Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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A Fosmid Cloning Strategy for Detecting the Widest Possible Spectrum of Microbes from the International Space Station Drinking Water System

  • Choi, Sangdun (Department of Molecular Science and Technology, Ajou University) ;
  • Chang, Mi Sook (Division of Biology, California Institute of Technology) ;
  • Stuecker, Tara (Jet Propulsion Laboratory, California Institute of Technology) ;
  • Chung, Christine (Division of Biology, California Institute of Technology) ;
  • Newcombe, David A. (Jet Propulsion Laboratory, California Institute of Technology) ;
  • Venkateswaran, Kasthuri (Jet Propulsion Laboratory, California Institute of Technology)
  • Received : 2012.10.06
  • Accepted : 2012.11.05
  • Published : 2012.12.31
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Abstract

In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular- weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing.

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References

  1. Garland JL, Alazraki MP, Atkinson CF, Finger BW. Evaluating the feasibility of biological waste processing for long term space missions. Acta Hortic 1998;469:71-78.
  2. Jones JG. Freshwater ecosystems: structure and response. Ecotoxicol Environ Saf 2001;50:107-113. https://doi.org/10.1006/eesa.2001.2079
  3. Wommack KE, Williamson KE, Helton RR, Bench SR, Winget DM. Methods for the isolation of viruses from environmental samples. Methods Mol Biol 2009;501:3-14.
  4. Williamson KE, Wommack KE, Radosevich M. Sampling natural viral communities from soil for culture-independent analyses. Appl Environ Microbiol 2003;69:6628-6633. https://doi.org/10.1128/AEM.69.11.6628-6633.2003
  5. Orcutt BN, Sylvan JB, Knab NJ, Edwards KJ. Microbial ecology of the dark ocean above, at, and below the seafloor. Microbiol Mol Biol Rev 2011;75:361-422. https://doi.org/10.1128/MMBR.00039-10
  6. Cunliffe M, Upstill-Goddard RC, Murrell JC. Microbiology of aquatic surface microlayers. FEMS Microbiol Rev 2011;35:233-246. https://doi.org/10.1111/j.1574-6976.2010.00246.x
  7. Stefanis C, Alexopoulos A, Voidarou C, Vavias S, Bezirtzoglou E. Principal methods for isolation and identification of soil microbial communities. Folia Microbiol (Praha) 2012 Jul 12 [Epub]. http://dx.doi.org/10.1007/s12223-012-0179-5.
  8. Singh J, Behal A, Singla N, Joshi A, Birbian N, Singh S, et al. Metagenomics: concept, methodology, ecological inference and recent advances. Biotechnol J 2009;4:480-494. https://doi.org/10.1002/biot.200800201
  9. Kim UJ, Shizuya H, de Jong PJ, Birren B, Simon MI. Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucleic Acids Res 1992;20:1083-1085. https://doi.org/10.1093/nar/20.5.1083
  10. Choi SD. Construction of chromosome-specific BAC libraries from the filamentous ascomycete Ashbya gossypii. Genomics Inform 2006;4:80-86.
  11. Dietrich FS, Voegeli S, Brachat S, Lerch A, Gates K, Steiner S, et al. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 2004;304:304-307. https://doi.org/10.1126/science.1095781
  12. Choi S, Wing RA. Construction of Bacterial Artificial Chromosome (BAC) Libraries. In: Plant Molecular Biology Manual (Gelvin S, Schilperoo R, eds.). 2nd ed. Norwell: Kluwer Academic Publishers, 2000. pp. 1-28.
  13. Berthet N, Reinhardt AK, Leclercq I, van Ooyen S, Batejat C, Dickinson P, et al. Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR. BMC Mol Biol 2008;9:77. https://doi.org/10.1186/1471-2199-9-77
  14. Kumar G, Garnova E, Reagin M, Vidali A. Improved multiple displacement amplification with phi29 DNA polymerase for genotyping of single human cells. Biotechniques 2008;44:879-890. https://doi.org/10.2144/000112755
  15. Yokouchi H, Fukuoka Y, Mukoyama D, Calugay R, Takeyama H, Matsunaga T. Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using phi29 polymerase. Environ Microbiol 2006;8:1155-1163. https://doi.org/10.1111/j.1462-2920.2006.01005.x
  16. Blanco L, Bernad A, Lazaro JM, Martin G, Garmendia C, Salas M. Highly efficient DNA synthesis by the phage phi 29 DNA polymerase: symmetrical mode of DNA replication. J Biol Chem 1989;264:8935-8940.
  17. Blanco L, Salas M. Relating structure to function in phi29 DNA polymerase. J Biol Chem 1996;271:8509-8512. https://doi.org/10.1074/jbc.271.15.8509
  18. Inoue-Nagata AK, Albuquerque LC, Rocha WB, Nagata T. A simple method for cloning the complete begomovirus genome using the bacteriophage phi29 DNA polymerase. J Virol Methods 2004;116:209-211. https://doi.org/10.1016/j.jviromet.2003.11.015
  19. Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 2001;11:1095-1099. https://doi.org/10.1101/gr.180501
  20. Alexandrino M, Grohmann E, Szewzyk R, Szewzyk U. Application of culture-independent methods to assess the bacteria removal efficiency of subsurface flow constructed wetlands. Water Sci Technol 2007;56:217-222. https://doi.org/10.2166/wst.2007.523
  21. Alexandrino M, Grohmann E, Szewzyk U. Optimization of PCR-based methods for rapid detection of Campylobacter jejuni, Campylobacter coli and Yersinia enterocolitica serovar 0:3 in wastewater samples. Water Res 2004;38:1340-1346. https://doi.org/10.1016/j.watres.2003.10.036
  22. Adachi E, Shimamura K, Wakamatsu S, Kodama H. Amplification of plant genomic DNA by Phi29 DNA polymerase for use in physical mapping of the hypermethylated genomic region. Plant Cell Rep 2004;23:144-147.
  23. Kuske CR, Banton KL, Adorada DL, Stark PC, Hill KK, Jackson PJ. Small-scale DNA sample preparation method for field PCR detection of microbial cells and spores in soil. Appl Environ Microbiol 1998;64:2463-2472.
  24. Stackebrandt E, Liesack W, Goebel BM. Bacterial diversity in a soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J 1993;7:232-236.
  25. Wilson KH, Blitchington RB. Human colonic biota studied by ribosomal DNA sequence analysis. Appl Environ Microbiol 1996;62:2273-2278.
  26. Wilson KH, Blitchington RB, Greene RC. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J Clin Microbiol 1990;28:1942-1946.
  27. Gage DJ. Infection and invasion of roots by symbiotic, nitrogen- fixing rhizobia during nodulation of temperate legumes. Microbiol Mol Biol Rev 2004;68:280-300. https://doi.org/10.1128/MMBR.68.2.280-300.2004
  28. Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, et al. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One 2010;5:e10433. https://doi.org/10.1371/journal.pone.0010433
  29. Mailloux BJ, Alexandrova E, Keimowitz AR, Wovkulich K, Freyer GA, Herron M, et al. Microbial mineral weathering for nutrient acquisition releases arsenic. Appl Environ Microbiol 2009;75:2558-2565. https://doi.org/10.1128/AEM.02440-07
  30. Manning G, Reiner DS, Lauwaet T, Dacre M, Smith A, Zhai Y, et al. The minimal kinome of Giardia lamblia illuminates early kinase evolution and unique parasite biology. Genome Biol 2011;12:R66. https://doi.org/10.1186/gb-2011-12-7-r66

Cited by

  1. Retraction: A Fosmid Cloning Strategy for Detecting the Widest Possible Spectrum of Microbes from the International Space Station Drinking Water System vol.11, pp.2, 2013, https://doi.org/10.5808/GI.2013.11.2.97