The role of regulation of cell speed in the behavior of Physarum polycephalum amoebae

Studies on the behavior of wild-type and mutant Physarum polycephalum amoebae have revealed that regulation of cell speed results in different patterns of cell dispersion in different environments and have shown that P. polycephalum can be used for genetic studies of the mechanisms responsible for this element of cell behavior. Colonies generated by clonal populations of amoebae growing on E. coli display alternate colony morphologies depending on the pH of the culture medium and the presence of live E. coli as a nutrient. In the larger ‘spreading colonies’ cells at the outside of a colony are dispersed over a wide band of bacteria while in the smaller ‘aggregate ring colonies’ most cells moving on bacteria are aggregated in a regularly shaped ring on a narrow band of bacteria at the border of the bacterial lawn created when amoebae completely consume the bacteria available in the colony center. Measurements of cell growth, the rate of colony expansion, and the rate of single cell movement show that cells in contact with bacteria move more slowly in aggregate ring than in spreading colonies. Moreover, since in aggregate ring colonies the rate of movement of cells in contact with bacteria is also reduced relative to that of cells moving on adjacent regions of the agar surface, inhibition of cell speed appears to be at least partially responsible for generating the aggregate ring morphology. Characterization of the behavior of a single locus mutant which generates spreading colonies under conditions where aggregate ring colonies are normally formed has provided additional evidence that a specific mechanism is involved in controlling the distribution of amoebae through regulation of cell speed. Furthermore, the studies of this mutant have shown that aberrant colony morphology can be used as an easily recognized phenotype for identifying and studying mutants with defects which affect the regulation of cell speed.     

Morphogenesis in cell colonies grown from Convolvulus cell suspensions plated on synthetic media

Filtered cell suspensions of cultured callus tissue derived from the roots of Convolvulus arvensis L. were plated out on synthetic agar nutrient media in petri plates. Cell colonies which formed from the single cells or small cell groups in the suspension showed a considerable range of developmental patterns depending upon the physical and chemical environment to which they were exposed. Variation of the auxin and kinin concentrations and the nature and concentration of the source of reduced N compounds had the most profound effects on colony development. High auxin favored cell enlargement, high kinin favored the development of compact colonies composed of many small cells. Both auxin and kinin were required for cell colony formation. Cell differentiation responses which were observed but not subject to experimental control included formation of starch- and crystal-storing cells, differentiation of tracheary elements, formation of cellular filaments, and development of chlorophyllous tissue. Organ initiation was studied in cell colonies developed directly from plated cell suspensions and in cell colonies subcultured on various nutrient media. Bud initiation was produced repeatedly on media containing NAA at 10^-8 to 10^-6 m combined with kinetin at 10^-6 m . Root initiation was induced infrequently and unpredictably. Once roots had been formed from cell colonies derived from cell suspensions, the roots could be subcultured and induced to form buds; these in turn grew into whole plants. Subculture of young cell colonies to media containing different combinations of growth substances made possible a study of the effects of auxin and kinin on organization of primordia by the cell colonies. By following marked single cells plated on synthetic media, it was possible to produce single-cell clones which under proper nutrient conditions were induced to form buds. The value of the combined techniques of cell suspension culture and cell plating for the study of the physical and chemical factors influencing cell differentiation and organized development are pointed out.     

Understanding the cause of false negative β‐d‐glucuronidase reactions in culture media containing fermentable carbohydrate

Aims:  To explain the basis for false negative β‐glucuronidase reactions seen with culture media containing lactose as a carbon and energy source. Methods and Results:  Escherichia coli strains were assessed for their reactions in culture media containing a β‐d ‐glucuronidase substrate either with or without lactose. An assay was developed to test for the expression of β‐d ‐glucuronidase at pH 5·0 and pH 7·2. Strains of E. coli that gave false negative glucuronidase reactions on media containing lactose generally expressed lower concentrations of the enzyme β‐d ‐glucuronidase than strains that gave positive results, although the difference was by no means consistent. Most strains that were negative on lactose‐containing media expressed virtually no β‐d ‐glucuronidase activity at pH 5·0. Examination of colonies on Membrane lactose glucuronide agar (MLGA) from lightly polluted water showed that c. 10% of the E. coli present failed to yield green colonies on MLGA. Conclusions:  E. coli that failed to produce green colonies on MLGA produced lower levels of β‐d ‐glucuronidase than did strains that formed green colonies, the difference being greater at pH 5·0 than pH 7·2. The false negative rate for E. coli 10% which is similar to that experienced in the study that originally described MLGA. Significance and Impact of the Study:  Strains of E. coli that fail to produce typical colonies on MLGA might produce lower concentrations of the enzyme β‐d ‐glucuronidase. Whilst the enzyme activity is sufficient to be detected at pH 7·2, fermentation of lactose significantly lowers the pH of the medium and can result in reduced enzyme activity and therefore lack of detection. The false negative rate of c. 10% would be difficult to detect in routine laboratories as it would represent 1% or less of yellow colonies being identified as E. coli (assuming E. coli accounts for 10% of the total coliform population in drinking water).     

Differentiated Gene Expression in Cells within Yeast Colonies

Yeast cells growing on solid media organize themselves into multicellular structures, colonies, exhibiting patterns specific for particular yeast strains. With the aim of identifying genes involved in regulations of the colony formation, we applied a new approach enabling the extensive screening of Saccharomyces cerevisiae genes, the expression of which is changed during colony development. We used the library of S. cerevisiae DNA fragments inserted in front of the lacZ gene lacking its own promoter. Colonies of transformants with a blue/white patterned morphotype, implying that the expression of the lacZ gene from the inserted yeast promoter is switched on and off during the colony formation, were isolated. We identified several genes with variable expression during colony morphogenesis, including CCR4, PAM1, MEP3, ADE5,7 and CAT2. S. cerevisiae strain deleted in the CCR4 gene forms colonies with less organized morphology when compared with the isogenic parental strain. The synchronization of the expression patterns of some of the isolated genes in neighboring colonies was observed.     

Assessment of survival during starvation ofEscherichia coli andKlebsiella pneumoniae in artificial urine: analysis of the kinetics of colony formation

A kinetic model of colony formation was proposed by Hattori, based on a count of the colonies that appear on a plate in successive short intervals of time. In this model, three parameters (,t _r and N) are defined, which reflect the ability of a bacterium to yield colonies and allow us to described the dynamics of bacterial populations in soil and ofE. coli at different growth phases. In this paper we report a reparametrization of the kinetic model of colony formation, with the aim of facilitating more accurate calculation of andt _r. Moreover, we observed that during the starvation ofE. coli andK. pneumoniae in urine, can be used to assess survival, since this parameter clearly decreases during starvation. Retardation time values (t _r) were similar inE. coli andK. pneumoniae throughout the starvation experimental period.     

The Alternative Role of Enterobactin as an Oxidative Stress Protector Allows Escherichia coli Colony Development

Numerous bacteria have evolved different iron uptake systems with the ability to make use of their own and heterologous siderophores. However, there is growing evidence attributing alternative roles for siderophores that might explain the potential adaptive advantages of microorganisms having multiple siderophore systems. In this work, we show the requirement of the siderophore enterobactin for Escherichia coli colony development in minimal media. We observed that a strain impaired in enterobactin production (entE mutant) was unable to form colonies on M9 agar medium meanwhile its growth was normal on LB agar medium. Given that, neither iron nor citrate supplementation restored colony growth, the role of enterobactin as an iron uptake-facilitator would not explain its requirement for colony development. The absence of colony development was reverted either by addition of enterobactin, the reducing agent ascorbic acid or by incubating in anaerobic culture conditions with no additives. Then, we associated the enterobactin requirement for colony development with its ability to reduce oxidative stress, which we found to be higher in media where the colony development was impaired (M9) compared with media where the strain was able to form colonies (LB). Since oxyR and soxS mutants (two major stress response regulators) formed colonies in M9 agar medium, we hypothesize that enterobactin could be an important piece in the oxidative stress response repertoire, particularly required in the context of colony formation. In addition, we show that enterobactin has to be hydrolyzed after reaching the cell cytoplasm in order to enable colony development. By favoring iron release, hydrolysis of the enterobactin-iron complex, not only would assure covering iron needs, but would also provide the cell with a molecule with exposed hydroxyl groups (hydrolyzed enterobactin). This molecule would be able to scavenge radicals and therefore reduce oxidative stress.     

Cell division across the volume of colonies of flavobacterium sp. 22

Six-day-old colonies ofFlavobacterium sp. 22 were studied by electron microscopy. Direct evidence was obtained of bacterial cell division across the entire colony volume, indicating that the colony growth ofFlavobacterium sp. 22 is not purely peripheral. It is argued that the colony shape is determined not only by peripheral growth but also by physical forces acting upon a droplet of liquid on the surface. For bacterial colonies developing on solid nutrient media, the intercellular matrix plays the role of such a liquid.     

Zeta Potential of Selected Bacteria in Drinking Water When Dead, Starved, or Exposed to Minimal and Rich Culture Media

The zeta potentials of E. coli, GFP (green fluorescence protein)-labeled E. coli, Salmonella Newport, and Pseudomonas sp. in different states (nutrient-starved and dead) and grown in rich and minimal media were measured. Capillary electrophoresis experiments were conducted to measure the zeta potential of the different cells suspended in a drinking water sample. Salmonella Newport strain showed a lower zeta potential compared to E. coli, GFP-labeled E. coli, and Pseudomonas sp. Starved E. coli cells had a lower zeta potential compared to E. coli cells grown under rich media conditions. Salmonella Newport cells grown in minimal media also had a lower zeta potential compared to rich, starved, and dead cells. The different bacterial cell types exhibited differences in size as well. These results suggest that when bacterial cells are present in drinking water they can exhibit significant heterogeneity in the size and zeta potential, depending on their physiological state.     

Observation of microorganism colonies using a scanning-laser-beam pH-sensing microscope

The extracellular pH-distribution of colonies of Saccharomyces cerevisiae (yeast) and Escherichia coli (E. coli) were observed using a newly-developed scanning-laser-beam pH-sensing microscope. Colonies were incubated either on top of agarose plates or between the pH-sensing surface and the agar. In the latter case, colony growth was observed in-situ. The colonies could be observed within a period as short as 8 h for E. coli. The pH-distribution profiles by the colonies were found to be very sharp, in agreement with simulation results.     

Growth patterns of yeast colonies depending on nutrient supply

Common theories of microbial growth and physiology are formulated exclusively in terms of the isolated microorganisms – especially bacteria. This is, however, an inadmissible simplification because it is obvious that the organization of microbial populations and colonies follows certain general rules. Bacterial colonies are able to generate complex interfacial growth patterns similar to those observed during diffusion-limited growth processes in non-living systems. One reason for these patterns is assumed to be the ability of many bacteria to swarm in an active manner on a substrate surface. Therefore the models of bacterial colony growth incorporate “random walkers”, which move actively in response to a gradient in the concentration of nutrients and communicate with each other by means of a chemotactic feedback. A selected number of yeasts were tested with regard to their colony growth patterns depending on the medium parameters such as nutrient concentration. Growth patterns similar to those which were described in literature for bacteria were also found in these experiments. It concerns in particular growth types like compact growth, fractal growth and dense-branching growth. This result allows a hypothesis to be formulated, that – especially in the case of fractal growth patterns – wandering of cells on a substrate surface may be induced by uncontrolled “swimming” on a thin water film caused by the metabolic activity (e.g. respiration) of the cells on the surface of the agar. Furthermore it was found that an interplay between changes in the individual morphology of yeast cells and the morphology transitions takes place. Such growth patterns are known for Candida sp. which are able to form pseudomycel and blastospores.     

Label-free identification of bacterial microcolonies via elastic scattering

Label‐free microcolony identification via elastic light scattering was investigated for three different genera: Salmonella enterica serovar Montevideo, Listeria monocytogenes F4244, and Escherichia coli DH5α. Microcolonies were defined as bacterial colonies in their late‐lag phase to early‐exponential phase with the diameter range of 100–200 µm. To link biophysical characteristics with corresponding scattering patterns, a phase contrast microscope and a confocal displacement meter were used to measure the colony diameter and its 3D height profile. The results indicated that the growth characteristics of microcolonies were encoded in their morphologies which correlated to the characteristic diffraction patterns. Proposed methodology was able to classify three genera based on comprehensive phenotypic map which incorporated growth speed, ring count, and colony diameter. While the proposed method illustrated the possibility of discriminating microcolonies in their early growth stage, more thorough biophysical understanding is needed to expand the technology to other species. Biotechnol. Bioeng. 2011; 108:637–644. © 2010 Wiley Periodicals, Inc.     

Applying dimorphic yeasts as model organisms to study mycelial growth: Part 1. Experimental investigation of the spatio-temporal development of filamentous yeast colonies

Colony development of the dimorphic yeasts Yarrowia lipolytica and Candida boidinii on solid agar substrates under glucose limitation served as a model system for mycelial development of higher filamentous fungi. Strong differences were observed in the behaviour of both yeasts: C. boidinii colonies reached a final colony extension which was small compared to the size of the growth field. They formed cell-density profiles which steeply declined along the colony radius and no biomass decay processes could be detected. The stop of colony extension coincided with the depletion of glucose from the growth substrate. These findings supported the hypothesis that glucose-limited C. boidinii colonies can be regarded as populations of single cells which grow according to a diffusion-limited growth mechanism. Y. lipolytica colonies continued to extend after the depletion of the primary nutrient resource, glucose, until the populations covered the entire growth field which was accomplished by utilization of mycelial biomass.     

COLONY FORMATION AND SEXUAL MORPHOGENESIS IN THE COCCOLITHOPHORE PLEUROCHRYSIS SP. (HAPTOPHYTA)1

Pleurochrysis sp. formed two types of symmetrical, diploid colonies on solid media: (i) single‐cell lineage (SCL) colonies and (ii) aggregation (AG) colonies. The first division of a single mother cell was asymmetric in ～54% of SCL colonies. These colonies developed at a slower rate than AG colonies. Diffusible molecules released from the cells acted like morphogens enhancing formation of AG colonies; their influence on chemotaxis of aggregating cells was dependent on concentration of the inoculum. Nitrogen depletion of diploid colonies induced sexual morphogenesis and colony patterning into inner and outer regions. The smaller innermost cells were surrounded by outer larger cells. Developmental mechanisms of colony formation were examined in relation to the heteromorphic, haplo‐diploid life cycle.     

Development of a multispectral light‐scatter sensor for bacterial colonies

We report a multispectral elastic‐light‐scatter instrument that can simultaneously detect three‐wavelength scatter patterns and associated optical densities from individual bacterial colonies, overcoming the limits of the single‐wavelength predecessor. Absorption measurements on liquid bacterial samples revealed that the spectroscopic information can indeed contribute to sample differentiability. New optical components, including a pellicle beam splitter and an optical cage system, were utilized for robust acquisition of multispectral images. Four different genera and seven shiga toxin producing E. coli serovars were analyzed; the acquired images showed differences in scattering characteristics among the tested organisms. In addition, colony‐based spectral optical‐density information was also collected. The optical model, which was developed using diffraction theory, correctly predicted wavelength‐related differences in scatter patterns, and was matched with the experimental results. Scatter‐pattern classification was performed using pseudo‐Zernike (GPZ) polynomials/moments by combining the features collected at all three wavelengths and selecting the best features via a random‐forest method. The data demonstrate that the selected features provide better classification rates than the same number of features from any single wavelength.

Three wavelength‐merged scatter pattern from E. coli.     

Agonistic behavior among colonies of the Formosan subterranean termite,Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae), from Florida and Hawaii: Lack of correlation with cuticular hydrocarbon composition

Cuticular hydrocarbon patterns of the Formosan subterranean termite, Coptotermes formosanus Shiraki, were similar among colonies from the same geographical location. Hydrocarbon patterns of Florida colonies were easily distinguished from those of Hawaii colonies by using canonical discriminant analysis. Groups of termites from the same colony did not fight one another when placed in an arena. Intercolonial aggression was not recorded among C. formosanuspopulations from Florida but three colonies from Hawaii fought with the other Hawaiian and three Florida colonies. Of the 12 colonies (six each from Florida and Hawaii) tested, 3 Florida colonies did not direct or receive aggression from any other colony. Cuticular hydrocarbon patterns were not correlated with agonistic behavior.     

Studies of Escherichia coli Cultured on RainbowTM Agar O157 with Particular Reference to Enterohaemorrhagic Escherichia coli (EHEC)

Rainbow^TM Agar O157 is designed for the rapid isolation and identification of enterohaemorrhagic Escherichia coli (EHEC), particularly O157, characterised by black colonies. Five-hundred-eighty-five E. coli strains, including O157, O111 and O113 serogroups from many sources were examined on Rainbow^TM Agar O157. EHEC O157 could readily be isolated and recognized uniquely by typical black colonies. Some other EHEC also stand out as blue-black, whereas O113 and some other EHEC strains were mauve, red or pink and indistinguishable from SLT-negative strains of E. coli.     

Thinking about Bacillus subtilis as a multicellular organism

Initial attempts to use colony morphogenesis as a tool to investigate bacterial multicellularity were limited by the fact that laboratory strains often have lost many of their developmental properties. Recent advances in elucidating the molecular mechanisms underlying colony morphogenesis have been made possible through the use of undomesticated strains. In particular, Bacillus subtilis has proven to be a remarkable model system to study colony morphogenesis because of its well-characterized developmental features. Genetic screens that analyze mutants defective in colony morphology have led to the discovery of an intricate regulatory network that controls the production of an extracellular matrix. This matrix is essential for the development of complex colony architecture characterized by aerial projections that serve as preferential sites for sporulation. While much progress has been made, the challenge for future studies will be to determine the underlying mechanisms that regulate development such that differentiation occurs in a spatially and temporally organized manner.     

Probabilistic transition from unstable predator-prey interaction to stable coexistence of Dictyostelium discoideum and Escherichia coli

Predator-prey interactions have been found at all levels within ecosystems. Despite their ecological ubiquity and importance, the process of transition to a stable coexistent state has been poorly verified experimentally. To investigate the stabilization process of predator-prey interactions, we previously constructed a reproducible experimental predator-prey system between Dictyostelium discoideum and Escherichia coli, and showed that the phenotypically changed E. coli contributed to stabilization of the system. In the present study, we focused on the transition to stable coexistence of both species after the phenotypic change in E. coli. Analysis of E. coli cells isolated from co-culture plates as single colony enabled us to readily identify the appearance of phenotypically changed E. coli that differed in colony morphology and growth rate. It was also demonstrated that two types of viscous colony, i.e., the dense-type and sparse-type, differing in spatial distribution of both species emerged probabilistically and all of the viscous colonies maintained stably were of the sparse-type. These results suggest that the phenotypically changed E. coli may produce two types of viscous colonies probabilistically. The difference in spatial distribution would affect localized interactions between both species and then cause probabilistic stabilization of predator-prey interactions.     

Occurrence ofEnterococcus spp. in waters

We studied 630 bacterial strains isolated from surface waters and determined as enterococci on the basis of their growth on Slanetz-Bartley agar in typical colonies. The strains were tested and characterized by several key conventional tests for basic differentiation of enterococci and by commercial test kits. We identified 135 strains ofE. fœcium (21%), 115E. fœcalis (18%), 30E. mundtii (5%), 27E. hirae (4%), 22E. casseliflavus (3%), 21E. gallinarum (3%), 17E. durans-E. hirae complex (3%), 5E. durans (1%), and 1 strain ofE. avium. 150 strains were classified only asEnterococcus sp. (25%) and 107 strains (17%) isolated from Slanetz-Bartley agar were not enterococci. We found that the non-enterococcal group consisted of other Gram-positive cocci and Gram-positive and Gram-negative rods. Based on the identification we tried to find a relation between taxonomic position of isolated strains and their colony morphology on Slanetz-Bartley agar. Out of the total of 523 identified enterococci, 345 strains (66%) formed purple colonies, 136 red colonies (26%), 37 pink colonies (7%) and 5 cream colored colonies (1%). There was no correlation among the color, size or colony morphology and the taxonomic characterization of enterococcal strains.