Abstract
DNA microarrays are well suited as a tool for analyzing functional gene diversity as well as community composition in aquatic environments. Microarrays allow for the semiquantitative characterization of target genes by means of specific hybridization of labeled target gene sequences, amplified from the environment, to the corresponding oligonucleotide probes on the slide. Specificity and sensitivity are determined by the probe design. In their current implementation, environmental DNA microarrays are useful for analyzing microbial communities as well as for analyzing the presence of functional genes involved in larger biogeochemical processes, such as nitrogen cycling. Here, we lay out a basic protocol to analyze genes in the environment, which can be applied to most target genes of interest.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Braker, G., Ayala-del-Rio, H. L., Devol, A. H., Fesefeldt, A., and Tiedje, J. M. (2001) Community structure of denitrifiers, Bacteria, and Archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl. Environ. Microbiol. 67, 1893–1901.
Schimel, D. S., Brown, V. B., Hibbard, K. A., Lund, C. P., and Archer, S. (1995) Aggregation of species properties for biogeochemical modeling: empirical results, in Linking Species and Ecosystems (Jones, C. G. and Lawton, J. H., eds.), Chapman and Hall, New York, pp. 209–214.
Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467–470.
Cho, J.-C. and Tiedje, J. M. (2002) Quantitative detection of microbial genes by using DNA microarrays. Appl. Environ. Microbiol. 68, 1425–1430.
Guschin, D. Y., Mobarry, B. K., Proudnikov, D., Stahl, D. A., Rittmann, B. E., and Mirzabekov, A. D. (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl. Environ. Microbiol. 63, 2397–2402.
Wu, L., Thompson, D. K., Li, G., Hurt, R. A., Tiedje, J. M., and Zhou, J. (2001) Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl. Environ. Microbiol. 67, 5780–5790.
Bouvier, T. C. and del Giorgio, P. A. (2002) Compositional changes in freeliving bacterial communities along a salinity gradient in two temperate estuaries. Limnol. Oceanogr. 47, 453–470.
Taroncher-Oldenburg, G., Griner, E. M., Francis, C. A., and Ward, B. B. (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl. Environ. Microbiol. 69, 1159–1171.
Braker, G., Fesefeldt, A., and Witzel, K. P. (1998) Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl. Environ. Microbiol. 64, 3769–3775.
Casciotti, K. and Ward, B. B. (2001) Dissimilatory nitrite reductase genes from autotrophic ammonia-oxidizing bacteria. Appl. Environ. Microbiol. 67, 2213–2221.
Song, B., Palleroni, N. J., and Haggblom, M. M. (2000) Isolation and characterization of diverse halobenzoate-degrading denitrifying bacteria from soils and sediments. Appl. Environ. Microbiol. 66, 3446–3453.
Song, B. and Ward, B. B. (2003) Nitrite reductase genes in halobenzoate degrading denitrifying bacteria and related species. FEMS Microbiol. Ecol. 43, 349–357.
Swofford, D. L. (2002) PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta (CD-ROM) Sinauer Associates, Inc, Sunderland MA.
Zuker, M., Mathews, D. H., and Turner, D. H. (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide, in RNA Biochemistry and Biotechnology (Barciszewski, J. and Clark, B. F. C., eds.), Kluwer Academic Publishers, Dordrecht, The Netherlands, pp. 11–43.
SantaLucia, J., Jr. (1998) A unified view of polymer, dumbbell, and oligonucleotides DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95, 1460–1465.
Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406–3415.
Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911–940.
Shalon, D., Smith, S. J., and Brown, P. O. (1996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6, 639–645.
Lee, M. T., Kuo, F. C., Whitmore, G. A., and Sklar, J. (2000). Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc. Natl. Acad. Sci. USA 18, 9834–9839.
Kerr, M. K., Martin, M., and Churchill, G. A. (2000) Analysis of variance for gene expression microarray. J. Comput. Biol. 7, 819–837.
Dudley, A. M., Aach, J., Steffen, M. A., and Church, G. M. (2002) Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Nat. Acad. Sci. USA 99, 7554–7559.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc.
About this protocol
Cite this protocol
Taroncher-Oldenburg, G., Ward, B.B. (2007). Oligonucleotide Microarrays for the Study of Coastal Microbial Communities. In: Hilario, E., Mackay, J. (eds) Protocols for Nucleic Acid Analysis by Nonradioactive Probes. Methods in Molecular Biology, vol 353. Humana Press. https://doi.org/10.1385/1-59745-229-7:301
Download citation
DOI: https://doi.org/10.1385/1-59745-229-7:301
Publisher Name: Humana Press
Print ISBN: 978-1-58829-430-2
Online ISBN: 978-1-59745-229-8
eBook Packages: Springer Protocols