Abstract
Rotifers are a key component of many freshwater ecosystems, but surveys of the composition of rotifer communities are limited by the labor-intensiveness of sample processing, particularly of non-planktonic taxa, and by the shortage of investigators qualified to identify a broad range of rotifer species. Additional problems are posed by species that must be identified from living specimens, and by members of cryptic species complexes. As DNA sequencing becomes easier and cheaper, it has become practical to obtain representative DNA sequences from identified rotifer species for use in genome-based surveys to determine which rotifers are present in a new sample, avoiding the difficulties of traditional surveys. Here we discuss two genome-based tools used in surveys of microbial communities: serial analysis of gene tags (SAGT) and microarray hybridization. SAGT is a method for inexpensively obtaining characteristic short DNA sequences from a sample that can both identify taxa for which the tag sequence is known and signal the presence of additional uncharacterized species. Microarray hybridization allows detection of DNA sequences in the sample that are identical or similar to sequences present on the microarray. We also report the construction and hybridization of a small microarray of rotifer sequences, demonstrating that this method can discriminate among bdelloid families, and is likely to make much finer discriminations if appropriate sequences are present on the microarray. These techniques are most powerful when combined with traditional systematics in collaborative efforts, which may be fostered through the data base of rotifer biology, WheelBase (http://jbpc.mbl.edu/wheelbase).
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Alexandre, I., S. Hamels, S. Dufour, J. Collet, N. Zammatteo, F. Longueville, J. L. Gala & J. Remacle, 2001. Colorimetric silver detection of DNA microarrays. Analytical Biochemistry 295: 1–8.
Amaral Zettler, L. A., F. Gomez, E. Zettler, B. G. Keenan, R. Amils & M. L. Sogin, 2002. Eukaryotic diversity in Spain’s River of Fire. Nature 417: 137.
Arndt, H., 1993. Rotifers as predators on components of the microbial web (bacteria, heterotrophic flagellates, ciliates) — a review. Hydrobiologia 255/256: 231–246.
Belosludtsev, Y., B. Iverson, S. Lemeshko, R. Eggers, R. Wiese, S. Lee, T. Powdrill & M. Hogan, 2001. DNA microarrays based on noncovalent oligonucleotide attachment and hybridization in two dimensions. Analytical Biochemistry 292: 250–256.
Birky, C. W., C. Wolf, H. Maugham, L. Herbertson & E. Henry, 2005. Speciation and selection without sex. Hydrobiologia 546: 29–45.
Bowtell, D. D., 1999. Options available — from start to finish — for obtaining expression data by microarray. Nature Genetics 21: 25–32.
Call, D. R., M. K. Borucki & F. J. Loge, 2003. Detection of bacterial pathogens in environmental samples using DNA microarrays. Journal of Microbiological Methods 53: 235–243.
Chandler, D. P., G. J. Newton, J. A. Small & D. S. Daly, 2003. Sequence versus structure for the direct detection of 16S rRNA on planar oligonucleotide microarrays. Applied and Environmental Microbiology 69: 2950–2958.
Christner, B. C., B. H. Kvitko 2nd & J. N. Reeve, 2003. Molecular identification of Bacteria and Eukarya inhabiting an Antarctic cryoconite hole. Extremophiles 7: 177–83.
Gómez, A., 2005. Molecular ecology of rotifers: from population differentiation to speciation. Hydrobiologia 546: 83–99.
Gomez, A., M. Serra, G. R. Carvalho & D. H. Lunt, 2002a. Speciation in ancient cryptic species complexes: evidence from the molecular phylogeny of Brachionus plicatilis (Rotifera). Evolution 56: 1431–1444.
Gomez, A., G. J. Adcock, D. H. Lunt & G. R. Carvalho, 2002b. The interplay between colonization history and gene flow in passively dispersing zooplankton: microsatellite analysis of rotifer resting egg banks. Journal of Evolutionary Biology 15: 158–171.
Hutchinson, G. E., 1967. A Treatise on Limnology, (vol. 2). John Wiley and Sons, New York, 115 pp.
Karsten, S. L., V. M. Deerlin, C. Sabatti, L. H. Gill & D. H. Geschwind, 2002. An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis. Nucleic Acids Research 30: E4.
Kysela, D. T., C. Palacios & M. L. Sogin, 2005. Serial analysis of V6/ribosomal sequence tags (SARST-V6): A novel method for efficient, high-throughput analysis of microbial community composition. Environmental Microbiology 7: 356–364.
Liu, W-T., & D. A. Stahl, 2001. Molecular approaches for the measurement of density, diversity, and phylogeny. In Manual of Environmental Microbiology, 2nd edn. ASM Press, Washington, DC, 114–134.
Mark Welch, D. B., 2000. Evidence from a protein-coding gene that acanthocephalans are rotifers. Invertebrate Biology 119: 17–26.
Mark Welch, D. B. & M. Meselson, 2000. Evidence for the evolution of bdelloid rotifers without sexual recombination or genetic exchange. Science 288: 1211–1215.
Mark Welch, J. L., D. B. Mark Welch & M. Meselson, 2004. Cytogenetic evidence for asexual evolution of bdelloid rotifers. Proceedings of the National Academy of Sciences (USA) 101: 1618–1621.
Polz, M. F., S. Bertilsson, S. G. Acinas & D. Hunt, 2003. A(r)ray of hope in analysis of the function and diversity of microbial communities. Biological Bulletin 204: 196–199.
Quackenbush, J., 2002. Microarray data normalization and transformation. Nature Genetics 32(supplement): 496–501.
Ricci, C. & M. Balsamo, 2000. The biology and ecology of lotic rotifers and gastrotrichs. Freshwater Biology 44: 15–28.
Rublee, P. A., 1998. Rotifers in arctic North America with particular reference to their role in microplankton community structure and response to ecosystem perturbations in Alaskan Arctic LTER lakes. Hydrobiologia 387/388: 153–160.
Sambrook, J., E. F. Fritsch & T. Maniatis, 1989. Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Press, New York.
Schena, M., D. Shalon, R. Heller, A. Chai, P. O. Brown & R. W. Davis, 1996. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proceedings of the National Academy of Sciences USA 93: 10614–10619.
Schmalenberger, A., F. Schwieger & C. C. Tebbe, 2001. Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling. Applied and Environmental Microbiology 617: 3557–3563.
Segers, H. & R. J. Shiel, 2005. Tale of a sleeping beauty: a new and easily cultured organism for experimental studies on bdelloid rotifers. Hydrobiologia 546: 141–145.
Small, J., D. R. Call, F. J. Brockman, T. M. Straub & D. P. Chandler, 2001. Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Applied and Environmental Microbiology 67: 4708–4716.
Spear, J. R., R. E. Ley, A. B. Berger & N. R. Pace, 2003. Complexity in natural microbial ecosystems: the Guerrero Negro experience. Biological Bulletin 204: 168–173.
Teske, A., K-U. Hinrichs, V. Edgcomb, A. Vera Gomez, D. Kysela, S. P. Sylva, M. L. Sogin & H. W. Jannasch, 2002. Microbial diversity of hydrothermal sediments in the Guaymas basin: evidence for anaerobic methanotrophic communities. Applied and Environmental Microbiology 68: 1994–2007.
Wallace, R. L. & C. Ricci, 2002. Rotifera. In Rundle, S. D., A. L. Robertson & J. M. Schmid-Araya, (eds), Freshwater Meiofauna: Biology and Ecology. Backhuys Publishers, Leiden (The Netherlands), 15–44.
Williamson, C. E., 1983. Invertebrate predation on planktonic rotifers. Hydrobiologia 104: 385–396.
Wu, L., D. K. Thompson, G. Li, R. A. Hurt, J. M. Tiedje & J. Zhou, 2001. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Applied and Environmental Microbiology 67: 5780–5790.
Ye, R. W., T. Wang, L. Bedzyk & K. M. Croker, 2001. Applications of DNA microarrays in microbial systems. Journal of Microbiological Methods 47: 257–272.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer
About this chapter
Cite this chapter
Welch, D.B.M., Welch, J.L.M. (2005). The potential of genomic approaches to rotifer ecology. In: Herzig, A., Gulati, R.D., Jersabek, C.D., May, L. (eds) Rotifera X. Developments in Hydrobiology, vol 181. Springer, Dordrecht. https://doi.org/10.1007/1-4020-4408-9_8
Download citation
DOI: https://doi.org/10.1007/1-4020-4408-9_8
Publisher Name: Springer, Dordrecht
Print ISBN: 978-1-4020-3493-0
Online ISBN: 978-1-4020-4408-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)