Functional group-specific traits drive phytoplankton dynamics in the oligotrophic ocean

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 44, 2015, Pages E5972-E5979

  Alexander, Harriet ^a,b   Rouco, Mónica ^c   Haley, Sheean T ^c   Wilson, Samuel T ^d   Karl, David M ^d   Dyhrman, Sonya T ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

^c Columbia University ^*  (United States)

^d UNIVERSITY OF HAWAII   (United States)

Author keywords

Biogeochemistry; Blooms; Ecological traits; Metatranscriptomics; Phytoplankton

Indexed keywords

FUNCTIONAL GROUP; MESSENGER RNA; METAL; TRANSCRIPTOME; VITAMIN; SEA WATER;

ALGAL BLOOM; ARTICLE; AUTOTROPHY; CARBON SEQUESTRATION; DIATOM; DINOFLAGELLATE; DNA CONTAMINATION; ENERGY METABOLISM; HAPTOPHYTA; HETEROTROPHY; MICROBIAL METABOLISM; NONHUMAN; NUTRIENT LOADING; OLIGOTROPHIC OCEAN; PHYTOPLANKTON; POPULATION STRUCTURE; PRIORITY JOURNAL; PURINE METABOLISM; SEA; SPECIES COMPOSITION; GROWTH, DEVELOPMENT AND AGING; PHYSIOLOGY;

OCEANS AND SEAS; PHYTOPLANKTON; SEAWATER;

EID: 84946606300     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1518165112     Document Type: Article

References (54)

1. Karl DM, Laws EA, Morris P, Williams PJL, Emerson S (2003) Global carbon cycle: Metabolic balance of the open sea. Nature 426(6962):32.
2. McAndrew P, et al. (2007) Metabolic response of oligotrophic plankton communities to deep water nutrient enrichment. Mar Ecol Prog Ser 332:63-75.
3. Karl DM, Church MJ, Dore JE, Letelier RM, Mahaffey C (2012) Predictable and efficient carbon sequestration in the North Pacific Ocean supported by symbiotic nitrogen fixation. Proc Natl Acad Sci USA 109(6):1842-1849.
4. Villareal TA, Brown CG, Brzezinski MA, Krause JW, Wilson C (2012) Summer diatom blooms in the North Pacific subtropical gyre: 2008-2009. PLoS One 7(4):e33109.
5. Villareal TA, Adornato L, Wilson C, Schoenbaechler CA (2011) Summer blooms of diatom-diazotroph assemblages and surface chlorophyll in the North Pacific Gyre: A disconnect. J Geophys Res 116(C3):C03001.
6. Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998) Primary production of the biosphere: Integrating terrestrial and oceanic components. Science 281(5374): 237-240.
7. López-Urrutia A, San Martin E, Harris RP, Irigoien X (2006) Scaling the metabolic balance of the oceans. Proc Natl Acad Sci USA 103(23):8739-8744.
8. Margalef R (1978) Life-forms of phytoplankton as survival alternatives in an unstable environment. Oceanol Acta 1(4):493-509.
9. Tilman D (1977) Resource competition between plankton algae: An experimental and theoretical approach. Ecology 58(2):338-348.
10. Cavender-Bares KK, Karl DM, Chisholm SW (2001) Nutrient gradients in the western North Atlantic Ocean: Relationship to microbial community structure and comparison to patterns in the Pacific Ocean. Deep Sea Res Part I Oceanogr Res Pap 48(11): 2373-2395.
11. Karl DM, et al. (2001) Ecological nitrogen-to-phosphorus stoichiometry at station ALOHA. Deep Sea Res Part II Top Stud Oceanogr 48(8-9):1529-1566.
12. Karl DM (2002) Nutrient dynamics in the deep blue sea. Trends Microbiol 10(9):410-418.
13. Benitez-Nelson CR, et al. (2007) Mesoscale eddies drive increased silica export in the subtropical Pacific Ocean. Science 316(5827):1017-1021.
14. Kim I-N, et al. (2014) Chemical oceanography. Increasing anthropogenic nitrogen in the North Pacific Ocean. Science 346(6213):1102-1106.
15. Cortés MYM, Bollmann J, Thierstein HHR (2001) Coccolithophore ecology at the HOT station ALOHA, Hawaii. Deep Sea Res Part II Top Stud Oceanogr 48(8-9):1957-1981.
16. Marchetti A, et al. (2012) Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. Proc Natl Acad Sci USA 109(6):E317-E325.
17. Alexander H, Jenkins BD, Rynearson TA, Dyhrman ST (2015) Metatranscriptome analyses indicate resource partitioning between diatoms in the field. Proc Natl Acad Sci USA 112(17):E2182-E2190.
18. Dupont CL, et al. (2015) Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. ISME J 9(5):1076-1092.
19. Pearson GA, et al. (2015) Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula. ISME J 9(10):2275-2289.
20. Ottesen EA, et al. (2014) Multispecies diel transcriptional oscillations in open ocean heterotrophic bacterial assemblages. Science 345(6193):207-212.
21. 2 via cAMP signalling and coordinated gene expression. Nat Clim Change 5(8):761-765.
22. Dyhrman ST, et al. (2012) The transcriptome and proteome of the diatom Thalassiosira pseudonana reveal a diverse phosphorus stress response. PLoS One 7(3):e33768.
23. Amin SA, et al. (2015) Interaction and signalling between a cosmopolitan phytoplankton and associated bacteria. Nature 522(7554):98-101.
24. Shi Y, McCarren J, DeLong EF (2012) Transcriptional responses of surface water marine microbial assemblages to deep-sea water amendment. Environ Microbiol 14(1): 191-206.
25. McCarren J, et al. (2010) Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea. Proc Natl Acad Sci USA 107(38):16420-16427.
26. De Vargas C, et al.; Tara Oceans Coordinators (2015) Eukaryotic plankton diversity in the sunlit ocean. Science 348(6237):1261605.
27. Villar E, et al.; Tara Oceans Coordinators (2015) Environmental characteristics of Agulhas rings affect interocean plankton transport. Science 348(6237): 1261447.
28. Keeling PJ, et al. (2014) The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLoS Biol 12(6):e1001889.
29. Letelier RM, et al. (1993) Temporal variability of phytoplankton community structure based on pigment analysis. Limnol Oceanogr 38(7):1420-1437.
30. Fontanez KM, Eppley JM, Samo TJ, Karl DM, DeLong EF (2015) Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre. Front Microbiol 6:469.
31. Moustafa A, et al. (2010) Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence. PLoS One 5(3):e9688.
32. Hackett JD, Anderson DM, Erdner DL, Bhattacharya D (2004) Dinoflagellates: A remarkable evolutionary experiment. Am J Bot 91(10):1523-1534.
33. Palenik BP, Henson SE (1997) The use of amides and other organic nitrogen sources by the phytoplankton Emiliania huxleyi. Limnol Oceanogr 42(7):1544-1551.
34. Winn CD, Karl DM (1984) Laboratory calibrations of the [h]adenine technique for measuring rates of RNA and DNA synthesis in marine microorganisms. Appl Environ Microbiol 47(4):835-842.
35. Silver MW, et al. (2010) Toxic diatoms and domoic acid in natural and iron enriched waters of the oceanic Pacific. Proc Natl Acad Sci USA 107(48):20762-20767.
36. Marchetti A, et al. (2005) Iron and silicic acid effects on phytoplankton productivity, diversity, and chemical composition in the central equatorial Pacific Ocean. Limnol Oceanogr 55(1):11-29.
37. Read BA, et al.; Emiliania huxleyi Annotation Consortium (2013) Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 499(7457): 209-213.
38. Wu Z, et al. (2010) Empirical bayes analysis of sequencing-based transcriptional profiling without replicates. BMC Bioinformatics 11(1):564.
39. Saito MA, et al. (2014) Multiple nutrient stresses at intersecting Pacific Ocean biomes detected by protein biomarkers. Science 345(6201):1173-1177.
40. Bertrand EM, et al. (2012) Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein. Proc Natl Acad Sci USA 109(26):E1762-E1771.
41. Bender SJ, Durkin CA, Berthiaume CT, Morales RL, Armbrust EV (2014) Transcriptional responses of three model diatoms to nitrate limitation of growth. Front Mar Sci 1:3.
42. Dyhrman ST, et al. (2006) Long serial analysis of gene expression for gene discovery and transcriptome profiling in the widespread marine coccolithophore Emiliania huxleyi. Appl Environ Microbiol 72(1):252-260.
43. Dyhrman ST, Palenik B (2003) Characterization of ectoenzyme activity and phosphateregulated proteins in the coccolithophorid Emiliania huxleyi. J Plankton Res 25(10): 1215-1225.
44. Xu Y, Wahlund TM, Feng L, Shaked Y, Morel FMM (2006) A novel alkaline phosphatase in the cocolithophore Emiliania huxleyi (Prymnesiophyceae) and its regulation by phosphorus. J Phycol 42(4):835-844.
45. Lessard EJ, Merico A, Tyrrell T (2005) Nitrate:phosphate ratios and Emiliania huxleyi blooms. Limnol Oceanogr 50(3):1020-1024.
46. Robinson MD, Oshlack A (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11(3):R25.
47. Litchman E, Klausmeier CA (2008) Trait-based community ecology of phytoplankton. Annu Rev Ecol Evol Syst 39(1):615-639.
48. Doney SC, et al. (2012) Climate change impacts on marine ecosystems. Annu Rev Mar Sci 4(1):11-37.
49. Parsons TR, Yoshiaki M, Lalli CM (1984) A Manual of Chemical & Biological Methods for Seawater Analysis (Pergamon, Oxford).
50. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26(5):589-595.
51. Anders S, Pyl PT, Huber W (2015) HTSeq-a Python framework to work with highthroughput sequencing data. Bioinformatics 31(2):166-169.
52. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: An automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35(Web Server issue):W182-W185.
53. Shi Y, Tyson GW, Eppley JM, DeLong EF (2011) Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. ISME J 5(6):999-1013.
54. Krzywinski M, et al. (2009) Circos: An information aesthetic for comparative genomics. Genome Res 19(9):1639-1645.