Academic literature on the topic 'Pelagomonas calceolata'

Abstract. In late 2004, the BIOSOPE cruise sailed between the equatorial influenced waters off Marquesas islands and the nutrient enriched waters of the Chilean upwelling. Along the way, it explored the Southeast Pacific gyre centred around Easter Island, which is probably the most oligotrophic oceanic region on earth. During this cruise, we undertook a vigorous effort to isolate novel photosynthetic picoplanktonic eukaryotes. Two strategies were attempted on board: enrichment of samples with culture medium and sorting of specific populations by flow cytometry based on chlorophyll fluorescence. Over 1900 pre-cultures were started and then further purified by flow cytometry, serial dilution or pipette isolation to yield a total of 212 strains. These strains were characterized morphologically and for more than 50% of them, genetically, through partial sequencing of the 18 S rRNA gene. Among the characterized strains, the largest number are stramenopiles (Heterokontophyta) with a record of 38 strains belonging to the species Pelagomonas calceolata (Pelagophyceae). Strains from the recently described genera Bolidomonas and Florenciella have been re-isolated for the first time since their description. Two other abundant groups are the Chlorophyta, especially Prasinophyceae, and the Haptophyta, especially the genera Phaeocystis and Emiliania. A limited number of heterotrophic flagellates have also been isolated, all of them closely related to known species. Finally over a dozen of unicellular cyanobacteria strains have been obtained, some forming unusual short chains. Overall our strategy was quite successful since it allowed us to isolate a large number of picoplankton strains but failed in two respects. First, apparently very few novel taxa have been obtained. One set of strains is related to Prasinoderma coloniale (Prasinococcales, Prasinophyceae) but their sequences are sufficiently different from the latter to probably belong to a new genus or species. The sequences of two other strains are phylogenetically affiliated to stramenopile environmental sequences, probably corresponding a new algal class. Second, very few strains have been obtained from the very oligotrophic central gyre itself. Future work should probably combine flow cytometry sorting with culture media and cultivation approaches specifically developed for oligotrophic water species.

Abstract. In late 2004, the BIOSOPE cruise sailed between the equatorial influenced waters off the Marquesas Islands and the nutrient enriched waters of the Chilean upwelling. Along the way, it explored the Southeast Pacific gyre centred around Easter Island, which is probably the most oligotrophic oceanic region on earth. During this cruise, we undertook a vigorous effort to isolate novel photosynthetic picoplanktonic eukaryotes. Two strategies were attempted on board: enrichment of filtered samples with culture medium and sorting of specific populations by flow cytometry based on size and chlorophyll fluorescence. Over 1900 pre-cultures were started and then further purified by flow cytometry, serial dilution or pipette isolation to yield a total of 212 strains. These strains were characterized morphologically and for more than 50% of them, genetically, through partial sequencing of the 18 S rRNA gene. Among the characterized strains, the largest number belongs to stramenopiles (Heterokontophyta) with a record of 38 strains belonging to the species Pelagomonas calceolata (Pelagophyceae). Strains from the recently described genera Bolidomonas and Florenciella have been re-isolated for the first time since their description. Two other abundant groups are the Chlorophyta, especially Prasinophyceae, and the Haptophyta, especially the genera Phaeocystis and Emiliania. A limited number of heterotrophic flagellates have also been isolated, all of them belonging to groups containing known species. Finally, over a dozen of unicellular cyanobacterial Synechococcus strains have been obtained, some forming unusual short chains. Overall our strategy was quite successful since it allowed us to isolate a large number of picoplankton strains. Still it failed in two respects. First, apparently very few novel taxa have been obtained. One set of strains is related to Prasinoderma coloniale (Prasinococcales, Prasinophyceae) but their sequences are sufficiently different from the latter to probably belong to a new genus or species. The sequences of two other strains, unfortunately later lost, were phylogenetically affiliated to stramenopile environmental sequences, probably corresponding to a new algal class. Second, very few strains have been obtained from the very oligotrophic central gyre itself. In order to be successful, future work in similar waters should probably combine flow cytometry sorting with culture media and cultivation approaches specifically developed for oligotrophic water species.

AbstractThe smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment.

Pelagophytes are abundant picophytoplankton within open ocean ecosystems and the causative algae of harmful brown tide blooms in estuaries. The physiological capabilities facilitating the ecological success of pelagophytes in these diverse ecosystems remains poorly understood. Here, we investigated the transcriptional response of two coastal pelagophytes (Aureococcus anophagefferens and Aureoumbra lagunensis) and two open ocean pelagophytes (Pelagococcus subviridis and Pelagomonas calceolata) to conditions commonly found within the marine ecosystems where they thrive: low concentrations of nitrogen (N), phosphorus (P), or light. OrthoMCL was used to generate a total of 62,653 orthologous groups (OGs) with only a small fraction of these OGs (2,776 or 4.4%) being shared among all four pelagophytes. Of the commonly shared OGs, 8% were significantly differentially abundant under low N, P, or light with the majority associated with energy and lipid metabolism. Distinct responses among pelagophytes included increased abundance of transcripts encoding phosphate transporters (Aureococcus) and transcripts encoding a pyrophosphatase (Aureococcus and Pelagomonas) under low P, the expression of a suite of organic nitrogen-degrading enzymes under low N (Aureoumbra and Pelagomonas), increased abundance of transcripts encoding flavodoxins relative to ferredoxins (Pelagomonas) and transcripts encoding lysophospholipase (Pelagococcus) under low light, and both increases and decreases in abundance of transcripts encoding selenoproteins in all pelagophytes except Pelagococcus. Collectively, this study provides new information on the expressed gene compliment of these poorly characterized taxa and demonstrates that these pelagophytes possess a combination of shared and unique physiological features that likely facilitate their adaptation to distinct environmental conditions.

Abstract The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756), and five strains of Aureoc. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984, and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 bp (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five Aureoc. anophagefferens strains varied slightly in length (42,401–42,621 bp) and were 99.4–100.0% identical. Gene content and order were highly conserved between the Aureoc. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in Aureoc. anophagefferens containingDNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. Although the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five Aureoc. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to nonbloom-forming species.

ABSTRACT Vitamin B 1 (thiamin) is a cofactor for critical enzymatic processes and is scarce in surface oceans. Several eukaryotic marine algal species thought to rely on exogenous thiamin are now known to grow equally well on the precursor 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), including the haptophyte Emiliania huxleyi . Because the thiamin biosynthetic capacities of the diverse and ecologically important haptophyte lineage are otherwise unknown, we investigated the pathway in transcriptomes and two genomes from 30 species representing six taxonomic orders. HMP synthase is missing in data from all studied taxa, but the pathway is otherwise complete, with some enzymatic variations. Experiments on axenic species from three orders demonstrated that equivalent growth rates were supported by 1 µM HMP or thiamin amendment. Cellular thiamin quotas were quantified in the oceanic phytoplankter E. huxleyi using the thiochrome assay. E. huxleyi exhibited luxury storage in standard algal medium [(1.16 ± 0.18) × 10 −6 pmol thiamin cell −1 ], whereas quotas in cultures grown under more environmentally relevant thiamin and HMP supplies [(2.22 ± 0.07) × 10 −7 or (1.58 ± 0.14) × 10 −7 pmol thiamin cell −1 , respectively] were significantly lower than luxury values and prior estimates. HMP and its salvage-related analog 4-amino-5-aminomethyl-2-methylpyrimidine (AmMP) supported higher growth than thiamin under environmentally relevant supply levels. These compounds also sustained growth of the stramenopile alga Pelagomonas calceolata . Together with identification of a salvage protein subfamily (TENA_E) in multiple phytoplankton, the results indicate that salvaged AmMP and exogenously acquired HMP are used by several groups for thiamin production. Our studies highlight the potential importance of thiamin pathway intermediates and their analogs in shaping phytoplankton community structure. IMPORTANCE The concept that vitamin B 1 (thiamin) availability in seawater controls the productivity and structure of eukaryotic phytoplankton communities has been discussed for half a century. We examined B 1 biosynthesis and salvage pathways in diverse phytoplankton species. These comparative genomic analyses as well as experiments show that phytoplankton thought to require exogenous B 1 not only utilize intermediate compounds to meet this need but also exhibit stronger growth on these compounds than on thiamin. Furthermore, oceanic phytoplankton have lower cellular thiamin quotas than previously reported, and salvage of intermediate compounds is likely a key mechanism for meeting B 1 requirements under environmentally relevant scenarios. Thus, several lines of evidence now suggest that availability of specific precursor molecules could be more important in structuring phytoplankton communities than the vitamin itself. This understanding of preferential compound utilization and thiamin quotas will improve biogeochemical model parameterization and highlights interaction networks among ocean microbes.

Les picoeucaryotes photosynthétiques (PPE) sont abondants dans tous les océans et constituent une part importante de la biomasse et de la production primaire. Les modèles climatiques prédisent une extension des zones oligotrophes dans les prochaines décennies ce qui pourrait fortement augmenter l'abondance et l'impact écologique des PPE. Parmi eux, la microalgue Pelagomonas calceolata (Stramenopiles/Pelagophyceae) est très largement répandue dans les océans (Worden et al., 2012) mais son rôle dans le cycle du carbone et son impact sur la chaine trophique restent méconnus (Dupont et al., 2015). Des analyses in situ et in vitro suggèrent que P. calceolata peut s'adapter aux variations environnementales grâce à une importante capacité de modulation de l'expression des gènes (Carradec et al., 2018 ; Dimier et al., 2009). L'objectif de cette thèse est de comprendre comment P. calceolata s'adapte aux variations environnementales des nombreux milieux qu'elle occupe. Dans le premier chapitre, le génome de P. calceolata est assemblé annoté puis comparé à ceux des autres PPEs. Grâce aux données de métagénomiques et métatranscriptomiques issues de l'expédition Tara Oceans, la biogéographie et de l'activité transcriptomique de P. calceolata dans les différentes conditions environnementales a permis de mieux comprendre la distribution présente et future de cette algue, et les gènes impliqués dans son succès écologique (Guérin et al 2022). Dans le deuxième chapitre, nous nous sommes particulièrement intéressés aux capacités d'acclimatation de P. calceolata face aux changements de quantité et de source d'azote. Les gènes différentiellement exprimés (DEG) chez P. calceolata en fonction de la concentration en nitrate dans les échantillons Tara Oceans ont été comparés avec ceux identifiés lors d'expériences de croissance en conditions contrôlées. P. calceolata a été cultivé dans des milieux déplétés en nitrate ou dans lesquelles le nitrate a été remplacé par de l'ammonium, de l'urée ou du cyanate. La comparaison des DEG issus du laboratoire avec ceux issus des données environnementales permet de mieux comprendre le métabolisme de cette microalgue face au manque de nitrate, quels mécanismes sont mis en place dans l'environnement pour faire face à la variabilité de la disponibilité du nitrate, notamment par sa capacité à utiliser des sources d'azote organique. Dans le troisième chapitre, nous avons voulu mieux comprendre comment la profondeur impacte la physiologie de P. calceolata. En effet, on retrouve P. calceolata dans des échantillons d'eaux provenant de la surface et au moins jusqu'à 200m de profondeur. Nous avons constaté que la profondeur d'échantillonnage impactait fortement l'expression des gènes de P. calceolata impliqués dans la photorespiration et dans les mécanismes de concentration du carbone. Lors de cette thèse de doctorat, la caractérisation des capacités d'adaptation de P. calceolata a permis de mieux comprendre comment la régulation transcriptomique lui permet d'être cosmopolite, et montre que cette microalgue peut servir d'organisme modèle grâce à la possibilité de l'étudier simultanément en laboratoire et dans des données multi-omiques environnementales
Photosynthetic picoeukaryotes (PPE) are abundant in all oceans and represent a significant proportion of biomass and primary production. Climate models predict an extension of oligotrophic areas in the following decades, which could greatly increase the abundance and ecological impact of PPEs. Among them, the microalga Pelagomonas calceolata (Stramenopiles/Pelagophyceae) is widely distributed in the oceans (Worden et al., 2012) but its role in the carbon cycle and its impact on the trophic chain remain poorly characterised (Dupont et al., 2015). In situ and in vitro analyses suggest that P. calceolata can adapt to environmental variations thanks to a significant capacity to modulate gene expression (Carradec et al., 2018; Dimier et al., 2009). The aim of this thesis is to understand how P. calceolata adapts to environmental variations in the many environments it lives in. In the first chapter, the P. calceolata genome is assembled, annotated and compared with those of other PPEs. Thanks to metagenomic and metatranscriptomic data from the Tara Oceans expedition, the biogeography and transcriptomic activity of P. calceolata under different environmental conditions has provided a better understanding of the present and future distribution of this alga, and the genes involved in its ecological success (Guérin et al 2022). In the second chapter, we focused on the acclimatisation habilites of P. calceolata to changing nitrogen quantities and sources. Differentially expressed genes (DEGs) in P. calceolata as a function of nitrate concentration in Tara Oceans samples were compared with those identified during growth experiments under controlled conditions. P. calceolata was grown in media depleted in nitrate or in which nitrate was replaced by ammonium, urea or cyanate. The comparison of DEGs obtained in the laboratory with those obtained from environmental data provides a better understanding of the metabolism of this microalga in the face of nitrate shortage, and of the mechanisms put in place in the environment to cope with variability in nitrate availability, in particular through its ability to use organic nitrogen sources. In the third chapter, we aimed to better understand how depth affects the physiology of P. calceolata. P. calceolata is found in water samples from the surface down to a depth of at least 200m. We found that sampling depth had a strong impact on the expression of P. calceolata genes involved in photorespiration and carbon concentration mechanisms. During this PhD thesis, the characterisation of the adaptive capacities of P. calceolata led to a better understanding of how transcriptomic regulation enables it to be cosmopolitan, and shows that this microalga can be used as a model organism thanks to the possibility of studying it simultaneously in the laboratory and in environmental multi-omics data