Data Accessibility and Benefit-Sharing Statement
Raw sequence reads and metadata are deposited in the Bioproject PRJNA769790. Scripts are available at the GitHub repository https://github.com/blancobercial/Protist_Time_Series.
References Cited
Agusti S, Lubián LM, Moreno-Ostos E, Estrada M, Duarte CM (2019) Projected Changes in Photosynthetic Picoplankton in a Warmer Subtropical Ocean. Frontiers in Marine Science 5 .
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology 215 , 403-410.
Andersen NG, Nielsen TG, Jakobsen HH, Munk P, Riemann L (2011) Distribution and production of plankton communities in the subtropical convergence zone of the Sargasso Sea. II. Protozooplankton and copepods.Marine Ecology Progress Series 426 , 71-86.
Arenovski AL, Lim EL, Caron DA (1995) Mixotrophic nanoplankton in oligotrophic surface waters of the Sargasso Sea may employ phagotrophy to obtain major nutrients. Journal of Plankton Research17 , 801-820.
Barker GM (2008) Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation.Biological Journal of the Linnean Society 76 , 165-194.
Biard T, Ohman MD (2020) Vertical niche definition of test-bearing protists (Rhizaria) into the twilight zone revealed by in situ imaging.Limnology and Oceanography 65 , 2583-2602.
Bjorbækmo MFM, Evenstad A, Røsæg LL, Krabberød AK, Logares R (2020) The planktonic protist interactome: where do we stand after a century of research? The ISME Journal 14 , 544-559.
Blanco-Bercial L (2020) Metabarcoding Analyses and Seasonality of the Zooplankton Community at BATS. Frontiers in Marine Science7 .
Bucklin A, Lindeque PK, Rodriguez-Ezpeleta N, Albaina A, Lehtiniemi M (2016) Metabarcoding of marine zooplankton: prospects, progress and pitfalls. Journal of Plankton Research 38 , 393-400.
Byung Cheol C, Sang Cheol N, Dong Han C (2000) Active ingestion of fluorescently labeled bacteria by mesopelagic heterotrophic nanoflagellates in the East Sea, Korea. Marine Ecology Progress Series 206 , 23-32.
Calbet A, Landry MR (2004) Phytoplankton growth, microzooplankton grazing, and carbon cycling in marine systems. Limnology and Oceanography 49 , 51-57.
Canals O, Obiol A, Muhovic I, Vaqué D, Massana R (2020) Ciliate diversity and distribution across horizontal and vertical scales in the open ocean. Molecular Ecology 29 , 2824-2839.
Caron DA, Hu SK (2019) Are We Overestimating Protistan Diversity in Nature? Trends in Microbiology 27 , 197-205.
Caron DA, Peele ER, Lim EL, Dennett MR (1999) Picoplankton and nanoplankton and their trophic coupling in surface waters of the Sargasso Sea south of Bermuda. Limnology and Oceanography44 , 259-272.
Choi CJ, Jimenez V, Needham DM, et al. (2020) Seasonal and Geographical Transitions in Eukaryotic Phytoplankton Community Structure in the Atlantic and Pacific Oceans. Frontiers in Microbiology11 .
Church MJ, Lomas MW, Muller-Karger F (2013) Sea change: Charting the course for biogeochemical ocean time-series research in a new millennium. Deep Sea Research Part II: Topical Studies in Oceanography 93 , 2-15.
Clarke KR, Gorley RN (2015) PRIMER v7: User Manual/Tutorial.PRIMER-E, Plymouth , 296.
Conte MH, Ralph N, Ross EH (2001) Seasonal and interannual variability in deep ocean particle fluxes at the Oceanic Flux Program (OFP)/Bermuda Atlantic Time Series (BATS) site in the western Sargasso Sea near Bermuda. Deep Sea Research Part II: Topical Studies in Oceanography 48 , 1471-1505.
Cotti-Rausch BE, Lomas MW, Lachenmyer EM, Baumann EG, Richardson TL (2020) Size-fractionated biomass and primary productivity of Sargasso Sea phytoplankton. Deep Sea Research Part I: Oceanographic Research Papers 156 , 103141.
de Vargas C, Audic S, Henry N, et al. (2015) Eukaryotic plankton diversity in the sunlit ocean. Science 348 .
del Campo J, Not F, Forn I, Sieracki ME, Massana R (2013) Taming the smallest predators of the oceans. The ISME Journal 7 , 351-358.
Duhamel S, Kim E, Sprung B, Anderson OR (2019) Small pigmented eukaryotes play a major role in carbon cycling in the P-depleted western subtropical North Atlantic, which may be supported by mixotrophy.Limnology and Oceanography 64 , 2424-2440.
Edgar RC (2016) UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing. bioRxiv , 081257.
Edwards KF (2019) Mixotrophy in nanoflagellates across environmental gradients in the ocean. Proceedings of the National Academy of Sciences 116 , 6211-6220.
Evelyn JL, Michael CM (1998) Microzooplankton herbivory and phytoplankton growth in the northwestern Sargasso Sea. Aquatic Microbial Ecology 16 , 173-188.
Faith DP (1992) Conservation evaluation and phylogenetic diversity.Biological Conservation 61 , 1-10.
Flynn KJ, Mitra A, Anestis K, et al. (2019) Mixotrophic protists and a new paradigm for marine ecology: where does plankton research go now? Journal of Plankton Research 41 , 375-391.
Giovannoni SJ, DeLong DF, Schmidt TM, Pace NR (1990) Tangentail flow filtration and preliminary phylogenetic analysis of marine picoplankton.Applied and Environmental Microbiology 56 , 2572-2575.
Gonçalves Leles S, Bruggeman J, Polimene L, et al. (2021) Differences in physiology explain succession of mixoplankton functional types and affect carbon fluxes in temperate seas. Progress in Oceanography 190 , 102481.
Gonçalves Leles S, Polimene L, Bruggeman J, et al. (2018) Modelling mixotrophic functional diversity and implications for ecosystem function. Journal of Plankton Research 40 , 627-642.
Gower JC (1966) Some distance properties of latent root and vector methods used in multivariate analysis. Biometrika 53 , 325-338.
Guillou L, Bachar D, Audic S, et al. (2013) The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Research 41 , D597-D604.
Holm S (1979) A Simple Sequentially Rejective Multiple Test Procedure.Scandinavian Journal of Statistics 6 , 65-70.
Irwin AJ, Oliver MJ (2009) Are ocean deserts getting larger?Geophysical Research Letters 36 .
Klaveness D, Shalchian-Tabrizi K, Thomsen HA, Eikrem W, Jakobsen KS (2005) Telonema antarcticum sp. nov., a common marine phagotrophic flagellate. International Journal of Systematic and Evolutionary Microbiology 55 , 2595-2604.
Koparde VN, Parikh HI, Bradley SP, Sheth NU (2017) MEEPTOOLS: a maximum expected error based FASTQ read filtering and trimming toolkit.International Journal of Computational Biology and Drug Design10 , 237-247.
Kwon S, Lee B, Yoon S (2014) CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing. BMC Bioinformatics 15 , S10.
Latorre F, Deutschmann IM, Labarre A, et al. (2021) Niche adaptation promoted the evolutionary diversification of tiny ocean predators. Proceedings of the National Academy of Sciences118 , e2020955118.
Legendre P, Gallagher ED (2001) Ecologically meaningful transformations for ordination of species data. Oecologia 129 , 271-280.
Lomas MW, Bates NR, Johnson RJ, et al. (2013) Two decades and counting: 24-years of sustained open ocean biogeochemical measurements in the Sargasso Sea. Deep Sea Research Part II: Topical Studies in Oceanography 93 , 16-32.
Luyten J, Pedlosky J, Stommel H (1983) The ventilated thermocline.Journal of Physical Oceanography 13 , 292-309.
Marçais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics27 , 764-770.
Massana R, del Campo J, Sieracki ME, Audic S, Logares R (2014) Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles. The ISME Journal 8 , 854-866.
Mitra A, Flynn KJ, Burkholder JM, et al. (2014) The role of mixotrophic protists in the biological carbon pump.Biogeosciences 11 , 995-1005.
Mitra A, Flynn KJ, Tillmann U, et al. (2016) Defining Planktonic Protist Functional Groups on Mechanisms for Energy and Nutrient Acquisition: Incorporation of Diverse Mixotrophic Strategies.Protist 167 , 106-120.
Not F, Gausling R, Azam F, Heidelberg JF, Worden AZ (2007) Vertical distribution of picoeukaryotic diversity in the Sargasso Sea.Environmental Microbiology 9 , 1233-1252.
Ollison GA, Hu SK, Mesrop LY, DeLong EF, Caron DA (2021) Come rain or shine: Depth not season shapes the active protistan community at station ALOHA in the North Pacific Subtropical Gyre. Deep Sea Research Part I: Oceanographic Research Papers 170 , 103494.
Orsi WD, Wilken S, del Campo J, et al. (2018) Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing. Environmental Microbiology 20 , 815-827.
Parikh HI, Koparde VN, Bradley SP, Buck GA, Sheth NU (2016) MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing. BMC Bioinformatics 17 , 491.
Place AR, Bowers HA, Bachvaroff TR, et al. (2012) Karlodinium veneficum—The little dinoflagellate with a big bite. Harmful Algae 14 , 179-195.
Quevedo M, Anadón R (2001) Protist control of phytoplankton growth in the subtropical north-east Atlantic. Marine Ecology Progress Series 221 , 29-38.
Riemann L, Nielsen TG, Kragh T, et al. (2011) Distribution and production of plankton communities in the subtropical convergence zone of the Sargasso Sea. I. Phytoplankton and bacterioplankton. Marine Ecology Progress Series 426 , 57-70.
Rocke E, Pachiadaki MG, Cobban A, Kujawinski EB, Edgcomb VP (2015) Protist Community Grazing on Prokaryotic Prey in Deep Ocean Water Masses. PLoS ONE 10 , e0124505.
Rognes T, Flouri T, Nichols B, Quince C, Mahé F (2016) VSEARCH: a versatile open source tool for metagenomics. PeerJ 4 , e2584.
Sanders RW, Berninger UG, Lim EL, Kemp PF, Caron DA (2000) Heterotrophic and mixotrophic nanoplankton predation on picoplankton in the Sargasso Sea and on Georges Bank. Marine Ecology Progress Series192 , 103-118.
Santoferrara LF (2019) Current practice in plankton metabarcoding: optimization and error management. Journal of Plankton Research41 , 571-582.
Schloss PD, Westcott SL, Ryabin T, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology 75 , 7537-7541.
Steinberg DK, Landry MR (2017) Zooplankton and the Ocean Carbon Cycle.Annual Review of Marine Science 9 , 413-444.
Stoeck T, Bass D, Nebel M, et al. (2010) Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water. Molecular Ecology 19 , 21-31.
Sunagawa S, Coelho LP, Chaffron S, et al. (2015) Structure and function of the global ocean microbiome. Science 348 .
Treusch AH, Demir-Hilton E, Vergin KL, et al. (2012) Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids. . The ISME Journal 6 , 481-492.
Treusch AH, Vergin KL, Finlay LA, et al. (2009) Seasonality and vertical structure of an ocean gyre microbial community. ISME Journal 3 , 1148-1163.
Voskamp A, Hof C, Biber MF, et al. (2020) Climate change impacts on the phylogenetic diversity of the world’s terrestrial birds: more than species numbers. bioRxiv , 2020.2012.2002.378216.
Worden AZ, Follows MJ, Giovannoni SJ, et al. (2015) Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes. Science 347 , 1257594.
Table 1. Hydrographic envelope for the vertical layers and season definitions. Vertical layers are defined based in density and the CTD-measured fluorescence. Seasons are defined based on the depth of the mixed layer (MLD), and the relative position of the deep Chla -max (DCM) with it.