Catastrophic and noncatastrophic population crashes in a bitrophic system with dynamic additional food provision to cooperative predators.

In this article we contemplate the dynamics of an additional food-provided prey-predator system. We assume that the behavior of cooperative predators induces fear in prey, which radically affects the prey's birth and death rates. We observe that the structural instability imposed by strong cooperative hunting among predators goes away with higher intensities of fear levels affecting the prey's reproductive output and mortality. High levels of prey refuge are not conducive to the survival of predators. In such a situation, adequate supply of high-quality additional food is favorable regarding the persistence and stability of the system. Interestingly, the system potentially exhibits two stable configurations under identical ecological conditions by allowing different bifurcation scenarios, including saddle-node and backward bifurcations, and associated hysteresis effects with prey refuge along with additional food quantity and quality. In the stochastic environment, the system experiences critical transitions through bifurcation-induced tipping events with time-varying additional food for predators. Enhanced disturbance events promote noise-induced switching and tipping events. Finally, our investigation explores whether impending population crashes resulting from the variability of additional food quantity and quality can reliably be predicted using early warning signals in the context of redshifted noise. Overall, our results may provide insights for finding control strategies in the context of community ecology.

Diverse nature of ClpX degradation motifs in Streptococcus mutans.

IMPORTANCE: Cytoplasmic Clp-related proteases play a major role in maintaining cellular proteome in bacteria. ClpX/P is one such proteolytic complex that is important for conserving protein homeostasis. In this study, we investigated the role of ClpX/P in Streptococcus mutans, an important oral pathogen. We identified several putative substrates whose cellular levels are regulated by ClpX/P in S. mutans and subsequently discovered several recognition motifs that are critical for degradation. Our study is the first comprehensive analysis of determining ClpX/P motifs in streptococci. We believe that identifying the substrates that are regulated by ClpX/P will enhance our understanding about virulence regulation in this important group of pathogens.

Nutrient enrichment and phytoplankton toxicity influence a diversity of complex dynamics in a fear-induced plankton-fish model.

In this paper, we contemplate the dynamics of an aquatic system consisting of three interacting species, phytoplankton, zooplankton, and fish. We assume that the evading risk of fish predation induces fear in zooplankton species, which affects its growth dynamics radically. On the other hand, zooplankton develop an anti-predator defense by taking temporary refuge. Interestingly, the system potentially exhibits multi-stable configurations under identical ecological conditions by allowing different bifurcation scenarios, including multiple saddle-node and transcritical bifurcations with varying levels of nutrients, strength of phytoplankton toxicity, zooplankton refuge size and the cost of fear imposed by fish population. Further, by adding Gaussian white noise, we have extended the deterministic system to its stochastic version. We find that white noise appears to regulate the survival and extinction of model species. Comprehensive numerical simulations are consistent with mathematical results prognosticated by linear analysis. Overall, our study may provide a new insight into the mechanisms of emergence and mitigation of plankton blooms.

Evolutionarily stable strategies to overcome Allee effect in predator-prey interaction.

Every successful species invasion is facilitated by both ecological and evolutionary mechanisms. The evolution of population's fitness related traits acts as functional adaptations to Allee effects. This trade-off increases predatory success at an expense of elevated death rate of potential predators. We address our queries employing an eco-evolutionary modeling approach that provides a means of circumventing inverse density-dependent effect. In the absence of evolution, the ecological system potentially exhibits multi-stable configurations under identical ecological conditions by allowing different bifurcation scenarios with the Allee effect. The model predicts a high risk of catastrophic extinction of interacting populations around different types of saddle-node bifurcations resulting from the increased Allee effect. We adopt the game-theoretic approach to derive the analytical conditions for the emergence of evolutionarily stable strategy (ESS) when the ecological system possesses asymptotically stable steady states as well as population cycles. We establish that ESSs occur at those values of adopted evolutionary strategies that are local optima of some functional forms of model parameters. Overall, our theoretical study provides important ecological insights in predicting successful biological invasions in the light of evolution.

Toxicity-mediated regime shifts in a contaminated nutrient-plankton system.

In this article, we contemplate the dynamics of a three-tier system of nutrient, phytoplankton, and zooplankton with a gestation delay of discrete type and a distributed delay in nutrient recycling. Phytoplankton secretion-mediated alteration in the grazing pattern of zooplankton is encapsulated by a Monod-Haldane functional response. We carry out global sensitivity analysis for identifying the crucial model parameters having a significant impact on zooplankton density. The system potentially exhibits bistable configurations under identical ecological conditions by allowing different bifurcation scenarios, including multiple saddle-node and transcritical bifurcations with varying input rates of nutrients and inhibitory effects of phytoplankton against zooplankton. We observe that the gestation delay in zooplankton is responsible for the emergence of noxious bloom events. Interestingly, when the delay parameter crosses a threshold, the system experiences chaotic disorder, which prognosticates the onset of irregular bloom. Furthermore, by adding Gaussian white noise, we have extended the deterministic model to its stochastic counterpart. We found that white noise appears to regulate the survival and extinction of interacting populations. Comprehensive numerical simulations are consistent with mathematical results prognosticated by linear analysis.

Synthesis of a Novel Lantibiotic Using Mutacin II Biosynthesis Apparatus.

Owing to extensive metagenomic studies, we now have access to numerous sequences of novel bacteriocin-like antimicrobial peptides encoded by various cultivable and noncultivable bacteria. However, relatively rarely, we even have access to these cultivable strains to examine the potency and the targets of the predicted bacteriocins. In this study, we evaluated a heterologous biosynthetic system to produce biologically active nonnative novel lantibiotics, which are modified bacteriocins. We chose Streptococcus mutans, a dental pathogen, as the host organism because it is genetically easy to manipulate and is inherently a prolific producer of various bacteriocins. We chose the S. mutans T8 strain as the host, which produces the lantibiotic mutacin II, to express 10 selected homologs of mutacin II identified from GenBank. These lantibiotic peptides either are novel or have been studied very minimally. The core regions of the selected lantibiotic peptides were fused to the leader sequence of the mutacin II peptide and integrated into the chromosome such that the core region of the native mutacin II was replaced with the new core sequences. By this approach, using the mutacin II biosynthesis machinery, we obtained one bioactive novel lantibiotic peptide with 52% different residues compared to the mutacin II core region. This unknown lantibiotic is encoded by Streptococcus agalactiae and Streptococcus ovuberis strains. Since this peptide displays some homology with nukacin ISK-1, we named it nukacin Spp. 2. This study demonstrated that the mutacin II biosynthesis machinery can be successfully used as an efficient system for the production of biologically active novel lantibiotics. IMPORTANCE In this study, we report for the first time that Streptococcus mutans can be used as a host to produce various nonnative lantibiotics. We showed that in the T8 strain, we could produce bioactive lacticin 481 and nukacin ISK-1, both of which are homologs of mutacin II, using T8's modification and secretion apparatus. Similarly, we also synthesized a novel bioactive lantibiotic, which we named nukacin Spp. 2.

Involvement of ClpE ATPase in Physiology of Streptococcus mutans.

Streptococcus mutans, a dental pathogen, harbors at least three Clp ATPases (ClpC, ClpE, and ClpX) that form complexes with ClpP protease and participate in regulated proteolysis. Among these, the function of ClpE ATPase is poorly understood. We have utilized an isogenic clpE-deficient strain derived from S. mutans UA159 and evaluated the role of ClpE in cellular physiology. We found that loss of ClpE leads to increased susceptibility against thiol stress but not to oxidative and thermal stress. Furthermore, we found that the mutant displays altered tolerance against some antibiotics and altered biofilm formation. We performed a label-free proteomic analysis by comparing the mutant with the wild-type UA159 strain under nonstressed conditions and found that ClpE modulates a relatively limited proteome in the cell compared to the proteomes modulated by ClpX and ClpP. Nevertheless, we found that ClpE deficiency leads to an overabundance of some cell wall synthesis enzymes, ribosomal proteins, and an unknown protease encoded by SMU.2153. Our proteomic data strongly support some of the stress-related phenotypes that we observed. Our study emphasizes the significance of ClpE in the physiology of S. mutans. IMPORTANCE When bacteria encounter environmental stresses, the expression of various proteins collectively known as heat shock proteins is induced. These heat shock proteins are necessary for cell survival specifically under conditions that induce protein denaturation. A subset of heat shock proteins known as the Clp proteolytic complex is required for the degradation of the misfolded proteins in the cell. The Clp proteolytic complex contains an ATPase and a protease. A specific Clp ATPase, ClpE, is uniquely present in Gram-positive bacteria, including streptococci. Here, we have studied the functional role of the ClpE protein in Streptococcus mutans, a dental pathogen. Our results suggest that ClpE is required for survival under certain antibiotic exposure and stress conditions but not others. Our results demonstrate that loss of ClpE leads to a significantly altered cellular proteome, and the analysis of those changes suggests that ClpE's functions in S. mutans are different from its functions in other Gram-positive bacteria.

Complete Genome Sequence of Streptococcus mutans Strain MD, Which Produces Highly Potent Mutacins.

Here, we report the complete genome sequence of Streptococcus mutans strain MD, which produces potent mutacins capable of inhibiting streptococci. MD is a relatively uncharacterized strain whose genome information was unavailable. This study provides useful information for comparative genomic study and for understanding the repertoire of mutacins in S. mutans.

Induction of clpP expression by cell-wall targeting antibiotics in Streptococcus mutans.

Streptococcus mutans is one of the major bacteria of the human oral cavity that is associated with dental caries. The pathogenicity of this bacterium is attributed to its ability to rapidly respond and adapt to the ever-changing conditions of the oral cavity. The major player in this adaptive response is ClpP, an intracellular protease involved in degradation of misfolded proteins during stress responses. S. mutans encodes a single clpP gene with an upstream region uniquely containing multiple tandem repeat sequences (RSs). Here, we explored expression of clpP with respect to various stresses and report some new findings. First, we found that at sub-inhibitory concentration, certain cell-wall damaging antibiotics were able to induce clpP expression. Specifically, third- and fourth-generation cephalosporins that target penicillin-binding protein 3 (PBP3) strongly enhanced the clpP expression. However, induction of clpP was weak when the first-generation cephalosporins with lower affinity to PBP3 were used. Surprisingly, carbapenems, which primarily target PBP2, induced expression of clpP the least. Second, we found that a single RS element was capable of inducing clpP expression as efficiently as with the wild-type seven RS elements. Third, we found that the RS-element-mediated modulation of clpP expression was strain dependent, suggesting that specific host factors might be involved in the transcription. And finally, we observed that ClpP regulates its own expression, as the expression of clpP-gusA was higher in a clpP-deficient mutant. This suggests that ClpP is involved in the degradation of activator(s) involved in its own transcription.

Modeling the avoidance behavior of zooplankton on phytoplankton infected by free viruses.

In any ecosystem, chaotic situations may arise from equilibrium state for different reasons. To overcome these chaotic situations, sometimes the system itself exhibits some mechanisms of self-adaptability. In this paper, we explore an eco-epidemiological model consisting of three aquatic groups: phytoplankton, zooplankton, and marine free viruses. We assume that the phytoplankton population is infected by external free viruses and zooplankton get affected on consumption of infected phytoplankton; also, the infected phytoplankton do not compete for resources with the susceptible one. In addition, we model a mechanism by which zooplankton recognize and avoid infected phytoplankton, at least when susceptible phytoplankton are present. The zooplankton extinction chance increases on increasing the force of infection or decreasing the intensity of avoidance. Further, when the viral infection triggers chaotic dynamics, high zooplankton avoidance intensity can stabilize again the system. Interestingly, for high avoidance intensity, nutrient enrichment has a destabilizing effect on the system dynamics, which is in line with the paradox of enrichment. Global sensitivity analysis helps to identify the most significant parameters that reduce the infected phytoplankton in the system. Finally, we compare the dynamics of the system by allowing the infected phytoplankton also to share resources with the susceptible phytoplankton. A gradual increase of the virus replication factor turns the system dynamics from chaos to doubling state to limit cycle to stable state and the system finally settles down to the zooplankton-free equilibrium point. Moreover, on increasing the intensity of avoidance, the system shows a transcritical bifurcation from the zooplankton-free equilibrium to the coexistence steady state and remains stable thereafter.

Ribosomal protein L4 of Lactobacillus rhamnosus LRB alters resistance to macrolides and other antibiotics.

Lactobacillus rhamnosus is an important lactic acid bacterium that is predominantly used as a probiotic supplement. This bacterium secretes immunomodulatory and antibacterial peptides that are necessary for the probiotic trait. This organism also occupies diverse ecological niches, such as gastrointestinal tracts and the oral cavity. Several studies have shown that L. rhamnosus is prone to spontaneous genome rearrangement irrespective of the ecological origins. We previously characterized an oral isolate of L. rhamnosus, LRB, which is genetically closely related to the widely used probiotic strain L. rhamnosus LGG. In this study, we isolated a nontargeted mutant that was particularly sensitive to acid stress. Using next generation sequencing, we further mapped the putative mutations in the genome and found that the mutant had acquired a deletion of 75 base pairs in the rplD gene that encodes the large ribosomal subunit L4. The mutant had a growth defect at 37°C and at ambient temperature. Further antibiotic sensitivity analyses indicated that the mutant is relatively more resistant to erythromycin and chloramphenicol; two antibiotics that target the 50S subunit. In contrast, the mutant was more sensitive to tetracycline, which targets the 30S subunit. Thus, it appears that nontargeted mutations could significantly alter the antibiotic resistance profile of L. rhamnosus. Our study raises concern that probiotic use of L. rhamnosus should be carefully monitored to avoid unintended consequences.

Characterization of a stress tolerance-defective mutant of Lactobacillus rhamnosus LRB.

Lactobacillus rhamnosus is a lactic acid bacterium that survives diverse ecological niches, including the human oral cavity and gastrointestinal tract. L. rhamnosus is an acidogenic bacterium that produces copious amounts of lactic acid. The organism is also considered as aciduric, since it can survive prolonged exposure to an acidic environment. For a probiotic bacterium such as L. rhamnosus, it is necessary to understand how this organism survives acid stress. In this study we used L. rhamnosus LRB to isolate one spontaneous mutant that was sensitive to acid stress. The mutant, which we named RBM1, also displayed sensitivity to a wide range of stresses including osmotic, thermal, and others. Using whole genome sequencing, we mapped the putative mutations in the mutant strain. It appears that three single nucleotide substitutions occurred in the mutant as compared to the wild-type LRB strain. Among those, the most relevant mutation occurred in the ftsH gene that created a single amino acid change in the protein. We performed a comparative proteomic study to understand the molecular basis for stress sensitivity and found that ~15% of the proteome is altered in the mutant strain. Our study suggests that generation of spontaneous mutants during L. rhamnosus colonization could drastically affect bacterial physiology and survival under stress conditions.

Effects of zooplankton selectivity on phytoplankton in an ecosystem affected by free-viruses and environmental toxins.

In the present study, we investigate the selective feeding of zooplankton on phytoplankton infected by free-viruses in the presence of environmental toxins in the marine ecosystem. The environmental toxins assume to decrease the growth rate of susceptible phytoplankton, and increase the death rate of infected phytoplankton and zooplankton. Global sensitivity analysis identifies important parameters of the system having crucial impact on the aquatic health. The coexistence equilibrium of the system stabilizes on increasing the parameters related to inhibition of phytoplankton growth due to environmental toxins and the force of infection, and destabilizes on increasing the carrying capacity of susceptible phytoplankton and preference of zooplankton on infected phytoplankton. The chance of extinction of free-viruses increases on increasing the preference of zooplankton on infected phytoplankton or decreasing the force of infection. Moreover, if the input rate of environmental toxins is high, then the system becomes zooplankton-free for higher values of force of infection. On increasing the values of preference of zooplankton on infected phytoplankton, the system exhibits transition from stable coexistence to oscillations around coexistence equilibrium to oscillations around disease-free equilibrium. We observe that the presence of free-viruses and environmental toxins in the system drive zooplankton population to very low equilibrium values but the ecological balance of the aquatic food web can be maintained by modulating the decay (depletion) rate of free-viruses (environmental toxins).

Complete Genome Sequence of Lactobacillus rhamnosus Strain LRB.

Lactobacillus rhamnosus is a Gram-positive facultative heterofermentative lactic acid bacterium. It is often isolated from the gastrointestinal tract, mouth, vagina, and fermented dairy products. We have isolated the L. rhamnosus strain LRB from a healthy baby tooth that had naturally fallen out. Here, we report the annotated whole-genome sequence of LRB.

SepM, a Streptococcal Protease Involved in Quorum Sensing, Displays Strict Substrate Specificity.

UNLABELLED: Streptococcus mutans, a causative agent of dental caries, relies on multiple quorum-sensing (QS) pathways that coordinate the expression of factors needed for colonization in the oral cavity. S. mutans uses small peptides as QS signaling molecules that typically are secreted into the outside milieu. Competence-stimulating peptide (CSP) is one such QS signaling molecule that functions through the ComDE two-component signal transduction pathway. CSP is secreted through NlmTE, a dedicated ABC transporter that cleaves off the N-terminal leader peptide to generate a mature peptide that is 21 residues long (CSP-21). We recently identified a surface-localized protease, SepM, which further cleaves the CSP-21 peptide at the C-terminal end and removes the last 3 residues to generate CSP-18. CSP-18 is the active QS molecule that interacts with the ComD sensor kinase to activate the QS pathway. In this study, we show that SepM specifically cleaves CSP-21 between the Ala18 and Leu19 residues. We also show that SepM recognizes only Ala at position 18 and Leu at position 19, although some CSP-18 variants with a substitution at position 18 can function equally as well as the QS peptide. Furthermore, we demonstrate that SepM homologs from other streptococci are capable of processing CSP-21 to generate functional CSP-18. IMPORTANCE: SepM is a membrane-associated streptococcal protease that processes competence-stimulating peptide (CSP) to generate an active quorum-sensing molecule in S. mutans. SepM belongs to the S16 family of serine proteases, and in this study, we found that SepM behaves as an endopeptidase. SepM displays strict substrate specificity and cleaves the peptide bond between the Ala and Leu residues. This is the first report of an endopeptidase that specifically cleaves these two residues.

Gene Regulation by the LiaSR Two-Component System in Streptococcus mutans.

The LiaSR two-component signal transduction system regulates cellular responses to several environmental stresses, including those that induce cell envelope damages. Downstream regulons of the LiaSR system have been implicated in tolerance to acid, antibiotics and detergents. In the dental pathogen Streptococcus mutans, the LiaSR system is necessary for tolerance against acid, antibiotics, and cell wall damaging stresses during growth in the oral cavity. To understand the molecular mechanisms by which LiaSR regulates gene expression, we created a mutant LiaR in which the conserved aspartic acid residue (the phosphorylation site), was changed to alanine residue (D58A). As expected, the LiaR-D58A variant was unable to acquire the phosphate group and bind to target promoters. We also noted that the predicted LiaR-binding motif upstream of the lia operon does not appear to be well conserved. Consistent with this observation, we found that LiaR was unable to bind to the promoter region of lia; however, we showed that LiaR was able to bind to the promoters of SMU.753, SMU.2084 and SMU.1727. Based on sequence analysis and DNA binding studies we proposed a new 25-bp conserved motif essential for LiaR binding. Introducing alterations at fully conserved positions in the 25-bp motif affected LiaR binding, and the binding was dependent on the combination of positions that were altered. By scanning the S. mutans genome for the occurrence of the newly defined LiaR binding motif, we identified the promoter of hrcA (encoding a key regulator of the heat shock response) that contains a LiaR binding motif, and we showed that hrcA is negatively regulated by the LiaSR system. Taken together our results suggest a putative role of the LiaSR system in heat shock responses of S. mutans.

A conserved streptococcal membrane protein, LsrS, exhibits a receptor-like function for lantibiotics.

Streptococcus mutans strain GS-5 produces a two-peptide lantibiotic, Smb, which displays inhibitory activity against a broad spectrum of bacteria, including other streptococci. For inhibition, lantibiotics must recognize specific receptor molecules present on the sensitive bacterial cells. However, so far no such receptor proteins have been identified for any lantibiotics. In this study, using a powerful transposon mutagenesis approach, we have identified in Streptococcus pyogenes a gene that exhibits a receptor-like function for Smb. The protein encoded by that gene, which we named LsrS, is a membrane protein belonging to the CAAX protease family. We also found that nisin, a monopeptide lantibiotic, requires LsrS for its optimum inhibitory activity. However, we found that LsrS is not required for inhibition by haloduracin and galolacticin, both of which are two-peptide lantibiotics closely related to Smb. LsrS appears to be a well-conserved protein that is present in many streptococci, including S. mutans. Inactivation of SMU.662, an LsrS homolog, in S. mutans strains UA159 and V403 rendered the cells refractory to Smb-mediated killing. Furthermore, overexpression of LsrS in S. mutans created cells more susceptible to Smb. Although LsrS and its homolog contain the CAAX protease domain, we demonstrate that inactivation of the putative active sites on the LsrS protein has no effect on its receptor-like function. This is the first report describing a highly conserved membrane protein that displays a receptor-like function for lantibiotics.

SMU.746-SMU.747, a putative membrane permease complex, is involved in aciduricity, acidogenesis, and biofilm formation in Streptococcus mutans.

Dental caries induced by Streptococcus mutans is one of the most prevalent chronic infectious diseases worldwide. The pathogenicity of S. mutans relies on the bacterium's ability to colonize tooth surfaces and survive a strongly acidic environment. We performed an ISS1 transposon mutagenesis to screen for acid-sensitive mutants of S. mutans and identified an SMU.746-SMU.747 gene cluster that is needed for aciduricity. SMU.746 and SMU.747 appear to be organized in an operon and encode a putative membrane-associated permease. SMU.746- and SMU.747-deficient mutants showed a reduced ability to grow in acidified medium. However, the short-term or long-term acid survival capacity and F1F0 ATPase activity remained unaffected in the mutants. Furthermore, deletion of both genes did not change cell membrane permeability and the oxidative and heat stress responses. Growth was severely affected even with slight acidification of the defined medium (pH 6.5). The ability of the mutant strain to acidify the defined medium during growth in the presence of glucose and sucrose was significantly reduced, although the glycolysis rate was only slightly affected. Surprisingly, deletion of the SMU.746-SMU.747 genes triggered increased biofilm formation in low-pH medium. The observed effects were more striking in a chemically defined medium. We speculate that the SMU.746-SMU.747 complex is responsible for amino acid transport, and we discuss its possible role in colonization and survival in the oral environment.

SmbFT, a putative ABC transporter complex, confers protection against the lantibiotic Smb in Streptococci.

Streptococcus mutans, a dental pathogen, secretes different kinds of lantibiotic and nonlantibiotic bacteriocins. For self-protection, a bacteriocin producer strain must possess one or more cognate immunity mechanisms. We report here the identification of one such immunity complex in S. mutans strain GS-5 that confers protection against Smb, a two-component lantibiotic. The immunity complex that we identified is an ABC transporter composed of two proteins: SmbF (the ATPase component) and SmbT (the permease component). Both of the protein-encoding genes are located within the smb locus. We show that GS-5 becomes sensitized to Smb upon deletion of smbT, which makes the ABC transporter nonfunctional. To establish the role SmbFT in providing immunity, we heterologously expressed this ABC transporter complex in four different sensitive streptococcal species and demonstrated that it can confer resistance against Smb. To explore the specificity of SmbFT in conferring resistance, we tested mutacin IV (a nonlantibiotic), nisin (a single peptide lantibiotics), and three peptide antibiotics (bacitracin, polymyxin B, and vancomycin). We found that SmbFT does not recognize these structurally different peptides. We then tested whether SmbFT can confer protection against haloduracin, another two-component lantibiotic that is structurally similar to Smb; SmbFT indeed conferred protection against haloduracin. SmbFT can also confer protection against an uncharacterized but structurally similar lantibiotic produced by Streptococcus gallolyticus. Our data suggest that SmbFT truly displays immunity function and confer protection against Smb and structurally similar lantibiotics.

Complete genome sequence of Streptococcus mutans GS-5, a serotype c strain.

Streptococcus mutans, a principal causative agent of dental caries, is considered to be the most cariogenic among all oral streptococci. Of the four S. mutans serotypes (c, e, f, and k), serotype c strains predominate in the oral cavity. Here, we present the complete genome sequence of S. mutans GS-5, a serotype c strain originally isolated from human carious lesions, which is extensively used as a laboratory strain worldwide.