Photosynthetic picoeukaryote assemblages in the South China Sea from the Pearl River estuary to the SEATS station

Aquatic Microbial Ecology

Volumn 71, Issue 3, 2014, Pages 271-284

  Wu, Wenxue ^a   Huang, Bangqin ^a   Zhong, Chao ^a  

^a XIAMEN UNIVERSITY   (China)

Author keywords

18S rDNA; Community structure; FISH TSA; Mamiellophyceae; Photosynthetic picoeukaryotes; South China Sea

Indexed keywords

EID: 84987652788     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame01681     Document Type: Article

References (84)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Amacher J, Neuer S, Anderson I, Massana R (2009) Molecular approach to determine contributions of protist community to particle flux. Deep-Sea Res I 56:2206-2215
3. Balzano S, Marie D, Gourvil P, Vaulot D (2012) Composition of the summer photosynthetic pico and nanoplankton communities in the Beaufort Sea assessed by T-RFLP and sequences of the 18S rRNA gene from flow cytometry sorted samples. ISME J 6:1480-1498
4. Blanchot J, André JM, Navarette C, Neveux J, Radenae MH (2001) Picophytoplankton in the equatorial Pacific: vertical distributions in the warm pool and in the high nutrient low chlorophyll conditions. Deep-Sea Res I 48:297-314
5. Caron DA, Countway PD, Savai P, Gast RJ and others (2009) Defining DNA-based operational taxonomic units for microbial-eukaryote ecology. Appl Environ Microbiol 75:5797-5808
6. Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540-552
7. Chen Y, Wang N, Zhang P, Zhou H, Qu L (2002) Molecular evidence identifies bloom-forming Phaeocystis (Prymnesiophyta) from coastal waters of southeast China as Phaeocystis globosa. Biochem Syst Ecol 30:15-22
8. Chen YL, Chen H, Karl DM, Takahashi M (2004) Nitrogen modulates phytoplankton growth in spring in the South China Sea. Cont Shelf Res 24:527-541
9. Chen B, Wang L, Song S, Huang B and others (2011) Comparisons of picophytoplankton abundance, size, and fluorescence between summer and winter in northern South China Sea. Cont Shelf Res 31:1527-1540
10. Collado-Fabbri S, Vaulot D, Ulloa O (2011) Structure and seasonal dynamics of the eukaryotic picophytoplankton community in a wind-driven coastal upwelling ecosystem. Limnol Oceanogr 56:2334-2346
11. Countway PD, Caron DA (2006) Abundance and distribution of Ostreococcus sp. in the San Pedro Channel, California, as revealed by quantitative PCR. Appl Environ Microbiol 72:2496-2506
12. Countway PD, Gast RJ, Savai P, Caron DA (2005) Protistan diversity estimates based on 18S rDNA from seawater incubations in the Western North Atlantic. J Eukaryot Microbiol 52:95-106
13. Cuvelier ML, Allen AE, Monier A, McCrow JP and others (2010) Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton. Proc Natl Acad Sci USA 107:14679-14684
14. Demir-Hilton E, Sudek S, Cuvelier ML, Gentemann CL and others (2011) Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus. ISME J 5:1095-1107
15. Dong HP, Wang DZ, Dai MH, Hong HS (2010) Characterization of particulate organic matter in the water column of the South China Sea using a shotgun proteomic approach. Limnol Oceanogr 55:1565-1578
16. Du C, Liu Z, Dai M, Kao SJ and others (2013) Impact of the Kuroshio intrusion on the nutrient inventory in the upper northern South China Sea: insights from an isopycnal mixing model. Biogeosciences 10:6419-6432
17. DuRand MD, Olson RJ, Chisholm SW (2001) Phytoplankton population dynamics at the Bermuda Atlantic Time-series station in the Sargasso Sea. Deep-Sea Res II 48:1983-2003
18. Fenchel T, Finlay BJ (2004) The ubiquity of small species: patterns of local and global diversity. BioScience 54:777-784
19. Finlay BJ (2002) Global dispersal of free-living microbial eukaryote species. Science 296:1061-1063
20. Fuller NJ, Campbell C, Allen DJ, Pitt FD and others (2006) Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids. Aquat Microb Ecol 43:79-93
21. Furuya K, Marumo R (1983) The structure of the phytoplankton community in the subsurface chlorophyll maxima in the western North Pacific Ocean. J Plankton Res 5:393-406
22. Furuya K, Hayashi M, Yabushita Y (1998) HPLC determination of phytoplankton pigments using N,N-dimethylformamide. J Oceanogr 54:199-203
23. Giovannoni SJ, DeLong EF, Olsen GJ, Pace NR (1988) Phylogenetic group-specific oligonucleotide probes for identification of single microbial cells. J Bacteriol 170:720-726
24. Green JC (1991) Phagotrophy in prymnesiophyte flagellates. In: Patterson DJ, Larsen J (eds) The biology of free-living heterotrophic flagellates. Syst Assoc Spec Vol 45:401-414
25. Guillou L, Moon-Van der Staay SY, Claustre H, Partensky F, Vaulot D (1999) Diversity and abundance of Bolidophyceae (Heterokonta) in two oceanic regions. Appl Environ Microbiol 65:4528-4536
26. Guillou L, Eikrem W, Chrétiennot-Dinet MJ, Le Gall F and others (2004) Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems. Protist 155:193-214
27. Harrison PJ, Yin K, Lee JHW, Gan J, Liu H (2008) Physical-biological coupling in the Pearl River Estuary. Cont Shelf Res 28:1405-1415
28. Hernández-Becerril DU, Aquino-Cruz A, Salas-De-León DA, Signoret-Poillon M, Monreal-Gómez MA (2012) Studies on picophytoplankton in the southern Gulf of Mexico: pigment analysis and potential importance of the picoeukaryote Prasinophyte Micromonas pusilla. Mar Biol Res 8:331-340
29. Hu J, Zheng Q, Sun Z, Tai CK (2012) Penetration of nonlinear Rossby eddies into South China Sea evidenced by cruise data. J Geophys Res 117, C03010, doi:10.1029/2011JC007525
30. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17:754-755
31. Jardillier L, Zubkov MV, Pearman J, Scanlan DJ (2010) Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean. ISME J 4:1180-1192
32. Kirkham AR, Jardillier LE, Holland R, Zubkov MV, Scanlan DJ (2011) Analysis of photosynthetic picoeukaryote community structure along an extended Ellett line transect in the northern North Atlantic reveals a dominance of novel prymnesiophyte and prasinophyte phylotypes. Deep-Sea Res I 58:733-744
33. Kirkham AR, Lepère C, Jardillier LE, Not F and others (2013) A global perspective on marine photosynthetic picoeukaryote community structure. ISME J 7:922-936
34. Latasa M, Scharek R, Le Gall F, Guillou L (2004) Pigment suites and taxonomic groups in Prasinophyceae. J Phycol 40:1149-1155
35. Li WKW (1994) Primary production of prochlorophytes, cyanobacteria, and eucaryotic ultraphytoplankton: measurements from flow cytometric sorting. Limnol Oceanogr 39:169-175
36. Li LY, Lin D, Chen JH, Wu SH and others (2010) Diversity and distribution of planktonic protists in the northern South China Sea. J Plankton Res 33:445-456
37. Liang WD, Yang YJ, Tang TY, Chuang WS (2008) Kuroshio in the Luzon Strait. J Geophys Res 113, C08048, doi: 10.1029/2007JC004609
38. Litchman E, Klausmeier CA, Schofield OM, Falkowski P (2007) The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level. Ecol Lett 10:1170-1181
39. Liu KK, Chao SY, Shaw PT, Gong GC and others (2002) Monsoon-forced chlorophyll distribution and primary production in the South China Sea: observations and a numerical study. Deep-Sea Res I 49:1387-1412
40. Liu H, Chang J, Tseng CM, Wen LS, Liu KK (2007) Seasonal variability of picoplankton in the Northern South China Sea at the SEATS station. Deep-Sea Res II 54:1602-1616
41. Liu H, Probert I, Uitz J, Claustre H and others (2009) Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans. Proc Natl Acad Sci USA 106:12803-12808
42. Lovejoy C, Vincent WF, Bonilla S, Roy S and others (2007) Distribution, phylogeny, and growth of cold-adapted picoprasinophytes in Arctic Seas. J Phycol 43:78-89
43. Mackey MD, Mackey DJ, Higgins HW, Wright SW (1996) CHEMTAX - a program for estimating class abundances from chemical markers: application to HPLC measurements of phytoplankton. Mar Ecol Prog Ser 144:265-283
44. Mackey DJ, Higgins HW, Mackey MD, Holdsworth D (1998) Algal class abundances in the western equatorial Pacific: estimation from HPLC measurements of chloroplast pigments using CHEMTAX. Deep-Sea Res I 45:1441-1468
45. Mackey DJ, Blanchot J, Higgins HW, Neveux J (2002) Phytoplankton abundances and community structure in the equatorial Pacific. Deep-Sea Res II 49:2561-2582
46. Marie D, Zhu F, Balagué V, Ras J, Vaulot D (2006) Eukaryotic picoplankton communities of the Mediterranean Sea in summer assessed by molecular approaches (DGGE, TTGE, QPCR). FEMS Microbiol Ecol 55:403-415
47. Marin B, Melkonian M (2010) Molecular phylogeny and classification of the Mamiellophyceae class. nov. (Chlorophyta) based on sequence comparisons of the nuclear- and plastid-encoded rRNA operons. Protist 161:304-336
48. McDonald SM, Sarno D, Scanlan DJ, Zingone A (2007) Genetic diversity of eukaryotic ultraphytoplankton in the Gulf of Naples during an annual cycle. Aquat Microb Ecol 50:75-89
49. Michaels AF, Silver MW (1988) Primary production, sinking fluxes and the microbial food web. Deep-Sea Res 35:473-490
50. Moon-van der Staay SY, van der Staay GW M, Guillou L, Vaulot D and others (2000) Abundance and diversity of prymnesiophytes in the picoplankton community from the equatorial Pacific Ocean inferred from 18S rDNA sequences. Limnol Oceanogr 45:98-109
51. Moon-van der Staay SY, De Wachter R, Vaulot D (2001) Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity. Nature 409:607-610
52. Ning X, Chai F, Xue H, Cai Y and others (2004) Physical-biological oceanographic coupling influencing phytoplankton and primary production in the South China Sea. J Geophys Res 109, C10005, doi:10.1029/2004JC002365
53. Not F, Simon N, Biegala IC, Vaulot D (2002) Application of fluorescent in situ hybridization coupled with tyramide signal amplification (FISH-TSA) to assess eukaryotic picoplankton composition. Aquat Microb Ecol 28:157-166
54. Not F, Latasa M, Marie D, Cariou T and others (2004) A single species, Micromonas pusilla (Prasinophyceae), dominates the eukaryotic picoplankton in the Western English Channel. Appl Environ Microbiol 70:4064-4072
55. Not F, Massana R, Latasa M, Marie D and others (2005) Late summer community composition and abundance of photosynthetic picoeukaryotes in Norwegian and Barents Seas. Limnol Oceanogr 50:1677-1686
56. Not F, Zapata M, Pazos Y, Campaña E, Doval M, Rodríguez F (2007) Size-fractionated phytoplankton diversity in the NW Iberian coast: a combination of microscopic, pigment and molecular analyses. Aquat Microb Ecol 49:255-265
57. Not F, Latasa M, Scharek R, Viprey M and others (2008) Protistan assemblages across the Indian Ocean, with a specific emphasis on the picoeukaryotes. Deep-Sea Res I 55:1456-1473
58. Not F, del Campo J, Balagué V, de Vargas C, Massana R (2009) New insights into the diversity of marine picoeukaryotes. PLoS ONE 4:e7143
59. O'Kelly CJ, Sierachi ME, Their EC, Hobson I (2003) A transient bloom of Ostreococcus (Chlorophyta, Prasinophyceae) in West Neck Bay, Long Island, New York. J Phycol 39:850-854
60. Pérez V, Fernández E, Marañón E, Serret P and others (2005) Latitudinal distribution of microbial plankton abundance, production, and respiration in the equatorial Atlantic in autumn 2000. Deep-Sea Res I 52:861-880
61. Richardson TL, Jackson GA (2007) Small phytoplankton and carbon export from the surface ocean. Science 315:838-840
62. Rodríguez F, Derelle E, Guillou L, Le Gall F and others (2005) Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae). Environ Microbiol 7:853-859
63. Schlitzer R (2011) Ocean data view. Available at http://odv.awi.de
64. Schloss PD, Westcott SL, Ryabin T, Hall JR and others (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537-7541
65. Shaw PT, Chao SY (1994) Surface circulation in the South China Sea. Deep-Sea Res I 41:1663-1683
66. Shi XL, Marie D, Jardillier L, Scanlan DJ, Vaulot D (2009) Groups without cultured representatives dominate eukaryotic picophytoplankton in the oligotrophic South East Pacific Ocean. PLoS ONE 4:e7657
67. Sievers F, Wilm A, Dineen DG, Gibson TJ and others (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7:539
68. Simon N, Le Bot N, Marie D, Partensky F, Vaulot D (1995) Fluorescent in situ hybridization with rRNA-targeted oligonucleotide probes to identify small phytoplankton by flow cytometry. Appl Environ Microbiol 61:2506-2513
69. Simon N, Campbell L, Örnolfsdottir E, Groben R and others (2000) Oligonucleotide probes for the identification of three algal groups by dot blot and fluorescent whole-cell hybridization. J Eukaryot Microbiol 47:76-84
70. Šlapeta J, López-García P, Moreira D (2006) Global dispersal and ancient cryptic species in the smallest marine eukaryotes. Mol Biol Evol 23:23-29
71. Tamura K, Peterson D, Peterson N, Stecher G and others (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731-2739
72. Treusch AH, Demir-Hilton E, Vergin KL, Worden AZ and others (2012) Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids. ISME J 6:481-492
73. Vaulot D, Le Gall F, Marie D, Guillou L, Partensky F (2004) The Roscoff Culture Collection (RCC): A collection dedicated to marine picoplankton. Nova Hedwigia 79:49-70
74. Viprey M, Guillou L, Ferréol M, Vaulot D (2008) Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach. Environ Microbiol 10:1804-1822
75. Wang DZ, Dong HP, Xie ZX, Dai MH, Hong HS (2011) Metaproteomic characterization of dissolved organic matter in the water column of the South China Sea. Limnol Oceanogr 56:1641-1652
76. Welschmeyer NA (1994) Fluorometric analysis of chlorophyll a in the presence of chlorophyll b and pheopigments. Limnol Oceanogr 39:1985-1992
77. Worden AZ (2006) Picoeukaryote diversity in coastal waters of the Pacific Ocean. Aquat Microb Ecol 43:165-175
78. Worden AZ, Nolan JK, Palenik B (2004) Assessing the dynamics and ecology of marine picophytoplankton: the importance of the eukaryotic component. Limnol Oceanogr 49:168-179
79. Worden AZ, Lee JH, Mock T, Rouzé P and others (2009) Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science 324:268-272
80. Xu J, Yin K, He L, Yuan Z and others (2008) Phosphorus limitation in the northern South China Sea during late summer: influence of the Pearl River. Deep-Sea Res I 55:1330-1342
81. Yuan J, Chen MY, Shao P, Zhou H and others (2004) Genetic diversity of small eukaryotes from the coastal waters of Nansha Islands in China. FEMS Microbiol Lett 240:163-170
82. Zhu F, Massana R, Not F, Marie D, Vaulot D (2005) Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol Ecol 52:79-92
83. Zubkov MV, Tarran GA (2008) High bacterivory by the smallest phytoplankton in the North Atlantic Ocean. Nature 455:224-226
84. Zubkov MV, Sleigh MA, Tarran GA, Burkill PH, Leakey RJG (1998) Picoplanktonic community structure on an Atlantic transect from 50° N to 50° S. Deep-Sea Res I 45:1339-1355