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Paul VG, Mormile MR. A case for the protection of saline and hypersaline environments: a microbiological perspective. FEMS Microbiol Ecol 2017; 93:3950317. [DOI: 10.1093/femsec/fix091] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/09/2017] [Indexed: 11/12/2022] Open
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van Zyl LJ, Nemavhulani S, Cass J, Cowan DA, Trindade M. Three novel bacteriophages isolated from the East African Rift Valley soda lakes. Virol J 2016; 13:204. [PMID: 27912769 PMCID: PMC5135824 DOI: 10.1186/s12985-016-0656-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 11/21/2016] [Indexed: 12/21/2022] Open
Abstract
Background Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and consequently few bacteriophages that infect bacteria from haloalkaline environments have been described. Methods Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on two different Bacillus species and one Paracoccus species using agar overlays. The growth characteristics of each phage in its host was investigated and the genome sequences determined and analysed by comparison with known phages. Results Phage Shbh1 belongs to the family Myoviridae while Mgbh1 and Shpa belong to the Siphoviridae family. Tetranucleotide usage frequencies and G + C content suggests that Shbh1 and Mgbh1 do not regularly infect, and have therefore not evolved with, the hosts they were isolated on here. Shbh1 was shown capable of infecting two different Bacillus species from the two different lakes demonstrating its potential broad-host range. Comparative analysis of their genome sequence with known phages revealed that, although novel, Shbh1 does share substantial amino acid similarity with previously described Bacillus infecting phages (Grass, phiNIT1 and phiAGATE) and belongs to the Bastille group, while Mgbh1 and Shpa are highly novel. Conclusion The addition of these phages to current databases should help with metagenome/metavirome annotation efforts. We describe a highly novel Paracoccus infecting virus (Shpa) which together with NgoΦ6 and vB_PmaS_IMEP1 is one of only three phages known to infect Paracoccus species but does not show similarity to these phages. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0656-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa.
| | - Shonisani Nemavhulani
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa
| | - James Cass
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa
| | - Donald Arthur Cowan
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa.,Department of Genetics, University of Pretoria, Pretoria, 0002, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville, Cape Town, 7535, South Africa
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Baxter BK, Gunde-Cimerman N, Oren A. Salty sisters: The women of halophiles. Front Microbiol 2014; 5:192. [PMID: 24926287 PMCID: PMC4045239 DOI: 10.3389/fmicb.2014.00192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/10/2014] [Indexed: 01/02/2023] Open
Abstract
A history of halophile research reveals the commitment of scientists to uncovering the secrets of the limits of life, in particular life in high salt concentration and under extreme osmotic pressure. During the last 40 years, halophile scientists have indeed made important contributions to extremophile research, and prior international halophiles congresses have documented both the historical and the current work. During this period of salty discoveries, female scientists, in general, have grown in number worldwide. But those who worked in the field when there were small numbers of women sometimes saw their important contributions overshadowed by their male counterparts. Recent studies suggest that modern female scientists experience gender bias in matters such as conference invitations and even representation among full professors. In the field of halophilic microbiology, what is the impact of gender bias? How has the participation of women changed over time? What do women uniquely contribute to this field? What are factors that impact current female scientists to a greater degree? This essay emphasizes the “her story” (not “history”) of halophile discovery.
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Affiliation(s)
- Bonnie K Baxter
- Great Salt Lake Institute, Westminster College Salt Lake City, UT, USA
| | - Nina Gunde-Cimerman
- Molecular Genetics and Microbiology, University of Ljubljana Ljubljana, Slovenia ; Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins Ljubljana, Slovenia
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem Givat Ram, Israel
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Boujelben I, Yarza P, Almansa C, Villamor J, Maalej S, Antón J, Santos F. Virioplankton community structure in Tunisian solar salterns. Appl Environ Microbiol 2012; 78:7429-37. [PMID: 22904045 PMCID: PMC3457115 DOI: 10.1128/aem.01793-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Accepted: 08/06/2012] [Indexed: 11/20/2022] Open
Abstract
The microbial community inhabiting Sfax solar salterns on the east coast of Tunisia has been studied by means of different molecular and culture-dependent tools that have unveiled the presence of novel microbial groups as well as a community structure different from that of other coastal hypersaline environments. We have focused on the study of the viral assemblages of these salterns and their changes along the salinity gradient and over time. Viruses from three ponds (C4, M1, and TS) encompassing salinities from moderately hypersaline to saturated (around 14, 19, and 35%, respectively) were sampled in May and October 2009 and analyzed by transmission electron microscopy (TEM) and pulsed-field gel electrophoresis (PFGE). Additionally, for all three October samples and the May TS sample, viral metagenomic DNA was cloned in fosmids, end sequenced, and analyzed. Viral concentration, as well as virus-to-cell ratios, increased along the salinity gradient, with around 10(10) virus-like particles (VLPs)/ml in close-to-saturation ponds, which represents the highest viral concentration reported so far for aquatic systems. Four distinct morphologies could be observed with TEM (spherical, tailed, spindled, and filamentous) but with various proportions in the different samples. Metagenomic analyses indicated that every pond harbored a distinct viral assemblage whose G+C content could be roughly correlated with that of the active part of the microbial community that may have constituted the putative hosts. As previously reported for hypersaline metaviromes, most sequences did not have matches in the databases, although some were conserved among the Sfax metaviromes. BLASTx, BLASTp, and dinucleotide frequency analyses indicated that (i) factors additional to salinity could be structuring viral communities and (ii) every metavirome had unique gene contents and dinucleotide frequencies. Comparison with hypersaline metaviromes available in the databases indicated that the viral assemblages present in close-to-saturation environments located thousands of kilometers apart presented some common traits among them in spite of their differences regarding the putative hosts. A small core metavirome for close-to-saturation systems was found that contained 7 sequences of around 100 nucleotides (nt) whose function was not hinted at by in silico search results, although it most likely represents properties essential for hyperhalophilic viruses.
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Affiliation(s)
- Ines Boujelben
- Département des Sciences de la Vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Pablo Yarza
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Cristina Almansa
- Servicios Técnicos de Investigación (SSTTI), Unidad de Microscopía, Universidad de Alicante, Alicante, Spain
| | - Judith Villamor
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Sami Maalej
- Département des Sciences de la Vie, Faculté des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
| | - Josefa Antón
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
- Instituto Multidisciplinar para el Estudio del Medio Ramón Margalef, Universidad de Alicante, Alicante, Spain
| | - Fernando Santos
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
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Casas V, Maloy S. Role of bacteriophage-encoded exotoxins in the evolution of bacterial pathogens. Future Microbiol 2012; 6:1461-73. [PMID: 22122442 DOI: 10.2217/fmb.11.124] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Recent advances in metagenomics research have generated a bounty of information that provides insight into the dynamic genetic exchange occurring between bacteriophage (phage) and their bacterial hosts. Metagenomic studies of the microbiomes from a variety of environments have shown that many of the genes sequenced are of phage origin. Among these genes are phage-encoded exotoxin genes. When phage that carry these genes infect an appropriate bacterial host, the bacterium undergoes lysogenic conversion, converting the bacterium from an avirulent strain to a pathogen that can cause human disease. Transfer of the exotoxin genes between bacteria has been shown to occur in marine environments, animal and human intestines and sewage treatment plants. Surprisingly, phage that encode exotoxin genes are commonly found in environments that lack the cognate bacteria commonly associated with the specific toxin-mediated disease and have been found to be associated with alternative environmental bacterial hosts. These findings suggest that the exotoxin genes may play a beneficial role for the bacterial host in nature, and that this environmental reservoir of exotoxin genes may play a role in the evolution of new bacterial pathogens.
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Affiliation(s)
- Veronica Casas
- Center for Microbial Sciences, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
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Santos F, Yarza P, Parro V, Meseguer I, Rosselló-Móra R, Antón J. Culture-independent approaches for studying viruses from hypersaline environments. Appl Environ Microbiol 2012; 78:1635-43. [PMID: 22247131 PMCID: PMC3298169 DOI: 10.1128/aem.07175-11] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hypersaline close-to-saturation environments harbor an extremely high concentration of virus-like particles, but the number of haloviruses isolated so far is still very low. Haloviruses can be directly studied from natural samples by using different culture-independent techniques that include transmission electron microscopy, pulsed-field gel electrophoresis, and different metagenomic approaches. Here, we review the findings of these studies, with a main focus on the metagenomic approaches. The analysis of bulk viral nucleic acids directly retrieved from the environment allows estimations of viral diversity, activity, and dynamics and tentative host assignment. Results point to a diverse and active viral community in constant interplay with its hosts and to a "hypersalineness" quality common to viral assemblages present in hypersaline environments that are thousands of kilometers away from each other.
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Affiliation(s)
- Fernando Santos
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
| | - Pablo Yarza
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
- Marine Microbiology Group, Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Esporles (Mallorca), Spain
| | - Víctor Parro
- Departamento de Evolución Molecular, Centro de Astrobiología (INTA-CSIC), Torrejón de Ardoz, Madrid, Spain
| | - Inmaculada Meseguer
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
- Departamento de Producción vegetal y Microbiología, Universidad Miguel Hernández, Elche, Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Esporles (Mallorca), Spain
| | - Josefa Antón
- Departamento de Fisiología, Genética y Microbiología, Universidad de Alicante, Alicante, Spain
- Instituto Multidisciplinar para el Estudio del Medio Ramón Margalef, Universidad de Alicante, Alicante, Spain
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Trade-offs between competition and defense specialists among unicellular planktonic organisms: the "killing the winner" hypothesis revisited. Microbiol Mol Biol Rev 2010; 74:42-57. [PMID: 20197498 DOI: 10.1128/mmbr.00034-09] [Citation(s) in RCA: 206] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A trade-off between strategies maximizing growth and minimizing losses appears to be a fundamental property of evolving biological entities existing in environments with limited resources. In the special case of unicellular planktonic organisms, the theoretical framework describing the trade-offs between competition and defense specialists is known as the "killing the winner" hypothesis (KtW). KtW describes how the availability of resources and the actions of predators (e.g., heterotrophic flagellates) and parasites (e.g., viruses) determine the composition and biogeochemical impact of such organisms. We extend KtW conceptually by introducing size- or shape-selective grazing of protozoans on prokaryotes into an idealized food web composed of prokaryotes, lytic viruses infecting prokaryotes, and protozoans. This results in a hierarchy analogous to a Russian doll, where KtW principles are at work on a lower level due to selective viral infection and on an upper level due to size- or shape-selective grazing by protozoans. Additionally, we critically discuss predictions and limitations of KtW in light of the recent literature, with particular focus on typically neglected aspects of KtW. Many aspects of KtW have been corroborated by in situ and experimental studies of isolates and natural communities. However, a thorough test of KtW is still hampered by current methodological limitations. In particular, the quantification of nutrient uptake rates of the competing prokaryotic populations and virus population-specific adsorption and decay rates appears to be the most daunting challenge for the years to come.
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Leblanc C, Caumont-Sarcos A, Comeau AM, Krisch HM. Isolation and genomic characterization of the first phage infecting Iodobacteria: ϕPLPE, a myovirus having a novel set of features. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:499-509. [PMID: 23765928 DOI: 10.1111/j.1758-2229.2009.00055.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The aquatic phage ϕPLPE infects a bacterium of the genus Iodobacter that are common inhabitants of rivers, streams and canals that produce violacein-like pigments. Our characterization of ϕPLPE reveals it to be a small, contractile-tailed phage whose 47.5 kb genome sequence is phylogenetically distant from all previously characterized phages. The genome has a generally modular organization (e.g. replication/recombination, structure/morphogenesis, lysis/lysogeny) and approximately half of its 84 open reading frames have no known homologues. It behaves as a virulent phage under the host growth conditions we have employed and, with the exception of an anti-repressor (ant) homologue, the genome lacks all the genes associated with a lysogenic lifestyle. Thus, either ϕPLPE was once a temperate phage that has lost most of its lysogeny cassette or it is a virulent phage that acquired an ant-like gene presumably for some function other than the control of lysogeny. The ϕPLPE genome has few bacterial gene homologues with the interesting exception of a putative acylhydrolase (acylase). This function has been implicated in bacterial quorum sensing since it degrades homoserine-lactone signalling molecules and can disrupt or modulate quorum signalling from either the emitter or its competitors. ϕPLPE may be an example of a phage co-opting components of the bacterial quorum-sensing apparatus to its own advantage.
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Affiliation(s)
- Cécile Leblanc
- Centre National de la Recherche Scientifique, LMGM, F-31000 Toulouse, France. Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, F-31000 Toulouse, France
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Choi S, Jeliazkov I, Jiang SC. Lysogens and free viruses in fresh, brackish, and marine waters: a Bayesian analysis. FEMS Microbiol Ecol 2009; 69:243-54. [PMID: 19508280 DOI: 10.1111/j.1574-6941.2009.00705.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A yearlong study was conducted to determine factors that affect the abundance and distribution of lysogens and free viruses at fresh-, brackish-, and saltwater stations in Newport Bay, CA. The viral and bacterial abundance were highest in the freshwater (average 1.1 x 10(8) and 1.1 x 10(7) mL(-1), respectively) and lowest in the marine water (average 0.4 x 10(8) and 0.5 x 10(7) mL(-1), respectively). Bacterial and viral counts were also several times higher during the summer than in winter. Approximately, 35% of the 141 samples were inducible in the presence of mitomycin C. The highest percentage of inducible lysogens was observed in marine waters (42%), while the lowest percentage was observed in the warmer freshwater (23%). A statistical model for the joint occurrence of lysogens and free viruses was formulated and estimated using Bayesian techniques to understand the key environmental determinants of viruses and lysogens. Our results support the existence of significant heterogeneity between the saltwater and freshwater sites. A parsimonious model that combines the two saltwater sites performs best among the specifications that were considered. Bacteria and water temperature were significant determinants of virus counts, whereas lysogen relationships are unclear. Importantly, conditional on the covariates, viruses and lysogen fractions exhibit robust negative correlation.
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Affiliation(s)
- Samuel Choi
- Environmental Health, Science and Policy, University of California, Irvine, CA, USA
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Serwer P, Hayes SJ, Thomas JA, Griess GA, Hardies SC. Rapid determination of genomic DNA length for new bacteriophages. Electrophoresis 2007; 28:1896-902. [PMID: 17480041 DOI: 10.1002/elps.200600672] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
dsDNA viruses with long genomes (>200 kb) are expected to be a major source of novel genes. To rapidly characterize the genomes of newly isolated dsDNA bacteriophages, we develop here a procedure for the PFGE of intact long DNA genomes from bacteriophage particles in unfractionated, infected cell lysates of either liquid or gelled cultures. The DNA used for PFGE is suitable for sequencing after extraction with phenol. The PFGE is tuned to the range of expected DNA lengths. This procedure bypasses the isolation of bacteriophage particles and is useful for PFGE analysis of DNA from dissected zones of bacteriophage plaques.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA.
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