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. (C) 2021 The Authors. Published by Elsevier GmbHThis work was supported by the IMPEKAB ANR 15-CE02-0011 grant and the Brittany Region ARED C16 1520A01, the Japan Society for Promotion of Science KAKENHI Grant No. K16K0-74750 for N. Suzuki and "the Cooperative Research Project with the Japan Science and Technology Agency (JST) and Centre National de la Recherche Scientifique (CNRS, France) "Morphomolecular Diversity Assessment of Ecologically, Evolutionary, and Geo-logically Relevant Marine Plankton (Radiolaria) ". We are grateful to the CNRS-Sorbonne University ABiMS bioinformatics platform (http://abims.sbroscoff.fr) for providing computational resources. The authors are grateful to the MOOSE observation national network (funded by CNRS-INSU and Research Infrastructure ILICO) which sustain the annual ship-based hydrographic sections in the northwestern Mediterranean Sea (MOOSEGE) , as well as John Dolan for hosting us multiple times at the Laboratoire d'Oceanographie of Villefranche sur Mer. We are greatly thankful to Cedric Berney for the phylogenetic advice and the valuable help on the interpretation of the "symbiotic" clade, as well as Vasily Zlatogursky for his contributions and feed-back on the heliozoan-like organism

Transcriptome analyses to investigate symbiotic relationships between marine protists

International audienceRhizaria are an important component of oceanic plankton communities worldwide. A number of species harbor eukaryotic microalgal symbionts, which are horizontally acquired in the environment at each generation. Although these photosymbioses are determinant for Rhizaria ability to thrive in oceanic ecosystems, the mechanisms for symbiotic interactions are unclear. Using high-throughput sequencing technology (i.e., 454), we generated large Expressed Sequence Tag (EST) datasets from four uncultured Rhizaria, an acantharian (Amphilonche elongata), two polycystines (Collozoum sp. and Spongosphaera streptacantha), and one phaeodarian (Aulacantha scolymantha). We assessed the main genetic features of the host/symbionts consortium (i.e., the holobiont) transcriptomes and found rRNA sequences affiliated to a wide range of bacteria and protists in all samples, suggesting that diverse microbial communities are associated with the holobionts. A particular focus was then carried out to search for genes potentially involved in symbiotic processes such as the presence of c-type lectins-coding genes, which are proteins that play a role in cell recognition among eukaryotes. Unigenes coding putative c-type lectin domains (CTLD) were found in the species bearing photosynthetic symbionts (A. elongata, Collozoum sp., and S. streptacantha) but not in the non-symbiotic one (A. scolymantha). More particularly, phylogenetic analyses group CTLDs from A. elongata and Collozoum sp. on a distinct branch from S. streptacantha CTLDs, which contained carbohydrate-binding motifs typically observed in other marine photosymbiosis. Our data suggest that similarly to other well-known marine photosymbiosis involving metazoans, the interactions of glycans with c-type lectins is likely involved in modulation of the host/symbiont specific recognition in Radiolaria

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

International audiencePlanktonic organisms play crucial roles in oceanic food webs and global biogeochemical cycles1, 2. Most of our knowledge about the ecological impact of large zooplankton stems from research on abundant and robust crustaceans, and in particular copepods3, 4. 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 reservoir5. 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 planet6 changes our understanding of marine planktonic ecosystems

Diversity of photosynthetic picoeukaryotes in eutrophic shallow lakes as assessed by combining flow cytometry cell-sorting and high throughput sequencing

Photosynthetic picoeukaryotes (PPE) are key components of primary production in marine and freshwater ecosystems. In contrast with those of marine environments, freshwater PPE groups have received little attention. In this work, we used flow cytometry cell sorting, microscopy and metabarcoding to investigate the composition of small photosynthetic eukaryote communities from six eutrophic shallow lakes in South America, Argentina. We compared the total molecular diversity obtained from PPE sorted populations as well as from filtered total plankton samples (FTP). Most reads obtained from sorted populations belonged to the classes: Trebouxiophyceae, Chlorophyceae and Bacillariophyceae. We retrieved sequences from non-photosynthetic groups, such as Chytridiomycetes and Ichthyosporea which contain a number of described parasites, indicating that these organisms were probably in association with the autotrophic cells sorted. Dominant groups among sorted PPEs were poorly represented in FTP and their richness was on average lower than in the sorted samples. A significant number of operational taxonomic units (OTUs) were exclusively found in sorting samples, emphasizing that sequences from FTP underestimate the diversity of PPE. Moreover, 22% of the OTUs found among the dominant groups had a low similarity (<95%) with reported sequences in public databases, demonstrating a high potential for novel diversity in these lakes.Fil: Metz, Sebastián Darío. Universidad Nacional de San Martin. Instituto Tecnológico de Chascomús - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Tecnológico de Chascomús; ArgentinaFil: Dos Santos, Adriana Lopes. Sorbonne University; Francia. Centre National de la Recherche Scientifique; Francia. Nanyang Technological University; SingapurFil: Castro Berman, Manuel. Universidad Nacional de San Martin. Instituto Tecnológico de Chascomús - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Tecnológico de Chascomús; ArgentinaFil: Bigeard, Estelle. Sorbonne University; Francia. Centre National de la Recherche Scientifique; Francia. Nanyang Technological University; SingapurFil: Licursi, Magdalena. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto Nacional de Limnología. Universidad Nacional del Litoral. Instituto Nacional de Limnología; ArgentinaFil: Not, Fabrice. Sorbonne University; Francia. Centre National de la Recherche Scientifique; FranciaFil: Lara, Enrique. University of Neuchatel; SuizaFil: Unrein, Fernando. Universidad Nacional de San Martin. Instituto Tecnológico de Chascomús - Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto Tecnológico de Chascomús; Argentin

A global perspective on marine photosynthetic picoeukaryote community structure

A central goal in ecology is to understand the factors affecting the temporal dynamics and spatial distribution of microorganisms and the underlying processes causing differences in community structure and composition. However, little is known in this respect for photosynthetic picoeukaryotes (PPEs), algae that are now recognised as major players in marine CO2 fixation. Here, we analysed dot blot hybridisation and cloning–sequencing data, using the plastid-encoded 16S rRNA gene, from seven research cruises that encompassed all four ocean biomes. We provide insights into global abundance, α- and β-diversity distribution and the environmental factors shaping PPE community structure and composition. At the class level, the most commonly encountered PPEs were Prymnesiophyceae and Chrysophyceae. These taxa displayed complementary distribution patterns, with peak abundances of Prymnesiophyceae and Chrysophyceae in waters of high (25:1) or low (12:1) nitrogen:phosphorus (N:P) ratio, respectively. Significant differences in phylogenetic composition of PPEs were demonstrated for higher taxonomic levels between ocean basins, using Unifrac analyses of clone library sequence data. Differences in composition were generally greater between basins (interbasins) than within a basin (intrabasin). These differences were primarily linked to taxonomic variation in the composition of Prymnesiophyceae and Prasinophyceae whereas Chrysophyceae were phylogenetically similar in all libraries. These data provide better knowledge of PPE community structure across the world ocean and are crucial in assessing their evolution and contribution to CO2 fixation, especially in the context of global climate change

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts

New Insights into the Diversity of Marine Picoeukaryotes

Over the last decade, culture-independent surveys of marine picoeukaryotic diversity based on 18S ribosomal DNA clone libraries have unveiled numerous sequences of novel high-rank taxa. This newfound diversity has significantly altered our understanding of marine microbial food webs and the evolution of eukaryotes. However, the current picture of marine eukaryotic biodiversity may be significantly skewed by PCR amplification biases, occurrence of rDNA genes in multiple copies within a single cell, and the capacity of DNA to persist as extracellular material. In this study we performed an analysis of the metagenomic dataset from the Global Ocean Survey (GOS) expedition, seeking eukaryotic ribosomal signatures. This PCR-free approach revealed similar phylogenetic patterns to clone library surveys, suggesting that PCR steps do not impose major biases in the exploration of environmental DNA. The different cell size fractions within the GOS dataset, however, displayed a distinct picture. High protistan diversity in the <0.8 µm size fraction, in particular sequences from radiolarians and ciliates (and their absence in the 0.8–3 µm fraction), suggest that most of the DNA in this fraction comes from extracellular material from larger cells. In addition, we compared the phylogenetic patterns from rDNA and reverse transcribed rRNA 18S clone libraries from the same sample harvested in the Mediterranean Sea. The libraries revealed major differences, with taxa such as pelagophytes or picobiliphytes only detected in the 18S rRNA library. MAST (Marine Stramenopiles) appeared as potentially prominent grazers and we observed a significant decrease in the contribution of alveolate and radiolarian sequences, which overwhelmingly dominated rDNA libraries. The rRNA approach appears to be less affected by taxon-specific rDNA copy number and likely better depicts the biogeochemical significance of marine protists

Role of small Rhizaria and diatoms in the pelagic silica production of the Sourther Ocean

We examined biogenic silica production and elementary composition (biogenic Si, particulate organic carbon and particulate organic nitrogen) of Rhizaria and diatoms in the upper 200 m along a transect in the Southwest Pacific sector of the Southern Ocean during austral summer (January–February 2019). From incubations using the 32Si radioisotope, silicic acid uptake rates were measured at 15 stations distributed in the Polar Front Zone, the Southern Antarctic Circumpolar Current and the Ross Sea Gyre. Rhizaria cells are heavily silicified (up to 7.6 nmol Si cell−1), displaying higher biogenic Si content than similar size specimens found in other areas of the global ocean, suggesting a higher degree of silicification of these organisms in the silicic acid rich Southern Ocean. Despite their high biogenic Si and carbon content, the Si/C molar ratio (average of 0.05 ± 0.03) is quite low compared to that of diatoms and relatively constant regardless of the environmental conditions. The direct measurements of Rhizaria's biogenic Si production (0.8–36.8 μmol Si m−2 d−1) are of the same order of magnitude than previous indirect estimations, confirming the importance of the Southern Ocean for the global Rhizaria silica production. However, diatoms largely dominated the biogenic Si standing stock and production of the euphotic layer, with low rhizarians' abundances and biogenic Si production (no more than 1%). In this manuscript, we discuss the Antarctic paradox of Rhizaria, that is, the potential high accumulation rates of biogenic Si due to Rhizaria in siliceous sediments despite their low production rates in surface waters.Versión del editor3,38

Symbiont Chloroplasts Remain Active During Bleaching-Like Response Induced by Thermal Stress in Collozoum pelagicum (Collodaria, Retaria)

Collodaria (Retaria) are important contributors to planktonic communities and biogeochemical processes (e.g., the biologic pump) in oligotrophic oceans. Similarly to corals, Collodaria live in symbiosis with dinoflagellate algae, a relationship that is thought to explain partly their ecological success. In the context of global change, the robustness of the symbiotic interaction, and potential subsequent bleaching events are of primary interest for oceanic ecosystems functioning. In the present study, we compared the ultrastructure, morphology, symbiont density, photosynthetic capacities and respiration rates of colonial Collodaria exposed to a range of temperatures corresponding to natural conditions (21°C), moderate (25°C), and high (28°C) thermal stress. We showed that symbiont density immediately decreased when temperature rose to 25°C, while the overall Collodaria holobiont metabolic activity increased. When temperature reached 28°C, the holobiont respiration nearly stopped and the host morphological structure was largely damaged, as if the host tolerance threshold has been crossed. Over the course of the experiment, the photosynthetic capacities of remaining algal symbionts were stable, chloroplasts being the last degraded organelles in the microalgae. These results contribute to a better characterization and understanding of temperature-induced bleaching processes in planktonic photosymbioses