GROWTH REQUIREMENTS OF BACTERIAL VIRUSES

Enhancing plant growth in biofertilizer-amended soil through nitrogen-transforming microbial communities

Biofertilizers have immense potential for enhancing agricultural productivity. However, there is still a need for clarification regarding the specific mechanisms through which these biofertilizers improve soil properties and stimulate plant growth. In this research, a bacterial agent was utilized to enhance plant growth and investigate the microbial modulation mechanism of soil nutrient turnover using metagenomic technology. The results demonstrated a significant increase in soil fast-acting nitrogen (by 46.7%) and fast-acting phosphorus (by 88.6%) upon application of the bacterial agent. This finding suggests that stimulated soil microbes contribute to enhanced nutrient transformation, ultimately leading to improved plant growth. Furthermore, the application of the bacterial agent had a notable impact on the accumulation of key genes involved in nitrogen cycling. Notably, it enhanced nitrification genes (amo, hao, and nar), while denitrification genes (nir and nor) showed a slight decrease. This indicates that ammonium oxidation may be the primary pathway for increasing fast-acting nitrogen in soils. Additionally, the bacterial agent influenced the composition and functional structure of the soil microbial community. Moreover, the metagenome-assembled genomes (MAGs) obtained from the soil microbial communities exhibited complementary metabolic processes, suggesting mutual nutrient exchange. These MAGs contained widely distributed and highly abundant genes encoding plant growth promotion (PGP) traits. These findings emphasize how soil microbial communities can enhance vegetation growth by increasing nutrient availability and regulating plant hormone production. This effect can be further enhanced by introducing inoculated microbial agents. In conclusion, this study provides novel insights into the mechanisms underlying the beneficial effects of biofertilizers on soil properties and plant growth. The significant increase in nutrient availability, modulation of key genes involved in nitrogen cycling, and the presence of MAGs encoding PGP traits highlight the potential of biofertilizers to improve agricultural practices. These findings have important implications for enhancing agricultural sustainability and productivity, with positive societal and environmental impacts.

Isolation, discrimination, and molecular detection of Listeria species from slaughtered cattle in Namwala District, Zambia

BACKGROUND

The food industry is increasingly becoming more scrutinized, given the frequency and intensity with which zoonotic diseases are being reported. Pathogen tracking has become more applicable with regards food safety. It is in this regard that the present study was formulated to track Listeria species. in freshly slaughtered cattle carcasses by utilizing standard and molecular biological techniques.

METHODS

A cross-sectional study design was conducted from March to December 2020 with 200 samples being equally collected in the rainy and dry seasons. A total of 180 and 20 swabs were aseptically collected from carcasses and the environment respectively. Samples were first subjected to pre-enrichment in half-strength Fraser broth followed by enrichment in full strength Fraser broth and subsequent plating on Listeria agar. Listeria growth characteristics were identified up to species level based on their morphological and biochemical characteristics. Further, molecular detection and phylogenetic analysis was conducted. Quantitative proportionate survey data were analyzed using Stata Version 15 software to estimate crude prevalence taking into account complex design at abattoir level. Factors associated with contamination were characterized using logistic regression. Sequences were analyzed using, Genetyyx version 12 and phylogenetic Mega.

RESULTS

Of the 200 samples, 19 were positive for Listeria species identified as L.innocua 14/19 (73.7%) and L. monocytogenes 5/19 (26.3%). All isolates were from freshly slaughtered carcasses, and none from environment. Siginificant differences in contamination levels were observed based on season: rainy season yielded 14 (73.6%) whilst the dry season 5 (26.3%). The L. monocytogenes strains showed a high degree of homogeneity on phylogenetic analysis and clustered based on abattoir. Seasonality was identified as a major determinant influencing contamination based on the final logistic regression model.

CONCLUSION

This study found evidence of L. monocytogenes contamination on traditionally raised beef carcasses across various abattoirs surveyed. The failure to find Listeria contamination on the abattoir environment may to a greater extent intimate cattle carccases as primary sources of contamination. However, a more comprerehnsive study incorporating different geographical regions is needed to conclusively ascertain these present findings.

The Production and Analysis of Biodegradable Polymers of Type of Medium-Chain-Length Polyhydroxyalkanoates (mcl-PHA) by Pseudomonas putida Strain for the Biomedical Engineering

BACKGROUND

Polyhydroxyalkanoates (PHAs) are bacteria-synthetized biopolymers under unbalanced growth conditions. These biopolymers are considered potential biomaterials for future applications for their biocompatibility and biodegradable features and potential biomaterials for future applications for their biocompatibility and biodegradable characteristics and their ability to be quickly produced and functionalize with strong mechanical resistance. This article is intended to perform microbial fermentation using Pseudomonas putida strain to show the amount of biopolymers of the type polyhydroxyalkanoates with medium-chain-length (mcl-PHA) obtained depending on the type and quantity of added precursors (glucose and fatty acids).

METHODS

It is important to understand the microbial interaction and mechanism involved in PHA biosynthetis.For these, several methods were used, such as: obtaining microbial biomass by using a Pseudomonas putida strain able of PHA-producing, analysis of biopolymer production by acetone extraction following the Soxhlet method, purification of biopolymer by methanol-ethanol treatment, followed by the estimation of biomass by spectrophotometric analysis and the measurement of the dry weight of cells and the quantification of the amount of biopolymer produced following the gas chromatographic method (GC).

RESULTS

The highest PHA yield was obtained using octanoic (17 mL in 2000 mL medium) and hexanoic acids (14 mL in 2000 mL medium) as precursors. Consequently, octanoic acid - octanoic acid, heptanoic acid - nonanoic acid, and octanoic acid - hexanoic acid were the mix of precursors that supported the amount of PHA obtained.

CONCLUSION

Of the 4 types of structurally related substrate, the strain Pseudomonas putida ICCF 319 prefers the C8 sublayer for an elastomeric PHA's biosynthesis with a composition in which the C8 monomer predominates over C6 and C10.

Microbial Arsenal of Antiviral Defenses - Part I

Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). Constant threat of phage infection is a major force that shapes evolution of the microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering have been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection, with a focus on novel systems discovered in recent years. First chapter covers defense associated with cell surface, role of small molecules, and innate immunity systems relying on DNA modification.

A growing microcolony can survive and support persistent propagation of virulent phages

Bacteria form colonies and secrete extracellular polymeric substances that surround the individual cells. These spatial structures are often associated with collaboration and quorum sensing between the bacteria. Here we investigate the mutual protection provided by spherical growth of a monoclonal colony during exposure to phages that proliferate on its surface. As a proof of concept we exposed growing colonies of Escherichia coli to a virulent mutant of phage P1. When the colony consists of less than [Formula: see text]50,000 members it is eliminated, while larger initial colonies allow long-term survival of both phage-resistant mutants and, importantly, colonies of mostly phage-sensitive members. A mathematical model predicts that colonies formed solely by phage-sensitive bacteria can survive because the growth of bacteria throughout the colony exceeds the killing of bacteria on the surface and pinpoints how the critical colony size depends on key parameters in the phage infection cycle.

Bio-Control of Salmonella Enteritidis in Foods Using Bacteriophages

Two lytic phages, vB_SenM-PA13076 (PA13076) and vB_SenM-PC2184 (PC2184), were isolated from chicken sewage and characterized with host strains Salmonella Enteritidis (SE) ATCC13076 and CVCC2184, respectively. Transmission electron microscopy revealed that they belonged to the family Myoviridae. The lytic abilities of these two phages in liquid culture showed 104 multiplicity of infection (MOI) was the best in inhibiting bacteria, with PC2184 exhibiting more activity than PA13076. The two phages exhibited broad host range within the genus Salmonella. Phage PA13076 and PC2184 had a lytic effect on 222 (71.4%) and 298 (95.8%) of the 311 epidemic Salmonella isolates, respectively. We tested the effectiveness of phage PA13076 and PC2184 as well as a cocktail combination of both in three different foods (chicken breast, pasteurized whole milk and Chinese cabbage) contaminated with SE. Samples were spiked with 1 × 10(4) CFU individual SE or a mixture of strains (ATCC13076 and CVCC2184), then treated with 1 × 10(8) PFU individual phage or a two phage cocktail, and incubated at 4 °C or 25 °C for 5 h. In general, the inhibitory effect of phage and phage cocktail was better at 4 °C than that at 25 °C, whereas the opposite result was observed in Chinese cabbage, and phage cocktail was better than either single phage. A significant reduction in bacterial numbers (1.5-4 log CFU/sample, p < 0.05) was observed in all tested foods. The two phages on the three food samples were relatively stable, especially at 4 ºC, with the phages exhibiting the greatest stability in milk. Our research shows that our phages have potential effectiveness as a bio-control agent of Salmonella in foods.

Resources, mortality, and disease ecology: Importance of positive feedbacks between host growth rate and pathogen dynamics

Resource theory and metabolic scaling theory suggest that the dynamics of a pathogen within a host should strongly depend upon the rate of host cell metabolism. Once an infection occurs, key ecological interactions occur on or within the host organism that determine whether the pathogen dies out, persists as a chronic infection, or grows to densities that lead to host death. We hypothesize that, in general, conditions favoring rapid host growth rates should amplify the replication and proliferation of both fungal and viral pathogens. If a host population experiences an increase in mortality, to persist it must have a higher growth rate, per host, often reflecting greater resource availability per capita. We hypothesize that this could indirectly foster the pathogen, which also benefits from increased within-host resource turnover. We first bring together in a short review a number of key prior studies which illustrate resource effects on viral and fungal pathogen dynamics. We then report new results from a semi-continuous cell culture experiment with SHIV, demonstrating that higher mortality rates indeed can promote viral proliferation. We develop a simple model that illustrates dynamical consequences of these resource effects, including interesting effects such as alternative stable states and oscillatory dynamics. Our paper contributes to a growing body of literature at the interface of ecology and infectious disease epidemiology, emphasizing that host abundances alone do not drive community dynamics: the physiological state and resource content of infected hosts also strongly influence host-pathogen interactions.

Chemical studies in host-virus interactions; a comparison of some properties of three mutant pairs of bacterial viruses, T2r and T2r, T4r and T4r, T6r and T6r

Various chemical and physiological aspects of the reproductive cycles of r⁺ and r strains of T2, T4, and T6 viruses have been examined and compared. These include the ultraviolet absorption spectra in which differences between r and r⁺ strains were not observed, though they were obtained in the case of T2, T4, and T6. Adsorption of T4 and T6 was found to require the adsorption cofactor l-tryptophane. Among the r and r⁺ strains of these viruses limiting tryptophane requirements for adsorption were found to be different. Some differences were observed in the one-step growth curves of these viruses under conditions of single and multiple infection. The turbidity-time relations of infected cultures were characteristically different. The rates of DNA and protein synthesis in the infected cells were found to be independent of the viruses used. Certain implications of the data have been discussed.

Chemical studies in host-virus interactions; the mutual reactivation of T2r virus inactivated by ultraviolet light and the synthesis of desoxyribose nucleic acid

A method has been described for following purine and pyrimidine synthesis in intact cells by measuring the ultraviolet absorption of a bacterial suspension. It has been shown that in cells infected with active virus, the rate of increase of ultraviolet absorption at 2600 Å corresponded to that of DNA, although preceding DNA synthesis slightly. The amount of separation of the curves in time was determined by the multiplicity of infection. Under conditions of mutual reactivation of ultraviolet-irradiated virus, DNA synthesis was inhibited but not the increase in ultraviolet absorption. Thus a continuing purine and pyrimidine synthesis was indicated by the increase in this function. When an intact virus particle could be found within these bacteria, however, DNA synthesis began at the rate characteristic of normal infections. Certain peculiarities of lysis in this system were noted. The significance of these observations for various genetic theories has been discussed. It would appear that Luria's hypothesis of independent gene pool synthesis has probably been disproven. It has also been shown that the lesion produced by irradiation of a virus particle with ultraviolet light probably occurs in the DNA of the particle. The validity of these conclusions will depend on a knowledge of the relation of virus protein synthesis to DNA synthesis in this system.

The intracellular growth of bacteriophages. I. Liberation of intracellular bacteriophage T4 by premature lysis with another phage or with cyanide

A method is described for liberating and estimating intracellular bacteriophage at any stage during the latent period by arresting phage growth and inducing premature lysis of the infected cells. This is brought about by placing the infected bacteria into the growth medium supplemented with 0.01 M cyanide and with a high titer T6 lysate. It was found in some of the later experiments that the T6 lysate is essential only during the first half of the latent period. Cyanide alone will induce lysis during the latter part of the latent period. Using this method on T4-infected bacteria it is found that during the first half of the latent period no phage particles, not even those originally infecting the bacteria, are recovered. This result is in agreement with the gradually emerging concept that a profound alteration of the infecting phage particle takes place before reproduction ensues. During the second half of the latent period mature phage is found to accumulate within the bacteria at a rate which is parallel to the approximately linear increase of intracellular DNA in this system. However, the phage production lags several minutes behind DNA production. When 5-methyltryptophan replaced cyanide as the metabolic inhibitor, similar results were obtained. The curves were, however, displaced several minutes to the left on the time axis. The results are compared with Latarjet's (16) data on x-radiation of infected bacteria and with Foster's data (18) concerning the effect of proflavine on infected bacteria. Essential agreement with both is apparent.

Effects of Escherichia coli physiology on growth of phage T7 in vivo and in silico

Phage development depends not only upon phage functions but also on the physiological state of the host, characterized by levels and activities of host cellular functions. We established Escherichia coli at different physiological states by continuous culture under different dilution rates and then measured its production of phage T7 during a single cycle of infection. We found that the intracellular eclipse time decreased and the rise rate increased as the growth rate of the host increased. To develop mechanistic insight, we extended a computer simulation for the growth of phage T7 to account for the physiology of its host. Literature data were used to establish mathematical correlations between host resources and the host growth rate; host resources included the amount of genomic DNA, pool sizes and elongation rates of RNA polymerases and ribosomes, pool sizes of amino acids and nucleoside triphosphates, and the cell volume. The in silico (simulated) dependence of the phage intracellular rise rate on the host growth rate gave quantitatively good agreement with our in vivo results, increasing fivefold for a 2.4-fold increase in host doublings per hour, and the simulated dependence of eclipse time on growth rate agreed qualitatively, deviating by a fixed delay. When the simulation was used to numerically uncouple host resources from the host growth rate, phage growth was found to be most sensitive to the host translation machinery, specifically, the level and elongation rate of the ribosomes. Finally, the simulation was used to follow how bottlenecks to phage growth shift in response to variations in host or phage functions.

Nucleuc acid synthesis in types 4 and 5 adenovirus-infected HeLa cells

Type 4 adenovirus infection of HeLa cells effected a marked increase in synthesis of the saline-soluble DNA fraction, but not the host-cell DNA (the water-soluble fraction). This was demonstrated by the marked increase in specific activity of saline-soluble DNA but not water-soluble DNA when P³²-inorganic phosphate or sodium formate-C¹⁴ was employed. When these isotopes were used to label cells before viral infection rather than during the process of viral propagation, the saline-soluble DNA from infected cells had a specific activity of 10 to 20 per cent less than that of uninfected cells, indicating that the saline-soluble DNA was synthesized both from prelabeled precursors of the cell pools and unlabeled materials from the medium. Saline-soluble DNA began to increase between 10 to 12 hours after viral infection and 3 to 4 hours before appearance of newly propagated infectious virus. The specific activity of the acid-soluble pool of infected cells also increased between 10 to 12 hours after viral inoculation when sodium formate-C¹⁴ was used as a radioisotope. When P³²-inorganic phosphate was utilized, the specific activity of infected-cell RNA was increased approximately the same relative amount as when total RNA was determined chemically; i.e., 30 to 40 per cent. With type 5 adenovirus, not only did a 3- to 5-fold increase in saline-soluble DNA occur, but also an increase was measured in specific activity of RNA when P³²-inorganic phosphate was used.

INHIBITORY ACTION OF PHAGE K ON STAPHYLOCOCCAL DEHYDROGENASES. II. ITS POSSIBLE RELATIONSHIP TO SENSITIZATION AND CELL LYSIS

Ralston, D. J. (University of California, Berkeley) and M. D. Perry. Inhibitory action of phage K on staphylococcal dehydrogenases. II. Its possible relationship to sensitization and cell lysis. J. Bacteriol. 86:740-748. 1963.-By measuring the reduction of the dye triphenyl tetrazolium chloride to the insoluble red formazan, an analysis was made of the inhibition by phage K of the dehydrogenase capacity of populations of Staphylococcus aureus K(1), to determine to what extent this might be associated with the ability of phage K to sensitize the cells-a reaction characterized by the conversion of the cell wall to susceptibility to lysis by the staphylococcal enzyme, virolysin. Increasing multiplicities of phage progressively increased the fractions of sensitized cells and also caused increasing inhibition of the dehydrogenase activity of the populations. The dehydrogenase activities of the sensitized fractions were compared with those of the nonsensitized fractions. Over a wide range of phage-bacterium ratios, the dehydrogenase activities of the sensitized fractions were found to be lower than those of the nonsensitized fractions. Microscopically, this was reflected by the appearance of large numbers of cells with a reduced amount of visible formazan granules. When lysin was added to the phage-treated cells, lysis occurred mainly from cell fractions which possessed little or no tetrazolium-reducing capacity. The data indicated that sensitization by phage was accompanied by a marked decrease in cellular dehydrogenase activity but was not associated with a complete inhibition of these enzymes. A comparison was made between the dehydrogenases of phage-sensitized cells and cells found to be "spontaneously" sensitive to virolysin, i.e., lysed by the enzyme without any prior exposure to phage. Like phage-sensitized cells, the spontaneously sensitized staphylococci possessed low dehydrogenase activity and lacked the capacity to support phage synthesis. In tests of a given cell preparation, the dehydrogenase levels of the phage-sensitized fractions were found to be close to, or even lower than, the level of the spontaneously sensitized fraction, suggesting that in S. aureus K(1) the sensitized state is associated in some manner with a reduction of the dehydrogenase activity to a critical level. There is as yet no evidence for any direct causal relationship between sensitization and dehydrogenase inhibition.

Whole-virus vaccine development by continuous culture on a complementing host

We have evaluated an adaptive strategy for generating whole-virus vaccines using a bacteriophage model. Wildtype phage T7 was cultivated in a two-stage continuous stirred-tank reactor (CSTR) utilizing a recombinant E. coli host that constitutively expressed T7 RNA polymerase, an essential enzyme of the early viral metabolism. Over the course of 180 generations a diversity of phage variants emerged, outgrew the wildtype, and were subsequently eclipsed by yet fitter variants, based on host-ranges, restriction patterns, and one-step growth responses of isolated clones. The fittest variant, which required complementation by the recombinant host in order to grow, deleted at least 12 percent of its genome and replicated twice as fast as the wildtype. Moreover, this variant was immunogenically indistinguishable from the wildtype, based on cross-reactivities of antisera raised against both. These results suggest the feasibility of the proposed strategy for the development of safe whole-virus vaccines.

Genetics of Rhodospirillaceae

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Phage Growth and Deoxyribonucleic Acid Synthesis in Escherichia coli Infected by a Thymine-Requiring Bacteriophage

Mathews, Christopher K. (Yale University, New Haven, Conn.). Phage growth and deoxyribonucleic acid synthesis in Escherichia coli infected by a thymine-requiring bacteriophage. J. Bacteriol. 90: 648–652. 1965.—Cultures of Escherichia coli B infected with a mutant strain of phage T4 which cannot induce the formation of thymidylate synthetase produce deoxyribonucleic acid (DNA) at about two-thirds the rate of cultures infected with the parent strain. Under certain conditions the yield of viable phage observed with the mutant is one-third of that brought about by the wild-type strain. Addition of thymine increases both DNA synthesis and phage production in cells infected by the mutant. It is suggested that the ability to induce thymidylate synthetase formation in infected cells confers a selective advantage on the wild-type strain.

KINETICS OF SYNTHESIS OF VARIOUS TYPES OF ANTIGENIC PROTEINS IN CELLS INFECTED WITH PSEUDORABIES VIRUS

Hamada, Chuya (Albert Einstein Medical Center, Philadelphia, Pa.), and Albert S. Kaplan. Kinetics of synthesis of various types of antigenic proteins in cells infected with pseudorabies virus. J. Bacteriol. 89:1328-1334. 1965.-By means of an indirect precipitation test, a determination was made of the rates of synthesis of various types of serologically specific proteins in rabbit kidney cells infected with pseudorabies virus. The rate of synthesis of cell-specific protein decreased after infection. During the early stages of the infective process, proteins which bear no precursor relationship to the viral particles (nonstructural viral proteins) and which cannot be detected in noninfected cells were formed. Almost concurrently with these nonstructural proteins, synthesis of virus precursor proteins began. The synthesis of these proteins preceded the formation of mature virus and continued until the end of the virus growth cycle.

RIFAMYCIN. XXXIII. ISOLATION OF ACTINOPHAGES ACTIVE ON STREPTOMYCES MEDITERRANEI AND CHARACTERISTICS OF PHAGE-RESISTANT STRAINS

Five actinophages highly specific for Streptomyces mediterranei were isolated from lysed broth cultures. Studies were performed on the effect of plating conditions on plaque formation. The development of phage-resistant strains of S. mediterranei not only eliminated the phage but also significantly increased rifamycin yields. The phage-resistant cultures proved to be more unstable than the original sensitive strain. Maintenance of the cultures as frozen vegetative mycelium assured culture stability and reproducibility of the results. Strict aseptic precautions throughout the laboratories and fermentation areas did not eliminate the danger of phage infection; effective control was obtained only with the introduction of resistant strains. S. mediterranei phages proved to be highly specific for calcium as an adsorption cofactor; addition of calcium-sequestering agents to sensitive mycelium completely prevented its lysis by the phage. The resistant strains developed were capable of adsorbing the phage and of releasing it without multiplication upon aging of the mycelium. No marked morphological, cultural, or biochemical differences were found among the various phage-resistant strains.

The protein coats or ghosts of coli phage T2. II. The biological functions

Phage coats or ghosts, composed entirely of protein, appear to be responsible for protecting the phage nucleic acid from degradation by factors in the surrounding medium; attachment of the virus to its susceptible host; and delivering the nucleic acid to the interior of the cell. In addition, the ghosts have a number of biological actions which resemble similar actions of the parent phage. Thus, they both "kill" cells, inhibit pentosenucleic acid formation, interfere with subsequent infection by other virus particles, block adaptive enzyme formation, induce or trigger lysis of the host, and cause a leakage of phosphorus-containing fragments from the cell. Results to date fail to demonstrate a direct involvement of the ghosts in the passage of genetic information to the progeny. Several of the above changes induced in the host cell following attachment of ghosts could be derived from an alteration in but a single metabolic reaction. The stoichiometry of the ghost-bacterial cell interaction is different from that of the parent phage. Experiments to distinguish between a variable response of the host cell to reaction at different sites and a state of heterogeneity in the ghost preparations suggest the former but they are not decisive.