Diversity and ecology of Radiolaria in modern oceans.

Among the many inhabitants of planktonic communities, several lineages have biomineralized intricate skeletons. These have existed for millions of years and include the Radiolaria, a group of marine protists, many of which bear delicate mineral skeletons of different natures. Radiolaria are well known for their paleontological signatures, but little is known about the ecology of modern assemblages. They are found from polar to tropical regions, in the sunlit layers of the ocean down to the deep and cold bathypelagic. They are closely involved in the biogeochemical cycles of silica, carbon and strontium sulfate, carrying important amounts of such elements to the deep ocean. However, relatively little is known on the actual extent of genetic diversity or biogeographic patterns. The rapid emergence and acceptance of molecular approaches have nevertheless led to major advances in our understanding of diversity within and evolutionary relationships between major radiolarian groups. Here, we review the state of knowledge relating to the classification, diversity and ecology of extant radiolarian orders, highlighting the substantial gaps in our understanding of the extent of their contribution to marine biodiversity and their role in marine food webs.

Machine learning techniques to characterize functional traits of plankton from image data.

Plankton imaging systems supported by automated classification and analysis have improved ecologists' ability to observe aquatic ecosystems. Today, we are on the cusp of reliably tracking plankton populations with a suite of lab-based and in situ tools, collecting imaging data at unprecedentedly fine spatial and temporal scales. But these data have potential well beyond examining the abundances of different taxa; the individual images themselves contain a wealth of information on functional traits. Here, we outline traits that could be measured from image data, suggest machine learning and computer vision approaches to extract functional trait information from the images, and discuss promising avenues for novel studies. The approaches we discuss are data agnostic and are broadly applicable to imagery of other aquatic or terrestrial organisms.

In situ imaging reveals the biomass of giant protists in the global ocean.

Planktonic organisms play crucial roles in oceanic food webs and global biogeochemical cycles. Most of our knowledge about the ecological impact of large zooplankton stems from research on abundant and robust crustaceans, and in particular copepods. A number of the other organisms that comprise planktonic communities are fragile, and therefore hard to sample and quantify, meaning that their abundances and effects on oceanic ecosystems are poorly understood. Here, using data from a worldwide in situ imaging survey of plankton larger than 600 µm, we show that a substantial part of the biomass of this size fraction consists of giant protists belonging to the Rhizaria, a super-group of mostly fragile unicellular marine organisms that includes the taxa Phaeodaria and Radiolaria (for example, orders Collodaria and Acantharia). Globally, we estimate that rhizarians in the top 200 m of world oceans represent a standing stock of 0.089 Pg carbon, equivalent to 5.2% of the total oceanic biota carbon reservoir. In the vast oligotrophic intertropical open oceans, rhizarian biomass is estimated to be equivalent to that of all other mesozooplankton (plankton in the size range 0.2-20 mm). The photosymbiotic association of many rhizarians with microalgae may be an important factor in explaining their distribution. The previously overlooked importance of these giant protists across the widest ecosystem on the planet changes our understanding of marine planktonic ecosystems.

Brandtodinium gen. nov. and B. nutricula comb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians.

Symbiotic interactions between pelagic hosts and microalgae have received little attention, although they are widespread in the photic layer of the world ocean, where they play a fundamental role in the ecology of the planktonic ecosystem. Polycystine radiolarians (including the orders Spumellaria, Collodaria and Nassellaria) are planktonic heterotrophic protists that are widely distributed and often abundant in the ocean. Many polycystines host symbiotic microalgae within their cytoplasm, mostly thought to be the dinoflagellate Scrippsiella nutricula, a species originally described by Karl Brandt in the late nineteenth century as Zooxanthella nutricula. The free-living stage of this dinoflagellate has never been characterized in terms of morphology and thecal plate tabulation. We examined morphological characters and sequenced conservative ribosomal markers of clonal cultures of the free-living stage of symbiotic dinoflagellates isolated from radiolarian hosts from the three polycystine orders. In addition, we sequenced symbiont genes directly from several polycystine-symbiont holobiont specimens from different oceanic regions. Thecal plate arrangement of the free-living stage does not match that of Scrippsiella or related genera, and LSU and SSU rDNA-based molecular phylogenies place these symbionts in a distinct clade within the Peridiniales. Both phylogenetic analyses and the comparison of morphological features of culture strains with those reported for other closely related species support the erection of a new genus that we name Brandtodinium gen. nov. and the recombination of S. nutricula as B. nutricula comb. nov.

Global census of the significance of giant mesopelagic protists to the marine carbon and silicon cycles.

Thriving in both epipelagic and mesopelagic layers, Rhizaria are biomineralizing protists, mixotrophs or flux-feeders, often reaching gigantic sizes. In situ imaging showed their contribution to oceanic carbon stock, but left their contribution to element cycling unquantified. Here, we compile a global dataset of 167,551 Underwater Vision Profiler 5 Rhizaria images, and apply machine learning models to predict their organic carbon and biogenic silica biomasses in the uppermost 1000 m. We estimate that Rhizaria represent up to 1.7% of mesozooplankton carbon biomass in the top 500 m. Rhizaria biomass, dominated by Phaeodaria, is more than twice as high in the mesopelagic than in the epipelagic layer. Globally, the carbon demand of mesopelagic, flux-feeding Phaeodaria reaches 0.46 Pg C y-1, representing 3.8 to 9.2% of gravitational carbon export. Furthermore, we show that Rhizaria are a unique source of biogenic silica production in the mesopelagic layer, where no other silicifiers are present. Our global census further highlights the importance of Rhizaria for ocean biogeochemistry.

A Morpho-molecular Perspective on the Diversity and Evolution of Spumellaria (Radiolaria).

Spumellaria (Radiolaria, Rhizaria) are holoplanktonic amoeboid protists, ubiquitous and abundant in the global ocean. Their silicified skeleton preserves very well in sediments, displaying an excellent fossil record extremely valuable for paleo-environmental reconstruction studies, from where most of their extant diversity and ecology have been inferred. This study represents a comprehensive classification of Spumellaria based on the combination of ribosomal taxonomic marker genes (rDNA) and morphological characteristics. In contrast to established taxonomic knowledge, we demonstrate that symmetry of the skeleton takes more importance than internal structures at high classification ranks. Such reconsideration allows gathering different morphologies with concentric structure and spherical or radial symmetry believed to belong to other Radiolaria orders from the fossil record, as for some Entactinaria families. Our calibrated molecular clock dates the origin of Spumellaria in the middle Cambrian (ca. 515 Ma), among the first radiolarian representatives in the fossil record. This study allows a direct connection between living specimens and extinct morphologies from the Cambrian, bringing both a standpoint for future molecular environmental surveys and a better understanding for paleo-environmental reconstruction analysis.

Time Calibrated Morpho-molecular Classification of Nassellaria (Radiolaria).

Nassellaria are marine protists belonging to the Radiolaria lineage (Rhizaria). Their skeleton, made of opaline silica, exhibit an excellent fossil record, extremely valuable in micro-paleontological studies for paleo-environmental reconstruction. Yet, to date very little is known about the extant diversity and ecology of Nassellaria in contemporary oceans, and most of it is inferred from their fossil record. Here we present an integrative classification of Nassellaria based on taxonomical marker genes (18S and 28S ribosomal DNA) and morphological characteristics obtained by optical and scanning electron microscopy imaging. Our phylogenetic analyses distinguished 11 main morpho-molecular clades relying essentially on the overall morphology of the skeleton and not on internal structures as previously considered. Using fossil calibrated molecular clock we estimated the origin of Nassellaria among radiolarians primitive forms in the Devonian (ca. 420 Ma), that gave rise to living nassellarian groups in the Triassic (ca. 250 Ma), during the biggest diversification event over their evolutionary history. This morpho-molecular framework provides both a new morphological classification easier to identify under light microscopy and the basis for future molecular ecology surveys. Altogether, it brings a new standpoint to improve our scarce understanding of the ecology and worldwide distribution of extant nassellarians.

High contribution of Rhizaria (Radiolaria) to vertical export in the California Current Ecosystem revealed by DNA metabarcoding.

Passive sinking of particulate organic matter (POM) is the main mechanism through which the biological pump transports surface primary production to the ocean interior. However, the contribution and variability of different biological sources to vertical export is not fully understood. Here, we use DNA metabarcoding of the 18S rRNA gene and particle interceptor traps (PITs) to characterize the taxonomic composition of particles sinking out of the photic layer in the California Current Ecosystem (CCE), a productive system with high export potential. The PITs included formalin-fixed and 'live' traps to investigate eukaryotic communities involved in the export and remineralization of sinking particles. Sequences affiliated with Radiolaria dominated the eukaryotic assemblage in fixed traps (90%), with Dinophyta and Metazoa making minor contributions. The prominence of Radiolaria decreased drastically in live traps, possibly due to selective consumption by copepods, heterotrophic nanoflagellates, and phaeodarians that were heavily enriched in these traps. These patterns were consistent across the water masses surveyed extending from the coast to offshore, despite major differences in productivity and trophic structure of the epipelagic plankton community. Our findings identify Radiolaria as major actors in export fluxes in the CCE.

Biogeography and diversity of Collodaria (Radiolaria) in the global ocean.

Collodaria are heterotrophic marine protists that exist either as large colonies composed of hundreds of cells or as large solitary cells. All described species so far harbour intracellular microalgae as photosymbionts. Although recent environmental diversity surveys based on molecular methods demonstrated their consistently high contribution to planktonic communities and their worldwide occurrence, our understanding of their diversity and biogeography is still very limited. Here we estimated the 18S ribosomal DNA (rDNA) gene copies per collodarian cell for solitary (5770±1960 small subunit (SSU) rDNA copies) and colonial specimens (37 474±17 799 SSU rDNA copies, for each individual cell within a colony) using single-specimen quantitative PCR. We then investigated the environmental diversity of Collodaria within the photic zone through the metabarcoding survey from the Tara Oceans expedition and found that the two collodarian families Collosphaeridae and Sphaerozoidae contributed the most to the collodarian diversity and encompassed mostly cosmopolitan taxa. Although the biogeographical patterns were homogeneous within each biogeochemical biome considered, we observed that coastal biomes were consistently less diverse than oceanic biomes and were dominated by the Sphaerozoidae while the Collosphaeridae were dominant in the open oceans. The significant relationships with six environmental variables suggest that collodarian diversity is influenced by the trophic status of oceanic provinces and increased towards more oligotrophic regions.

Towards an Integrative Morpho-molecular Classification of the Collodaria (Polycystinea, Radiolaria).

Collodaria are ubiquitous and abundant marine radiolarian (Rhizaria) protists. They occur as either large colonies or solitary specimens, and, unlike most radiolarians, some taxa lack silicified structures. Collodarians are known to play an important role in oceanic food webs as both active predators and hosts of symbiotic microalgae, yet very little is known about their diversity and evolution. Taxonomic delineation of collodarians is challenging and only a few species have been genetically characterized. Here we investigated collodarian diversity using phylogenetic analyses of both nuclear small (18S) and large (28S) subunits of the ribosomal DNA, including 124 new sequences from 75 collodarians sampled worldwide. The resulting molecular phylogeny was compared to morphology-based classification. Our analyses distinguished the monophyletic clade of skeleton-less and spicule-bearing Sphaerozoidae from the sister clades Collosphaeridae (skeleton-bearing) and Collophidiidae (skeleton-less), while the Thalassicollidae was not retrieved as a monophyletic clade. Detailed morphological examination with electron microscopy combined with molecular analyses revealed many discrepancies, such as a mix between solitary and colonial species, co-existence of skeleton-less and skeleton-bearing specimens within the Collosphaeridae, as well as complex intraspecific variability in silicified structures. Such observations challenge a morphology-based classification and highlight the pertinence of an integrative taxonomic approach to study collodarian diversity.