Skip to main content Accessibility help
Hostname: page-component-56f9d74cfd-mtzzk Total loading time: 0.664 Render date: 2022-06-25T21:32:33.308Z Has data issue: true Feature Flags: { "shouldUseShareProductTool": true, "shouldUseHypothesis": true, "isUnsiloEnabled": true, "useRatesEcommerce": false, "useNewApi": true }

9 - Protist systematics, ecology and next generation sequencing

from Part II - Next Generation Biodiversity Science

Published online by Cambridge University Press:  05 June 2016

David Bass
Sciences, The Natural History Museum, London, UK
Thomas Bell
Imperial College London, Silwood Park Campus, Ascot, UK
Peter D. Olson
Natural History Museum, London
Joseph Hughes
University of Glasgow
James A. Cotton
Wellcome Trust Sanger Institute, Cambridge
Get access


Protist taxonomy in context

The increasing availability over the past two decades of gene sequence data for protists has fired an energetic and rapidly moving field of taxonomic development and debate, in response to many exciting and often very surprising findings. The classic subdivisions of microbial eukaryotes into four main groups – amoeboid organisms, flagellates, ciliates and sporozoa (a group of parasites) – formulated in the 19th century and current throughout a large part of the 20th appeals because of its simplicity, but almost could not be more wrong. The history of protist taxonomy is not the subject of this chapter, but a diversity of perspectives can be found in (among others) Adl et al. (2005; 2007; 2012), Cavalier-Smith (1998), Corliss (1984), Levine et al. (1980), Walker et al. (2011) and references therein. There are several characteristics of protists that have contributed to this taxonomic turbulence. Their size makes detailed observation non-trivial; individual approaches, skills and tools applied to morphological taxonomic studies have varied significantly over time, and continue to do so. Their single-celled and/or non-differentiated forms do not offer many easily observable characters for either the taxonomist or natural selection to work on. A consequence of the latter is extremely high levels of convergent evolution at different evolutionary scales. Some very striking examples of convergence have been revealed by molecular phylogenetic analyses, which demonstrate the extent to which the pre-molecular subdivision of protists was incorrect (e.g. Nikolaev et al. 2004; Richards and Talbot 2007; Richards et al. 2011; S. D. Brown et al. 2012).

Some other important factors contributing to taxonomic difficulties are (1) the unknown sexual status of most protists and therefore the inapplicability and/or uncertainty of applying the biological species concept (sex is known for some but many are presumed asexual at least in the mid to long term), (2) highly incomplete and patchy knowledge of the diversity of many protist groups and regions of the eukaryote Tree of Life in which knowledge of lineage diversity and biology is generally poor, (3) the absence of a generally agreed or applicable species concept for most protist groups, and (4) difficulty of culturing many lineages.

Publisher: Cambridge University Press
Print publication year: 2016

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)


Adl, S. M., Leander, B. S., Simpson, A. G., et al. (2007). Diversity, nomenclature, and taxonomy of protists. Systematic Biology, 56, 684–9.CrossRefGoogle ScholarPubMed
Adl, S. M., Simpson, A. G., Farmer, M. A., et al. (2005). The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology, 52, 399–451.CrossRefGoogle ScholarPubMed
Adl, S. M., Simpson, A. G., Lane, C. E., et al. (2012). The revised classification of eukaryotes. Journal of Eukaryotic Microbiology, 59, 429–514.CrossRefGoogle ScholarPubMed
Álvarez, I. and Wendel, J. F. (2003). Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution, 29, 417–34.CrossRefGoogle ScholarPubMed
Amaral-Zettler, L. A., McCliment, E. A., Ducklow, H. W. and Huse, S. M. (2009). A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE, 4, e6372.CrossRefGoogle ScholarPubMed
Amato, A., Kooistra, W. H., Levialdi, C. F., et al. (2007). Reproductive isolation among sympatric cryptic species in marine diatoms. Protist, 158, 193–207.CrossRefGoogle ScholarPubMed
Bachy, C., Dolan, J. R., López-García, P., Deschamps, P. and Moreira, D. (2012). Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study. The ISME Journal, 7, 244–55.Google ScholarPubMed
Barraclough, T. G., Birky, C. W. Jr and Burt, A. (2003). Diversification in sexual and asexual organisms. Evolution, 57, 2166–72.CrossRefGoogle ScholarPubMed
Barraclough, T. G., Hughes, M., Ashford-Hodges, N. and Fujisawa, T. (2009). Inferring evolutionarily significant units of bacterial diversity from broad environmental surveys of single-locus data. Biology Letters, 5, 425–8.CrossRefGoogle ScholarPubMed
Bass, D. and Boenigk, J. (2011). Everything is everywhere, a 21st century de-reconstruction. In Biogeography of Microscopic Organisms, Is Everything Everywhere? ed. Fontaneto, D.. Systematics Association Special Volume 79. Cambridge, Cambridge University Press, pp. 88–110.Google Scholar
Bass, D., Howe, A. T., Mylnikov, A. P., et al. (2009). Phylogeny and classification of Cercomonadida, Cercomonas, Eocercomonas, Paracercomonas, and Cavernomonas gen. n. Protist 160, 483–521.Google ScholarPubMed
Bass, D., Richards, T. A., Matthai, L., Marsh, V. and Cavalier-Smith, T. (2007). DNA evidence for global dispersal and probable endemicity of protozoa. BMC Evolutionary Biology, 7, 162.CrossRefGoogle ScholarPubMed
Bass, D., Stentiford, G. D., Littlewood, T. D. and Hartikainen, H. (2015). Diverse applications of environmental DNA methods in parasitology. Trends in Parasitology, 31, 499–513.CrossRefGoogle ScholarPubMed
Bass, D., Yabuki, A., Santini, S., Romac, S. and Berney, C. (2012). Reticulamoeba is a long branched granofilosean (Cercozoa) that is missing from sequence databases. PLoS One, 7, e49090.CrossRefGoogle ScholarPubMed
Behnke, A., Engel, M., Christen, R., Nebel, M., Klein, R. R. and Stoeck, T. (2011). Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions. Environmental Microbiology, 13, 340–9.CrossRefGoogle ScholarPubMed
Bellemain, E., Carlsen, T., Brochmann, C., Coissac, E., Taberlet, P. and Kauserud, H. (2010). ITS as an environmental DNA barcode for fungi, an in silico approach reveals potential PCR biases. BMC Microbiology, 10, 189.CrossRefGoogle Scholar
Berney, C., Romac, S., Mahé, F., Santini, S., Siano, R. and Bass, D. (2013). Vampires in the oceans: predatory cercozoan amoebae in marine habitats. The ISME Journal, 7, 2387–99.CrossRefGoogle ScholarPubMed
Bik, H. M., Porazinska, D. L., Creer, S., Caporaso, J. G., Knight, R. and Thomas, W. K. (2012). Sequencing our way towards understanding global eukaryotic biodiversity. Trends in Ecology and Evolution, 27, 233–43.CrossRefGoogle ScholarPubMed
Bittner, L., Gobet, A., Audic, S., et al. (2012). Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. Molecular Ecology, 22, 87–101.Google ScholarPubMed
Blaxter, M., Mann, J., Chapman, T., et al. (2005). Defining operational taxonomic units using DNA barcode data. Philosophical Transactions of the Royal Society of London B-Biological Sciences, 360, 1935–43.CrossRefGoogle ScholarPubMed
Boenigk, J., Ereshefsky, M., Hoef-Emden, K., Mallet, J. and Bass, D. (2012). Concepts in protistology: species definitions and boundaries. European Journal of Protistology, 48, 96–102.CrossRefGoogle ScholarPubMed
Brabender, M., Kiss, A. K., Domonell, A., Nitsche, F. and Arndt, H. (2012). Phylogenetic and morphological diversity of novel soil cercomonad species with a description of two new genera (Nucleocercomonas and Metabolomonas). Protist, 163, 495–528.CrossRefGoogle Scholar
Brown, M. W., Kolisko, M., Silberman, J. D. and Roger, A. J. (2012). Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria. Current Biology, 22, 1123–7.CrossRefGoogle ScholarPubMed
Brown, S. D., Armstrong, K. F. and Cruickshank, R. H. (2012). Molecular phylogenetics of a South Pacific sap beetle species complex (Carpophilus spp., Coleoptera, Nitidulidae). Molecular Phylogenetics and Evolution, 64, 428–40.CrossRefGoogle Scholar
Buée, M., Reich, M., Murat, C., et al. (2009). 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytologis, 184, 449–56.CrossRefGoogle ScholarPubMed
Burki, F. (2014). The eukaryotic tree of life from a global phylogenomic perspective. Cold Spring Harbor Perspectives in Biology, 6(5), a016147.CrossRefGoogle ScholarPubMed
Caisová, L., Marin, B. and Melkonian, M. (2011). A close-up view on ITS2 evolution and speciation: a case study in the Ulvophyceae (Chlorophyta, Viridiplantae). BMC Evolutionary Biology, 11, 262.CrossRefGoogle Scholar
Cavalier-Smith, T. (1998). A revised six-kingdom system of life. Biological Reviews of the Cambridge Philosophical Society, 73, 203–66.CrossRefGoogle ScholarPubMed
Cavalier-Smith, T. and Chao, E. E. (2010). Phylogeny and evolution of Apusomonadida (Protozoa, Apusozoa): new genera and species. Protist, 161, 549–76.CrossRefGoogle ScholarPubMed
Chambouvet, A., Richards, T. A., Bass, D. and Neuhauser, S. (2015). Revealing micro-parasite diversity using brute force molecular techniques and gently persuasive microscopy in aquatic environments. In Parasite Diversity and Diversification, ed. Morand, S., Brasnov, B. R. and Littlewood, D. T. J.. Cambridge, Cambridge University Press.CrossRef
Chan, C. X. and Ragan, M. A. (2013). Next-generation phylogenomics. Biology Direct, 8, 3.CrossRefGoogle ScholarPubMed
China Plant BOL Group, Li, D. Z., Gao, L. M., et al. (2011). Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proceedings of the National Academy of Sciences of the United States of America, 108, 19641–6.Google ScholarPubMed
Coleman, A. W. (2007). Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Research, 35, 3322–9.CrossRefGoogle ScholarPubMed
Coleman, A. W. (2009). Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide. Molecular Phylogenetics and Evolution, 50, 197–203.CrossRefGoogle Scholar
Corliss, J. O. (1984). The kingdom Protista and its 45 phyla. Biosystems, 17, 87–126.CrossRefGoogle ScholarPubMed
Creer, S., Fonseca, V. G., Porazinska, D. L., et al. (2010). Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Molecular Ecology, 19 (Suppl 1), 4–20.CrossRefGoogle ScholarPubMed
del Campo, J., Not, F., Forn, I., Sieracki, M. E. and Massana, R. (2013). Taming the smallest predators of the oceans. The ISME Journal, 7(2), 351–8.CrossRefGoogle ScholarPubMed
de Vargas, C., Audic, S., Henry, N., et al. (2015). Eukaryotic plankton diversity in the sunlit ocean. Science, 348(6237). doi: 10.1126/science.1261605.CrossRefGoogle ScholarPubMed
Dunthorn, M., Otto, J., Berger, S. A., et al. (2014). Placing environmental next-generation sequencing amplicons from microbial eukaryotes into a phylogenetic context. Molecular Biology and Evolution, 31, 993–1009.CrossRefGoogle ScholarPubMed
Dupont, A. Ö. C., Griffiths, R. I., Bell, T. and Bass, D. (2016). Differences in soil micro-eukaryotic communities over soil pH gradients are strongly driven by parasites and saprotrophs. Environmental Microbiology, in press.CrossRef
Edgcomb, V., Orsi, W, Bunje, J. et al. (2011). Protistan microbial observatory in the Cariaco Basin, Caribbean. I. Pyrosequencing vs Sanger insights into species richness. The ISME Journal, 5, 1344–56.CrossRefGoogle ScholarPubMed
Evans, S. N. and Matsen, F. A. (2012). The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples. Journal of the Royal Statistical Society. Series B, Statistical Methodology, 74, 569–92.CrossRefGoogle ScholarPubMed
Fonseca, V. G., Carvalho, G. R., Sung, W., et al. (2010). Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature Communications, 1, 98.CrossRefGoogle ScholarPubMed
Fonseca, V. G., Nichols, B., Lallias, D., et al. (2012). Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Research, 40, e66.CrossRefGoogle ScholarPubMed
Garzón, C., Geiser, D. M. and Moorman, G. W. (2005). Amplified fragment length polymorphism analysis and internal transcribed spacer and coxII sequences reveal a species boundary within Pythium irregulare. Phytopathology, 95, 1489–98.CrossRefGoogle ScholarPubMed
Geisen, S., Laros, I., Vizcaíno, A., Bonkowski, M., de Groot, G. A. (2015a). Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa. Molecular Ecology, 24(17), 4556–69.CrossRefGoogle ScholarPubMed
Geisen, S., Tveit, A. T., Clark, I. M., et al. (2015b). Metatranscriptomic census of active protists in soils. The ISME Journal, 9(10), 2178–90.CrossRefGoogle ScholarPubMed
Gilles, A., Meglécz, E., Pech, N., Ferreira, S., Malausa, T. and Martin, J-F. (2011). Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics, 12, 245.CrossRefGoogle ScholarPubMed
Glücksman, E., Bell, T., Griffiths, R. I. and Bass, D. (2010). Closely related protist strains have different grazing impacts on natural bacterial communities. Environmental Microbiology, 12, 3105–13.CrossRefGoogle ScholarPubMed
Guillou, L., Bachar, D., Audic, S., et al. (2013). The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Research, 41 (Database issue), D597–604.Google ScholarPubMed
Hartikainen, H., Stentiford, G. D., Bateman, K. S., et al. (2014). Mikrocytids are a broadly distributed and divergent radiation of parasites in aquatic invertebrates. Current Biology, 24, 807–12.CrossRefGoogle ScholarPubMed
Heinrichs, G., de Hoog, G. S. and Haase, G. (2012). Barcode identifiers as a practical tool for reliable species assignment of medically important black yeast species. Journal of Clinical Microbiology, 50, 3023–30.CrossRefGoogle ScholarPubMed
Hess, D. and Melkonian, M. (2013). The mystery of Clade X: Ociraptor gen. nov. and Viridiraptor gen. nov. are highly specialized, algivorous amoeba-flagellates (Glissomonadida, Cercozoa). Protist, 164, 706–47.CrossRef
Heywood, J. L., Sieracki, M. E., Bellows, W., Poulton, N. J. and Stepanauskas, R. (2011). Capturing diversity of marine heterotrophic protists: one cell at a time. The ISME Journal, 5(4), 674–84.CrossRefGoogle ScholarPubMed
Howe, A. T., Bass, D., Chao, E. E. and Cavalier-Smith, T. (2011a). New genera, species, and improved phylogeny of Glissomonadida (Cercozoa). Protist, 162, 710–22.CrossRefGoogle Scholar
Howe, A. T., Bass, D., Scoble, J., et al. (2011b). Novel cultured protists identify deep-branching environmental DNA clades of Cercozoa: new genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia. Protist, 162, 332–72.CrossRefGoogle ScholarPubMed
Howe, A. T., Bass, D., Vickerman, K., Chao, E.E-Y. and Cavalier-Smith, T. (2009). Phylogeny, taxonomy, and astounding genetic diversity of Glissomonadida ord. nov., the dominant gliding zooflagellates in soil (Protozoa, Cercozoa). Protist, 160, 159–89.CrossRefGoogle Scholar
Jeon, S., Bunge, J., Leslin, C., Stoeck, T., Hong, S. and Epstein, S. S. (2008). Environmental rRNA inventories miss over half of protistan diversity. BMC Microbiology, 8, 222.CrossRefGoogle ScholarPubMed
Jones, M. D. M., Forn, I., Gadhela, C., et al. (2011). Discovery of novel intermediate forms redefines the fungal tree of life. Nature, 474, 200–3.CrossRefGoogle ScholarPubMed
Jumpponen, A. and Jones, K. L. (2009). Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytologist, 184, 438–48.CrossRefGoogle ScholarPubMed
Karpov, S. A., Bass, D., Mylnikov, A. P. and Cavalier-Smith, T. (2006). Molecular phylogeny of Cercomonadidae and kinetid patterns of Cercomonas and Eocercomonas gen. nov. (Cercomonadida, Cercozoa). Protist, 157, 125–58.CrossRefGoogle Scholar
Kiontke, K. C., Félix, M. A., Ailion, M., et al. (2011). A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits. BMC Evolutionary Biology, 11, 339.CrossRefGoogle ScholarPubMed
Koeppel, A., Perry, E. B., Sikorski, J., et al. (2008). Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. Proceedings of the National Academy of Sciences of the United States of America, 105, 2504–9.CrossRefGoogle ScholarPubMed
Kubartová, A., Ottosson, E., Dahlberg, A. and Stenlid, J. (2012). Patterns of fungal communities among and within decaying logs, revealed by 454 sequencing. Molecular Ecology, 18, 4514–32.Google Scholar
Kunin, V., Engelbrektson, A., Ochmann, H. and Hugenholtz, P. (2009). Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environmental Microbiology, 12, 118–23.Google ScholarPubMed
Lecroq, B., Lejzerowicz, F., Bachar, D., et al. (2011). Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments. Proceedings of the National Academy of Sciences of the United States of Americ, 108, 13177–82.CrossRefGoogle ScholarPubMed
Levine, N. D., Corliss, J. O., Cox, F. E., et al. (1980). A newly revised classification of the protozoa. Journal of Protozoology, 27, 37–58.CrossRefGoogle ScholarPubMed
Liu, L., Li, Y., Li, S., et al. (2012). Comparison of next-generation sequencing systems. Journal of Biomedicine and Biotechnology, 2012, Article ID 251364.CrossRefGoogle ScholarPubMed
Logares, R., Audic, S., Bass, D., et al. (2014). Patterns of rare and abundant marine microbial eukaryotes. Current Biology, 24, 813–21.CrossRefGoogle ScholarPubMed
Logares, R., Audic, S., Santini, S., Pernice, M. C., de Vargas, C. and Massana, R. (2012). Diversity patterns and activity of uncultured flagellates unveiled with pyrosequencing. The ISME Journal, 6, 1823–33.CrossRefGoogle ScholarPubMed
Loman, N. J., Misra, R. V., Dallman, T. J., et al. (2012). Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotechnology, 30, 434–41.Google ScholarPubMed
Marinho, M. A., Junqueira, A. C. and Azeredo-Espin, A. M. (2011). Evaluation of the internal transcribed spacer 2 (ITS2) as a molecular marker for phylogenetic inference using sequence and secondary structure information in blow flies (Diptera, Calliphoridae). Genetica, 139, 1189–207.CrossRefGoogle Scholar
Massana, R., Unrein, F., Rodríguez-Martínez, R., et al. (2009). Grazing rates and functional diversity of uncultured heterotrophic flagellates. The ISME Journal, 3, 588–96.CrossRefGoogle ScholarPubMed
Matsen, F. A., Hoffman, N. G., Gallagher, A. and Stamatakis, A. (2012). A format for phylogenetic placements. PLoS One, 7, e31009.CrossRefGoogle ScholarPubMed
Matsen, F. A., Kodner, R. B. and Armbrust, E. V. (2010). pplacer, linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics, 11, 538.CrossRefGoogle ScholarPubMed
Medinger, R., Nolte, V., Vinay Pandey, R., et al. (2010). Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Molecular Ecology, 19, 32–40.CrossRefGoogle Scholar
Merget, B., Koetschan, C., Hackl, T., et al. (2012). The ITS2 database. Journal of Visualised Experiments, 61, 3806.Google Scholar
Moreira, D. and López-García, P. (2002). The molecular ecology of microbial eukaryotes unveils a hidden world. Trends in Microbiology, 10, 31–8.CrossRefGoogle ScholarPubMed
Müller, T., Philippi, N., Dandekar, T., Schultz, J. and Wolf, M. (2007). Distinguishing species. RNA, 13, 1469–72.CrossRefGoogle ScholarPubMed
Nassonova, E., Smirnov, A., Fahrni, J. and Pawlowski, J. (2010). Barcoding amoebae: comparison of SSU, ITS and COI genes as tools for molecular identification of naked lobose amoebae. Protist, 161, 102–15.CrossRefGoogle ScholarPubMed
Nekrutenko, A. and Taylor, J. (2012). Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nature Reviews Genetics, 13, 667–62.CrossRefGoogle ScholarPubMed
Nesnidal, M. P., Helmkampf, M., Bruchhaus, I., El-Matbouli, M. and Hausdorf, B. (2013). Agent of whirling disease meets orphan worm: phylogenomic analyses firmly place myxozoa in cnidaria. PLoS One, 8, e54576.CrossRefGoogle ScholarPubMed
Nikolaev, S. I., Berney, C., Fahrni, J. F., et al. (2004). The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proceedings of the National Academy of Sciences of the United States of America, 101, 8066–71.CrossRefGoogle ScholarPubMed
Nilsson, R. H., Kristiansson, E., Ryberg, M., Hallenberg, N. and Larsson, K. H. (2008). Intraspecific ITS variability in the Kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evolutionary Bioinformatics, 4, 193–201.CrossRefGoogle ScholarPubMed
Pawlowski, J., Audic, S., Adl, S., et al. (2012). CBOL Protist Working Group: barcoding eukaryotic richness beyond the animal, plant and fungal kingdoms. PLoS Biology, 10, e1001419.CrossRefGoogle Scholar
Quail, M. A., Smith, M., Coupland, P., et al. (2012). A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosicences and Ilumina MiSeq sequencers. BMC Genomics, 13, 341.CrossRefGoogle Scholar
Richards, T. A. and Bass, D. (2005). Molecular screening of free-living microbial eukaryotes: diversity and distribution using a meta-analysis. Current Opinions in Microbiology, 8, 240–52.CrossRefGoogle ScholarPubMed
Richards, T. A., Soanes, D. M., Jones, M. D., et al. (2011). Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proceedings of the National Academy of Sciences of the United States of America, 108, 15258–63.CrossRefGoogle ScholarPubMed
Richards, T. A. and Talbot, N. J. (2007). Plant parasitic oomycetes such as phytophthora species contain genes derived from three eukaryotic lineages. Plant Signaling and Behavior, 2, 112–14.CrossRefGoogle ScholarPubMed
Shokralla, S., Spall, J. L., Gibson, J. F. and Hajibabaei, M. (2012). Next-generation sequencing technologies for environmental DNA research. Molecular Ecology, 21, 1794–805.CrossRefGoogle ScholarPubMed
Song, J., Shi, L., Li, D., et al. (2012). Extensive pyrosequencing reveals frequent intra-genomic variations of internal transcribed spacer regions of nuclear ribosomal DNA. PLoS One, 7, e43971.CrossRefGoogle ScholarPubMed
Stoeck, T., Bass, D., Nebel, M., et al. (2010). Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology, 19 (Supp. 1), 21–31.CrossRefGoogle ScholarPubMed
Stoeck, T., Zuendorf, A., Breiner, H. W. and Behnke, A. (2007). A molecular approach to identify active microbes in environmental eukaryote clone libraries. Microbial Ecology, 53, 328–39.CrossRefGoogle ScholarPubMed
Tarcz, S. (2013). Intraspecific differentiation of Paramecium novaurelia strains (Ciliophora, Protozoa) inferred from phylogenetic analysis of ribosomal and mitochondrial DNA variation. European Journal of Protistology, 49, 50–61.CrossRefGoogle ScholarPubMed
Walker, G., Dorrell, R. A., Schlacht, A. and Dacks, J. B. (2011). Eukaryotic systematic: a 2011 user's guide for cell biologists and parasitologists. Parasitology, 138, 1638–63.CrossRefGoogle ScholarPubMed
Whiteley, A. S., Jenkins, S., Waite, I., et al. (2012). Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) platform. Journal of Microbiological Methods, 91, 80–8.CrossRefGoogle ScholarPubMed
Wuyts, J., Van de Peer, Y., Winkelmans, T. and De Wachter, R. (2002). The European database on small subunit ribosomal RNA. Nucleic Acids Research, 30, 183–5.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the or variations. ‘’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats