead of nitrogen transport. Further, we observed that ntrC knockout mutation led extended lag phase and slow growth, made ΔntrC mutant unable to compete with wild-type S. Typhimurium in both static and fluctuating nutrient condition. In addition to this, ΔntrC knockout mutant was unable to survive long-term nitrogen starvation (150 days). The nutrient recycling assays and gene expression studies revealed that ntrC gene is essential for rapid recycling of nutrients from the dead cells. Moreover, in the absence of ntrC gene, magnesium limits the nutrient recycling efficiency of S. Typhimurium. Therefore, the ntrC gene, which is often studied with respect to nitrogen scavenging in a low nitrogen growing condition, is required even in the adequate supply of nitrogen to maintain optimal growth and fast exit from the lag phase. Hence, we conclude that, the ntrC expression is essential for competitive fitness of S. Typhimurium under the low and fluctuating nutrient condition. IMPORTANCE S. Typhimurium, both in host and external environment, faces enormous competition from other microorganisms. The competition may take place either in static or in fluctuating nutrient conditions. Thus, how S. Typhimurium survives under such overlapping stress conditions remained unclear. Therefore, using S. Typhimurium as model organism we report that a global regulator NtrC, found in enteric bacteria like Escherichia coli and Salmonella, activates the set of genes and operons involved in rapid adaptation and efficient nutrient recycling/scavenging. These properties enable cells to compete with other microbes under the characteristic feast-or-famine lifestyle of S. Typhimurium. Therefore, this work helps us to understand the starvation physiology of the enteric bacterial pathogen S. Typhimurium.

Aeromonas sobria as a potential candidate for bioremediation of heavy metal from contaminated environments

The uncontrolled discharge of industrial wastes causes the accumulation of high heavy metal concentrations in soil and water, leading to many health issues. In the present study, a Gram-negative Aeromonas sobria was isolated from heavily contaminated soil in the Tanjaro area, southwest of Sulaymaniyah city in the Kurdistan Region of Iraq; then, we assessed its ability to uptake heavy metals. A. sobria was molecularly identified based on the partial amplification of 16S rRNA using novel primers. The sequence was aligned with 33 strains to analyze phylogenetic relationships by maximum likelihood. Based on maximum tolerance concentration (MTC), A. sobria could withstand Zn, Cu, and Ni at concentrations of 5, 6, and 8 mM, respectively. ICP-OES data confirmed that A. sobria reduced 54.89% (0.549 mM) of the Cu, 62.33% (0.623 mM) of the Ni, and 36.41% (0.364 mM) of the Zn after 72 h in the culture medium. Transmission electron microscopy (TEM) showed that A. sobria accumulated both Cu and Ni, whereas biosorption was suggested for the Zn. These findings suggest that metal-resistant A. sobria could be a promising candidate for heavy metal bioremediation in polluted areas. However, more broadly, research is required to assess the feasibility of exploiting A. sobria in situ.

Enhancing cell resistance for production of mixed microbiological reference materials with Salmonella and coliforms by freeze-drying

The reference material (RM) is a technical requirement for the quality assurance of analytical results and proficiency tests or interlaboratory comparisons. Microbiological RMs are most available in the dehydrated form, mainly by freeze-drying, and maintaining bacterial survival after preparation is a challenge. Thus, obtaining the most resistant cells is essential. Considering that bacteria present cross-response to dehydration after being submitted to an array of stress conditions, this study aimed to evaluate the influence of growth conditions on enterobacteria for the production of mixed microbiological RMs by freeze-drying in skim milk powder. Salmonella enterica serovar Enteritidis, Cronobacter sakazakii, Escherichia coli, and Citrobacter freundii were grown in a minimal medium with 0.5 M NaCl and 0 to 5.0 mM of manganese sulfate (MnSO4) until stationary phase. Salmonella Enteritidis presented an increased resistance to dehydration in the presence of Mn, while C. sakazakii was the most resistant to freeze-drying and further storage for 90 days. Mixed microbiological RMs were produced by freeze-drying and containing Salmonella Enteritidis and coliforms in skim milk powder with 100 mM of trehalose and the Salmonella survival rate was 91.2 to 93.6%. The mixed RM was stable after 30 days at -20 °C, and Salmonella and coliforms were detected by different methods being, the Rambach Agar the best for the bacterial differentiation. The results showed that the culture conditions applied in this study resulted in bacterial cells being more resistant to dehydration, freeze-drying, and stabilization for the production of mixed microbiological RMs more stable and homogeneous.

Impact of Lactobacillus-originated metabolites on enterohemorrhagic E. coli in rumen fluid

Rumen is one of the richest microbial ecosystems naturally harboring many zoonotic pathogens. Controlling the colonization of cattle originated zoonotic pathogens in rumen, particularly enterohemorrhagic Escherichia coli (EHEC), is critical in reducing foodborne enteric diseases in humans. In this study, we aimed to inhibit the growth of EHEC in a simulated rumen system with collected rumen fluids (RFs) using live probiotics, synbiotics, and their metabolites. EHEC inoculated RF was treated with live wild type Lactobacillus casei (LCwt), LCwt with 0.5% peanut flour (LCwt+PF), an engineered LC capable of overexpressing linoleate isomerase (LCCLA), and their metabolites collected in cell-free culture supernatants (CFCSwt, CFCSwt+PF, and CFCSCLA) at various time points. A growth stimulatory effect toward Lactobacillus spp. was exerted by all CFCS, while the EHEC was suppressed. Among other treatments only LCwt+PF reduced EHEC by 2.68 logs after 72 h. This observation was also supported by metataxonomic analysis. A reduction in Bacteroidetes and Proteobacteria while increase in Firmicutes was observed at 48 h by the presence of CFCSs as compared to the control. Our observation implies probiotic-originated metabolites modulate rumen microbiota positively which can be deployed to control the transmission of cattle-borne pathogens specifically EHEC.

The stationary phase-specific sRNA FimR2 is a multifunctional regulator of bacterial motility, biofilm formation and virulence

Bacterial pathogens employ a plethora of virulence factors for host invasion, and their use is tightly regulated to maximize infection efficiency and manage resources in a nutrient-limited environment. Here we show that during Escherichia coli stationary phase the 3' UTR-derived small non-coding RNA FimR2 regulates fimbrial and flagellar biosynthesis at the post-transcriptional level, leading to biofilm formation as the dominant mode of survival under conditions of nutrient depletion. FimR2 interacts with the translational regulator CsrA, antagonizing its functions and firmly tightening control over motility and biofilm formation. Generated through RNase E cleavage, FimR2 regulates stationary phase biology by fine-tuning target mRNA levels independently of the chaperones Hfq and ProQ. The Salmonella enterica orthologue of FimR2 induces effector protein secretion by the type III secretion system and stimulates infection, thus linking the sRNA to virulence. This work reveals the importance of bacterial sRNAs in modulating various aspects of bacterial physiology including stationary phase and virulence.

Elucidation of Iron(III) Bioleaching Properties of Gram-Positive Bacteria

Microbial-based iron reduction is an emerging technology used as an alternative to conventional chemical-based iron reduction. The iron reduction in kaolin refinement is vital for enhancing its commercial value. Extensive studies on microbial-based iron reduction mainly focus on Gram-negative bacteria, whereas little is understood about Gram-positive bacteria's mechanism and potential application. This study aims to investigate the iron-reducing mechanism of two Gram-positive bacterial isolates, Bacillus cereus (B. cereus) and Staphylococcus aureus (S. aureus). By varying the growth environment of bacteria and monitoring the biochemical changes during the process of iron reduction, the results show that Gram-positive bacterial iron reduction performance depends on the medium composition, differing from Gram-negative bacteria-based reduction processes. Nitrogen-rich medium facilitates the microbial basification of the medium, where the alkaline conditions impact the microbial iron reduction process by altering the gene expression involved in intracellular pH homeostasis and microbial growth. This discovery will contribute to the mineral refining processes and promote the development of microbial-based bioprocesses for ore purification, while also laying the foundation for investigating other Gram-positive bacterial iron-reducing ability.

Rapid Profiling of Metabolic Perturbations to Antibiotics in Living Bacteria by Induced Electrospray Ionization Mass Spectrometry

Rapid monitoring of real bacterial metabolic perturbations to antibiotics may be helpful to better understand the mechanisms of action and more targeted treatment. In this study, the real metabolic responses to antibiotic treatment in living bacteria were profiled rapidly by induced electrospray ionization mass spectrometry. Significant metabolic perturbations were profiled after antibiotic treatment compared with untreated bacteria. Similar and unique metabolic responses were observed with different antibiotic treatments. Further multivariable analysis was performed to determine significant metabolites as potential biomarkers. Moreover, different metabolic disturbances were detected for serial dilutions of antibiotic treatments. Overall, combined with induced electrospray ionization mass spectrometry, the rapid and real bacterial metabolic status caused by antibiotics was monitored, suggesting the potential application of our method in mechanism exploration and clinical diagnosis.

Integrated changes in thermal stability and proteome abundance during altered nutrient states in Escherichia coli and human cells

Altered thermal solubility measurement techniques are emerging as powerful tools to assess ligand binding, post-translational modification, protein-protein interactions, and many other cellular processes that affect protein state under various cellular conditions. Thermal solubility or stability profiling techniques are enabled on a global proteomic scale by employing isobaric tagging reagents that facilitate multiplexing capacity required to measure changes in the proteome across thermal gradients. Key among these is thermal proteomic profiling (TPP), which requires 8-10 isobaric tags per gradient and generation of multiple proteomic datasets to measure different replicates and conditions. Furthermore, using TPP to measure protein thermal stability state across different conditions may also require measurements of differential protein abundance. Here, we use the proteome integral stability alteration (PISA) assay, a higher throughput version of TPP, to measure global changes in protein thermal stability normalized to their protein abundance. We explore the use of this approach to determine changes in protein state between logarithmic and stationary phase Escherichia coli as well as glucose-starved human Hek293T cells. We observed protein intensity-corrected PISA changes in 290 and 350 proteins due to stationary phase transition in E. coli and glucose starvation, respectively. These data reveal several examples of proteins that were not previously associated with nutrient states by abundance alone. These include E. coli proteins such as putative acyl-CoA dehydrogenase (aidB) and chaperedoxin (cnoX) as well as human RAB vesicle trafficking proteins and many others which may indicate their involvement in metabolic diseases such as cancer.

Permanent, Antimicrobial Coating to Rapidly Kill and Prevent Transmission of Bacteria, Fungi, Influenza, and SARS-CoV-2

Microbial adhesion and contamination on shared surfaces can lead to life-threatening infections with serious impacts on public health, economy, and clinical practices. The traditional use of chemical disinfectants for sanitization of surfaces, however, comes with its share of health risks, such as hazardous effects on the eyes, skin, and respiratory tract, carcinogenicity, as well as environmental toxicity. To address this, we have developed a nonleaching quaternary small molecule (QSM)-based sprayable coating which can be fabricated on a wide range of surfaces such as nylon, polyethylene, surgical mask, paper, acrylate, and rubber in a one-step, photocuring technique. This contact-active coating killed pathogenic bacteria and fungi including drug-resistant strains of Staphylococcus aureus and Candida albicans within 15-30 min of contact. QSM coatings withstood multiple washes, highlighting their durability. Interestingly, the coated surfaces exhibited rapid killing of pathogens, leading to the prevention of their transmission upon contact. The coating showed membrane disruption of bacterial cells in fluorescence and electron microscopic investigations. Along with bacteria and fungi, QSM-coated surfaces also showed the complete killing of high loads of influenza (H1N1) and SARS-CoV-2 viruses within 30 min of exposure. To our knowledge, this is the first report of a coating for multipurpose materials applied in high-touch public places, hospital equipment, and clinical consumables, rapidly killing drug-resistant bacteria, fungi, influenza virus, and SARS-CoV-2.

Immobilized Stenotrophomonas maltophilia KB2 in Naproxen Degradation

Immobilization is a commonly used method in response to the need to increase the resistance of microorganisms to the toxic effects of xenobiotics. In this study, a plant sponge from Luffa cylindrica was used as a carrier for the immobilization of the Stenotrophomonas maltophilia KB2 strain since such a carrier meets the criteria for high-quality carriers, i.e., low price and biodegradability. The optimal immobilization conditions were established as a temperature of 30 °C, pH 7.2, incubation time of 72 h, and an optical density of the culture of 1.4. The strain immobilized in such conditions was used for the biodegradation of naproxen, and an average rate of degradation of 3.8 µg/hour was obtained under cometabolic conditions with glucose. The obtained results indicate that a microbiological preparation based on immobilized cells on a luffa sponge can be used in bioremediation processes where it is necessary to remove the introduced carrier.

Transient Complexity of E. coli Lipidome Is Explained by Fatty Acyl Synthesis and Cyclopropanation

In the case of many bacteria, such as Escherichia coli, the composition of lipid molecules, termed the lipidome, temporally adapts to different environmental conditions and thus modifies membrane properties to permit growth and survival. Details of the relationship between the environment and lipidome composition are lacking, particularly for growing cultures under either favourable or under stress conditions. Here, we highlight compositional lipidome changes by describing the dynamics of molecular species throughout culture-growth phases. We show a steady cyclopropanation of fatty acyl chains, which acts as a driver for lipid diversity. There is a bias for the cyclopropanation of shorter fatty acyl chains (FA 16:1) over longer ones (FA 18:1), which likely reflects a thermodynamic phenomenon. Additionally, we observe a nearly two-fold increase in saturated fatty acyl chains in response to the presence of ampicillin and chloramphenicol, with consequences for membrane fluidity and elasticity, and ultimately bacterial stress tolerance. Our study provides the detailed quantitative lipidome composition of three E. coli strains across culture-growth phases and at the level of the fatty acyl chains and provides a general reference for phospholipid composition changes in response to perturbations. Thus, lipidome diversity is largely transient and the consequence of lipid synthesis and cyclopropanation.

Filamentous morphology of bacterial pathogens: regulatory factors and control strategies

Several studies have demonstrated that when exposed to physical, chemical, and biological stresses in the environment, many bacteria (Gram-positive and Gram-negative) change their morphology from a normal cell to a filamentous shape. The formation of filamentous morphology is one of the survival strategies against environmental stress and protection against phagocytosis or protist predators. Numerous pathogenic bacteria have shown filamentous morphologies when examined in vivo or in vitro. During infection, certain pathogenic bacteria adopt a filamentous shape inside the cell to avoid phagocytosis by immune cells. Filamentous morphology has also been seen in biofilms formed on biotic or abiotic surfaces by certain bacteria. As a result, in addition to protecting against phagocytosis by immune cells or predators, the filamentous shape aids in biofilm adhesion or colonization to biotic or abiotic surfaces. Furthermore, these filamentous morphologies of bacterial pathogens lead to antimicrobial drug resistance. Clinically, filamentous morphology has become one of the most serious challenges in treating bacterial infection. The current review went into great detail about the various factors involved in the change of filamentous morphology and the underlying mechanisms. In addition, the review discussed a control strategy for suppressing filamentous morphology in order to combat bacterial infections. Understanding the mechanism underlying the filamentous morphology induced by various environmental conditions will aid in drug development and lessen the virulence of bacterial pathogens. KEY POINTS: • The bacterial filamentation morphology is one of the survival mechanisms against several environmental stress conditions and protection from phagocytosis by host cells and protist predators. • The filamentous morphologies in bacterial pathogens contribute to enhanced biofilm formation, which develops resistance properties against antimicrobial drugs. • Filamentous morphology has become one of the major hurdles in treating bacterial infection, hence controlling strategies employed for inhibiting the filamentation morphology from combating bacterial infections.

The Gene Expression Profile Differs in Growth Phases of the Bifidobacterium Longum Culture

To date, transcriptomics have been widely and successfully employed to study gene expression in different cell growth phases of bacteria. Since bifidobacteria represent a major component of the gut microbiota of a healthy human that is associated with numerous health benefits for the host, it is important to study them using transcriptomics. In this study, we applied the RNA-Seq technique to study global gene expression of B. longum at different growth phases in order to better understand the response of bifidobacterial cells to the specific conditions of the human gut. We have shown that in the lag phase, ABC transporters, whose function may be linked to active substrate utilization, are increasingly expressed due to preparation for cell division. In the exponential phase, the functions of activated genes include synthesis of amino acids (alanine and arginine), energy metabolism (glycolysis/gluconeogenesis and nitrogen metabolism), and translation, all of which promote active cell division, leading to exponential growth of the culture. In the stationary phase, we observed a decrease in the expression of genes involved in the control of the rate of cell division and an increase in the expression of genes involved in defense-related metabolic pathways. We surmise that the latter ensures cell survival in the nutrient-deprived conditions of the stationary growth phase.

Improvement of fitness and biocontrol properties of Pseudomonas putida via an extracellular heme peroxidase

The extracellular 373‐kDa PehA heme peroxidase of Pseudomonas putida KT2440 has two enzymatic domains which depend on heme cofactor for their peroxidase activity. A null pehA mutant was generated to examine the impact of PehA in rhizosphere colonization competence and the induction of plant systemic resistance (ISR). This mutant was not markedly hampered in colonization efficiency. However, increase in pehA dosage enhanced colonization fitness about 30 fold in the root and 900 fold in the root apex. In vitro assays with purified His‐tagged enzymatic domains of PehA indicated that heme‐dependent peroxidase activity was required for the enhancement of root tip colonization. Evaluation of live/dead cells confirmed that overexpression of pehA had a positive effect on bacterial cell viability. Following root colonization of rice plants by KT2440 strain, the incidence of rice blast caused by Magnaporthe oryzae was reduced by 65% and the severity of this disease was also diminished in comparison to non‐treated plants. An increase in the pehA dosage was also beneficial for the control of rice blast as compared with gene inactivation. The results suggest that PehA helps P. putida to cope with the plant‐imposed oxidative stress leading to enhanced colonization ability and concomitant ISR‐elicitation.

Phosphite synthetic auxotrophy as an effective biocontainment strategy for the industrial chassis Pseudomonas putida

The inclusion of biosafety strategies into strain engineering pipelines is crucial for safe-by-design biobased processes. This in turn might enable a more rapid regulatory acceptance of bioengineered organisms in both industrial and environmental applications. For this reason, we equipped the industrially relevant microbial chassis Pseudomonas putida KT2440 with an effective biocontainment strategy based on a synthetic dependency on phosphite, which is generally not readily available in the environment. The produced PSAG-9 strain was first engineered to assimilate phosphite through the genome-integration of a phosphite dehydrogenase and a phosphite-specific transport complex. Subsequently, to deter the strain from growing on naturally assimilated phosphate, all native genes related to its transport were identified and deleted generating a strain unable to grow on media containing any phosphorous source other than phosphite. PSAG-9 exhibited fitness levels with phosphite similar to those of the wild type with phosphate, and low levels of escape frequency. Beyond biosafety, this strategy endowed P. putida with the capacity to be cultured under non-sterile conditions using phosphite as the sole phosphorous source with a reduced risk of contamination by other microbes, while displaying enhanced NADH regenerative capacity. These industrially beneficial features complement the metabolic advantages for which this species is known for, thereby strengthening it as a synthetic biology chassis with potential uses in industry, with suitability towards environmental release.

The growth-survival trade-off is hard-wired in the Lactococcus lactis gene regulation network

Most microbes reside in oligotrophic environments for extended periods of time, requiring survival strategies that maintain proliferative capacity. We demonstrate that the non-spore-forming Lactococcus lactis KF147 progressively activates the expression of stress-associated functions in response to the declining growth rate elicited by prolonged retentostat cultivation, which coincides with up to 10⁴ -fold increased stress tolerance. Our findings provide a quantified view of the transcription and stress-tolerance adaptations underlying the growth-survival trade-off in L. lactis, and exemplify the hard-wiring of this trade-off in the lactococcal gene regulation network.

Metabolites characterisation of endophytic Phyllosticta fallopiae L67 isolated from Aloe vera with antimicrobial activity on diabetic wound microorganisms

This study aimed to assess the antimicrobial activity of endophytic Phyllosticta fallopiae L67 isolated from Aloe vera against diabetic wound microorganisms and characterise their active fraction for biologically important metabolites. The dichloromethane (DCM) extract exhibited the most significant activity with inhibition zones ranging from 11.33 to 38.33 mm. The minimal inhibitory and lethality concentrations of DCM extract ranged from 78.13 to 2500.00 µg/ml and 625.00 to 5000.00 µg/ml, respectively. The extract showed teratogenicity and lethality in the zebrafish model, where peritoneal and hepatic oedema occurred at 62.50 µg/ml, and no abnormality appeared at 31.25 µg/ml. The extract also inhibited more than 82% biofilm formation. Bioassay-guided fractionation on DCM extract yielded 18 fractions and the most active fraction was subjected to UPLC-QTOF-MS/MS analysis. Flavones, stilbenes, flavanonols, isoflavonoids, phenolic glycosides and phenol derivatives were detected. In conclusion, endophytic P. fallopiae possessed bioactive metabolites with significant antimicrobial activity against diabetic wound microorganisms.

Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains

Homomers are prevalent in bacterial proteomes, particularly among core metabolic enzymes. Homomerization is often key to function and regulation, and interfaces that facilitate the formation of homomeric enzymes are subject to intense evolutionary change. However, our understanding of the molecular mechanisms that drive evolutionary variation in homomeric complexes is still lacking. How is the diversification of protein interfaces linked to variation in functional regulation and structural integrity of homomeric complexes? To address this question, we studied quaternary structure evolution of bacterial methionine S-adenosyltransferases (MATs)-dihedral homotetramers formed along a large and conserved dimeric interface harboring two active sites, and a small, recently evolved, interdimeric interface. Here, we show that diversity in the physicochemical properties of small interfaces is directly linked to variability in the kinetic stability of MAT quaternary complexes and in modes of their functional regulation. Specifically, hydrophobic interactions within the small interface of Escherichia coli MAT render the functional homotetramer kinetically stable yet impose severe aggregation constraints on complex assembly. These constraints are alleviated by electrostatic interactions that accelerate dimer-dimer assembly. In contrast, Neisseria gonorrhoeae MAT adopts a nonfunctional dimeric state due to the low hydrophobicity of its small interface and the high flexibility of its active site loops, which perturbs small interface integrity. Remarkably, in the presence of methionine and ATP, N. gonorrhoeae MAT undergoes substrate-induced assembly into a functional tetrameric state. We suggest that evolution acts on the interdimeric interfaces of MATs to tailor the regulation of their activity and stability to unique organismal needs.

Roles of SmeYZ, SbiAB, and SmeDEF Efflux Systems in Iron Homeostasis of Stenotrophomonas maltophilia

Stenotrophomonas maltophilia, a nonfermenting Gram-negative rod, is frequently isolated from the environment and is emerging as a multidrug-resistant global opportunistic pathogen. S. maltophilia harbors eight RND-type efflux pumps that contribute to multidrug resistance and physiological functions. Among the eight efflux pumps, SmeYZ pump is constitutively highly expressed. In our previous study, we demonstrated that loss-of-function of the SmeYZ pump results in pleiotropic phenotypes, including abolished swimming motility, decreased secreted protease activity, and compromised tolerance to oxidative stress and antibiotics. In this study, we attempted to elucidate the underlying mechanisms responsible for ΔsmeYZ-mediated pleiotropic phenotypes. RNA-seq transcriptome analysis and subsequent confirmation with qRT-PCR revealed that smeYZ mutant experienced an iron starvation response because the genes involved in the synthesis and uptake of stenobactin, the sole siderophore of S. maltophilia, were significantly upregulated. We further verified that smeYZ mutant had low intracellular iron levels via inductively coupled plasma mass spectrometry (ICP-MS). Also, KJΔYZ was more sensitive to 2,2'-dipyridyl (DIP), a ferrous iron chelator, in comparison with the wild type. The contribution of SmeYZ, SmeDEF, and SbiAB pumps to stenobactin secretion was suggested by qRT-PCR and further verified by Chrome Azurol S (CAS) activity, iron source utilization, and cell viability assays. We also demonstrated that loss-of-function of SmeYZ led to the compensatory upregulation of SbiAB and SmeDEF pumps for stenobactin secretion. The overexpression of the SbiAB pump resulted in a reduction in intracellular iron levels, which may be the key factor responsible for the ΔsmeYZ-mediated pleiotropic phenotypes, except for antibiotic extrusion. IMPORTANCE Efflux pumps display high efficiency of drug extrusion, which underlies their roles in multidrug resistance. In addition, efflux pumps have physiological functions, and their expression is tightly regulated by various environmental and physiological signals. Functional redundancy of efflux pumps is commonly observed, and mutual regulation occurs among these functionally redundant pumps in a bacterium. Stenotrophomonas maltophilia is an opportunistic pathogen that shows intrinsic multi-drug resistance. In this study, we demonstrated that SmeYZ, SbiAB, and SmeDEF efflux pumps of S. maltophilia display functional redundancy in siderophore secretion. Inactivation of smeYZ led to the upregulation of smeDEF and sbiAB. Unexpectedly, sbiAB overexpression resulted in the reduction of intracellular iron levels, which led to pleiotropic defects in smeYZ mutant. This study demonstrates a previously unidentified connection between efflux pumps, siderophore secretion, and intracellular iron levels in S. maltophilia.

A human bone infection organ model for biomaterial research

The aim of this work was to establish an organ model for staphylococcal infection of human bone samples and to investigate the influence and efficacy of a microporous β-tricalcium phosphate ceramic (β-TCP, RMS Foundation) loaded with hydrogels (alginate, alginate-di-aldehyde (ADA)-gelatin) and clindamycin on infected human bone tissue over a period of 28 days. For this purpose, human tibia plateaus, collected during total knee replacement surgery, were used as a source of bone material. Samples were infected with S. aureus ATCC29213 and treated with differently loaded β-TCP composites (alginate +/- clindamycin, ADA-gelatin +/- clindamycin, unloaded). The loading of the composites was carried out by means of a flow chamber. The infection was observed for 28 days, quantifying bacteria in the medium and the osseus material on day 1, 7, 14, 21 and 28. All samples were histologically processed for bone vitality evaluation. Bone infection could be consistently performed within the organ model. In addition, a strong reduction in bacterial counts was recorded in the groups treated with ADA-gelatin + clindamycin and alginate + clindamycin, while the bacterial count in the control groups remained constant. No significant differences between groups could be observed in the number of lacunae filled with osteocytes suggesting no differences in bone vitality among groups. In an ex-vivo human bone infection model, over a period of 28 days bacterial growth could be reduced by treatment with ADA-Gel + CLI and ALG + CLI -releasing β-TCP composites. This could be relevant for its clinical use. Further work will be necessary to improve the loading of β-TCP and the bone infection organ model itself. STATEMENT OF SIGNIFICANCE: The common treatment of bone infections is debridement and systemic administration of antibiotics. In some cases, antibiotic-containing carriers are already used, but these must be removed again. Our work is intended to show another treatment option. The scaffold we have developed, made of a calcium phosphate ceramic and a hydrogel as the active substance carrier, can, in addition to releasing the active substance, also assume a load-bearing function of the bone and is biodegradable. In addition, the model we developed can also be used for the analysis and treatment of bone infections other than those of the musculoskeletal system. More importantly, it can also serve as a substitute for previously used animal experiments.

The role of sigma factor competition in bacterial adaptation under prolonged starvation

The study of adaptive microbial evolution in the laboratory can illuminate the genetic mechanisms of gaining fitness under a pre-defined set of selection factors. Laboratory evolution of bacteria under long-term starvation has gained importance in recent years because of its ability to uncover adaptive strategies that overcome prolonged nutrient limitation, a condition often encountered by natural microbes. In this evolutionary paradigm, bacteria are maintained in an energy-restricted environment in a growth phase called long-term stationary phase (LTSP). This phase is characterized by a stable, viable population size and highly dynamic genetic changes. Multiple independent iterations of LTSP evolution experiments have given rise to mutants that are slow-growing compared to the ancestor. Although the antagonistic regulation between rapid growth and the stress response is well-known in bacteria (especially Escherichia coli), the growth deficit of many LTSP-adapted mutants has not been explored in detail. In this review, I pinpoint the trade-off between growth and stress response as a dominant driver of evolutionary strategies under prolonged starvation. Focusing on mainly E. coli-based research, I discuss the various affectors and regulators of the competition between sigma factors to occupy their targets on the genome, and assess its effect on growth advantage in stationary phase (GASP). Finally, I comment on some crucial issues that hinder the progress of the field, including identification of novel metabolites in nutrient-depleted media, and the importance of using multidisciplinary research to resolve them.

Plant pathogenic bacterium can rapidly evolve tolerance to an antimicrobial plant allelochemical

Crop losses to plant pathogens are a growing threat to global food security and more effective control strategies are urgently required. Biofumigation, an agricultural technique where Brassica plant tissues are mulched into soils to release antimicrobial plant allelochemicals called isothiocyanates (ITCs), has been proposed as an environmentally friendly alternative to agrochemicals. Whilst biofumigation has been shown to suppress a range of plant pathogens, its effects on plant pathogenic bacteria remain largely unexplored. Here, we used a laboratory model system to compare the efficacy of different types of ITCs against Ralstonia solanacearum plant bacterial pathogen. Additionally, we evaluated the potential for ITC-tolerance evolution under high, intermediate, and low transfer frequency ITC exposure treatments. We found that allyl-ITC was the most efficient compound at suppressing R. solanacearum growth, and its efficacy was not improved when combined with other types of ITCs. Despite consistent pathogen growth suppression, ITC tolerance evolution was observed in the low transfer frequency exposure treatment, leading to cross-tolerance to ampicillin beta-lactam antibiotic. Mechanistically, tolerance was linked to insertion sequence movement at four positions in genes that were potentially associated with stress responses (H-NS histone like protein), cell growth and competitiveness (acyltransferase), iron storage ([2-Fe-2S]-binding protein) and calcium ion sequestration (calcium-binding protein). Interestingly, pathogen adaptation to the growth media also indirectly selected for increased ITC tolerance through potential adaptations linked with metabolism and antibiotic resistance (dehydrogenase-like protein) and transmembrane protein movement (Tat pathway signal protein). Together, our results suggest that R. solanacearum can rapidly evolve tolerance to allyl-ITC plant allelochemical which could constrain the long-term efficiency of biofumigation biocontrol and potentially shape pathogen evolution with plants.

Intracellular biosensor-based dynamic regulation to manipulate gene expression at the spatiotemporal level

The use of intracellular, biosensor-based dynamic regulation strategies to regulate and improve the production of useful compounds have progressed significantly over previous decades. By employing such an approach, it is possible to simultaneously realize high productivity and optimum growth states. However, industrial fermentation conditions contain a mixture of high- and low-performance non-genetic variants, as well as young and aged cells at all growth phases. Such significant individual variations would hinder the precise controlling of metabolic flux at the single-cell level to achieve high productivity at the macroscopic population level. Intracellular biosensors, as the regulatory centers of metabolic networks, can real-time sense intra- and extracellular conditions and, thus, could be synthetically adapted to balance the biomass formation and overproduction of compounds by individual cells. Herein, we highlight advances in the designing and engineering approaches to intracellular biosensors. Then, the spatiotemporal properties of biosensors associated with the distribution of inducers are compared. Also discussed is the use of such biosensors to dynamically control the cellular metabolic flux. Such biosensors could achieve single-cell regulation or collective regulation goals, depending on whether or not the inducer distribution is only intracellular.

Shared in planta population and transcriptomic features of nonpathogenic members of endophytic phyllosphere microbiota

Plants evolved in an environment colonized by a vast number of microbes, which collectively constitute the plant microbiota. The majority of microbiota taxa are nonpathogenic and may be beneficial to plants under certain ecological or environmental conditions. We conducted experiments to understand the features of long-term interactions of nonpathogenic microbiota members with plants. We found that a multiplication–death equilibrium explained the shared long-term static populations of nonpathogenic bacteria and that in planta bacterial transcriptomic signatures were characteristic of the stationary phase, a physiological state in which stress protection responses are induced. These results may have significant implications in understanding the bulk of “nonpathogenic” plant–microbiota interactions that occur in agricultural and natural ecosystems.

Plants and animals are in constant association with a variety of microbes. Although much is known about how pathogenic and symbiotic microbes interact with plants, less is known about the population dynamics, adaptive traits, and transcriptional features of the vast number of microbes that make up the bulk of the plant microbiota. The majority of microbiota taxa are either commensal, natural mutants of pathogens, or pathogens that encounter strong immune responses due to plant recognition of pathogen effectors. How these “nonpathogenic” microbes interact with plants is poorly understood, especially during long-term, steady-state interactions, which are more reflective of plant–microbiota interactions in nature. In this study, we embarked upon long-term population and in planta transcriptomic studies of commensal endophytic bacteria and compared them to nonpathogenic or effector-triggered immunity-inducing strains of the bacterial pathogen Pseudomonas syringae. Our results led to the discovery of multiplication–death equilibrium as a common basis for the shared long-term static population densities of these bacteria. A comprehensive in planta transcriptomic analysis using multiple time points after inoculation revealed a striking similarity between the transcriptomic features of nonpathogenic P. syringae to that of bacteria in stationary phase in vitro, a metabolically active physiological state in which the production of adaptive secondary metabolites and stress responses are induced. We propose that the long-term population and transcriptomic features of nonpathogenic bacteria captured in this study likely reflect the physiological steady state encountered by the bulk of endophytic microbiota—excluding virulent pathogens—in their life-long interactions with plants in nature.

Absence of Ribosome Modulation Factor Alters Growth and Competitive Fitness of Escherichia coli

During stationary phase in Escherichia coli, the expression of the ribosome modulation factor (RMF) protein participates in the dimerization of two 70S ribosomes, ultimately creating a 100S particle. 100S ribosomes are commonly thought to function to preserve ribosomes as growth ceases and cells begin to catabolize intracellular components, including proteins, during their transition into stationary phase. Here, we show that the rates of stationary-phase ribosomal degradation are increased in an rmf mutant strain that cannot produce 100S ribosomes, resulting in deficiencies in outgrowth upon reinoculation into fresh medium. Upon coinoculation in LB medium, the mutant exhibits a delay in entry into log phase, differences in growth rates, and an overall reduction in relative fitness during competition. Unexpectedly, the rmf mutant exhibited shorter generation times than wild-type cells during log phase, both in monoculture and during competition. These doubling times of ∼13 min suggest that failure to maintain ribosomal balance affects the control of cell division. Though the timing of entry into and exit from log phase is altered, 100S ribosomes are not essential for long-term viability of the rmf mutant when grown in monoculture.

IMPORTANCE Ribosomes are the sole source in any cell for new protein synthesis that is vital to maintain life. While ribosomes are frequently consumed as sources of nutrients under low-nutrient conditions, some ribosomes appear to be preserved for later use. The failure to maintain the availability of these ribosomes can lead to a dire consequence upon the influx of new nutrients, as cells are unable to efficiently replenish their metabolic machinery. It is important to study the repercussions, consequences, and mechanisms of survival in cells that cannot properly maintain the availability of their ribosomes in order to better understand their mechanisms of survival during competition under nutrient-depleted conditions.

The cellular slime mold Fonticula alba forms a dynamic, multicellular collective while feeding on bacteria

Multicellularity evolved in fungi and animals, or the opisthokonts, from their common amoeboflagellate ancestor but resulted in strikingly distinct cellular organizations. The origins of this multicellularity divergence are not known. The stark mechanistic differences that underlie the two groups and the lack of information about ancestral cellular organizations limits progress in this field. We discovered a new type of invasive multicellular behavior in Fonticula alba, a unique species in the opisthokont tree, which has a simple, bacteria-feeding sorocarpic amoeba lifestyle. This invasive multicellularity follows germination dependent on the bacterial culture state, after which amoebae coalesce to form dynamic collectives that invade virgin bacterial resources. This bacteria-dependent social behavior emerges from amoeba density and allows for rapid and directed invasion. The motile collectives have animal-like properties but also hyphal-like search and invasive behavior. These surprising findings enrich the diverse multicellularities present within the opisthokont lineage and offer a new perspective on fungal origins.

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Unexpected bacterial-state-dependent culture conditions for Fonticula alba

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A multicellular invasion of bacterial food resources that is distinct from fruiting

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A leader-led invasive collectivity that is an emergent property

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Insights into the origins of invasive hyphal and fruiting multicellularity in dikarya

An ultrasensitive microfluidic approach reveals correlations between the physico-chemical and biological activity of experimental peptide antibiotics

Antimicrobial resistance challenges the ability of modern medicine to contain infections. Given the dire need for new antimicrobials, polypeptide antibiotics hold particular promise. These agents hit multiple targets in bacteria starting with their most exposed regions-their membranes. However, suitable approaches to quantify the efficacy of polypeptide antibiotics at the membrane and cellular level have been lacking. Here, we employ two complementary microfluidic platforms to probe the structure-activity relationships of two experimental series of polypeptide antibiotics. We reveal strong correlations between each peptide's physicochemical activity at the membrane level and biological activity at the cellular level. We achieve this knowledge by assaying the membranolytic activities of the compounds on hundreds of individual giant lipid vesicles, and by quantifying phenotypic responses within clonal bacterial populations with single-cell resolution. Our strategy proved capable of detecting differential responses for peptides with single amino acid substitutions between them, and can accelerate the rational design and development of peptide antimicrobials.

Experimental Evolution of Anticipatory Regulation in Escherichia coli

Environmental cues in an ecological niche are often temporal in nature. For instance, in temperate climates, temperature is higher in daytime compared to during night. In response to these temporal cues, bacteria have been known to exhibit anticipatory regulation, whereby triggering response to a yet to appear cue. Such an anticipatory response in known to enhance Darwinian fitness, and hence, is likely an important feature of regulatory networks in microorganisms. However, the conditions under which an anticipatory response evolves as an adaptive response are not known. In this work, we develop a quantitative model to study response of a population to two temporal environmental cues, and predict variables which are likely important for evolution of anticipatory regulatory response. We follow this with experimental evolution of Escherichia coli in alternating environments of rhamnose and paraquat for ∼850 generations. We demonstrate that growth in this cyclical environment leads to evolution of anticipatory regulation. As a result, pre-exposure to rhamnose leads to a greater fitness in paraquat environment. Genome sequencing reveals that this anticipatory regulation is encoded via mutations in global regulators. Overall, our study contributes to understanding of how environment shapes the topology of regulatory networks in an organism.

Study of the contribution of active defense mechanisms to ciprofloxacin tolerance in Escherichia coli growing at different rates

Using rpoS, tolC, ompF, and recA knockouts, we investigated their effect on the physiological response and lethality of ciprofloxacin in E. coli growing at different rates on glucose, succinate or acetate. We have shown that, regardless of the strain, the degree of changes in respiration, membrane potential, NAD⁺/NADH ratio, ATP and glutathione (GSH) strongly depends on the initial growth rate and the degree of its inhibition. The deletion of the regulator of the general stress response RpoS, although it influenced the expression of antioxidant genes, did not significantly affect the tolerance to ciprofloxacin at all growth rates. The mutant lacking TolC, which is a component of many E. coli efflux pumps, showed the same sensitivity to ciprofloxacin as the parent. The absence of porin OmpF slowed down the entry of ciprofloxacin into cells, prolonged growth and shifted the optimal bactericidal concentration towards higher values. Deficiency of RecA, a regulator of the SOS response, dramatically altered the late phase of the SOS response (SOS-dependent cell death), preventing respiratory inhibition and a drop in membrane potential. The recA mutation inverted GSH fluxes across the membrane and abolished ciprofloxacin-induced H₂S production. All studied mutants showed an inverse linear relationship between logCFU ml^-1 and the specific growth rate. Mutations shifted the plot of this dependence relative to the parental strain according to their significance for ciprofloxacin tolerance. The crucial role of the SOS system is confirmed by dramatic shift down of this plot in the recA mutant.

Evolutionary Dynamics of Asexual Hypermutators Adapting to a Novel Environment

How microbes adapt to a novel environment is a central question in evolutionary biology. Although adaptive evolution must be fueled by beneficial mutations, whether higher mutation rates facilitate the rate of adaptive evolution remains unclear. To address this question, we cultured Escherichia coli hypermutating populations, in which a defective methyl-directed mismatch repair pathway causes a 140-fold increase in single-nucleotide mutation rates. In parallel with wild-type E. coli, populations were cultured in tubes containing Luria-Bertani broth, a complex medium known to promote the evolution of subpopulation structure. After 900 days of evolution, in three transfer schemes with different population-size bottlenecks, hypermutators always exhibited similar levels of improved fitness as controls. Fluctuation tests revealed that the mutation rates of hypermutator lines converged evolutionarily on those of wild-type populations, which may have contributed to the absence of fitness differences. Further genome-sequence analysis revealed that, although hypermutator populations have higher rates of genomic evolution, this largely reflects strong genetic linkage. Despite these linkage effects, the evolved population exhibits parallelism in fixed mutations, including those potentially related to biofilm formation, transcription regulation, and mutation-rate evolution. Together, these results are generally inconsistent with a hypothesized positive relationship between the mutation rate and the adaptive speed of evolution, and provide insight into how clonal adaptation occurs in novel environments.

Enhanced polyhydroxybutyrate production from acid whey through determination of process and metabolic limiting factors

To sustainably produce biodegradable polyhydroxybutyrate (PHB), this study investigated effects of process and metabolic limiting factors during bioconversion of acid whey (AW) to PHB, offering economic and environmental advantages for dairy industry. Recombinant Escherichia coli LSBJ was used to achieve high PHB yields by utilizing both lactose and lactic acid as carbon source. Up to 85% PHB accumulation was achieved during growth on the synthetic AW. Growth on raw AW had the highest PHB yield of 4 g/L and a high substrate utilization efficiency (95%). Notably, ratios of lactate: lactose and C/N impacted metabolic flux and PHB yields. Maintaining the fermentation pH enhanced PHB production. Furthermore, additives of inorganic nitrogen sources, minerals and trace metals promoted PHB production from AW. The study improves the understanding of factors affecting utilization of AW and demonstrated the high PHB yields using recombinant E. coli that could be leveraged to design a sustainable process.

Enzyme Activity of Cellulolytic Bacteria from Biological Education and Research Forest Floor Andalas University

<b>Background and Objective:</b> The composition of the waste consists mostly of plant biomass. Cellulose is the largest component of plant biomass and cellulolytic bacteria are needed to degrade it. This study aimed to determine enzyme activity possessed by bacterial isolates from Biological Education and Research Forest floor Andalas University. <b>Materials and Methods:</b> The isolation stage was carried out with NA (Nutrient agar) medium, Screening with CMC (Carboxymethyl Cellulose) medium with congo red dye and enzyme activity testing was carried out using the Nelson-Somogyi method. <b>Results:</b> We found 16 bacterial isolates obtained from Biological Education and Research Forest Floor Andalas University, 10 of them were positive for cellulolytic bacteria with the highest cellulolytic index value of 2.59 on FFB 2 isolates. <b>Conclusion:</b> The bacterial isolate with the best enzyme activity value was FFB 2 isolate 0.166 U mL<sup>1</sup> for 72 hrs.

Development of an Autoinducible Plasmid for Recombinant Protein Production

BACKGROUND

The production of recombinant proteins in E. coli involves such factors as host strains, expression vectors, culture media, and induction methods. The typical procedure to produce heterologous proteins consists of the following: (1) insertion of the target gene into a suitable vector to construct an overexpression plasmid, (2) transformation of a strain specialized for protein production with the constructed plasmid DNA, (3) growth of the host in a suitable medium and induction of the protein production at a right moment, and (4) further growth to get the maximum yield. There are hurdles involved in each of these steps, and researchers have developed many materials or methods, which often require special recipes or procedures.

OBJECTIVE

To eliminate the special requirements for the recombinant protein production by using readily available materials. Also to save time and effort in the routine protein production work.

METHOD

We started with a vector capable of producing a target protein fused to the C-terminus of the maltose binding protein (MBP). The mCherry (red fluorescent protein) gene was fused to MBP. It acted as a reporter in the initial screening procedure. The original lethal gene (barnase) was replaced with sacB. We chose 3 stationary phase promoters, and made hybrids of them by mixing halves from each one. The T5 promoter was replaced with these stationary phase promoters or their hybrids. The best plasmid was selected by the color intensity of the cell pellet. MBP and GST genes were inserted in place of sacB, and their production yields were compared with the original plasmid in the conventional way of expression.

RESULTS

We constructed an expression plasmid with an autoinducible promoter working in a host that was not specially designed for protein production and in a TB medium which did not contain any secret ingredient, nor was difficult to prepare unlike Studier's defined medium. This plasmid also contains a color indicator which turns red when protein production is successful. We tested our system with the maltose binding protein (MBP) and the glutathione S-transferase (GST), and showed that both proteins were produced to a level comparable to what the commercial medium and/or the specialized strain yielded.

CONCLUSION

We developed a plasmid equipped with an autoinducible promoter, a hybrid of the two promoters which were activated at the stationary phase. This plasmid does not need a special E. coli strain nor a sophisticated nor an expensive medium. It produces an intense red (or pink) color, which can be used as an indicator of a successful production of the target protein and as a predictive measure of the amount of the produced target protein. We speculate that this plasmid will have its greatest advantage when growing cells at low temperatures which would inevitably take a long time.  .

Changes in the distribution of membrane lipids during growth of Thermotoga maritima at different temperatures: Indications for the potential mechanism of biosynthesis of ether-bound diabolic acid (membrane-spanning) lipids

Membrane-spanning lipids are present in a wide variety of archaea but they are rarely in bacteria. Nevertheless, the (hyper)thermophilic members of the order Thermotogales harbor tetraester, tetraether, and mixed ether/ester membrane-spanning lipids mostly composed of core lipids derived from diabolic acids, C_30, C₃₂ and C₃₄ dicarboxylic acids with two adjacent mid-chain methyl substituents. Lipid analysis of Thermotoga maritima across growth phases revealed a decrease of the relative abundance of fatty acids together with an increase of diabolic acids with independence of growth temperature. We also identified isomers of C₃₀ and C₃₂ diabolic acids, i.e. dicarboxylic acids with only one methyl group at C-15. Their distribution suggests they are products of the condensation reaction but preferably produced when the length of the acyl chains is not optimal. In comparison with growth at the optimal temperature of 80°C, an increase of glycerol ether-derived lipids was observed at 55°C. Besides, our analysis only detected diabolic acid-containing intact polar lipids with phosphoglycerol (PG) headgroups. Considering these findings, we hypothesize a biosynthetic pathway for the synthesis of membrane-spanning lipids based on PG polar lipid formation, suggesting that the protein catalyzing this process could be a membrane protein. We also identified, by genomic and protein domain analyses, a gene coding for a putative plasmalogen synthase homologue in T. maritima, which is also present in other bacteria producing sn1-alkyl ether lipids but not plasmalogens, suggesting it could be involved in the conversion of the ester to ether bond in the diabolic acids bound in membrane-spanning lipids. Importance Membrane-spanning lipids are unique compounds found in most archaeal membranes, but they are also present in specific bacterial groups like the Thermotogales. The synthesis and physiological role of membrane-spanning lipids in bacteria represent an evolutionary and biochemical open question that points to the differentiation of the membrane lipids composition. Understanding the formation of membrane-spanning lipids is crucial to solving this question and identifying the enzymatic and biochemical mechanism performing this procedure. In the present work, we found changes at the core lipid level, and we propose that the growth phase drives the biosynthesis of these lipids rather than temperature. Our results identified physiological conditions influencing the membrane-spanning lipids biosynthetic process which can further clarify the pathway leading to the biosynthesis of these compounds.

Cellular Self-Digestion and Persistence in Bacteria

Cellular self-digestion is an evolutionarily conserved process occurring in prokaryotic cells that enables survival under stressful conditions by recycling essential energy molecules. Self-digestion, which is triggered by extracellular stress conditions, such as nutrient depletion and overpopulation, induces degradation of intracellular components. This self-inflicted damage renders the bacterium less fit to produce building blocks and resume growth upon exposure to fresh nutrients. However, self-digestion may also provide temporary protection from antibiotics until the self-digestion-mediated damage is repaired. In fact, many persistence mechanisms identified to date may be directly or indirectly related to self-digestion, as these processes are also mediated by many degradative enzymes, including proteases and ribonucleases (RNases). In this review article, we will discuss the potential roles of self-digestion in bacterial persistence.

Biodesulfurization Induces Reprogramming of Sulfur Metabolism in Rhodococcus qingshengii IGTS8: Proteomics and Untargeted Metabolomics

Sulfur metabolism in fuel-biodesulfurizing bacteria and the underlying physiological adaptations are not understood, which has impeded the development of a commercially viable bioprocess for fuel desulfurization. To fill these knowledge gaps, we performed comparative proteomics and untargeted metabolomics in cultures of the biodesulfurization reference strain Rhodococcus qingshengii IGTS8 grown on either inorganic sulfate or the diesel-borne organosulfur compound dibenzothiophene as a sole sulfur source. Dibenzothiophene significantly altered the biosynthesis of many sulfur metabolism proteins and metabolites in a growth phase-dependent manner, which enabled us to reconstruct the first experimental model for sulfur metabolism in a fuel-biodesulfurizing bacterium. All key pathways related to assimilatory sulfur metabolism were represented in the sulfur proteome, including uptake of the sulfur sources, sulfur acquisition, and assimilatory sulfate reduction, in addition to biosynthesis of key sulfur-containing metabolites such as S-adenosylmethionine, coenzyme A, biotin, thiamin, molybdenum cofactor, mycothiol, and ergothioneine (low-molecular weight thiols). Fifty-two proteins exhibited significantly different abundance during at least one growth phase. Sixteen proteins were uniquely detected and 47 proteins were significantly more abundant in the dibenzothiophene culture during at least one growth phase. The sulfate-free dibenzothiophene-containing culture reacted to sulfate starvation by restricting sulfur assimilation, enforcing sulfur-sparing, and maintaining redox homeostasis. Biodesulfurization triggered alternative pathways for sulfur assimilation different from those operating in the inorganic sulfate culture. Sulfur metabolism reprogramming and metabolic switches in the dibenzothiophene culture were manifested in limiting sulfite reduction and biosynthesis of cysteine, while boosting the production of methionine via the cobalamin-independent pathway, as well as the biosynthesis of the redox buffers mycothiol and ergothioneine. The omics data underscore the key role of sulfur metabolism in shaping the biodesulfurization phenotype and highlight potential targets for improving the biodesulfurization catalytic activity via metabolic engineering.

IMPORTANCE For many decades, research on biodesulfurization of fossil fuels was conducted amid a large gap in knowledge of sulfur metabolism and its regulation in fuel-biodesulfurizing bacteria, which has impeded the development of a commercially viable bioprocess. In addition, lack of understanding of biodesulfurization-associated metabolic and physiological adaptations prohibited the development of efficient biodesulfurizers. Our integrated omics-based findings reveal the assimilatory sulfur metabolism in the biodesulfurization reference strain Rhodococcus qingshengii IGTS8 and show how sulfur metabolism and oxidative stress response were remodeled and orchestrated to shape the biodesulfurization phenotype. Our findings not only explain the frequently encountered low catalytic activity of native fuel-biodesulfurizing bacteria but also uncover unprecedented potential targets in sulfur metabolism that could be exploited via metabolic engineering to boost the biodesulfurization catalytic activity, a prerequisite for commercial application.

Cell Wall Biology of Vibrio cholerae

Most bacteria are protected from environmental offenses by a cell wall consisting of strong yet elastic peptidoglycan. The cell wall is essential for preserving bacterial morphology and viability, and thus the enzymes involved in the production and turnover of peptidoglycan have become preferred targets for many of our most successful antibiotics. In the past decades, Vibrio cholerae, the gram-negative pathogen causing the diarrheal disease cholera, has become a major model for understanding cell wall genetics, biochemistry, and physiology. More than 100 articles have shed light on novel cell wall genetic determinants, regulatory links, and adaptive mechanisms. Here we provide the first comprehensive review of V. cholerae's cell wall biology and genetics. Special emphasis is placed on the similarities and differences with Escherichia coli, the paradigm for understanding cell wall metabolism and chemical structure in gram-negative bacteria.

Water-Soluble Humic Materials Modulating Metabolism and Triggering Stress Defense in Sinorhizobium fredii

Bacteria have evolved a series of mechanisms to maintain their survival and reproduction in changeable and stressful environments. In-depth understanding of these mechanisms can allow for better developing and utilizing of bacteria with various biological functions. In this study, we found that water-soluble humic materials (WSHM), a well-known environment-friendly plant growth biostimulant, significantly promoted the free-living growth and survival of Sinorhizobium fredii CCBAU45436 in a bell-shaped, dose-dependent manner, along with more-efficient carbon source consumption and relief of medium acidification. By using RNA-Seq analysis, a total of 1,136 genes significantly up-/downregulated by external addition of WSHM were identified under test conditions. These differentially expressed genes (DEGs) were enriched in functional categories related to carbon/nitrogen metabolism, cellular stress response, and genetic information processing. Further protein-protein interaction (PPI) network analysis and reverse genetic engineering indicated that WSHM might reprogram the transcriptome through inhibiting the expression of key hub gene rsh, which encodes a bifunctional enzyme catalyzing synthesis and hydrolysis of the "magic spot" (p)ppGpp. In addition, the root colonization and viability in soil of S. fredii CCBAU45436 were increased by WSHM. These findings provide us with new insights into how WSHM benefit bacterial adaptations and demonstrate great application value to be a unique inoculant additive. IMPORTANCE Sinorhizobium fredii CCBAU45436 is a highly effective, fast-growing rhizobium that can establish symbiosis with multiple soybean cultivars. However, it is difficult to maintain the high-density effective viable cells in the rhizobial inoculant for the stressful conditions during production, storage, transport, and application. Here, we showed that WSHM greatly increased the viable cells of S. fredii CCBAU45436 in culture, modulating metabolism and triggering stress defense. The root colonization and viability in soil of S. fredii CCBAU45436 were also increased by WSHM. Our results shed new insights into the effects of WSHM on bacteria and the importance of metabolism and stress defense during the bacteria's whole life. In addition, the functional mechanism of WSHM may provide candidate genes for improving environmental adaptability and application potential of bacteria through genetic engineering.

Microbial population dynamics and evolutionary outcomes under extreme energy limitation

Microorganisms commonly inhabit energy-limited ecosystems where cellular maintenance and reproduction is highly constrained. To gain insight into how individuals persist under such conditions, we derived demographic parameters from a collection of 21 heterotrophic bacterial taxa by censusing 100 populations in an effectively closed system for 1,000 d. All but one taxon survived prolonged resource scarcity, yielding estimated times to extinction ranging over four orders of magnitude from 100 to 105 y. Our findings corroborate reports of long-lived bacteria recovered from ancient environmental samples, while providing insight into mechanisms of persistence. As death rates declined over time, lifespan was extended through the scavenging of dead cells. Although reproduction was suppressed in the absence of exogenous resources, populations continued to evolve. Hundreds of mutations were acquired, contributing to genome-wide signatures of purifying selection as well as molecular signals of adaptation. Consistent ecological and evolutionary dynamics indicate that distantly related bacteria respond to energy limitation in a similar and predictable manner, which likely contributes to the stability and robustness of microbial life.

Endurance of extremely prolonged nutrient prevention across kingdoms of life

Numerous observations demonstrate that microorganisms can survive very long periods of nutrient deprivation and starvation. Moreover, it is evident that prolonged periods of starvation are a feature of many habitats, and many cells in all kingdoms of life are found in prolonged starvation conditions. Bacteria exhibit a range of responses to long-term starvation. These include genetic adaptations such as the long-term stationary phase and the growth advantage in stationary phase phenotypes characterized by mutations in stress-signaling genes and elevated mutation rates. Here, we suggest using the term "endurance of prolonged nutrient prevention" (EPNP phase), to describe this phase, which was also recently described in eukaryotes. Here, we review this literature and describe the current knowledge about the adaptations to very long-term starvation conditions in bacteria and eukaryotes, its conceptual and structural conservation across all kingdoms of life, and point out possible directions that merit further research.

Removal of peptidoglycan and inhibition of active cellular processes leads to daptomycin tolerance in Enterococcus faecalis

Daptomycin is a cyclic lipopeptide antibiotic used in the clinic for treatment of severe enterococcal infections. Recent reports indicate that daptomycin targets active cellular processes, specifically, peptidoglycan biosynthesis. Within, we examined the efficacy of daptomycin against Enterococcus faecalis under a range of environmental growth conditions including inhibitors that target active cellular processes. Daptomycin was far less effective against cells in late stationary phase compared to cells in exponential phase, and this was independent of cellular ATP levels. Further, the addition of either the de novo protein synthesis inhibitor chloramphenicol or the fatty acid biosynthesis inhibitor cerulenin induced survival against daptomycin far better than controls. Alterations in metabolites associated with peptidoglycan synthesis correlated with protection against daptomycin. This was further supported as removal of peptidoglycan induced physiological daptomycin tolerance, a synergistic relation between daptomycin and fosfomycin, an inhibitor of the fist committed step peptidoglycan synthesis, was observed, as well as an additive effect when daptomycin was combined with ampicillin, which targets crosslinking of peptidoglycan strands. Removal of the peptidoglycan of Enterococcus faecium, Staphylococcus aureus, and Bacillus subtilis also resulted in significant protection against daptomycin in comparison to whole cells with intact cell walls. Based on these observations, we conclude that bacterial growth phase and metabolic activity, as well as the presence/absence of peptidoglycan are major contributors to the efficacy of daptomycin.

DNA cytosine methyltransferase enhances viability during prolonged stationary phase in Escherichia coli

In Escherichia coli, DNA cytosine methyltransferase (Dcm) methylates the second cytosine in the sequence 5'CCWGG3' generating 5-methylcytosine. Dcm is not associated with a cognate restriction enzyme, suggesting Dcm impacts facets of bacterial physiology outside of restriction-modification systems. Other than gene expression changes, there are few phenotypes that have been identified in strains with natural or engineered Dcm loss, and thus Dcm function has remained an enigma. Herein, we demonstrate that Dcm does not impact bacterial growth under optimal and selected stress conditions. However, Dcm does impact viability in long-term stationary phase competition experiments. Dcm+ cells outcompete cells lacking dcm under different conditions. Dcm knockout cells have more RpoS-dependent HPII catalase activity than wild-type cells. Thus, the impact of Dcm on stationary phase may involve changes in RpoS activity. Overall, our data reveal a new role for Dcm during long-term stationary phase.

sRNA-mediated RNA processing regulates bacterial cell division

Tight control of cell division is essential for survival of most organisms. For prokaryotes, the regulatory mechanisms involved in the control of cell division are mostly unknown. We show that the small non-coding sRNA StsR has an important role in controlling cell division and growth in the alpha-proteobacterium Rhodobacter sphaeroides. StsR is strongly induced by stress conditions and in stationary phase by the alternative sigma factors RpoHI/HII, thereby providing a regulatory link between cell division and environmental cues. Compared to the wild type, a mutant lacking StsR enters stationary phase later and more rapidly resumes growth after stationary phase. A target of StsR is UpsM, the most abundant sRNA in the exponential phase. It is derived from partial transcriptional termination within the 5' untranslated region of the mRNA of the division and cell wall (dcw) gene cluster. StsR binds to UpsM as well as to the 5' UTR of the dcw mRNA and the sRNA-sRNA and sRNA-mRNA interactions lead to a conformational change that triggers cleavage by the ribonuclease RNase E, affecting the level of dcw mRNAs and limiting growth. These findings provide interesting new insights into the role of sRNA-mediated regulation of cell division during the adaptation to environmental changes.

Spatiotemporal dynamics of growth and death within spherical bacterial colonies

Bacterial growth within colonies and biofilms is heterogeneous. Local reduction of growth rates has been associated with tolerance against various antibiotics. However, spatial gradients of growth rates are poorly characterized in three-dimensional bacterial colonies. Here, we report two spatially resolved methods for measuring growth rates in bacterial colonies. As bacteria grow and divide, they generate a velocity field that is directly related to the growth rates. We derive profiles of growth rates from the velocity field and show that they are consistent with the profiles obtained by single-cell-counting. Using these methods, we reveal that even small colonies initiated with a few thousand cells of the human pathogen Neisseria gonorrhoeae develop a steep gradient of growth rates within two generations. Furthermore, we show that stringent response decelerates growth inhibition at the colony center. Based on our results, we suggest that aggregation-related growth inhibition can protect gonococci from external stresses even at early biofilm stages.

Investigations on the influence of energy source on time-dependent hormesis: A case study of sulfadoxine to Aliivibrio fischeri in different cultivation systems

Hormesis is a biphasic dose-response relationship featured by low-dose stimulation and high-dose inhibition. Although the hormetic phenomenon has been extensively studied over the past decades, there is little information regarding the influence of energy source on the occurrence of hormesis, especially the time-dependent one. In this study, to explore the role of cultivation system's energy source in time-dependent hormesis, the toxic dose-responses of Aliivibrio fischeri (A. fischeri) bioluminescence to Sulfadoxine (SDX) during 24 h were determined in four cultivation systems with different energy source conditions. The results indicated that the time-dependent hormetic effects were induced by SDX in all cultivation systems: SDX triggered hormetic phenomenon on the bioluminescence at each growth stage over 24 h in the cultivation systems with sufficient and insufficient energy source; due to the diauxic growth of A. fischeri under multiple energy source conditions, the hormetic effects of SDX gradually disappeared after the preferred energy source was used up. It was speculated that the inhibitory action of SDX was derived from its interaction with DHPS to impede the synthesis of proteins, and SDX bound with AC to upregulate the quorum sensing (QS) system to exhibit the stimulatory action. Comparing the time-dependent hormesis in each cultivation system, it was obtained that the energy source could impact the hourly maximum stimulatory rate, the EC₅₀ of SDX, and the time point that hormesis occurred, which might result from the influence of energy source on the stimulatory and inhibitory actions of SDX through regulating the metabolic system (individual level) and QS system (group level) of bacteria. This study clarifies the importance of energy source for hormesis occurrence, which may further promote the development of hormesis.

Tracking bacterial lineages in complex and dynamic environments with applications for growth control and persistence

As bacteria transition from exponential to stationary phase, they change substantially in size, morphology, growth and expression profiles. These responses also vary between individual cells, but it has proved difficult to track cell lineages along the growth curve to determine the progression of events or correlations between how individual cells enter and exit dormancy. Here, we developed a platform for tracking more than 10⁵ parallel cell lineages in dense and changing cultures, independently validating that the imaged cells closely track batch populations. Initial applications show that for both Escherichia coli and Bacillus subtilis, growth changes from an 'adder' mode in exponential phase to mixed 'adder-timers' entering stationary phase, and then a near-perfect 'sizer' upon exit-creating broadly distributed cell sizes in stationary phase but rapidly returning to narrowly distributed sizes upon exit. Furthermore, cells that undergo more divisions when entering stationary phase suffer reduced survival after long periods of dormancy but are the only cells observed that persist following antibiotic treatment.