Papers by Claudia Pogoreutz
Fungi and Fungi-Like Entities
Coral Reef Microbiome, 2025
Coral microbiology research has long focused on the composition and functional roles of prokaryot... more Coral microbiology research has long focused on the composition and functional roles of prokaryotic organisms, but microeukaryotic communities, including the enigmatic fungi remain a poorly understood “black box” within coral and other holobionts. Here, we summarise what is known and hypothesised about the diversity, functional traits and potential, and chemodiversity of coral- and reef-associated fungi and fungi-like organisms (FLOs). Finally, we briefly outline the challenges associated with the characterization of marine fungi and provide a perspective for future studies to elucidate the biology, chemical ecology, and organismal interactions of marine fungi and FLOs within coral reef holobionts and their potentially far-reaching roles in coral reef ecosystem functioning and health.
Coral Reefs, 2024
Animal holobionts constitute diverse yet interconnected landscapes of microenvironments that harb... more Animal holobionts constitute diverse yet interconnected landscapes of microenvironments that harbor specific bacterial communities with distinct functions. An increasing body of literature suggests a partitioning and distinct functional profiles of bacterial communities across shark microenvironments, which has led to the proposition that beneficial bacterial functions may contribute to shark health. Here, we provide a first assessment of bacterial communities in different microenvironments of black-tip reef sharks (Carcharhinus melanopterus), the most abundant reef shark species across the Indo-West Pacific. Collecting samples from 34 sharks from the Amirante Islands, Seychelles, we characterized the corresponding bacterial communities of two external skin locations, within the buccal cavity, and of the cloaca (representing the gut microbiome) using 16S rRNA gene amplicon sequencing. Overall, shark-associated bacterial communities were distinct from seawater, and skin, buccal, and cloaca samples were distinct from each other. Shark cloaca samples and seawater exhibited lower bacterial alpha diversity and richness compared to the other microenvironments. Predicted functional profiles and Linear Discriminant Effect Size analysis suggest potential differences in metabolic pathways present in the different shark-associated bacterial communities and in the seawater. Taxonomy-based functional inference suggests cloaca-associated bacterial communities specialize in the consumption and breakdown of various food items. Taken together, our data suggest distinct bacterial niche habitats within the 'microbial landscape' of black-tip reef sharks, as indicated by distinct bacterial communities and their predicted metabolic functions. Future (meta)genomic and functional work will help reveal potential roles of bacteria in the health of their shark hosts. Keywords Marine bacteria • Fish microbiome • Skin microbiome • Gut microbiome • Western Indian Ocean
Data for "Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis
Zenodo (CERN European Organization for Nuclear Research), Jun 9, 2023
Tara Pacific CDIV ITS2 Symbiodiniaceae data release
Zenodo (CERN European Organization for Nuclear Research), Mar 2, 2022
The coral microbiome in sickness, in health and in a changing world
Nature reviews. Microbiology, Mar 4, 2024
Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthr... more Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.
Tara Pacific 18S-based coral host genetic analysis data release version 1
This dataset contains 4 tables and 3 sets of figures related to the primary analysis of the 18S m... more This dataset contains 4 tables and 3 sets of figures related to the primary analysis of the 18S metabarcoding sequencing output. This dataset is only concerned with the identity of the coral host (i.e. not additional protist diversity). The samples included in this dataset have a 'sample-material_label' value of 'CORAL' and 'sampling-protocol_label' value of 'SEQ-CS4L'. They represent the coral samples collected at all 32 of the islands visited in the Tara Pacific expedition.
Additional file 1 of Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities
Additional file 1. Novel ITS2 Sequances.
Symbiotic nutrient exchange enhances the long-term survival of cassiosomes, the autonomous stinging-cell structures of <i>Cassiopea</i>
mSphere, Dec 12, 2023
Medusae of the widely distributed upside-down jellyfish Cassiopea release autonomous, mobile stin... more Medusae of the widely distributed upside-down jellyfish Cassiopea release autonomous, mobile stinging structures. These so-called cassiosomes play a role in predator defense and prey capture, and are major contributors to &quot;contactless&quot; stinging incidents in (sub-)tropical shallow waters. While the presence of endosymbiotic dinoflagellates in cassiosomes has previously been observed, their potential contribution to the metabolism and long-term survival of cassiosomes is unknown. Combining stable isotope labeling and correlative scanning electron microscopy and nanoscale secon dary ion mass spectrometry imaging with a long-term in vitro experiment, our study reveals a mutualistic symbiosis based on nutritional exchanges in dinoflagellate-bearing cassiosomes. We show that organic carbon input from the dinoflagellates fuels the metabolism of the host tissue and enables anabolic nitrogen assimilation. This symbiotic nutrient exchange enhances the life span of cassiosomes for at least one month in vitro. Overall, our study demonstrates that cassiosomes, in analogy with Cassiopea medusae, are photosymbiotic holobionts. Cassiosomes, which are easily accessible under aquarium conditions, promise to be a powerful new miniaturized model system for in-depth ultrastructural and molecular investigation of cnidarian photosymbioses.
Microbiome diversity underpins coral bleaching dynamics of Seychelles reefs during the 2016 El Niño-mass bleaching
Pocillopora verrucosa metagenome
The coral structural framework is crucial for maintaining reef ecosystem function and services. I... more The coral structural framework is crucial for maintaining reef ecosystem function and services. In the central Red Sea, a naturally high alkalinity is beneficial to reef growth, but rising water temperatures impair the calcification capacity of reef-building organisms. However, it is currently unknown how beneficial and detrimental factors affect the balance between calcification and erosion, and thereby the overall growth of the reef framework. To provide insight into present-day carbonate budgets and reef growth dynamics in the central Red Sea, we measured in situ net-accretion and net-erosion rates (G net) by deployment of limestone blocks and estimated census-based carbonate budgets (G budget) in four reef sites along a cross-shelf gradient (25 km). We assessed abiotic variables (i.e., temperature, inorganic nutrients, and carbonate system variables) and biotic drivers (i.e., calcifier and bioeroder abundances). On average, total alkalinity A T (2346-2431 µmol kg-1), aragonite saturation state (4.5-5.2 Ω a), and pCO 2 (283-315 µatm) were close to estimates of pre-industrial global ocean surface waters. Despite these calcification-favorable carbonate system conditions, G net and G budget encompassed positive (offshore) and negative net-production (midshore-lagoon and exposed nearshore site) estimates. Notably, G budget maxima were lower compared to reef growth from pristine Indian Ocean sites. Yet, a comparison with historical data from the northern Red Sea suggests that overall reef growth in the Red Sea has likely remained similar since 1995. When assessing sites across the shelf gradient, A T correlated well with reef growth rates (ρ = 0.89), while temperature was a weaker, negative correlate (ρ =-0.71). Further, A T explained about 65 % of G budget in a best fitting distance-based linear model. Interestingly, parrotfish abundances added up to 82% of explained variation, further substantiating recent studies highlighting the importance of parrotfish to reef ecosystem function. Our study provides a baseline that will be particularly useful in assessing future trajectories of reef growth capacities in the Red Sea under continuous ocean warming and acidification. .
Biogeosciences, Oct 26, 2018
The structural framework provided by corals is crucial for reef ecosystem function and services, ... more The structural framework provided by corals is crucial for reef ecosystem function and services, but high seawater temperatures can be detrimental to the calcification capacity of reef-building organisms. The Red Sea is very warm, but total alkalinity (TA) is naturally high and beneficial for reef accretion. To date, we know little about how such detrimental and beneficial abiotic factors affect each other and the balance between calcification and erosion on Red Sea coral reefs, i.e., overall reef growth, in this unique ocean basin. To provide estimates of present-day reef growth dynamics in the central Red Sea, we measured two metrics of reef growth, i.e., in situ net-accretion/-erosion rates (G net) determined by deployment of limestone blocks and ecosystem-scale carbonate budgets (G budget), along a crossshelf gradient (25 km, encompassing nearshore, midshore, and offshore reefs). Along this gradient, we assessed multiple abiotic (i.e., temperature, salinity, diurnal pH fluctuation, inorganic nutrients, and TA) and biotic (i.e., calcifier and epilithic bioeroder communities) variables. Both reef growth metrics revealed similar patterns from nearshore to offshore: net-erosive, neutral, and net-accretion states. The average cross-shelf G budget was 0.66 kg CaCO 3 m −2 yr −1 , with the highest budget of 2.44 kg CaCO 3 m −2 yr −1 measured in the offshore reef. These data are comparable to the contemporary G budgets from the western Atlantic and Indian oceans, but lie well below "optimal reef production" (5-10 kg CaCO 3 m −2 yr −1) and below maxima recently recorded in remote high coral cover reef sites. However, the erosive forces observed in the Red Sea nearshore reef contributed less than observed elsewhere. A higher TA accompanied reef growth across the shelf gradient, whereas stronger diurnal pH fluctuations were associated with negative carbonate budgets. Noteworthy for this oligotrophic region was the positive effect of phosphate, which is a central micronutrient for reef building corals. While parrotfish contributed substantially to bioerosion, our dataset also highlights coralline algae as important local reef builders. Altogether, our study establishes a baseline for reef growth in the central Red Sea that should be useful in assessing trajectories of reef growth capacity under current and future ocean scenarios. protection, among others (Moberg and Folke, 1999; Reaka-Kudla, 1997). Biogenic calcification, erosion, and dissolution contribute to the formation of the reef framework constructed of calcium carbonate (CaCO 3 , mainly aragonite). The balance of carbonate loss and accretion is influenced by biotic and abiotic factors. On a reef scale, the main antagonists are calcifying benthic communities on the one hand,
bioRxiv (Cold Spring Harbor Laboratory), Jun 12, 2023
Global warming is causing large-scale disruption of cnidarian-Symbiodiniaceae symbioses fundament... more Global warming is causing large-scale disruption of cnidarian-Symbiodiniaceae symbioses fundamental to major marine ecosystems, such as coral reefs. However, the mechanisms by which heat stress perturbs these symbiotic partnerships remain poorly understood. In this context, the upside-down jellyfish Cassiopea has emerged as a powerful experimental model system. We combined a controlled heat stress experiment with isotope labeling and correlative SEM-NanoSIMS imaging to show that host starvation is a central component in the chain of events that ultimately leads to the collapse of the Cassiopea holobiont. Heat stress caused an increase in catabolic activity and a depletion of carbon reserves in the unfed host, concurrent with a reduction in the supply of photosynthates from its algal symbionts. This state of host starvation was accompanied by pronounced in hospite degradation of algal symbionts, which may be a distinct feature of the heat stress response of Cassiopea. Interestingly, this loss of symbionts by degradation was to a large extent concealed by body shrinkage of the starving animals, resulting in what could be referred to as 'invisible' bleaching. Overall, our study highlights the importance of the nutritional status in the heat stress response of the Cassiopea holobiont. Compared with other symbiotic cnidarians, the large mesoglea of Cassiopea, with its structural sugar and protein content, may constitute an energy reservoir capable of delaying starvation. It seems plausible that this anatomical feature at least partly contributes to the relatively high stress tolerance of these animals in our warming oceans.
Medusae of the widely distributed and locally invasive upside-down jellyfishCassiopearelease auto... more Medusae of the widely distributed and locally invasive upside-down jellyfishCassiopearelease autonomous, mobile stinging structures. These so-called cassiosomes are a major contributor to ‘contactless’ stinging incidents in (sub-)tropical shallow waters. While the presence of endosymbiotic dinoflagellates in cassiosomes has previously been observed, their potential contribution to the metabolism and long-term survival of cassiosomes is unknown. Combining stable isotope labeling and correlative SEM and NanoSIMS imaging with a long-termin vitroexperiment, this study reveals a mutualistic symbiosis based on nutritional exchanges in dinoflagellate-bearing cassiosomes. We were able to show that organic carbon input from the dinoflagellates fuels the metabolism of the host tissue and enables anabolic nitrogen assimilation. Thanks to this symbiotic nutrient exchange, cassiosomes showed enhanced survival in the light compared to dark conditions for at least one monthin vitro. Overall, this ...
Skin microbiome of black-tip reef shark (Carcharhinus melanopterus)
The coral microbiome in sickness, in health and in a changing world
Nature Reviews Microbiology, 2024
Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthr... more Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.
Microbiome, 2024
Background Global warming is causing large-scale disruption of cnidarian-Symbiodiniaceae symbiose... more Background Global warming is causing large-scale disruption of cnidarian-Symbiodiniaceae symbioses fundamental to major marine ecosystems, such as coral reefs. However, the mechanisms by which heat stress perturbs these symbiotic partnerships remain poorly understood. In this context, the upside-down jellyfish Cassiopea has emerged as a powerful experimental model system. Results We combined a controlled heat stress experiment with isotope labeling and correlative SEM-NanoSIMS imaging to show that host starvation is a central component in the chain of events that ultimately leads to the collapse of the Cassiopea holobiont. Heat stress caused an increase in catabolic activity and a depletion of carbon reserves in the unfed host, concurrent with a reduction in the supply of photosynthates from its algal symbionts. This state of host starvation was accompanied by pronounced in hospite degradation of algal symbionts, which may be a distinct feature of the heat stress response of Cassiopea. Interestingly, this loss of symbionts by degradation was concealed by body shrinkage of the starving animals, resulting in what could be referred to as "invisible" bleaching. Conclusions Overall, our study highlights the importance of the nutritional status in the heat stress response of the Cassiopea holobiont. Compared with other symbiotic cnidarians, the large mesoglea of Cassiopea, with its structural sugar and protein content, may constitute an energy reservoir capable of delaying starvation. It seems plausible that this anatomical feature at least partly contributes to the relatively high stress tolerance of these animals in rapidly warming oceans.
Trends in Microbiology, 2024
Stony corals are poster child holobionts due to their intimate association with diverse microorga... more Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral-Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum. Endozoicomonas is a global associate of corals Stony corals (see Glossary) are complex marine animal holobionts associated with diverse microorganisms from all domains of life, specifically microeukaryotes (algae, fungi, and other protists), prokaryotes (Bacteria and Archaea), and viruses [1,2]. The realization that these microbial associates take up diverse functional niches has shaped a view in which they may influence the health and fitness of the coral holobiont. Coral-associated bacterial communities in particular are taxonomically and functionally diverse, species-specific, and respond to environmental fluctuations [1,3,4].
mSphere, 2023
Medusae of the widely distributed upside-down jellyfish Cassiopea release autonomous, mobile stin... more Medusae of the widely distributed upside-down jellyfish Cassiopea release autonomous, mobile stinging structures. These so-called cassiosomes play a role in predator defense and prey capture, and are major contributors to "contactless" stinging incidents in (sub-)tropical shallow waters. While the presence of endosymbiotic dinoflagellates in cassiosomes has previously been observed, their potential contribution to the metabolism and long-term survival of cassiosomes is unknown. Combining stable isotope labeling and correlative scanning electron microscopy and nanoscale secon dary ion mass spectrometry imaging with a long-term in vitro experiment, our study reveals a mutualistic symbiosis based on nutritional exchanges in dinoflagellate-bearing cassiosomes. We show that organic carbon input from the dinoflagellates fuels the metabolism of the host tissue and enables anabolic nitrogen assimilation. This symbiotic nutrient exchange enhances the life span of cassiosomes for at least one month in vitro. Overall, our study demonstrates that cassiosomes, in analogy with Cassiopea medusae, are photosymbiotic holobionts. Cassiosomes, which are easily accessible under aquarium conditions, promise to be a powerful new miniaturized model system for in-depth ultrastructural and molecular investigation of cnidarian photosymbioses.
Symbiodinium response parameters
Overview of Symbiodinium response paramters (density, chl content, relative clade community compo... more Overview of Symbiodinium response paramters (density, chl content, relative clade community composition) for both experiments. Data were obtained using flow cytometry (density & chl) and MiSeq sequencing (ITS Symbiodinium sequence composition). All units are identical to those reported in the manuscript
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Papers by Claudia Pogoreutz