Regular Rods Research Articles

Isolation, characterization, and U(VI)-reducing potential of a facultatively anaerobic, acid-resistant Bacterium from Low-pH, nitrate- and U(VI)-contaminated subsurface sediment and description of Salmonella subterranea sp. nov.

A facultatively anaerobic, acid-resistant bacterium, designated strain FRCl, was isolated from a low-pH, nitrate- and U(VI)-contaminated subsurface sediment at site FW-024 at the Natural and Accelerated Bioremediation Research Field Research Center in Oak Ridge, Tenn. Strain FRCl was enriched at pH 4.5 in minimal medium with nitrate as the electron acceptor, hydrogen as the electron donor, and acetate as the carbon source. Clones with 16S ribosomal DNA (rDNA) sequences identical to the sequence of strain FRCl were also detected in a U(VI)-reducing enrichment culture derived from the same sediment. Cells of strain FRCl were gram-negative motile regular rods 2.0 to 3.4 micro m long and 0.7 to 0.9 microm in diameter. Strain FRCl was positive for indole production, by the methyl red test, and for ornithine decarboxylase; it was negative by the Voges-Proskauer test (for acetylmethylcarbinol production), for urea hydrolysis, for arginine dihydrolase, for lysine decarboxylase, for phenylalanine deaminase, for H(2)S production, and for gelatin hydrolysis. Strain FRCl was capable of using O(2), NO(3)(-), S(2)O(3)(2-), fumarate, and malate as terminal electron acceptors and of reducing U(VI) in the cell suspension. Analysis of the 16S rDNA sequence of the isolate indicated that this strain was 96.4% similar to Salmonella bongori and 96.3% similar to Enterobacter cloacae. Physiological and phylogenetic analyses suggested that strain FRCl belongs to the genus Salmonella and represents a new species, Salmonella subterranea sp. nov.

Crystalline phase in the ultrahigh molecular‐weight polyethylene gel solution and xerogel

AbstractThe transverse and longitudinal sizes of crystallites in thermoreversible polyethylene gels and xerogels were measured using wide‐angle X‐ray scattering and a low‐frequency Raman spectroscopy, and were found to be 10–40 and 4–5 nm, respectively. The experimental data evidence the imperfection of primary crystallites in both dimensions. The gel‐to‐solid transition results in gaining the direct interaction between crystalline entities with increasing the cracking, on the one hand, and forming the clusters of stacked crystalline platelets linked with regular molecular rods, on the other hand. These contact interaction leads, in addition, to the coiling of a great part of regular sequences that emanate from the crystallite cores to the amorphous region. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 373–378, 2003

CMEIAS: A Computer-Aided System for the Image Analysis of Bacterial Morphotypes in Microbial Communities.

A major challenge in microbial ecology is to develop reliable and facile methods of computer-assisted microscopy that can analyze digital images of complex microbial communities at single cell resolution, and compute useful quantitative characteristics of their organization and structure without cultivation. Here we describe a computer-aided interactive system to analyze the high degree of morphological diversity in growing microbial communities revealed by phase-contrast microscopy. The system, called "CMEIAS" (Center for Microbial Ecology Image Analysis System) consists of several custom plug-ins for UTHSCSA ImageTool, a free downloadable image analysis program operating on a personal computer in a Windows NT environment. CMEIAS uses various measurement features and two object classifiers to extract size and shape measurements of segmented, digital images of microorganisms and classify them into their appropriate morphotype. The first object classifier uses a single measurement feature to analyze relatively simple communities containing only a few morphotypes (e.g., regular rods, cocci, filaments). A second new hierarchical tree classifier uses an optimized subset of multiple measurement features to analyze significantly more complex communities containing greater morphological diversity than ever before possible. This CMEIAS shape classifier automatically categorizes each cell into one of 11 predominant bacterial morphotypes, including cocci, spirals, curved rods, U-shaped rods, regular straight rods, unbranched filaments, ellipsoids, clubs, rods with extended prostheca, rudimentary branched rods, and branched filaments. The training and testing images for development and evaluation of the CMEIAS classifier were obtained from 1,937 phase-contrast grayscale digital images of various diverse communities. The CMEIAS shape classifier had an accuracy of 96.0% on a training set of 1,471 cells and 97.0% on a test set of 4,270 cells representing all 11 bacterial morphotype classes, indicating that accurate classification of rich morphological diversity in microbial communities is now possible. An interactive edit feature was added to address the main sources of error in automatic shape classification, enabling the operator to inspect the assigned morphotype of each bacterium based on visual recognition of its distinctive pseudocolor, reassign it to another morphotype class if necessary, and add up to five other morphotypes to the classification scheme. The shape classifier reports on the number and types of different morphotypes present and the abundance among each of them, thus providing the data needed to compute the morphological diversity within the microbial community. An example of how CMEIAS can augment the analysis of microbial community structure is illustrated by studies of morphological diversity as an indicator of dynamic ecological succession following a nutrient shift-up perturbation in two continuously fed, anaerobic bioreactors with morphologically distinct start communities. Various steps to minimize the limitations of computer-assisted microscopy to classify bacterial morphotypes using CMEIAS are described. In summary, CMEIAS is an accurate, robust, flexible semiautomatic computing tool that can significantly enhance the ability to quantitate bacterial morphotype diversity and should serve as a useful adjunct to the analysis of microbial community structure. This first version of CMEIAS will be released as free, downloadable plug-ins so it can provide wide application in studies of microbial ecology.

THE BACTERIAL FLORA IN BOTTLED NATURAL MINERAL WATER SOLD IN ITALY

ABSTRACTThe heterotrophic plate counts of 31 glass and 40 plastic (PVC) bottled mineral waters were examined and found to be generally low. The bacterial flora, isolated from Plate Count Agar plates, incubated at 37C, was composed of gramnegative, nonfermentative rods, gram‐positive, catalase positive cocci and gram‐positive, regular and irregular rods. Indicator pathogenic bacteria were analyzed both with the standard method and after resuscitation. Neither fecal streptococci nor Pseudomonas aeruginosa were isolated from any of the sample examined; coliform were found with either the standard or resuscitation method, while Staphylococcus aureus was detected only with the resuscitation method. The results obtained indicate the need of using, as routine, the resuscitation treatment to recover the injured indicator or pathogenic organisms.

Limited range fractality of randomly adsorbed rods

Multiple resolution analysis of two dimensional structures composed of randomly adsorbed penetrable rods, for densities below the percolation threshold, has been carried out using box-counting functions. It is found that at relevant resolutions, for box sizes, r, between cutoffs given by the average rod length 〈l〉 and the average inter-rod distance r1, these systems exhibit apparent fractal behavior. It is shown that unlike the case of randomly distributed isotropic objects, the upper cutoff r1 is not only a function of the coverage but also depends on the excluded volume, averaged over the orientational distribution. Moreover, the apparent fractal dimension also depends on the orientational distributions of the rods and decreases as it becomes more anisotropic. For box sizes smaller than 〈l〉 the box counting function is determined by the internal structure of the rods, whether simple or itself fractal. Two examples are considered—one of regular rods of one dimensional structure and rods which are trimmed into a Cantor set structure which are fractals themselves. The models examined are relevant to adsorption of linear molecules and fibers, liquid crystals, stress induced fractures, and edge imperfections in metal catalysts. We thus obtain a distinction between two ranges of length scales: r<〈l〉, where the internal structure of the adsorbed objects is probed and 〈l〉<r<r1, where their distribution is probed, both of which may exhibit fractal behavior. This distinction is relevant to the large class of systems which exhibit aggregation of a finite density of fractal-like clusters, which includes surface growth in molecular beam epitaxy and diffusion-limited-cluster-cluster-aggregation models.

The relative abundance and seawater requirements of gram-positive bacteria in near-shore tropical marine samples

The relative abundance of gram-positive bacteria in a variety of near-shore marine samples was determined using the KOH method. Gram-positive bacteria accounted for 14%, 25%, 31 %, and 12%, respectively, of the colony-forming bacteria obtained from seawater, sediments, and the surfaces of algae and invertebrates. A total of 481 gram-positive strains were isolated representing a wide range of morphological groups including regular and irregular rods, cocci, and actinomycetes. Seventy-seven percent of the strains characterized did not form spores and were aerobic, catalase-positive rods with regular to irregular cell morphologies. Eighty-two percent of the strains tested showed an obligate requirement of seawater for growth. None of the cocci tested required seawater or sodium for growth. This is the first report documenting that gram-positive bacteria can compose a large percentage of the culturable, heterotrophic bacteria associated with the surfaces of tropical marine algae.

Phylogenetic relationship of the fish pathogenic Renibacterium salmoninarum to Arthrobacter, Micrococcus and related taxa

The phylogenetic position of the obligate fish pathogenic Gram-positive eubacterium Renibacterium salmoninarum was determined by the 16S ribosomal RNA cataloguing approach. Comparison of the catalogue to those of more than 165 Gram-positive organisms from 50 genera revealed that R. salmoninarum is a member of the actinomycetes subdivision. As derived from similarity coefficients (SAB values), this organism is related to a subgroup harbouring morphologically and chemotaxonomically rather heterogeneous taxa, including Anthrobacter, Micrococcus, Cellulomonas, Jonesia, Promicromonospora, Stomatococcus and Brevibacterium. Thus, the inclusion of organisms characterized by regular rods increases the phenotypic variability of this phylogenetically coherent group.

Phylogenetic relationship of the fish pathogenicRenibacterium salmoninarumtoArthrobacter, Micrococcusand related taxa

The phylogenetic position of the obligate fish pathogenic Gram-positive eubacterium Renibacterium salmoninarum was determined by the 16S ribosomal RNA cataloguing approach. Comparison of the catalogue to those of more than 165 Gram-positive organisms from 50 genera revealed that R. salmoninarum is a member of the actinomycetes subdivision. As derived from similarity coefficients (SAB values), this organism is related to a subgroup harbouring morphologically and chemotaxonomically rather heterogeneous taxa, including Anthrobacter, Micrococcus, Cellulomonas, Jonesia, Promicromonospora, Stomatococcus and Brevibacterium. Thus, the inclusion of organisms characterized by regular rods increases the phenotypic variability of this phylogenetically coherent group.

Oligotrophic bacteria from rendzina forest soil.

Oligotrophic bacteria were shown to exist abundantly in all layers of a rendzina forest soil throughout the year. Two-hundred-three oligotrophic bacteria were isolated from forest soil (Aoba, Sendai) at different layers (L, F, H and A layers) throughout the year, and their morphological and physiological characteristics were examined. A high proportion (95%) of the isolated oligotrophs were Gram-negative, non-spore forming bacteria. Based on the cell shape, the isolates were divided into four groups: regular rods, curved/spiral bacteria, irregular rods, and buddin and/or prosthecate bacteria. Each group of bacteria is discussed in relation to the physiological characteristics. Notably oligotrophic bacteria of different cell types showed a marked zonal distribution in respect to profile depth.

Changes in the bacterial community after application of oily sludge to soil

The changes in the bacterial flora after application of oily sludge and fertilizer to two different soils, both sandy, but one somewhat richer in organic material, have been studied. Application of oily sludge and fertilizer to the soils had no influence on direct counts. The CFUs increased in the low-organic soil when sludge was applied, but did not change in the richer soil by the same treatment. When both sludge and fertilizer were applied together, strong increases in CFUs were found in both soils. Application of fertilizer together with sludge excluded sporeforming rods and actinomycetes from the poorer soil and strongly stimulated pleomorphic rods+ cocci and non-sporeforming regular rods. The same treatment of the richer soil resulted in an enhancement of CFUs of all tested groups.

Isolation and characterization of alkaline phosphatase-containing granules (phosphasomes) from human polymorphonuclear leucocytes.

Human polymorphonuclear leucocytes were homogenized in isotonic sucrose and subjected to analytical subcellular fractionation by centrifugation on a discontinuous sucrose density gradient to produce a phosphasome-enriched fraction, contaminated primarily by plasma membrane. Experiments to separate these membrane fractions by centrifugation on gradients of Nycodenz or Percoll, or by toroidal coil counter current chromatography, were unsuccessful. Fractionation carried out on neutrophils previously suspended in isotonic sucrose containing a low concentration of digitonin resulted in the preparation of a highly purified phosphasome fraction, free of plasma membrane components. Electron-microscope cytochemistry of the purified fraction identified the phosphasomes as regular and irregular-shaped spheres and rods, the alkaline phosphatase being associated with the inner aspect of the vesicle membrane. These granule structures were very similar to phosphasomes observed in intact neutrophils. A proportion of the endoplasmic reticulum and Golgi membrane marker enzymes remained associated with the phosphasomes throughout the separation procedures.

Oligotrophic bacteria on organic debris and plant roots in a paddy field soil

The distribution of heterotrophic bacteria on organic debris and roots of rice plants in a paddy field were studied. The heterotrophic bacteria consisted of two main groups: those which grew on full-strength nutrient broth (NB) and those which did not grow on NB but on a 100-fold dilution of NB (DNB). The latter group was called ‘DNB organisms’ and were considered to be oligotrophic. In both manured and unmanured soils, DNB organisms were predominant in the bacterial communities on organic debris and the rice roots throughout most of the entire period of rice cultivation, although a transient decrease in the proportion of DNB organisms was observed immediately after an application of manure. Morphological and physiological characteristics of DNB isolates from organic debris and rice roots were studied: five types of cell shape were observed, (1) regular rods, (2) filament-forming rods, (3) irregular rods, (4) prosthecate organisms and (5) large oval cells. Regular rods (42% of the total DNB isolates) and irregular rods (46%) were abundant. The ecological roles of DNB organisms in paddy soil are discussed in relation to their physiological characteristics.

Gravitational field of vacuum domain walls and strings

The gravitational properties of vacuum domain walls and strings are studied in the linear approximation of general relativity. These properties are shown to be very different from those of regular massive planes and rods. It is argued that the domain walls are gravitationally unstable and collapse at a certain time $\ensuremath{\sim}{t}_{c}$ after their creation. If the vacuum walls ever existed, they must have disappeared at $t<{t}_{c}$.

Nebela tuberculata comb. nov. (Arcellinida), its History and Ultrastructure

SYNOPSIS. The name Nebela tuberculata comb. nov. is proposed for the testate ameba formerly known as Difflugia tuberculata (Wallich, 1864) Archer, 1867. The generic reassignment is based upon the test construction material which is shown, by electronmicrographs and X‐ray diffraction, to be autogenous regular and irregular silicious rods. A brief history of the animal is recounted utilizing works of several authors who have encountered the ameba over the last century.

Correlation between morphology and stress—strain properties of three block copolymers i. stress-softening effect

The stress-softening effect, which comes out when SBS three block copolymers are stretched, is taken into consideration and the conclusion is reached that it is due to a disruption of the polystyrene continuous phase, according to the hypothesis of other authors. This conclusion is supported by two kinds of experiments performed on samples having a well known and simple morphology. First of all by stress-strain measurements on specimens previously swollen: it can be seen that the stress-softening effect disappears as soon as the structure of the material is completely modified by the treatment. Secondly by the direct observation at the electron microscope of the structure after the deformation. This shows how the original continuous and regular polystyrene rods of the “single crystal” assume a string of pearl structure which finally is irreversibly disrupted.

Cell division, macromolecular synthesis and morphology dependent on the state of the envelope in a mutant of Klebsiella pneumoniae.

SUMMARY: Mutant Mir M7 of Klebsiella pneumoniae exhibits a pH-dependent morphological interconversion; growing cells are rod-shaped at pH 5·5 but round at pH 7. Round cells cannot divide or make DNA, RNA and proteins at pH 5·5. At this pH, cell division and DNA synthesis are resumed either when substances such as Mg2+, Na+, sucrose or spermine are added to the growth medium or immediately after the appearance of a normal rod morphology. Round cells, but not rods or the wild type, are lysed by low concentrations of detergents and are killed by Mdl-amino acids. Their growth rate is not improved by vigorous aeration and they make spheroplasts at an incubation temperature of 8 °C. This behaviour is the opposite of that of rods and the original strain. The transition from rods to round cells at pH 7 does not occur when cell division is inhibited by penicillin. Round cells must divide several times in an acid medium to give regular and uniform rods. The possibility of a different state of the membrane in round and rod-shaped cells and a dependence of cell division, DNA synthesis, and morphology on the state of the membrane are discussed.

Reversible Denaturierung des Proteins aus Tabakmosaikvirus

The protein of TMV is denaturated after extraction by phenol, precipitation with methanol and resolution in 0.1 M NaOH or 8 M urea. The denaturated protein could be transformed to the native state. The following criteria were used for the differentiation between the denaturated and the native state: solubility in neutral aqueous medium, aggregation to regular viruslike rods, reconstitution to infectious virus with ribonucleic acid and the serological specificity.

The development of the straight rod type of Lactobacillus bifidus.

Summary: Microscopical examinations of several Lactobacillus bifidus strains have shown that the ‘bifid’ morphology of the cells, which seems to predominate in vivo, is readily changed on subcultivation in different media in vitro. At first highly branched and larger forms occur, and from these mycelial branched filaments develop. The mycelial cells may swell, in which case intensely staining coccoid granules can be detected in the cells. Ultimately, the filaments break up, and give rise to the development of regular short straight rods. Obviously these straight rods appear from the coccoid granules.