Abstract
Diatoms play a fundamental role at the base of the polar marine food web. In the Southern Ocean, low iron concentrations and light levels control diatom abundance and distribution. Diatoms must therefore employ strategies that allow them to cope when iron and/or light availability is growth limiting. Through a combination of physiological and molecular-based approaches, we have investigated the physiological response to variable iron concentrations and light levels along with the expressed gene repertoires of nine newly isolated diatoms from the Western Antarctic Peninsula (WAP) region of the Southern Ocean. The diatoms ranged across five orders of magnitude in biovolume and displayed various degrees of susceptibility to low iron and light availability. Under the performed laboratory culture conditions, the growth rates of most diatoms decreased more due to low light level rather than low iron concentrations. Additionally, most diatoms were not subject to further reductions in growth rates when grown under combined low-light and iron-limiting conditions, indicating they are less likely to be co-limited by an additive effect. By sequencing the transcriptomes of these diatoms, we identified genes that likely facilitate their growth under variable iron and light conditions commonly present in the Southern Ocean. Specifically, we investigated the presence of 20 key genes involved in iron acquisition and homeostasis, iron usage in photosynthesis and nitrogen assimilation, and protection from reactive oxygen species. When comparing gene repertoires of recently sequenced transcriptomes of diatoms isolated from around the globe, the prevalence of certain genes exhibited biogeographical patterns that clearly distinguish Southern Ocean diatoms from those isolated from other regions.
Similar content being viewed by others
References
Agusti S, Duarte CM (2000) Experimental induction of a large phytoplankton bloom in Antarctic coastal waters. Mar Ecol Prog Ser 206:73–85. https://doi.org/10.3354/meps206073
Alderkamp AC, Kulk G, Buma AGJ et al (2012) The effect of iron limitation on the photophysiology of Phaeocystis antarctica (prymnesiophyceae) and Fragilariopsis cylindrus (bacillariophyceae) under dynamic irradiance. J Phycol 48:45–59. https://doi.org/10.1111/j.1529-8817.2011.01098.x
Allen AE, Laroche J, Maheswari U et al (2008) Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation. Proc Natl Acad Sci 105:10438–10443. https://doi.org/10.1073/pnas.0711370105
Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215:403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Arrigo KR, van Dijken GL, Bushinsky S (2008) Primary production in the Southern Ocean, 1997–2006. J Geophys Res 113:C08004. https://doi.org/10.1029/2007JC004551
Arrigo KR, Mills MM, Kropuenske LR et al (2010) Photophysiology in two major southern ocean phytoplankton taxa: photosynthesis and growth of Phaeocystis antarctica and Fragilariopsis cylindrus under different irradiance levels. Integr Comp Biol 50:950–966. https://doi.org/10.1093/icb/icq021
Bailleul B, Berne N, Murik O et al (2015) Energetic coupling between plastids and mitochondria drives CO2 assimilation in diatoms. Nature 524:366–369. https://doi.org/10.1038/nature14599
Baxter CJ, Redestig H, Schauer N et al (2007) The metabolic response of heterotrophic Arabidopsis cells to oxidative stress. Plant Physiol 143:312–325. https://doi.org/10.1104/pp.106.090431
Behrenfeld MJ, Milligan AJ (2013) Photophysiological expressions of iron stress in phytoplankton. Ann Rev Mar Sci 5:217–246. https://doi.org/10.1146/annurev-marine-121211-172356
Blain S, Quéguiner B, Armand L et al (2007) Effect of natural iron fertilization on carbon sequestration in the Southern Ocean. Nature 446:1070–1074. https://doi.org/10.1038/nature05700
Botebol H, Lesuisse E, Sutak R et al (2015) Central role for ferritin in the day/night regulation of iron homeostasis in marine phytoplankton. Proc Natl Acad Sci 112:1–6. https://doi.org/10.1073/pnas.1506074112
Bowler C, Allen AE, Badger JH et al (2008) The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature Lett. 456:239–244
Boyd PW (2002) Environmental factors controlling phytoplankton processes in the Southern Ocean. J Phycol 38:844–861
Boyd PW, Watson AJ, Law CS et al (2000) A mesoscale phytoplankton bloom in the polar Southern Ocean stimulated by iron fertilization. Nature 407:695–702. https://doi.org/10.1038/35037500
Boyd PW, Crossley AC, DiTullio GR et al (2001) Control of phytoplankton growth by iron supply and irradiance in the subantarctic Southern Ocean: experimental results from the SAZ Project. J Geophys Res 106:31573. https://doi.org/10.1029/2000JC000348
Boyd PW, Jickells T, Law CS et al (2007) Mesoscale iron enrichment experiments 1993-2005: synthesis and future directions. Science 315:612–617. https://doi.org/10.1126/science.1131669
Brand LE, Guillard RL, Murphy LS (1981) A method for the rapid and precise determination of acclimated phytoplankton reproductions rates. J Plankton Res 3:193–201
Cassar N, Bender ML, Barnett BA et al (2007) The Southern Ocean biological response to aeolian iron deposition. Science 317:1067–1070. https://doi.org/10.1126/science.1144602
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340
Edwards R, Sedwick P, Land E (2001) Iron in East Antarctic snow-implications for atmospheric iron deposition and algal production in Antarctic waters. Geophys Res Lett 28:3907–3910. https://doi.org/10.1029/2001GL012867
Eppley RW, Rogers JN, McCarthy JJ (1969) Half-saturation constants for uptake of nitrate and ammonium by marine phytoplankton. Limnol Oceanogr 14:912–920
Erdner DL, Price NM, Doucette GJ et al (1999) Characterization of ferredoxin and flavodoxin as markers of iron limitation in marine phytoplankton. Mar Ecol Prog Ser 184:43–53
Feng Y, Hare CE, Rose JM et al (2010) Interactive effects of iron, irradiance and CO2 on Ross Sea phytoplankton. Deep Res Part I Oceanogr Res Pap 57:368–383. https://doi.org/10.1016/j.dsr.2009.10.013
Fuhrman JA, Schwalbach MS, Stingl U (2008) Proteorhodopsins: an array of physiological roles? Nat Rev Microbiol 6:488–494
Gorbunov MY, Falkowski PG (2005) Fluorescence induction and relaxation (FIRe) technique and instrumentation for monitoring photosynthetic processes and primary production. In: Van der Est A, Bruce D (eds) Photosynthesis: fundamental aspects to global perspectives: proceedings of the 13th international congress on photosynthesis, Allen and Unwin, London, pp 1029–1031
Grabherr MG, Haas BJ, Yassour M et al (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652. https://doi.org/10.1038/nbt.1883
Greene RM, York N, Geider RJ, Falkowski PG (1991) Effect of iron limitation on photosynthesis in a marine diatom. Limnol Oceanogr 36:1772–1782
Groussman RD, Parker MS, Armbrust EV (2015) Diversity and evolutionary history of iron metabolism genes in diatoms. PLoS ONE 10:e0129081. https://doi.org/10.1371/journal.pone.0129081
Hillebrand H, Dürselen CD, Kirschtel D et al (1999) Biovolume calculation for pelagic and benthic microalgae. J Phycol 35:403–424. https://doi.org/10.1046/j.1529-8817.1999.3520403.x
Hoppe CJM, Holtz LM, Trimborn S, Rost B (2015) Ocean acidification decreases the light-use efficiency in an Antarctic diatom under dynamic but not constant light. New Phytol 207:159–171. https://doi.org/10.1111/nph.13334
Hubbard KA, Rocap G, Armbrust EV (2008) Inter- and intraspecific community structure within the diatom genus Pseudo-nitzschia (Bacillariophyceae). J Phycol 44:637–649. https://doi.org/10.1111/j.1529-8817.2008.00518.x
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian Protein Metabolism. Academic Press, New York, pp 21-132.
Kanehisa M, Goto S, Hattori M et al (2006) From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34:D354–D357. https://doi.org/10.1093/nar/gkj102
Kearse M, Moir R, Wilson A et al (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649. https://doi.org/10.1093/bioinformatics/bts199
Keeling PJ, Burki F, Wilcox HM 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:e1001889. https://doi.org/10.1371/journal.pbio.1001889
Kropuenske LR, Mills MM, van Dijken GL et al (2009) Photophysiology in two major Southern Ocean phytoplankton taxa: photoprotection in Phaeocystis antarctica and Fragilariopsis cylindrus. Limnol Oceanogr 54:1176–1196. https://doi.org/10.4319/lo.2009.54.4.1176
Kustka AB, Allen AE, Morel FMM (2007) Sequence analysis and transcriptional regulation of iron acquisition genes in two marine diatoms. J. Phycol. 43:715–729. https://doi.org/10.1111/j.1529-8817.2007.00359.x
La Roche J, Boyd PW, McKay RML, Geider RJ (1996) Flavodoxin as an in situ marker for iron stress in phytoplankton. Nature 382:802–805
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923
Li B, Ruotti V, Stewart RM et al (2009) RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 26:493–500. https://doi.org/10.1093/bioinformatics/btp692
Lis H, Shaked Y, Kranzler C et al (2015) Iron bioavailability to phytoplankton: an empirical approach. ISME J 9:1003–1013. https://doi.org/10.1038/ismej.2014.199
Lommer M, Specht M, Roy AS et al (2012) Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation. Genome Biol 13:R66. https://doi.org/10.1186/gb-2012-13-7-r66
MacIntyre HL, Cullen JJ (2005) Using cultures to investigate the physiological ecology of microalgae. In: Andersen RA (ed) Algal Culturuing Techniques. Academic Press, New York, pp 287–326
Maldonado MT, Allen AE, Chong JS et al (2006) Copper-dependent iron transport in coastal and oceanic diatoms. Limnol Oceanogr 51:1729–1743. https://doi.org/10.4319/lo.2006.51.4.1729
Marchetti A, Harrison PJ (2007) Coupled changes in the cell morphology and the elemental (C, N, and Si) composition of the pennate diatom Pseudo-nitzschia due to iron deficiency. Limnol Oceanogr 52:2270–2284
Marchetti A, Maldonado MT (2016) Iron. In: Borowitzka MA et al (eds) Developments in applied phycology. Springer, Switzerland, pp 233–279
Marchetti A, Parker MS, Moccia LP et al (2009) Ferritin is used for iron storage in bloom-forming marine pennate diatoms. Nature 457:467–470. https://doi.org/10.1038/nature07539
Marchetti A, Schruth DM, Durkin CA et al (2012) Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. Proc Natl Acad Sci USA 109:E317–E325. https://doi.org/10.1073/pnas.1118408109
Marchetti A, Catlett D, Hopkinson BM et al (2015) Marine diatom proteorhodopsins and their potential role in coping with low iron availability. ISME J 9:1–4. https://doi.org/10.1038/ismej.2015.74
Martin JH (1990) Glacial-interglacial CO2 change: the iron hypothesis. Paleoceanography 5:1–13. https://doi.org/10.1029/pa005i001p00001
Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12:671–682. https://doi.org/10.1038/nrg3068
Medlin L, Elwood HJ, Stickel S, Sogin ML (1988) The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene 71:491–499. https://doi.org/10.1016/0378-1119(88)90066-2
Mock T, Otillar RP, Strauss J et al (2017) Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature Lett 541:536–540. https://doi.org/10.1038/nature20803
Montes-Hugo M, Martinson D, Ducklow HW et al (2009) Recent changes in phytoplankton communities associated with rapid regional climate change along Western Antarctic Peninsula. Science 323:1470–1473. https://doi.org/10.1126/science.1164533
Moore JK, Abbott MR (2000) Phytoplankton chlorophyll distributions and primary production in the Southern Ocean. J Geophys Res 105:28709. https://doi.org/10.1029/1999JC000043
Moriya Y, Itoh M, Okuda S et al (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:182–185. https://doi.org/10.1093/nar/gkm321
Morrissey J, Bowler C (2012) Iron utilization in marine cyanobacteria and eukaryotic algae. Front Microbiol 3:1–13. https://doi.org/10.3389/fmicb.2012.00043
Morrissey J, Sutak R, Paz-Yepes J et al (2015) A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake. Curr Biol 25:364–371. https://doi.org/10.1016/j.cub.2014.12.004
Mortazavi A, Williams BA, McCue K et al (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628. https://doi.org/10.1038/nmeth.1226
Nawrocki WJ, Tourasse NJ, Taly A et al (2014) The plastid terminal oxidase: its elusive function points to multiple contributions to plastid physiology. Annu Rev Plant Biol 66:150112150216002. https://doi.org/10.1146/annurev-arplant-043014-114744
Oshlack A, Wakefield M (2009) Transcript length bias in RNA-seq data confounds systems biology. Biol Direct 4:14. https://doi.org/10.1186/1745-6150-4-14
Pankowski A, Mcminn A (2008) Iron availability regulates growth, photosynthesis, and production of ferredoxin and flavodoxin in Antarctic sea ice diatoms. Aquat Biol 4:273–288. https://doi.org/10.3354/ab00116
Peers G, Price NM (2006) Copper-containing plastocyanin used for electron transport by an oceanic diatom. Nature 441:341–344. https://doi.org/10.1038/nature04630
Peters E, Thomas DN (1996) Prolonged darkness and diatom mortality I: marine antarctic species. J Exp Mar Bio Ecol 207:25–41. https://doi.org/10.1016/S0022-0981(96)02520-8
Petrou K, Trimborn S, Rost B et al (2014) The impact of iron limitation on the physiology of the Antarctic diatom Chaetoceros simplex. Mar Biol 161:925–937. https://doi.org/10.1007/s00227-014-2392-z
Raven JA (1990) Predictions of Mn and Fe use efficiencies of phototrophic growth as a function of light availability for growth and of C assimilation pathway. New Phytol 116:1–18. https://doi.org/10.1111/j.1469-8137.1990.tb00505.x
Raven JA (2013) Iron acquisition and allocation in stramenopile algae. J Exp Bot 64:2119–2127. https://doi.org/10.1093/jxb/ert121
Raven JA, Evans MCW, Korb RE (1999) The role of trace metals in photosynthetic electron transport in O2-evolving organisms. Photosynth Res 60:111–149. https://doi.org/10.1023/a:1006282714942
Richardson TL, Cullen JJ (1995) Changes in buoyancy and chemical composition during growth of a coastal marine diatom: ecological and biogeochemical consequences. Mar Ecol Prog Ser 128:77–90. https://doi.org/10.3354/meps128077
Saba GK, Fraser WR, Saba VS et al (2014) Winter and spring controls on the summer food web of the coastal West Antarctic Peninsula. Nature Comm 5:4318. https://doi.org/10.1038/ncomms
Sallée J-B, Speer KG, Rintoul SR (2010) Zonally asymmetric response of the Southern Ocean mixed-layer depth to the Southern Annular Mode. Nat Geosci 3:273–279. https://doi.org/10.1038/ngeo812
Schrader PS, Milligan AJ, Behrenfeld MJ (2011) Surplus photosynthetic antennae complexes underlie diagnostics of iron limitation in a cyanobacterium. PLoS ONE. https://doi.org/10.1371/journal.pone.0018753
Simão FA, Waterhouse RM, Ioannidis P et al (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212. https://doi.org/10.1093/bioinformatics/btv351
Smetacek V, Klaas C, Strass VH et al (2012) Deep carbon export from a Southern Ocean iron-fertilized diatom bloom. Nature 487:313–319. https://doi.org/10.1038/nature11229
Smith WOJR, Ainley DG, Arrigo KR (2014) The oceanography and ecology of the Ross Sea. Ann Rev Mar Sci 6:469–487. https://doi.org/10.1146/annurev-marine-010213-135114
Strzepek RF, Harrison PJ (2004) Photosynthetic architecture differs in coastal and oceanic diatoms. Nature 431:689–692. https://doi.org/10.1038/nature02954
Strzepek RF, Maldonado MT, Hunter KA et al (2011) Adaptive strategies by Southern Ocean phytoplankton to lessen iron limitation: uptake of organically complexed iron and reduced cellular iron requirements. Limnol Oceanogr 56:1983–2002. https://doi.org/10.4319/lo.2011.56.6.1983
Strzepek RF, Hunter KA, Frew RD et al (2012) Iron-light interactions differ in Southern Ocean phytoplankton. Limnol Oceanogr 57:1182–1200. https://doi.org/10.4319/lo.2012.57.4.1182
Suggett DJ, Moore CM, Hickman AE, Geider RJ (2009) Interpretation of fast repetition rate (FRR) fluorescence: signatures of phytoplankton community structure versus physiological state. Mar Ecol Prog Ser 376:1–19. https://doi.org/10.3354/meps07830
Sunda WG, Huntsman SA (1995) Iron uptake and growth limitation in oceanic and coastal phytoplankton. Mar Chem 50:189–206. https://doi.org/10.1016/0304-4203(95)00035-P
Sunda WG, Huntsman SA (1997) Interrelated influence of iron, light and cell size on marine phytoplankton growth. Nature 390:389–392. https://doi.org/10.1038/37093
Timmermans KR, Davey MS, Van der Wagt B et al (2001) Co-limitation by iron and light of Chaetoceros brevis, C. dichaeta and C. calcitrans (Bacillariophyceae). Mar Ecol Prog Ser 217:287–297. https://doi.org/10.3354/meps217287
Timmermans KR, Van Der Wagt B, de Baar HJW (2004) Growth rates, half saturation constants, and silicate, nitrate, and phosphate depletion in relation to iron availability of four large open-ocean diatoms from the Southern Ocean. Limnol Oceanogr 49:2141–2151. https://doi.org/10.4319/lo.2004.49.6.2141
van Oijen T, van Leeuwe MA, Gieskes WW, de Baar HJ (2004) Effects of iron limitation on photosynthesis and carbohydrate metabolism in the Antarctic diatom Chaetoceros brevis (Bacillariophyceae). Eur J Phycol 39:161–171. https://doi.org/10.1080/0967026042000202127
Venables HJ, Clarke A, Meredith MP (2013) Wintertime controls on summer stratification and productivity at the western Antarctic Peninsula. Limnol Oceanogr 58:1035–1047. https://doi.org/10.4319/lo.2013.58.3.1035
Yoshida K, Terashima I, Noguchi K (2007) Up-regulation of mitochondrial alternative oxidase concomitant with chloroplast over-reduction by excess light. Plant Cell Physiol 48:606–614. https://doi.org/10.1093/pcp/pcm033
Acknowledgements
This study was funded by the National Science Foundation Grant PLR1341479 awarded to AM, and NSF Grant OPP1043339 to NC. MMETSP was funded in part by the Gordon and Betty Moore Foundation through Grant 2637 to the National Center for Genome Resources. CMM was primarily supported by a Gates Millennium Fellowship. We thank S. Nelson and J. Benjamin for assistance with diatom culturing, M. Kanke and J. Kim for scripting assistance, and B. MacGregor and W. Sunda for helpful comments on the manuscript.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Moreno, C.M., Lin, Y., Davies, S. et al. Examination of gene repertoires and physiological responses to iron and light limitation in Southern Ocean diatoms. Polar Biol 41, 679–696 (2018). https://doi.org/10.1007/s00300-017-2228-7
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00300-017-2228-7