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The Pelagic Light-Dependent Microbiome

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The Marine Microbiome

Part of the book series: The Microbiomes of Humans, Animals, Plants, and the Environment ((MHAPE,volume 3))

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Abstract

The pelagic sunlit zone or euphotic zone is defined as the lit surface of the ocean down to a depth where enough light penetrates to allow photosynthesis. Typically, the depth at which photosynthesis still exceeds respiration coincides with the depth at which the light intensity is attenuated to 1% of the sea surface irradiance. The composition of the light-dependent pelagic microbiome is both a function of light availability and spectral quality, as well as the strength of the water column stratification relative to turbulent mixing. Solar radiation provides the energy source for the pelagic light-dependent microbiome. However, additional environmental factors affecting the surface layer of the ocean make this environment spatially and temporally variable. Latitude has a combined effect on photoperiod, seasonal light levels, and temperature regimes. Overall, the microbiome inhabiting the euphotic zone in the ocean is adapted to steep gradients in light, temperature, salinity, and nutrient concentrations that can occur on local spatial scales. The three main categories of microorganisms that conserve energy from sunlight are the cyanobacteria and eukaryotic microalgae who carry out oxygenic photosynthesis, the aerobic anoxygenic photosynthetic bacteria (AAnPB) that perform photoheterotrophy, and proteorhodopsin-containing bacteria which synthesize ATP via a light-driven proton pump. Organisms within all three groups are taxonomically diverse and are adapted to cope with rapidly changing environmental conditions. Although the energy flow through the euphotic zone is controlled by primary producers that carry out carbon fixation via oxygenic photosynthesis, the microbiome in this layer of the ocean is additionally composed of heterotrophic, mixotrophic, and symbiotic microorganisms who interact with primary producers either in a predatory role or as nutrient recyclers.

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References

  • Aguirre LE, Ouyang L, Elfwing A, Hedblom M, Wulff A, Inganäs O (2018) Diatom frustules protect DNA from ultraviolet light. Sci Rep 8:1–6

    Article  CAS  Google Scholar 

  • Agusti S, González-Gordillo JI, Vaqué D, Estrada M, Cerezo MI, Salazar G et al (2015) Ubiquitous healthy diatoms in the deep sea confirm deep carbon injection by the biological pump. Nat Commun 6:1–8

    Article  CAS  Google Scholar 

  • Allen AE, LaRoche J, Maheswari U, Lommer M, Schauer N, Lopez PJ et al (2008) Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation. Proc Natl Acad Sci U S A 105:10438–10443

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bais AF, Bernhard G, McKenzie RL, Aucamp PJ, Young PJ, Ilyas M et al (2019) Ozone-climate interactions and effects on solar ultraviolet radiation. Photochem Photobiol Sci 18:602–640

    Article  CAS  PubMed  Google Scholar 

  • Bais AF, McKenzie RL, Bernhard G, Aucamp PJ, Ilyas M, Madronich S et al (2015) Ozone depletion and climate change: impacts on UV radiation. Photochem Photobiol Sci 14:19–52

    Article  CAS  PubMed  Google Scholar 

  • Baldry K, Strutton PG, Hill NA, Boyd PW (2020) Subsurface chlorophyll-a maxima in the Southern Ocean. Front Mar Sci 7:671

    Article  Google Scholar 

  • Bar-On YM, Phillips R, Milo R (2018) The biomass distribution on earth. Proc Natl Acad Sci U S A 115:6506–6511

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bebout BM, Garcia-Pichel F (1995) UV B-induced vertical migrations of cyanobacteria in a microbial mat. Appl Environ Microbiol 61:4215–4222

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Becker JW, Hogle SL, Rosendo K, Chisholm SW (2019) Co-culture and biogeography of Prochlorococcus and SAR11. ISME J 13:1506–1519

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Behnke J, LaRoche J (2020) Iron uptake proteins in algae and the role of iron starvation-induced proteins (ISIPs). Eur J Phycol 55:339–360

    Article  CAS  Google Scholar 

  • Beier S, Gálvez MJ, Molina V, Sarthou G, Quéroué F, Blain S et al (2015) The transcriptional regulation of the glyoxylate cycle in SAR11 in response to iron fertilization in the Southern Ocean. Environ Microbiol Rep 7:427–434

    Article  CAS  PubMed  Google Scholar 

  • Béja O, Spudich EN, Spudich JL, Leclerc M, DeLong EF (2001) Proteorhodopsin phototrophy in the ocean. Nature 411:786–789

    Article  PubMed  Google Scholar 

  • Berube PM, Rasmussen A, Braakman R, Stepanauskas R, Chisholm SW (2019) Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus. elife 8:e41043

    Article  PubMed  PubMed Central  Google Scholar 

  • Biller SJ, Schubotz F, Roggensack SE, Thompson AW, Summons RE, Chisholm SW (2014) Bacterial vesicles in marine ecosystems. Science 343:183–186

    Article  CAS  PubMed  Google Scholar 

  • Blain S, Tagliabue A (2016) In: Tréguer P (ed) Iron cycle in oceans. ISTE Ltd, London, UK

    Chapter  Google Scholar 

  • Boeuf D, Lami R, Cunnington E, Jeanthon C (2016) Summer abundance and distribution of proteorhodopsin genes in the western arctic ocean. Front Microbiol 7:1–12

    Article  Google Scholar 

  • Bolaños LM, Choi CJ, Worden AZ, Baetge N, Carlson CA, Giovannoni S (2021) Seasonality of the microbial community composition in the North Atlantic. Front Mar Sci 8:1–16

    Article  Google Scholar 

  • Bolaños LM, Karp-Boss L, Choi CJ, Worden AZ, Graff JR, Haëntjens N et al (2020) Small phytoplankton dominate western North Atlantic biomass. ISME J 14:1663–1674

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bouchard JN, Roy S, Ferreyra G, Campbell DA, Curtosi A (2005) Ultraviolet-B effects on photosystem II efficiency of natural phytoplankton communities from Antarctica. Polar Biol 28:607–618

    Article  Google Scholar 

  • Boyd PW, Jickells T, Law CS, Blain S, Boyle EA, Buesseler KO et al (2007) Mesoscale iron enrichment experiments 1993-2005: synthesis and future directions. Science 315:612–617

    Article  CAS  PubMed  Google Scholar 

  • Browning TJ, Al-Hashem AA, Hopwood MJ, Engel A, Belkin IM, Wakefield ED et al (2021) Iron regulation of North Atlantic eddy phytoplankton productivity. Geophys Res Lett 48:e2020GL091403

    Article  Google Scholar 

  • Buesseler KO, Boyd PW, Black EE, Siegel DA (2020) Metrics that matter for assessing the ocean biological carbon pump. Proc Natl Acad Sci U S A 117:9679–9687

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Buma AGJ, van Hannen EJ, Veldhuis MJW, Gieskes WWC (1996) UV-B induces DNA damage and DNA synthesis delay in the marine diatom Cyclotella sp. Sci Mar 60:101–106

    CAS  Google Scholar 

  • Buma AGJ, De Boer MK, Boelen P (2001) Depth distributions of DNA damage in Antarctic marine phyto- and bacterioplankton exposed to summertime UV radiation. J Phycol 37:200–208

    Article  CAS  Google Scholar 

  • Buttigieg PL, Fadeev E, Bienhold C, Hehemann L, Pierre O, Boetius A (2018) Marine microbes in 4D–using time series observation to assess the dynamics of the ocean microbiome and its links to ocean health. Curr Opin Microbiol 43:169–185

    Article  PubMed  Google Scholar 

  • Campbell D, Eriksson MJ, Öquist G, Gustafsson P, Clarke AK (1998) The cyanobacterium Synechococcus resists UV-B by exchanging photosystem II reaction-center D1 proteins. Proc Natl Acad Sci U S A 95:364–369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Canals O, Obiol A, Muhovic I, Vaqué D, Massana R (2020) Ciliate diversity and distribution across horizontal and vertical scales in the open ocean. Mol Ecol 29:2824–2839

    Article  CAS  PubMed  Google Scholar 

  • Caputi L, Carradec Q, Eveillard D, Kirilovsky A, Pelletier E, Pierella Karlusich JJ et al (2019) Community-level responses to iron availability in open ocean plankton ecosystems. Global Biogeochem Cycles 33:391–419

    Article  CAS  Google Scholar 

  • Carlson CA, Del Giorgio PA, Herndl GJ (2007) Microbes and the dissipation of energy and respiration: from cells to ecosystems. Oceanography 20:89–100

    Article  Google Scholar 

  • Castenholz RW, Garcia-Pichel F (2013) Cyanobacterial responses to UV radiation. In: Whitton BA (ed) Ecology of cyanobacteria II: their diversity in space and time. Springer, Netherlands, pp 481–499

    Google Scholar 

  • Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ et al (2019) Scientists’ warning to humanity: microorganisms and climate change. Nat Rev Microbiol 17:569–586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Choi CJ, Jimenez V, Needham DM, Poirier C, Bachy C, Alexander H et al (2020) Seasonal and geographical transitions in eukaryotic phytoplankton community structure in the Atlantic and Pacific oceans. Front Microbiol 11:542372

    Article  PubMed  PubMed Central  Google Scholar 

  • Church MJ, Wai B, Karl DM, DeLong EF (2010) Abundances of crenarchaeal amoA genes and transcripts in the Pacific Ocean. Environ Microbiol 12:679–688

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Coesel S, Mangogna M, Ishikawa T, Heijde M, Rogato A, Finazzi G et al (2009) Diatom PtCPF1 is a new cryptochrome/photolyase family member with DNA repair and transcription regulation activity. EMBO Rep 10:655–661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cohen NR, McIlvin MR, Moran DM, Held NA, Saunders JK, Hawco NJ et al (2021) Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the Central Pacific Ocean. Nat Microbiol 6:173–186

    Article  CAS  PubMed  Google Scholar 

  • Cullen JJ (2015) Subsurface chlorophyll maximum layers: enduring enigma or mystery solved? Annu Rev Mar Sci 7:207–239

    Article  Google Scholar 

  • Dall’Olmo G, Dingle J, Polimene L, Brewin RJW, Claustre H (2016) Substantial energy input to the mesopelagic ecosystem from the seasonal mixed-layer pump. Nat Geosci 9:820–823

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • De Tommasi E, Congestri R, Dardano P, De Luca AC, Managò S, Rea I et al (2018) UV-shielding and wavelength conversion by centric diatom nanopatterned frustules. Sci Rep 8:1–14

    Article  CAS  Google Scholar 

  • De Vargas C, Audic S, Henry N, Decelle J, Mahé F, Logares R et al (2015) Eukaryotic plankton diversity in the sunlit ocean. Science 348:1–12

    Article  CAS  Google Scholar 

  • Debeljak P, Toulza E, Beier S, Blain S, Obernosterer I (2019) Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes. Environ Microbiol 21:2360–2374

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dlugosch L, Poehlein A, Wemheuer B, Pfeiffer B, Giebel H-A, Daniel R, Simon M (2021) Nitrogen availability drives gene length of dominant prokaryotes and diversity of genes acquiring Nitrogen-species in oceanic systems. bioRxiv 2021.01.10.426031:1–26

    Google Scholar 

  • Doblin MA, Petrou K, Sinutok S, Seymour JR, Messer LF, Brown MV et al (2016) Nutrient uplift in a cyclonic eddy increases diversity, primary productivity and iron demand of microbial communities relative to a western boundary current. PeerJ 4:e1973

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Dos Santos AL, Gourvil P, Tragin M, Noël MH, Decelle J, Romac S et al (2017) Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters. ISME J 11:512–528

    Article  Google Scholar 

  • Dudok de Wit T, Kopp G, Fröhlich C, Schöll M (2017) Methodology to create a new total solar irradiance record: making a composite out of multiple data records. Geophys Res Lett 44:1196–1203

    Article  Google Scholar 

  • Dupouy C, Frouin R, Tedetti M, Maillard M, Rodier M, Lombard F et al (2018) Diazotrophic Trichodesmium impact on UV-vis radiance and pigment composition in the western tropical South Pacific. Biogeosciences 15:5249–5269

    Article  CAS  Google Scholar 

  • Dyhrman ST, Chappell PD, Haley ST, Moffett JW, Orchard ED, Waterbury JB et al (2006) Phosphonate utilization by the globally important marine diazotroph Trichodesmium. Nature 439:68–71

    Article  CAS  PubMed  Google Scholar 

  • Edwards KF (2019) Mixotrophy in nanoflagellates across environmental gradients in the ocean. Proc Natl Acad Sci U S A 116:6211–6220

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Falkowski PG (1994) The role of phytoplankton photosynthesis in global biogeochemical cycles. Photosynth Res 39:235–258

    Article  CAS  PubMed  Google Scholar 

  • Falkowski PG, Katz ME, Knoll AH, Quigg A, Raven JA, Schofield O et al (2004) The evolution of modern eukaryotic phytoplankton. Science 305:354–360

    Article  CAS  PubMed  Google Scholar 

  • Falkowski PG, Laroche J (1991) Acclimation to spectral irradiance in algae. J Phycol 27:8–14

    Article  Google Scholar 

  • Field CB, Behrenfeld MJ, Randerson JT, Falkowski P (1998) Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281:237–240

    Article  CAS  PubMed  Google Scholar 

  • Fiore C, Alexander H, Kido Soule M, Kujawinski E (2020) A phosphate starvation response gene (psr1-like) is present and expressed in Micromonas pusilla and other marine algae. Aquat Microb Ecol 86:29–46

    Article  Google Scholar 

  • Flegontova O, Flegontov P, Malviya S, Audic S, Wincker P, de Vargas C et al (2016) Extreme diversity of diplonemid eukaryotes in the ocean. Curr Biol 26:3060–3065

    Article  CAS  PubMed  Google Scholar 

  • Flombaum P, Wang WL, Primeau FW, Martiny AC (2020) Global picophytoplankton niche partitioning predicts overall positive response to ocean warming. Nat Geosci 13:116–120

    Article  CAS  Google Scholar 

  • Flynn KJ, Mitra A (2009) Building the “perfect beast”: modelling mixotrophic plankton. J Plankton Res 31:965–992

    Article  CAS  Google Scholar 

  • Fragoso GM, Poulton AJ, Yashayaev IM, Head EJH, Johnsen G, Purdie DA (2018) Diatom biogeography from the Labrador Sea revealed through a trait-based approach. Front Mar Sci 5:297

    Article  Google Scholar 

  • Franks PJS (2015) Marine science. ICES J Mar Sci 72:1897–1907

    Article  Google Scholar 

  • Freyria NJ, Joli N, Lovejoy C (2021) A decadal perspective on north water microbial eukaryotes as Arctic Ocean sentinels. Sci Rep 11:1–14

    Article  CAS  Google Scholar 

  • Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, Naeem S (2006) Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci U S A 103:13104–13109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fuhrman JA, Steele JA, Hewson I, Schwalbach MS, Brown MV, Green JL et al (2008) A latitudinal diversity gradient in planktonic marine bacteria. Proc Natl Acad Sci U S A 105:7774–7778

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao K, Helbling E, Häder D, Hutchins D (2012) Responses of marine primary producers to interactions between ocean acidification, solar radiation, and warming. Mar Ecol Prog Ser 470:167–189

    Article  CAS  Google Scholar 

  • Gao Q, Garcia-Pichel F (2011) Microbial ultraviolet sunscreens. Nat Rev Microbiol 9:791–802

    Article  CAS  PubMed  Google Scholar 

  • Garcia-Corral LS, Holding JM, Carrillo-de-Albornoz P, Steckbauer A, Pérez-Lorenzo M, Navarro N et al (2017a) Effects of UVB radiation on net community production in the upper global ocean. Glob Ecol Biogeogr 26:54–64

    Article  Google Scholar 

  • Garcia-Corral LS, Holding JM, Carrillo-de-Albornoz P, Steckbauer A, Pérez-Lorenzo M, Navarro N et al (2017b) Temperature dependence of plankton community metabolism in the subtropical and tropical oceans. Global Biogeochem Cycles 31:1141–1154

    Article  CAS  Google Scholar 

  • Gardner WD, Chung SP, Richardson MJ, Walsh ID (1995) The oceanic mixed-layer pump. Deep Sea Res Part II: Topical Studies in Oceanography 42:757–775

    Article  Google Scholar 

  • Geider RJ, La Roche J (2002) Redfield revisited: variability of C:N:P in marine microalgae and its biochemical basis. Eur J Phycol 37:1–17

    Article  Google Scholar 

  • Giovannoni SJ (2017) SAR11 bacteria: the most abundant plankton in the oceans. Annu Rev Mar Sci 9:231–255

    Article  Google Scholar 

  • Gómez-Consarnau L, González JM, Coll-Lladó M, Gourdon P, Pascher T, Neutze R et al (2007) Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature 445:210–213

    Article  PubMed  CAS  Google Scholar 

  • Gómez-Consarnau L, Raven JA, Levine NM, Cutter LS, Wang D, Seegers B et al (2019) Microbial rhodopsins are major contributors to the solar energy captured in the sea. Sci Adv 5:1–8

    Article  CAS  Google Scholar 

  • Grébert T, Doré H, Partensky F, Farrant GK, Boss ES, Picheral M et al (2018) Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria. Proc Natl Acad Sci U S A 115:E2010–E2019

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Grébert T, Nguyen AA, Pokhrel S, Joseph KL, Ratin M, Dufour L et al (2021) Molecular basis of an alternative dual-enzyme system for light color acclimation of marine Synechococcus cyanobacteria. Proc Natl Acad Sci U S A 118:e2019715118

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Guidi L, Chaffron S, Bittner L, Eveillard D, Larhlimi A, Roux S et al (2016) Plankton networks driving carbon export in the oligotrophic ocean. Nature 532:465–470

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo Z, Zhang H, Lin S (2014) Light-promoted rhodopsin expression and starvation survival in the marine dinoflagellate Oxyrrhis marina. PLoS One 9:1–23

    Article  Google Scholar 

  • Harding K, Turk-Kubo KA, Sipler RE, Mills MM, Bronk DA, Zehr JP (2018) Symbiotic unicellular cyanobacteria fix nitrogen in the Arctic Ocean. Proc Natl Acad Sci U S A 115:13371–13375

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holtrop T, Huisman J, Stomp M, Biersteker L, Aerts J, Grébert T et al (2020) Vibrational modes of water predict spectral niches for photosynthesis in lakes and oceans. Nat Ecol Evol 5:55–66

    Article  PubMed  Google Scholar 

  • Ibarbalz FM, Henry N, Brandão MC, Martini S, Busseni G, Byrne H et al (2019) Global trends in marine plankton diversity across kingdoms of life. Cell 179:1084–1097

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Iuculano F, Álverez-Salgado XA, Otero J, Catalá TS, Sobrino C, Duarte CM et al (2019) Patterns and drivers of UV absorbing chromophoric dissolved organic matter in the euphotic layer of the open ocean. Front Mar Sci 6:1–19

    Article  Google Scholar 

  • Jiao N, Herndl GJ, Hansell DA, Benner R, Kattner G, Wilhelm SW et al (2010) Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean. Nat Rev Microbiol 8:593–559

    Article  CAS  PubMed  Google Scholar 

  • Jickells TD (2005) Global iron connections between desert dust, ocean biogeochemistry, and climate. Science 308:67–71

    Article  CAS  PubMed  Google Scholar 

  • Johnson ZI, Zinser ER, Coe A, Mcnulty NP, Woodward EMS, Chisholm SW (2006) Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311:1737–1741

    Article  CAS  PubMed  Google Scholar 

  • Kemp AES, Villareal TA (2018) The case of the diatoms and the muddled mandalas: time to recognize diatom adaptations to stratified waters. Prog Oceanogr 167:138–149

    Article  Google Scholar 

  • Kessler N, Armoza-Zvuloni R, Wang S, Basu S, Weber PK, Stuart RK et al (2020) Selective collection of iron-rich dust particles by natural Trichodesmium colonies. ISME J 14:91–103

    Article  CAS  PubMed  Google Scholar 

  • Kirchman DL, Hanson TE (2013) Bioenergetics of photoheterotrophic bacteria in the oceans. Environ Microbiol Rep 5:188–199

    Article  CAS  PubMed  Google Scholar 

  • Kirk JTO (1994) Light and photosynthesis in aquatic ecosystems. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Koedooder C, Guéneuguès A, Van Geersdaële R, Vergé V, Bouget FY, Labreuche Y et al (2018) The role of the glyoxylate shunt in the acclimation to iron limitation in marine heterotrophic bacteria. Front Mar Sci 5:1–12

    Article  Google Scholar 

  • Koedooder C, Van Geersdaële R, Guéneuguès A, Bouget F-Y, Obernosterer I, Blain S (2020) The interplay between iron limitation, light, and carbon in the proteorhodopsin containing Photobacterium angustum S14. FEMS Microbiol Ecol 103:1–12

    Google Scholar 

  • Kraemer S, Ramachandran A, Colatriano D, Lovejoy C, Walsh DA (2020) Diversity and biogeography of SAR11 bacteria from the Arctic Ocean. ISME J 14:79–90

    Article  PubMed  Google Scholar 

  • Krause JW, Schulz IK, Rowe KA, Dobbins W, Winding MHS, Sejr MK et al (2019) Silicic acid limitation drives bloom termination and potential carbon sequestration in an Arctic bloom. Sci Rep 9:1–11

    Article  CAS  Google Scholar 

  • Krupke A, Musat N, LaRoche J, Mohr W, Fuchs BM, Amann RI et al (2013) In situ identification and N2 and C fixation rates of uncultivated cyanobacteria populations. Syst Appl Microbiol 36:259–271

    Article  CAS  PubMed  Google Scholar 

  • LaRoche J, Boyd PW, McKay RML, Geider RJ (1996) Flavodoxin as an in situ marker for iron stress in phytoplankton. Nature 382:802–805

    Article  CAS  Google Scholar 

  • Lacour L, Briggs N, Claustre H, Ardyna M, Dall’Olmo G (2019) The intraseasonal dynamics of the mixed layer pump in the subpolar North Atlantic Ocean: a biogeochemical-Argo float approach. Global Biogeochem Cycles 33:266–281

    Article  CAS  Google Scholar 

  • Lampe RH, Mann EL, Cohen NR, Till CP, Thamatrakoln K, Brzezinski MA et al (2018) Different iron storage strategies among bloom-forming diatoms. Proc Natl Acad Sci 115:E12275–E12284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langlois R, Mills MM, Ridame C, Croot P, LaRoche J (2012) Diazotrophic bacteria respond to Saharan dust additions. Mar Ecol Prog Ser 470:1–14

    Article  CAS  Google Scholar 

  • Leblanc K, Quéguiner B, Diaz F, Cornet V, Michel-Rodriguez M, Durrieu De Madron X et al (2018) Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export. Nat Commun 9:1–12

    Article  CAS  Google Scholar 

  • Legendre L, Rivkin RB, Weinbauer MG, Guidi L, Uitz J (2015) The microbial carbon pump concept: potential biogeochemical significance in the globally changing ocean. Prog Oceanogr 134:432–450

    Article  Google Scholar 

  • Letelier RM, White AE, Bidigare RR, Barone B, Church MJ, Karl DM (2017) Light absorption by phytoplankton in the North Pacific subtropical gyre. Limnol Oceanogr 62:1526–1540

    Article  Google Scholar 

  • Li Q, Edwards KF, Schvarcz CR, Selph KE, Steward GF (2021) Plasticity in the grazing ecophysiology of Florenciella (Dichtyochophyceae), a mixotrophic nanoflagellate that consumes Prochlorococcus and other bacteria. Limnol Oceanogr 66:47–60

    Article  CAS  Google Scholar 

  • Liefer JD, Garg A, Fyfe MH, Irwin AJ, Benner I, Brown CM et al (2019) The macromolecular basis of phytoplankton C:N:P under nitrogen starvation. Front Microbiol 10:1–16

    Article  Google Scholar 

  • Lima-Mendez G, Faust K, Henry N, Decelle J, Colin S, Carcillo F et al (2015) Determinants of community structure in the global plankton interactome. Science 348:1–10

    Article  CAS  Google Scholar 

  • Longhurst A (1995) Seasonal cycles of pelagic production and consumption. Prog Oceanogr 36:77–167

    Article  Google Scholar 

  • López-Pérez M, Haro-Moreno JM, Coutinho FH, Martinez-Garcia M, Rodriguez-Valera F (2020) The evolutionary success of the marine bacterium SAR11 analyzed through a metagenomic perspective. mSystems 5:1–13

    Article  Google Scholar 

  • Lucas-Lledo JI, Lynch M (2009) Evolution of mutation rates: phylogenomic analysis of the photolyase/cryptochrome family. Mol Biol Evol 26:1143–1153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Malmstrom RR, Coe A, Kettler GC, Martiny AC, Frias-lopez J, Zinser ER et al (2010) Temporal dynamics of Prochlorococcus ecotypes in the Atlantic and Pacific oceans. ISME J 4:1252–1264

    Article  PubMed  Google Scholar 

  • Man D, Wang W, Sabehi G, Aravind L, Post AF, Massana R et al (2003) Diversification and spectral tuning in marine proteorhodopsins. EMBO J 22:1725–1731

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Manck LE, Espinoza JL, Dupont CL, Barbeau KA (2020) Transcriptomic study of substrate-specific transport mechanisms for iron and carbon in the marine copiotroph Alteromonas macleodii. mSystems 5:1–16

    Article  Google Scholar 

  • Marchetti A (2019) A global perspective on iron and plankton through the Tara oceans lens. Global Biogeochem Cycles 33:239–242

    Article  CAS  Google Scholar 

  • Marra JF, Lance VP, Vaillancourt RD, Hargreaves BR (2014) Resolving the ocean’s euphotic zone. Deep Res Part I Oceanogr Res Pap 83:45–50

    Article  Google Scholar 

  • Martínez-Pérez C, Mohr W, Löscher CR, Dekaezemacker J, Littmann S, Yilmaz P et al (2016) The small unicellular diazotrophic symbiont, UCYN-A, is a key player in the marine nitrogen cycle. Nat Microbiol 1:16163

    Article  PubMed  CAS  Google Scholar 

  • McQuaid JB, Kustka AB, Oborník M, Horák A, McCrow JP, Karas BJ et al (2018) Carbonate-sensitive phytotransferrin controls high-affinity iron uptake in diatoms. Nature 555:534–537

    Article  CAS  PubMed  Google Scholar 

  • Mills MM, Moore CM, Langlois R, Milne A, Achterberg EP, Nachtigall K et al (2008) Nitrogen and phosphorus co-limitation of bacterial productivity and growth in the oligotrophic sub-tropical North Atlantic. Limnol Oceanogr 53:824–834

    Article  CAS  Google Scholar 

  • Mills MM, Turk-Kubo KA, van Dijken GL, Henke BA, Harding K, Wilson ST et al (2020) Unusual marine cyanobacteria/haptophyte symbiosis relies on N2 fixation even in N-rich environments. ISME J 14:2395–2406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moisander PH, Beinart RA, Hewson I, White AE, Johnson KS, Carlson CA et al (2010) Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain. Science 327:1512–1514

    Article  CAS  PubMed  Google Scholar 

  • Moore CM, Mills MM, Arrigo KR, Berman-Frank I, Bopp L, Boyd PW et al (2013) Processes and patterns of oceanic nutrient limitation. Nat Geosci 6:701–710

    Article  CAS  Google Scholar 

  • Moore CM, Mills MM, Langlois R, Milne A, Achterberg EP, LaRoche J et al (2008) Relative influence of nitrogen and phosphorous availability on phytoplankton physiology and productivity in the oligotrophic sub-tropical North Atlantic Ocean. Limnol Oceanogr 53:291–305

    Article  CAS  Google Scholar 

  • Moreira-Coello V, Mouriño-Carballido B, Marañón E et al (2017) Biological N2 fixation in the upwelling region off NW Iberia: magnitude, relevance, and players. Front Mar Sci 4:303

    Article  Google Scholar 

  • Morel FMM, Lam PJ, Saito MA (2020) Trace metal substitution in marine phytoplankton. Annu Rev Earth Planet Sci 48:491–517

    Article  CAS  Google Scholar 

  • Moreno AR, Martiny AC (2018) Ecological stoichiometry of ocean plankton. Annu Rev Mar Sci 10:43–69

    Article  Google Scholar 

  • Muñoz-Marín MC, Gómez-Baena G, López-Lozano A, Moreno-Cabezuelo JA, Díez J, García-Fernández JM (2020) Mixotrophy in marine picocyanobacteria: use of organic compounds by Prochlorococcus and Synechococcus. ISME J 14:1065–1073

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nishitani G, Yamaguchi M (2018) Seasonal succession of ciliate Mesodinium spp. with red, green, or mixed plastids and their association with cryptophyte prey. Sci Rep 8:1–9

    Article  Google Scholar 

  • Nonoyama K, Nawaly G, Tsuji M et al (2019) Metabolic innovations underpinning the origin and diversification of the diatom chloroplast. Biomol Ther 9:322

    CAS  Google Scholar 

  • Núñez-Pons L, Avila C, Romano G, Verde C, Giordano D (2018) UV-protective compounds in marine organisms from the southern ocean. Mar Drugs 16:336

    Article  PubMed Central  CAS  Google Scholar 

  • Obernosterer I, Fourquez M, Blain S (2015) Fe and C co-limitation of heterotrophic bacteria in the naturally fertilized region off the Kerguelen Islands. Biogeosciences 12:1983–1992

    Article  Google Scholar 

  • Olson DK, Yoshizawa S, Boeuf D, Iwasaki W, Delong EF (2018) Proteorhodopsin variability and distribution in the North Pacific subtropical gyre. ISME J 12:1047–1060

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Overmans S, Agustí S (2019) Latitudinal gradient of UV attenuation along the highly transparent Red Sea Basin. Photochem Photobiol 95:1267–1279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Owens SA, Pike S, Buesseler KO (2015) Thorium-234 as a tracer of particle dynamics and upper ocean export in the Atlantic Ocean. Deep Res Part II Top Stud Oceanogr 116:42–59

    Article  CAS  Google Scholar 

  • Oziel L, Baudena A, Ardyna M, Massicotte P, Randelhoff A, Sallée JB, Ingvaldsen RB, Devred E, Babin M (2020) Faster Atlantic currents drive poleward expansion of temperate phytoplankton in the Arctic Ocean. Nat Commun 11:1–8

    Article  CAS  Google Scholar 

  • Pachiadaki MG, Brown JM, Brown J, Bezuidt O, Berube PM, Biller SJ et al (2019) Charting the complexity of the marine microbiome through single-cell genomics. Cell 179:1623–1635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pedneault E, Galand PE, Potvin M, Tremblay JÉ, Lovejoy C (2014) Archaeal amoA and ureC genes and their transcriptional activity in the Arctic Ocean. Sci Rep 4:4661

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pierella Karlusich JJ, Ibarbalz FM, Bowler C (2020) Phytoplankton in the Tara Ocean. Annu Rev Mar Sci 12:233–265

    Article  Google Scholar 

  • Pinhassi J, DeLong EF, Béjà O, González JM, Pedrós-Alió C (2016) Marine bacterial and archaeal ion-pumping rhodopsins: genetic diversity, physiology, and ecology. Microbiol Mol Biol Rev 80:929–954

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Polimene L, Sailley S, Clark D, Mitra A, Allen JI (2017) Biological or microbial carbon pump? The role of phytoplankton stoichiometry in ocean carbon sequestration. J Plankton Res 39:180–186

    CAS  Google Scholar 

  • Quigg A, Irwin AJ, Finkel ZV (2011) Evolutionary inheritance of elemental stoichiometry in phytoplankton. Proc R Soc B Biol Sci 278:526–534

    Article  Google Scholar 

  • Ratten J-M, LaRoche J, Desai DK, Shelley RU, Landing WM, Boyle E et al (2015) Sources of iron and phosphate affect the distribution of diazotrophs in the North Atlantic. Deep Res Part II Top Stud Oceanogr 116:332–341

    Article  CAS  Google Scholar 

  • Read RW, Berube PM, Biller SJ, Neveux I, Cubillos-Ruiz A, Chisholm SW et al (2017) Nitrogen cost minimization is promoted by structural changes in the transcriptome of N-deprived Prochlorococcus cells. ISME J 11:2267–2278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Redfield A (1958) The biological control of chemical factors in the environment. Amercian Sci 46:205–221

    CAS  Google Scholar 

  • Richter D, Watteaux R, Vannier T, Leconte J, Frémont P, Reygondeau G, Maillet N, et al. (2020) Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems. bioRxiv 867739:1–38

    Google Scholar 

  • Righetti D, Vogt M, Gruber N, Psomas A, Zimmermann NE (2019) Global pattern of phytoplankton diversity driven by temperature and environmental variability. Sci Adv 5:1–11

    Article  Google Scholar 

  • Rijkenberg MJA, Fischer AC, Kroon JJ, Gerringa LJA, Timmermans KR, Wolterbeek HT et al (2005) The influence of UV irradiation on the photoreduction of iron in the Southern Ocean. Mar Chem 93:119–129

    Article  CAS  Google Scholar 

  • Roth-Rosenberg D, Aharonovich D, Luzzatto-Knaan T, Vogts A, Zoccarato L, Eigemann F et al (2020) Prochlorococcus cells rely on microbial interactions rather than on chlorotic resting stages to survive long-term nutrient starvation. MBio 11:1–13

    Article  Google Scholar 

  • Saito MA, Goepfert TJ, Ritt JT (2008) Some thoughts on the concept of colimitation: three definitions and the importance of bioavailability. Limnol Oceanogr 53:276–290

    Article  CAS  Google Scholar 

  • Santoro AE, Richter RA, Dupont CL (2019) Planktonic marine archaea. Annu Rev Mar Sci 11:131–158

    Article  Google Scholar 

  • Sargent EC, Hitchcock A, Johansson SA, Langlois R, Moore CM, LaRoche J et al (2016) Evidence for polyploidy in the globally important diazotroph Trichodesmium. FEMS Microbiol Lett 363:fnw244

    Article  PubMed  CAS  Google Scholar 

  • Shenhav L, Zeevi D (2020) Resource conservation manifests in the genetic code. Science 370:683–687

    Article  CAS  PubMed  Google Scholar 

  • Shiozaki T, Fujiwara A, Ijichi M, Harada N, Nishino S, Nishi S et al (2018) Diazotroph community structure and the role of nitrogen fixation in the nitrogen cycle in the Chukchi Sea (western Arctic Ocean). Limnol Oceanogr 63:2191–2205

    Article  CAS  Google Scholar 

  • Sinha RP, Häder DP (2002) UV-induced DNA damage and repair: a review. Photochem Photobiol Sci 1:225–236

    Article  CAS  PubMed  Google Scholar 

  • Smyth TJ (2011) Penetration of UV irradiance into the global ocean. J Geophys Res Ocean 116:1–12

    Article  Google Scholar 

  • Stoecker DK, Hansen PJ, Caron DA, Mitra A (2017) Mixotrophy in the marine plankton. Annu Rev Mar Sci 9:311–335

    Article  Google Scholar 

  • Stomp M, Huisman J, Stal LJ, Matthijs HCP (2007) Colorful niches of phototrophic microorganisms shaped by vibrations of the water molecule. ISME J 1:271–282

    Article  CAS  PubMed  Google Scholar 

  • Strzepek RF, Boyd PW, Sunda WG (2019) Photosynthetic adaptation to low iron, light, and temperature in Southern Ocean phytoplankton. Proc Natl Acad Sci U S A 116:4388–4393

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Strzepek RF, Harrison PJ (2004) Photosynthetic architecture differs in coastal and oceanic diatoms. Nature 431:689–692

    Article  CAS  PubMed  Google Scholar 

  • Sunagawa S, Acinas SG, Bork P, Bowler C, Acinas SG, Babin M et al (2020) Tara oceans: towards global ocean ecosystems biology. Nat Rev Microbiol 18:428–445

    Article  CAS  PubMed  Google Scholar 

  • Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G et al (2015) Structure and function of the global ocean microbiome. Science 348:1261359

    Article  PubMed  CAS  Google Scholar 

  • Sunda WG (2012) Feedback interactions between trace metal nutrients and phytoplankton in the ocean. Front Microbiol 3:204

    Article  PubMed  PubMed Central  Google Scholar 

  • Sunda WG, Huntsman SA (1995) Cobalt and zinc interreplacement in marine phytoplankton: biological and geochemical implications. Limnol Oceanogr 40:1404–1417

    Article  CAS  Google Scholar 

  • Tang W, Cassar N (2019) Data-driven modeling of the distribution of diazotrophs in the global ocean. Geophys Res Lett 46:12258–12269

    Article  Google Scholar 

  • Tedetti M, Sempéré R (2006) Penetration of ultraviolet radiation in the marine environment. A review. Photochem Photobiol 82:389–397

    Article  CAS  PubMed  Google Scholar 

  • Tedetti M, Sempéré R, Vasilkov A, Charrière B, Nérini D, Miller WL et al (2007) High penetration of ultraviolet radiation in the south East Pacific waters. Geophys Res Lett 34:1–5

    Article  Google Scholar 

  • Tillmann U (2003) Kill and eat your predator: a winning strategy of the planktonic flagellate Prymnesium parvum. Aquat Microb Ecol 32:73–84

    Article  Google Scholar 

  • Tong S, Hutchins DA, Gao K (2019) Physiological and biochemical responses of Emiliania huxleyi to ocean acidification and warming are modulated by UV radiation. Biogeosciences 16:561–572

    Article  CAS  Google Scholar 

  • Tréguer P, Bowler C, Moriceau B, Dutkiewicz S, Gehlen M, Aumont O et al (2018) Influence of diatom diversity on the ocean biological carbon pump. Nat Geosci 11:27–37

    Article  CAS  Google Scholar 

  • Twining BS, Antipova O, Chappell PD, Cohen NR, Jacquot JE, Mann EL et al (2020) Taxonomic and nutrient controls on phytoplankton iron quotas in the ocean. Limnol Oceanogr Lett 6:96–106

    Article  CAS  Google Scholar 

  • Tyrrell T (1999) The relative influences of nitrogen and phosphorus on oceanic primary production. Nature 400:525–531

    Article  CAS  Google Scholar 

  • Van Mooy BAS, Fredricks HF, Pedler BE, Dyhrman ST, Karl DM, Koblížek M et al (2009) Phytoplankton in the ocean use non-phosphorus lipids in response to phosphorus scarcity. Nature 458:69–72

    Article  PubMed  CAS  Google Scholar 

  • Wagner S, Schubotz F, Kaiser K, Hallmann C, Waska H, Rossel PE et al (2020) Soothsaying DOM: a current perspective on the future of oceanic dissolved organic carbon. Front Mar Sci 7:1–17

    Article  Google Scholar 

  • Wang Y, Lee Z, Wei J, Shang S, Wang M, Lai W (2021) Extending satellite ocean color remote sensing to the near-blue ultraviolet bands. Remote Sens Environ 253:112228

    Article  Google Scholar 

  • Ward BA, Cael BB, Collins S, Young CR (2021) Selective constraints on global plankton dispersal. Proc Natl Acad Sci U S A 118:e2007388118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Watanabe S (2020) Cyanobacterial multi-copy chromosomes and their replication. Biosci Biotechnol Biochem 84:1309–1321

    Article  CAS  PubMed  Google Scholar 

  • Westrich JR, Ebling AM, Landing WM, Joyner JL, Kemp KM, Griffin DW et al (2016) Saharan dust nutrients promote vibrio bloom formation in marine surface waters. Proc Natl Acad Sci U S A 113:5964–5969

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Westrich JR, Griffin DW, Westphal DL, Lipp EK (2018) Vibrio population dynamics in mid-Atlantic surface waters during Saharan dust events. Front Mar Sci 5:1–9

    Article  Google Scholar 

  • Wietz M, Bienhold C, Metfies K, Torres-Valdés S, Von Appen W-J, Salter I, Boetius A, Wegener A (2021) The polar night shift: annual dynamics and drivers of microbial community structure in the Arctic Ocean physical oceanography of the Polar Seas. bioRxiv 2021.04.08.436999

    Google Scholar 

  • Wirtz K, Smith SL (2020) Vertical migration by bulk phytoplankton sustains biodiversity and nutrient input to the surface ocean. Sci Rep 10:1–13

    Article  CAS  Google Scholar 

  • Worden AZ, Not F (2008) Ecology and diversity of picoeukaryotes. In: Kirchman DL (ed) Microbial ecology of the oceans, 2nd edn. Wiley-Blackwell, New Jersey, pp 159–205

    Chapter  Google Scholar 

  • Xu J, Bach LT, Schulz KG, Zhao W, Gao K, Riebesell U (2016) The role of coccoliths in protecting Emiliania huxleyi against stressful light and UV radiation. Biogeosciences 13:4637–4643

    Article  CAS  Google Scholar 

  • Yelton AP, Acinas SG, Sunagawa S, Bork P, Pedrós-Alió C, Chisholm SW (2016) Global genetic capacity for mixotrophy in marine picocyanobacteria. ISME J 10:2946–2957

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yurkov VV, Beatty JT (1998) Aerobic anoxygenic phototrophic bacteria. Microbiol Mol Biol Rev 62:695–724

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zehr JP, Shilova IN, Farnelid HM, Muñoz-Marín M del C, Turk-Kubo KA, Fowler D, et al. (2016) Unusual marine unicellular symbiosis with the nitrogen-fixing cyanobacterium UCYN-A. Nat Microbiol 2:16214

    Article  PubMed  CAS  Google Scholar 

  • Zepp RG, Erickson DJ, Paul ND, Sulzberger B (2007) Interactive effects of solar UV radiation and climate change on biogeochemical cycling. Photochem Photobiol Sci 6:286–300

    Article  CAS  PubMed  Google Scholar 

  • Zhu Z, Fu F, Qu P, Mak EWK, Jiang H, Zhang R et al (2020) Interactions between ultraviolet radiation exposure and phosphorus limitation in the marine nitrogen-fixing cyanobacteria Trichodesmium and Crocosphaera. Limnol Oceanogr 65:363–376

    Article  CAS  Google Scholar 

  • Zhuang Y, Jin H, Chen J, Ren J, Zhang Y, Lan M et al (2020) Phytoplankton community structure at subsurface chlorophyll maxima on the Western Arctic shelf: patterns, causes, and ecological importance. J Geophys Res Biogeosciences 125:1–15

    Article  Google Scholar 

  • Zorz J, Willis C, Comeau AM, Langille MGI, Johnson CL, Li WKW et al (2019) Drivers of regional bacterial community structure and diversity in the Northwest Atlantic Ocean. Front Microbiol 10:1–24

    Article  CAS  Google Scholar 

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  1. Department of Biology, Dalhousie University, NS, Halifax, Canada

    Julie LaRoche & Brent M. Robicheau

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    Lucas J. Stal

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    Mariana Silvia Cretoiu

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LaRoche, J., Robicheau, B.M. (2022). The Pelagic Light-Dependent Microbiome. In: Stal, L.J., Cretoiu, M.S. (eds) The Marine Microbiome. The Microbiomes of Humans, Animals, Plants, and the Environment, vol 3. Springer, Cham. https://doi.org/10.1007/978-3-030-90383-1_9

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