- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Recently Accepted Articles ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 240175, 11 pages
The World Bacterial Biogeography and Biodiversity through Databases: A Case Study of NCBI Nucleotide Database and GBIF Database
1Microbiology Group, Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, USTHB, BP 32, EL ALIA, Bab Ezzouar, Algiers, Algeria
2Environmental Microbiology, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
Received 14 March 2013; Revised 11 July 2013; Accepted 13 August 2013
Academic Editor: Konstantinos Mavrommatis
Copyright © 2013 Okba Selama 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.
- J. B. H. Martiny, B. J. M. Bohannan, J. H. Brown et al., “Microbial biogeography: putting microorganisms on the map,” Nature Reviews Microbiology, vol. 4, no. 2, pp. 102–112, 2006.
- C. B. Cox and P. D. Moore, Biogeography: An Ecological and Evolutionary Approach, Blackwell Science, Oxford, UK, 2000.
- J. H. Brown, B. R. Riddle, and M. V. Lomolino, Biogeography, Sinauer Associates, Sunderland, Mass, USA, 2005.
- I. M. Head, J. R. Saunders, and R. W. Pickup, “Microbial evolution, diversity, and ecology: a decade of ribosomal RNA analysis of uncultivated microorganisms,” Microbial Ecology, vol. 35, no. 1, pp. 1–21, 1998.
- A. E. Mccaig, L. A. Glover, and J. I. Prosser, “Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures,” Applied and Environmental Microbiology, vol. 65, no. 4, pp. 1721–1730, 1999.
- N. Bano, S. Ruffin, B. Ransom, and J. T. Hollibaugh, “Phylogenetic composition of arctic ocean archaeal assemblages and comparison with antarctic assemblages,” Applied and Environmental Microbiology, vol. 70, no. 2, pp. 781–789, 2004.
- J. C. Venter, K. Remington, J. F. Heidelberg et al., “Environmental genome shotgun sequencing of the sargasso sea,” Science, vol. 304, no. 5667, pp. 66–74, 2004.
- R. I. Griffiths, B. C. Thomson, P. James, T. Bell, M. Bailey, and A. S. Whiteley, “The bacterial biogeography of British soils,” Environmental Microbiology, vol. 13, no. 6, pp. 1642–1654, 2011.
- E. Pagaling, H. Wang, M. Venables et al., “Microbial biogeography of six salt lakes in Inner Mongolia, China, and a salt lake in Argentina,” Applied and Environmental Microbiology, vol. 75, no. 18, pp. 5750–5760, 2009.
- A. D. Chapman, “Quality control and validation of point-sourced environmental resource data,” in Spatial Accuracy Assessment: Land Information Uncertainty in Natural Resources, K. Lowell and A. Jaton, Eds., pp. 409–418, Ann Arbor Press, Chelsea, Mich, USA, 1999.
- A. D. Chapman, “Uses of Primary Species-Occurrence Data, version 1.0,” Report for the Global Biodiversity Information Facility, Copenhagen, Denmark, 2005.
- A. D. Chapman, “Principles of Data Quality, version 1.0,” Report for the Global Biodiversity Information Facility, Copenhagen, Denmark, 2005.
- The Global Biodiversity Information Facility, http://data.gbif.org/welcome.htm.
- NCBI Nucleotide Database, http://www.ncbi.nlm.nih.gov/nuccore.
- Bandwidth place, http://www.bandwidthplace.com/.
- Controlled vocabulary for /country qualifier, http://www.insdc.org/country.html.
- S. Federhen, “The NCBI taxonomy database,” Nucleic Acids Research, vol. 40, Database issue, pp. D136–D143, 2012.
- NCBI Taxonomy, http://www.ncbi.nlm.nih.gov/taxonomy.
- M. Ruggiero, D. Gordon, N. Bailly, P. Kirk, and D. Nicolson, “The catalogue of life taxonomic classification,” in Species 2000 & ITIS Catalogue of Life, 2011 Annual Checklist, F. A. Bisby, Y. R. Roskov, A. Culham et al., Eds., Part A, Species 2000, Reading, UK, 2nd edition, 2011.
- The Global Biodiversity Information Facility, The species portal, http://data.gbif.org/species/.
- GBIF Database occurrence search webpage, http://data.gbif.org/occurrences/.
- Python, http://www.python.org/about/.
- E. Sayers, “A general introduction to the E-utilities,” 2009, http://www.ncbi.nlm.nih.gov/books/NBK25497/#chapter2.Introduction.
- Biopython, http://biopython.org/wiki/Biopython.
- A. South, “rworldmap: new R package for mapping global data,” The R Journal, vol. 3, no. 1, pp. 35–43, 2011.
- The R Project for Statistical Computing, http://www.r-project.org/.
- White House Office of Science and Technology Policy, “The 2014 budget: a world-leading commitment to science & research,” 2013, www.whitehouse.gov/ostp, http://www.whitehouse.gov/sites/default/files/microsites/ostp/2014_R&Dbudget_overview.pdf.
- J. H. Brown and M. V. Lomolino, Biogeography, Sinauer, Sunderland, Mass, USA, 2nd edition, 1998.
- W. B. Whitman, D. C. Coleman, and W. J. Wiebe, “Prokaryotes: the unseen majority,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 12, pp. 6578–6583, 1998.
- P. Hugenholtz, B. M. Goebel, and N. R. Pace, “Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity,” Journal of Bacteriology, vol. 180, no. 18, pp. 4765–4774, 1998.
- J. I. Prosser, B. J. M. Bohannan, T. P. Curtis et al., “The role of ecological theory in microbial ecology,” Nature Reviews Microbiology, vol. 5, no. 5, pp. 384–392, 2007.
- M. C. Horner-Devine, M. Lage, J. B. Hughes, and B. J. M. Bohannan, “A taxa-area relationship for bacteria,” Nature, vol. 432, no. 7018, pp. 750–753, 2004.
- J. Green and B. J. M. Bohannan, “Spatial scaling of microbial biodiversity,” Trends in Ecology and Evolution, vol. 21, no. 9, pp. 501–507, 2006.
- D. R. Nemergut, E. K. Costello, M. Hamady et al., “Global patterns in the biogeography of bacterial taxa,” Environmental Microbiology, vol. 13, no. 1, pp. 135–144, 2011.
- J. C. Cho and J. M. Tiedje, “Biogeography and degree of endemicity of fluorescent Pseudomonas strains in soil,” Applied and Environmental Microbiology, vol. 66, no. 12, pp. 5448–5456, 2000.
- R. J. Whitaker, D. W. Grogan, and J. W. Taylor, “Geographic barriers isolate endemic populations of hyperthermophilic archaea,” Science, vol. 301, no. 5635, pp. 976–978, 2003.
- H. Chu, N. Fierer, C. L. Lauber, J. G. Caporaso, R. Knight, and P. Grogan, “Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes,” Environmental Microbiology, vol. 12, no. 11, pp. 2998–3006, 2010.
- N. Fierer and R. B. Jackson, “The diversity and biogeography of soil bacterial communities,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 3, pp. 626–631, 2006.
- K. van der Gucht, K. Cottenie, K. Muylaert et al., “The power of species sorting: local factors drive bacterial community composition over a wide range of spatial scales,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 51, pp. 20404–20409, 2007.
- M. C. Horner-Devine, J. M. Silver, M. A. Leibold et al., “A comparison of taxon co-occurrence patterns for macro- and microorganisms,” Ecology, vol. 88, no. 6, pp. 1345–1353, 2007.
- D. Remsen, B. Ko, V. Chavan, and M. Raymond, Getting Started: An Overview of Data Publishing in the GBIF Network, Global Biodiversity Information Facility, Copenhagen, Denmark, 2011, http://links.gbif.org/getting_started_publishing_en_v1.
- The Earth Microbiome Project, http://www.earthmicrobiome.org/.