Protist 18S rRNA gene sequence analysis reveals multiple sources of organic matter contributing to turbidity maxima of the Columbia River estuary

Marine Ecology Progress Series

Volumn 438, Issue , 2011, Pages 19-31

  Herfort, Lydie ^a   Peterson, Tawnya D ^a   McCue, Lee Ann ^b   Zuber, Peter ^a  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Columbia River estuary; Estuarine turbidity maxima; Organic matter

Indexed keywords

CHLOROPHYLL A; CLONE; DETRITUS; DIATOM; GENE EXPRESSION; MARINE ECOSYSTEM; MOLECULAR ANALYSIS; ORGANIC MATTER; PHYLOGENY; PHYTOPLANKTON; PROTIST; SURFACE WATER; TURBIDITY;

COLUMBIA ESTUARY; UNITED STATES;

BACILLARIOPHYTA; KATABLEPHARIS; MASTIGOPHORA (FLAGELLATES); MYRIONECTA RUBRA; PROTISTA;

EID: 80053596583     PISSN: 01718630     EISSN: None     Source Type: Journal    
DOI: 10.3354/meps09303     Document Type: Article

References (40)

1. Amspoker MC, McIntire CD (1986) Effects of sedimentary processes and salinity on the diatom flora of the Columbia River estuary. Bot Mar 29: 391-399
2. Bell EM, Laybourn-Parry J (1999) Annual plankton dynamics in an Antarctic saline lake. Freshw Biol 41: 507-519 (Pubitemid 29324046)
3. 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
4. Crump BC, Baross JA (1996) Particle-attached bacteria and heterotrophic plankton associated with the Columbia River estuary turbidity maxima. Mar Ecol Prog Ser 138: 265-273
5. Crump BC, Baross JA, Simenstad CA (1998) Dominance of particle-attached bacteria in the Columbia River estuary, USA. Aquat Microb Ecol 14: 7-18 (Pubitemid 128474839)
6. Crump BC, Armbrust EV, Baross JA (1999) Phylogenetic analysis of particle-attached and free-living bacterial communities in the Columbia River, its estuary and the adjacent coastal ocean. Appl Environ Microbiol 65: 3192-3204 (Pubitemid 29315598)
7. Diez B, Pedros-Alio C, Massana R (2001) Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing. Appl Environ Microbiol 67: 2932-2941 (Pubitemid 33644756)
8. Domaizon I, Viboud S, Fontvieille D (2003) Taxon-specific and seasonal variations in flagellates grazing on heterotrophic bacteria in the oligotrophic Lake Annecy-importance of mixotrophy. FEMS Microbiol Ecol 46: 317-329 (Pubitemid 37494873)
9. Fenchel T, Hansen PJ (2006) Motile behavior of the bloomforming ciliate Mesodinium rubrum. Mar Biol Res 2: 33-40
10. Frey BE, Lara-Lara R, Small LF (1984) Water column primary production in the Columbia River estuary. Columbia River Estuary Data Development Program, Astoria, OR
11. Goodwin TW(1971) Algal carotenoids. In: Goodwin TW (ed) Aspects of terpenoid chemistry and biochemistry. Academic Press, London, p 315-356
12. Haertel L, Osterberg C, Curl H, Park PK (1969) Nutrient and plankton ecology of the Columbia River estuary. Ecology 50: 962-978
13. Hedges JI, Stern JH (1984) Carbon and nitrogen determinations of carbonate-containing solids. Limnol Oceanogr 29: 663-666
14. Herfort L, Peterson TD, McCue LA, Crump BC and others (2011) Myrionecta rubra population genetic diversity and its cryptophyte chloroplast specificity in recurrent red tides in the Columbia River estuary. Aquat Microb Ecol 62: 85-97
15. Jay DA (1984) Circulatory processes in the Columbia River Estuary. Columbia River Estuary Data Development Program, Astoria, OR
16. Jay DA, Musiak JD (1996) Internal tidal asymmetry in channel flows: origins and consequences. In: Pattiaratchi C (ed) Mixing processes in estuaries and coastal seas. American Geophysical Union, Coastal and Estuarine Sciences Monograph, Washington, DC, p 219-258
17. Lara-Lara JR, Frey BE, Small LF (1990a) Primary production in the Columbia River estuary. I. Spatial and temporal variability of properties. Pac Sci 44: 17-37 (Pubitemid 20426867)
18. Lara-Lara JR, Frey BE, Small LF (1990b) Primary production in the Columbia River estuary. II. Grazing losses, transport and a phytoplankton carbon budget. Pac Sci 44: 38-50 (Pubitemid 20426868)
19. Lefranc M, Thenot A, Lepere C, Debroas D (2005) Genetic diversity of small eukaryotes in lakes differing by their trophic status. Appl Environ Microbiol 71: 5935-5942 (Pubitemid 41456887)
20. Lindholm T (1985) Mesodinium rubrum-a unique photosynthetic ciliate. Adv Aquat Microbiol 3: 1-48
21. López-Garcia P, Rodriguez-Valera F, Pedros-Alio C, Moreira D (2001) Unexpected diversity of small eukaryotes in deep-sea Antarctic plankton. Nature 409: 603-607 (Pubitemid 32154809)
22. McManus GB, Katz LA (2009) Molecular and morphological methods for identifying plankton: what makes a successful marriage? J Plankton Res 31: 1119-1129
23. 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 (Pubitemid 32154810)
24. Neal VT (1972) Physical aspects of the Columbia River and its estuary. In: Pruter AT, Alverson DL (eds) The Columbia River estuary and adjacent ocean waters. University of Washington Press, Seattle, WA, p 19-40
25. Ploug H, Zimmermann-Timm H, Schweitzer B (2002) Microbial communities and respiration on aggregates in the Elbe Estuary, Germany. Aquat Microb Ecol 27: 241-248 (Pubitemid 34465938)
26. Prahl FG, Small LF, Eversmeyer B (1997) Biogeochemical characterization of suspended particulate matter in the Columbia River estuary. Mar Ecol Prog Ser 160: 173-184 (Pubitemid 28069539)
27. Prasad AKSK, Nienow JA, Livingston RJ (1990) The genus Cyclotella (Bacillariophyta) in Choctawhatchee Bay, Florida, with special reference to C. striata and C. choctawhatcheeana sp. nov. Phycologia 29: 418-436
28. Savin MC, Martin JL, LeGresley M, Giewat M, Rooney- Varga J (2004) Plankton diversity in the Bay of Fundy as measured by morphological and molecular methods. Microb Ecol 48: 51-65 (Pubitemid 39160988)
29. Simenstad CA, Small LF, McIntire CD (1990) Consumption processes and food web structure in the Columbia River Estuary. Prog Oceanogr 25: 271-297
30. Simenstad CA, Morgan CA, Cordell JR, Baross JA (1994) Flux, passive retention, and active residence of zooplankton in Columbia River estuarine turbidity maxima. In: Dyer KR, Orth BJ (eds) Changes in fluxes in estuaries: implications from science to management. ECSA22/ERF Symp, Plymouth, September 1992. Olsen & Olsen Press, Fredensborg, p 473-484
31. Slapeta J, López-García P, Moreira D (2006) Present status of the molecular ecology of kathablepharids. Protist 157: 7-11 (Pubitemid 43220712)
32. Small LF, Morgan SR (1994) Phytoplankton attributes in the turbidity maximum of the Columbia River Estuary, USA. In: Dyer K, Orth R (eds) Changing particle fluxes in estuaries: implications from science to management. ECSAERF22 Symp, Plymouth, September 1992. Olsen & Olsen Press, Fredensborg, p 465-472
33. Small LF, Prahl FG (2004) A particle conveyor belt process in the Columbia River estuary: evidence from chlorophyll a and particulate organic carbon. Estuaries 27: 999-1013
34. Small LF, McIntire CD, MacDonald KB, Lara-Lara JR, Frey BE, Amspoker MC, Winfield T (1990) Primary production, plant and detrital biomass, and particle transport in the Columbia River estuary. Prog Oceanogr 25: 175-210
35. Stoermer EF, Smol JP (1999) The diatoms: application for the environmental and earth sciences. Cambridge University Press, Cambridge
36. Sullivan BE, Prahl FG, Small LF, Covert PA (2001) Seasonality of phytoplankton production in the Columbia River: a natural or anthropogenic pattern? Geochim Cosmochim Acta 65: 1125-1139
37. Utermöhl H (1931) Neue Wege in der quantitativen Erfassung des Planktons (mit besonderer Berücksichtigung des Ultraplanktons). Verh Int Verein Theor Angew Limnol 5: 567-596
38. Utermöhl H (1958) Zur Vervollkommnung der quantitativen Phytoplankton-Methodik. Mitt Int Ver Theor Angew Limnol 9: 1-38
39. Verardo DJ, Froelich PN, McIntyre A (1990) Determination of organic carbon and nitrogen in marine sediments using the Carlo Erba NA-1500 analyzer. Deep-Sea Res I 37: 157-165
40. Wright SW, Jeffrey SW, Mantoura RFC, Llewellyn CA, Bjornland T, Repeta D, Welschmeyer N (1991) Improved HPLC method for the analysis of chlorophylls and carotenoids from marine phytoplankton. Mar Ecol Prog Ser 77: 183-196