Morphology, Ultrastructure, and Mitochondrial Genome of the Marine Non-Photosynthetic Bicosoecid Cafileria marina Gen. et sp. nov.

Jírsová, Dagmar; Füssy, Zoltán; Richtová, Jitka; Gruber, Ansgar; Oborník, Miroslav

doi:10.3390/microorganisms7080240

Cited by 7 publications

(7 citation statements)

References 81 publications

(104 reference statements)

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“…Moreover, the retrieval of eukaryotic members affiliated with Bikosea and Placididae, mainly from the A. fusiformi phycosphere, is consistent with their size, Bikosea being on average 3–4 μm wide and 5–6 μm length, (Jirsová et al., 2019) and Placididae, 3–10 μm length and 2–7 μm wide, (Rybarski et al., 2021), which are essentially larger than Picocystis. While being previously retrieved in hypersaline environments, the Bikosea ecology remains unclear (Jirsová et al., 2019; Park & Simpson, 2015). The presence of several Chlorophyceae OTUs affiliated with the Lobomonas genus in both phycospheres is highly interesting as we did not detect those OTUs in the large ecosystemic studies we previously performed (Bernard et al., 2019; Hugoni et al., 2018), suggesting that we missed those OTUs because of the large scale employed, proving further value to the microscaled studies as performed here.…”

Section: Discussionmentioning

confidence: 65%

Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome

Bruto,

Oger,

Got

et al. 2023

Molecular Ecology

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Microorganisms are key contributors of aquatic biogeochemical cycles but their microscale ecology remains largely unexplored, especially interactions occurring between phytoplankton and microorganisms in the phycosphere, that is the region immediately surrounding phytoplankton cells. The current study aimed to provide evidence of the phycosphere taking advantage of a unique hypersaline, hyperalkaline ecosystem, Lake Dziani Dzaha (Mayotte), where two phytoplanktonic species permanently co‐dominate: a cyanobacterium, Arthrospira fusiformis, and a green microalga, Picocystis salinarum. To assay phycospheric microbial diversity from in situ sampling, we set up a flow cytometry cell‐sorting methodology for both phytoplanktonic populations, coupled with metabarcoding and comparative microbiome diversity. We focused on archaeal communities as they represent a non‐negligible part of the phycospheric diversity, however their role is poorly understood. This work is the first which successfully explores in situ archaeal diversity distribution showing contrasted phycospheric compositions, with P. salinarum phycosphere notably enriched in Woesearchaeales OTUs while A. fusiformis phycosphere was enriched in methanogenic lineages affiliated OTUs such as Methanomicrobiales or Methanofastidiosales. Most archaeal OTUs, including Woesearchaeales considered in literature as symbionts, were either ubiquitous or specific of the free‐living microbiome (i.e. present in the 3–0.2 μm fraction). Seminally, several archaeal OTUs were enriched from the free‐living microbiome to the phytoplankton phycospheres, suggesting (i) either the inhibition or decrease of other OTUs, or (ii) the selection of specific OTUs resulting from the physical influence of phytoplanktonic species on surrounding Archaea.

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Section: Discussionmentioning

confidence: 65%

Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome

Bruto,

Oger,

Got

et al. 2023

Molecular Ecology

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“…Almost all the ciliate sequences are grouped in the crown of clade II; these sequences were previously identified as a different sub-class of E(z) named the Enhancer-of-zeste-like protein Ezl (Frapporti et al 2019). The one Naegleria gruberi (Discoba) E(z) homolog and all Cafileria marina (Jirsová et al 2019) (stramenopiles) homologs cluster in the same clade. Clade III contains all the rhodophyte sequences, including the recently identified homologs in Cyanidioschyzon merolae (Mikulski et al 2017) and the E(z) homologs of the newly discovered family Rhodelphidae (Gawryluk et al 2019; Burki et al 2020) (fig.…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

Sharaf

Vijayanathan

Oborník

et al. 2021

Preprint

Self Cite

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Polycomb Repressive Complex 2 (PRC2) is involved in establishing transcriptionally silent chromatin states through its ability to methylate lysine 27 of histone H3 by the catalytic subunit Enhancer of zeste [E(z)]. Polycomb group (PcG) proteins play a crucial role in the maintenance of cell identity and in developmental regulation. Previously, the diversity of PRC2 subunits within some eukaryotic lineages has been reported and its presence in early eukaryotic evolution has been hypothesized. So far however, systematic survey of the presence of PRC2 subunits in species of all eukaryotic lineages is missing. Here, we report the diversity of PRC2 core subunit proteins in different eukaryotic supergroups with emphasis on the early-diverged lineages and explore the molecular evolution of PRC2 subunits by phylogenetics. In detail, we investigate the SET-domain protein sequences and their evolution across the four domains of life and particularly focus on the structural diversity of the SET-domain subfamily containing E(z), the catalytic subunit of PRC2. We show that PRC2 subunits are already present in early eukaryotic lineages, strengthening the support for PRC2 emergence prior to diversification of eukaryotes. We identify a common presence of E(z) and ESC, suggesting that Su(z)12 may have emerged later and/or may be dispensable from the evolutionarily conserved functional core of PRC2. Furthermore, our results broaden our understanding of the E(z) evolution within the SET-domain protein family, suggesting possibilities of function evolution. Through this, we shed light on a possible emerging point of the PRC2 and the evolution of its function in eukaryotes.

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“…The larger sizes of the Saprolegniales and Pythiales mitogenomes are due to duplication events in several genes 120 . The mitochondrial genome of Cafileria marina represents the Bigyra 122 . It is a circular molecule of 43 Kb, which has the same gene content as Amoebozoa mitogenomes 122 .…”

Section: Other Eukaryote Mitogenome Structuresmentioning

confidence: 99%

“…The mitochondrial genome of Cafileria marina represents the Bigyra 122 . It is a circular molecule of 43 Kb, which has the same gene content as Amoebozoa mitogenomes 122 . Remarkably, the nad11 gene in many Heterokonta is split into two fragments; in several groups (for example, all Eustigmatophyceae, some Bacillariophyceae, and some Bygira), one of the fragments is relocated to the nuclear genome 118 .…”

Section: Other Eukaryote Mitogenome Structuresmentioning

confidence: 99%

Recent advances in understanding mitochondrial genome diversity

Zardoya

2020

F1000Res

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Ever since its discovery, the double-stranded DNA contained in the mitochondria of eukaryotes has fascinated researchers because of its bacterial endosymbiotic origin, crucial role in encoding subunits of the respiratory complexes, compact nature, and specific inheritance mechanisms. In the last few years, high-throughput sequencing techniques have accelerated the sequencing of mitochondrial genomes (mitogenomes) and uncovered the great diversity of organizations, gene contents, and modes of replication and transcription found in living eukaryotes. Some early divergent lineages of unicellular eukaryotes retain certain synteny and gene content resembling those observed in the genomes of alphaproteobacteria (the inferred closest living group of mitochondria), whereas others adapted to anaerobic environments have drastically reduced or even lost the mitogenome. In the three main multicellular lineages of eukaryotes, mitogenomes have pursued diverse evolutionary trajectories in which different types of molecules (circular versus linear and single versus multipartite), gene structures (with or without self-splicing introns), gene contents, gene orders, genetic codes, and transfer RNA editing mechanisms have been selected. Whereas animals have evolved a rather compact mitochondrial genome between 11 and 50 Kb in length with a highly conserved gene content in bilaterians, plants exhibit large mitochondrial genomes of 66 Kb to 11.3 Mb with large intergenic repetitions prone to recombination, and fungal mitogenomes have intermediate sizes of 12 to 236 Kb.

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Morphology, Ultrastructure, and Mitochondrial Genome of the Marine Non-Photosynthetic Bicosoecid Cafileria marina Gen. et sp. nov.

Cited by 7 publications

References 81 publications

Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome

Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome

Phylogenetic profiling suggests early origin of the core subunits of Polycomb Repressive Complex 2 (PRC2)

Recent advances in understanding mitochondrial genome diversity

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