"My enemy's enemy is my friend." Using phages to fight bacteria. Bradbury, J. (2004). Lancet 363:624-625. [first paragraph] Bacteriophages, viruses that prey upon bacteria, typically attack only a single bacterial strain. This specificity, together with the killing capacity of "phages", says phage researcher Martin Loessner, makes them the "natural enemies" of bacteria. "We are now endeavouring to make this enemy our friend", says Loessner, a professor of food microbiology at the Swiss Federal Institute of Technology in Zurich, turning phages into potentially important allies in our battle against bacteria.
Pressure inactivation kinetics of phage l cI 857. Chen, H., Joerger, R. D., Kingsley, D. H., Hoover, D. G. (2004). Journal of Food Protection 67:505-511. Inactivation curves of phage lambda cI 857 inactivated by high hydrostatic pressure were obtained at three pressure levels (300, 350, and 400 MPa) in buffered media and ultrahigh-temperature 2% reduced fat milk. Pressurization of phage lambda in buffered media at 300 MPa for 300 min, 350 MPa for 36 min, and 400 MPa for 8 min reduced the titer of phage lambda by 7.5, 6.7, and 7.7 log, respectively. Pressurization of phage lambda in milk at 300 MPa for 400 min, 350 MPa for 80 min, and 400 MPa for 20 min reduced the titer of phage lambda by 5.4, 6.4, and 7.1 log, respectively. Tailing was observed in all inactivation curves, indicating that the linear model was not adequate for describing these curves. Among the three nonlinear models studied, the Weibull and log-logistic models consistently produced best fits to all inactivation curves, and the modified Gompertz model the poorest. Because there were no significant differences in the values of shape factor (n) for suspension medium buffer, we reduced the number of parameters in the Weibull model from two to one by setting n at the mean value. The simplified Weibull model produced a fit comparable to the full model. Additionally, the simplified Weibull model allowed predictions to be made at pressures different from the experimental pressures. Menstruum was found to significantly affect the pressure resistance of phage lambda. Comparison of pressure inactivation of hepatitis A virus and phage lambda indicated that phage lambda is more sensitive to pressure than hepatitis A virus in Dulbecco's modified Eagle medium with 10% fetal bovine sera
New dawn for phage therapy. Dixon, B. (2004). The Lancet infectious diseases 4:186. [first two paragraphs] Perhaps Antony Twort was 10 years too early in publishing his father Frederick's biography. A marvellous portrait of the eccentric co-discoverer of the bacteriophage, whose work helped to usher in the era of molecular biology, the book appeared only after numerous rejections from publishers (Lancet Infect Dis 2003; 3: 58). It also received little review attention, because literary editors are largely unaware of the role of science and scientists in shaping the modern world. ¶ However, the decade since publication of In Focus, Out of Step (Stroud, UK: Alan Sutton) has seen increasing interest in phages, especially in administering them therapeutically. Most recently there have been promising advances towards real applications. Now, thanks to work in Vienna, Austria, the major obstacle to phage therapy seems well on the way to being removed. At a time when antibiotic resistance is provoking real concern even in the most sober quarters, this is excellent news.
Removal of coliphages in secondary effluent by microfiltration-mechanisms of removal and impact of operating parameters. Farahbakhsh, K., Smith, D. W. (2004). Water Research 38:585-592. The efficacy of a microfiltration (MF) pilot plant in removing somatic coliphages (referred hereafter as coliphages) present in the secondary effluent was evaluated during this study. The impact of operating parameters such as feed coliphage concentrations, permeate flux and membrane fouling on the removal of coliphages by the MF plant was investigated. The study showed that membrane fouling was beneficial for removing coliphages by MF. It was also shown that the removal of coliphages by MF was initially governed by adsorption on membrane surface or in membrane pores. As the membrane fouled, however, the removal of coliphages was primarily governed by direct interception on the cake layer formed on the surface of the membrane. Increases in feed coliphage concentrations resulted in the passage of larger numbers of coliphages when the MF was clean but had little impact on the passage of coliphages when the membrane became fouled. Increasing permeate flux lowered log-removal values (LRVs) for the clean membrane but resulted in an initial increase in LRVs for the fouled membrane followed by a drop in LRVs with further increases in permeate flux
Big questions, small worlds: microbial model systems in ecology. Jessep, C. M., Kassen, R., Forde, S. E., Kerr, B., Buckling, A., Rainey, P. B., Bohannan, B. J. M. (2004). Trends in Ecology and Evolution 19:189-197. Although many biologists have embraced microbial model systems as tools to address genetic and physiological questions, the explicit use of microbial communities as model systems in ecology has traditionally been more restricted. Here, we highlight recent studies that use laboratory-based microbial model systems to address ecological questions. Such studies have significantly advanced our understanding of processes that have proven difficult to study in field systems, including the genetic and biochemical underpinnings of traits involved in ecological interactions, and the ecological differences driving evolutionary change. The use of microbial model systems is not without criticism, however. Many ecologists have voiced concern that microbial microcosm experiments are too simplified, contrived, and small in spatial and temporal scale to adequately address ecological questions. We argue that these concerns reflect a misunderstanding of the purpose of microcosm studies. It is the simplicity of microbial model systems that makes them such powerful tools for the study of ecology; such simplicity allows the high degrees of experimental control and replication necessary to address many questions that are inaccessible through field observation or experimentation. Furthermore, the tractability of the microbial model systems also allows ecologists to bridge ecological and evolutionary questions, and to analyze experiments post hoc to better understand the mechanisms underlying particular results.
Population and evolutionary dynamics of phage therapy. Levin, B. R., Bull, J. J. (2004). Nat. Rev. Microbiol. 2:166-173. Following a sixty-year hiatus in western medicine, bacteriophages (phages) are again being advocated for treating and preventing bacterial infections. Are attempts to use phages for clinical and environmental applications more likely to succeed now than in the past? Will phage therapy and prophylaxis suffer the same fates as antibiotics--treatment failure due to acquired resistance and ever-increasing frequencies of resistant pathogens? Here, the population and evolutionary dynamics of bacterial-phage interactions that are relevant to phage therapy and prophylaxis are reviewed and illustrated with computer simulations
Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes. Liu, M., Gingery, M., Doulatov, S. R., Liu, Y., Hodes, A., Baker, S., Davis, P., Simmonds, M., Churcher, C., Mungall, K., Quail, M. A., Preston, A., Harvill, E. T., Maskell, D. J., Eiserling, F. A., Parkhill, J., Miller, J. F. (2004). Journal of Bacteriology 186:1503-1517. Liu et al. recently described a group of related temperate bacteriophages that infect Bordetella subspecies and undergo a unique template-dependent, reverse transcriptase-mediated tropism switching phenomenon (Liu et al., Science 295: 2091-2094, 2002). Tropism switching results from the introduction of single nucleotide substitutions at defined locations in the VR1 (variable region 1) segment of the mtd (major tropism determinant) gene, which determines specificity for receptors on host bacteria. In this report, we describe the complete nucleotide sequences of the 42.5- to 42.7-kb double-stranded DNA genomes of three related phage isolates and characterize two additional regions of variability. Forty-nine coding sequences were identified. Of these coding sequences, bbp36 contained VR2 (variable region 2), which is highly dynamic and consists of a variable number of identical 19-bp repeats separated by one of three 5-bp spacers, and bpm encodes a DNA adenine methylase with unusual site specificity and a homopolymer tract that functions as a hotspot for frameshift mutations. Morphological and sequence analysis suggests that these Bordetella phage are genetic hybrids of P22 and T7 family genomes, lending further support to the idea that regions encoding protein domains, single genes, or blocks of genes are readily exchanged between bacterial and phage genomes. Bordetella bacteriophages are capable of transducing genetic markers in vitro, and by using animal models, we demonstrated that lysogenic conversion can take place in the mouse respiratory tract during infection
Characterizing spontaneous induction of Stx encoding phages using a selectable reporter system. Livny, J., Friedman, D. I. (2004). Molecular Microbiology 51:1691-1704. Shiga toxin (Stx) genes in Stx producing Escherichia coli (STEC) are encoded in prophages of the lambda family, such as H-19B. The subpopulation of STEC lysogens with induced prophages has been postulated to contribute significantly to Stx production and release. To study induced STEC, we developed a selectable in vivo expression technology, SIVET, a reporter system adapted from the RIVET system. The SIVET lysogen has a defective H-19B prophage encoding the TnpR resolvase gene downstream of the phage PR promoter and a cat gene with an inserted tet gene flanked by targets for the TnpR resolvase. Expression of resolvase results in excision of tet , restoring a functional cat gene; induced lysogens survive and are chloramphenicol resistant. Using SIVET we show that: (i) approximately 0.005% of the H-19B lysogens are spontaneously induced per generation during growth in LB. (ii) Variations in cellular physiology (e.g. RecA protein) rather than in levels of expressed repressor explain why members of a lysogen population are spontaneously induced. (iii) A greater fraction of lysogens with stx encoding prophages are induced compared to lysogens with non-Stx encoding prophages, suggesting increased sensitivity to inducing signal(s) has been selected in Stx encoding prophages. (iv) Only a small fraction of the lysogens in a culture spontaneously induce and when the lysogen carries two lambdoid prophages with different repressor/ operators, 933W and H-19B, usually both prophages in the same cell are induced.
Bacteriophage contamination: is there a simple method to reduce its deleterious effects in laboratory cultures and biotechnological factories? Los, M., Czyz, A., Sell, E., Wegrzyn, A., Neubauer, P., Wegrzyn, G. (2004). Journal of applied genetics 45:111-120. Infection of bacterial cultures by bacteriophages as well as prophage induction in the host cells are serious problems in both research and biotechnological laboratories. Generally, prevention strategies (like good laboratory/factory hygiene, sterilisation, decontamination and disinfection) are necessary to avoid bacteriophage contamination. However, it is well known that no matter how good the laboratory/factory practice and hygiene are, bacteriophage infections occur from time to time. The use of immunised or resistant bacterial strains against specific phages may be helpful, but properties of the genetically modified strains resistant to phages are often worse (from the point of view of a researcher or a biotechnological company) than those of the parental, phage-sensitive strains. In this article we review recent results that may provide a simple way to minimise deleterious effects of bacteriophage infection and prophage induction. It appears that low bacterial growth rates result in a significant inhibition of lytic development of various bacteriophages. Moreover, spontaneous prophage induction is less frequent in slowly growing bacteria
Evolutionary potential of an RNA virus. Makeyev, E. V., Bamford, D. H. (2004). Journal of Virology 78:2114-2120. RNA viruses are remarkably adaptable to changing environments. This is medically important because it enables pathogenic viruses to escape the immune response and chemotherapy and is of considerable theoretical interest since it allows the investigation of evolutionary processes within convenient time scales. A number of earlier studies have addressed the dynamics of adapting RNA virus populations. However, it has been difficult to monitor the trajectory of molecular changes in RNA genomes in response to selective pressures. To address the problem, we developed a novel in vitro evolution system based on a recombinant double-stranded RNA bacteriophage, phi 6, containing a beta-lactamase (bla) gene marker. Carrier-state bacterial cells are resistant to ampicillin, and after several passages, they become resistant to high concentrations of another beta-lactam antibiotic, cefotaxime, due to mutations in the virus-borne bla gene. We monitored the changes in bla cDNAs induced by cefotaxime selection and observed an initial explosion in sequence variants with multiple mutations throughout the gene. After four passages, a stable, homogeneous population of bla sequences containing three specific nonsynonymous mutations was established. Of these, two mutations (E104K and G238S) have been previously reported for beta-lactamases from cefotaxime-resistant bacterial isolates. These results extend our understanding of the molecular mechanisms of viral adaptation and also demonstrate the possibility of using an RNA virus as a vehicle for directed evolution of heterologous proteins.
Rapid detection of Escherichia coli O157:H7 by using green fluorescent protein-labeled PP01 bacteriophage. Oda, M., Morita, M., Unno, H., Tanji, Y. (2004). Applied and Environmental Microbiology 70:527-534. A previously isolated T-even-type PP01 bacteriophage was used to detect its host cell, Escherichia coli O157:H7. The phage small outer capsid (SOC) protein was used as a platform to present a marker protein, green fluorescent protein (GFP), on the phage capsid. The DNA fragment around soc was amplified by PCR and sequenced. The gene alignment of soc and its upstream region was g56-soc.2-soc.1-soc, which is the same as that for T2 phage. GFP was introduced into the C- and N-terminal regions of SOC to produce recombinant phages PP01-GFP/SOC and PP01-SOC/GFP, respectively. Fusion of GFP to SOC did not change the host range of PP01. On the contrary, the binding affinity of the recombinant phages to the host cell increased. However, the stability of the recombinant phages in alkaline solution decreased. Adsorption of the GFP-labeled PP01 phages to the E. coli cell surface enabled visualization of cells under a fluorescence microscope. GFP-labeled PP01 phage was not only adsorbed on culturable E. coli cells but also on viable but nonculturable or pasteurized cells. The coexistence of insensitive E. coli K-12 (W3110) cells did not influence the specificity and affinity of GFP-labeled PP01 adsorption on E. coli O157:H7. After a 10-min incubation with GFP-labeled PP01 phage at a multiplicity of infection of 1,000 at 4ºC, E. coli O157:H7 cells could be visualized by fluorescence microscopy. The GFP-labeled PP01 phage could be a rapid and sensitive tool for E. coli O157:H7 detection
Estimation of septic tank setback distances based on transport of E. coli and F-RNA phages. Pang, L., Close, M., Goltz, M., Sinton, L., Davies, H., Hall, C., Stanton, G. (2004). Environment International 29:907-921. Setback distances between septic tank systems and the shorelines of Lake Okareka, New Zealand were determined from model simulations for a worst-case scenario, using the highest hydraulic conductivity and gradient measured in the field, removal rates of the microbial indicators (Escherichia coli and F-RNA phages) determined from a column experiment, and maximum values of the design criteria for the disposal system, and assuming an absence of an unsaturated zone, a continuous discharge of the raw effluent from a failed or non-complying treatment system (both indicators at concentrations of 1x107 counts/100 ml) into the groundwater and no sorption of pathogens in the aquifer. Modelling results suggest that the minimal setback distances were 16 m to satisfy the New Zealand Recreational Water Quality Guidelines for E. coli <126 per 100 ml (Ministry for the Environment, 1999) and 48 m to meet the Drinking-Water Standards for New Zealand 2000 for enteric virus <1 per 100 l (Ministry of Health, 2000). These distances may be applicable for other lakeshores in pumice sand aquifers with groundwater velocities <7 m/day. Findings of laboratory column and batch experiments provided an insight into the microbial attenuation and transport processes in pumice sand aquifers. Bacterial removal was predominately through filtration (87-88%) and partially by die-off (12-13%), while viral removal was by both die-off (45%) and filtration (55%). In addition, microbial die-off in groundwater without aquifer material (i.e., free microbes) was much lower than die-off in groundwater with aquifer material (i.e., sorbed microbes) and contributed only 2-6% to the total removal. This implies that the setback distances estimated from die-off rates for the free microbes, determined in the laboratory without considering aquifer media and other removal processes, which are often reported in the literature, could be larger than necessary
The Pasteurella multocida toxin is encoded within a lysogenic bacteriophage. Pullinger, G. D., Bevir, T., Lax, A. J. (2004). Molecular Microbiology 51:255-269. Toxigenic strains of Pasteurella multocida produce a 146 kDa toxin (PMT) that acts as a potent mitogen. Sequence analysis of the structural gene for PMT, toxA, previously suggested it was horizontally acquired, because it had a low G + C content relative to the P. multocida genome. To address this, the sequence of DNA flanking toxA was determined. The sequence analysis showed the presence of homologues to bacteriophage tail protein genes and a bacteriophage antirepressor, suggesting that the toxin gene resides within a prophage. In addition to phage genes, the toxA flanking DNA contained a homologue of a restriction/modification system that was shown to be functional. The presence of a bacteriophage was demonstrated in spent medium from toxigenic P. multocida isolates. Its production was increased by mitomycin C addition, a treatment that is known to induce the lytic cycle of many temperate bacteriophages. The genomes of bacteriophages from three different toxigenic P. multocida strains had similar but not identical restriction profiles, and were approximately 45-50 kb in length. The prophages from two of these had integrated at the same site in the chromosome, in a tRNA gene. Southern blot analysis confirmed that these bacteriophages contained the toxA gene.
The genome and proteome of coliphage T1. Roberts, M. D., Martin, N. L., Kropinski, A. M. (2004). Virology 318:245-266. The genome of enterobacterial phage T1 has been sequenced, revealing that its 50.7-kb terminally redundant, circularly permuted sequence contains 48,836 bp of nonredundant nucleotides. Seventy-seven open reading frames (ORFs) were identified, with a high percentage of small genes located at the termini of the genomes displaying no homology to existing phage or prophage proteins. Of the genes showing homologs (47%), we identified those involved in host DNA degradation (three endonucleases) and T1 replication (DNA helicase, primase, and single-stranded DNA-binding proteins) and recombination (RecE and Erf homologs). While the tail genes showed homology to those from temperate coliphage N15, the capsid biosynthetic genes were unique. Phage proteins were resolved by 2D gel electrophoresis, and mass spectrometry was used to identify several of the spots including the major head, portal, and tail proteins, thus verifying the annotation
Immunological factors that affect the in vivo fate of T7 phage in the mouse. Srivastava, A. S., Kaido, T., Carrier, E. (2004). Journal of Virological Methods 115:99-104. Phage display is a powerful method to study organ and tissue specific addresses. As part of our studies on the in vivo panning of tissue-homing peptide libraries, we examined the survival of T7 phage in the blood of C57BL/6J mice to estimate the half-life of T7 phage and the factors responsible for its inactivation. Amplified and purified T7 phage particles with or without random peptide library inserts were injected intravenously into the tail vein of wild-type (C57BL/6J) and immunocompromized (C57BL/6J) female mice. In wild-type mice, both the parent phage as well as phage carrying a peptide library were eliminated quickly from the blood, with only approximately 1% survival of detectable infectious phage after 60 min of injection. In SCID (C57BL/6J-Prkdcscid) mice, phage titers were stable over the same period of time with or without peptide library, suggesting a role for either B- or T cells or both in phage inactivation. The presumed role of B cell was indicated by demonstration of stable phage in the B-cell deficient mouse (C57BL/10-Igh-6tm1Cgn). In other immunocompromized mice, the phage titers were unstable, similar to that found in wild-type mice. In no case, was there a difference between phage with or without random peptide library. These data indicate that the presence of random C-X7-C peptides on the T7 phage coat protein does not affect the clearance of the phage in murine blood. Most likely, host immune factors play a role in the neutralization of T7 phage in blood by reacting with B-cell dependent immunoglobin
Are viruses driving microbial diversification and diversity? Weinbauer, M. G., Rassoulzadegan, F. (2004). Environmental microbiology 6:1-11. Viruses can influence the genetic diversity of prokaryotes in various ways. They can affect the community composition of prokaryotes by 'killing the winner' and keeping in check competitive dominants. This may sustain species richness and the amount of information encoded in genomes. Viruses can also transfer (viral and host) genes between species. Such mechanisms have probably influenced the speciation of prokaryotes. Whole-genome sequencing has clearly revealed the importance of (virus-mediated) gene transfer. However, its significance for the ecological performance of aquatic microbial communities is only poorly studied, although the few available reports indicate a large potential. Here, we present data supporting the hypothesis that viral genes and viral activity generate genetic variability of prokaryotes and are a driving force for ecological functioning and evolutionary change
Ecology of Prokaryotic Viruses. Weinbauer, M. G. (2004). FEMS Microbiology Reviews 28:127-181. The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses ("phages") in marine, freshwater and soil systems from a "virus point of view". The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by "killing the winner" and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.
Impact of virioplankton on archaeal and bacterial community richness as assessed in seawater batch cultures. Winter, C., Smit, A., Herndl, G. J., Weinbauer, M. G. (2004). Applied and Environmental Microbiology 70:804-813. During cruises in the tropical Atlantic Ocean (January to February 2000) and the southern North Sea (December 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. Prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. Batch cultures with microwave-inactivated viruses and without viruses served as controls. The apparent richness of archaeal and bacterial communities was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA gene fragments. Although the estimated richness of the prokaryotic communities generally was greatly reduced within the first 24 h of incubation due to confinement, the effects of virus amendment were detected at the level of individual operational taxonomic units (OTUs) in the T-RFLP patterns of both groups, Archaea and Bacteria. One group of OTUs was detected in the control samples but was absent from the virus-treated samples. This negative response of OTUs to virus amendment probably was caused by viral lysis. Additionally, we found OTUs not responding to the amendments, and several OTUs exhibited variable responses to the addition of inactive or active viruses. Therefore, we conclude that individual members of pelagic archaeal and bacterial communities can be differently affected by the presence of virioplankton.
Genotoxicity of water extracts from the River Yamuna at Mathura, India. Aleem, A., Malik, A. (2003). Environmental Toxicology 18:69-77. Water samples were collected from the River Yamuna at Mathura, India, and concentrated by using XAD resins (Amberlite XAD-4 and XAD-8) and liquid-liquid extraction procedures. The genotoxicities of the extracted water samples were evaluated by the Ames Salmonella/mammalian microsome test, DNA repair of defective mutants, and bacteriophage lambda systems. The results of the Salmonella test demonstrated that the XAD-concentrated water samples had maximum mutagenicity with the TA98 strain, both with and without metabolic activation. The XAD-concentrated water samples collected in the summer showed maximum mutagenic responses compared with those collected in other seasons, whereas the liquid-liquid extracted samples exhibited maximum mutagenic activity during the postmonsoon season. The damage brought about during DNA repair of defective mutants in the presence of XAD-concentrated water samples was found to be remarkably high compared with the liquid-liquid extracted water samples at a dose level of 20 microL/mL of culture. All the mutants invariably exhibited significant decline in their colony-forming units compared with their isogenic wild-type counterparts. Survival was decreased by 86.7% and 65.1% in the polA(-) strain after 6 h of treatment with XAD-concentrated and liquid-liquid extracted water samples, respectively. A significant decrease in the survival of bacteriophage lambda was also observed when treated with test samples. The damage was more pronounced in lexA mutants when the phage was treated with XAD-concentrated samples. The recA, lexA, and polA mutants of E. coli K-12 were found to be sensitive to the test samples, suggesting damage to the DNA of exposed cells as well as to the role of recA+, lexA+, and polA+ genes in coping with the hazardous effect of the pollutants. The results demonstrated substantial genotoxicity and mutagenicity in the water samples tested
AFV1, a novel virus infecting hyperthermophilic archaea of the genus Acidianus. Bettstetter, M., Peng, X., Garrett, R. A., Prangishvili, D. (2003). Virology 315:68-79 We describe a novel virus, AFV1, of the hyperthermophilic archaeal genus Acidianus. Filamentous virions are covered with a lipid envelope and contain at least five different proteins with molecular masses in the range of 23-130 kDa and a 20.8-kb-long linear double-stranded DNA. The virus has been assigned to the family Lipothrixviridae on the basis of morphotypic characteristics. Host range is confined to several strains of Acidianus and the virus persists in its hosts in a stable carrier state. The latent period of virus infection is about 4 h. Viral DNA was sequenced and sequence similarities were found to the lipothrixvirus SIFV, the rudiviruses SIRV1 and SIRV2, as well as to conjugative plasmids and chromosomes of the genus Sulfolobus. Exceptionally for the linear genomes of archaeal viruses, many short direct repeats, with the sequence TTGTT or close variants thereof, are closely clustered over 300 bp at each end of the genome. They are reminiscent of the telomeric ends of linear eukaryal chromosomes.
Dynamic of isolation of the Phytopathogenic bacteria's phages from a leaf and a root of sugar beet. Andriychuk, O. M., Semchuk, L. I., Romashov, S. A., Ignatenko, T. A., Yatskovska, L. I., Boyko, A. L. (2003). Bulletin of the University of Kiev, series Biology . Research on studying the dynamics of phage's isolation to indicatory cultures Pseudomonas, Xanthomonas, Erwinia, which formed groups on certain taxonomicaly attributes is carried out: 1 - some strains which represents the pathovars of the certain species (8 strain); 2 - strains which represent species of the certain genus (13 strain); 3 - certain genus of phytopathogenic bacteria (Pseudomonas, Xanthomonas, Erwinia). Such bacteria can represents the taxonomic hierarchy and represents the model of microflora field agrocenoses. Research of phage's isolation from plants and roots of sugar beet has shown the presence of various phage's isolates by a character of the lytic abilities to the used indicatory bacteria. The direct isolation of phages to 13 indicators strains and a ultra-violet induction of lysogenic microflorae were carried out. Researches carried out in dynamics during 14 months continuously. During the warm period for the analysis selected leaves of sugar beet, roots selected during all year. The reveals wide spectrum of phages was characteristic both for free, and for ultra-violet induction phages.
Detection of the phytopathogenic bacteria' phages in Antarctica. Boyko, A. L., Semchuk, L. I., Voytsitsky, V. M., Andriychuk, O. M., Romashev, S. A., Ignatenko, T. O., Yatskovska, L. I., Vaschenko, V. M., Delimat, A. (2003). Agroeclogical magazine 12-15. During expedition to the Ukrainian Antarctic station " Academician Vernadsky " in 2003 testes of a thawed snow and a ground from islands of the Argentina archipelago have been taken. The analysis on presence of phytopathogenic bacteria phages Xanthomonas, Burkholderia, Erwinia and Pseudomonas. has shown lytic activity practically in all tests. For the most of them the titres of phages was 1-10 PFU/ml, and 6 gave high spontaneous production of the investigated phages - 106 PFU/ml. Processing of the tests by UV-radiation with the purpose of an lysogenic microflorae induction caused the inactivation of phages up to individual negative colonies. Discussion of the received results from the point of view of the investigated region's features is offered.
Detection of phages of phytopathogenic bacterias Pseudomonas, Xanthomonas, Erwinia and Bacillus in agrocenosises. Boyko, A. L., Semchuk, L. I., Romashev, S. A., Andriychuk, O. M., Yatskovska, L. I. (2003). Agroecological magazine 24-26. Studied the diffusion of phytopathogenic bacteria' bacteriophages of in [sic] Kiev area. The samplings conducted on plantations of sugar-beet. Among discharged bacteriophages the main specific weight was made by phages [of] Xanthomonas beticola. In samples [of] seeds of sugar-beet the phages are not detected. Their influencing on number of a pathogenic microflora in biocenoses is discussed.
Evaluation of F+ RNA and DNA coliphages as source-specific indicators of fecal contamination in surface waters. Cole, D., Long, S. C., Sobsey, M. D. (2003). Applied and Environmental Microbiology 69:6507-6514. Male-specific (F+) coliphages have been investigated as viral indicators of fecal contamination that may provide source-specific information for impacted environmental waters. This study examined the presence and proportions of the different subgroups of F+ coliphages in a variety of fecal wastes and surface waters with well-defined potential waste impacts. Municipal wastewater samples had high proportions of F+ DNA and group II and III F+ RNA coliphages. Bovine wastewaters also contained a high proportion of F+ DNA coliphages, but group I and IV F+ RNA coliphages predominated. Swine wastewaters contained approximately equal proportions of F+ DNA and RNA coliphages, and group I and III F+ RNA coliphages were most common. Waterfowl (gull and goose) feces contained almost exclusively F+ RNA coliphages of groups I and IV. No F+ coliphages were isolated from the feces of the other species examined. F+ coliphage recovery from surface waters was influenced by precipitation events and animal or human land use. There were no significant differences in coliphage density among land use categories. Significant seasonal variation was observed in the proportions of F+ DNA and RNA coliphages. Group I F+ RNA coliphages were the vast majority (90%) of those recovered from surface waters. The percentage of group I F+ RNA coliphages detected was greatest at background sites, and the percentage of group II F+ RNA coliphages was highest at human-impacted sites. Monitoring of F+ coliphage groups can indicate the presence and major sources of microbial inputs to surface waters, but environmental effects on the relative occurrence of different groups need to be considered
Shigella dysenteriae type 1-specific bacteriophage from environmental waters in Bangladesh. Faruque, S. M., Chowdhury, N., Khan, R., Hasan, M. R., Nahar, J., Islam, M. J., Yamasaki, S., Ghosh, A. N., Nair, G. B., Sack, D. A. (2003). Applied and Environmental Microbiology 69:7028-7031. Shigella dysenteriae type 1 is the causative agent of the most severe form of bacillary dysentery, which occurs as epidemics in many developing countries. We isolated a bacteriophage from surface water samples from Bangladesh that specifically lyses strains of S. dysenteriae type 1. This phage, designated SF-9, belongs to the Podoviridae family and has a 41-kb double-stranded DNA genome. Further screening of water samples for the prevalence of the phage revealed 9 of 71 (12.6%) water samples which were positive for the phage. These water samples were also positive in PCR assays for one or more S. dysenteriae type 1-specific genes, including ipaBCD and stx1, and live S. dysenteriae type 1 was isolated from three phage-positive samples. The results of this study suggest that phage SF-9 may have epidemiological applications in tracing the presence of S. dysenteriae type 1 in environmental waters
The physical environment affects cyanophage communities in British Columbia inlets. Frederickson, C. M., Short, S. M., Suttle, C. A. (2003). Microbial Ecology 46:348-357. Little is known about the natural distribution of viruses that infect the photosynthetically important group of marine prokaryotes, the cyanobacteria. The current investigation reveals that the structure of cyanophage communities is dependent on water column structure. PCR was used to amplify a fragment of the cyanomyovirus gene (g) 20, which codes for the portal vertex protein. Denaturing gradient gel electrophoresis (DGGE) of PCR amplified g20 gene fragments was used to examine variations in cyanophage community structure in three inlets in British Columbia, Canada. Qualitative examination of denaturing gradient gels revealed cyanophage community patterns that reflected the physical structure of the water column as indicated by temperature and salinity. Based on mobility of PCR fragments in the DGGE gels, some cyanophages appeared to be widespread, while others were observed only at specific depths. Cyanophage communities within Salmon Inlet were more related to one another than to communities from either Malaspina Inlet or Pendrell Sound. As well, surface communities in Malaspina Inlet and Pendrell Sound were different when compared to communities at depth. In the same two locations, distinct differences in community composition were observed in communities that coincided with depths of high chlorophyll fluorescence. The observed community shifts over small distances (only a few meters in depth or inlets separated by less than 100 km) support the idea that cyanophage communities separated by small spatial scales develop independently of each other as a result isolation by water column stratification or land mass separation, which may ultimately lead to changes in the distribution or composition of the host community
Bacteriophage ecology and plants. Gill, J. J., Abedon, S. T. (2003). APSnet Feature http://www.apsnet.org/online/feature/phages/. Plant biology cannot be fully appreciated absent microbial flora, and plant-associated bacteria are incompletely understood without an awareness of phage -- the viruses of prokaryotes. Phage have been found in association with "buds, leaves, root nodules (leguminous plants), roots, rotting fruit, seeds, stems and straw; crown gall tumors… healthy or diseased alfalfa, barley, beans, broccoli, Brussels sprouts, buckwheat, clover, cotton, cucumber, lucerne, mulberry, oats peas, peach trees, radish, rutabaga, ryegrass, rye, timothy, tobacco, tomatoes, [and] wheat" (4). In this overview we consider the myriad ways that phage can impact ecologically on plant-associated bacteria.
Bacteriophage treatment of a severe Escherichia coli respiratory infection in broiler chickens. Huff, W. E., Huff, G. R., Rath, N. C., Balog, J. M., Donoghue, A. M. (2003). Avian Diseases 47:1399-1405. A bacteriophage to a serotype 02, nonmotile Escherichia coli was isolated from municipal waste treatment facilities and poultry processing plants. A study was conducted to determine the efficacy of multiple vs. single intramuscular (i.m.) injections of bacteriophage to treat a severe E. coli respiratory infection. The birds were challenged at 7 days of age by injection of 6 x 104 colony-forming units (cfu) of E. coli into the thoracic air sac followed by an i.m. injection into the thigh with either heat-killed or active bacteriophage. There were 16 treatments with three replicate pens of 10 birds. There were four control treatments, which included untreated birds, birds injected with either heat-killed or active bacteriophage, and birds challenged only with E. coli. In the remaining treatments, birds were injected with heat-killed or active bacteriophage either once immediately after E. coli challenge or immediately after challenge and at 8 and 9 days of age, once at 8 days of age or at 8, 9, and 10 days of age, and once at 9 days of age or at 9, 10, and 11 days of age. Mortality was significantly decreased from 57% to 13% in the birds given a single i.m. injection of bacteriophage immediately after E. coli challenge, and there was complete recovery in birds treated immediately after challenge and at 8 and 9 days of age, which was a significant improvement from the single injection treatment. There was a significant reduction in mortality from 57% to 10% in the birds treated with bacteriophage once at 8 days of age and those birds treated at 8, 9, and 10 days of age, with no difference between single or multiple treatments. The mortality in the single or multiple phage treated birds that started at 9 days of age was reduced from 57% to 28% and 27%, respectively, but was not statistically different from the control. These data suggest that bacteriophage can be an effective treatment when administered early in this experimental E. coli respiratory disease and that early multiple treatments are better than a single treatment. The efficacy of bacteriophage treatment diminishes as it is delayed, with no difference between single or multiple treatments. Bacteriophage may provide an effective alternative to antibiotics, but like antibiotic therapy, the effectiveness of phage to rescue animals decreases the longer treatment is delayed in the disease process
Lateral gene transfer: when will adolescence end? Lawrence, J. G., Hendrix, R. W. (2003). Molecular Microbiology 50:739-749. The scope and impact of horizontal gene transfer (HGT) in Bacteria and Archaea has grown from a topic largely ignored by the microbiological community to a hot-button issue gaining staunch supporters (on particular points of view) at a seemingly ever-increasing rate. Opinions range from HGT being a phenomenon with minor impact on overall microbial evolution and diversification to HGT being so rampant as to obfuscate any opportunities for elucidating microbial evolution - especially organismal phylogeny - from sequence comparisons. This contentious issue has been fuelled by the influx of complete genome sequences, which has allowed for a more detailed examination of this question than previously afforded. We propose that the lack of common ground upon which to formulate consensus viewpoints probably stems from the absence of answers to four critical questions. If addressed, they could clarify concepts, reject tenuous speculation and solidify a robust foundation for the integration of HGT into a framework for long-term microbial evolution, regardless of the intellectual camp in which you reside. Here, we examine these issues, why their answers shape the outcome of this debate and the progress being made to address them.
Diagnostic and therapeutic applications of lytic phages. Mandeville, R., Griffiths, M., Goodridge, L., McIntyre, L., Ilenchuk, T. T. (2003). Analytical Letters 36:3241-3259. The ability of lytic phages to rapidly kill and lyse infected bacteria, the specificity of phages for particular bacteria, and the ability of phages to increase in number during the infection process make phages excellent potential diagnostic and therapeutic agents for fighting bacterial disease. However, temperate phages are of little use in phage diagnostics and therapy.
Use of fluorescently labeled phage in the detection and identification of bacterial species. Mosier-Boss, P. A., Lieberman, S. H., Andrews, J. M., Rohwer, F. L., Wegley, L. E., Breitbart, M. (2003). Applied spectroscopy 57:1138-1144. Phages are viruses whose hosts are bacterial cells. They identify their hosts by specific receptor molecules on the outside of the host cell. Once the phages find their specific receptors, they bind to the bacterial cell and inject their nucleic acid inside the cell. The binding between phage and host can be so specific that only certain strains of a single species can be infected. In this communication, the specificity of phage P22 for Salmonella typhimurium LT2 is exploited to allow the detection of Salmonella in the presence of other bacterial species. In particular, the dsDNA of P22 is bound to SYBR gold, a highly sensitive, fluorescent nucleic acid stain. When multiple phages infect the same cell, the fluorescence emissions of the phage DNA inside the cell allow it to be imaged using an epifluorescence microscope. The advantages of using phages as the bacterial recognition element in a sensor over antibodies are discussed
Detection of the phytopathogenic bacteria phages in the gills of the Black Sea fishes. Semchuk, L. I., Stepanova, O. A., Boyko, A. L., Romashev, S. A., Andriychuk, O. M., Ignatenko, T. O., Yatskovska, L. I. (2003). Bulletin of the University of Kiev. , series Biology . A biological activity of phages, isolated from the gills of Black Sea fishes, to phytopathogenic bacteria was studied. It was shown the capacity of the testing cultures to support the phages reproduction during the definite time.
Viral abundance and a high proportion of lysogens suggest that viruses are important members of the microbial community in the Gulf of Trieste. Stopar, D., Cerne, A., Zigman, M., Poljsak-Prijatelj, M., Turk, V. (2003). Microbial Ecology 46:249-256. Epifluorescence microscopy and transmission electron microscopy were applied to study virioplankton community in the Gulf of Trieste (northern Adriatic Sea). The total viral abundance was in a range between 2.5 x 109/L and 2.9 x 1010/L and was positively correlated with trophic status of the environment. Viruslike particles were significantly correlated with bacterial abundance in all samples studied. Correlations with other physicochemical or biological parameters were not significant. The data suggest that, because of the substantial fraction of tailed viruses present (26%), bacteriophages are an important component of the virioplankton community in the Gulf of Trieste. The abundance of viruslike particles in the seawater changed at hour intervals in a range from 1.3 x 109/L to 5.1 x 109/L. A significant fraction (71%) of the bacterial isolates was inducible in vitro by mitomycin C, and a high occurrence (51%) of lysogenic isolates with more than one phage morphotype present in the lysate was detected. The presence of lysogenic bacteria in the seawater was confirmed in situ with a mitomycin C induction experiment on the natural bacterial population. Results suggest that virioplankton is an abundant component of the microbial community in the Gulf of Trieste
Transduction of porcine enteropathogenic Escherichia coli with a derivative of a shiga toxin 2-encoding bacteriophage in a porcine ligated ileal loop system. Tóth, I., Schmidt, H., Dow, M., Malik, A., Oswald, E., Nagy, B. (2003). Applied and Environmental Microbiology 69:7242-7247. In this study, we have investigated the ability of detoxified Shiga toxin (Stx)-converting bacteriophages F3538 (Dstx(2)::cat) (H. Schmidt et al., Appl. Environ. Microbiol. 65:3855-3861, 1999) and H-19B::Tn10d-bla (D. W. Acheson et al., Infect. Immun. 66:4496-4498, 1998) to lysogenize enteropathogenic Escherichia coli (EPEC) strains in vivo. We were able to transduce the porcine EPEC strain 1390 (O45) with F3538 (Dstx(2)::cat) in porcine ligated ileal loops but not the human EPEC prototype strain E2348/69 (O127). Neither strain 1390 nor strain E2348/69 was lysogenized under these in vivo conditions when E. coli K-12 containing H-19B::Tn10d-bla was used as the stx1 phage donor. The repeated success in the in vivo transduction of an Stx2-encoding phage to a porcine EPEC strain in pig loops was in contrast to failures in the in vitro trials with these and other EPEC strains. These results indicate that in vivo conditions are more effective for transduction of Stx2-encoding phages than in vitro conditions
Searching for the advantages of virus sex. Turner, P. E. (2003). Origins of Life and Evolution of the Biosphere 33:95-108. Sex (genetic exchange) is a nearly universal phenomenon in biological populations. But this is surprising given the costs associated with sex. For example, sex tends to break apart co-adapted genes, and sex causes a female to inefficiently contribute only half the genes to her offspring. Why then did sex evolve? One famous model poses that sex evolved to combat Muller's ratchet, the mutational load that accrues when harmful mutations drift to high frequencies in populations of small size. In contrast, the Fisher-Muller Hypothesis predicts that sex evolved to promote genetic variation that speeds adaptation in novel environments. Sexual mechanisms occur in viruses, which feature high rates of deleterious mutation and frequent exposure to novel or changing environments. Thus, confirmation of one or both hypotheses would shed light on the selective advantages of virus sex. Experimental evolution has been used to test these classic models in the RNA bacteriophage f6, a virus that experiences sex via reassortment of its chromosomal segments. Empirical data suggest that sex might have originated in f6 to assist in purging deleterious mutations from the genome. However, results do not support the idea that sex evolved because it provides beneficial variation in novel environments. Rather, experiments show that too much sex can be bad for f6; promiscuity allows selfish viruses to evolve and spread their inferior genes to subsequent generations. Here I discuss various explanations for the evolution of segmentation in RNA viruses, and the added cost of sex when large numbers of viruses co-infect the same cell
Rapid selection of phage-resistant mutants in Streptococcus thermophilus by immunoselection and cell sorting. Viscardi, M., Capparelli, R., Iannelli, D. (2003). International Journal of Food Microbiology 89:223-231. Immunoselection and flow cytometry allowed the isolation from Streptococcus thermophilus strain Str31 of double mutants displaying resistance to the phage f31 and good acid production. Strain Str31 is very sensitive to phage f31. This phage-host system seemed therefore particularly suitable to test the validity of the selection method adopted in this study. Mutants were stable with respect to both characters. The isolation of the double mutants required 4 to 5 days. The approach does not involve genetic manipulations and can therefore be an alternative to genetic engineering when this technology cannot be applied
Bacteriophages as an efficient therapy for antibiotic-resistant septicemia in man. Weber-Dabrowska, B., Mulczyk, M., Gorski, A. (2003). Transplantation proceedings 35:1385-1386. [first paragraph] Acute bacterial infection-induced sepsis, with shock, metabolic acidosis, oliguria, or hypoxemia, remains a major medical challenge, especially at a time when experts believe that we may be returning to the pre-antibiotic era, arising from increasing antibiotic resistance In the USA alone there are at least 500,000 cases of sepsis annually, with mortality rates ranging from 30% to 50% (ie, 150,000 to 250,000 deaths). Assuming a U.S. population of approximately 270 million and a total world population of >6 billion, this would mean at least 11 million cases of sepsis worldwide with at least 3 to 5 million deaths annually (or probably more, as American health-care standards are generally much higher than in many other countries). Several treatments designed to reduce sepsis-associated mortality have been unsuccessful; therefore, finding an effective new therapy for sepsis is urgently needed.
Lysogeny and virus-induced mortality of bacterioplankton in surface, deep, and anoxic waters. Weinbauer, M., Brettar, I., Höfle, M. (2003). Limnology and Oceanography 48:1457-1465. Lysogeny (bacteria containing inducible prophages) and lytic viral infection (bacteria in a lytic stage of infection) were investigated at the community level in contrasting marine environments such as estuarine versus offshore waters, surface versus deep waters, and oxic versus anoxic waters in the Mediterranean and Baltic Seas. The frequency of lysogenic cells (FLC) in bacterioplankton communities ranged from not detectable to 84% as estimated by prophage induction due to mitomycin C, and highest values were typically found in deep waters (800–2,000 m). Transmission electron microscopy based estimates of virus-induced mortality of bacterioplankton (VMB) ranged from a few percent to 71%, and highest values were found in anoxic waters of the Baltic Sea. FLC and the frequency of infected cells (FIC) were related in form of a negative power function indicating that environments exist where one of the two viral life strategies prevails. Across all investigated environments, FLC was negatively related to bacterial abundance and production, whereas FIC showed a positive relationship with viral and bacterial parameters. FIC was higher and FLC was lower in moderately productive estuarine and offshore surface waters than in less productive mesopelagic and deep waters. Thus, lysogeny seems to be a survival strategy at low host abundance and activity, whereas high host abundance and activity seems to favor the lytic life cycle. The key process for the prevalence of lytic infection compared to prophage replication at high host abundance could be competition due to outnumbering. Between 11% and 88% (average, 35%) of the bacteria contained a functional (lytic or lysogenic) viral genome.
Comparing the effects of resource enrichment and grazing on viral production in a meso-eutrophic reservoir. Weinbauer, M. G., Christaki, U., Nedoma, J., Simek, K. (2003). Aquatic Microbial Ecology 31:137-144. As viral production depends on bacteria, factors which influence bacterial production should also impact viral production. Likewise, viruses and heterotrophic nanoflagellates (HNF) both exploit bacterial prey, so HNF grazing could influence interactions between viruses and bacteria. To examine these relationships, we examined samples from experiments in which natural bacterial populations were subjected to relaxation of nutrient limitation and different levels of grazing pressure from HNF. We observed that stimulation of bacterial production and abundance with the relaxation of nutrient limitation resulted in a higher standing stock of viruses, higher viral production and also a higher virus-induced lysis rate of bacterioplankton. These relationships suggest that the relative effect of virus-induced mortality is higher in more productive environments. We found that viral abundance, viral production and virus-induced mortality of bacteria was highest in the treatments in which grazing rates on bacteria by HNF were highest, and lowest in the treatments where no eukaryotic predators were present. Thus, high grazing rates were associated with high virus production rates. The resource enrichment had a stronger effect on viral production and infection of bacteria than grazing. Averaged over time for single treatments, viruses lysed a significant portion (range, 18 to 66%) of the bacterial production per day.
Sampling natural viral communities from soil for culture-independent analyses. Williamson, K. E., Wommack, K. E., Radosevich, M. (2003). Applied and Environmental Microbiology 69:6628-6633. An essential first step in investigations of viruses in soil is the evaluation of viral recovery methods suitable for subsequent culture-independent analyses. In this study, four elution buffers (10% beef extract, 250 mM glycine buffer, 10 mM sodium pyrophosphate, and 1% potassium citrate) and three enumeration techniques (plaque assay, epifluorescence microscopy [EFM], and transmission electron microscopy [TEM]) were compared to determine the best method of extracting autochthonous bacteriophages from two Delaware agricultural soils. Beef extract and glycine buffer were the most effective in eluting viable phages inoculated into soils (up to 29% recovery); however, extraction efficiency varied significantly with phage strain. Potassium citrate eluted the highest numbers of virus-like particles from both soils based on enumerations by EFM (mean, 5.3 x 108 g of dry soil-1), but specific soil-eluant combinations posed significant problems to enumeration by EFM. Observations of virus-like particles under TEM gave confidence that the particles were, in fact, phages, but TEM enumerations yielded measurements of phage abundance (mean, 1.5 x 108 g of dry soil-1) that were about five times lower. Clearly, the measurement of phage abundance in soils varies with both the extraction and enumeration methodology; thus, it is important to assess multiple extraction and enumeration approaches prior to undertaking ecological studies of phages in a particular soil
Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. Lawrence, J. G., Hatfull, G. F., Hendrix, R. W. (2002). Journal of Bacteriology 184:4891-4905. The practice of classifying organisms into hierarchical groups originated with Aristotle and was codified into nearly immutable biological law by Linnaeus. The heart of taxonomy is the biological species, which forms the foundation for higher levels of classification. Whereas species have long been established among sexual eukaryotes, achieving a meaningful species concept for prokaryotes has been an onerous task and has proven exceedingly difficult for describing viruses and bacteriophages. Moreover, the assembly of viral "species" into higher-order taxonomic groupings has been even more tenuous, since these groupings were based initially on limited numbers of morphological features and more recently on overall genomic similarities. The wealth of nucleotide sequence information that catalyzed a revolution in the taxonomy of free-living organisms necessitates a reevaluation of the concept of viral species, genera, families, and higher levels of classification. Just as microbiologists discarded dubious morphological traits in favor of more accurate molecular yardsticks of evolutionary change, virologists can gain new insight into viral evolution through the rigorous analyses afforded by the molecular phylogenetics of viral genes. For bacteriophages, such dissections of genomic sequences reveal fundamental flaws in the Linnaean paradigm that necessitate a new view of viral evolution, classification, and taxonomy.
The adaptation and survival of phages in nature. Semchuk, L. I., Ignatenko, T., Romashev, S. A., Andriychuk, O., Yatskovska, L. (2002). Bulletin of the University of Kiev, series Biology 38:54-56. The short analyse of the phage's properties changing, their evolution and survival adaptation in the environment is given.
Detection of populations of phages of phytopathogenic bacterias and their biological properties. Boyko, A. L., Semchuk, L. I., Romashev, S. A., Andriychuk, L. N. (2001). Bulletin of the Agroscience 51-53. Excreted bacteriophages to X. axonopodis pv. beticola, E. carÏtovora, P. syringae pv. atrofaciens in the Kiev area. The bacteriophages showed specific specificity, were look-alike on morphology, sizes, are stable at long-term storage and in range pH 4-10. The role of populations of phages in biocenoses and capability of indication of pathogens with their help is discussed.
Ecological and biological aspects of research phages phytopathogenic bacteria. Semchuk, L. I., Andriychuk, E. M., Romashev, S. A., JatskÏvska, L. I. (2001). Bulletin of the University of Kiev, series Biology N35:11-13. Investigated features of biology and ecology of phages of phytopathogenic bacteria Xanthomonas and Pseudomonas on sowings of sugar beet.
Effect of resource supply rate on host-pathogen dynamics. Bohannan, B. J. M. (2000). in Bell, C. R., Brylinsky, M., Johnson-Green, P. (eds.) Microbial Biosystems: New Frontiers. Atlantic Canada Society for Microbial Ecology, Halifax, Canada. The dynamics of model host cell (E. coli) and model pathogen (bacteriophage) populations were studied in chemostats with different resource supply rates. Resource supply rate was manipulated by altering the concentration of the limiting resource (glucose) in the incoming media. Population responses to increased resource supply rate were influenced strongly by the vulnerability of the host cells to infection. When the host cell population consisted entirely of cells equally vulnerable to infection, both pathogen and host cells responded to increased resource supply rate with an increase in their average densities. In contrast, when the host cell contained some cells that were less vulnerable to infection (i.e., partially phage-resistant E. coli), only the pathogen population responded to increased supply rate with a significant increase in average density. Furthermore, when the host cell population contained some cells completely invulnerable to infection (i.e., phage-resistant E. coli) only the host cell population responded to increased supply rate with an increase in average density. These responses were in general agreement with the predictions of mechanistic models of resource-consumer interactions.
Genetic analysis of a bacterial genetic exchange element: the gene transfer agent of Rhodobacter capsulatus. Lang, A. S., Beatty, J. T. (2000). Proceedings of the National Academy of Sciences, USA 97:859-864. An unusual system of genetic exchange exists in the purple nonsulfur bacterium Rhodobacter capsulatus. DNA transmission is mediated by a small bacteriophage-like particle called the gene transfer agent (GTA) that transfers random 4.5-kb segments of the producing cell's genome to recipient cells, where allelic replacement occurs. This paper presents the results of gene cloning, analysis, and mutagenesis experiments that show that GTA resembles a defective prophage related to bacteriophages from diverse genera of bacteria, which has been adopted by R. capsulatus for genetic exchange. A pair of cellular proteins, CckA and CtrA, appear to constitute part of a sensor kinase/response regulator signaling pathway that is required for expression of GTA structural genes. This signaling pathway controls growth-phase-dependent regulation of GTA gene messages, yielding maximal gene expression in the stationary phase. We suggest that GTA is an ancient prophage remnant that has evolved in concert with the bacterial genome, resulting in a genetic exchange process controlled by the bacterial cell.
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