Characterization and complete genome sequence of Privateer, a highly prolate Proteus mirabilis podophage

The Gram-negative bacterium Proteus mirabilis causes a large proportion of catheter-associated urinary tract infections, which are among the world’s most common nosocomial infections. Here, we characterize P. mirabilis bacteriophage Privateer, a prolate podophage of the C3 morphotype isolated from Texas wastewater treatment plant activated sludge. Basic characterization assays demonstrated Privateer has a latent period of ~40 min and average burst size around 140. In the 90.7 kb Privateer genome, 43 functions were assigned for the 144 predicted protein-coding genes. Genes encoding DNA replication proteins, DNA modification proteins, four tRNAs, lysis proteins, and structural proteins were identified. Cesium-gradient purified Privateer particles analyzed via LC-MS/MS verified the presence of several predicted structural proteins, including a longer, minor capsid protein apparently produced by translational frameshift. Comparative analysis demonstrated Privateer shares 83% nucleotide similarity with Cronobacter phage vB_CsaP_009, but low nucleotide similarity with other known phages. Predicted structural proteins in Privateer appear to have evolutionary relationships with other prolate podophages, in particular the Kuraviruses

Isolation and characterization of wetland VSW-3, a novel lytic cold-active bacteriophage of Pseudomonas fluorescens

Wetlands are often called the “kidneys of the Earth” and contribute substantially to environmental improvement. Pseudomonas fluorescens is a major contaminant of milk products and causes the spoilage of refrigerated foods and fresh poultry. In this study, we isolated and characterized a lytic cold-active bacteriophage named VSW-3 together with P. fluorescens SW-3 cells from the Napahai wetland in China. Electron microscopy showed that VSW-3 had an icosahedral head (56 nm) and a tapering tail (20 nm × 12 nm) and a genome size of approximate 40 kb. On the basis of the top-scoring hits in the BLASTP analysis, VSW-3 showed a high degree of module similarity to the Pseudomonas phages Andromeda and Bf7. The latent and burst periods were 45 and 20 min, respectively, with an average burst size of 90 phage particles per infected cell. The pH and thermal stability of VSW-3 were also explored. The optimal pH was found to be 7.0 and the activity decreased rapidly when the temperature exceeded 60 °C. VSW-3 is a cold-active bacteriophage, hence, it is important to research its ability to prevent product contamination caused by P. fluorescens and to characterize its relationship with its host P. fluorescens in the future.

Isolation and Characterization of an Aeromonas punctata Bacteriophage

AnAeromonas punctatabacteriophage, named as DH1, was isolated from East Lake, Wuhan city, China. Morphologically, phage DH1 showed a typicalMyoviridaestructure consisting of an isometric head (50 nm in diameter) and a visible tail. The bacteriophage had a latent period of about 90 minutes and an average burst size of about 125 PFU•Cell-1. Restriction enzyme pattern of the bacteriophage’s genome showed that the genome is a double-stranded DNA and about 34kb in size. The sequenced genomic fragments showed highly similarities to gp04 and gp16 sequence of otherMyoviridaebacteriophages at protein level.

Discrete Distributional Differential Expression (D3E) - A Tool for Gene Expression Analysis of Single-cell RNA-seq Data

The advent of high throughput RNA-seq at the single-cell level has opened up new opportunities to elucidate the heterogeneity of gene expression. One of the most widespread applications of RNA-seq is to identify genes which are differentially expressed (DE) between two experimental conditions. Here, we present a discrete, distributional method for differential gene expression (D3E), a novel algorithm specifically designed for single-cell RNA-seq data. We use synthetic data to evaluate D3E, demonstrating that it can detect changes in expression, even when the mean level remains unchanged. D3E is based on an analytically tractable stochastic model, and thus it provides additional biological insights by quantifying biologically meaningful properties, such as the average burst size and frequency. We use D3E to investigate experimental data, and with the help of the underlying model, we directly test hypotheses about the driving mechanism behind changes in gene expression.

Identification of Cyanophage Ma-LBP and Infection of the Cyanobacterium Microcystis aeruginosa from an Australian Subtropical Lake by the Virus

ABSTRACT Viruses can control the structure of bacterial communities in aquatic environments. The aim of this project was to determine if cyanophages (viruses specific to cyanobacteria) could exert a controlling influence on the abundance of the potentially toxic cyanobacterium Microcystis aeruginosa (host). M. aeruginosa was isolated, cultured, and characterized from a subtropical monomictic lake—Lake Baroon, Sunshine Coast, Queensland, Australia. The viral communities in the lake were separated from cyanobacterial grazers by filtration and chloroform washing. The natural lake viral cocktail was incubated with the M. aeruginosa host growing under optimal light and nutrient conditions. The specific growth rate of the host was 0.023 h−1; generation time, 30.2 h. Within 6 days, the host abundance decreased by 95%. The density of the cyanophage was positively correlated with the rate of M. aeruginosa cell lysis (r 2 = 0.95). The cyanophage replication time was 11.2 h, with an average burst size of 28 viral particles per host cell. However, in 3 weeks, the cultured host community recovered, possibly because the host developed resistance (immunity) to the cyanophage. The multiplicity of infection was determined to be 2,890 virus-like particles/cultured host cell, using an undiluted lake viral population. Transmission electron microscopy showed that two types of virus were likely controlling the host cyanobacterial abundance. Both viruses displayed T7-like morphology and belonged to the Podoviridiae group (short tails) of viruses that we called cyanophage Ma-LBP. In Lake Baroon, the number of the cyanophage Ma-LBP was 5.6 × 104 cyanophage · ml−1, representing 0.23% of the natural viral population of 2.46 × 107 · ml−1. Our results showed that this cyanophage could be a major natural control mechanism of M. aeruginosa abundance in aquatic ecosystems like Lake Baroon. Future studies of potentially toxic cyanobacterial blooms need to consider factors that influence cyanophage attachment, infectivity, and lysis of their host alongside the physical and chemical parameters that drive cyanobacterial growth and production.

Isolation and characterization of two bacteriophages of a stem-nodulating Rhizobium strain from Sesbania rostrata

Two rhizobiophages, RS1 and RS2, were isolated in Senegal from a soil sample and dry stem nodules of Sesbania rostrata, a tropical legume that is infected by two categories of Rhizobium strains: "stem strains," which nodulate both roots and stems (type strain, ORS571), and "root strains," which induce effective nodules only on roots. Both phages were found to have a host range restricted to ORS571; all root strains were found to be resistant. By electron microscopy, phage RS1 showed an hexagonal head 63 nm wide and a tail 87 nm long; phage RS2 revealed an hexagonal head 60 nm wide. Characterization of phage growth cycle by one-step growth experiments showed that the latent period was ca. 75 min for RS1 and ca. 4 h for RS2, that the rise period lasted ca. 2 h for both RS1 and RS2, and that the average burst size was ca. 100 for RS1 and 130 for RS2. Temperature denaturation occurred at 60–65 °C (RS1) and 45–50 °C (RS2). Serum neutralization tests revealed that the phages were not serologically related. In contrast to RS1, RS2 appeared to be temperate, since stable lysogens were isolated.

INFLUENCE OF SELECTED HERBICIDES IN PHAGES OF SOME SOIL BACTERIA

Various concentrations of paraquat, atrazine, simazine, linuron, diuron, and paraquat in combinations with each including simazine + diuron, and terbacil alone, did not inhibit lytic activity of four bacteriophages of Agrobacterium radiobacter, three bacteriophages of Rhizobium meliloti, three bacteriophages of R. trifolii, or two bacteriophages of Streptomyces chrysomallus. Generally, the herbicides had no effect on the neutralization of radiobacterphage PR-1001 with its homologous antiserum, the length of the latent period, the percent adsorption or the average burst size. In contrast, paraquat concentrations from 20 to 400 μg∙mL−1 gradually reduced the adsorption from 38 to 21% and the average burst size from 67 to 9 in the PR-1001:R-1001 phage: host system. The same concentrations, however, showed no effect on the particle attachment or the length of the latent period.

Partial characterization of a new C3-type capsule-dissolving phage of Streptococcus cremoris

A viscous, ropy, sour milk product, called 'viili,' is produced in Finland. Capsule-forming strains of Streptococcus cremoris are the typical starters for this product. Occasionally fermentation fails and results in a non-ropy clot. The reasons for these failures, however, are obscure. In one batch of spoiled 'viili,' a new C3-type bacteriophage, termed KSY1, was isolated. The head of the phage was about 230 nm long and about 50 nm wide and the tail was 35 nm long and carried a complex collar structure. Upon infection of a number of encapsulated cultures of S. cremoris with KSY1, the cocci, though not serving as a host of the phage, lost their capsules. A capsuleless strain, S. cremoris 249, served as a host. The latent period was about 150 min and the average burst size 80. The buoyant density of KSY1 was 1.436 g/cm3.

Properties of psychrophilic bacteriophage specific for Micrococcus cryophilus

A bacteriophage infective for the obligate psychrophile, Micrococcus cryophilus, was isolated from sewage. The host range is limited to this species. Phage and host DNA are similar in G–C content. The bacteriophage has an average burst size of 290 at 20 °C and 50 at 3.5 °C. The phage is thermosensitive, being 99.9% inactivated in 5 min at 45 °C. This is the first report of the isolation of bacteriophage infective for gram-positive psychrophiles.