Bacterial Population Size Research Articles

Rice straw decomposition affects diversity and dynamics of soil fungal community, but not bacteria

Straw decomposition increased amounts of soil organic carbon and changed microbial biomass. But the different impacts of rice straw decomposition on the succession of bacterial and fungal community composition in field conditions were poorly understood. The objective of this study was to investigate the development of soil bacterial and fungal communities during rice straw decomposition in field conditions, and the relationship between soil chemical/physical properties and the evolution of microbial communities. A 1-year field study (90, 180, 270, and 360 days) was conducted, including the straw decomposition soil and control (no straw decomposition soil). The bulk soil samples (0–15-cm depths) from three replicate plots per treatment were collected for the analysis of soil properties and of microbial diversity parameters. Soil bacterial and fungal community structures and population sizes were determined by applying PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR). The bacterial and fungal community diversity was evaluated using the following parameters: Shannon–Wiener diversity index, richness, and evenness. Moreover, the relationship between soil properties and the changes of microbial communities was analyzed using redundancy analysis (RDA). The results showed that, in contrast to bacteria, the soil fungal population size and diversity indices were significantly increased during different time points of rice straw decomposition, and reached to the highest value at 360 days. When compared with the bacterial DGGE profiles, the fungal DGGE profiles significantly changed between the straw decomposition soil and control, and the dominant soil fungal genera varied apparently. Bacterial 16S ribosomal RNA (rRNA) and fungal 18S rRNA gene sequences obtained from the main DGGE bands were further sequenced, among which Penicillium sp., Aspergillus sp., and Acremonium sp. have the ability to degrade cellulose. RDA suggested that the soil available P, organic C, pH, and bulk density were the main factors influencing the variation in the fungal community structures and diversities. The fungal community structures displayed distinct successions during rice straw decomposition. But such finding was not observed in bacterial communities. The ratio of fungi to bacteria measured by qPCR was higher in the straw decomposition soil compared with the findings in control, indicating that fungi predominated in straw decomposition. Especially, our study deduced that the diversified cellulolytic fungal genera highly enriched in rice straw decomposition soils had great potential of mining novel cellulose-decomposing enzymes.

The DinJ/RelE Toxin-Antitoxin System Suppresses Bacterial Proliferation and Virulence of Xylella fastidiosa in Grapevine.

Xylella fastidiosa, the causal agent of Pierce's disease of grapes, is a slow-growing, xylem-limited, bacterial pathogen. Disease progression is characterized by systemic spread of the bacterium through xylem vessel networks, causing leaf-scorching symptoms, senescence, and vine decline. It appears to be advantageous to this pathogen to avoid excessive blockage of xylem vessels, because living bacterial cells are generally found in plant tissue with low bacterial cell density and minimal scorching symptoms. The DinJ/RelE toxin-antitoxin system is characterized here for a role in controlling bacterial proliferation and population size during plant colonization. The DinJ/RelE locus is transcribed from two separate promoters, allowing for coexpression of antitoxin DinJ with endoribonuclease toxin RelE, in addition to independent expression of RelE. The ratio of antitoxin/toxin expressed is dependent on bacterial growth conditions, with lower amounts of antitoxin present under conditions designed to mimic grapevine xylem sap. A knockout mutant of DinJ/RelE exhibits a hypervirulent phenotype, with higher bacterial populations and increased symptom development and plant decline. It is likely that DinJ/RelE acts to prevent excessive population growth, contributing to the ability of the pathogen to spread systemically without completely blocking the xylem vessels and increasing probability of acquisition by the insect vector.

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut.

The relative role of drift versus selection underlying the evolution of bacterial species within the gut microbiota remains poorly understood. The large sizes of bacterial populations in this environment suggest that even adaptive mutations with weak effects, thought to be the most frequently occurring, could substantially contribute to a rapid pace of evolutionary change in the gut. We followed the emergence of intra-species diversity in a commensal Escherichia coli strain that previously acquired an adaptive mutation with strong effect during one week of colonization of the mouse gut. Following this first step, which consisted of inactivating a metabolic operon, one third of the subsequent adaptive mutations were found to have a selective effect as high as the first. Nevertheless, the order of the adaptive steps was strongly affected by a mutational hotspot with an exceptionally high mutation rate of 10−5. The pattern of polymorphism emerging in the populations evolving within different hosts was characterized by periodic selection, which reduced diversity, but also frequency-dependent selection, actively maintaining genetic diversity. Furthermore, the continuous emergence of similar phenotypes due to distinct mutations, known as clonal interference, was pervasive. Evolutionary change within the gut is therefore highly repeatable within and across hosts, with adaptive mutations of selection coefficients as strong as 12% accumulating without strong constraints on genetic background. In vivo competitive assays showed that one of the second steps (focA) exhibited positive epistasis with the first, while another (dcuB) exhibited negative epistasis. The data shows that strong effect adaptive mutations continuously recur in gut commensal bacterial species.

Changes in the activity and abundance of the soil microbial community in response to the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP)

The application of organic and inorganic fertilizers to soil can result in increased gaseous emissions, such as NH3, N2O, CO2, and CH4, as well as nitrate leaching, contributing to climate warming and ground and surface water pollution, particularly in regions with hot climates, where high temperatures and high soil nitrification rates often occur. The use of nitrification inhibitors (NIs) has been shown to effectively decrease nitrogen (N) losses from the soil-plant system. Non-disruptive laboratory incubation experiments were conducted to assess the extent to which temperature (20 and 30 °C) and nutrient source (mineral and organic fertilizers) influence the rate of carbon (C)- and N-related microbial processes in soil in response to the NI 3,4-dimethylpyrazole phosphate (DMPP). Furthermore, short-term changes in the ability of microbes to degrade C substrates were evaluated in disruptive soil microcosms using microbial community-level physiological profiling and the abundance of the bacterial 16S rRNA gene as a measure of total bacterial population size. DMPP reduced net nitrification after 2 and 4 weeks of incubation at 30 and 20 °C by an average of 78.3 and 84.5 %, respectively, and with similar dynamics for mineral or organic fertilization. The addition of labile organic matter with cattle effluent led to a rapid increase in C mineralization that was significantly reduced by DMPP at both temperatures, whereas no changes could be detected after the addition of mineral fertilizer. The culturable heterotrophic microorganisms showed metabolic diversification in the oxidation of C sources, with organic fertilizer playing a major role in the substrate utilization patterns during the first week of incubation and the DMPP effects prevailing from day 14 until day 28. Furthermore, the copy number of the bacterial 16S rRNA gene was reduced by the application of DMPP and organic fertilizer after 28 days. Our results show the marked efficiency of DMPP as an NI at elevated temperatures of incubation and when associated with both mineral and organic fertilization, providing support for its use as a tool to mitigate N losses in Mediterranean ecosystems. However, we also observed impaired C respiration rates and bacterial abundances, as well as shifts in community-level physiological profiles in soil, possibly indicating a short-term effect of DMPP and organic fertilizers on non-target C-related processes and microorganisms.

Computational prospecting the great viral unknown.

Bacteriophages play an important role in host-driven biological processes by controlling bacterial population size, horizontally transferring genes between hosts and expressing host-derived genes to alter host metabolism. Metagenomics provides the genetic basis for understanding the interplay between uncultured bacteria, their phage and the environment. In particular, viral metagenomes (viromes) are providing new insight into phage-encoded host genes (i.e. auxiliary metabolic genes; AMGs) that reprogram host metabolism during infection. Yet, despite deep sequencing efforts of viral communities, the majority of sequences have no match to known proteins. Reference-independent computational techniques, such as protein clustering, contig spectra and ecological profiling are overcoming these barriers to examine both the known and unknown components of viromes. As the field of viral metagenomics progresses, a critical assessment of tools is required as the majority of algorithms have been developed for analyzing bacteria. The aim of this paper is to offer an overview of current computational methodologies for virome analysis and to provide an example of reference-independent approaches using human skin viromes. Additionally, we present methods to carefully validate AMGs from host contamination. Despite computational challenges, these new methods offer novel insights into the diversity and functional roles of phages in diverse environments.

Queuing Models for Abstracting Interactions in Bacterial Communities

Microbial communities play a significant role in bioremediation, plant growth, human and animal digestion, global elemental cycles including the carbon-cycle, and water treatment. They are also posed to be the engines of renewable energy via microbial fuel cells, which can reverse the process of electrosynthesis. Microbial communication regulates many virulence mechanisms used by bacteria. Thus, it is of fundamental importance to understand interactions in microbial communities and to develop predictive tools that help control them, in order to aid the design of systems exploiting bacterial capabilities. This position paper explores how abstractions from communications, networking and information theory can play a role in understanding and modeling bacterial interactions. In particular, two forms of interactions in bacterial systems will be examined: electron transfer and quorum sensing . While the diffusion of chemical signals has been heavily studied, electron transfer occurring in living cells and its role in cell–cell interaction is less understood. Recent experimental observations open up new frontiers in the design of microbial systems based on electron transfer, which may coexist with the more well-known interaction strategies based on molecular diffusion. In quorum sensing, the concentration of certain signature chemical compounds emitted by the bacteria is used to estimate the bacterial population size, so as to activate collective behaviors. In this position paper, queuing models for electron transfer are summarized and adapted to provide new models for quorum sensing. These models are stochastic, and thus capture the inherent randomness exhibited by cell colonies in nature. It is shown that queuing models allow the characterization of the state of a single cell as a function of interactions with other cells and the environment, thus enabling the construction of an information theoretic framework, while being amenable to complexity reduction using methods based on statistical physics and wireless network design.

Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine.

ABSTRACTThe zebrafish, Danio rerio, is a powerful model for studying bacterial colonization of the vertebrate intestine, but the genes required by commensal bacteria to colonize the zebrafish gut have not yet been interrogated on a genome-wide level. Here we apply a high-throughput transposon mutagenesis screen to Aeromonas veronii Hm21 and Vibrio sp. strain ZWU0020 during their colonization of the zebrafish intestine alone and in competition with each other, as well as in different colonization orders. We use these transposon-tagged libraries to track bacterial population sizes in different colonization regimes and to identify gene functions required during these processes. We show that intraspecific, but not interspecific, competition with a previously established bacterial population greatly reduces the ability of these two bacterial species to colonize. Further, using a simple binomial sampling model, we show that under conditions of interspecific competition, genes required for colonization cannot be identified because of the population bottleneck experienced by the second colonizer. When bacteria colonize the intestine alone or at the same time as the other species, we find shared suites of functional requirements for colonization by the two species, including a prominent role for chemotaxis and motility, regardless of the presence of another species.

Quantitative Analysis of Lysobacter Predation.

Bacteria of the genus Lysobacter are considered to be facultative predators that use a feeding strategy similar to that of myxobacteria. Experimental data supporting this assumption, however, are scarce. Therefore, the predatory activities of three Lysobacter species were tested in the prey spot plate assay and in the lawn predation assay, which are commonly used to analyze myxobacterial predation. Surprisingly, only one of the tested Lysobacter species showed predatory behavior in the two assays. This result suggested that not all Lysobacter strains are predatory or, alternatively, that the assays were not appropriate for determining the predatory potential of this bacterial group. To differentiate between the two scenarios, predation was tested in a CFU-based bioassay. For this purpose, defined numbers of Lysobacter cells were mixed together with potential prey bacteria featuring phenotypic markers, such as distinctive pigmentation or antibiotic resistance. After 24 h, cocultivated cells were streaked out on agar plates and sizes of bacterial populations were individually determined by counting the respective colonies. Using the CFU-based predation assay, we observed that Lysobacter spp. strongly antagonized other bacteria under nutrient-deficient conditions. Simultaneously, the Lysobacter population was increasing, which together with the killing of the cocultured bacteria indicated predation. Variation of the predator/prey ratio revealed that all three Lysobacter species tested needed to outnumber their prey for efficient predation, suggesting that they exclusively practiced group predation. In summary, the CFU-based predation assay not only enabled the quantification of prey killing and consumption by Lysobacter spp. but also provided insights into their mode of predation.

Genetic variation for induced and basal resistance against leaf pathogen Pseudomonas syringae pv. tomato DC3000 among Arabidopsis thaliana accessions.

In Arabidopsis thaliana, significant efforts to determine the effect of naturally occurring variation between phenotypically divergent accessions on different biotic or abiotic stresses are underway. Although it is usually assumed that induced systemic resistance (ISR) against pathogen will covary with plant genetic variation, this assumption has not been tested rigorously in previous experiments. Here, we investigated heritable variation in resistance as well as Penicillium simplicissimum GP17-2-mediated ISR to the bacteria Pseudomonas syringae pv. tomato DC3000 (Pst) among a worldwide collection of accessions of A. thaliana. In this study, 75 Arabidopsis accessions were screened against the bacteria Pst following induction and non-induction treatment and their resistance levels were determined by measuring three components of A. thaliana resistance (infected leaf number, disease severity and pathogen growth). We observed extensive quantitative variation in the number of infected leaves, severity of disease symptoms and the bacterial population size among 75 accessions of A. thaliana infected with Pst. On the contrary, about a two-third of the accessions (49 accessions) showed a reduction in infected leaf number, disease severity and pathogen proliferation after treatment with GP17-2, indicating that GP17-2 induction of resistance is ecotype specific in Arabidopsis. The level of suppression was more pronounced for percent disease severity and pathogen proliferation than for number of infected leaves in ISR-inducible accessions. Accessions non-responsive to GP17-2 treatment generally appeared to be associated with higher basal resistance to infection by Pst. Future study with these parental lines employing a variety of crossing schemes may facilitate identification of major trait loci responsible for GP17-2-mediated ISR in Arabidopsis.

Soil microbial community composition rather than litter quality is linked with soil organic carbon chemical composition in plantations in subtropical China

Purpose Native broadleaf plantations are increasingly being developed as an alternative to coniferous plantations. This studyexaminedtherelationshipsamonglittercarbon(C)quality, soil microbial community composition, and soil organic C (SOC) chemical properties in plantations and how they were affected by tree species. Materials and methods The solid-state 13 C nuclear magnetic resonance spectroscopy (NMR) technique was used to examine SOC chemical composition, and litter and fine root C quality in four plantations of native tree species (Pinus massoniana, Castanopsis hystrix, Michelia macclurei, and Mytilaria laosensis) in Pingxiang, Guangxi Zhuang AutonomousRegion,insubtropicalChina.Soilmicrobialbiomass C and nitrogen (N) were determined by the chloroform fumigation-extraction method and soil bacterial and fungal biomass were measured with the phospholipid fatty acid (PLFA) technique. Results and discussion The proportions of O-alkyl C, alkyl C, aromatic C, and carbonyl C in SOC and the alkyl/O-alkyl C ratio (A/O-A) in litter and fine root samples, soil microbial C and N, microbial C/N ratios, and the amount of PLFAs were significantly different among the four plantations of different species. SOC in the 0–10-cm layer had 43–49 % O-alkyl C, 24–34 % alkyl C, 14–17 % aromatic C, and 9–11 % carbonyl C in SOC. The microbial C/N ratio, the amount of total PLFAs, and bacterial and Gram-positive bacterial population sizes were linked to the proportion of alkyl C in SOC and the A/O-A ratio in soil. The proportion of alkyl C in SOC was not related to the proportion of alkyl C in litter or fine root samples. Conclusions The microbial community composition rather than plant litter or fine root quality was linked to chemical composition of SOC in the studied subtropical plantations. Future research should place more emphasis on the processes involved in the formation of SOC and their association with the microbial community.

Allochthonous bioaugmentation in ex situ treatment of crude oil-polluted sediments in the presence of an effective degrading indigenous microbiome

Oil-polluted sediment bioremediation depends on both physicochemical and biological parameters, but the effect of the latter cannot be evaluated without the optimization of the former. We aimed in optimizing the physicochemical parameters related to biodegradation by applying an ex-situ landfarming set-up combined with biostimulation to oil-polluted sediment, in order to determine the added effect of bioaugmentation by four allochthonous oil-degrading bacterial consortia in relation to the degradation efficiency of the indigenous community. We monitored hydrocarbon degradation, sediment ecotoxicity and hydrolytic activity, bacterial population sizes and bacterial community dynamics, characterizing the dominant taxa through time and at each treatment. We observed no significant differences in total degradation, but increased ecotoxicity between the different treatments receiving both biostimulation and bioaugmentation and the biostimulated-only control. Moreover, the added allochthonous bacteria quickly perished and were rarely detected, their addition inducing minimal shifts in community structure although it altered the distribution of the residual hydrocarbons in two treatments. Therefore, we concluded that biodegradation was mostly performed by the autochthonous populations while bioaugmentation, in contrast to biostimulation, did not enhance the remediation process. Our results indicate that when environmental conditions are optimized, the indigenous microbiome at a polluted site will likely outperform any allochthonous consortium.

Root exudate profiling of maize seedlings inoculated with Herbaspirillum seropedicaeand humic acids

AbstractBackgroundCo-inoculation of maize withHerbaspirillum seropedicaeand humic substances increases the sizes of plant-associated bacterial populations and enhances grain yields under laboratory and field conditions. Root exudation is a key mechanism in the regulation of plant-bacterial interactions in the rhizosphere; humic matter supplementation is known to change the exudation of H+ions and organic acids from maize roots. Our starting premise was thatH. seropedicaeand humic acids would modify maize seedling exudation profiles. We postulated that a better understanding of these shifts in exudate profiles might be useful in improving the chemical environment to promote better performance of plant growth-promoting bacteria delivered as bioinoculants. Thus, root exudates of maize were collected and analyzed by gas chromatography-mass spectrometry (GC-MS) and proton nuclear magnetic resonance (1H NMR).ResultsNitrogenous compounds, fatty acids, organic acids, steroids, and terpenoid derivatives were the main structural moieties found in root exudates. Significant changes in exudation patterns occurred 14 days after the initiation of experiments. Quantities of fatty acids, phenols, and organic acids exuded by seedlings treated with humic acids alone differed from the quantities exuded in other treatments. Seedlings treated withH. seropedicaeorH. seropedicaein combination with humic acids exuded a diversity of nitrogenous compounds, most of which had heterocyclic structures. Twenty-one days after initiating the experiment, seedlings treated withH. seropedicaealone exuded elevated quantities of steroids and terpenoid derivatives related to precursors of gibberellic acids (kaurenoic acids).ConclusionsChanges in root exudation profiles induced by our treatments became most marked 14 and 21 days after initiation of the experiment; on those days, we observed (i) increased fatty acid exudation from seedlings treated only with humic acids and (ii) increased exudations of nitrogenated compounds and terpenes from seedlings treated only withH. seropedicae. Improved knowledge on the effects of bacterial inoculants and supplementation with humates on plant exudate composition may contribute substantially to improved understanding of plant metabolic responses and lead to new approaches in the use of selected compounds as additives in bioinoculant formulations that will modulate the cross-talk between bacteria and plants, thereby improving crop yields.

Reductive genome evolution at both ends of the bacterial population size spectrum.

Bacterial genomes show substantial variations in size. The smallest bacterial genomes are those of endocellular symbionts of eukaryotic hosts, which have undergone massive genome reduction and show patterns that are consistent with the degenerative processes that are predicted to occur in species with small effective population sizes. However, similar genome reduction is found in some free-living marine cyanobacteria that are characterized by extremely large populations. In this Opinion article, we discuss the different hypotheses that have been proposed to account for this reductive genome evolution at both ends of the bacterial population size spectrum.

Carbon Mineralization and Microbial Attributes in Straw-Amended Soils as Affected by Moisture Levels

An 80-d incubation experiment was conducted to investigate straw decomposition, the priming effect and microbial characteristics in a non-fertilized soil (soil 1) and a long-term organic manure-fertilized soil (soil 2) with and without 13C-labeled maize straw amendment under different moisture levels. The soil 2 showed a markedly higher priming effect, microbial biomass C (Cmic), and β-glucosidase activity, and more abundant populations of bacteria and fungi than the soil 1. Also, soil CO2 emission, Cmic, β-glucosidase activity, and bacterial and fungal population sizes were substantially enhanced by straw amendment. In the presence of straw, the amount of straw mineralization and assimilation by microbes in the soil at 55% of water holding capacity (WHC) were significantly higher by 31% and 17%, respectively, compared to those at 25% of WHC. In contrast, β-glucosidase activity and fungal population size were both enhanced as the moisture content decreased. Cmic decreased as straw availability decreased, which was mainly attributed to the reduction of straw-derived Cmic. Amended soils, except the amended soil 2 at 25% of WHC, had a more abundant fungal population as straw availability decreased, indicating that fungal decomposability of added straw was independent of straw availability. Non-metric multidimensional scaling analysis based on fungal denatured gradient gel electrophoresis band patterns showed that shifts in the fungal community structure occurred as water and straw availability varied. The results indirectly suggest that soil fungi are able to adjust their degradation activity to water and straw availability by regulating their community structure.

Interaction of rumen bacteria as assumed by colonization patterns on untreated and alkali‐treated rice straw

Colonization patterns of representative rumen bacteria were compared between untreated rice straw (UTS) and sodium hydroxide-treated rice straw (SHTS). UTS and SHTS were incubated in the rumen of sheep for 10 min, 1, 2, 6, 12, 24, 48 and 96 h using the nylon bag method. The population sizes of 13 representative bacterial species or groups were quantified by real-time PCR. The total bacterial population size (abundance) was similar in both UTS and SHTS. Fibrobacter succinogenes showed a higher population size compared to other fibrolytic species and was detected at a higher level in SHTS (3.7%) than in UTS (2.6%). Ruminococcus albus and Ruminococcus flavefaciens were also detected at higher levels in SHTS (0.15% and 0.29%) than in UTS (0.03% and 0.18%). Population sizes of non-fibrolytic species, such as Selenomonas ruminantium, Anaerovibrio lipolytica and Succinivibrio dextrinosolvens were higher in UTS than in SHTS. Coefficient of determination (r(2) ) on population changes between bacterial species or groups were higher in UTS than in SHTS, suggesting the necessity of stronger bacterial interactions for UTS digestion. Therefore, not only colonization of fibrolytic species, but also synergistic interactions between different bacterial species may be key to the ruminal digestion of rice straw.

The ecological roles of Bacillus thuringiensis within phyllosphere environments

Bacillus thuringiensis (Bt) is one of the most used bio-control agents to control plant insects, but little is known about its effect on the microbial population and communities on plant leaves. With the culture dependent method, it has been observed that the dynamics of Bt within the phyllosphere varied dependent on both the doses of Bt sprayed on the leaves and the plant species, however, Bt’s population size kept stable at about 1000cfug−1 after 15d since inoculation. By comparing the bacterial abundances and community structures within the phyllosphere of three plant species, we confirmed that Bt at the doses of 1.5×107 and 1.5×109 cfumL−1 respectively did not significantly influence the natural bacterial population size on the leaf surfaces based on culture dependent assay. However, based on culture independent denaturing gradient gel electrophoresis (DGGE), Shannon–Wiener index (H′) and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) analysis, Bt has a significant influence on the bacterial communities within the phyllosphere of amaranth and cotton, but not rice. These results indicate that Bt exhibits different behaviors and ecological roles on the microbial diversity within the phyllosphere, and its environmental safety has to be concerned and evaluated in the future.

Menaquinone (Vitamin K2) Enhancement of <i>Staphylococcus aureus</i> Biofilm Formation

During infection, Staphylococcus aureus is exposed to exogenous menaquinone which is essential for the human blood clotting cascade. The effect of exogenous menaquinone on S. aureus phenotypic expression is not known. To test whether menaquinone affects expression of virulence-associated phenotypes, methicillin-sensitive (MSSA) and -resistant (MRSA) S. aureus strains (n = 8) were grown in the presence of menaquinone (0.001 - 12 μg/ml). Capsule production, biofilm formation (plastic and fibronectin-coated microtiter plates) and carotenoid levels were determined spectrophotometrically after growth in Mueller Hinton broth (MH; 24-hr, 37°C). All experiments were, at minimum, done in triplicate and repeated twice. Menaquinone at physiologic levels (0.01 μg/ml MH) significantly increased (p 0.05) biofilm formation on plastic in a manner that was bacterial population size dependent. In addition, menaquinone (0.05 - 4 μg/ml) significantly increased (p 0.05) biofilm formation on fibronectin-coated surfaces for four MSSA strains and one MRSA strain by two to six-fold as compared to medium controls. However, menaquinone had no effect on capsule production or cell-associated carotenoid levels. Menaquinone’s effect on biofilm formation on fibronectin-coated surfaces appears to be regulated by sarA. These findings are the first to demonstrate that a vitamin at concentrations reported in humans affects S. aureus virulence-associated phenotypes.

Deciphering Bacterial Universal Language by Detecting the Quorum Sensing Signal, Autoinducer-2, with a Whole-Cell Sensing System

Bacteria communicate with neighboring bacteria of the same species or of other species by means of chemical signaling molecules. The concentration of such signaling molecules is proportional to the bacterial population size; upon reaching a threshold concentration, corresponding to a threshold cell density, certain specialized genes are expressed. This system of communication among bacteria is known as quorum sensing (QS). QS regulates diverse behaviors, such as formation of biofilms and production of pathogenic factors. Autoinducer-2 (AI-2) is a QS signaling molecule that is used for interspecies communication by both Gram-positive and Gram-negative bacteria. Bacteria are known to play an important role in many diseases, from infections to chronic inflammation. Therefore, QS is involved in a variety of disorders of bacterial origin or where bacteria play a crucial pathogenic role. One such condition is inflammatory bowel disease (IBD), a chronic inflammation of the gastrointestinal (GI) tract that includes debilitating diseases, such as ulcerative colitis (UC) and Crohn's disease (CD). To date, noninvasive methods are unavailable for the diagnosis and monitoring of IBD. We hypothesized that detection of QS molecules in physiological samples, specifically saliva and stool specimens, would provide with a method for the noninvasive, early diagnosis and monitoring of IBD conditions. To that end, we developed and optimized a whole-cell sensing system for AI-2, which is based on Vibrio harveyi strain BB170. Furthermore, we standardized and applied the biosensing system for the quantitative detection of AI-2 in saliva, stool, and intestinal samples from IBD patients.

Stochastic Models for a Chemostat and Long-Time Behavior

We introduce two stochastic chemostat models consisting of a coupled population-nutrient process reflecting the interaction between the nutrient and the bacteria in the chemostat with finite volume. The nutrient concentration evolves continuously but depends on the population size, while the population size is a birth-and-death process with coefficients depending on time through the nutrient concentration. The nutrient is shared by the bacteria and creates a regulation of the bacterial population size. The latter and the fluctuations due to the random births and deaths of individuals make the population go almost surely to extinction. Therefore, we are interested in the long-time behavior of the bacterial population conditioned to nonextinction. We prove the global existence of the process and its almost-sure extinction. The existence of quasistationary distributions is obtained based on a general fixed-point argument. Moreover, we prove the absolute continuity of the nutrient distribution when conditioned to a fixed number of individuals and the smoothness of the corresponding densities.

Stochastic Models for a Chemostat and Long-Time Behavior

We introduce two stochastic chemostat models consisting of a coupled population-nutrient process reflecting the interaction between the nutrient and the bacteria in the chemostat with finite volume. The nutrient concentration evolves continuously but depends on the population size, while the population size is a birth-and-death process with coefficients depending on time through the nutrient concentration. The nutrient is shared by the bacteria and creates a regulation of the bacterial population size. The latter and the fluctuations due to the random births and deaths of individuals make the population go almost surely to extinction. Therefore, we are interested in the long-time behavior of the bacterial population conditioned to nonextinction. We prove the global existence of the process and its almost-sure extinction. The existence of quasistationary distributions is obtained based on a general fixed-point argument. Moreover, we prove the absolute continuity of the nutrient distribution when conditioned to a fixed number of individuals and the smoothness of the corresponding densities.