Chapter 90 : Characterization of Microeukaryota in Natural Environments

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Microeukaryotes, including fungi and protists, are important members of communities within natural environments. This chapter focuses exclusively on available molecular approaches for investigating microeukaryote assemblages within various natural environments. Oligotrophic environments generally require more sampling effort to obtain adequate biomass for molecular characterization than do more nutrient-rich environments. Sediment sampling achieved by the implementation of sterile mud samplers and coring devices has been described for hydrothermal sediments and anoxic sediments. The 18S rRNA gene contains both conserved and variable regions that can be exploited for characterization of the microeukaryote assemblages within an environment. Multiple PCRs containing amplicons of expected size can be pooled to minimize bias from single reactions. Immunological approaches have proven useful in ecological studies for the detection and enumeration of microeukaryotes. Quantitative real-time PCR uses the rate of accumulation of amplified target DNA during the PCR to estimate the copy number of the target in the original sample. Denaturing gradient gel electrophoresis is a PCR-based method in which the amplified 18S rRNA gene fragments are separated by polyacrylamide gel electrophoresis containing a linearly increasing gradient of denaturant.

Citation: Strap J. 2007. Characterization of Microeukaryota in Natural Environments, p 1112-1121. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch90
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1. Altschul, S. F.,, W. Gish,, W. Miller,, E. W. Myers, and, D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403410.
2. Amann, R.,, and W. Ludwig. 2000. Ribosomal RNA-targeted nucleic acid probes for studies in microbial ecology. FEMS Microbiol. Rev. 24: 555565.
3. Amann, R.,, W. Ludwig, and, K. Schleifer. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143169.
4. Amann, R. I.,, B. J. Binder,, R. J. Olson,, S. W. Chisholm,, R. Devereux, and, D. A. Stahl. 1990. Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl. Environ. Microbiol. 56: 19191925.
5. Amaral Zettler, L. A.,, M. A. Messerli,, A. D. Laatsch,, P. J. S. Smith, and, M. L. Sogin. 2003. From genes to genomes: beyond biodiversity in Spain’s Rio Tinto. Biol. Bull. 204: 205209.
6. Anderson, D. M.,, B. A. Keafer,, D. M. Kulis,, R. M. Waters, and, R. Nuzzi. 1993. An immunofluorescent survey of the brown tide chrysophyte Aureococcus anophagefferans along the northeast coast of the United States. J. Plankton Res. 15: 563580.
7. Arndt, H.,, D. Dietrich,, B. Auer,, E.-J. Cleven,, T. Grafenhan,, M. Weitere, and, A. P. Mylnikov. 2000. Functional diversity of heterotrophic flagellates in aquatic ecosystems. In B. S. C. Leadbeater and, J. C. Green (ed.), The Flagellates: Unity, Diversity and Evolution. Taylor and Francis, London, United Kingdom.
8. Baker, B. J.,, M. A. Lutz,, S. C. Dawson,, P. L. Bond, and, J. F. Banfield. 2004. Metabolically active eukaryotic communities in extremely acidic mine drainage. Appl. Environ. Microbiol. 70: 62646271.
9. Baldauf, S. L. 2003. Phylogeny for the faint of heart: a tutorial. Trends Genet. 19: 345351.
10. Bass, D.,, and T. Cavalier-Smith. 2004. Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). Int. J. Syst. Evol. Microbiol. 54: 23932404.
11. Borneman, J.,, and R. J. Hartin. 2000. PCR primers that amplify fungal rRNA genes from environmental samples. Appl. Environ. Microbiol. 66: 43564360.
12. Bossio, D. A.,, and K. M. Scow. 1998. Impacts of carbon and flooding on soil microbial communities: phospholipid fatty acid profiles and substrate utilisation patterns. Microb. Ecol. 35: 265278.
13. Bowers, H. A.,, T. Tengs,, H. B. J. Glasgow,, J. M. Burkholder,, P. A. Rublee, and, D. W. Oldach. 2000. Development of real-time PCR assays for rapid detection of Pfiesteria piscicida and related dinoflagellates. Appl. Environ. Microbiol. 66: 46414648.
14. Buchan, A.,, S. Y. Newell,, M. Butler,, E. J. Biers,, J. T. Hollibaugh, and, M. A. Moran. 2003. Dynamics of bacterial and fungal communities on decaying salt marsh grass. Appl. Environ. Microbiol. 69: 66766687.
15. Campbell, L.,, P. Shapiro, and, E. Haugen. 1994. Immunochemical characterization of eukaryotic ultraplankton from the Atlantic and Pacific oceans. J. Plankton Res. 16: 3551.
16. Caron, D. A.,, R. J. Gast,, E. L. Lim, and, M. R. Dennett. 1999. Protistan community structure: molecular approaches for answering ecological questions. Hydrobiologia 401: 215227.
17. Casamayor, E. O.,, R. Massana,, S. Benlloch,, L. Ovreas,, B. Diez,, V. J. Goddard,, J. M. Gasol,, I. Joint,, F. Rodriguez-Valera, and, C. Pedros-Alio. 2002. Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multi-pond solar saltern. Environ. Microbiol. 4: 338348.
18. Chandler, D. P.,, J. K. Fredrickson, and, F. J. Brockman. 1997. Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol. Ecol. 6: 475483.
19. Chandler, D. P.,, C. A. Wagnon, and, H. Bolton, Jr. 1998. Reverse transcriptase (RT) inhibition of PCR at low concentrations of template and its implications for quantitative RT-PCR. Appl. Environ. Microbiol. 64: 669677.
20. Chao, A. 1987. Estimating the population-size for capture recapture data with unequal catchability. Biometrics 43: 783791.
21. Chao, A.,, and S. M. Lee. 1992. Estimating the number of classes via sample coverage. J. Am. Stat. Assoc. 87: 210217.
22. Christner, B. C.,, B. H. Kvitko, and, J. N. Reeve. 2003. Molecular identification of bacteria and eukarya inhabiting an Antarctic cryoconite hole. Extremophiles 7: 14251430.
23. Corinaldesi, C.,, R. Danovaro, and, A. Dell’Anno. 2005. Simultaneous recovery of extracellular and intracellular DNA suitable for molecular studies from marine sediments. Appl. Environ. Microbiol. 71: 4650.
24. Countway, P. D.,, R. J. Gast,, P. Savai, and, D. A. Caron. 2005. Protistan diversity estimates based on 18S rDNA from seawater incubations in the Western North Atlantic. J. Eukaryot. Microbiol. 52: 95106.
25. Coyne, K. J.,, and S. C. Cary. 2005. Molecular approaches to the investigation of viable dinoflagellate cysts in natural sediments from estuarine environments. J. Eukaryot. Microbiol. 52: 9094.
26. Coyne, K. J.,, D. A. Hutchins,, C. E. Hare, and, S. C. Cary. 2001. Assessing temporal and spatial variability in Pfiesteria piscicida distributions using molecular probing techniques. Aquat. Microb. Ecol. 24: 275285.
27. Darling, K. F.,, D. Kroon,, C. M. Wade, and, A. J. Leigh Brown. 1996. Molecular phylogeny of the planktonic Foraminifera. J. Foraminifer. Res. 26: 324330.
28. Dawson, S. C.,, and N. R. Pace. 2002. Novel kingdomlevel eukaryotic diversity in anoxic environments. Proc. Natl. Acad. Sci. USA 99: 83248329.
29. DeLong, E. F.,, G. S. Wickham, and, N. R. Pace. 1989. Phylogenetic stains: ribosomal RNA-based probes for the identification of single cells. Science 243: 13601363.
30. de Souza, F. A.,, G. A. Kowalchuk,, P. Leeflang,, J. A. van Veen, and, E. Smit. 2004. PCR-denaturing gradient gel electrophoresis profiling of inter- and intraspecies 18S rRNA gene sequence heterogeneity is an accurate and sensitive method to assess species diversity of arbuscular mycorrhizal fungi of the genus Gigaspora. Appl. Environ. Microbiol. 70: 14131424.
31. Diez, B.,, C. Pedros-Alio,, T. L. Marsh, and, R. Massana. 2001. Application of denaturing gradient gel electrophoresis (DGGE) to study the diversity of marine picoeukaryotic assemblages and comparison of DGGE with other molecular techniques. Appl. Environ. Microbiol. 67: 29422951.
32. Diez, B.,, C. Pedros-Alio, and, R. Massana. 2001. Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Appl. Environ. Microbiol. 67: 29322941.
33. Elwood, H. J.,, G. J. Olsen, and, M. L. Sogin. 1985. The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata. Mol. Biol. Evol. 2: 399410.
34. Erwin, D. P.,, I. K. Erickson,, M. E. Delwiche,, F. S. Colwell,, J. L. Strap, and, R. L. Crawford. 2005. Diversity of oxygenase genes from methane- and ammonia-oxidizing bacteria in the Eastern Snake River Plain Aquifer. Appl. Environ. Microbiol. 71: 20162025.
35. Farrelly, V.,, F. Rainey, and, E. Stackebrandt. 1995. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microbiol. 61: 27982801.
36. Fuhrman, J. A.,, D. E. Comeau,, A. Hagstrom, and, A. M. Chan. 1988. Extraction from natural planktonic microorganisms of DNA suitable for molecular biological studies. Appl. Environ. Microbiol. 54: 14261429.
37. Galand, P. E.,, S. Saarnio,, H. Fritze, and, K. Yrjala. 2002. Depth related diversity of methanogen Archaea in Finnish oligotrophic fen. FEMS Microbiol. Ecol. 42: 441449.
38. Gast, R. J.,, M. R. Dennett, and, D. A. Caron. 2004. Characterization of protistan assemblages in the Ross Sea, Antarctica, by denaturing gradient gel electrophoresis. Appl. Environ. Microbiol. 70: 20282037.
39. Giovannoni, S. J.,, E. F. DeLong,, G. J. Olsen, and, N. R. Pace. 1988. Phylogenetic group-specific oligodeoxynucleotide probes for identification of single microbial cells. J. Bacteriol. 170: 720726.
40. Gonzalez, J. M.,, M. C. Portillo, and, C. Saiz-Jimenez. 2005. Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments. Environ. Microbiol. 7: 10241028.
41. Good, I. J. 1953. The population frequency of species and the estimation of population parameters. Biometrika 40: 237264.
42. Griffiths, R. I.,, A. S. Whiteley,, A. G. O’Donnell, and, M. J. Bailey. 2000. Rapid method for coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl. Environ. Microbiol. 66: 54885491.
43. Gruebl, T.,, M. E. Frischer,, M. Sheppard,, M. Neumann,, A. N. Maurer, and, R. F. Lee. 2002. Development of an 18S rRNA gene targeted PCR-based diagnostic for the blue crab parasite Hematodinium sp. Dis. Aquat. Org. 49: 6170.
44. Hackl, E.,, S. Zechmeister-Boltenstern,, L. Bodrossy, and, A. Sessitsch. 2004. Comparison of diversities and compositions of bacterial populations inhabiting natural forest soils. Appl. Environ. Microbiol. 70: 50575065.
45. Hermsen, C. C.,, D. S. C. Telgt,, E. H. P. Linders,, L. Van De Locht,, W. M. C. Eling,, E. Mensink, and, R. W. Sauerwein. 2001. Detection of Plasmodium falciparum malaria parasites in vivo by real-time quantitative PCR. Mol. Biochem. Parasitol. 118: 247251.
46. Huber, T.,, G. Faulkner, and, P. Hugenholtz. 2004. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 23172319.
47. Hughes, J. B.,, J. J. Hellmann,, T. H. Ricketts, and, B. J. M. Bohannan. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl. Environ. Microbiol. 67: 43994406.
48. Hunt, J.,, L. Boddy,, P. F. Randerson, and, H. J. Rogers. 2004. An evaluation of 18S rDNA approaches for the study of fungal diversity in grassland soils. Microb. Ecol. 47: 385395.
49. Karnati, S. K. R.,, Z. Yu,, J. T. Sylvester,, B. A. Dehority,, M. Morrison, and, J. L. Firkins. 2003. Technical note: specific PCR amplification of protozoal 18S rDNA sequences from DNA extracted from ruminal samples of cows. J. Anim. Sci. 81: 812815.
50. Kinner, N. E.,, R. W. Harvey,, D. M. Shay,, D. W. Metge, and, A. Warren. 2002. Field evidence for a protistan role in an organically-contaminated aquifer. Environ. Sci. Technol. 36: 43124318.
51. Kitts, C. L. 2001. Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics. Curr. Issues Intest. Microbiol. 2001: 1725.
52. Koide, R. T. 2005. Nucleic acid isolation from ecological samples—fungal associations, mycorrhizae. Methods Enzymol. 395: 5872.
53. Kuhlman, K. R.,, W. G. Fusco,, M. T. La Duc,, L. B. Allenbach,, C. L. Ball,, G. M. Kuhlman,, R. C. Anderson,, I. K. Erickson,, T. Stuecker,, J. Benardini,, J. L. Strap, and, R. L. Crawford. 2006. Diversity of microorganisms within rock varnish in the Whipple Mountains, California. Appl. Environ. Microbiol. 72: 17081715.
54. Kumar, Y.,, R. Westram,, S. Behrens,, B. Fuchs,, F. O. Glöckner,, R. Amann,, H. Meier, and, W. Ludwig. 2005. Graphical representation of ribosomal RNA probe accessibility data using ARB software package. BMC Bioinformatics 6: 61.
55. Lane, D. J. 1991. 16S/23S rRNA sequencing, p. 115–175. In E. Stackebrandt and, M. Goodfellow (ed.), Nucleic Acid Techniques in Bacterial Systematics. John Wiley and Sons, New York, N.Y.
56. Lange, M.,, L. Guillou,, D. Vaulot,, N. Simon,, R. I. Amann,, W. Ludwig, and, L. K. Medlin. 1996. Identification of the class Prymnesiophyceae and the genus Phaeocyctis with ribosomal RNA-targeted nucleic acid probes detected by flow cytometry. J. Phycol. 32: 858868.
57. Lawley, B.,, S. Ripley,, P. Bridge, and, P. Convey. 2004. Molecular analysis of geographic patterns of eukaryotic diversity in Antarctic soils. Appl. Environ. Microbiol. 70: 59635972.
58. Lefranc, M.,, A. Thenot,, C. Lepere, and, D. Debroas. 2005. Genetic diversity of small eukaryotes in lakes differing by their trophic status. Appl. Environ. Microbiol. 71: 59355942.
59. Liesack, W.,, H. Weyland, and, E. Stackebrandt. 1991. Potential risks of gene amplification by PCR as determined by 16S rDNA analysis of a mixed-culture of strict barophilic bacteria. Microb. Ecol. 21: 191198.
60. Lim, E.,, D. Caron, and, E. Delong. 1996. Development and field application of a quantitative method for examining natural assemblages of protists with oligonucleotide probes. Appl. Environ. Microbiol. 62: 14161423.
61. Lim, E. L.,, L. A. Amaral,, D. A. Caron, and, E. F. DeLong. 1993. Application of rRNA-based probes for observing marine nanoplanktonic protists. Appl. Environ. Microbiol. 59: 16471655.
62. Lin, M. H.,, T. C. Chen,, T. T. Kuo,, C. C. Tseng, and, C. P. Tseng. 2000. Real-time PCR for quantitative detection of Toxoplasma gondii. J. Clin. Microbiol. 38: 41214125.
63. Lin, S.,, and E. J. Carpenter. 1996. An empirical protocol for whole-cell immunofluorescence of marine phytoplankton. J. Phycol. 32: 10831094.
64. Lio, P.,, and N. Goldman. 1998. Models of molecular evolution and phylogeny. Genome Res. 8: 12331244.
65. López-Garcia, P.,, H. Philippe,, F. Gail, and, D. Moreira. 2003. Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the Mid-Atlantic Ridge. Proc. Natl. Acad. Sci. USA 100: 697702.
66. López-Garcia, P.,, F. Rodriguez-Valera,, C. Pedros-Alio, and, D. Moreira. 2001. Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409: 603607.
67. Lord, N. S.,, C. W. Kaplan,, P. Shank,, C. L. Kitts, and, S. L. Elrod. 2002. Assessment of fungal diversity using terminal restriction fragment (TRF) pattern analysis: comparison of 18S and ITS ribosomal regions. FEMS Micro-biol. Ecol. 42: 327337.
68. Loy, A.,, M. Horn, and, M. Wagner. 2003. probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res. 31: 514516.
69. Maidak, B. L.,, J. R. Cole,, T. G. Lilburn,, C. T. Parker, Jr.,, P. R. Saxman,, R. J. Farris,, G. M. Garrity,, G. J. Olsen,, T. M. Schmidt, and, J. M. Tiedje. 2001. The RDPII (Ribosomal Database Project). Nucleic Acids Res. 29: 173174.
70. Mallatt, J. M.,, J. R. Garey, and, J. W. Shultz. 2004. Ecdysozoan phylogeny and Bayesian inference: first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol. Phylogenet. Evol. 31: 178191.
71. Marsh, T. L. 2005. Culture-independent microbial community analysis with terminal restriction fragment length polymorphism. Methods Enzymol. 397: 308329.
72. Marsh, T. L.,, W. T. Liu,, L. J. Forney, and, H. Cheng. 1998. Beginning a molecular analysis of the eukaryal community in activated sludge. Water. Sci. Technol. 37: 455460.
73. Marsh, T. L.,, P. Saxman,, J. Cole, and, J. Tiedje. 2000. Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Appl. Environ. Microbiol. 66: 36163620.
74. Martin, A. P. 2002. Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl. Environ. Microbiol. 68: 36733682.
75. Massana, R.,, J. Castresana,, V. Balague,, L. Guillou,, K. Romari,, A. Groisillier,, K. Valentin, and, C. Pedros-Alio. 2004. Phylogenetic and ecological analysis of novel marine stramenopiles. Appl. Environ. Microbiol. 70: 35283534.
76. Massana, R.,, L. Guillou,, B. Diez, and, C. Pedros-Alio. 2002. Unveiling the organisms behind novel eukaryotic ribosomal DNA sequences from the ocean. Appl. Environ. Microbiol. 68: 45544558.
77. Medlin, L.,, H. J. Elwood,, S. Stickel, and, M. L. Sogin. 1988. The characterization of enzymatically amplified eukaryotic 16S-like RNA-coding regions. Gene 71: 491499.
78. Mendoza, H.,, V. López-Rodas,, S. González-Gil,, A. Aguilera, and, E. Costas. 1995. Use of polyclonal antisera and blocking of the antibodies in the identification of marine dinoflagellates: species-specific and clone-specific antisera angainst Gymnodinium and Alexandrium. J. Exp. Mar. Biol. Ecol. 186: 103115.
79. Miller, D. N.,, J. E. Bryant,, E. L. Madsen, and, W. C. Ghiorse. 1999. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65: 4715- 4724.
80. Moon-van der Staay, S. Y.,, R. De Wachter, and, D. Vaulot. 2001. Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409: 607610.
81. Moon-van der Staay, S. Y.,, G. W. M. van der Staay,, L. Guillou,, D. Vaulot,, H. Claustre, and, L. K. Medlin. 2000. Abundance and diversity of prymnesiophytes in the picoplankton community from the equatorial Pacific Ocean inferred from 18S rDNA sequences. Limnol. Oceanogr. 45: 98109.
82. More, M.,, J. Herrick,, M. Silva,, W. Ghiorse, and, E. Madsen. 1994. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl. Environ. Microbiol. 60: 15721580.
83. Moyer, C. L.,, J. M. Tiedje,, F. C. Dobbs, and, D. M. Karl. 1996. A computer-simulated restriction fragment length polymorphism analysis of bacterial small-subunit rRNA genes: efficacy of selected tetrameric restriction enzymes for studies of microbial diversity in nature. Appl. Environ. Microbiol. 62: 25012507.
84. Mullins, T. D.,, T. B. Britschgi,, R. I. Krest, and, S. J. Giovannoni. 1995. Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities. Limnol. Oceanogr. 39: 148158.
85. Muyzer, G.,, E. C. de Waal, and, A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of poly-merase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59: 695700.
86. Nei, M.,, and W. H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76: 52695273.
87. Nikolcheva, L.,, and F. Barlocher. 2004. Taxon-specific fungal primers reveal unexpectedly high diversity during leaf decomposition in a stream. Mycol. Prog. 3: 4150.
88. Nikolcheva, L.,, A. Cockshutt, and, F. Barlocher. 2003. Determining diversity of freshwater fungi on decaying leaves: comparison of traditional and molecular approaches. Appl. Environ. Microbiol. 69: 25482554.
89. Not, F.,, M. Latasa,, D. Marie,, T. Cariou,, D. Vaulot, and, N. Simon. 2004. A single species, Micromonas pusilla (Prasinophyceae), dominates the eukaryotic picoplankton in the Western English Channel. Appl. Environ. Microbiol. 70: 40644072.
90. Ogram, A. V.,, G. S. Sayler, and, T. T. Barkay. 1988. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7: 5766.
91. Okazaki, K.,, T. Iwaoka,, N. Murakami,, K. Ichimi, and, S. Montani. 2001. Production of monoclonal antibody against Scrippsiella trochoidea cysts and its application to analysis during cyst formation and enzyme-linked immunosorbent assay. Biosci. Biotechnol. Biochem. 65: 470473.
92. Palumbo, A. V.,, L. S. Fisher,, M. Z. Martin,, Z. K. Yang,, J. R. Tarver,, S. D. Wullschleger, and, W. L. Daniels. 2004. Application of emerging tools and techniques for measuring carbon and microbial communities in reclaimed mine soils. Environ. Manag. 33: S518S527.
93. Picard, C.,, C. Ponsonnet,, E. Paget,, X. Nesme, and, P. Simonet. 1992. Detection and enumeration of bacteria in soil by direct DNA extraction and polymerase chain reaction. Appl. Environ. Microbiol. 58: 27172722.
94. Polz, M. F.,, and C. M. Cavannaugh. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl. Environ. Microbiol. 64: 37243730.
95. Richards, T. A.,, A. A. Veprtiskiy,, D. E. Gouliamova, and, S. A. Nierzwicki-Bauer. 2005. The molecular diversity of freshwater picoeukaryotes from an oligotrophic lake reveals diverse, distinctive and globally dispersed lineages. Environ. Microbiol. 7: 14131425.
96. Rod’kina, S. A. 2003. Comparative characterization of the microbial community in two species of sponges from Sea of Japan using fatty acid markers. Russ. J. Mar. Biol. 29: 255258.
97. Romari, K.,, and D. Vaulot. 2004. Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. Limnol. Oceanogr. 49: 784798.
98. Romestand, B.,, J. Torreilles, and, P. Roch. 2001. Production of monoclonal antibodies against the protozoa, Perkinsus marinus: estimation of parasite multiplication in vitro. Aquat. Living Resour. 14: 351357.
99. Savin, M. C.,, J. L. Martin,, M. LeGresley,, M. Giewat, and, J. Rooney-Varga. 2004. Plankton diversity in the Bay of Fundy as measured by morphological and molecular methods. Microb. Ecol. 48: 5165.
100. Schabereiter-Gurtner, C.,, G. Pinar,, W. Lubitz, and, S. Rolleke. 2001. Analysis of fungal communities on historical church window glass by denaturing gradient gel electrophoresis and phylogenetic 18S rDNA sequence analysis. J. Microbiol. Methods 47: 345354.
101. Schloss, P. D.,, and J. Handelsman. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71: 15011506.
102. Schloss, P. D.,, B. R. Larget, and, J. Handelsman. 2004. Integration of microbial ecology and statistics: a test to compare gene libraries. Appl. Environ. Microbiol. 70: 54855492.
103. Schneider, S.,, D. Roessli, and, L. Excoffier. 2000. Arlequin ver. 2.000: a software for population genetics data analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva, Switzerland.
104. Shapiro, L. P.,, L. Campbell, and, E. M. Haugen. 1989. Immunochemical recognition of phytoplankton species. Mar. Ecol. Prog. Ser. 57: 219224.
105. Sherr, E. B.,, and B. F. Sherr. 2002. Significance of predation by protists in aquatic microbial food webs. Antonie Leeuwenhoek 81: 293308.
106. Simon, N.,, J. Brenner,, B. Edvardsen, and, L. Medlin. 1997. The identification of Chrysochromulina and Prymnesium species (Haptophyta, Prymnesiophyceae) using fluorescent or chemiluminescent oligonucleotide probes: a means for improving studies on toxic algae. Eur. J. Phycol. 32: 393401.
107. Simon, N.,, L. Campbell,, E. Ornolfsdottir,, R. Groben,, L. Guillou,, L. Lange, and, L. K. Medlin. 2000. Oligonucleotide probes for the identification of three algal groups by dot blot and fluorescent whole-cell hybridization. J. Eukaryot. Microbiol. 47: 7684.
108. Simon, N.,, N. LeBot,, D. Marie,, F. Partensky, and, D. Vaulot. 1995. Fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes to identify small phytoplankton by flow cytometry. Appl. Environ. Micro-biol. 61: 25062513.
109. Singleton, D. R.,, M. A. Furlong,, S. L. Rathbun, and, W. B. Whitman. 2001. Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl. Environ. Microbiol. 67: 43744376.
110. Slapeta, J.,, D. Moreira, and, P. Lopez-Garcia. 2005. The extent of protist diversity: insights from molecular ecology of freshwater eukaryotes. Proc. R. Soc. Ser. B. 272: 20732081.
111. Smit, E.,, P. Leeflang,, B. Glandorf,, J. D. van Elsas, and, K. Wernars. 1999. Analysis of fungal diversity in the wheat rhizosphere by sequencing of cloned PCR-amplified genes encoding 18S rRNA and temperature gradient gel electrophoresis. Appl. Environ. Microbiol. 65: 26142621.
112. Sogin, M. L. 1990. Amplification of ribosomal RNA genes for molecular evolution studies, p. 307–322. In M. A. Innis,, D. H. Gelfand,, J. J. Sninsky, and, T. J. White (ed.), PCR Protocols: a Guide to Methods and Applications. Academic Press, Inc., New York, N.Y.
113. Somerville, C. C.,, I. T. Knight,, W. L. Straube, and, R. R. Colwell. 1989. Simple, rapid method for direct isolation of nucleic acids from aquatic environments. Appl. Environ. Microbiol. 55: 548554.
114. Stoeck, T.,, and S. Epstein. 2003. Novel eukaryotic lineages inferred from small-subunit rRNA analyses of oxygen-depleted marine environments. Appl. Environ. Microbiol. 69: 26572663.
115. Stoeck, T.,, G. T. Taylor, and, S. S. Epstein. 2003. Novel eukaryotes from the permanently anoxic Cariaco Basin (Caribbean Sea). Appl. Environ. Microbiol. 69: 56565663.
116. Strap, J. L.,, F. S. Colwell, and, R. L. Crawford. Eukaryotic diversity in planktonic and biofilm populations within the subsurface of the Snake River Plain Aquifer. Submitted for publication.
117. Suzuki, M.,, and S. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62: 625630.
118. Takishita, K.,, H. Miyake,, M. Kawato, and, T. Maruyama. 2005. Genetic diversity of microbial eukaryotes in anoxic sediment around fumaroles on a submarine cladera floor based on the small-subunit rDNA phylogeny. Extremophiles 9: 185196.
119. Tebbe, C. C.,, and W. Vahjen. 1993. Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant DNA from bacteria and a yeast. Appl. Environ. Microbiol. 59: 26572665.
120. Thompson, J. D.,, T. J. Gibson,, F. Plewniak,, F. Jeanmougin, and, D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25: 48764882.
121. Tsai, Y.-L.,, and B. H. Olson. 1991. Rapid method for direct extraction of DNA from soil and sediments. Appl. Environ. Microbiol. 57: 10701074.
122. van Hannen, E. J.,, M. P. Agterveld,, H. J. Gons, and, H. J. Laanbroek. 1998. Revealing genetic diversity of eukaryotic microorganisms in aquatic environments by denaturing gradient gel electrophoresis. J. Phycol. 34: 206213.
123. Vestal, J. R.,, and D. C. White. 1989. Lipid analysis in microbial ecology. Bioscience 39: 535541.
124. Vilgalys, R.,, and M. Hester. 1990. Rapid genetic identification and mapping of enzymatically amplifed ribosomal DNA from several Cryptococcus species. J. Bacteriol. 172: 42384246.
125. von Wintzingerode, F.,, U. B. Gobel, and, E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21: 213229.
126. Vrieling, E. G.,, and D. M. Anderson. 1996. Immunofluorescence in phytoplankton research: applications and potential. J. Phycol. 32: 116.
127. Weisse, T. 2002. The significance of inter- and intraspecific variation in bacterivorous and herbivorous protists. Antonie Leeuwenhoek 81: 327341.
128. Whelan, S.,, P. Lio, and, N. Goldman. 2001. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet. 17: 262272.
129. White, D. C.,, W. M. Davis,, J. S. Nickels,, J. D. King, and, R. J. Bobbie. 1979. Determination of the sedimentary microbial biomass by extractable lipid phosphate. Oecologia 40: 5162.
130. White, D. C.,, H. C. Pinkart, and, D. Ringelberg. 1997. Biomass measurements: biochemical approaches, p. 91–101. In C. J. Hurst,, G. R. Knudsen,, M. J. McInerney,, L. D. Stetzenbach, and, M. V. Walter (ed.), Manual of Environmental Microbiology. American Society for Microbiology, Washington, D.C.
131. White, T. J.,, T. Bruns,, S. Lee, and, J. Taylor. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, p. 315–322. In M. A. Innis,, D. H. Gelfand,, J. J. Sninsky, and, T. J. White (ed.), PCR Protocols: a Guide to Methods and Applications. Academic Press, Inc., New York, N.Y.
132. Willerslev, E.,, A. J. Hansen,, B. Christensen,, J. P. Steffensen, and, P. Arctander. 1999. Diversity of Holocene life forms in fossil glacier ice. Proc. Natl. Acad. Sci. USA 96: 80178021.
133. Zelles, L. 1999. Fatty acid patterns of phospholipids and lipopolysaccharides in the characterisation of microbial communities in soil: a review. Biol. Fertil. Soils 29: 111129.
134. Zhu, F.,, R. Massana,, F. Not,, D. Marie, and, D. Vaulot. 2005. Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol. Ecol. 52: 7992.


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18S rRNA gene primers

Citation: Strap J. 2007. Characterization of Microeukaryota in Natural Environments, p 1112-1121. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch90

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