Table of Contents Author Guidelines Submit a Manuscript
Archaea
Volume 2015, Article ID 875784, 12 pages
http://dx.doi.org/10.1155/2015/875784
Research Article

De Novo Sequences of Haloquadratum walsbyi from Lake Tyrrell, Australia, Reveal a Variable Genomic Landscape

1Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089, USA
2Cooperative Institute for Research in Environmental Sciences, CIRES Building, Room 318, University of Colorado Boulder, Boulder, CO 80309, USA
3Department of Environmental Science, Policy and Management, University of California, Berkeley, 54 Mulford Hall, Berkeley, CA 94720, USA
4Research School of Earth Sciences, The Australian National University, Canberra, ACT 0200, Australia
5Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0202, USA
6Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA 92093, USA

Received 19 June 2014; Revised 2 September 2014; Accepted 16 September 2014

Academic Editor: Timothy Williams

Copyright © 2015 Benjamin J. Tully et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. I. Bodaker, I. Sharon, M. T. Suzuki et al., “Comparative community genomics in the Dead Sea: an increasingly extreme environment,” ISME Journal, vol. 4, no. 3, pp. 399–407, 2010. View at Publisher · View at Google Scholar · View at Scopus
  2. I. Boujelben, M. Gomariz, M. Martínez-García et al., “Spatial and seasonal prokaryotic community dynamics in ponds of increasing salinity of Sfax solar saltern in Tunisia,” Antonie van Leeuwenhoek, vol. 101, no. 4, pp. 845–857, 2012. View at Publisher · View at Google Scholar · View at Scopus
  3. C. Demergasso, L. Escudero, E. O. Casamayor, G. Chong, V. Balagué, and C. Pedrós-Alió, “Novelty and spatio-temporal heterogeneity in the bacterial diversity of hypersaline Lake Tebenquiche (Salar de Atacama),” Extremophiles, vol. 12, no. 4, pp. 491–504, 2008. View at Publisher · View at Google Scholar · View at Scopus
  4. D. Oh, K. Porter, B. Russ, D. Burns, and M. Dyall-Smith, “Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds,” Extremophiles, vol. 14, no. 2, pp. 161–169, 2010. View at Publisher · View at Google Scholar · View at Scopus
  5. A. Oren, “Life at high salt concentrations,” in The Prokaryotes, E. Rosenberg, E. F. DeLong, S. Lory, E. Stackebrandt, and F. Thompson, Eds., pp. 421–440, Springer, Berlin, Germany, 2013. View at Google Scholar
  6. A.-Ş. Andrei, H. L. Banciu, and A. Oren, “Living with salt: metabolic and phylogenetic diversity of archaea inhabiting saline ecosystems,” FEMS Microbiology Letters, vol. 330, no. 1, pp. 1–9, 2012. View at Publisher · View at Google Scholar · View at Scopus
  7. A. E. Walsby, “A square bacterium,” Nature, vol. 283, no. 5742, pp. 69–71, 1980. View at Publisher · View at Google Scholar · View at Scopus
  8. H. Bolhuis, “Walsby's square archaeon,” in Adaptation of Life at High Salt Concentrations in Archaea, Bacteria, and Eukarya, N. Gunde-Cimerman, A. Oren, and A. Plemenitas, Eds., pp. 185–199, 2005. View at Google Scholar
  9. H. Bolhuis, E. M. Te Poele, and F. Rodriguez-Valera, “Isolation and cultivation of Walsby's square archaeon,” Environmental Microbiology, vol. 6, no. 12, pp. 1287–1291, 2004. View at Publisher · View at Google Scholar · View at Scopus
  10. H. Bolhuis, P. Palm, A. Wende et al., “The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity,” BMC Genomics, vol. 7, article 169, 2006. View at Publisher · View at Google Scholar · View at Scopus
  11. O. Béjá, E. N. Spudich, J. L. Spudich, M. Leclerc, and E. F. DeLong, “Proteorhodopsin phototrophy in the ocean,” Nature, vol. 411, no. 6839, pp. 786–789, 2001. View at Publisher · View at Google Scholar · View at Scopus
  12. J. E. Sherwood, F. Stagnitti, M. J. Kokkinn, and W. D. Williams, “Dissolved-oxygen concentrations in hypersaline waters,” Limnology and Oceanography, vol. 36, no. 2, pp. 235–250, 1991. View at Publisher · View at Google Scholar
  13. B. A. Legault, A. Lopez-Lopez, J. C. Alba-Casado et al., “Environmental genomics of “Haloquadratum walsbyi” in a saltern crystallizer indicates a large pool of accessory genes in an otherwise coherent species,” BMC Genomics, vol. 7, article 171, 2006. View at Publisher · View at Google Scholar · View at Scopus
  14. S. Podell, J. A. Ugalde, P. Narasingarao, J. F. Banfield, K. B. Heidelberg, and E. E. Allen, “Assembly-driven community genomics of a hypersaline microbial ecosystem,” PLoS ONE, vol. 8, no. 4, Article ID e61692, 2013. View at Publisher · View at Google Scholar · View at Scopus
  15. A. H. Treusch, A. Kletzin, G. Raddatz et al., “Characterization of large-insert DNA libraries from soil for environmental genomic studies of Archaea,” Environmental Microbiology, vol. 6, no. 9, pp. 970–980, 2004. View at Publisher · View at Google Scholar · View at Scopus
  16. S. J. Giovannoni, H. J. Tripp, S. Givan et al., “Genetics: genome streamlining in a cosmopolitan oceanic bacterium,” Science, vol. 309, no. 5738, pp. 1242–1245, 2005. View at Publisher · View at Google Scholar · View at Scopus
  17. N. F. W. Saunders, T. Thomas, P. M. G. Curmi et al., “Mechanisms of thermal adaptatation revealed from genomes of the anatarctic Archaea Methanogenium frigidum and Methanacoccoides burtonii,” Genome Research, vol. 13, no. 7, pp. 1580–1588, 2003. View at Publisher · View at Google Scholar · View at Scopus
  18. D. G. Burns, H. M. Camakaris, P. H. Janssen, and M. L. Dyall-Smith, “Cultivation of Walsby's square haloarchaeon,” FEMS Microbiology Letters, vol. 238, no. 2, pp. 469–473, 2004. View at Publisher · View at Google Scholar · View at Scopus
  19. M. L. Dyall-Smith, F. Pfeiffer, K. Klee et al., “Haloquadratum walsbyi: Limited Diversity in a Global Pond,” PLoS ONE, vol. 6, no. 6, Article ID e20968, 2011. View at Publisher · View at Google Scholar · View at Scopus
  20. S. Cuadros-Orellana, A.-B. Martin-Cuadrado, B. Legault et al., “Genomic plasticity in prokaryotes: the case of the square haloarchaeon,” The ISME Journal, vol. 1, no. 3, pp. 235–245, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. P. Narasingarao, S. Podell, J. A. Ugalde et al., “De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities,” ISME Journal, vol. 6, no. 1, pp. 81–93, 2012. View at Publisher · View at Google Scholar · View at Scopus
  22. S. Podell, J. B. Emerson, C. M. Jones et al., “Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community,” ISME Journal, vol. 8, no. 5, pp. 979–990, 2014. View at Publisher · View at Google Scholar · View at Scopus
  23. J. B. Emerson, B. C. Thomas, K. Andrade, E. E. Allen, K. B. Heidelberg, and J. F. Banfielda, “Dynamic viral populations in hypersaline systems as revealed by metagenomic assembly,” Applied and Environmental Microbiology, vol. 78, no. 17, pp. 6309–6320, 2012. View at Publisher · View at Google Scholar · View at Scopus
  24. J. B. Emerson, K. Andrade, B. C. Thomas et al., “Virus-host and CRISPR dynamics in archaea-dominated hypersaline Lake tyrrell, Victoria, Australia,” Archaea, vol. 2013, Article ID 370871, 12 pages, 2013. View at Publisher · View at Google Scholar · View at Scopus
  25. K. B. Heidelberg, W. C. Nelson, J. B. Holm, N. Eisenkolb, K. Andrade, and J. B. Emerson, “Characterization of eukaryotic microbial diversity in hypersaline lake tyrrell, australia,” Frontiers in Microbiology, vol. 4, Article ID Article 115, 2013. View at Publisher · View at Google Scholar · View at Scopus
  26. Y. Peng, H. C. M. Leung, S. M. Yiu, and F. Y. L. Chin, “IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth,” Bioinformatics, vol. 28, no. 11, Article ID bts174, pp. 1420–1428, 2012. View at Publisher · View at Google Scholar · View at Scopus
  27. H. Li and R. Durbin, “Fast and accurate short read alignment with Burrows-Wheeler transform,” Bioinformatics, vol. 25, no. 14, pp. 1754–1760, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. V. Iverson, R. M. Morris, C. D. Frazar, C. T. Berthiaume, R. L. Morales, and E. V. Armbrust, “Untangling genomes from metagenomes: revealing an uncultured class of marine euryarchaeota,” Science, vol. 335, no. 6068, pp. 587–590, 2012. View at Publisher · View at Google Scholar · View at Scopus
  29. M. Rho, H. Tang, and Y. Ye, “FragGeneScan: predicting genes in short and error-prone reads,” Nucleic Acids Research, vol. 38, no. 20, p. e191, 2010. View at Publisher · View at Google Scholar · View at Scopus
  30. R. K. Aziz, D. Bartels, A. Best et al., “The RAST Server: rapid annotations using subsystems technology,” BMC Genomics, vol. 9, article 75, 2008. View at Publisher · View at Google Scholar · View at Scopus
  31. V. M. Markowitz, F. Korzeniewski, K. Palaniappan et al., “The integrated microbial genomes (IMG) system,” Nucleic Acids Research, vol. 34, pp. D344–D348, 2006. View at Publisher · View at Google Scholar · View at Scopus
  32. P. D. Schloss, S. L. Westcott, T. Ryabin et al., “Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities,” Applied and Environmental Microbiology, vol. 75, no. 23, pp. 7537–7541, 2009. View at Publisher · View at Google Scholar · View at Scopus
  33. A. E. Darling, B. Mau, and N. T. Perna, “Progressivemauve: multiple genome alignment with gene gain, loss and rearrangement,” PLoS ONE, vol. 5, no. 6, Article ID e11147, 2010. View at Publisher · View at Google Scholar · View at Scopus
  34. J. D. Thompson, D. G. Higgins, and T. J. Gibson, “Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994. View at Publisher · View at Google Scholar · View at Scopus
  35. T. N. Petersen, S. Brunak, G. von Heijne, and H. Nielsen, “SignalP 4.0: discriminating signal peptides from transmembrane regions,” Nature Methods, vol. 8, no. 10, pp. 785–786, 2011. View at Publisher · View at Google Scholar · View at Scopus
  36. S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997. View at Publisher · View at Google Scholar · View at Scopus
  37. M. Nishihara, T. Yamazaki, T. Oshima, and Y. Koga, “sn-Glycerol-1-phosphate-forming activities in Archaea: separation of archaeal phospholipid biosynthesis and glycerol catabolism by glycerophosphate enantiomers,” Journal of Bacteriology, vol. 181, no. 4, pp. 1330–1333, 1999. View at Google Scholar · View at Scopus