Coastal upwelling regions are among the most productive marine ecosystems but may be threatened by amplified ocean acidification. Increased acidification is hypothesized to reduce iron bioavailability for phytoplankton thereby expanding iron limitation and impacting primary production. Here we show from community to molecular levels that phytoplankton in an upwelling region respond to short-term acidification exposure with iron uptake pathways and strategies that reduce cellular iron demand. A combined physiological and multi-omics approach was applied to trace metal clean incubations that introduced 1200 ppm CO2 for up to four days. Although variable, molecular-level responses indicate a prioritization of iron uptake pathways that are less hindered by acidification and reductions in iron utilization. Growth, nutrient uptake, and community compositions remained largely unaffected suggesting that these mechanisms may confer short-term resistance to acidification; however, we speculate that cellular iron demand is only temporarily satisfied, and longer-term acidification exposure without increased iron inputs may result in increased iron stress.

Biology Centre Institute of Parasitology Czech Academy of Sciences 370 05 České Budějovice CZ Czechia

Department of Biology and Institute for Comparative Genomics Dalhousie University 1355 Oxford St Halifax NS B3H 4R2 Canada

Faculty of Science University of South Bohemia 370 05 České Budějovice CZ Czechia

Geosciences Research Division Scripps Institution of Oceanography University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA

Integrative Oceanography Division Scripps Institution of Oceanography University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA

Microbial and Environmental Genomics J Craig Venter Institute 4120 Capricorn Lane La Jolla CA 92037 USA

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Joos F, Spahni R. Rates of change in natural and anthropogenic radiative forcing over the past 20,000 years. Proc. Natl. Acad. Sci. USA. 2008;105:1425–1430. doi: 10.1073/pnas.0707386105. PubMed DOI PMC

Keeling, C. D. et al. in A history of atmospheric CO2and its effects on plants, animals, and ecosystems 83-113 (Springer, 2005).

Tripati AK, Roberts CD, Eagle RA. Coupling of CO2 and Ice Sheet Stability Over Major Climate Transitions of the Last 20 Million Years. Science. 2009;326:1394–1397. doi: 10.1126/science.1178296. PubMed DOI

Gruber N, et al. The oceanic sink for anthropogenic CO2 from 1994 to 2007. Science. 2019;363:1193–1199. doi: 10.1126/science.aau5153. PubMed DOI

Capone DG, Hutchins DA. Microbial biogeochemistry of coastal upwelling regimes in a changing ocean. Nat. Geosci. 2013;6:711–717. doi: 10.1038/ngeo1916. DOI

Leinweber A, Gruber N. Variability and trends of ocean acidification in the Southern California Current System: A time series from Santa Monica Bay. J. Geophys. Res. Oceans. 2013;118:3622–3633. doi: 10.1002/jgrc.20259. DOI

Hauri C, et al. Spatiotemporal variability and long-term trends of ocean acidification in the California Current System. Biogeosciences. 2013;10:193–216. doi: 10.5194/bg-10-193-2013. DOI

Feely RA, Sabine CL, Hernandez-Ayon JM, Ianson D, Hales B. Evidence for upwelling of corrosive “Acidified” water onto the continental shelf. Science. 2008;320:1490–1492. doi: 10.1126/science.1155676. PubMed DOI

Osborne EB, Thunell RC, Gruber N, Feely RA, Benitez-Nelson CR. Decadal variability in twentieth-century ocean acidification in the California Current Ecosystem. Nat. Geosci. 2020;13:43–49. doi: 10.1038/s41561-019-0499-z. DOI

Mackey KRM, Morris JJ, Morel FMM, Kranz SA. Response of photosynthesis to ocean acidification. Oceanography. 2015;28:74–91. doi: 10.5670/oceanog.2015.33. DOI

Bach LT, Taucher J. CO2 effects on diatoms: a synthesis of more than a decade of ocean acidification experiments with natural communities. Ocean Sci. 2019;15:1159–1175. doi: 10.5194/os-15-1159-2019. DOI

Hutchins D, et al. Phytoplankton iron limitation in the Humboldt Current and Peru Upwelling. Limnol. Oceanogr. 2002;47:997–1011. doi: 10.4319/lo.2002.47.4.0997. DOI

Bruland KW, Rue EL, Smith GJ. Iron and macronutrients in California coastal upwelling regimes: Implications for diatom blooms. Limnol. Oceanogr. 2001;46:1661–1674. doi: 10.4319/lo.2001.46.7.1661. DOI

Till CP, et al. The iron limitation mosaic in the California Current System: Factors governing Fe availability in the shelf/near-shelf region. Limnol. Oceanogr. 2019;64:109–123. doi: 10.1002/lno.11022. DOI

Moore CM, et al. Processes and patterns of oceanic nutrient limitation. Nat. Geosci. 2013;6:701–710. doi: 10.1038/ngeo1765. DOI

Hutchins DA, Boyd PW. Marine phytoplankton and the changing ocean iron cycle. Nat. Clim. Change. 2016;6:1072. doi: 10.1038/nclimate3147. DOI

Shi D, Xu Y, Hopkinson BM, Morel FMM. Effect of Ocean Acidification on Iron Availability to Marine Phytoplankton. Science. 2010;327:676–679. doi: 10.1126/science.1183517. PubMed DOI

McQuaid JB, et al. Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms. Nature. 2018;555:534. doi: 10.1038/nature25982. PubMed DOI

Boyd PW, et al. Why are biotic iron pools uniform across high- and low-iron pelagic ecosystems? Glob. Biogeochem. Cycles. 2015;29:1028–1043. doi: 10.1002/2014GB005014. DOI

Avendaño, L., Gledhill, M., Achterberg, E. P., Rérolle, V. M. C. & Schlosser, C. Influence of ocean acidification on the organic complexation of iron and copper in Northwest European Shelf Seas; a Combined Observational and Model Study. Front. Mar. Sci.3, 58 (2016).

Gledhill M, van den Berg CMG, Nolting RF, Timmermans KR. Variability in the speciation of iron in the northern North Sea. Mar. Chem. 1998;59:283–300. doi: 10.1016/S0304-4203(97)00097-2. DOI

Stockdale A, Tipping E, Lofts S, Mortimer RJG. Effect of ocean acidification on organic and inorganic speciation of trace metals. Environ. Sci. Technol. 2016;50:1906–1913. doi: 10.1021/acs.est.5b05624. PubMed DOI

Gledhill M, Achterberg EP, Li K, Mohamed KN, Rijkenberg MJA. Influence of ocean acidification on the complexation of iron and copper by organic ligands in estuarine waters. Mar. Chem. 2015;177:421–433. doi: 10.1016/j.marchem.2015.03.016. DOI

Zhu K, et al. Influence of pH and dissolved organic matter on iron speciation and apparent iron solubility in the peruvian shelf and slope region. Environ. Sci. Technol. 2021;55:9372–9383. doi: 10.1021/acs.est.1c02477. PubMed DOI

Breitbarth E, et al. Ocean acidification affects iron speciation during a coastal seawater mesocosm experiment. Biogeosciences. 2010;7:1065–1073. doi: 10.5194/bg-7-1065-2010. DOI

Lorenzo MR, Segovia M, Cullen JT, Maldonado MT. Particulate trace metal dynamics in response to increased CO2 and iron availability in a coastal mesocosm experiment. Biogeosciences. 2020;17:757–770. doi: 10.5194/bg-17-757-2020. DOI

Sugie K, et al. Synergistic effects of pCO2 and iron availability on nutrient consumption ratio of the Bering Sea phytoplankton community. Biogeosciences. 2013;10:6309–6321. doi: 10.5194/bg-10-6309-2013. DOI

Endo H, Sugie K, Yoshimura T, Suzuki K. Effects of CO2 and iron availability on rbcL gene expression in Bering Sea diatoms. Biogeosciences. 2015;12:2247–2259. doi: 10.5194/bg-12-2247-2015. DOI

Trimborn S, et al. Iron sources alter the response of Southern Ocean phytoplankton to ocean acidification. Mar. Ecol. Prog. Ser. 2017;578:35–50. doi: 10.3354/meps12250. DOI

Pausch, F. et al. Responses of a natural phytoplankton community from the drake passage to two predicted climate change scenarios. Front. Mar. Sci.9, 759501 (2022).

Endo H, Yoshimura T, Kataoka T, Suzuki K. Effects of CO2 and iron availability on phytoplankton and eubacterial community compositions in the northwest subarctic Pacific. J. Exp. Mar. Biol. Ecol. 2013;439:160–175. doi: 10.1016/j.jembe.2012.11.003. DOI

Yoshimura T, et al. Impacts of elevated CO2 on particulate and dissolved organic matter production: microcosm experiments using iron-deficient plankton communities in open subarctic waters. J. Oceanogr. 2013;69:601–618. doi: 10.1007/s10872-013-0196-2. DOI

Yoshimura T, et al. Organic matter production response to CO2 increase in open subarctic plankton communities: Comparison of six microcosm experiments under iron-limited and -enriched bloom conditions. Deep Sea Res. Part I: Oceanogr. Res. Pap. 2014;94:1–14. doi: 10.1016/j.dsr.2014.08.004. DOI

Feng Y, et al. Interactive effects of iron, irradiance and CO2 on Ross Sea phytoplankton. Deep Sea Res. Part I: Oceanogr. Res. Pap. 2010;57:368–383. doi: 10.1016/j.dsr.2009.10.013. DOI

Hopkinson BM, Xu Y, Shi D, McGinn PJ, Morel FMM. The effect of CO2 on the photosynthetic physiology of phytoplankton in the Gulf of Alaska. Limnol. Oceanogr. 2010;55:2011–2024. doi: 10.4319/lo.2010.55.5.2011. DOI

Chen, M., Wang, W.-X. & Guo, L. Phase partitioning and solubility of iron in natural seawater controlled by dissolved organic matter. Global Biogeochem. Cycles18, GB4013 (2004).

Mausz MA, et al. High CO2 concentration and iron availability determine the metabolic inventory in an Emiliania huxleyi-dominated phytoplankton community. Environ. Microbiol. 2020;22:3863–3882. doi: 10.1111/1462-2920.15160. PubMed DOI

Segovia M, et al. Iron availability modulates the effects of future CO2 levels within the marine planktonic food web. Mar. Ecol. Prog. Ser. 2017;565:17–33. doi: 10.3354/meps12025. DOI

Hoppe CJM, et al. Iron limitation modulates ocean acidification effects on southern ocean phytoplankton communities. PLOS ONE. 2013;8:e79890. doi: 10.1371/journal.pone.0079890. PubMed DOI PMC

Borer PM, Sulzberger B, Reichard P, Kraemer SM. Effect of siderophores on the light-induced dissolution of colloidal iron (III) (hydr)oxides. Mar. Chem. 2005;93:179–193. doi: 10.1016/j.marchem.2004.08.006. DOI

Tortell PD, Reinfelder JR, Morel FMM. Active uptake of bicarbonate by diatoms. Nature. 1997;390:243–244. doi: 10.1038/36765. PubMed DOI

Tortell PD, Rau GH, Morel FMM. Inorganic carbon acquisition in coastal Pacific phytoplankton communities. Limnol. Oceanogr. 2000;45:1485–1500. doi: 10.4319/lo.2000.45.7.1485. DOI

Tortell PD, DiTullio GR, Sigman DM, Morel FMM. CO2 effects on taxonomic composition and nutrient utilization in an Equatorial Pacific phytoplankton assemblage. Mar. Ecol. Prog. Ser. 2002;236:37–43. doi: 10.3354/meps236037. DOI

Osma, N. et al. Response of phytoplankton assemblages from naturally acidic coastal ecosystems to elevated pCO2. Front. Mar. Sci.7, 323 (2020).

Vargas CA, et al. Species-specific responses to ocean acidification should account for local adaptation and adaptive plasticity. Nat. Ecol. Evol. 2017;1:0084. doi: 10.1038/s41559-017-0084. PubMed DOI

Joint I, Doney SC, Karl DM. Will ocean acidification affect marine microbes? ISME J. 2011;5:1–7. doi: 10.1038/ismej.2010.79. PubMed DOI PMC

Valenzuela JJ, et al. Ocean acidification conditions increase resilience of marine diatoms. Nat. Comm. 2018;9:2328. doi: 10.1038/s41467-018-04742-3. PubMed DOI PMC

Beszteri S, Thoms S, Benes V, Harms L, Trimborn S. The response of three Southern Ocean phytoplankton species to ocean acidification and light availability: a transcriptomic study. Protist. 2018;169:958–975. doi: 10.1016/j.protis.2018.08.003. PubMed DOI

Jones BM, et al. Responses of the emiliania huxleyi proteome to ocean acidification. PLOS ONE. 2013;8:e61868. doi: 10.1371/journal.pone.0061868. PubMed DOI PMC

Turi G, Lachkar Z, Gruber N. Spatiotemporal variability and drivers of pCO2 and air–sea CO2 fluxes in the California Current System: an eddy-resolving modeling study. Biogeosciences. 2014;11:671–690. doi: 10.5194/bg-11-671-2014. DOI

Fiechter J, et al. Air‐sea CO2 fluxes in the California Current: Impacts of model resolution and coastal topography. Glob. Biogeochem. Cycles. 2014;28:371–385. doi: 10.1002/2013GB004683. DOI

Bundy RM, Biller DV, Buck KN, Bruland KW, Barbeau KA. Distinct pools of dissolved iron-binding ligands in the surface and benthic boundary layer of the California Current. Limnol. Oceanogr. 2014;59:769–787. doi: 10.4319/lo.2014.59.3.0769. DOI

Hogle SL, et al. Pervasive iron limitation at subsurface chlorophyll maxima of the California Current. Proc. Natl. Acad. Sci. USA. 2018;115:13300–13305. doi: 10.1073/pnas.1813192115. PubMed DOI PMC

Forsch, K. O. et al. Iron limitation and biogeochemical effects in southern California Current coastal upwelling filaments. J. Geophys. Res. Oceans128, e2023JC019961 (2023).

Hutchins DA, Bruland KW. Iron-limited diatom growth and Si:N uptake ratios in a coastal upwelling regime. Nature. 1998;393:561–564. doi: 10.1038/31203. DOI

Wang XJ, Behrenfeld M, Le Borgne R, Murtugudde R, Boss E. Regulation of phytoplankton carbon to chlorophyll ratio by light, nutrients and temperature in the Equatorial Pacific Ocean: a basin-scale model. Biogeosciences. 2009;6:391–404. doi: 10.5194/bg-6-391-2009. DOI

Marchetti, A. & Maldonado, M. T. in The Physiology of Microalgae (eds M. A. Borowitzka, J. Beardall & J. A. Raven) 233-279 (Springer International Publishing, 2016).

Trimborn S, Hoppe CJM, Taylor BB, Bracher A, Hassler C. Physiological characteristics of open ocean and coastal phytoplankton communities of Western Antarctic Peninsula and Drake Passage waters. Deep Sea Res. Part I: Oceanogr. Res. Pap. 2015;98:115–124. doi: 10.1016/j.dsr.2014.12.010. DOI

Maldonado MT, Price NM. Reduction and transport of organically bound iron by Thalassiosira Oceanica (Bacillariophyceae) J. Phycol. 2001;37:298–310. doi: 10.1046/j.1529-8817.2001.037002298.x. DOI

Maldonado MT, Price NM. Utilization of iron bound to strong organic ligands by plankton communities in the subarctic Pacific Ocean. Deep Sea Res. Part II: Topical Stud. Oceanogr. 1999;46:2447–2473. doi: 10.1016/S0967-0645(99)00071-5. DOI

Malviya S, et al. Insights into global diatom distribution and diversity in the world’s ocean. Proc. Natl. Acad. Sci. USA. 2016;113:E1516–E1525. doi: 10.1073/pnas.1509523113. PubMed DOI PMC

James CC, et al. Influence of nutrient supply on plankton microbiome biodiversity and distribution in a coastal upwelling region. Nat. Commun. 2022;13:2448. doi: 10.1038/s41467-022-30139-4. PubMed DOI PMC

Demir-Hilton E, et al. Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus. ISME J. 2011;5:1095–1107. doi: 10.1038/ismej.2010.209. PubMed DOI PMC

Worden AZ, et al. Global distribution of a wild alga revealed by targeted metagenomics. Curr. Biol. 2012;22:R675–R677. doi: 10.1016/j.cub.2012.07.054. PubMed DOI

Dupont CL, et al. Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. ISME J. 2015;9:1076–1092. doi: 10.1038/ismej.2014.198. PubMed DOI PMC

Sunagawa S, et al. Structure and function of the global ocean microbiome. Science. 2015;348:1261359. doi: 10.1126/science.1261359. PubMed DOI

Buchan A, González JM, Moran MA. Overview of the Marine Roseobacter Lineage. Appl. Environ. Microbiol. 2005;71:5665–5677. doi: 10.1128/AEM.71.10.5665-5677.2005. PubMed DOI PMC

Hoarfrost A, et al. Global ecotypes in the ubiquitous marine clade SAR86. ISME J. 2020;14:178–188. doi: 10.1038/s41396-019-0516-7. PubMed DOI PMC

Dutkiewicz S, et al. Impact of ocean acidification on the structure of future phytoplankton communities. Nat. Clim. Change. 2015;5:1002–1006. doi: 10.1038/nclimate2722. DOI

Edvardsen B, et al. Phylogenetic reconstructions of the Haptophyta inferred from 18S ribosomal DNA sequences and available morphological data. Phycologia. 2000;39:19–35. doi: 10.2216/i0031-8884-39-1-19.1. DOI

Kazamia E, et al. Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms. Sci. Adv. 2018;4:eaar4536. doi: 10.1126/sciadv.aar4536. PubMed DOI PMC

Behnke, J. & LaRoche, J. Iron uptake proteins in algae and the role of Iron Starvation-Induced Proteins (ISIPs). Eur. J. Phycol.55, 339–360 (2020).

Cohen NR, et al. Variations in diatom transcriptional responses to changes in iron availability across ocean provinces. Front Mar. Sci. 2017;4:360. doi: 10.3389/fmars.2017.00360. DOI

Smith SR, et al. Transcriptional orchestration of the global cellular response of a model pennate diatom to diel light cycling under iron limitation. PLOS Genet. 2016;12:e1006490. doi: 10.1371/journal.pgen.1006490. PubMed DOI PMC

McCain JSP, Allen AE, Bertrand EM. Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom. ISME J. 2022;16:569–579. doi: 10.1038/s41396-021-01084-9. PubMed DOI PMC

Blaby-Haas CE, Merchant SS. Comparative and functional algal genomics. Annu. Rev. Plant Biol. 2019;70:605–638. doi: 10.1146/annurev-arplant-050718-095841. PubMed DOI

Allen AE, et al. Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation. Proc. Natl Acad. Sci. USA. 2008;105:10438–10443. doi: 10.1073/pnas.0711370105. PubMed DOI PMC

Lommer M, et al. Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation. Genome Biol. 2012;13:R66. doi: 10.1186/gb-2012-13-7-r66. PubMed DOI PMC

Blaby-Haas CE, Merchant SS. The ins and outs of algal metal transport. Biochim Biophys. Acta Mol. Cell Res. 2012;1823:1531–1552. doi: 10.1016/j.bbamcr.2012.04.010. PubMed DOI PMC

Harrison GI, Morel FM. Response of the marine diatom Thalassiosira weissflogii to iron stress. Limnol. Oceanogr. 1986;31:989–997. doi: 10.4319/lo.1986.31.5.0989. DOI

Lampe RH, et al. Different iron storage strategies among bloom-forming diatoms. Proc. Natl. Acad. Sci. USA. 2018;115:E12275–E12284. doi: 10.1073/pnas.1805243115. PubMed DOI PMC

Ibuot A, Dean AP, Pittman JK. Multi-genomic analysis of the cation diffusion facilitator transporters from algae. Metallomics. 2020;12:617–630. doi: 10.1039/d0mt00009d. PubMed DOI

Coale, T. H., Bertrand, E. M., Lampe, R. H. & Allen, A. E. in The Molecular Life of Diatoms (eds A. Falciatore & T. Mock) 567-604 (Springer International Publishing, 2022).

Sutak R, et al. A comparative study of iron uptake mechanisms in marine microalgae: iron binding at the cell surface is a critical step. Plant Physiol. 2012;160:2271–2284. doi: 10.1104/pp.112.204156. PubMed DOI PMC

Kustka AB, Allen AE, Morel FMM. Sequence analysis and transcriptional regulation of iron acquistion gens in two marine diatoms. J. Phycol. 2007;43:715–729. doi: 10.1111/j.1529-8817.2007.00359.x. DOI

Staudenmaier H, Van Hove B, Yaraghi Z, Braun V. Nucleotide sequences of the fecBCDE genes and locations of the proteins suggest a periplasmic-binding-protein-dependent transport mechanism for iron(III) dicitrate in Escherichia coli. J. Bacteriol. 1989;171:2626. doi: 10.1128/jb.171.5.2626-2633.1989. PubMed DOI PMC

Khan AA, Quigley JG. Heme and FLVCR-related transporter families SLC48 and SLC49. Mol. Asp. Med. 2013;34:669–682. doi: 10.1016/j.mam.2012.07.013. PubMed DOI PMC

Hutchins DA, Witter AE, Butler A, Luther GW. Competition among marine phytoplankton for different chelated iron species. Nature. 1999;400:858–861. doi: 10.1038/23680. DOI

Coale TH, et al. Reduction-dependent siderophore assimilation in a model pennate diatom. Proc. Natl. Acad. Sci. USA. 2019;116:23609–23617. doi: 10.1073/pnas.1907234116. PubMed DOI PMC

Behnke J, Cai Y, Gu H, LaRoche J. Short-term response to iron resupply in an iron-limited open ocean diatom reveals rapid decay of iron-responsive transcripts. PLOS ONE. 2023;18:e0280827. doi: 10.1371/journal.pone.0280827. PubMed DOI PMC

Turnšek J, et al. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife. 2021;10:e52770. doi: 10.7554/eLife.52770. PubMed DOI PMC

Paddock ML, et al. MitoNEET is a uniquely folded 2Fe–2S outer mitochondrial membrane protein stabilized by pioglitazone. Proc. Natl. Acad. Sci. 2007;104:14342–14347. doi: 10.1073/pnas.0707189104. PubMed DOI PMC

Urzica EI, et al. Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage. Plant Cell. 2012;24:3921–3948. doi: 10.1105/tpc.112.102491. PubMed DOI PMC

Peers G, Price NM. Copper-containing plastocyanin used for electron transport by an oceanic diatom. Nature. 2006;441:341–344. doi: 10.1038/nature04630. PubMed DOI

Groussman RD, Parker MS, Armbrust EV. Diversity and evolutionary history of iron metabolism genes in diatoms. PLoS ONE. 2015;10:e0129081. doi: 10.1371/journal.pone.0129081. PubMed DOI PMC

Raven JA. The iron and molybdenum use efficiencies of plant growth with different energy, carbon and nitrogen sources. New Phytol. 1988;109:279–287. doi: 10.1111/j.1469-8137.1988.tb04196.x. DOI

Fuster DG, Alexander RT. Traditional and emerging roles for the SLC9 Na+/H+ exchangers. Pflügers Arch. 2014;466:61–76. doi: 10.1007/s00424-013-1408-8. PubMed DOI

Botebol H, et al. Central role for ferritin in the day/night regulation of iron homeostasis in marine phytoplankton. Proc. Natl. Acad. Sci. USA. 2015;112:14652–14657. doi: 10.1073/pnas.1506074112. PubMed DOI PMC

Matsuda Y, Hopkinson BM, Nakajima K, Dupont CL, Tsuji Y. Mechanisms of carbon dioxide acquisition and CO2 sensing in marine diatoms: a gateway to carbon metabolism. Philos. Trans. R. Soc. Lond. B. 2017;372:20160403. doi: 10.1098/rstb.2016.0403. PubMed DOI PMC

Morel, F. M. M., Lam, P. J. & Saito, M. A. Trace metal substitution in marine phytoplankton. Ann. Rev. Earth Planet. Sci.48, 491–517 (2020).

Samukawa M, Shen C, Hopkinson BM, Matsuda Y. Localization of putative carbonic anhydrases in the marine diatom, Thalassiosira pseudonana. Photosynth Res. 2014;121:235–249. doi: 10.1007/s11120-014-9967-x. PubMed DOI

Jensen EL, Clement R, Kosta A, Maberly SC, Gontero B. A new widespread subclass of carbonic anhydrase in marine phytoplankton. ISME J. 2019;13:2094–2106. doi: 10.1038/s41396-019-0426-8. PubMed DOI PMC

Hennon GMM, et al. Diatom acclimation to elevated CO2 via cAMP signalling and coordinated gene expression. Nat. Clim. Change. 2015;5:761–765. doi: 10.1038/nclimate2683. DOI

Crawfurd KJ, Raven JA, Wheeler GL, Baxter EJ, Joint I. The Response of Thalassiosira pseudonana to long-term exposure to increased CO2 and decreased pH. PLOS ONE. 2011;6:e26695. doi: 10.1371/journal.pone.0026695. PubMed DOI PMC

Nakajima K, Tanaka A, Matsuda Y. SLC4 family transporters in a marine diatom directly pump bicarbonate from seawater. Proc. Natl. Acad. Sci. USA. 2013;110:1767–1772. doi: 10.1073/pnas.1216234110. PubMed DOI PMC

Shaked Y, Buck KN, Mellett T, Maldonado MT. Insights into the bioavailability of oceanic dissolved Fe from phytoplankton uptake kinetics. ISME J. 2020;14:1182–1193. doi: 10.1038/s41396-020-0597-3. PubMed DOI PMC

Boyd PW, Lennartz ST, Glover DM, Doney SC. Biological ramifications of climate-change-mediated oceanic multi-stressors. Nat. Clim. Change. 2014;5:71. doi: 10.1038/nclimate2441. DOI

Chrachri A, Hopkinson BM, Flynn K, Brownlee C, Wheeler GL. Dynamic changes in carbonate chemistry in the microenvironment around single marine phytoplankton cells. Nat. Comm. 2018;9:74. doi: 10.1038/s41467-017-02426-y. PubMed DOI PMC

Shen C, Hopkinson BM. Size scaling of extracellular carbonic anhydrase activity in centric marine diatoms. J. Phycol. 2015;51:255–263. doi: 10.1111/jpy.12269. PubMed DOI

Riebesell U, et al. Enhanced biological carbon consumption in a high CO2 ocean. Nature. 2007;450:545–548. doi: 10.1038/nature06267. PubMed DOI

Hurd CL, et al. Ocean acidification as a multiple driver: how interactions between changing seawater carbonate parameters affect marine life. Mar. Freshw. Res. 2020;71:263–274. doi: 10.1071/MF19267. DOI

Scheffer M, et al. Early-warning signals for critical transitions. Nature. 2009;461:53–59. doi: 10.1038/nature08227. PubMed DOI

Sunda, W. G., Price, N. M. & Morel, F. M. Algal Culturing Techniques4, 35–63 (2005).

Hunter JD. Matplotlib: A 2D graphics environment. Comput Sci. Eng. 2007;9:90–95. doi: 10.1109/MCSE.2007.55. DOI

Dickson, A. G., Sabine, C. L. & Christian, J. R. Guide to best practices for ocean CO2measurements. (North Pacific Marine Science Organization, 2007).

Lewis, E. & Wallace, D. Program developed for CO2 system calculations. (Environmental System Science Data Infrastructure for a Virtual Ecosystem, 1998).

Mehrbach C, Culberson C, Hawley J, Pytkowicx R. Measurement of the apparent dissociation constants of carbonic acid in seawater at atmospheric pressure 1. Limnol. Oceanogr. 1973;18:897–907. doi: 10.4319/lo.1973.18.6.0897. DOI

Dickson A, Millero FJ. A comparison of the equilibrium constants for the dissociation of carbonic acid in seawater media. Deep Sea Res. Part A. Oceanogr. Res. Pap. 1987;34:1733–1743. doi: 10.1016/0198-0149(87)90021-5. DOI

Dickson AG. Thermodynamics of the dissociation of boric acid in synthetic seawater from 273.15 to 318.15 K. Deep Sea Res. Part A. Oceanogr. Res. Pap. 1990;37:755–766. doi: 10.1016/0198-0149(90)90004-F. DOI

Uppstrom L. The boron/chlorinity ratio of deep-sea water from the Pacific Ocean. Deep Sea Res. 1974;21:161–162.

Lohan MC, Aguilar-Islas AM, Bruland KW. Direct determination of iron in acidified (pH 1.7) seawater samples by flow injection analysis with catalytic spectrophotometric detection: Application and intercomparison. Limnol. Oceanogr.-Meth. 2006;4:164–171. doi: 10.4319/lom.2006.4.164. DOI

King, A. L. & Barbeau, K. A. Dissolved iron and macronutrient distributions in the southern California Current System. J. Geophys. Res. Oceans116, C03018 (2011).

Stukel MR, Ohman MD, Benitez-Nelson CR, Landry MR. Contributions of mesozooplankton to vertical carbon export in a coastal upwelling system. Mar. Ecol. Prog. Ser. 2013;491:47–65. doi: 10.3354/meps10453. DOI

Tang D, Morel FMM. Distinguishing between cellular and Fe-oxide-associated trace elements in phytoplankton. Mar. Chem. 2006;98:18–30. doi: 10.1016/j.marchem.2005.06.003. DOI

Parada AE, Needham DM, Fuhrman JA. Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples. Environ. Microbiol. 2016;18:1403–1414. doi: 10.1111/1462-2920.13023. PubMed DOI

Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM. A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLOS ONE. 2009;4:e6372. doi: 10.1371/journal.pone.0006372. PubMed DOI PMC

Bolyen E, et al. Reproducible, interactive, scalable, and extensible microbiome data science using QIIME 2. Nat. Biotechnol. 2019;37:852–857. doi: 10.1038/s41587-019-0209-9. PubMed DOI PMC

Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal; Vol 17, No 1: Next Generation Sequencing Data Analysis (2011).

Callahan BJ, et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods. 2016;13:581–583. doi: 10.1038/nmeth.3869. PubMed DOI PMC

Pedregosa F, et al. Scikit-learn: Machine learning in Python. J. Mach. Learn. Res. 2011;12:2825–2830.

Bokulich NA, et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin. Microbiome. 2018;6:90. doi: 10.1186/s40168-018-0470-z. PubMed DOI PMC

Pruesse E, et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007;35:7188–7196. doi: 10.1093/nar/gkm864. PubMed DOI PMC

Guillou L, et al. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 2012;41:D597–D604. doi: 10.1093/nar/gks1160. PubMed DOI PMC

Kruskal WH, Wallis WA. Use of ranks in one-criterion variance analysis. J. Am. Stat. Assoc. 1952;47:583–621. doi: 10.1080/01621459.1952.10483441. DOI

Anderson MJ. A new method for non‐parametric multivariate analysis of variance. Austral Ecol. 2001;26:32–46.

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. doi: 10.1186/s13059-014-0550-8. PubMed DOI PMC

McMurdie PJ, Holmes S. Waste not, want not: Why rarefying microbiome data is inadmissible. PLOS Comput. Biol. 2014;10:e1003531. doi: 10.1371/journal.pcbi.1003531. PubMed DOI PMC

Weiss S, et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017;5:27. doi: 10.1186/s40168-017-0237-y. PubMed DOI PMC

Benjamini Y, Hochberg Y. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. B. 1995;57:289–300.

Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. PubMed DOI PMC

Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016;32:3047–3048. doi: 10.1093/bioinformatics/btw354. PubMed DOI PMC

Grabherr MG, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotech. 2011;29:644–652. doi: 10.1038/nbt.1883. PubMed DOI PMC

Robertson G, et al. De novo assembly and analysis of RNA-seq data. Nat. Meth. 2010;7:909–912. doi: 10.1038/nmeth.1517. PubMed DOI

Tang S, Lomsadze A, Borodovsky M. Identification of protein coding regions in RNA transcripts. Nucleic Acids Res. 2015;43:e78. doi: 10.1093/nar/gkv227. PubMed DOI PMC

Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–3217. doi: 10.1093/bioinformatics/bts611. PubMed DOI

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat. Meth. 2012;9:357–359. doi: 10.1038/nmeth.1923. PubMed DOI PMC

Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat. Methods. 2015;12:59–60. doi: 10.1038/nmeth.3176. PubMed DOI

Bertrand EM, et al. Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge. Proc. Natl. Acad. Sci. USA. 2015;112:9938–9943. doi: 10.1073/pnas.1501615112. PubMed DOI PMC

Podell S, Gaasterland T. DarkHorse: a method for genome-wide prediction of horizontal gene transfer. Genome Biol. 2007;8:R16. doi: 10.1186/gb-2007-8-2-r16. PubMed DOI PMC

Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol. 2019;20:238. doi: 10.1186/s13059-019-1832-y. PubMed DOI PMC

Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 2017;45:D353–D361. doi: 10.1093/nar/gkw1092. PubMed DOI PMC

Aramaki T, et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2019;36:2251–2252. doi: 10.1093/bioinformatics/btz859. PubMed DOI PMC

Cohen, N. R., Alexander, H., Krinos, A. I., Hu, S. K. & Lampe, R. H. Marine microeukaryote metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications. Front. Mar. Sci.9, 867007 (2022).

Saito MA, Bulygin VV, Moran DM, Taylor C, Scholin C. Examination of microbial proteome preservation techniques applicable to autonomous environmental sample collection. Front Microbiol. 2011;2:215–215. doi: 10.3389/fmicb.2011.00215. PubMed DOI PMC

Cruaud P, et al. Open the SterivexTM casing: An easy and effective way to improve DNA extraction yields. Limnol. Oceanogr.-Meth. 2017;15:1015–1020. doi: 10.1002/lom3.10221. DOI

Hulstaert N, et al. ThermoRawFileParser: modular, scalable, and cross-platform RAW file conversion. J. Proteome Res. 2019;19:537–542. doi: 10.1021/acs.jproteome.9b00328. PubMed DOI PMC

Kim S, Pevzner PA. MS-GF+ makes progress towards a universal database search tool for proteomics. Nat. Comm. 2014;5:1–10. doi: 10.1038/ncomms6277. PubMed DOI PMC

Röst HL, et al. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat. Methods. 2016;13:741–748. doi: 10.1038/nmeth.3959. PubMed DOI

Weisser H, Choudhary JS. Targeted feature detection for data-dependent shotgun proteomics. J. Proteome Res. 2017;16:2964–2974. doi: 10.1021/acs.jproteome.7b00248. PubMed DOI PMC

Langley SR, Mayr M. Comparative analysis of statistical methods used for detecting differential expression in label-free mass spectrometry proteomics. J. Proteom. 2015;129:83–92. doi: 10.1016/j.jprot.2015.07.012. PubMed DOI

Keeling PJ, et al. The marine microbial eukaryote transcriptome sequencing project (MMETSP): Illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing. PLOS Biol. 2014;12:e1001889. doi: 10.1371/journal.pbio.1001889. PubMed DOI PMC

Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007;35:D61–D65. doi: 10.1093/nar/gkl842. PubMed DOI PMC

Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–2461. doi: 10.1093/bioinformatics/btq461. PubMed DOI

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 2013;30:772–780. doi: 10.1093/molbev/mst010. PubMed DOI PMC

Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–1973. doi: 10.1093/bioinformatics/btp348. PubMed DOI PMC

Gouy M, Guindon S, Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 2010;27:221–224. doi: 10.1093/molbev/msp259. PubMed DOI

Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods. 2017;14:587–589. doi: 10.1038/nmeth.4285. PubMed DOI PMC

Minh BQ, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 2020;37:1530–1534. doi: 10.1093/molbev/msaa015. PubMed DOI PMC

Perez-Riverol Y, et al. The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res. 2019;47:D442–D450. doi: 10.1093/nar/gky1106. PubMed DOI PMC