Censusing marine eukaryotic diversity in the twenty-first century

Philosophical Transactions of the Royal Society B: Biological Sciences

Volumn 371, Issue 1702, 2016, Pages

  Leray, Matthieu ^a   Knowlton, Nancy ^a  

^a DEPARTMENT OF PALEOBIOLOGY   (United States)

Author keywords

18S; Meiofauna; Metabarcoding; Plankton; Protist

Indexed keywords

EUKARYOTE; GENETIC ANALYSIS; KNOWLEDGE; MARINE ENVIRONMENT; MEIOFAUNA; MOLECULAR ANALYSIS; MORPHOLOGY; PLANKTON; PROTIST; TAXONOMY;

EUKARYOTA; PROKARYOTA; PROTISTA;

AQUATIC SPECIES; BIODIVERSITY; CLASSIFICATION; DNA BARCODING; ENVIRONMENTAL PROTECTION; EUKARYOTE; MARINE BIOLOGY; PROCEDURES; SEA;

AQUATIC ORGANISMS; BIODIVERSITY; CONSERVATION OF NATURAL RESOURCES; DNA BARCODING, TAXONOMIC; EUKARYOTA; MARINE BIOLOGY; OCEANS AND SEAS;

EID: 84982840798     PISSN: 09628436     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rstb.2015.0331     Document Type: Review

References (111)

1. McCauley DJ, Pinsky ML, Palumbi SR, Estes JA, Joyce FH, Warner RR. 2015 Marine defaunation: animal loss in the global ocean. Science 347, 1255641. (doi:10.1126/science.1255641)
2. Azam F, Fenchel T, Field JG, Gray JC, Meyer-Reil LA, Thingstad F. 1983 The ecological role of watercolumn microbes in the sea. Mar. Ecol. Prog. Ser. 10, 257-264. (doi:10.3354/meps010257)
3. Appeltans W et al. 2012 The magnitude of global marine species diversity. Curr. Biol. 22, 2189-2202. (doi:10.1016/j.cub.2012.09.036)
4. Costello MJ, Wilson S, Houlding B. 2012 Predicting total global species richness using rates of species description and estimates of taxonomic effort. Syst. Biol. 61, 871-883. (doi:10.1093/sysbio/syr080)
5. Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B. 2011 How many species are there on Earth and in the Ocean? PLoS Biol. 9, e1001127. (doi:10.1371/ journal.pbio.1001127)
6. Bouchet P, Lozouet P, Maestrati P, Heros V. 2002 Assessing the magnitude of species richness in tropical marine environments: exceptionally high numbers of molluscs at a New Caledonia site. Biol. J. Linn. Soc. 75, 421-436. (doi:10.1046/j. 1095-8312.2002.00052.x)
7. Mees J et al. 2015 World Register of Marine Species. See http://www.marinespecies.org (accessed 17 October 2015).
8. Jefferson TA, Rosenbaum HC. 2014 Taxonomic revision of the humpback dolphins (Sousa spp.), and description of a new species from Australia. Mar. Mammal Sci. 30, 1494-1541. (doi:10.1111/mms.12152)
9. Ley PDe. 2000 Lost in worm space: phylogeny and morphology as road maps to nematode diversity. Nematology 2, 9-16. (doi:10.1163/ 156854100508854)
10. Wägele H, Klussmann-Kolb A, Kuhlmann M, Haszprunar G, Lindberg D, Koch A, Wägele JW. 2011 The taxonomist—an endangered race. A practical proposal for its survival. Front. Zool. 8, 25. (doi:10. 1186/1742-9994-8-25)
11. Hughes TP, Bellwood DR, Connolly SR. 2002 Biodiversity hotspots, centres of endemicity, and the conservation of coral reefs. Ecol. Lett. 5, 775-784. (doi:10.1046/j.1461-0248.2002.00383.x)
12. Fisher R, Radford BT, Knowlton N, Brainard RE, Michaelis FB, Caley MJ. 2011 Global mismatch between research effort and conservation needs of tropical coral reefs. Conserv. Lett. 4, 64-72. (doi:10. 1111/j.1755-263X.2010.00146.x)
13. Hebert PDN, Cywinska A, Ball SL, DeWaard JR. 2003 Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B 270, 313-321. (doi:10.1098/ rspb.2002.2218)
14. CBOL Plant Working Group. 2009 A DNA barcode for land plants. Proc. Natl Acad. Sci. USA 106, 12 794-12 797. (doi:10.1073/pnas.0905845106)
15. Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W. 2012 Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc. Natl Acad. Sci. USA 109, 6241-6246. (doi:10.1073/pnas.1117018109)
16. Pawlowski J et al. 2012 CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol. 10, e1001419. (doi:10.1371/journal.pbio.1001419)
17. Ratnasingham S, Hebert PDN. 2007 BOLD: The Barcode of Life Data System (www.barcodinglife.org). Mol. Ecol. Notes 7, 355-364. (doi:10.1111/j.1471-8286.2007.01678.x)
18. Guillou L et al. 2013 The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41, D597-D604. (doi:10.1093/nar/gks1160)
19. Albano PG, Sabelli B, Bouchet P. 2011 The challenge of small and rare species in marine biodiversity surveys: microgastropod diversity in a complex tropical coastal environment. Biodivers. Conserv. 20, 3223-3237. (doi:10.1007/s10531-011-0117-x)
20. Hajibabaei M. 2012 The golden age of DNA metasystematics. Trends Genet. 28, 535-537. (doi:10.1016/j.tig.2012.08.001)
21. Jonasson J, Olofsson M, Monstein H-J. 2002 Classification, identification and subtyping of bacteria based on pyrosequencing and signature matching of 16S rDNA fragments. APMIS 110, 263-272. (doi:10.1034/j.1600-0463.2002. 100309.x)
22. Sogin ML, Morrison HG, Huber JA, Mark Welch D, Huse SM, Neal PR, Arrieta JM, Herndl GJ. 2006 Microbial diversity in the deep sea and the underexplored ‘rare biosphere’. Proc. Natl Acad. Sci. USA 103, 12 115-12 120. (doi:10.1073/pnas. 0605127103)
23. Hajibabaei M, Shokralla S, Zhou X, Singer GAC, Baird DJ. 2011 Environmental barcoding: a nextgeneration sequencing approach for biomonitoring applications using river benthos. PLoS ONE 6, e17497. (doi:10.1371/journal.pone.0017497)
24. Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E. 2012 Towards next-generation biodiversity assessment using DNA metabarcoding. Mol. Ecol. 21, 2045-2050. (doi:10.1111/j.1365-294X.2012.05470.x)
25. Fonseca VG et al. 2010 Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nat. Commun. 1, 98. (doi:10. 1038/ncomms1095)
26. Fonseca VG et al. 2014 Metagenetic analysis of patterns of distribution and diversity of marine meiobenthic eukaryotes. Glob. Ecol. Biogeogr. 23, 1293-1302. (doi:10.1111/geb.12223)
27. Brannock P, Waits D, Sharma J, Halanych K. 2014 High-throughput sequencing characterizes intertidal meiofaunal communities in northern Gulf of Mexico (Dauphin Island and Mobile Bay, Alabama). Biol. Bull. 227, 161-174.
28. Pawlowski J, Christen R, Lecroq B, Bachar D, Shahbazkia HR, Amaral-Zettler L, Guillou L. 2011 Eukaryotic richness in the abyss: insights from pyrotag sequencing. PLoS ONE 6, e18169. (doi:10. 1371/journal.pone.0018169)
29. Guardiola M, Uriz MJ, Taberlet P, Coissac E, Wangensteen S, Turon X. 2015 Deep-sea, deepsequencing: metabarcoding extracellular DNA from sediments of marine canyons. PLoS ONE 10, e0139633. (doi:10.1371/journal.pone.0139633)
30. Bik HM, Sung W, De Ley P, Baldwin JG, Sharma J, Rocha-Olivares A, Thomas WK. 2012 Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments. Mol. Ecol. 21, 1048-1059. (doi:10.1111/j.1365-294X.2011.05297.x)
31. Chariton AA, Stephenson S, Morgan MJ, Steven ADL, Colloff MJ, Court LN, Hardy CM. 2015 Metabarcoding of benthic eukaryote communities predicts the ecological condition of estuaries. Environ. Pollut. 203, 165-174. (doi:10.1016/j. envpol.2015.03.047)
32. Chariton AA, Court LN, Hartley DM, Colloff MJ, Hardy CM. 2010 Ecological assessment of estuarine sediments by pyrosequencing eukaryotic ribosomal DNA. Front. Ecol. Environ. 8, 233-238. (doi:10. 1890/090115)
33. Lallias D et al. 2015 Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems. ISME J. 9, 1208-1221. (doi:10.1038/ismej.2014.213)
34. Cowart DA, Pinheiro M, Mouchel O, Maguer M, Grall J, Mine´ J, Arnaud-Haond S. 2015 Metabarcoding is powerful yet still blind: a comparative analysis of morphological and molecular surveys of seagrass communities. PLoS ONE 10, e0117562. (doi:10. 1371/journal.pone.0117562)
35. Leray M, Knowlton N. 2015 DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proc. Natl Acad. Sci. USA 112, 2076-2081. (doi:10.1073/pnas. 1424997112)
36. Pearman JK, El-Sherbiny MM, Lanzen A, Al-Aidaroos AM, Irigoien X. 2014 Zooplankton diversity across three Red Sea reefs using pyrosequencing. Front. Mar. Sci. 1, 1-11. (doi:10.3389/fmars.2014.00027)
37. Pearman JK, Irigoien X. 2015 Assessment of zooplankton community composition along a depth profile in the central Red Sea. PLoS ONE 10, e0133487. (doi:10.1371/journal.pone.0133487)
38. Hirai J, Yasuike M, Fujiwara A, Nakamura Y, Hamaoka S, Katakura S, Takano Y, Nagai S. 2015 Effects of plankton net characteristics on metagenetic community analysis of metazoan zooplankton in a coastal marine ecosystem. J. Exp. Mar. Biol. Ecol. 469, 36-43. (doi:10.1016/j.jembe. 2015.04.011)
39. Hirai J, Tsuda A. 2015 Metagenetic community analysis of epipelagic planktonic copepods in the tropical and subtropical Pacific. Mar. Ecol. Prog. Ser. 534, 65-78. (doi:10.3354/meps11404)
40. Hirai J, Kuriyama M, Ichikawa T, Hidaka K, Tsuda A. 2015 A metagenetic approach for revealing community structure of marine planktonic copepods. Mol. Ecol. Resour. 15, 68-80. (doi:10. 1111/1755-0998.12294)
41. de Vargas C et al. 2015 Eukaryotic plankton diversity in the sunlit ocean. Science 348, 1261605. (doi:10. 1126/science.1261605)
42. Lindeque PK, Parry HE, Harmer RA, Somerfield PJ, Atkinson A. 2013 Next generation sequencing reveals the hidden diversity of zooplankton assemblages. PLoS ONE 8, e81327. (doi:10.1371/ journal.pone.0081327)
43. Logares R et al. 2014 Patterns of rare and abundant marine microbial eukaryotes. Curr. Biol. 24, 813-821. (doi:10.1016/j.cub.2014.02.050)
44. Massana R, Pernice M, Bunge JA, del Campo J. 2011 Sequence diversity and novelty of natural assemblages of picoeukaryotes from the Indian Ocean. ISME J. 5, 184-195. (doi:10.1038/ismej. 2010.104)
45. Cheung MK, Au CH, Chu KH, Kwan HS, Wong CK. 2010 Composition and genetic diversity of picoeukaryotes in subtropical coastal waters as revealed by 454 pyrosequencing. ISME J. 4, 1053-1059. (doi:10.1038/ismej.2010.26)
46. Not F, del Campo J, Balague´ V, de Vargas C, Massana R. 2009 New insights into the diversity of marine picoeukaryotes. PLoS ONE 4, e7143. (doi:10. 1371/journal.pone.0007143)
47. Kramer MJ, Bellwood O, Bellwood DR. 2013 The trophic importance of algal turfs for coral reef fishes: the crustacean link. Coral Reefs 32, 575-583. (doi:10.1007/s00338-013-1009-1)
48. Bik HM, Halanych KM, Sharma J, Thomas WK. 2012 Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill. PLoS ONE 7, e38550. (doi:10.1371/journal. pone.0038550)
49. Leray M, Meyer CP, Mills SC. 2015 Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet. PeerJ 3, e1047. (doi:10.7717/peerj.1047)
50. Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N, Ranwez V, Boehm JT, Machida RJ. 2013 A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front. Zool. 10, 34. (doi:10.1186/1742-9994-10-34)
51. Deagle BE, Chiaradia A, McInnes J, Jarman SN. 2010 Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out? Conserv. Genet. 11, 2039-2048. (doi:10.1007/ s10592-010-0096-6)
52. Zaiko A, Martinez JL, Schmidt-Petersen J, Ribicic D, Samuiloviene A, Garcia-Vazquez E. 2015 Metabarcoding approach for the ballast water surveillance-an advantageous solution or an awkward challenge? Mar. Pollut. Bull. 92, 25-34. (doi:10.1016/j.marpolbul.2015.01.008)
53. Warwick RM, Clarke KR. 1996 Relationships between body-size, species abundance and diversity in marine benthic assemblages: facts or artefacts? J. Exp. Mar. Biol. Ecol. 202, 63-71. (doi:10.1016/ 0022-0981(96)00031-7)
54. Fenchel T. 1993 There are more small than large species? Oikos 68, 375-378. (doi:10.2307/3544855)
55. May RM. 1988 How many species are there on Earth? Science 241, 1441-1449. (doi:10.1126/ science.241.4872.1441)
56. Caron DA, Countway PD, Jones AC, Kim DY, Schnetzer A. 2012 Marine protistan diversity. Annu. Rev. Mar. Sci. 4, 467-493. (doi:10.1146/annurevmarine-120709-142802)
57. Santoferrara LF, Grattepanche J-D, Katz LA, Mcmanus GB. 2014 Pyrosequencing for assessing diversity of eukaryotic microbes: analysis of data on marine planktonic ciliates and comparison with traditional methods. Environ. Microbiol. 16, 2752-2763. (doi:10.1111/1462-2920.12380)
58. Georges C, Monchy S, Genitsaris S, Christaki U. 2014 Protist community composition during early phytoplankton blooms in the naturally ironfertilized Kerguelen area (Southern Ocean). Biogeosci. Discuss. 11, 11 179-11 215. (doi:10. 5194/bg-11-5847-2014)
59. Brown MV, Philip GK, Bunge JA, Smith MC, Bissett A, Lauro FM, Fuhrman JA, Donachie SP. 2009 Microbial community structure in the North Pacific ocean. ISME J. 3, 1374-1386. (doi:10.5194/bg-11-5847-2014)
60. Yu L, Zhang W, Liu L, Yang J. 2015 Determining microeukaryotic plankton community around Xiamen Island, Southeast China, using Illumina MiSeq and PCR-DGGE techniques. PLoS ONE 10, e0127721. (doi:10.1371/journal.pone.0127721)
61. Logares R, Audic S, Santini S, Pernice MC, de Vargas C, Massana R. 2012 Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing. ISME J. 6, 1823-1833. (doi:10.1038/ismej.2012.36)
62. Bittner L et al. 2013 Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay. Mol. Ecol. 22, 87-101. (doi:10.1111/ mec.12108)
63. Lecroq B, Lejzerowicz F, Bachar D, Christen R, Esling P, Baerlocher L, Østerås M, Farinelli L, Pawlowski J. 2011 Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments. Proc. Natl Acad. Sci. USA 108, 13 177-13 182. (doi:10.1073/pnas.1018426108)
64. Bass D, Cavalier-Smith T. 2004 Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). Int. J. Syst. Evol. Microbiol. 54, 2393-2404. (doi:10. 1099/ijs.0.63229-0)
65. Bernhard JM, Edgcomb VP, Visscher PT, McIntyre-Wressnig A, Summons RE, Bouxsein ML, Louis L, Jeglinski M. 2013 Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas. Proc. Natl Acad. Sci. USA 110, 9830-9834. (doi:10.1073/pnas. 1221721110)
66. del Campo J, Ruiz-Trillo I. 2013 Environmental survey meta-analysis reveals hidden diversity among unicellular opisthokonts. Mol. Biol. Evol. 30, 802-805. (doi:10.1093/molbev/mst006)
67. Not F, Valentin K, Romari K, Lovejoy C, Massana R, Töbe K, Vaulot D, Medlin LK. 2007 Picobiliphytes: a marine picoplanktonic algal group with unknown affinities to other eukaryotes. Science 315, 253-255. (doi:10.1126/science.1136264)
68. Kim E, Harrison JW, Sudek S, Jones MDM, Wilcox HM, Richards TA, Worden AZ, Archibald JM. 2011 Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life. Proc. Natl Acad. Sci. USA 108, 1496-1500. (doi:10.1073/pnas. 1013337108)
69. Pawlowski J. 2013 The new micro-kingdoms of eukaryotes. BMC Biol. 11, 40-41. (doi:10.1186/ 1741-7007-11-40)
70. Platt HM, Warwick RM. 1980 The significance of freeliving nematodes to the littoral ecosystem. In The Shore Environment-2 Ecosystems (eds JH Price, DEG Irvine), pp. 729-759. London, UK: Academic Press.
71. Lambshead PJD, Boucher G. 2003 Marine nematode deep-sea biodiversity-hyperdiverse or hype? J. Biogeogr. 30, 475-485. (doi:10.1046/j.1365-2699.2003.00843.x)
72. Blaxter M, Mann J, Chapman T, Thomas F, Whitton C, Floyd R, Abebe E. 2005 Defining operational taxonomic units using DNA barcode data. Phil. Trans. R. Soc. B 360, 1935-1943. (doi:10.1098/rstb. 2005.1725)
73. Floyd R, Abebe E, Papert A, Blaxter M. 2002 Molecular barcodes for soil nematode identification. Mol. Ecol. 11, 839-850. (doi:10.1046/j.1365-294X. 2002.01485.x)
74. Creer S et al. 2011 Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises. Mol. Ecol. 19, 4-20. (doi:10.1111/j.1365-294X.2009.04473.x)
75. Radziejewska T, Stańkowska-Radziun M. 1979 Intertidal meiofauna of Recherchefjorden and Mablukta, West. Spitsbergen. Sarsia 64, 253-258. (doi:10.1080/00364827.1979.10411385)
76. Martens PM, Schockaert ER. 1986 The importance of turbellarians in the marine meiobenthos: a review. Hydrobiologia 132, 295-303. (doi:10.1007/ BF00046263)
77. Beaugrand G, Brander KM, Alistair Lindley J, Souissi S, Reid PC. 2003 Plankton effect on cod recruitment in the North Sea. Nature 426, 661-664. (doi:10. 1038/nature02164)
78. Alve E. 1995 Benthic foraminiferal responses to estuarine pollution; a review. J. Foraminifer. Res. 25, 190-203. (doi:10.2113/gsjfr.25.3.190)
79. Pawlowski J, Esling P, Lejzerowicz F, Cedhagen T, Wilding TA. 2014 Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities. Mol. Ecol. Resour. 14, 1129-1140. (doi:10.1111/1755-0998.12261)
80. Pochon X, Wood SA, Keeley NB, Lejzerowicz F, Esling P, Drew J, Pawlowski J. 2015 Accurate assessment of the impact of salmon farming on benthic sediment enrichment using foraminiferal metabarcoding. Mar. Pollut. Bull. 100, 370-382. (doi:10.1016/j. marpolbul.2015.08.022)
81. Lejzerowicz F, Esling P, Pillet L, Wilding TA, Black KD, Pawlowski J. 2015 High-throughput sequencing and morphology perform equally well for benthic monitoring of marine ecosystems. Sci. Rep. 5, 13932. (doi:10.1038/srep13932)
82. Aylagas E, Borja A, Rodríguez-Ezpeleta N. 2014 Environmental status assessment using DNA metabarcoding: towards a genetics based Marine Biotic Index (gAMBI). PLoS ONE 9, e90529. (doi:10. 1371/journal.pone.0090529)
83. Pochon X, Bott NJ, Smith KF, Wood SA. 2013 Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests. PLoS ONE 8, e73935. (doi:10.1371/journal.pone.0073935)
84. Fenchel T, Finlay BJ. 2004 The ubiquity of small species: patterns of local and global diversity. Bioscience 54, 777-784. (doi:10.1641/0006-3568(2004)054[0777:TUOSSP]2.0.CO;2)
85. Finlay BJ. 2002 Global dispersal of free-living microbial eukaryote species. Science 296, 1061-1063. (doi:10.1126/science.1070710)
86. Kopf A et al. 2015 The ocean sampling day consortium. Gigascience 4, 27. (doi:10.1186/s13742-015-0066-5)
87. Bik HM, Porazinska DL, Creer S, Caporaso JG, Knight R, Thomas WK. 2012 Sequencing our way towards understanding global eukaryotic biodiversity. Trends Ecol. Evol. 27, 233-243. (doi:10.1016/j.tree.2011. 11.010)
88. Huse SM, Welch DM, Morrison HG, Sogin ML. 2010 Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ. Microbiol. 12, 1889-1898. (doi:10.1111/j.1462-2920.2010. 02193.x)
89. Sun Y, Cai Y, Huse SM, Knight R, Farmerie WG, Wang X, Mai V. 2012 A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Brief. Bioinform. 13, 107-121. (doi:10.1093/bib/bbr009)
90. Brannock PM, Halanych KM. 2015 Meiofaunal community analysis by high-throughput sequencing: comparison of extraction, quality filtering, and clustering methods. Mar. Genomics 23, 67-75. (doi:10.1016/j.margen.2015.05.007)
91. Oliver AK, Brown SP, Callaham MA, Jumpponen A. 2015 Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15%. Fungal Ecol. 15, 86-89. (doi:10.1016/j.funeco.2015.03.003)
92. Elbrecht V, Leese F. 2015 Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass—sequence relationships with an innovative metabarcoding protocol. PLoS ONE 10, e0130324. (doi:10.1371/journal.pone. 0130324)
93. Zhan A, He S, Brown EA, Chain FJJ, Therriault TW, Abbott CL, Heath DD, Cristescu ME, MacIsaac HJ. 2014 Reproducibility of pyrosequencing data for biodiversity assessment in complex communities. Methods Ecol. Evol. 5, 881-890. (doi:10.1111/2041-210X.12230)
94. Rossberg AG, Rogers T, McKane AJ. 2014 Current noise-removal methods can create false signals in ecogenomic data. Proc. R. Soc. B 281, 20140191. (doi:10.1098/rspb.2014.0191)
95. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011 UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194-2200. (doi:10.1093/bioinformatics/btr381)
96. Porazinska DL, Giblin-Davis RM, Sung W, Thomas WK. 2012 The nature and frequency of chimeras in eukaryotic metagenetic samples. J. Nematol. 44, 18-25.
97. Fonseca VG, Nichols B, Lallias D, Quince C, Carvalho GR, Power DM, Creer S. 2012 Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses. Nucleic Acids Res. 40, e66. (doi:10.1093/ nar/gks002)
98. Flynn JM, Brown EA, Chain FJJ, MacIsaac HJ, Cristescu ME. 2015 Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods. Ecol. Evol. 5, 2252-2266. (doi:10.1002/ece3.1497)
99. Brown EA, Chain FJJ, Crease TJ, MacIsaac HJ, Cristescu ME. 2015 Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities? Ecol. Evol. 5, 2234-2251. (doi:10.1002/ece3.1485)
100. Decelle J, Romac S, Sasaki E, Not F, Mahe´ F. 2014 Intracellular diversity of the V4 and V9 regions of the 18S rRNA in marine protists (radiolarians) assessed by high-throughput sequencing. PLoS ONE 9, e104297. (doi:10.1371/journal.pone.0104297)
101. Tang CQ, Leasi F, Obertegger U, Kieneke A, Barraclough TG, Fontaneto D. 2012 The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. Proc. Natl Acad. Sci. USA 109, 16 208-16 212. (doi:10.1073/pnas.1209160109)
102. Wu S, Xiong J, Yu Y. 2015 Taxonomic resolutions based on 18S rRNA genes: a case study of subclass copepoda. PLoS ONE 10, e0131498. (doi:10.1371/ journal.pone.0131498)
103. Mohrbeck I, Raupach MJ, Martínez Arbizu P, Knebelsberger T, Laakmann S. 2015 Highthroughput sequencing-the key to rapid biodiversity assessment of marine metazoa? PLoS ONE 10, e0140342. (doi:10.1371/journal.pone.0140342)
104. Hoef-Emden K, Küpper FC, Andersen RA. 2007 Meeting report: Sloan Foundation Workshop to resolve problems relating to the taxonomy of microorganisms and to culture collections arising from the barcoding initiatives; Portland ME, November 6-7, 2006. Protist 158, 135-137. (doi:10.1016/j.protis.2007.02.001)
105. Piganeau G, Eyre-Walker A, Jancek S, Grimsley N, Moreau H. 2011 How and why DNA barcodes underestimate the diversity of microbial eukaryotes. PLoS ONE 6, e16342. (doi:10.1371/journal.pone. 0016342)
106. Mahe´ F, Rognes T, Quince C, de Vargas C, Dunthorn M. 2014 Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2, e593. (doi:10. 7717/peerj.593)
107. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO. 2013 The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590-D596. (doi:10.1093/nar/ gks1219)
108. Srivathsan A, Sha JCM, Vogler AP, Meier R. 2015 Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf-feeding monkey (Pygathrix nemaeus). Mol. Ecol. Resour. 15, 250-261. (doi:10.1111/1755-0998.12302)
109. Hadziavdic K, Lekang K, Lanzen A, Jonassen I, Thompson EM, Troedsson C. 2014 Characterization of the 18S rRNA gene for designing universal eukaryote specific primers. PLoS ONE 9, e87624. (doi:10.1371/journal.pone.0087624)
110. Machida RJ, Kweskin M, Knowlton N. 2012 PCR primers for metazoan mitochondrial 12S ribosomal DNA sequences. PLoS ONE 7, e35887. (doi:10.1371/ journal.pone.0035887)
111. Duffy JE, Amaral-Zettler LA, Fautin DG, Paulay G, Rynearson TA, Sosik HM, Stachowicz JJ. 2013 Envisioning a marine biodiversity observation network. Bioscience 63, 350-361. (doi:10.1525/bio. 2013.63.5.8)