New accomplishments and approaches for assessing protistan diversity and ecology in natural ecosystems

BioScience

Volumn 59, Issue 4, 2009, Pages 287-299

  Caron, David A ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Biogeography; Diversity; Microbial ecology; Molecular ecology; Protists

Indexed keywords

ALGAE; ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; PROTISTA; PROTOZOA;

EID: 67649791192     PISSN: 00063568     EISSN: None     Source Type: Journal    
DOI: 10.1525/bio.2009.59.4.7     Document Type: Article

References (80)

1. Adl SM, et al. 2005. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology 52:399-451.
2. Alexander M. 1961. Introduction to Soil Microbiology. New York: Wiley.
3. Baas Becking LGM. 1934. Geobiologie of inleiding tot de milieukunde. The Hague: W. P. Van Stockkum and Zoon.
4. Bass D, Cavalier-Smith T. 2004. Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa). International Journal of Systematic and Evolutionary Microbiology 54: 2393-2404.
5. Bé AWH. 1977. An ecological, zoogeographic and taxonomic review of recent planktonic forminifera. Pages 1-100 in Ramsay ATS, ed. Oceanic Micropaleontology. New York: Academic Press.
6. Bent SJ, Peirson JD, Forney LJ. 2007. Measuring species richness based on microbial community fingerprints: The emperor has no clothes. Applied and Environmental Microbiology 73: 2399.
7. Berney C, Fahrni J, Pawlowski J. 2004. How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys. BMC Biology 4: 2-13.
8. Blaxter ML. 2004. The promise of a DNA taxonomy. Philosophical Transactions of the Royal Society of London B 359:669-679.
9. Boenigk J, Pfandl K, Garstecki T, Harms H, Novarino G, Chatzinotas A. 2006. Evidence for geographic isolation and signs of endemism within a protistan morphospecies. Applied and Environmental Microbiology 72:5159-5164.
10. Bonowski M. 2004. Protozoa and plant growth: The microbial loop in soil revisited. New Phytologist 162: 617-631.
11. Campbell NA, Reece JB. 2007. Biology. New York: Benjamin Cummings.
12. Caron DA, Schnetzer A. 2007. Protistan community structure. Pages 454-468 in Hurst CJ, Crawford RL, Garland JL, Lipson DA, Mills AL, Stetzenbach LD, eds. Manual of Environmental Microbiology. Washington (DC): ASM Press.
13. Caron DA, Dam HG, Kremer P, Lessard EJ, Madin LP, Malone TC, Napp JM, Peele ER, Roman MR, Youngbluth MJ. 1995. The contribution of micro-organisms to particulate carbon and nitrogen in surface waters of the Sargasso Sea near Bermuda. Deep-Sea Research I 42: 943-972.
14. Caron DA, Countway PD, Brown MV. 2004. The growing contributions of molecular biology and immunology to protistan ecology: Molecular signatures as ecological tools. Journal of Eukaryotic Microbiology 51: 38-48.
15. Chantangsi C, Lynn DH, Brandl MT, Cole JC, Hetrick N, Ikonomi P. 2007. Barcoding ciliates: A comprehensive study of 75 isolates of the genus Tetrahymena. International Journal of Systematic and Evolutionary Microbiology 57:2412-2423.
16. Chao A, Lee SM. 1992. Estimating the number of classes via sample coverage. Journal of the American Statistical Association 87: 210-217.
17. Countway PD, Caron DA. 2006. Abundance and distribution of Ostreo-coccus sp. in the San Pedro Channel, California (USA) revealed by qPCR. Applied and Environmental Microbiology 72: 2496-2506.
18. Countway PD, Gast RJ, Savai P, Caron DA. 2005. Protistan diversity estimates based on 18S rDNA from seawater incubations in the western North Atlantic. Journal of Eukaryotic Microbiology 52: 95-106.
19. Countway PD, Gast RJ, Dennett MR, Savai P, Rose JM, Caron DA. 2007. Distinct protistan assemblages characterize the euphoric zone and deep sea (2500 m) of the western N. Atlantic (Sargasso Sea and Gulf Stream). Environmental Microbiology 9:1219-1232.
20. Danovaro R, Luna GM, Dell-Anno A, Pietrangeli B. 2007. Measuring species richness based on microbial community fingerprints: The emperor has no clothes: Authors' reply. Applied and Environmental Microbiology 73: 2399-2401.
21. Dawson SC, Pace NR. 2002. Novel kingdom-level eukaryotic diversity in anoxic environments. Proceedings of the National Academy of Sciences 99: 8324-8329.
22. de Wit R, Bouvier T. 2006. 'Everything is everywhere, but, the environment selects'; what did Baas Becking and Beijerinck really say? Environmental Microbiology 8: 755-758.
23. Dolven JK, Lindqvist C, Albert VA, Bjorklund KR, Yuasa T, Takahashi O, Mayama S. 2007. Molecular diversity of alveolates associated with neritic North Atlantic radiolarians. Protist 158: 65-76.
24. Ebach MC, Holdrege C. 2005. More taxonomy, not DNA barcoding. BioScience 55: 822-823.
25. Epstein S, López-García P. 2007. "Missing" protists: A molecular perspective. Biodiversity and Conservation 17: 261-276.
26. Evans KM, Wortley AH, Mann DG. 2007. An assessment of potential diatom "barcode" genes (cox 1, rbc L, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). Protist 158: 349-364.
27. Fawley MJ, Fawley KP, Buchheim MA. 2004. Molecular diversity among communities of freshwater microchlorophytes. Microbial Ecology 48: 489-499.
28. Fenchel T. 2005. Cosmopolitan microbes and their 'cryptic' species. Aquatic Microbial Ecology 41: 49-54.
29. Finlay BJ, Clarke KJ. 1999. Ubiquitous dispersal of microbial species. Nature 400: 828.
30. Finlay BJ, Fenchel T. 1999. Divergent perspectives on protist species richness. Protist 150: 229-233.
31. Foissner W. 2006. Biogeography and dispersal of micro-organisms: A review emphasizing protists. Acta Protozoologica 45: 111-136.
32. Gast RJ, Dennett MR, Caron DA. 2004. Characterization of protistan assemblages in the Ross Sea, Antarctica by denaturing gradient gel electrophoresis. Applied and Environmental Microbiology 70: 2028-2037.
33. Griffiths BS, Kuan HL, Ritz K, Glover LA, McCaig AE, Fenwick C. 2004. The relationship between microbial community structure and functional stability, tested experimentally in an upland pasture soil. Microbial Ecology 47:104-113.
34. Groisillier A, Massana R, Valentin K, Vaulot D, Guillou L. 2006. Genetic diversity and habitats of two enigmatic marine alveolate lineages. Aquatic Microbial Ecology 42: 277-291.
35. Guillou L, Chrétiennot-Dinet M-J, Medlin LK, Claustre H, Loiseaux-de Goer S, Vaulot D. 1999. Bolidomonas: A new genus with two species belonging to a new algal class, the Bolidophyceae (Heterokonta). Journal of Phycology 35: 368-381.
36. Harper JT, Waanders E, Keeling PJ. 2005. On the monophyly of chrom-alveolates using a six-protein phylogeny of eukaryotes. International Journal of Systematic and Evolutionary Microbiology 55: 487-496.
37. Hoef-Emden K. 2007. Revision of the genus Cryptomonas (Cryptophyceae) II: Incongruences between the classical morphospecies concept and molecular phylogeny in smaller pyrenoid-less cells. Phycologia 46: 402-428.
38. Hughes JB, Hellmann JJ. 2005. The application of rarefaction techniques to molecular inventories of microbial diversity. Methods in Enzymology 397: 292-308.
39. Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJM. 2001. Counting the uncountable: Statistical approaches to estimating microbial diversity. Applied and Environmental Microbiology 67: 4399-4406.
40. Karl DM. 2007. Microbial oceanography: Paradigms, processes and promise. Nature Reviews Microbiology 5: 759-769.
41. Kawachi M, Atsumi M, Ikemoto H, Miyachi S. 2002. Pinguiochrysis pyriformis gen. et sp. nov. (Pinguiophyceae), a new picoplanktonic alga isolated from the Pacific Ocean. Phycological Research 50: 49-56.
42. Kent AD, Smith DJ, Benson BJ, Triplett EW. 2003. Web-based phylogenetic assignment tool for the analysis of terminal restriction fragment length polymorphism profiles of microbial communities. Applied and Environmental Microbiology 69: 6768-6776.
43. La Claire JW II. 2006. Analysis of expressed sequence tags from the harmful alga, Prymnesium parvum (Prymnesiophyceae, Haptophyceae). Marine Biotechnology 8: 534-546.
44. Lidie KB, Ryan JC, Barbier M, Van Dolah FM. 2005. Gene expression in Florida red tide dinoflagellate Karenia brevis: Analysis of an expressed sequence tag library and development of a DNA microarray. Marine Biotechnology 7:481-493.
45. López-García P, López-López A, Moreira D, Rodríguez-Valera F. 2001a. Diversity of free-living prokaryotes from a deep-sea site at the Antarctic Polar Front. FEMS Microbiology Ecology 36:193-202.
46. López-García P, Rodríguez-Valera F, Pedrós-Alió C, Moreira D. 2001b. Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409:603-607.
47. Lovejoy C, Massana R, Pedrós-Alío C. 2006. Diversity and distribution of marine microbial eukaryotes in the Arctic Ocean and adjacent seas. Applied and Environmental Microbiology 72:3085-3095.
48. Lovejoy C, Vincent WF, Bonilla S, Roy S, Martineau M-J, Terrado R, Potvin M, Massana R, Pedrós-Alió C. 2007. Distribution, phylogeny and growth of cold-adapted picoprasinophytes in Arctic Seas. Journal of Phycology 43: 78-89.
49. Ludwig W, et al. 2004. ARB: A software environment for sequence data. Nucleic Acids Research 32: 1363-1371.
50. Malone TC. 1971. The relative importance of nannoplankton and net-plankton as primary producers in tropical oceanic and neritic phyto-plankton communities. Limnology and Oceanography 16: 633-639.
51. Massana R, Castresana J, Balagué V, Guillou L, Romari K, Groisillier A, Valentin K, Pedrós-Alió C. 2004a. Phylogenetic and ecological analysis of novel marine stramenopiles. Applied and Environmental Microbiology 70: 3528-3534.
52. Massana R, Balague V, Guillou L, Pedros-Alio C. 2004b. Picoeukaryotic diversity in an oligotrophic coastal site studied by molecular and culturing approaches. FEMS Microbiology Ecology 50:231-243.
53. Massana R, Guillou L, Terrado R, Forn I, Pedrós-Alió C. 2006. Growth of uncultured heterotrophic flagellates in unamended seawater incubations. Aquatic Microbial Ecology 45: 171-180.
54. Modeo L, Petroni G, Rosati G, Montagnes DJS. 2003. A multidisciplinary approach to describe protists: Redescriptions of Novistrombidium testaceum and Strombidium inclinatum Montagnes, Taylor and Lynn 1990 (Ciliophora, Oligotrichia). Journal of Eukaryotic Microbiology 50: 175-189.
55. Moreira D, López-García P. 2003. Are hydrothermal vents oases for parasitic protists? Trends in Parasitology 19:556-558.
56. Naeem S, Shibin L. 1997. Biodiversity enhances ecosystem stability. Nature 390: 507-509.
57. O'Brien HE, Parrent JL, Jackson JA, Moncalvo J-M, Vilgalys R. 2005. Fungal community analysis by large-scale sequencing of environmental samples. Applied and Environmental Microbiology 71: 5544-5550.
58. Olson RJ, Chisholm SW, Zettler ER, Altabet MA, Dusenberry JA. 1990. Spatial and temporal distributions of prochlorophyte picoplankton in the North Atlantic Ocean. Deep-Sea Research 37: 1033-1051.
59. Pedrós-Alió C. 2006. Microbial diversity: Can it be determined? Trends in Microbiology 14: 257-263.
60. Pomeroy LR. 1974. The ocean's food web, a changing paradigm. BioScience 24: 499-504.
61. Popels LC, Cary SC, Hutchines DA, Forbes R, Pustizzi F, Gobler CJ, Coyne KJ. 2003. The use of quantitative polymerase chain reaction for the detection and enumeration of the harmful alga Aureococcus anophagef-ferens in environmental samples along the United States East Coast. Limnology and Oceanography 48: 92-102.
62. Richards TA, Bass D. 2005. Molecular screening of free-living microbial eukaryotes: Diversity and distribution using a meta-analysis. Current Opinion in Microbiology 8: 240-252.
63. Romari K, Vaulot D. 2004. Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences. Limnology and Oceanography 49:784-798.
64. Rubinoff D, Cameron S, Will K. 2006. Genomic perspective on the shortcomings of mitochondrial DNA for "barcoding" identification. Journal of Heredity 97: 581-594.
65. Rynearson TA, Armbrust EV 2004. Genetic differentiation among populations of the planktonic marine diatom Ditylum brightwellii (Bacillario-phyceae). Journal of Phycology 40: 34-43.
66. Sáez AG, Probert I, Geisen M, Quinn P, Young JR, Medlin LK. 2003. Pseudo-cryptic speciation in coccolithophores. Proceedings of the National Academy of Sciences 100: 7163-7168.
67. Schloss PD, Handelsman J. 2004. Status of the microbial census. Microbiology and Molecular Biology Reviews 68: 686-691.
68. Scholin CA, Buck KR, Britschgi T, Cangelosi G, Chavez FP. 1996. Identification of Pseudo-nitzschia australis (Bacillariophyceae) using rRNA-targeted probes in whole cell and sandwich hybridization formats. Phycologia 35: 190-197.
69. Sherr BF, Sherr EB, Caron DA, Vaulot D, Worden AZ. 2007. Oceanic protists. Oceanography 20: 102-106.
70. Sherr EB, Sherr BE 2002. Significance of predation by protists in aquatic microbial food webs. Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology 81: 293-308.
71. Sieburth JM. 1979. Sea Microbes. New York: Oxford University Press.
72. Simpson AGB, Roger AJ. 2004. The real 'kingdoms' of eukaryotes. Current Biology 14: R693-696.
73. Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arrieta JM, Herndl GJ. 2006. Microbial diversity in the deep sea and the under-explored "rare biosphere." Proceedings of the National Academy of Sciences 103: 12115-12120.
74. Stoeck T, Hayward B, Taylor GT, Varela R, Epstein SS. 2006. A multiple PCR-primer approach to access the microeukaryotic diversity in environmental samples. Protist 157: 31-43.
75. Stoeck T, Zuendorf A, Behnke A, Breiner H.-W. 2007. A molecular approach to identify active microbes in environmental eukaryote clone libraries. Microbial Ecology 53:328-339.
76. Suttle CA. 2005. Viruses in the sea. Nature 437: 356-361.
77. von Wintzingerode F, Gobel UB, Stackebrandt E. 1997. Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews 21: 213-229.
78. Vrieling EG, Anderson DM. 1996. Immunofluorescence in phytoplankton research: Applications and potential. Journal of Phycology 32: 1-16.
79. Wahlund TM, Hadaegh AR, Clark R, Nguyen B, Fanelli M, Read BA. 2004. Analysis of expressed sequence tags from calcifying cells of marine coc-colithophorid (Emiliania huxleyi). Marine Biotechnology 6: 278-290.
80. Whittaker RH. 1969. New concepts of kingdoms of organisms. Science 163: 150-160.