A Comparison of the Maximal Growth Rates of Various Bacteria under Optimal Conditions

Density-dependent effects are the main determinants of variation in growth dynamics between closely related bacterial strains

Although closely related, bacterial strains from the same species show significant diversity in their growth and death dynamics. Yet, our understanding of the relationship between the kinetic parameters that dictate these dynamics is still lacking. Here, we measured the growth and death dynamics of 11 strains of Escherichia coli originating from different hosts and show that the growth patterns are clustered into three major classes with typical growth rates, maximal fold change, and death rates. To infer the underlying phenotypic parameters that govern the dynamics, we developed a phenomenological mathematical model that accounts not only for growth rate and its dependence on resource availability, but also for death rates and density-dependent growth inhibition. We show that density-dependent growth is essential for capturing the variability in growth dynamics between the strains. Indeed, the main parameter determining the dynamics is the typical density at which they slow down their growth, rather than the maximal growth rate or death rate. Moreover, we show that the phenotypic landscape resides within a two-dimensional plane spanned by resource utilization efficiency, death rate, and density-dependent growth inhibition. In this phenotypic plane, we identify three clusters that correspond to the growth pattern classes. Overall, our results reveal the tradeoffs between growth parameters that constrain bacterial adaptation.

Reduced Level of Tear Antimicrobial and Immunomodulatory Proteins as a Possible Reason for Higher Ocular Infections in Diabetic Patients

(1) Background: Diabetes mellitus is one of the most common metabolic disorders and a risk factor for bacterial ocular infections. Our aim was to examine the antibacterial activity of tears from patients with diabetes mellitus with and without diabetic retinopathy and to link this activity to the level of tear proteins. (2) Methods: Non-stimulated basal tears were collected from 39 eyes of 35 subjects. The antibacterial activity of tear pools was tested against pathogenic Staphylococcus aureus ATCC 29213, Escherichia coli ATCC 26922 and Pseudomonas aeruginosa ATCC 27853 strains. The levels of 10 antimicrobial and immunomodulatory proteins were analyzed in the individual tear samples of the studied groups by SRM-based targeted mass spectrometry analysis. (3) Results: Disease stage-specific antimicrobial effect was observed in case of Staphylococcus aureus ATCC 29213 strain, and a non-disease specific inhibitory effect was observed in case of Pseudomonas aeruginosa ATCC 27853 strain. Changes in the levels of the studied antimicrobial and immunomodulatory proteins in the tears of the studied groups were also observed. (4) Conclusions: The higher ocular infection rate observed in diabetic patients may be the consequence of the decreased antimicrobial activity of tears possibly caused by the changes in the levels of antimicrobial and immunomodulatory proteins.

Using sliding mode observers to estimate BtuB concentration from measured vitamin B12 concentration

A simple model for the B12-riboswitch regulatory network in Escherichia coli is first described and the same analysis is applied when changing the strain to Salmonella enterica. Model validation is undertaken by linking the dynamics of the riboswitch model to bacterial growth and comparing the results obtained with in vivo experimental measurements. Measurements of bacterial growth are relatively straightforward to obtain experimentally, but experimental measurements relating to the operation of the riboswitch are more difficult. Using the validated model, sliding mode observer design methods are used to estimate BtuB given measurements of the concentration of vitamin B12. The sliding mode approach is selected because of its inherent robustness properties as well as for the ease of implementation. Validation of the estimates of BtuB produced by the observer is undertaken by comparing the BtuB and vitamin B12 concentrations estimated from the observer with green fluorescent protein production and the concentration of vitamin B12 obtained experimentally. These experimental results also provide further validation of the underpinning mathematical model. The results establish that using a sliding mode observer as a soft sensor is a useful approach to explore the operation of a vitamin B12 riboswitch given measurements of the concentration of vitamin B12.

A synthesis of bacterial and archaeal phenotypic trait data

A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients.

Threshold effect of growth rate on population variability of Escherichia coli cell lengths

A long-standing question in biology is the effect of growth on cell size. Here, we estimate the effect of Escherichia coli growth rate (r) on population cell size distributions by estimating the coefficient of variation of cell lengths (CV_L) from image analysis of fixed cells in DIC microscopy. We find that the CV_L is constant at growth rates less than one division per hour, whereas above this threshold, CV_L increases with an increase in the growth rate. We hypothesize that stochastic inhibition of cell division owing to replication stalling by a RecA-dependent mechanism, combined with the growth rate threshold of multi-fork replication (according to Cooper and Helmstetter), could form the basis of such a threshold effect. We proceed to test our hypothesis by increasing the frequency of stochastic stalling of replication forks with hydroxyurea (HU) treatment and find that cell length variability increases only when the growth rate exceeds this threshold. The population effect is also reproduced in single-cell studies using agar-pad cultures and 'mother machine'-based experiments to achieve synchrony. To test the role of RecA, critical for the repair of stalled replication forks, we examine the CV_L of E. coli ΔrecA cells. We find cell length variability in the mutant to be greater than wild-type, a phenotype that is rescued by plasmid-based RecA expression. Additionally, we find that RecA-GFP protein recruitment to nucleoids is more frequent at growth rates exceeding the growth rate threshold and is further enhanced on HU treatment. Thus, we find growth rates greater than a threshold result in increased E. coli cell lengths in the population, and this effect is, at least in part, mediated by RecA recruitment to the nucleoid and stochastic inhibition of division.

Threshold effect of growth rate on population variability of Escherichia coli cell lengths

A long-standing question in biology is the effect of growth on cell size. Here, we estimate the effect of Escherichia coli growth rate (r) on population cell size distributions by estimating the coefficient of variation of cell lengths (CV_L) from image analysis of fixed cells in DIC microscopy. We find that the CV_L is constant at growth rates less than one division per hour, whereas above this threshold, CV_L increases with an increase in the growth rate. We hypothesize that stochastic inhibition of cell division owing to replication stalling by a RecA-dependent mechanism, combined with the growth rate threshold of multi-fork replication (according to Cooper and Helmstetter), could form the basis of such a threshold effect. We proceed to test our hypothesis by increasing the frequency of stochastic stalling of replication forks with hydroxyurea (HU) treatment and find that cell length variability increases only when the growth rate exceeds this threshold. The population effect is also reproduced in single-cell studies using agar-pad cultures and 'mother machine'-based experiments to achieve synchrony. To test the role of RecA, critical for the repair of stalled replication forks, we examine the CV_L of E. coli ΔrecA cells. We find cell length variability in the mutant to be greater than wild-type, a phenotype that is rescued by plasmid-based RecA expression. Additionally, we find that RecA-GFP protein recruitment to nucleoids is more frequent at growth rates exceeding the growth rate threshold and is further enhanced on HU treatment. Thus, we find growth rates greater than a threshold result in increased E. coli cell lengths in the population, and this effect is, at least in part, mediated by RecA recruitment to the nucleoid and stochastic inhibition of division.

Population expansions shared among coexisting bacterial lineages are revealed by genetic evidence

Comparative population studies can help elucidate the influence of historical events upon current patterns of biodiversity among taxa that coexist in a given geographic area. In particular, comparative assessments derived from population genetics and coalescent theory have been used to investigate population dynamics of bacterial pathogens in order to understand disease epidemics. In contrast, and despite the ecological relevance of non-host associated and naturally occurring bacteria, there is little understanding of the processes determining their diversity. Here we analyzed the patterns of genetic diversity in coexisting populations of three genera of bacteria (Bacillus, Exiguobacterium, and Pseudomonas) that are abundant in the aquatic systems of the Cuatro Cienegas Basin, Mexico. We tested the hypothesis that a common habitat leaves a signature upon the genetic variation present in bacterial populations, independent of phylogenetic relationships. We used multilocus markers to assess genetic diversity and (1) performed comparative phylogenetic analyses, (2) described the genetic structure of bacterial populations, (3) calculated descriptive parameters of genetic diversity, (4) performed neutrality tests, and (5) conducted coalescent-based historical reconstructions. Our results show a trend of synchronic expansions across most populations independent of both lineage and sampling site. Thus, we provide empirical evidence supporting the analysis of coexisting bacterial lineages in natural environments to advance our understanding of bacterial evolution beyond medical or health-related microbes.

Microbial life under extreme energy limitation

A great number of the bacteria and archaea on Earth are found in subsurface environments in a physiological state that is poorly represented or explained by laboratory cultures. Microbial cells in these very stable and oligotrophic settings catabolize 10⁴- to 10⁶-fold more slowly than model organisms in nutrient-rich cultures, turn over biomass on timescales of centuries to millennia rather than hours to days, and subsist with energy fluxes that are 1,000-fold lower than the typical culture-based estimates of maintenance requirements. To reconcile this disparate state of being with our knowledge of microbial physiology will require a revised understanding of microbial energy requirements, including identifying the factors that comprise true basal maintenance and the adaptations that might serve to minimize these factors.

Localization and fate of Escherichia coli in hematogenous pyelonephritis

1. Hematogenous E. coli pyelonephritis was produced in rats. The localization of the organisms and the persistence of bacterial antigens was followed by fluorescent antibody techniques as well as by standard histological and bacteriological methods. 2. Salient sequential features were as follows: Single organisms passed through vessel walls into the renal interstitium and began multiplication and subsequently evoked a leucocytic response. Bacterial multiplication did not occur in glomeruli or renal tubular cells. Bacteria did not appear within renal tubular lumina until microabscesses were well developed in the renal interstitium. Bacteriuria appeared late and represented secondary invasion rather than filtration of organisms. The infection healed spontaneously but, while sterile, the parenchymal scars contained large amounts of residual bacterial antigen. The persistence of bacterial antigen did not result in continuing inflammatory changes or progressive scarring. 3. The persistence of bacterial antigens is postulated to constitute a major antigenic stimulus responsible for active immunity in experimental hematogenous pyelonephritis.

Coliform bacteria from aquatic sources in Fiji

Coliform bacteria were abundant in water and bivalve molluscs in the rivers and present to a lesser extent in the coastal areas of Fiji. The rivers fed by treated sewage were highly polluted. There was a noticeable increase in concentration of coliforms in bivalve molluscs. It was also found that these bacteria could survive and grow in river water and seawater over a 5-d period, and had a rapid growth rate in nutrient broth under ideal laboratory conditions. They were characterized by the API 20E identification system.

Salmonella suppression by known populations of bacteria in flies

Survivorship of Salmonella typhimurium, Streptococcus faecalis, Proteus mirabilis, and Pseudomonas aeruginosa was studied in dibiotic and tribiotic interactions in vitro and in various regions of the digestive tract of the blow fly, Calliphora vicina. In dibiotic interactions, Salmonella typhimurium dominated Streptococcus faecalis and was dominated by P. mirabilis, but in neither case was it eliminated from the larval gut. In tribiotic interactions, there was synergic suppression and a definite trend toward elimination of Salmonella typhimurium from the gut. This trend approaches but does not match the total exclusion of S. typhimurium from the gut of maggots with a normal flora. Bacterial survival in the gut of the fly is discussed in relation to doubling time, sweep-out rate of the maggot and prepupal gut, and the midgut bactericide.

Life at high temperatures. Evolutionary, ecological, and biochemical significance of organisms living in hot springs is discussed

The time is now ripe for a concerted attack on the evolutionary, ecological, and molecular aspects of life at high temperatures. Hot springs provide nearly ideal ecosystems for such study, since they are natural environments of great antiquity and relative constancy, where organisms have evolved to meet the environmental challenges of high temperatures. Even from our present limited knowledge, we can draw a number of conclusions.

Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes

Eagon, R. G. (University of Georgia, Athens). Pseudomonas natriegens, a marine bacterium with a generation time of less than 10 minutes. J. Bacteriol. 83:736-737. 1962.-Pseudomonas natriegens, a marine microorganism, was demonstrated to have a generation time of 9.8 min. This is the shortest generation time reported to date. Optimal growth occurred at 37 C in brain heart infusion broth supplemented with 1.5% sea salt.

BACTERIAL DISSIMILATION OF STREPTOMYCIN

Klein, Dolph (Rutgers, The State University, New Brunswick, N. J.), and David Pramer . Bacterial dissimilation of streptomycin. J. Bacteriol. 82: 505–510. 1961.—The influence of various nutritional and environmental factors on the dissimilation of streptomycin by a pseudomonad isolated from soil was investigated, and conditions most suitable for growth of the bacterium, in a medium that contained streptomycin as a sole source of energy, nitrogen, and organic carbon, were determined. Development of the bacterium as measured by plate counts was correlated with degradation of streptomycin as measured by both biological and spectrophotometric assay procedures.

Periodic analyses of culture filtrates indicated that the three constituent moieties of the streptomycin molecule underwent simultaneous transformation when the antibiotic was degraded microbiologically. Washed cell suspensions were capable of immediate and rapid oxidation of streptomycin, dihydrostreptomycin, and hydroxystreptomycin, but cell-free sonic extracts, in the absence and presence of cofactors, did not oxidize streptomycin or any of a number of derivatives or degradation products of the antibiotic. Evidence was obtained that the bacterial dissimilation of streptomycin involves an oxidation system in which methylene blue can act as hydrogen acceptor.