Eukaryotic plankton diversity in the sunlit ocean

Abstract

Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during the circumglobal Tara Oceans expedition. We analyzed 18S ribosomal DNA sequences across the intermediate plankton-size spectrum from the smallest unicellular eukaryotes (protists, >0.8 micrometers) to small animals of a few millimeters. Eukaryotic ribosomal diversity saturated at~150,000 operational taxonomic units, about one-third of which could not be assigned to known eukaryotic groups. Diversity emerged at all taxonomic levels, both within the groups comprising the~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies. Most eukaryotic plankton biodiversity belonged to heterotrophic protistan groups, particularly those known to be parasites or symbiotic hosts.T he sunlit surface layer of the world'soceans functionsasagiantbiogeoch emicalmem-brane between the atmosphere and the ocean interior (1). This biome includes plank-ton communities that fix CO 2 and other elements into biological matter, which then enters the food web. This biological matter can be remineralized or exported to the deeper ocean, where it may be sequestered over ecological to geological time scales. Studies of this biome have typically focused on either conspicuous phyto-or zooplankton at the larger end of the organismal size spectrum or microbes (prokaryotes and viruses) at the smaller end. In this work, we studied the taxonomic and ecological diversity of the intermediate size spectrum (from 0.8 mmtoafew millimeters), which includes all unicellular eukary-otes (protists) and ranges from the smallest pro-tistan cells to small animals (2). The ecological biodiversity of marine planktonic protists has been analyzed using Sanger (3-5) and high-throughput (6, 7) sequencing of mainly ribosomal DNA (rDNA) gene markers, on relatively small taxonomic and/or geographical scales, unveiling key new groups of phagotrophs (8), parasites (9), and phototrophs (10). We sequenced 18S rDNA metabarcodes up to local and global saturations from size-fractionated plankton communities sampled systematically across the world tropical and temperate sunlit oceans. A global metabarcoding approachTo explore patterns of photic-zone eukaryotic plankton biodiversity, we generated ~766 million raw rDNA sequence reads from 334 plankton samples collected during the circumglobal Tara Oceans expedition (11). At each of 47 stations, plankton communities were sampled at two water-column depths corresponding to the main hydrographic structures of the photic zone: subsurface mixed-layer waters and the deep chlorophyll maximum (DCM) at the top of the thermocline. A low-shear, nonintrusive peristaltic pump and plankton nets of...

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

“…As in a recent sampling of the sunlit surface layer of the world's open oceans 11 , more protist OTUs were detected than animals (4,374, of which 39% were assigned to the Arthropoda), plants (3,089) and fungi (17,849) combined (Supplementary Table 1). The OTUs found in the samples may not all correspond to soil-dwelling species: some of these hyperdiverse protists and other eukaryotes could be a shadow of the tree-canopy communities from cells that have rained down from above.…”

“…DNA was isolated using the PowerSoil DNA Elution Accessory Kit (Mo Bio). Like other large-scale sequencing studies 11,49 , only DNA was used in this study, not RNA, which can also be retained in sediments, even ancient ones 50,51 . See Supplementary Fig.…”

“…Reads from the open oceans came from the Tara Oceans consortium 11 . Starting with the Tara Oceans raw reads (Sequence Read Archive accession numbers: PRJEB6610 and PRJEB7315) allowed us to treat the sequencing data with the same bioinformatic pipeline.…”

“…To evaluate if macroorganismic diversity patterns are reflected at the microbial scale with protists, we conducted an environmental DNA metabarcoding study by sampling soils in 279 locations in a variety of lowland Neotropical forest types in La Selva Biological Station, Costa Rica, Barro Colorado Island, Panama and Tiputini Biodiversity Station, Ecuador. This metabarcoding approach has the power to uncover known and new taxa on a massive scale 11 . By amplifying DNA extracted from the soils with broadly targeted primers for the V4 region of 18S rRNA and sequencing it using the Illumina MiSeq platform, we were able to detect most eukaryotic lineages, and assess the diversity and relative dominance of free-living and parasitic lineages.…”

Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies

“…Interestingly, both Pearson and Spearman rank correlations were typically strongest for the nuclear 18S rDNA marker. Many studies have shown strong correlations between biovolume and 18S copy number for a range of eukaryotic taxa, including metazoans (Godhe et al., 2008; de Vargas et al., 2015; Zhu, Massana, Not, Marie, & Vaulot, 2005). Several factors could reduce the strength of the correlation between biomass and HTS reads in this study, including using separate samples for DNA‐based and morphology‐based identification, and estimating biomass using conversion factors rather than direct measurement.…”