Diversity of phytoplankton nitrate transporter sequences from isolated single cells and mixed samples from the East China Sea and mRNA quantification

Applied and Environmental Microbiology

Volumn 77, Issue 1, 2011, Pages 122-130

  Kang, Lee Kuo ^a   Wang, Hsuan Fan ^a   Chang, Jeng ^a  

^a NATIONAL TAIWAN OCEAN UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE RNA; CELL METHODS; DEGENERATE PRIMERS; EAST CHINA SEA; HIGH SPECIFICITY; MARINE DIATOMS; MIXED SAMPLES; MIXED SPECIES; MRNA LEVEL; NITRATE TRANSPORTERS; NITROGEN DEFICIENCY; PCR PRIMERS; PHYLOGENETIC ANALYSIS; PHYTOPLANKTON SAMPLES; PRIMER DESIGN; QUANTITATIVE PCR; SEQUENCE ALIGNMENTS; SEQUENCE DATABASE; SEQUENCE DIVERSITY; SINGLE CELLS; TARGET SPECIES; TRANSCRIPT LEVEL;

ALGAE CONTROL; GENE EXPRESSION; NUCLEIC ACIDS; PHYTOPLANKTON; RNA;

POLYMERASE CHAIN REACTION;

ANION TRANSPORT PROTEIN; MESSENGER RNA; NITRATE TRANSPORTERS; PRIMER DNA;

ABUNDANCE; DATABASE; DIATOM; GENE EXPRESSION; MARINE ECOSYSTEM; MITOCHONDRIAL DNA; NITRATE; PHYTOPLANKTON; POLYMERASE CHAIN REACTION; SPECIES DIVERSITY;

ARTICLE; CHINA; CLUSTER ANALYSIS; DIATOM; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYTOPLANKTON; SEA; SEQUENCE HOMOLOGY;

ANION TRANSPORT PROTEINS; CHINA; CLUSTER ANALYSIS; DIATOMS; DNA PRIMERS; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; OCEANS AND SEAS; PHYLOGENY; PHYTOPLANKTON; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

EAST CHINA SEA; PACIFIC OCEAN;

BACILLARIOPHYTA; NITZSCHIA ALBA;

EID: 79251638075     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01315-10     Document Type: Article

References (50)

1. Adhitya, A., F. I. M. Thomas, and B. B. Ward. 2007. Diversity of assimilatory nitrate reductase genes from plankton and epiphytes associated with a seagrass bed. Microb. Ecol. 54:587-597.
2. Allen, A. E., B. B. Ward, and B. K. Song. 2005. Characterization of diatom (Bacillariophyceae) nitrate reductase genes and their detection in marine phytoplankton communities. J. Phycol. 41:95-104.
3. Alverson, A. J. 2007. Strong purifying selection in the silicon transporters of marine and freshwater diatoms. Limnol. Oceanogr. 52:1420-1429.
4. Applied Biosystems. 1997. Relative quantitation of gene expression: ABI PRISM 7700 sequence detection system. PerkinElmer, Foster City, CA.
5. Armbrust, E. V. 2000. Structural features of nuclear genes in the centric diatom Thalassiosira weissflogii (Bacillariophyceae). J. Phycol. 36:942-946.
6. Armbrust, E. V., J. A. Berges, C. Bowler, B. R. Green, et al. 2004. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science 306:79-86.
7. Baker, G. C., J. J. Smith, and D. A. Cowan. 2003. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 55:541-555.
8. Bru, D., F. Martin-Laurent, and L. Philippot. 2008. Quantification of the detrimental effect of a single primer-template mismatch by real-time PCR using the 16S rRNA gene as an example. Appl. Environ. Microbiol. 74:1660-1663.
9. Chen, Y. L. L. 2000. Comparisons of primary productivity and phytoplankton size structure in the marginal regions of southern East China Sea. Cont. Shelf Res. 20:437-458.
10. Chung, C. C., S. P. L. Hwang, and J. Chang. 2003. Identification of a high-affinity phosphate transporter gene in a pransiophyte alga, Tetraselmis chui, and its expression under nutrient limitation. Appl. Environ. Microbiol. 69:754-759.
11. Clark, C. G. 1992. DNA purification from polysaccharide-rich cells, p. D-3.1-D-3.2. In J. J. Lee and A. T. Soldo (ed.), Protocols in protozoology. Society of Protozoology, Lawrence, KS.
12. Crawford, N. M., and A. D. M. Glass. 1998. Molecular and physiological aspects of nitrate uptake in plants. Trends Plant Sci. 3:389-395.
13. Dortch, Q. 1990. The interaction between ammonium and nitrate uptake in phytoplankton. Mar. Ecol. Prog. Ser. 61:183-201.
14. Duff, R. J., H. Ball, and P. J. Lavrentyev. 2008. Application of combined morphological-molecular approaches to the identification of planktonic protists from environmental samples. J. Eukaryot. Microbiol. 55:306-312.
15. Edvardsen, B., K. Shalchian-Tabrizi, K. S. Jakobsen, L. K. Medlin, E. Dahl, S. Brubak, and E. Paasche. 2003. Genetic variability and molecular phylogeny of Dinophysis species (Dinophyceae) from Norwegian waters inferred from single cell analyses of rDNA. J. Phycol. 39:395-408.
16. Field, C. B., M. J. Behrenfeld, J. T. Randerson, and P. Falkowski. 1998. Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281:237-240.
17. Forney, L. J., X. Zhou, and C. J. Brown. 2004. Molecular microbial ecology: land of the one-eyed king. Curr. Opin. Microbiol. 7:210-220.
18. Galvan, A., and E. Fernandez. 2001. Eukaryotic nitrate and nitrite transporters. Cell. Mol. Life Sci. 58:225-233.
19. Ghedira, R., N. Papazova, M. Vuylsteke, T. Ruttink, I. Taverniers, and M. De Loose. 2009. Assessment of primer/template mismatch effects on realtime PCR amplification of target taxa for GMO quantification. J. Agric. Food Chem. 57:9370-9377.
20. a.Guillard, R. R. L. 1983. Culture of phytoplankton for feeding marine invertebrates, p. 108-132. In C. J. Berg (ed.), Culture of marine invertebrates. Hutchinson Ross Publishing Co., Stroudsburg, PA.
21. Hahn, S., X. Y. Zhong, and W. Holzgreve. 2002. Single cell PCR in laser capture microscopy. Laser capture microscopy and microdissection. Methods Enzymol. 356:295-301.
22. Hahn, S., X. Y. Zhong, C. Troeger, R. Burgemeister, K. Gloning, and W. Holzgreve. 2000. Current applications of single-cell PCR. Cell. Mol. Life Sci. 57:96-105.
23. Handy, S. M., T. R. Bachvaroff, R. E. Timme, D. W. Coats, S. Kim, and C. F. Delwiche. 2009. Phylogeny of four Dinophysiacean genera (Dinophyceae, Dinophysiales) based on rDNA sequences from single cells and environmental samples. J. Phycol. 45:1163-1174.
24. Hildebrand, M., and K. Dahlin. 2000. Nitrate transporter genes from the diatom Cylindrotheca fusiformis (Bacillariophyceae): mRNA levels controlled by nitrogen source and by the cell cycle. J. Phycol. 36:702-713.
25. Howarth, R. W., and R. Marino. 2006. Nitrogen as the limiting nutrient for eutrophication in coastal marine ecosystems: evolving views over three decades. Limnol. Oceanogr. 51:364-376.
26. John, D. E., S. S. Patterson, and J. H. Paul. 2007. Phytoplankton-group specific quantitative polymerase chain reaction assays for RuBisCO mRNA transcripts in seawater. Mar. Biotechnol. 9:747-759.
27. Kang, L. K., S. P. L. Hwang, G. C. Gong, H. J. Lin, P. C. Chen, and J. Chang. 2007. Influences of nitrogen deficiency on the transcript levels of ammonium transporter, nitrate transporter and glutamine synthetase genes in Isochrysis galbana (Isochrysidales, Haptophyta). Phycologia 46:521-533.
28. Kang, L. K., S. P. L. Hwang, H. J. Lin, P. C. Chen, and J. Chang. 2009. Establishment of minimal and maximal transcript levels for nitrate transporter genes for detecting nitrogen deficiency in the marine phytoplankton Isochrysis galbana (Prymnesiophyceae) and Thalassiosira pseudonana (Bacillariophyceae). J. Phycol. 45:864-872.
29. Keane, T., C. Creevey, M. Pentony, T. Naughton, and J. McInerney. 2006. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol. Biol. 6:29.
30. Ki, J. S., and M. S. Han. 2005. Sequence-based diagnostics and phylogenetic approach of uncultured freshwater dinoflagellate Peridinium (Dinophyceae) species, based on single-cell sequencing of rDNA. J. Appl. Phycol. 17:147-153.
31. Ki, J. S., and M. S. Han. 2007. Rapid molecular identification of the harmful freshwater dinoflagellate Peridinium in various life stages using genus-specific single-cell PCR. J. Appl. Phycol. 19:467-470.
32. Ki, J. S., G. Y. Jang, and M. S. Han. 2004. Integrated method for single-cell DNA extraction, PCR amplification, and sequencing of ribosomal DNA from harmful dinoflagellates Cochlodinium polykrikoides and Alexandrium catenella. Mar. Biotechnol. 6:587-593.
33. Kudela, R. M., W. P. Cochlan, and R. C. Dugdale. 1997. Carbon and nitrogen uptake response to light by phytoplankton during an upwelling event. J. Plankton Res. 19:609-630.
34. Kwok, S., D. E. Kellogg, N. Mckinney, D. Spasic, L. Goda, C. Levenson, and J. J. Sninsky. 1990. Effects of primer template mismatches on the polymerase chain reaction-human immunodeficiency virus type-1 model studies. Nucleic Acids Res. 18:999-1005.
35. Liu, H. C., G. C. Gong, and J. Chang. 2010. Lateral water exchange between shelf-margin upwelling and Kuroshio waters influences phosphorus stress in microphytoplankton. Mar. Ecol. Prog. Ser. 409:121-130.
36. - uptake and assimilation: comparison of diatoms and dinoflagellates at several growth temperatures. Mar. Biol. 133:541-551.
37. Lomas, M. W., and P. M. Glibert. 2000. Comparisons of nitrate uptake, storage, and reduction in marine diatoms and flagellates. J. Phycol. 36:903-913.
38. Lynn, D. H., and M. Pinheiro. 2009. A survey of polymerase chain reaction (PCR) amplification studies of unicellular protists using single-cell PCR. J. Eukaryot. Microbiol. 56:406-412.
39. Nygaard, V., and E. Hovig. 2006. Options available for profiling small samples: a review of sample amplification technology when combined with microarray profiling. Nucleic Acids Res. 34:996-1014.
40. Poirier, G. M. C., and M. G. Erlander. 1998. Postdifferential display: parallel processing of candidates using small amounts of RNA. Methods 16:444-452.
41. Raes, J., and P. Bork. 2008. Molecular eco-systems biology: towards an understanding of community function. Nat. Rev. Microbiol. 6:693-699.
42. Siaut, M., M. Heijde, M. Mangogna, A. Montsant, et al. 2007. Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum. Gene 406:23-35.
43. Slot, J. C., K. N. Hallstrom, P. B. Matheny, and D. S. Hibbett. 2007. Diversification of NRT2 and the origin of its fungal homolog. Mol. Biol. Evol. 24:1731-1743.
44. Song, B., and B. B. Ward. 2007. Molecular cloning and characterization of high-affinity nitrate transporters in marine phytoplankton. J. Phycol. 43:542-552.
45. Takano, Y., and T. Horiguchi. 2006. Acquiring scanning electron microscopical, light microscopical and multiple gene sequence data from a single dinoflagellate cell. J. Phycol. 42:251-256.
46. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
47. Wadenback, J., D. Clapham, D. Craig, R. Sederoff, G. Peter, S. Von Arnold, and U. Egertsdotter. 2005. Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays. BMC Genomics 6:61.
48. Wang, E., L. D. Miller, G. A. Ohnmacht, E. T. Liu, and F. M. Marincola. 2000. High-fidelity mRNA amplification for gene profiling. Nature Biotechnol. 18:457-459.
49. Wawrik, B., J. H. Paul, and F. R. Tabita. 2002. Real-time PCR quantification of rbcL (ribulose-1,5-bisphosphate carboxylase/oxygenase) mRNA in diatoms and pelagophytes. Appl. Environ. Microbiol. 68:3771-3779.
50. Wilkerson, F. P., R. C. Dugdale, R. M. Kudela, and F. P. Chavez. 2000. Biomass and productivity in Monterey Bay, California: contribution of the large phytoplankton. Deep Sea Res. Part II Top. Stud. Oceanogr. 47:1003-1022.