Next-generation environmental diversity surveys of foraminifera: Preparing the future

Biological Bulletin

Volumn 227, Issue 2, 2014, Pages 93-106

  Pawlowski, J ^a   Lejzerowicz, F ^a   Esling, P ^b  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b IRCAM   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DATA SET; FORAMINIFERA; GENERATION TIME; GENETIC ANALYSIS; MARINE ENVIRONMENT; MORPHOLOGY; SPECIES DIVERSITY; SURVEY; TAXONOMY;

FORAMINIFERA;

BIODIVERSITY; CLASSIFICATION; ENVIRONMENT; FORAMINIFER; HIGH THROUGHPUT SEQUENCING; RESEARCH; STANDARDS; TRENDS;

BIODIVERSITY; ENVIRONMENT; FORAMINIFERA; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; RESEARCH;

EID: 84911415683     PISSN: 00063185     EISSN: None     Source Type: Journal    
DOI: 10.1086/BBLv227n2p93     Document Type: Review

References (109)

1. Acinas, S. G., R. Sarma-Rupavtarm, V. Klepac-Ceraj, and M. F. Polz. 2005. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl. Environ. Microbiol. 71: 8966-8969.
2. Aird, D., M. G. Ross, W. S. Chen, M. Danielsson, T. Fennell, C. Russ, D. B. Jaff, C. Nusbaum, and A. Gnirke. 2011. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12: R18.
3. Amend, A. S., K. A. Seifert, and T. D. Bruns. 2010. Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol. Ecol. 19: 5555-5565.
4. Andersen, K., K. L. Bird, M. Rasmussen, J. Haile, H. Breuning-Madsen, K. H. Kjaer, L. Orlando, M. T. P. Gilbert, and E. Willerslev. 2012. Meta-barcoding of 'dirt'DNA from soil reflects vertebrate biodiversity. Mol. Ecol. 21: 1966-1979.
5. Berney, C., J. Fahrni, and J. Pawlowski. 2004. How many novel eukaryotic "kingdoms"? Pitfalls and limitations of environmental DNA surveys. BMC Biol. 2: 13.
6. Bernhard, J. M., V. P. Edgcomb, P. T. Visscher, A. McIntyre-Wressnig, R. E. Summons, M. L. Bouxsein, L. Louis, and M. Jeglinski. 2013. Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas. Proc. Natl. Acad. Sci. USA 110: 9830-9834.
7. Berry, D., K. B. Mahfoudh, M. Wagner, and A. Loy. 2011. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification. Appl. Environ. Microbiol. 77: 7846-7849.
8. Boenigk, J., M. Ereshefsky, K. Hoef-Emden, J. Mallet, and D. Bass. 2012. Concepts in protistology: species definitions and boundaries. Eur. J. Protistol. 48: 96-102.
9. Bokulich, N. A., S. Subramanian, J. J. Faith, D. Gevers, J. I. Gordon, R. Knight, D. A. Mills, and J. G. Caporaso. 2012. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat. Methods 10: 57-59.
10. Bunge, J., L. Woodard, D. Böhning, J. A. Foster, S. Connolly, and H. K. Allen. 2012. Estimating population diversity with CatchAll. Bioinformatics 28: 1045-1047.
11. Buzas, M. A., and S. J. Culver. 1991. Species diversity and dispersal of benthic foraminifera. Bioscience 41: 483-489.
12. Caporaso, J. G., C. L. Lauber, W. A. Walters, D. Berg-Lyons, C. A. Lozupone, P. J. Turnbaugh, N. Fierer, and R. Knight. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc. Natl. Acad. Sci. USA 108: 4516-4522.
13. Carew, M. E., V. J. Pettigrove, L. Metzeling, and A. A. Hoffmann. 2013. Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species. Front. Zool. 10: 45.
14. Carlsen, T., A. B. Aas, D. L. Lindner, T. Vråstad, T. Schumacher, and H. Kauserud. 2012. Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies? Fungal Ecol. 5: 747-749.
15. Caron, D. A., P. D. Countway, P. Savai, R. J. Gast, A. Schnetzer, S. D. Moorthi, M. R. Dennett, D. M. Moran, and A. C. Jones. 2009. Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Appl. Environ. Microbiol. 75: 5797-5808.
16. Chao, A., and J. Bunge. 2002. Estimating the number of species in a stochastic abundance model. Biometrics 58: 531-539.
17. Darling, K. F., and C. M. Wade. 2008. The genetic diversity of planktic foraminifera and the global distribution of ribosomal RNA genotypes. Mar. Micropaleontol. 67: 216-238.
18. Darling, K. F., M. Kucera, and C. M. Wade. 2007. Global molecular phylogeography reveals persistent Arctic circumpolar isolation in a marine planktonic protist. Proc. Natl. Acad. Sci. USA 104: 5002-5007.
19. Deagle, B. E., A. C. Thomas, A. K. Shaffer, A. W. Trites, and S. N. Jarman. 2013. Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? Mol. Ecol. Resour. 13: 620-633.
20. Debenay, J.-P. 2012. A Guide to 1, 000 Foraminifera from Southwestern Pacific, New Caledonia. IRD Editions Marseille/Publication Scientifiques du Muséum, Paris. p. 378.
21. Degnan, P. H., and H. Ochman. 2011. Illumina-based analysis of microbial community diversity. ISME J. 6: 183-194.
22. Dell'Anno, A., and R. Danovaro. 2005. Extracellular DNA plays a key role in deep-sea ecosystem functioning. Science 309: 2179.
23. Dellinger, M., A. Labat, L. Perrouault, and P. Grellier. 2014. Haplomyxa saranae gen. nov. et sp. nov., a new naked freshwater foraminifer. Protist 165: 317-329.
24. de Vargas, C., R. Norris, L. Zaninetti, S. W. Gibb, and J. Pawlowski. 1999. Molecular evidence of cryptic speciation in planktonic foraminifers and their relation to oceanic provinces. Proc. Natl. Acad. Sci. USA 96: 2864-2868.
25. Dunthorn, M., J. Klier, J. Bunge, and T. Stoeck. 2012. Comparing the hyper-variable V4 and V9 regions of the small subunit rDNA for assessment of ciliate environmental diversity. J. Eukaryot. Microbiol. 59: 185-187.
26. Dunthorn, M., J. Otto, S. A. Berger, A. Stamatakis, F. Mahé, S. Romac, C. de Vargas, S. Audic, BioMarKs Consortium, A. Stock, F. Kauff, and T. Stoeck. 2014. Placing environmental next generation sequencing amplicons from microbial eukaryotes into a phylogenetic context. Mol. Biol. Evol. 31: 993-1009.
27. Edgar, R. C., B. J. Haas, J. C. Clemente, C. Quince, and R. Knight. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
28. Edgcomb, V. P., J. M. Bernhard, R. E. Summons, W. Orsi, D. Beaudoin, and P. T. Visscher. 2014. Active eukaryotes in microbialites from Highborne Cay, Bahamas, and Hamelin Pool (Shark Bay), Australia. ISME J. 8: 418-429.
29. Egge, E., L. Bittner, T. Andersen, S. Audic, C. de Vargas, and B. Edvardsen. 2013. 454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes. PLoS One 8: e74371.
30. Fonseca, V. G., B. Nichols, D. Lallias, C. Quince, G. R. Carvalho, D. M. Power, and S. Creer. 2012. Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Res. 40: e66-e66.
31. Glöckner, G., N. Hülsmann, M. Schleicher, A. A. Noegel, L. Eichinger, C. Gallinger, J. Pawlowski, R. Sierra, U. Euteneuer, L. Pillet et al. 2014. The genome of the foraminiferan Reticulomyxa filosa. Curr. Biol. 24: 11-18.
32. Godhe, A., M. E. Asplund, K. Höm, V. Saravanan, A. Tyagi, and I. Karunasagar. 2008. Quantification of diatom and dinoflagellate biomasses in coastal marine seawater samples by real-time PCR. Appl. Environ. Microbiol. 74: 7174-7182.
33. Gonzalez, J. M., M. C. Portillo, P. Belda-Ferre, and A. Mira. 2012. Amplification by PCR artificially reduces the proportion of the rare biosphere in microbial communities. PLoS One 7: e29973.
34. Gooday, A. J., and F. J. Jorissen. 2012. Benthic foraminiferal biogeography: controls on global distribution patterns in deep-water settings. Annu. Rev. Marine Sci. 4: 237-262.
35. Gray, J. S., and M. Elliott. 2009. Ecology of Marine Sediments: From Science to Management. Oxford University Press, Oxford.
36. Grimm, G. W., K. Stögerer, K. T. Ertan, H. Kitazato, M. Kucera, V. Hemleben, and C. Hemleben. 2007. Diversity of rDNA in Chilostomella: Molecular differentiation patterns and putative hermit types. Mar. Micropaleontol. 62: 75-90.
37. Habura, A., J. Pawlowski, S. D. Hanes, and S. S. Bowser. 2004. Unexpected foraminiferal diversity revealed by small-subunit rRNA analysis of Antarctic sediment. J. Eukaryot. Microbiol. 51: 173-179.
38. Habura, A., S. T. Goldstein, S. Broderick, and S. S. Bowser. 2008. A bush, not a tree: the extraordinary diversity of cold-water basal foraminiferans extends to warm-water environments. Limnol. Oceanogr. 53: 1339-1351.
39. Hayward, B. W., M. Holzmann, H. R. Grenfell, and J. Pawlowski. 2004. Morphological distinction of molecular types in Ammonia-towards a taxonomic revision of the world's most common and misidentified foraminiferal genus. Mar. Micropaleontol. 50: 237-271.
40. Hayward, B. W., H. R. Grenfell, C. M. Reid, and K. A. Hayward. 1999. Recent New Zealand Shallow-Water Benthic Foraminifera: Taxonomy, Ecologic Distribution, Biogeography, and Use in Paleoenvironmental Assessment, Institute of Geological & Nuclear Sciences Monograph, Vol. 21. Institute of Geological and Nuclear Sciences, Wellington, New Zealand. 258 pp.
41. Hayward, B. W., M. Holzmann, H. R. Grenfell, and J. Pawlowski. 2004. Morphological distinction of molecular types in Ammonia-towards a taxonomic revision of the world's most common and misidentified foraminiferal genus. Mar. Micropaleontol. 50: 237-271.
42. Hayward, B. W., H. R. Grenfell, A. T. Sabaa, H. L. Neil, and M. A. Buzas. 2010. Recent New Zealand Deep-Water Benthic Foraminifera: Taxonomy, Ecologic Distribution, Biogeography, and Use in Paleoenvironmental Assessment, Institute of Geological & Nuclear Sciences Monograph, Vol. 26. Institute of Geological and Nuclear Sciences, Wellington, New Zealand. 363 pp.
43. Heyse, G., F. Jönsson, W.-J. Chang, and H. J. Lipps. 2010. RNAdependent control of gene amplification. Proc. Natl. Acad. Sci. USA 107: 22134-22139.
44. Hoef-Emden, K. 2012. Pitfalls of establishing DNA barcoding systems in protists: the Cryptophyceae as a test case. PloS One 7: e43652.
45. Holzmann, M., and J. Pawlowski. 2002. Freshwater foraminiferans from Lake Geneva: past and present. J. Foraminiferal Res. 32: 344-350.
46. Holzmann, M., W. Piller, and J. Pawlowski. 1996. Sequence variations in large-subunit ribosomal RNA gene of Ammonia (Foraminifera, Protozoa) and their evolutionary implications. J. Mol. Evol. 43: 145-151.
47. Holzmann, M., A. Habura, H. Giles, S. S. Bowser, and J. Pawlowski. 2003. Freshwater foraminiferans revealed by analysis of environmental DNA samples. J. Eukaryot. Microbiol. 50: 135-139.
48. Huber, J. A., H. G. Morrison, S. M. Huse, P. R. Neal, M. L. Sogin, and D. B. Mark Welch. 2009. Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. Environ. Microbiol. 11: 1292-1302.
49. Kim, E., J. W. Harrison, S. Sudek, M. D. Jones, H. M. Wilcox, T. A. Richards, A. Z. Worden, and J. M. Archibald. 2011. Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proc. Natl. Acad. Sci. USA 108: 1496-1500.
50. Kircher, M., S. Sawyer, and M. Meyer. 2012. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40: e3.
51. Koski, L. B., and G. B. Golding. 2001. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52: 540-542.
52. Kozich, J. J., S. L. Westcott, N. T. Baxter, S. K. Highlander, and P. D. Schloss. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl. Environ. Microbiol. 79: 5112-5120.
53. Kunin, V., A. Engelbrektson, H. Ochman, and P. Hugenholtz. 2010. Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ. Microbiol. 12: 118-123.
54. Langlet, D., E. Geslin, C. Baal, E. Metzger, F. Lejzerowicz, B. Riedel, M. Zuschin, J. Pawlowski, M. Stachowitsch, and F. J. Jorissen. 2013. Foraminiferal survival after long-term in situ experimentally induced anoxia. Biogeoscience 10: 7463-7480.
55. Lecroq, B., F. Lejzerowicz, R. Christen, P. Esling, L. Baerlocher, M. Osteras, L. Farinelli, and J. Pawlowski. 2011. Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments. Proc. Natl. Acad. Sci. USA 108: 13177-13182.
56. Lejzerowicz, F., J. Pawlowski, L. Fraissinet-Tachet, and R. Marmeisse. 2010. Molecular evidence for widespread occurrence of Foraminifera in soils. Environ. Microbiol. 12: 2518-2526.
57. Lejzerowicz, F., I. Voltsky, and J. Pawlowski. 2013a. Identifying active foraminifera in the Sea of Japan using metatranscriptomic approach. Deep-Sea Res. II 86-87: 214-220.
58. Lejzerowicz, F., M. Majewski, W. Szczuciński, J. Decelle, C. Obadia, P. Martinez Arbizu, and J. Pawlowski. 2013b. Ancient DNA complements microfossil record in deep-sea subsurface sediments. Biol. Lett. 9: 20130238.
59. Lejzerowicz, F., P. Esling, and J. Pawlowski. 2014. Patchiness of deep-sea benthic Foraminifera across the Southern Ocean: insights from high-throughput DNA sequencing. Deep-Sea Res. II, doi:/10. 1016/j. dsr2. 2014. 07. 018.
60. Leung, K., H. Zahn, T. Leaver, K. M. Konwar, N. W. Hanson, A. P. Pagé, C.-C. Lo, P. S. Chain, S. J. Hallam, and C. L. Hansen. 2012. A programmable droplet-based microfluidic device applied to multiparameter analysis of single microbes and microbial communities. Proc. Natl. Acad. Sci. USA 109: 7665-7670.
61. Loeblich, A. R., and H. Tappan. 1988. Foraminiferal Genera and Their Classification, 2 Vols. Van Nostrand Reinhold, New York.
62. Logares, R., S. Audic, S. Santini, M. C. Pernice, C. de Vargas, and R. Massana. 2012. Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing. ISME J. 6: 1823-1833.
63. Logares, R., S. Audic, D. Bass, L. Bittner, C. Boutte, R. Christen, J.-M. Claverie, J. Decelle, J. R. Dolan, M. Dunthorn et al. 2014. Patterns of rare and abundant marine microbial eukaryotes. Curr. Biol. 24: 1-9.
64. Mason, V. C., G. Li, K. M. Helgen, and W. J. Murphy. 2011. Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens. Genome Res. 21: 1695-1704.
65. Massana, R., J. del Campo, M. E. Sieracki, S. Audic, and R. Logares. 2014. Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles. ISME J. 8: 854-66.
66. Medinger, R., V. Nolte, R. V. Pandey, S. Jost, B. Ottenwälder, C. Schlötterer, and J. Boenigk. 2010. Diversity in a hidden world: potential and limitation of next-generation sequencing for surveys of molecular diversity of eukaryotic microorganisms. Mol Ecol. 19 Suppl. 1: 32-40.
67. Mikhalevich, V. I. 2013. New insight into the systematics and evolution of the foraminifera. Micropaleontology 59: 493-527.
68. Minoche, A. E., J. C. Dohm, and H. Himmelbauer. 2011. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol. 12: R112.
69. Moodley, L. 1990. "Squatter" behaviour of soft-shelled foraminifera. Mar. Micropaleontol. 16: 149-153.
70. Morard, R., F. Quillévéré, G. Escarguel, Y. Ujiie, T. de Garidel-Thoron, R. D. Norris, and C. de Vargas. 2009. Morphological recognition of cryptic species in the planktonic foraminifera Orbulina universa. Mar. Micropaleontol. 71: 148-165.
71. Murray, J. W. 2006. Ecology and Applications of Benthic Foraminifera. Cambridge University Press, Cambridge.
72. Murray, J. W. 2007. Biodiversity of living benthic foraminifera: how many species are there? Mar. Micropaleontol. 63: 163-176.
73. Naviaux, R. K., B. Good, J. D. McPherson, D. L. Steffen, D. Markusic, B. Ransom, and J. Corbeil. 2005. Sand DNA: a genetic library of life at the water's edge. Mar. Ecol. Progr. Ser. 301: 9-22.
74. Orsi, W., J. F. Biddle, and V. Edgcomb. 2013. Deep sequencing of subseafloor eukaryotic rRNA reveals active fungi across marine subsurface provinces. PloS One 8: e56335.
75. Parfrey, L. W., and L. A. Katz. 2010. Genome dynamics are influenced by food source in Allogromia laticollaris strain CSH (Foraminifera). Genome Biol. Evol. 2: 678-685.
76. Parfrey, L. W., D. J. G. Lahr, and L. A. Katz. 2008. The dynamic nature of eukaryotic genomes. Mol. Biol. Evol. 25: 787-794.
77. Pawłowska, J., F. Lejzerowicz, P. Esling, W. Szczuciński, M. Zajączkowski, and J. Pawlowski. 2014. Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium. Geobiology 12: 277-288.
78. Pawlowski, J. 2000. Introduction to the molecular systematics of foraminifera: Micropaleontology 46 Suppl. 1: 1-12.
79. Pawlowski, J., and M. Holzmann. 2014. A plea for DNA barcoding of Foraminifera. J. Foraminiferal Res. 44: 62-67.
80. Pawlowski, J., and B. Lecroq. 2010. Short rDNA barcodes for species identification in foraminifera. J. Eukaryot. Microbiol. 57: 197-205.
81. Pawlowski, J., I. Bolivar, J. F. Fahrni, C. de Vargas, M. Gouy, and L. Zaninetti. 1997. Extreme differences in rates of molecular evolution of foraminifera revealed by comparison of ribosomal DNA sequences and the fossil record, Mol. Biol. Evol. 14: 498-505.
82. Pawlowski, J., I. Bolivar, J. Fahrni, C. de Vargas, and S. S. Bowser. 1999. Molecular evidence that Reticulomyxa filosa is a freshwater naked foraminifer. J. Eukaryot. Microbiol. 46: 612-617.
83. Pawlowski, J., J. F. Fahrni, U. Brykczynska, A. Habura, and S. S. Bowser. 2002. Molecular data reveal high taxonomic diversity of allogromiid Foraminifera in Explorers Cove (McMurdo Sound, Antarctica). Polar Biol. 25: 96-105.
84. Pawlowski, J., M. Holzmann, C. Berney, J. Fahrni, A. J. Gooday, T. Cedhagen, A. Habura, and S. S. Bowser. 2003. The evolution of early Foraminifera, Proc. Natl. Acad. Sci. 100: 11494-11498.
85. Pawlowski J., J. Fahrni, B. Lecroq, D. Longet, N. Cornelius, L. Excoffier, T. Cedhagen, and A. J. Gooday. 2007. Bipolar gene flow in deep-sea benthic foraminifera. Mol. Ecol. 16: 4089-4096.
86. Pawlowski, J., W. Majewski, D. Longet, J. Guiard, T. Cedhagen, A. J. Gooday, S. Korsun, A. Habura, and S. S. Bowser. 2008. Genetic differentiation between Arctic and Antarctic monothalamous foraminifera. Polar Biol. 31: 1205-1216.
87. Pawlowski, J., D. Fontaine, A. Aranda da Silva, and J. Guiard. 2011a. Novel lineages of Southern Ocean deep-sea foraminifera revealed by environmental DNA sequencing. Deep-Sea Research II 58: 1996-2003.
88. Pawlowski, J., R. Christen, B. Lecroq, D. Bachar, H. R. Shahbazkia, L. Amaral-Zettler, and L. Guillou. 2011b. Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS One 6: e18169.
89. Pawlowski, J., S. Audic, S. Adl, D. Bass, L. Belbahri, C. Berney, S. S. Bowser, I. Cepicka, J. Decelle, M. Dunthorn et al. 2012. CBOL Protist Working Group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol. 10: e1001419.
90. Pawlowski, J., M. Holzmann, and J. Tyszka. 2013. New supraordinal classification of Foraminifera: molecules meet morphology. Mar. Micropaleontol. 100: 1-10.
91. Pawlowski, J., P. Esling, F. Lejzerowicz, T. Cedhagen, and T. A. Wilding. 2014. Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities. Mol. Ecol. Res. 14: 1129-1140.
92. Pernice, M. C., R. Logares, L. Guillou, and R. Massana. 2013. General patterns of diversity in major marine microeukaryote lineages. PLoS One 8: e57170.
93. Pillet, L., D. Fontaine, and J. Pawlowski. 2012. Intra-genomic rRNA polymorphism and morphological variation in Elphidium macellum suggest inter-specific hybridization in foraminifera. PLoS One 7: e32373.
94. Pillet, L., I. Voltski, and J. Pawlowski. 2013. Molecular phylogeny of Elphidiidae (Foraminifera). Mar. Micropaleontol. 103: 1-14.
95. Prokopowich, C. D., T. R. Gregory, and T. J. Crease. 2003. The correlation between rDNA copy number and genome size in eukaryotes. Genome 46: 48-50.
96. Schnitker, D. 1974. Ecotypic variation in Ammonia beccarii (Linné): J. Foraminiferal Res. 4: 217-223.
97. Sen Gupta, B. K. 1999. Systematics of modern Foraminifera. Pp. 7-36 in Modern Foraminifera, B. K. Sen Gupta, ed. Kluwer Academic Publishers, Dordrecht.
98. Shi, X. L., C. Lepère, D. J. Scanlan, and D. Vaulot. 2011. Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean. PLoS One 6: e18979.
99. Stern, R. F., A. Horak, R. L. Andrew, M.-A. Coffroth, R. A. Andersen, F. C. Küpper, I. Jameson, M. Hoppenrath, B. Véron, F. Kasai et al. 2010. Environmental barcoding reveals massive dinoflagellate diversity in marine environments. PLoS One 5: e13991.
100. Stevens, J. L., R. L. Jackson, and J. B. Olson. 2013. Slowing PCR ramp speed reduces chimera formation from environmental samples. J. Microbiol. Methods 93: 203-205.
101. Stoeck, T., A. Zuendorf, H. W. Breiner, and A. Behnke. 2007. A molecular approach to identify active microbes in environmental eukaryote clone libraries. Microb. Ecol. 53: 328-339.
102. Tsuchiya, M., H. Kitazato, and J. Pawlowski, 2003. Analysis of Internal Transcribed Spacer of ribosomal DNA reveals cryptic speciation in Planoglabratella opercularis: J. Foraminiferal Res. 33: 285-293.
103. van Velzen, R., E. Weitschek, G. Felici, and F. T. Bakker. 2012. DNA barcoding of recently diverged species: relative performance of matching methods. PLoS One 7: e30490.
104. Vlassov, V. V., P. P. Laktionov, and E. Y. Rykova. 2007. Extracellular nucleic acids. Bioessays 29: 654-667.
105. Weber, A. A.-T., and J. Pawlowski. 2013. Can abundance of protists be inferred from sequence data: a case study of Foraminifera. PLoS One 8: e56739.
106. Weber, A. A.-T., and J. Pawlowski. 2014. Wide occurrence of SSU rDNA intragenomic polymorphism in Foraminifera and its implications for molecular species identification. Protist 165: 645-661.
107. Zhan, A., M. Hulak, F. Sylvester, X. Huang, A. A. Adebayo, C. L. Abbott, S. L. Adamowicz, D. D. Heath, M. E. Cristescu, and H. J. MacIsaac. 2013. High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods Ecol. Evol. 4: 558-565.
108. Zhang, T., and H. H. P. Fang. 2006. Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Appl. Microbiol. Biotechnol. 70: 281-28.
109. 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: 79-92.