Docteur MARIA CIOBANU

Bibliographie

• Parasitic connections: a patescibacterial epibiont, its methylotrophic gammaproteobacterial host, and their phages

  2026

  ArticlemBio

• Metagenome-derived virus-microbe ratios across ecosystems

  2023

  ArticleThe International Society of Microbiologial Ecology Journal

• Description of Gloeomargarita ahousahtiae sp. nov. (Gloeomargaritales), a thermophilic cyanobacterium with intracellular carbonate inclusions

  2023

  ArticleEuropean Journal of Phycology

• Biomineralization of amorphous Fe-, Mn- and Si-rich mineral phases by cyanobacteria under oxic and alkaline conditions

  2023

  ArticleBiogeosciences

• Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies

  2022

  ArticleSystematic Biology

• Independent Size Expansions and Intron Proliferation in Red Algal Plastid and Mitochondrial Genomes

  2022

  ArticleGenome Biology and Evolution

• Expanding the molecular and morphological diversity of Apusomonadida, a deep‐branching group of gliding bacterivorous protists

  2022

  ArticleJournal of Eukaryotic Microbiology

• Deglacial to Holocene environmental changes in the northern Ligurian Sea: The dual influence of regional climate variability and large-scale intermediate Mediterranean circulation

  2021

  ArticlePalaeogeography, Palaeoclimatology, Palaeoecology

Source : HAL — archive ouverte CCSD/CNRS (couvre articles, chapitres EMC, communications congrès, thèses).

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Top publications · les plus citées

• 1

  Metagenome-derived virus-microbe ratios across ecosystems

  The ISME journal · 2023

  📚 38 citations🎯 RCR 4.59Top 9% NIH🔓 Open Access📄 PDF gratuit ↗

  Lire l'abstract Crossref ↓

  Abstract It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa–200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ~13 fold and in plankton from marine and saline waters by ~2–4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.

• 2

  In-depth analyses of deep subsurface sediments using 454-pyrosequencing reveals a reservoir of buried fungal communities at record-breaking depths

  FEMS microbiology ecology · 2014

  📚 30 citations🎯 RCR 1.24🔓 Open Access📄 PDF gratuit ↗

  Lire l'abstract Crossref ↓

  Abstract The deep subseafloor, extending from a few centimeters below the sediment surface to several hundred meters into sedimentary deposits, constitutes the deep biosphere and harbors an unexpected microbial diversity. Several studies have described the occurrence, turnover, activity and function of subseafloor prokaryotes; however, subsurface eukaryotic communities still remain largely underexplored. Ribosomal RNA surveys of superficial and near-surface marine sediments have revealed an unexpected diversity of active eukaryotic communities, but knowledge of the diversity of deep subseafloor microeukaryotes is still scarce. Here, we investigated the vertical distribution of DNA and RNA fungal signatures within subseafloor sediments of the Canterbury basin (New Zealand) by 454 pyrotag sequencing of fungal genetic markers. Different shifts between the fungal classes of Tremellomycetes, Sordariomycetes, Eurotiomycetes, Saccharomycetes, Wallemiomycetes, Dothideomycetes, Exobasidiomycetes and Microbotryomycetes were observed. These data provide direct evidence that fungal communities occur at record depths in deep sediments of the Canterbury basin and extend the depth limit of fungal presence and activity, respectively 1740 and 346 mbsf. As most of the fungal sequences retrieved have a cosmopolitan distribution, it indicates that fungi are able to adapt to the deep subseafloor conditions at record-depth and must play important ecological roles in biogeochemical cycles.

• 3

  Phylogenomics Supports the Monophyly of Aphelids and Fungi and Identifies New Molecular Synapomorphies

  Systematic biology · 2023

  📚 23 citations🎯 RCR 3.78Top 12% NIH🔓 Open Access

  Lire l'abstract Crossref ↓

  Abstract The supergroup Holomycota, composed of Fungi and several related lineages of unicellular organisms (Nucleariida, Rozellida, Microsporidia, and Aphelida), represents one of the major branches in the phylogeny of eukaryotes. Nevertheless, except for the well-established position of Nucleariida as the first holomycotan branch to diverge, the relationships among the other lineages have so far remained unresolved largely owing to the lack of molecular data for some groups. This was notably the case aphelids, a poorly known group of endobiotic phagotrophic protists that feed on algae with cellulose walls. The first molecular phylogenies including aphelids supported their sister relationship with Rozellida and Microsporidia which, collectively, formed a new group called Opisthosporidia (the “Opisthosporidia hypothesis”). However, recent phylogenomic analyses including massive sequence data from two aphelid genera, Paraphelidium and Amoeboaphelidium, suggested that the aphelids are sister to fungi (the “Aphelida $+$ Fungi hypothesis”). Should this position be confirmed, aphelids would be key to understanding the early evolution of Holomycota and the origin of Fungi. Here, we carry out phylogenomic analyses with an expanded taxonomic sampling for aphelids after sequencing the transcriptomes of two species of the genus Aphelidium (Aphelidium insulamus and Aphelidium tribonematis) in order to test these competing hypotheses. Our new phylogenomic analyses including species from the three known aphelid genera strongly rejected the Opisthosporidia hypothesis. Furthermore, comparative genomic analyses further supported the Aphelida $+$ Fungi hypothesis via the identification of 19 orthologous genes exclusively shared by these two lineages. Seven of them originated from ancient horizontal gene transfer events predating the aphelid–fungal split and the remaining 12 likely evolved de novo, constituting additional molecular synapomorphies for this clade. Ancestral trait reconstruction based on our well-resolved phylogeny of Holomycota suggests that the progenitor of both fungi and rozellids, was aphelid-like, having an amoeboflagellate state and likely preying endobiotically on cellulose-containing, cell-walled organisms. Two lineages, which we propose to call Phytophagea and Opisthophagea, evolved from this ancestor. Phytophagea, grouping aphelids and classical fungi, mainly specialized in endobiotic predation of algal cells. Fungi emerged from this lineage after losing phagotrophy in favor of osmotrophy. Opisthophagea, grouping rozellids and Microsporidia, became parasites, mostly of chitin-containing hosts. This lineage entered a progressive reductive process that resulted in a unique lifestyle, especially in the highly derived Microsporidia. [Aphelida, fungi, Holomycota, horizontal gene transfer, phylogenomics, synapomorphy.]

Publications scientifiques (13) — classées par pathologie

Source PubMed · Recherche par auteur (homonymes possibles, vérifier l'affiliation).

Datasets & protocoles partagés

• IODP Expedition 317, Hole U1352B - Well Logging Data

  Dataset2021Zenodo

  Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of

• IODP Expedition 317, Hole U1351B - Well Logging Data

  Dataset2021Zenodo

  Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of

• IODP Expedition 317, Hole U1352C - Well Logging Data

  Dataset2021Zenodo

  Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of

• IODP Expedition 317, Hole U1351C - Well Logging Data

  Dataset2021Zenodo

  Logging data are measurements of physical properties of the formation surrounding a borehole, acquired in situ after completion of coring (wireline logging) or during drilling (Logging-While-Drilling, LWD). The range of

• Expanding the molecular and morphological diversity of Apusomonadida, a deep-branching group of gliding bacterivorous protists

  Dataset2024figshare

  Multiple sequences alignments and phylogenetic trees from the analyses of apusomonads, including four strains of the known species Multimonas media, Podomonas capensis and Apusomonas proboscidea, Mylnikovia oxoniensis (p

• Molecular and morphological characterisation of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida

  Dataset2023figshare

  Multiple sequences alignments and phylogenetic trees from the analyses of ancyromonads, including 14 new isolates. Most of them belong to three new and genetically divergent genera: <em>Caraotamonas</em>, <em>Nyramonas</

Source : DataCite — DOIs pour datasets, logiciels, protocoles, registres patient. Hors articles (déjà couverts).

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