Nicole Dubilier

Nicole Dubilier
Max Planck Institute for Marine Microbiology | MPI · Max Planck Institute for Marine Microbiology

About

166
Publications
35,264
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7,710
Citations
Citations since 2017
63 Research Items
4230 Citations
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20172018201920202021202220230200400600800
20172018201920202021202220230200400600800

Publications

Publications (166)
Article
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Background Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longe...
Preprint
In addition to abundant animal communities, corals from all ocean depths support diverse microbial associates that are important to coral health. While some of these microbes have been classified taxonomically, understanding the metabolic potential of coral-associated bacteria and how they interact with their coral hosts is limited by a lack of gen...
Article
Full-text available
Seagrasses are among the most efficient sinks of carbon dioxide on Earth. While carbon sequestration in terrestrial plants is linked to the microorganisms living in their soils, the interactions of seagrasses with their rhizospheres are poorly understood. Here, we show that the seagrass, Posidonia oceanica excretes sugars, mainly sucrose, into its...
Preprint
Full-text available
Sterols are lipids that regulate multiple processes in eukaryotic cells, and are essential components of cellular membranes. Sterols are currently assumed to be kingdom specific, with phytosterol synthesis restricted to plants while animals are only able to synthesize cholesterol. Here, we challenge this assumption by demonstrating that the marine...
Article
Full-text available
Possibly the last discovery of a previously unknown major ecosystem on Earth was made just over half a century ago, when researchers found teaming communities of animals flourishing two and a half kilometers below the ocean surface at hydrothermal vents. We now know that these highly productive ecosystems are based on nutritional symbioses between...
Article
Full-text available
How and when symbionts are acquired by their animal hosts has a profound impact on the ecology and evolution of the symbiosis. Understanding symbiont acquisition is particularly challenging in deep-sea organisms because early life stages are so rarely found. Here, we collected early developmental stages of three deep-sea bathymodioline species from...
Article
Full-text available
The composition and diversity of animal microbiomes is shaped by a variety of factors, many of them interacting, such as host traits, the environment, and biogeography. Hybrid zones, in which the ranges of two host species meet and hybrids are found, provide natural experiments for determining the drivers of microbiome communities, but have not bee...
Preprint
Full-text available
Many animals are obligately associated with microbial symbionts that provide essential services such as nutrition or protection against predators. It is assumed that in such obligate associations fidelity between the host and its symbionts must be high to ensure the evolutionary success of the symbiosis. We show here that this is not the case in ma...
Preprint
Full-text available
In obligate symbioses, partner fidelity plays a central role in maintaining the stability of the association across multiple host generations. Fidelity has been well studied in hosts with a very restricted diversity of symbionts, but little is known about how fidelity is maintained in hosts with multiple co-occurring symbionts. The marine annelid O...
Preprint
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Sulfur-oxidizing Thioglobaceae , often referred to as SUP05 and Arctic96BD clades, are widespread and common to hydrothermal vents and oxygen minimum zones. They impact global biogeochemical cycles and exhibit a variety of host-associated and free-living lifestyles. The evolutionary driving forces that led to the versatility, adoption of multiple l...
Preprint
Full-text available
Corals form diverse and valuable communities at all ocean depths. Unfortunately, they face a variety of threats, including increasing ocean temperatures, disease, and pollutants from human activities. But another less-expected threat may cause stress to ocean corals. Apicomplexans are a large group of parasites that cause major human diseases inclu...
Preprint
Full-text available
Symbiotic associations between animals and microorganisms are widespread and have a profound impact on the ecology, behaviour, physiology, and evolution of the host. Research on deep-sea mussels of the genus Bathymodiolus has revealed how chemosynthetic symbionts sustain their host with energy, allowing them to survive in the nutrient-poor environm...
Article
Symbioses between chemosynthetic bacteria and eukaryotic hosts can be found almost everywhere in the ocean, from shallow-water seagrass beds and coral reef sediments to the deep sea. Yet no one knew these existed until 45 years ago, when teeming communities of animals were found thriving at hydrothermal vents two and a half kilometers below the sea...
Preprint
The composition and diversity of animal microbiomes is shaped by a variety of factors, many of them interacting, such as host traits, the environment, and biogeography. Hybrid zones, in which the ranges of two host species meet and hybrids are found, provide natural experiments for determining the drivers of microbiome communities, but have not bee...
Article
Full-text available
Here, we present two high-quality, draft metagenome-assembled genomes of deltaproteobacterial OalgDelta3 endosymbionts from the gutless marine worm Olavius algarvensis . Their 16S rRNA gene sequences share 98% identity with Delta3 endosymbionts of related host species Olavius ilvae (GenBank accession no. AJ620501 ) and Inanidrilus exumae (GenBank a...
Article
Full-text available
Here, we present high-quality metagenome-assembled genome sequences of two closely related deltaproteobacterial endosymbionts from the gutless marine worm Olavius algarvensis (Annelida). The first is an improved draft genome sequence of the previously described sulfate-reducing symbiont Delta1. The second is from a closely related, recently discove...
Preprint
Full-text available
The karyorelictean ciliate Kentrophoros lacks a defined oral apparatus but has a dense coat of symbiotic bacteria that it consumes by phagocytosis. Body size, shape, and nuclear characters are variable in this genus. We formally describe a new species, K. magnus from Elba (Italy), which has unusual folding of its symbiont-bearing surface into pouch...
Article
Full-text available
Background Apicomplexans are the causative agents of major human diseases such as malaria and toxoplasmosis. A novel group of apicomplexans, recently named corallicolids, have been detected in corals inhabiting tropical shallow reefs. These apicomplexans may represent a transitional lifestyle between free-living phototrophs and obligate parasites....
Article
Full-text available
Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defence molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a scale relevant to microbial interactions. Here, we...
Preprint
Cnidarians are known for their symbiotic relationships, yet no known association exists between corals and chemoautotrophic microbes. Deep-sea corals, which support diverse animal communities in the Gulf of Mexico, are often found on authigenic carbonate in association with cold seeps. Sulfur-oxidizing chemoautotrophic bacteria of the SUP05 cluster...
Article
Full-text available
Nontargeted approaches using metabolomics to analyze metabolites that occur in the oceans is less developed than those for terrestrial and limnic ecosystems. One of the challenges in marine metabolomics is that salt limits metabolite analysis in seawater to methods requiring salt removal. Building on previous sample preparation methods for metabolo...
Article
Full-text available
Genetic diversity of closely related free-living microorganisms is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Accordingly, strain diversity is assumed to be highly restricted in intracellular bacteria associated with animals. Here, we sequenced metagenomes and met...
Preprint
Seagrasses are one of the most efficient natural sinks of carbon dioxide on Earth. Despite covering less than 0.1 % of coastal regions, they have the capacity to bury up to 10 % of marine organic matter and can bury the same amount of carbon 35 times faster than tropical rainforests. On land, the soils ability to sequestrate carbon is intimately li...
Article
Full-text available
Most autotrophs use the Calvin–Benson–Bassham (CBB) cycle for carbon fixation. In contrast, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (“Candidatus Thiobarba”) of deep-sea mussels that have acquir...
Conference Paper
Full-text available
The three-dimensional (3D) architecture of organs, tissues and cells together with the spatial distribution of specific molecules, both enables and drives the close interactions between hosts and microbes. To image the 3D anatomy and molecular composition of an animal-microbe system at a single cell scale we developed a correlative workflow combini...
Article
Full-text available
Placozoa is an enigmatic phylum of simple, microscopic, marine metazoans1,2. Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host3–6. We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic a...
Preprint
Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defense molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a scale relevant to microbial interactions. Here, we...
Article
Full-text available
Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast,...
Article
Full-text available
Many animals and protists depend on symbiotic sulfur-oxidizing bacteria as their main food source. These bacteria use energy from oxidizing inorganic sulfur compounds to make biomass autotrophically from CO 2 , serving as primary producers for their hosts. Here we describe a clade of nonautotrophic sulfur-oxidizing symbionts, “ Candidatus Kentron,”...
Preprint
Full-text available
Deep-sea bathymodioline mussels gain their nutrition from intracellular bacterial symbionts. Their sulfur-oxidizing (SOX) symbionts were recently shown to encode abundant toxin-related genes (TRGs) in their genomes, which may play a role in beneficial host-microbe interactions. Here, we compared TRGs in the genomes of SOX symbionts from 10 bathymod...
Preprint
Full-text available
paragraph Placozoa is an enigmatic phylum of simple, microscopic, marine metazoans. Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host. We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteom...
Preprint
Full-text available
Spatial metabolomics describes the location and chemistry of small molecules involved in metabolic phenotypes, defense molecules and chemical interactions in natural communities. Most current techniques are unable to spatially link the genotype and metabolic phenotype of microorganisms in situ at a scale relevant to microbial interactions. Here, we...
Preprint
Full-text available
Since the discovery of symbioses between sulfur-oxidizing (thiotrophic) bacteria and invertebrates at hydrothermal vents over 40 years ago, it has been assumed that autotrophic fixation of CO 2 by the symbionts drives these nutritional associations. In this study, we investigated Candidatus Kentron, the clade of symbionts hosted by Kentrophoros , a...
Preprint
Full-text available
Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast,...
Preprint
Full-text available
Genetic diversity of closely-related free-living microbes is widespread and underpins ecosystem functioning, but most evolutionary theories predict that it destabilizes intimate mutualisms. Indeed, symbiont strain diversity has long assumed to be restricted in intracellular bacteria associated with animals. Here, we sequenced the metagenomes and me...
Article
Full-text available
Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts...
Article
Full-text available
Primary production on Earth is dependent on autotrophic carbon fixation, which leads to the incorporation of carbon dioxide into biomass. Multiple metabolic pathways have been described for autotrophic carbon fixation, but most autotrophic organisms were assumed to have the genes for only one of these pathways. Our finding of a cultivable bacterium...
Preprint
Full-text available
Although the majority of known autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts ("Candidatus Thiobarba") of deep-sea mussels tha...
Poster
Full-text available
Ca. Endonucleobacter (Oceanospirillales, Hahellaceae) is an intranuclear pathogen of bathymodiolin mussels related to Endozoicomonas. After a single Ca. Endonucleobacter cell invades the host nucleus, it proliferates up to 80,000 bacteria, increasing the volume of the nucleus up to 50 fold. At the end of the infectious cycle the host cell bursts an...
Preprint
Full-text available
Very few bacteria are able to fix carbon via both the reverse tricarboxylic acid (rTCA) and the Calvin-Benson-Bassham (CBB) cycles, such as symbiotic, sulfur-oxidizing bacteria that are the sole carbon source for the marine tubeworm Riftia pachyptila , the fastest growing invertebrate. To date, this co-existence of two carbon fixation pathways had...
Preprint
Metabolomic footprinting, or exometabolomics, seeks to describe the complex chemical space surrounding cells. However, metabolite detection is hampered by negative matrix effects, especially when samples originate from high salt-content environments. We propose a sample preparation method for the untargeted exometabolomic analysis of seawater by ga...
Article
Full-text available
Gutless phallodrilines are marine annelid worms without a mouth or gut, which live in an obligate association with multiple bacterial endosymbionts that supply them with nutrition. In this study, we discovered an unusual symbiont community in the gutless phallodriline Inanidrilus exumae that differs markedly from the microbiomes of all 22 of the ot...
Chapter
Blühende symbiontische Gemeinschaften aus Tieren und chemosynthetischen Bakterien leben weit entfernt unter der Meeresoberfläche auf dem kargen Boden der Tiefsee. Obwohl nie ein Sonnenstrahl dorthin vordringt und nur eine verschwindend geringe Menge an Nahrung diese lebensfeindlichen Regionen erreicht, sind die chemosynthetischen Symbiosen der Tief...
Article
Full-text available
Symbioses between eukaryotes and sulfur-oxidizing (thiotrophic) bacteria have convergently evolved multiple times. Although well described in at least eight classes of metazoan animals, almost nothing is known about the evolution of thiotrophic symbioses in microbial eukaryotes (protists). In this study, we characterized the symbioses between mouth...
Article
Full-text available
Cycloclasticus bacteria are ubiquitous in oil-rich regions of the ocean and are known for their ability to degrade polycyclic aromatic hydrocarbons (PAHs). In this study, we describe Cycloclasticus that have established a symbiosis with Bathymodiolus heckerae mussels and poecilosclerid sponges from asphalt-rich, deep-sea oil seeps at Campeche Knoll...
Article
Full-text available
Background The gutless marine worm Olavius algarvensis has a completely reduced digestive and excretory system, and lives in an obligate nutritional symbiosis with bacterial symbionts. While considerable knowledge has been gained of the symbionts, the host has remained largely unstudied. Here, we generated transcriptomes and proteomes of O. algarve...
Article
Full-text available
The hydrothermal vent mussel Bathymodiolus azoricus lives in an intimate symbiosis with two types of chemosynthetic Gammaproteobacteria in its gills: a sulfur oxidizer and a methane oxidizer. Despite numerous investigations over the last decades, the degree of interdependence between the three symbiotic partners, their individual metabolic contribu...
Article
Full-text available
Bathymodiolus mussels dominate animal communities at many hydrothermal vents and cold seeps. Essential to the mussels' ecological and evolutionary success is their association with symbiotic methane- and sulfide-oxidizing gammaproteobacteria, which provide them with nutrition. In addition to these well-known gammaproteobacterial endosymbionts, we f...
Article
Deep-sea hydrothermal vents are patchily distributed ecosystems inhabited by specialized animal populations that are textbook meta-populations. Many vent-associated species have free-swimming, dispersive larvae that can establish connections between remote populations. However, connectivity patterns among hydrothermal vents are still poorly underst...
Article
Full-text available
The level of integration between associated partners can range from ectosymbioses to extracellular and intracellular endosymbioses, and this range has been assumed to reflect a continuum from less intimate to evolutionarily highly stable associations. In this study, we examined the specificity and evolutionary history of marine symbioses in a group...
Data
Molecular biological methods were used to investigate the microbial diversity and community structure in intertidal sandy sediments near the island of Sylt (Wadden Sea) at a site which was characterized for transport and mineralization rates in de Beer et al., (2005, hdl:10013/epic.21375). The sampling was performed during low tide in the middle of...
Data
Fig. S1. Epifluorescence images of O. algarvensis symbionts on a filter. Symbiont cells are the same as in Fig. 6. Images in the left and right columns show in the top row the composite CARD‐FISH signals of all fluorescence channels, followed in the second row by the epifluorescence images of symbiont cells with the sulfur‐oxidizing symbionts targe...