Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

Abstract

Among eukaryotes, four major phytoplankton lineages are responsible for marine photosynthesis; prymnesiophytes, alveolates, stramenopiles, and prasinophytes. Contributions by individual taxa, however, are not well known, and genomes have been analyzed from only the latter two lineages. Tiny "picoplanktonic" members of the prymnesiophyte lineage have long been inferred to be ecologically important but remain poorly characterized. Here, we examine pico-prymnesiophyte evolutionary history and ecology using cultivation-independent methods. 18S rRNA gene analysis showed picoprymnesiophytes belonged to broadly distributed uncultivated taxa. Therefore, we used targeted metagenomics to analyze uncultured pico-prymnesiophytes sorted by flow cytometry from subtropical North Atlantic waters. The data reveal a composite nuclear-encoded gene repertoire with strong green-lineage affiliations, which contrasts with the evolutionary history indicated by the plastid genome. Measured pico-prymnesiophyte growth rates were rapid in this region, resulting in primary production contributions similar to the cyanobacterium Prochlorococcus. On average, picoprymnesiophytes formed 25% of global picophytoplankton biomass, with differing contributions in five biogeographical provinces spanning tropical to subpolar systems. Elements likely contributing to success include high gene density and genes potentially involved in defense and nutrient uptake. Our findings have implications reaching beyond pico-prymnesiophytes, to the prasinophytes and stramenopiles. For example, prevalence of putative Ni-containing superoxide dismutases (SODs), instead of Fe-containing SODs, seems to be a common adaptation among eukaryotic phytoplankton for reducing Fe quotas in low-Fe modern oceans. Moreover, highly mosaic gene repertoires, although compositionally distinct for each major eukaryotic lineage, now seem to be an underlying facet of successful marine phytoplankton.comparative genomics | primary production | prymnesiophytes | marine photosynthesis | haptophytes G lobal primary production is partitioned equally among terrestrial and marine ecosystems, each accounting for ≈50 gigatons of carbon per year (1). The phytoplankton responsible for marine primary production include the cyanobacteria, Prochlorococcus and Synechococcus, and a multitude of eukaryotic phytoplankton, such as diatoms, dinoflagellates, prasinophytes, and prymnesiophytes (2-4). Most oceanic phytoplankton are "picoplanktonic" (<2-3 μm diameter) and have high surface area to volume ratios, an advantage in open-ocean low-nutrient conditions (5-8). Despite the importance of eukaryotic phytoplankton to carbon cycling only six genomes have been sequenced and analyzed comparatively, all being from diatoms and prasinophytes. These revealed greater differentiation than anticipated on the basis of 18S rRNA gene analyses (9-11). The observed genomic divergence is associated with major differences in physiology and niche adaptation (10).Pigment-based estimates indicate that prymnesiophytes, also know...

A global perspective on marine photosynthetic picoeukaryote community structure

“…Together, these data suggest large global distributions of pico-sized prymnesiophytes, which contribute significantly to marine primary production (Cuvelier et al, 2010;Jardillier et al, 2010) even though they mostly lack cultured representatives. The success of these organisms could be because of mixotrophic behaviour (that is, an ability to supplement their phototrophic physiology by preying on bacterioplankton).…”

“…The x-axis explains 9.3% and the y-axis explains 3.8% of the variation in dot blot hybridisation data. this respect, metagenomic analysis of a natural picoprymnesiophyte population revealed a mosaic gene repertoire including specific adaptations for growth in oligotrophic environments (Cuvelier et al, 2010), conditions that may represent a driver of niche differentiation. Furthermore, light availability has been shown to be associated with niche partitioning in prokaryotic picophytoplankton (Moore et al, 1998;West and Scanlan, 1999) and within the prasinophyte genus Ostreococcus , and may also drive the niche adaptation process in the Prymnesiophyceae.…”

“…In particular, cloning and sequencing of both nuclear (for example, see Moon van der Staay et al, 2001;Not et al, 2008) and plastid (for example, see Fuller et al, 2006b;MacDonald et al, 2007;Lepère et al, 2009) small subunit rRNA genes have revealed a vast, previously unsuspected diversity within this assemblage. This focus is largely because of the increased recognition of PPEs as key contributors to phytoplankton biomass and primary production across various marine pelagic ecosystems (Li, 1994;Worden et al, 2004;Richardson and Jackson, 2007;Cuvelier et al, 2010;Jardillier et al, 2010;Grob et al, 2011). Moreover, PPEs have recently been shown to be key bacterivores controlling bacterioplankton abundance in both temperate (Zubkov and Tarran, 2008) and oligotrophic gyre (Hartmann et al, 2012) waters.…”

Mixotrophic haptophytes are key bacterial grazers in oligotrophic coastal waters

“…Environmental surveys using molecular approaches have revealed a high contribution and diversity of haptophytes (Prymnesiophyceae) among the small photosynthetic eukaryotes in marine (Fuller et al, 2006;Liu et al, 2009;Cuvelier et al, 2010;Shi et al, 2011;Treusch et al, 2012) but also in some freshwater ecosystems (Bielewicz et al, 2011;Kong et al, 2012). In addition, Jardillier et al (2010) estimated that haptophytes are responsible for a very significant percentage of the total CO 2 fixation in the tropical and subtropical Northeast Atlantic Ocean.…”

Coupling FACS and Genomic Methods for the Characterization of Uncultivated Symbionts

“…While several high-throughput flow sorters are available, the BD Biosciences Influx™ Cell Sorter has been the FACS of choice for several recent studies on uncultivated symbionts Cuvelier, et al, 2010;Tripp, et al, 2010;Vaulot, et al, 2012). The Influx™ can be equipped with ten laser paths supporting collection of 24 data parameters, with the choice of lasers dependent on target cell types.…”