Skip to main content
SpringerLink
Log in

An examination of the bacteriophages and bacteria of the Namib desert

  • Articles
  • Published:
The Journal of Microbiology Aims and scope Submit manuscript

Abstract

Bacteria and their viruses (called bacteriophages, or phages), have been found in virtually every ecological niche on Earth. Arid regions, including their most extreme form called deserts, represent the single largest ecosystem type on the Earth’s terrestrial surface. The Namib desert is believed to be the oldest (80 million years) desert. We report here an initial analysis of bacteriophages isolated from the Namib desert using a combination of electron microscopy and genomic approaches. The virus-like particles observed by electron microscopy revealed 20 seemingly different phage-like morphologies and sizes belonging to the Myoviridae and Siphoviridae families of tailed phages. Pulsed-field gel electrophoresis revealed a majority of phage genomes of 55∼65 kb in length, with genomes of approximately 200, 300, and 350 kb also observable. Sample sequencing of cloned phage DNA fragments revealed that approximately 50% appeared to be of bacterial origin. Of the remaining DNA sequences, approximately 50% displayed no significant match to any sequence in the databases. The majority of the 16S rDNA sequences amplified from DNA extracted from the sand displayed considerable (94∼98%) homology to members of the Firmicutes, and in particular to members of the genus Bacillus, though members of the Bacteroidetes, Planctomycetes, Chloroflexi, and 8-Proteobacteria groups were also observed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Ackermann, H.W. and M.S. DuBow. 1987. Viruses of Procaryotes, Volumes 1 and 2. CRC Press, Cleveland, OH, USA.

    Google Scholar 

  • Ackermann, H.W. and M.S. DuBow. 2000. Myoviridae, siphoviridae, podoviridae, p. 69–109. In M.H.V. Van Regenmortel, D.H.L. Bishop, E.B. Carstens, M.K. Estes, S.M. Lemon, J. Maniloff, M.A. Mayo, D.J. McGeoch, C.R. Pringle, and R.B. Wickner (eds.), Virus taxonomy: Classification of viruses. Seventh report of the international committee on taxonomy of viruses. Academic Press, San Diego, CA, USA.

    Google Scholar 

  • Amann, R.I., W. Ludwig, and K.H. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169.

    PubMed  CAS  Google Scholar 

  • Antranikian, G., C.E. Vorgias, and C. Bertoldo. 2005. Extreme environments as a resource for microorganisms and novel bio-catalysts. Adv. Biochem. Eng. Biotechnol. 96, 219–262.

    PubMed  CAS  Google Scholar 

  • Borriss, M., E. Helmke, R. Hanschke, and T. Schweder. 2003. Isolation and characterization of marine psychrophilic phage-host systems from arctic sea ice. Extremophiles 7, 377–384.

    Article  PubMed  CAS  Google Scholar 

  • Breitbart, M., B. Felts, S. Kelley, J.M. Mahaffy, J. Nulton, P. Salamon, and F. Rohwer. 2004. Diversity and population structure of a near-shore marine-sediment viral community. Proc. Biol. Sci. 271, 565–574.

    Article  PubMed  Google Scholar 

  • Breitbart, M. and F. Rohwer. 2005. Here a virus, there a virus, everywhere the same virus? Trends Microbiol. 13, 278–284.

    Article  PubMed  CAS  Google Scholar 

  • Breitbart, M., P. Salamon, B. Andresen, J.M. Mahaffy, A.M. Segall, D. Mead, F. Azam, and F. Rohwer. 2002. Genomic analysis of uncultured marine viral communities. Proc. Natl. Acad. Sci. USA 99, 14250–14255.

    Article  PubMed  CAS  Google Scholar 

  • Burke, A. 2001. Determining landscape function and ecosystem dynamics: Contribution to ecological restoration in the southern Namib desert. Ambio 30, 29–36.

    Article  PubMed  CAS  Google Scholar 

  • Canchaya, C., C. Proux, G. Fournous, A. Bruttin, and H. Brussow. 2003. Prophage genomics. Microbiol. Mol. Biol. Rev. 67, 238–276.

    Article  PubMed  CAS  Google Scholar 

  • Chanal, A., V. Chapon, K. Benzerara, M. Barakat, R. Christen, W. Achouak, F. Barras, and T. Heulin. 2006. The desert of Tataouine: An extreme environment that hosts a wide diversity of microorganisms and radiotolerant bacteria. Environ. Microbiol. 8, 514–525.

    Article  PubMed  CAS  Google Scholar 

  • Crump, B., E.V. Armbrust, and J.A. Baross. 1999. Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia river, its estuary, and the adjacent coastal ocean. Appl. Environ. Microbiol. 65, 3192–3204.

    PubMed  CAS  Google Scholar 

  • Davey, M.E. and G.A. O’Toole. 2000. Microbial biofilms: From ecology to molecular genetics. Microbiol. Mol. Biol. Rev. 64, 847–867.

    Article  PubMed  CAS  Google Scholar 

  • Donlan, R. 2002. Biofilms: Microbial life on surfaces. Emerg. Infect. Dis. 8, 881–890.

    PubMed  Google Scholar 

  • Dunbar, J., S.M. Barns, L.O. Ticknor, and C.R. Kuske. 2002. Empirical and theoretical bacterial diversity in four Arizona soils. Appl. Environ. Microbiol. 68, 3035–3045.

    Article  PubMed  CAS  Google Scholar 

  • Elasri, M.O. and R.V. Miller. 1999. Study of the response of a bio-film bacterial community to UV radiation. Appl. Environ. Microbiol. 65, 2025–2031.

    PubMed  CAS  Google Scholar 

  • Elasri, M.O., T. Reid, S. Hutchens, and R.V. Miller. 2000. Response of a Pseudomonas aeruginosa biofilm community to DNA-damaging chemical agents. FEMS Microbiol. Ecol. 33, 21–25.

    Article  CAS  Google Scholar 

  • Forterre, P. 2001. New viruses for the new millennium. Trends Microbiol. 9, 114.

    Article  PubMed  CAS  Google Scholar 

  • Fouts, D.E. 2006. Phage finder: Automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res. 34, 5839–5851.

    Article  PubMed  CAS  Google Scholar 

  • Fuhrman, J.A. 1999. Marine viruses and their biogeochemical and ecological effects. Nature 399, 541–548.

    Article  PubMed  CAS  Google Scholar 

  • Gallardo, A.W.S. 1995. Factors determining soil microbial biomass and nutrient immobilization in desert soils. Biogeochemistry 28, 55–68.

    Article  Google Scholar 

  • Garcia-Pichel, F., A. Lopez-Cortes, and U. Nubel. 2001. Phylogenetic and morphological diversity of Cyanobacteria in soil desert crusts from the Colorado plateau. Appl. Environ. Microbiol. 67, 1902–1910.

    Article  PubMed  CAS  Google Scholar 

  • Geslin, C., M. Le Romancer, M. Gaillard, G. Erauso, and D. Prieur. 2003. Observation of virus-like particles in high temperature enrichment cultures from deep-sea hydrothermal vents. Res. Microbiol. 154, 303–307.

    Article  PubMed  Google Scholar 

  • Heulin, T., M. Barakat, R. Christen, M. Lesourd, L. Sutra, G. De Luca, and W. Achouak. 2003. Ramlibacter tataouinensis gen. Nov., sp. Nov., and Ramlibacter henchirensis sp. Nov., cyst-producing bacteria isolated from subdesert soil in Tunisia. Int. J. Syst. Evol. Microbiol. 53, 589–594.

    Article  PubMed  CAS  Google Scholar 

  • Khemayan, K., T. Pasharawipas, O. Puiprom, S. Sriurairatana, O. Suthienkul, and T.W. Flegel. 2006. Unstable lysogeny and pseudolysogeny in Vibrio harveyi Siphovirus-like phage 1. Appl. Environ. Microbiol. 72, 1355–1363.

    Article  PubMed  CAS  Google Scholar 

  • Kwan, T., J. Liu, M.S. DuBow, P. Gros, and J. Pelletier. 2005. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc. Natl. Acad. Sci. USA 102, 5174–5179.

    Article  PubMed  CAS  Google Scholar 

  • Lucchini, S., F. Desiere, and H. Brussow. 1999. Comparative genomics of Streptococcus thermophilus phage species supports a modular evolution theory. J. Virol. 8647–8656.

  • Mann, N. 2003. Phages of the marine Cyanobacterial picophyto-plankton. FEMS Microbiol. Rev. 27, 17–34.

    Article  PubMed  CAS  Google Scholar 

  • Nagesha, H.S., M. Yu, and L.F. Wang. 1996. Application of linker-ligation-PCR for construction of phage display epitope libraries. J. Virol. Methods 60, 147–154.

    Article  PubMed  CAS  Google Scholar 

  • Nagy, M.L., A. Perez, and F. Garcia-Pichel. 2005. The prokaryotic diversity of biological soil crusts in the Sonoran desert (Organ Pipe Cactus national monument, AZ). FEMS Microbiol. Ecol. 54, 233–245.

    Article  PubMed  CAS  Google Scholar 

  • Peduzzi, P. and F. Schiemer. 2004. Bacteria and viruses in the water column of tropical freshwater reservoirs. Environ. Microbiol. 6, 707–715.

    Article  PubMed  Google Scholar 

  • Peng, X., H. Blum, Q. She, S. Mallok, K. Brugger, R.A. Garrett, W. Zillig, and D. Prangishvili. 2001. Sequences and replication of genomes of the Archeal Rudiviruses sirv1 and sirv2: Relationships to the Archeal Lipothrixvirus sifv and some eukaryal viruses. Virology 291, 226–234.

    Article  PubMed  CAS  Google Scholar 

  • Prangishvili, D., P. Forterre, and R.A. Garrett. 2006. Viruses of the Archaea: A unifying view. Nat. Rev. Microbiol. 4, 837–848.

    Article  PubMed  CAS  Google Scholar 

  • Prangishvili, D. and R.A. Garrett. 2005. Viruses of hyperthermophilic Crenarchaea. Trends Microbiol. 13, 535–542.

    Article  PubMed  CAS  Google Scholar 

  • Prigent, M., M. Leroy, F. Confalonieri, M. Dutertre, and M.S. DuBow. 2005. A diversity of bacteriophage forms and genomes can be isolated from the surface sands of the Sahara desert. Extremophiles 9, 289–296.

    Article  PubMed  CAS  Google Scholar 

  • Reasoner, D.J. and E.E. Geldreich. 1985. A new medium for the enumeration and subculture of bacteria from potable water. Appl. Environ. Microbiol. 49, 1–7.

    PubMed  CAS  Google Scholar 

  • Rice, G., K. Stedman, J. Snyder, B. Wiedenheft, D. Willits, S. Brumfield, T. McDermott, and M.J. Young. 2001. Viruses from extreme thermal environments. Proc. Natl. Acad. Sci. USA 98, 13341–13345.

    Article  PubMed  CAS  Google Scholar 

  • Ripp, S. and R.V. Miller. 1997. The role of pseudolysogeny in bacter-iophage-host interactions in a natural freshwater environment. Microbiology 143, 2065–2070.

    Article  CAS  Google Scholar 

  • Ripp, S. and R.V. Miller. 1998. Dynamics of the pseudolysogenic response in slowly growing cells of Pseudomonas aeruginosa. Microbiology 144, 2225–2232.

    PubMed  CAS  Google Scholar 

  • Rohwer, F. 2003. Global phage diversity. Cell 113, 141.

    Article  PubMed  CAS  Google Scholar 

  • Romero, P., R. López, and E. García. 2004. Genomic organization and molecular analysis of the inducible prophage EJ-1, a mosaic myovirus from an atypical Pneumococcus. Virology 322, 239–252.

    Article  PubMed  CAS  Google Scholar 

  • Satyanarayana, T., C. Raghukumar, and S. Shivaji. 2005. Extremophilic microbes: diversity and perspectives. Curr. Sci. 89, 78–90.

    Google Scholar 

  • Vettori, C., G. Stotzky, M. Yoder, and E. Gallori. 1999. Interaction between bacteriophage PBS1 and clay minerals and transduction of Bacillus subtilis by clay-phage complexes. Environ. Microbiol. 1, 347–355.

    Article  PubMed  CAS  Google Scholar 

  • Vincent, W., J.A. Gibson, R. Pienitz, V. Villeneuve, P.A. Broady, P.B. Hamilton, and C. Howard-Williams. 2000. Ice shelf microbial ecosystems in the high arctic and implications for life on snowball earth. Naturwissenschaften 87, 137–141.

    Article  PubMed  CAS  Google Scholar 

  • Williamson, K., M. Radosevich, D.W. Smith, and K.E. Wommack. 2007. Incidence of lysogeny within temperate and extreme soil environments. Environ. Microbiol. 9, 2563–2574.

    Article  PubMed  CAS  Google Scholar 

  • Williamson, K., M. Radosevich, and K.E. Wommack. 2005. Abundance and diversity of viruses in six Delaware soils. Appl. Environ. Microbiol. 71, 3119–3125.

    Article  PubMed  CAS  Google Scholar 

  • Williamson, K., K.E. Wommack, and M. Radosevich. 2003. Sampling natural viral communities from soil for culture-independent analyses. Appl. Environ. Microbiol. 69, 6628–6633.

    Article  PubMed  CAS  Google Scholar 

  • Wommack, K.E. and R.R. Colwell. 2000. Virioplankton: Viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64, 69–114.

    Article  PubMed  CAS  Google Scholar 

  • Wood, H.E., M.T. Dawson, K.M. Devine, and D.J. McConnell. 1990. Characterization of PBS-X, a defective prophage of Bacillus subtilis. J. Bacteriol. 172, 2667–2674.

    PubMed  CAS  Google Scholar 

  • Zhou, J., M.A. Bruns, and J.M. Tiedje. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62, 316–322.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratoire de Génomique et Biodiversité Microbienne des Biofilms, Université Paris-Sud 11, Institut de Génétique et Microbiologie, CNRS UMR 8621, Bâtiment 409, 91405, Orsay, France

    Eric Prestel, Sylvie Salamitou & Michael S. DuBow

Authors
  1. Eric Prestel
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sylvie Salamitou
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Michael S. DuBow
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Michael S. DuBow.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Prestel, E., Salamitou, S. & DuBow, M.S. An examination of the bacteriophages and bacteria of the Namib desert. J Microbiol. 46, 364–372 (2008). https://doi.org/10.1007/s12275-008-0007-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-008-0007-4

Keywords

Search

Navigation