Chapter 41
Investigating Bacterial Diversity Along Alkaline Hot-Spring Thermal Gradients by Barcoded Pyrosequencing
Book Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
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This chapter contains sections titled:
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Introduction
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Materials and Methods
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Results and Discussion
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Software and Internet Resources
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References
SOFTWARE AND INTERNET RESOURCES
- BioEdit (http://www.mbio.ncsu.edu/BioEdit/bioedit. html)
- CAP3 Assembly Program (http://seq.cs.iastate.edu/)
- EcoSim (http://homepages.together.net/∼gentsmin/ecosim.htm)
- NCBI BLAST (http://blast.ncbi.nlm.nih.gov/)
- Primer version 5.0 (Plymouth Marine Laboratory, UK)
- Ribosomal Database Project (http://rdp.cme.msu.edu/)
- REFERENCES
- Altschul SF, Gish W, Miller W, Myers E, Lipman D. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403–410.
- Bryant DA, Costas AMG, Maresca JA, A. Chew GM, Klatt CG, et al. 2007. Candidatus Chloracidobacterium thermophilum: An aerobic phototrophic Acidobacterium. Science 317: 523–526.
- DasSarma S, Fleischmann EF. 1995. Archaea: A Laboratory Manual—Halophiles. New York: Cold Spring Harbor Laboratory Press, pp. 269–272.
- Gotelli NJ. 1999. How do communities come together? Science 286: 1684–1685.
- Gotelli NJ, Entsminger GL. 2001. EcoSim: Null models software for ecology. Version 7.0. Acquired Intelligence Inc. & Kesey-Bear.
- Gotelli NJ, McCabe DJ. 2002. Species co-occurrence: A meta-analysis of J. M. Diamond's assembly rules model. Ecology 83: 2091–2096.
- Hall TA. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Series 41: 95–98.
- Hansen MC, Tolker-Neilson T, Givskov M, Molin S. 1998. Biased 16S rDNA PCR amplification caused by interference from DNA flanking template region. FEMS Microbiol. Ecol. 26: 141–149.
- Horner-Devine MC, Silver JM, Leibold MA, Bohannan, BJM, Colwell RK, et al. 2007. A comparison of taxon co-occurrence patterns for macro- and microorganisms. Ecology 88: 1345–1353.
- Huang X, Madan A. 2006. CAP3: A DNA sequence assembly program. Genome Res. 9: 868–877.
- Madigan MT, Brock TD. 1975. Photosynthetic sulfide oxidation by Chloroflexus aurantiacus, a filamentous, photosynthetic, gliding bacterium. J. Bacteriol. 122: 782–784.
- Margulies M, Egholm M, Altman WE, Attiya S, Bader JS et al. 2005. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376–380.
-
McCune B, Grace JB. 2002. Analysis of Ecological Communities. Gleneden Beach, OR: MjM Software Design.
10.1046/j.1439-0310.2002.00768.x Google Scholar
- Miller SR, Castenholz RW. 2000. Evolution of thermotolerance in hot spring cyanobacteria of the genus Synechococcus. Appl. Environ. Microbiol. 66: 4222–4229.
- Miller SR, Strong AL, Jones KL, Ungerer MC. 2009. Bar-coded pyrosequencing reveals shared bacterial community properties along the temperature gradients of two alkaline hot springs in Yellowstone National Park. Appl. Environ. Microbiol. 75: 4565–4572.
- Prosser JI, Bohannan BJM, Curtis TP, Ellis RJ, Firestone MK et al. 2007. The role of ecological theory in microbial ecology. Nat. Rev. Microbiol. 5: 384–392.
- Stone L, Roberts A. 1990. The checkerboard score and species distributions. Oecologia 85: 74–79.
- van der Meer MTJ, Schouten S, Sinninghe Damste JS, de Leeuw JW, Ward DM. 2003. Compound-specific isotopic fractionation patterns suggest different carbon metabolisms among Chloroflexus-like bacteria in hot-spring microbial mats. Appl. Environ. Microbiol. 69: 6000–6006.
- Ward DM, Tayne TA, Anderson KL, Bateson MM. 1987. Community structure and interactions among community members in hot spring cyanobacterial mats. Symp. Soc. Gen. Microbiol. 41: 179–210.
- Ward DM, Ferris MJ, Nold SC, Bateson MM. 1998. A natural view of microbial diversity within hot spring cyanobacterial mat communities. Microbiol. Mol. Biol. Rev. 62: 1353–1370.
