New Bacillus bacteriophage species

Prevalence and Diversity Analysis of Candidate Prophages to Provide An Understanding on Their Roles in Bacillus Thuringiensis

Bacillus thuringiensis (Bt) is widely used in producing biological insecticides. Phage contaminations during Bt fermentation can cause severe losses of yields. Lots of strategies have been engaged to control extrinsic phage contamination during Bt fermentation, but their effectiveness is low. In this study, the candidate endogenous prophages (prophages) in 61 Bt chromosomes that had been deposited in GenBank database were analyzed. The results revealed that all chromosomes contained prophage regions, and 398 candidate prophage regions were predicted, including 135 putative complete prophages and 263 incomplete prophage regions. These putative complete prophages showed highly diverse genetic backgrounds. The inducibility of the prophages of ten Bt strains (4AJ1, 4BD1, HD-1, HD-29, HD-73, HD-521, BMB171, 4CC1, CT-43, and HD-1011) was tested, and the results showed that seven of the ten strains’ prophages were inducible. These induced phages belonged to the Siphoviridae family and exhibited a broad host spectrum against the non-original strains. The culture supernatants of the two strains (BMB171, 4CC1) could lyse Bt cells, but no virions were observed, which was speculated to be caused by lysin. The functional analysis of the putative complete prophage proteins indicated that some proteins, such as antibiotic resistance-associated proteins and restriction endonucleases, might increase the fitness of the Bt strains to different environments. The findings of this study provided understanding on the high prevalence and diversity of Bt prophages, as well as pointed out the role of prophages in the life cycle of Bt.

Isolation and characterization of glacier VMY22, a novel lytic cold-active bacteriophage of Bacillus cereus

As a unique ecological system with low temperature and low nutrient levels, glaciers are considered a "living fossil" for the research of evolution. In this work, a lytic cold-active bacteriophage designated VMY22 against Bacillus cereus MYB41-22 was isolated from Mingyong Glacier in China, and its characteristics were studied. Electron microscopy revealed that VMY22 has an icosahedral head (59.2 nm in length, 31.9 nm in width) and a tail (43.2 nm in length). Bacteriophage VMY22 was classified as a Podoviridae with an approximate genome size of 18 to 20 kb. A one-step growth curve revealed that the latent and the burst periods were 70 and 70 min, respectively, with an average burst size of 78 bacteriophage particles per infected cell. The pH and thermal stability of bacteriophage VMY22 were also investigated. The maximum stability of the bacteriophage was observed to be at pH 8.0 and it was comparatively stable at pH 5.0-9.0. As VMY22 is a cold-active bacteriophage with low production temperature, its characterization and the relationship between MYB41-22 and Bacillus cereus bacteriophage deserve further study.

Phages preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis: past, present and future

Many bacteriophages (phages) have been widely studied due to their major role in virulence evolution of bacterial pathogens. However, less attention has been paid to phages preying on bacteria from the Bacillus cereus group and their contribution to the bacterial genetic pool has been disregarded. Therefore, this review brings together the main information for the B. cereus group phages, from their discovery to their modern biotechnological applications. A special focus is given to phages infecting Bacillus anthracis, B. cereus and Bacillus thuringiensis. These phages belong to the Myoviridae, Siphoviridae, Podoviridae and Tectiviridae families. For the sake of clarity, several phage categories have been made according to significant characteristics such as lifestyles and lysogenic states. The main categories comprise the transducing phages, phages with a chromosomal or plasmidial prophage state, γ-like phages and jumbo-phages. The current genomic characterization of some of these phages is also addressed throughout this work and some promising applications are discussed here.

A giant Pseudomonas phage from Poland

A novel giant phage of the family Myoviridae is described. Pseudomonas phage PA5oct was isolated from a sewage sample from an irrigated field near Wroclaw, Poland. The virion morphology indicates that PA5oct differs from known giant phages. The phage has a head of about 131 nm in diameter and a tail of 136 × 19 nm. Phage PA5oct contains a genome of approximately 375 kbp and differs in size from any tailed phages known. PA5oct was further characterized by determination of its latent period and burst size and its sensitivity to heating, chloroform, and pH.

Occurrence of Bacillus thuringiensis and their phages in Yemen soil

Bacillus thuringiensis (Bt) isolates were found in all samples of soil in nine Governorates of Yemen. From 384 isolates of Bacillus recovered from these soil samples after acetate selection, 104 isolates (27.1 %) were Bt. Five isolates of Bt were selected and insecticidal activity was tested against Culex pipiens, Callosobruchus maculatus and Spodoptera littoralis. The Bt isolate YH18 gave toxicity to all tested insects larvae. This study extended to isolate phages active against the selected Bt isolates. Five phages were isolated and classified into two groups of tailed phages. Four phages with long non-contractile tails and hexagonal heads (Siphoviridae) and one phage with very short tail and isometric head (Podoviridae). Susceptibility of selected Bt to infect by these phages was studied by spot-test technique. Also the Bt isolate no YH18 was resistant to all tested phages. This is the first report illustrates the diversity and the abundance of Bt and Bt phage in Yemen soil.

Genomic analysis of a phage and prophage from a Bacillus thuringiensis strain

Bacteriophages have been found to be the most abundant and also potentially most diverse biological entities on Earth. In the present study, Bacillus phages were isolated rapidly and shown to have a high degree of diversity. The genomes of a newly isolated phage, phiCM3, and a prophage, proCM3, from the Bacillus thuringiensis strain YM-03 were sequenced and characterized. Comparative genome analysis showed that the phiCM3 genome is highly similar to the genomes of eight other Bacillus phages and seven of these phages were classified as the Wβ group of phages. Analysis of the differential evolution of the genes in the Wβ-group phages indicated that the genes encoding the antirepressor and tail fibre protein were more highly conserved than those encoding the major capsid protein, DNA replication protein, and RNA polymerase σ factor, which might have diverged to acquire mechanisms suitable for survival in different microbial hosts. Genome analysis of proCM3 revealed that proCM3 might be a defective phage because of mutations in the minor structural protein, and it was not inducible by mitomycin C treatment. The proCM3 genome was similar to those of two lytic Bacillus phages in sequence, but had a different genomic structure, composed of three regions in a different order. These data suggest that the three phages might have had a common ancestor and that genome rearrangement might have occurred during evolution. The findings of this study enrich our current knowledge of Bacillus phage diversity and evolution, especially for the Wβ-group and TP21-L-like phages, and may help the development of practical applications of Bacillus phages.

Existence of lysogenic bacteriophages in Bacillus thuringiensis type strains

We screened the existence of bacteriophages in 67 Bacillus thuringiensis type strains by phage DNA extraction and PCR using phage terminase small subunit (TerS)-specific primers to the supernatants and the precipitated pellets of Bt cultures, and by transmission electron microscopy. The various bacteriophages were observed from the supernatants of 22 type strains. Ten type strains showed the extracted phage DNAs and the amplified fragment by TerS PCR but 12 type strains showed only the phage DNAs. Their morphological characteristic suggests that they belong to Family Siphoviridae which had a long tail and symmetrical head.

Genome sequence and analysis of a broad-host range lytic bacteriophage that infects the Bacillus cereus group

BACKGROUND

Comparatively little information is available on members of the Myoviridae infecting low G+C content, Gram-positive host bacteria of the family Firmicutes. While numerous Bacillus phages have been isolated up till now only very few Bacillus cereus phages have been characterized in detail.

RESULTS

Here we present data on the large, virulent, broad-host-range B. cereus phage vB_BceM_Bc431v3 (Bc431v3). Bc431v3 features a 158,618 bp dsDNA genome, encompassing 239 putative open reading frames (ORFs) and, 20 tRNA genes encoding 17 different amino acids. Since pulsed-field gel electrophoresis indicated that the genome of this phage has a mass of 155-158 kb Bc431v3 DNA appears not to contain long terminal repeats that are found in the genome of Bacillus phage SPO1.

CONCLUSIONS

Bc431v3 displays significant sequence similarity, at the protein level, to B. cereus phage BCP78, Listeria phage A511 and Enterococcus phage ØEF24C and other morphologically related phages infecting Firmicutes such as Staphylococcus phage K and Lactobacillus phage LP65. Based on these data we suggest that Bc431v3 should be included as a member of the Spounavirinae; however, because of all the diverse taxonomical information has been addressed recently, it is difficult to determine the genus. The Bc431v3 phage contains some highly unusual genes such as gp143 encoding putative tRNAHis guanylyltransferase. In addition, it carries some genes that appear to be related to the host sporulation regulators. These are: gp098, which encodes a putative segregation protein related to FstK/SpoIIIE DNA transporters; gp105, a putative segregation protein; gp108, RNA polymerase sigma factor F/B; and, gp109 encoding RNA polymerase sigma factor G.

Genome characteristics of a novel phage from Bacillus thuringiensis showing high similarity with phage from Bacillus cereus

Bacillus thuringiensis is an important entomopathogenic bacterium belongs to the Bacillus cereus group, which also includes B. anthracis and B. cereus. Several genomes of phages originating from this group had been sequenced, but no genome of Siphoviridae phage from B. thuringiensis has been reported. We recently sequenced and analyzed the genome of a novel phage, BtCS33, from a B. thuringiensis strain, subsp. kurstaki CS33, and compared the gneome of this phage to other phages of the B. cereus group. BtCS33 was the first Siphoviridae phage among the sequenced B. thuringiensis phages. It produced small, turbid plaques on bacterial plates and had a narrow host range. BtCS33 possessed a linear, double-stranded DNA genome of 41,992 bp with 57 putative open reading frames (ORFs). It had a typical genome structure consisting of three modules: the "late" region, the "lysogeny-lysis" region and the "early" region. BtCS33 exhibited high similarity with several phages, B. cereus phage Wβ and some variants of Wβ, in genome organization and the amino acid sequences of structural proteins. There were two ORFs, ORF22 and ORF35, in the genome of BtCS33 that were also found in the genomes of B. cereus phage Wβ and may be involved in regulating sporulation of the host cell. Based on these observations and analysis of phylogenetic trees, we deduced that B. thuringiensis phage BtCS33 and B. cereus phage Wβ may have a common distant ancestor.

Characterization of Bacillus phage-K2 isolated from chungkookjang, a fermented soybean foodstuff

An investigation of a virulent Bacillus phage-K2 (named Bp-K2) isolated from chungkookjang (a fermented soybean foodstuff) was made. Bp-K2 differed in infectivity against a number of Bacillus subtilis strains including starter strains of chungkookjang and natto, being more infectious to Bacillus strains isolated from the chungkookjang, but much less active against a natto strain. Bp-K2 is a small DNA phage whose genome size is about 21 kb. Bp-K2 is a tailed bacteriophage with an isometric icosahedral head (50 nm long on the lateral side, 80 nm wide), a long contractile sheath (85-90 nm × 28 nm), a thin tail fiber (80-85 nm long, 10 nm wide), and a basal plate (29 nm long, 47 nm wide) with a number of spikes, but no collar. The details of the structures of Bp-K2 differ from natto phage ϕBN100 as well as other known Bacillus phages such as SPO1-like or ϕ 29-like viruses. These data suggest that Bp-K2 would be a new member of the Myoviridae family of Bacillus bacteriophages.

The SPO1-related bacteriophages

A large and diverse group of bacteriophages has been termed 'SPO1-like viruses'. To date, molecular data and genome sequences are available for Bacillus phage SPO1 and eight related phages infecting members of other bacterial genera. Many additional bacteriophages have been described as SPO1-related, but very few data are available for most of them. We present an overview of putative 'SPO1-like viruses' and shall discuss the available data in view of the recently proposed expansion of this group of bacteriophages to the tentative subfamily Spounavirinae. Characteristics of SPO1-related phages include (a) the host organisms are Firmicutes; (b) members are strictly virulent myoviruses; (c) all phages feature common morphological properties; (d) the phage genome consists of a terminally redundant, non-permuted dsDNA molecule of 127-157 kb in size; and (e) phages share considerable amino acid homology. The number of phages isolated consistent with these parameters is large, suggesting a ubiquitous nature of this group of viruses.

Detailed genomic analysis of the Wbeta and gamma phages infecting Bacillus anthracis: implications for evolution of environmental fitness and antibiotic resistance

Phage-mediated lysis has been an essential laboratory tool for rapidly identifying Bacillus anthracis for more than 40 years, relying on the gamma phage derivative of a Bacillus cereus prophage called W. The complete genomic sequences of the temperate W phage, referred to as Wbeta, and its lytic variant gamma were determined and found to encode 53 open reading frames each, spanning 40,864 bp and 37,373 bp, respectively. Direct comparison of the genomes showed that gamma evolved through mutations at key loci controlling host recognition, lysogenic growth, and possibly host phenotypic modification. Included are a cluster of point mutations at the gp14 tail fiber locus of gamma, encoding a protein that, when fused to green fluorescent protein, binds specifically to B. anthracis. A large 2,003-bp deletion was also identified at the gamma lysogeny module, explaining its shift from a temperate to a lytic lifestyle. Finally, evidence of recombination was observed at a dicistronic Wbeta locus, encoding putative bacterial cell surface-modifying proteins, replaced in gamma with a locus, likely obtained from a B. anthracis prophage, encoding demonstrable fosfomycin resistance. Reverse transcriptase PCR analysis confirmed strong induction at the dicistronic Wbeta locus and at four other phage loci in B. anthracis and/or B. cereus lysogens. In all, this study represents the first genomic and functional description of two historically important phages and is part of a broader investigation into contributions of phage to the B. anthracis life cycle. Initial findings suggest that lysogeny of B. anthracis promotes ecological adaptation, rather than virulence, as with other gram-positive pathogens.

Tailed bacteriophages: the order caudovirales

Tailed bacteriophages have a common origin and constitute an order with three families, named Caudovirales. Their structured tail is unique. Tailed phages share a series of high-level taxonomic properties and show many facultative features that are unique or rare in viruses, for example, tail appendages and unusual bases. They share with other viruses, especially herpesviruses, elements of morphogenesis and life-style that are attributed to convergent evolution. Tailed phages present three types of lysogeny, exemplified by phages lambda, Mu, and P1. Lysogeny appears as a secondary property acquired by horizontal gene transfer. Amino acid sequence alignments (notably of DNA polymerases, integrases, and peptidoglycan hydrolases) indicate frequent events of horizontal gene transfer in tailed phages. Common capsid and tail proteins have not been detected. Tailed phages possibly evolved from small protein shells with a few genes sufficient for some basal level of productive infection. This early stage can no longer be traced. At one point, this precursor phage became perfected. Some of its features were perfect enough to be transmitted until today. It is tempting to list major present-day properties of tailed phages in the past tense to construct a tentative history of these viruses: 1. Tailed phages originated in the early Precambrian, long before eukaryotes and their viruses. 2. The ur-tailed phage, already a quite evolved virus, had an icosahedral head of about 60 nm in diameter and a long non-contractile tail with sixfold symmetry. The capsid contained a single molecule of dsDNA of about 50 kb, and the tail was probably provided with a fixation apparatus. Head and tail were held together by a connector. a. The particle contained no lipids, was heavier than most viruses to come, and had a high DNA content proportional to its capsid size (about 50%). b. Most of its DNA coded for structural proteins. Morphopoietic genes clustered at one end of the genome, with head genes preceding tail genes. Lytic enzymes were probably coded for. A part of the phage genome was nonessential and possibly bacterial. Were tailed phages general transductants since the beginning? 3. The virus infected its host from the outside, injecting its DNA. Replication involved transcription in several waves and formation of DNA concatemers. Novel phages were released by burst of the infected cell after lysis of host membranes by a peptidoglycan hydrolase (and a holin?). a. Capsids were assembled from a starting point, the connector, and around a scaffold. They underwent an elaborate maturation process involving protein cleavage and capsid expansion. Heads and tails were assembled separately and joined later. b. The DNA was cut to size and entered preformed capsids by a headful mechanism. 4. Subsequently, tailed phages diversified by: a. Evolving contractile or short tails and elongated heads. b. Exchanging genes or gene fragments with other phages. c. Becoming temperate by acquiring an integrase-excisionase complex, plasmid parts, or transposons. d. Acquiring DNA and RNA polymerases and other replication enzymes. e. Exchanging lysin genes with their hosts. f. Losing the ability to form concatemers as a consequence of acquiring transposons (Mu) or proteinprimed DNA polymerases (phi 29). Present-day tailed phages appear as chimeras, but their monophyletic origin is still inscribed in their morphology, genome structure, and replication strategy. It may also be evident in the three-dimensional structure of capsid and tail proteins. It is unlikely to be found in amino acid sequences because constitutive proteins must be so old that relationships were obliterated and most or all replication-, lysogeny-, and lysis-related proteins appear to have been borrowed. However, the sum of tailed phage properties and behavior is so characteristic that tailed phages cannot be confused with other viruses.

Three Bacillus cereus bacteriophage endolysins are unrelated but reveal high homology to cell wall hydrolases from different bacilli

The ply genes encoding the endolysin proteins from Bacillus cereus phages Bastille, TP21, and 12826 were identified, cloned, and sequenced. The endolysins could be overproduced in Escherichia coli (up to 20% of total cellular protein), and the recombinant proteins were purified by a two-step chromatographical procedure. All three enzymes induced rapid and specific lysis of viable cells of several Bacillus species, with highest activity on B. cereus and B. thuringiensis. Ply12 and Ply21 were experimentally shown to be N-acetylmuramoyl-L-alanine amidases (EC 3.5.1.28). No apparent holin genes were found adjacent to the ply genes. However, Ply21 may be endowed with a signal peptide which could play a role in timing of cell lysis by the cytoplasmic phage endolysin. The individual lytic enzymes (PlyBa, 41.1 kDa; Ply21, 29.5 kDa, Ply12, 27.7 kDa) show remarkable heterogeneity, i.e., their amino acid sequences reveal only little homology. The N-terminal part of Ply21 was found to be almost identical to the catalytic domains of a Bacillus sp. cell wall hydrolase (CwlSP) and an autolysin of B. subtilis (CwlA). The C terminus of PlyBa contains a 77-amino-acid sequence repeat which is also homologous to the binding domain of CwlSP. Ply12 shows homology to the major autolysins from B. subtilis and E. coli. Comparison with database sequences indicated a modular organization of the phage lysis proteins where the enzymatic activity is located in the N-terminal region and the C-termini are responsible for specific recognition and binding of Bacillus peptidoglycan. We speculate that the close relationship of the phage enzymes and cell wall autolysins is based upon horizontal gene transfer among different Bacillus phages and their hosts.

Phage typing of Bacillus subtilis and B. thuringiensis

Phage typing schemes for Bacillus subtilis and B. thuringiensis were constructed using 98 phages and 743 bacterial strains. Most phages were host-species-specific. Phages were classified by electron microscopy. The B. subtilis scheme includes 10 phages and 29 phage types. The B. thuringiensis scheme comprises 8 phages and 25 phage types and can be applied to B. cereus. There is no correlation between H antigen serotypes and phagovars in B. thuringiensis. Characteristics of typing phages are described for identity control.

Classification of Acinetobacter phages

Eight phage species and type viruses are proposed. They belong to the Myoviridae, Siphoviridae, and Podoviridae families of tailed phages and are characterized by a combination of morphological and physicochemical properties. An unusual siphovirus species has an elongated head and transverse tail disks.

Bacteriophages from Bombyx mori

Preparations of silkworm larvae contained two large phages with contractile tails (Myoviridae). One phage was active on Pseudomonas paucimobilis. The other, not cultivated, was one of the largest viruses known.