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Abstract Fossilized remains of marine calcifiers constitute the physical basis for reconstructions of both deep ocean and sea-surface temperatures going back millions of years, but paleoclimate records derived from their isotope and trace-element chemistry can be biased by diagenesis. Experiments simulating diagenesis in the presence of an 18O-rich seawater analogue were conducted with modern and 14 Myr old foraminifera (Ammonia sp.) tests to investigate their relative susceptibility to oxygen isotope exchange. The fossilized tests were of exceptional preservation and similar to modern tests in terms of structure and crystalline organization, but had experienced partial loss of embedded organic structures, thus a priori offering fewer preferential pathways for porewaters to penetrate the tests. NanoSIMS imaging revealed that oxygen isotope exchange was pervasive in fossil tests, with isotopic exchange occurring at approximately half the rate of modern tests. The results unequivocally show that fossil biocalcites are metastable and remain more susceptible to isotope exchange than abiotic calcites millions of years after sedimentation and burial.

Abstract In contrast to abiotically formed carbonates, biogenetic carbonates have been observed to be nanocomposite, organo-mineral structures, the basic build-blocks of which are particles of quasi-uniform size (10–100 nm) organized into complex higher-order hierarchical structures, typically with highly controlled crystal-axis alignments. Some of these characteristics serve as criteria for inferring a biological origin and the state of preservation of fossil carbonate materials, and to determine whether the biomineralization process was biologically induced or controlled. Here we show that a calcium storage structure formed by the American lobster, a gastrolith initially consisting of amorphous calcium carbonate (ACC) and amorphous calcium phosphate (ACP), post-mortem can crystallize into (thus secondary) calcite with structural properties strongly influenced by the inherited organic matrix. This secondary calcite meets many structural criteria for biominerals (thus called the biomorphic calcite), but differs in trace element distributions (e.g., P and Mg). Such observations refine the capability to determine whether a fossil carbonates can be attributed to biogenic processes, with implications for the record of life on Earth and other terrestrial planets.

Abstract Coral reefs are among the most diverse ecosystems on our planet, and essential to the livelihood of hundreds of millions of people who depend on them for food security, income from tourism and coastal protection. Unfortunately, most coral reefs are existentially threatened by global climate change and local anthropogenic pressures. To better understand the dynamics underlying deterioration of reefs, monitoring at high spatial and temporal resolution is key. However, conventional monitoring methods for quantifying coral cover and species abundance are limited in scale due to the extensive manual labor required. Although computer vision tools have been employed to aid in this process, in particular structure‐from‐motion (SfM) photogrammetry for 3D mapping and deep neural networks for image segmentation, analysis of the data products creates a bottleneck, effectively limiting their scalability. This paper presents a new paradigm for mapping underwater environments from ego‐motion video, unifying 3D mapping systems that use machine learning to adapt to challenging conditions under water, combined with a modern approach for semantic segmentation of images. The method is exemplified on coral reefs in the northern Gulf of Aqaba, Red Sea, demonstrating high‐precision 3D semantic mapping at unprecedented scale with significantly reduced required labor costs: given a trained model, a 100 m video transect acquired within 5 min of diving with a cheap consumer‐grade camera can be fully automatically transformed into a semantic point cloud within 5 min. We demonstrate the spatial accuracy of our method and the semantic segmentation performance (of at least 80% total accuracy), and publish a large dataset of ego‐motion videos from the northern Gulf of Aqaba, along with a dataset of video frames annotated for dense semantic segmentation of benthic classes. Our approach significantly scales up coral reef monitoring by taking a leap towards fully automatic analysis of video transects. The method advances coral reef transects by reducing the labor, equipment, logistics, and computing cost. This can help to inform conservation policies more efficiently. The underlying computational method of learning‐based Structure‐from‐Motion has broad implications for fast low‐cost mapping of underwater environments other than coral reefs.

Abstract 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. Video Abstract

Abstract Efficient nutrient recycling underpins the ecological success of cnidarian-algal symbioses in oligotrophic waters. In these symbioses, nitrogen limitation restricts the growth of algal endosymbionts in hospite and stimulates their release of photosynthates to the cnidarian host. However, the mechanisms controlling nitrogen availability and their role in symbiosis regulation remain poorly understood. Here, we studied the metabolic regulation of symbiotic nitrogen cycling in the sea anemone Aiptasia by experimentally altering labile carbon availability in a series of experiments. Combining 13C and 15N stable isotope labeling experiments with physiological analyses and NanoSIMS imaging, we show that the competition for environmental ammonium between the host and its algal symbionts is regulated by labile carbon availability. Light regimes optimal for algal photosynthesis increase carbon availability in the holobiont and stimulate nitrogen assimilation in the host metabolism. Consequently, algal symbiont densities are lowest under optimal environmental conditions and increase toward the lower and upper light tolerance limits of the symbiosis. This metabolic regulation promotes efficient carbon recycling in a stable symbiosis across a wide range of environmental conditions. Yet, the dependence on resource competition may favor parasitic interactions, explaining the instability of the cnidarian-algal symbiosis as environmental conditions in the Anthropocene shift towards its tolerance limits.

Abstract In Parkinson’s disease, pathogenic factors such as the intraneuronal accumulation of the protein α-synuclein affect key metabolic processes. New approaches are required to understand how metabolic dysregulations cause degeneration of vulnerable subtypes of neurons in the brain. Here, we apply correlative electron microscopy and NanoSIMS isotopic imaging to map and quantify 13C enrichments in dopaminergic neurons at the subcellular level after pulse-chase administration of 13C-labeled glucose. To model a condition leading to neurodegeneration in Parkinson’s disease, human α-synuclein was unilaterally overexpressed in the substantia nigra of one brain hemisphere in rats. When comparing neurons overexpressing α-synuclein to those located in the control hemisphere, the carbon anabolism and turnover rates revealed metabolic anomalies in specific neuronal compartments and organelles. Overexpression of α-synuclein enhanced the overall carbon turnover in nigral neurons, despite a lower relative incorporation of carbon inside the nucleus. Furthermore, mitochondria and Golgi apparatus showed metabolic defects consistent with the effects of α-synuclein on inter-organellar communication. By revealing changes in the kinetics of carbon anabolism and turnover at the subcellular level, this approach can be used to explore how neurodegeneration unfolds in specific subpopulations of neurons.

Abstract Background The development of nanoscale secondary ion mass spectrometry (NanoSIMS) has revolutionized the study of biological tissues by enabling, e.g., the visualization and quantification of metabolic processes at subcellular length scales. However, the associated sample preparation methods all result in some degree of tissue morphology distortion and loss of soluble compounds. To overcome these limitations an entirely cryogenic sample preparation and imaging workflow is required. Results Here, we report the development of a CryoNanoSIMS instrument that can perform isotope imaging of both positive and negative secondary ions from flat block-face surfaces of vitrified biological tissues with a mass- and image resolution comparable to that of a conventional NanoSIMS. This capability is illustrated with nitrogen isotope as well as trace element mapping of freshwater hydrozoan Green Hydra tissue following uptake of 15N-enriched ammonium. Conclusion With a cryo-workflow that includes vitrification by high pressure freezing, cryo-planing of the sample surface, and cryo-SEM imaging, the CryoNanoSIMS enables correlative ultrastructure and isotopic or elemental imaging of biological tissues in their most pristine post-mortem state. This opens new horizons in the study of fundamental processes at the tissue- and (sub)cellular level. Teaser CryoNanoSIMS: subcellular mapping of chemical and isotopic compositions of biological tissues in their most pristine post-mortem state.

Abstract The oxygen isotopic compositions of fossil foraminifera tests constitute a continuous proxy record of deep-ocean and sea-surface temperatures spanning the last 120 million years. Here, by incubating foraminifera tests in 18O-enriched artificial seawater analogues, we demonstrate that the oxygen isotopic composition of optically translucent, i.e., glassy, fossil foraminifera calcite tests can be measurably altered at low temperatures through rapid oxygen grain-boundary diffusion without any visible ultrastructural changes. Oxygen grain boundary diffusion occurs sufficiently fast in foraminifera tests that, under normal upper oceanic sediment conditions, their grain boundaries will be in oxygen isotopic equilibrium with the surrounding pore fluids on a time scale of

Abstract Otoliths are calcium carbonate components of the stato-acoustical organ responsible for hearing and maintenance of the body balance in teleost fish. During their formation, control over, e.g., morphology and carbonate polymorph is influenced by complex insoluble collagen-like protein and soluble non-collagenous protein assemblages; many of these proteins are incorporated into their aragonite crystal structure. However, in the fossil record these proteins are considered lost through diagenetic processes, hampering studies of past biomineralization mechanisms. Here we report the presence of 11 fish-specific proteins (and several isoforms) in Miocene (ca. 14.8–14.6 Ma) phycid hake otoliths. These fossil otoliths were preserved in water-impermeable clays and exhibit microscopic and crystallographic features indistinguishable from modern representatives, consistent with an exceptionally pristine state of preservation. Indeed, these fossil otoliths retain ca. 10% of the proteins sequenced from modern counterparts, including proteins specific to inner ear development, such as otolin-1-like proteins involved in the arrangement of the otoliths into the sensory epithelium and otogelin/otogelin-like proteins that are located in the acellular membranes of the inner ear in modern fish. The specificity of these proteins excludes the possibility of external contamination. Identification of a fraction of identical proteins in modern and fossil phycid hake otoliths implies a highly conserved inner ear biomineralization process through time.

Abstract The coral-algal symbiosis is maintained by a constant and limited nitrogen availability in the holobiont. Denitrifiers, i.e., prokaryotes reducing nitrate/nitrite to dinitrogen, could contribute to maintaining the nitrogen limitation in the coral holobiont, however the effect of host and algal identity on their community is still unknown. Using the coral model Aiptasia, we quantified and characterized the denitrifier community in a full-factorial design combining two hosts (CC7 and H2) and two strains of algal symbionts of the family Symbiodiniaceae (SSA01 and SSB01). Strikingly, relative abundance of denitrifiers increased by up to 22-fold in photosymbiotic Aiptasia compared to their aposymbiotic (i.e., algal-depleted) counterparts. In line with this, while the denitrifier community in aposymbiotic Aiptasia was largely dominated by diet-associated Halomonas, we observed an increasing relative abundance of an unclassified bacterium in photosymbiotic CC7, and Ketobacter in photosymbiotic H2, respectively. Pronounced changes in denitrifier communities of Aiptasia with Symbiodinium linucheae strain SSA01 aligned with the higher photosynthetic carbon availability of these holobionts compared to Aiptasia with Breviolum minutum strain SSB01. Our results reveal that the presence of algal symbionts increases abundance and alters community structure of denitrifiers in Aiptasia. Thereby, patterns in denitrifier community likely reflect the nutritional status of aposymbiotic vs. symbiotic holobionts. Such a passive regulation of denitrifiers may contribute to maintaining the nitrogen limitation required for the functioning of the cnidarian-algal symbiosis.

IntroductionThe jellyfish Cassiopea has a conspicuous lifestyle, positioning itself upside-down on sediments in shallow waters thereby exposing its photosynthetic endosymbionts (Symbiodiniaceae) to light. Several studies have shown how the photosymbionts benefit the jellyfish host in terms of nutrition and O2 availability, but little is known about the internal physico-chemical microenvironment of Cassiopea during light–dark periods.MethodsHere, we used fiber-optic sensors to investigate how light is modulated at the water-tissue interface of Cassiopea sp. and how light is scattered inside host tissue. We additionally used electrochemical and fiber-optic microsensors to investigate the dynamics of O2 and pH in response to changes in the light availability in intact living specimens of Cassiopea sp.Results and discussionMapping of photon scalar irradiance revealed a distinct spatial heterogeneity over different anatomical structures of the host, where oral arms and the manubrium had overall higher light availability, while shaded parts underneath the oral arms and the bell had less light available. White host pigmentation, especially in the bell tissue, showed higher light availability relative to similar bell tissue without white pigmentation. Microprofiles of scalar irradiance into white pigmented bell tissue showed intense light scattering and enhanced light penetration, while light was rapidly attenuated over the upper 0.5 mm in tissue with symbionts only. Depth profiles of O2 concentration into bell tissue of live jellyfish showed increasing concentration with depth into the mesoglea, with no apparent saturation point during light periods. O2 was slowly depleted in the mesoglea in darkness, and O2 concentration remained higher than ambient water in large (> 6 cm diameter) individuals, even after 50 min in darkness. Light–dark shifts in large medusae showed that the mesoglea slowly turns from a net sink during photoperiods into a net source of O2 during darkness. In contrast, small medusae showed a more dramatic change in O2 concentration, with rapid O2 buildup/consumption in response to light–dark shifts; in a manner similar to corals. These effects on O2 production/consumption were also reflected in moderate pH fluctuations within the mesoglea. The mesoglea thus buffers O2 and pH dynamics during dark-periods.

Paleoclimate reconstructions commonly use oxygen isotope compositions from fossil foraminifera tests as proxies. Here, the authors show that these tests exchange O-isotopes with surrounding fluids, with implications for paleotemperature records.

Starch is the major form of energy storage in plant cells and forms discrete, semi-crystalline granules within plastids. Here the authors use electron tomography and nanoSIMS to show that Arabidopsis starch granules initiate in stromal pockets between thylakoid membranes that coalesce before growing anisotropically.

Nitrogen and sulfur are key elements in the biogeochemical cycles of marine ecosystems to which benthic foraminifera contribute significantly. Yet, cell-specific assimilation of ammonium, nitrate and sulfate by these protists is poorly characterized and understood across their wide range of species-specific trophic strategies. For example, detailed knowledge about ammonium and sulfate assimilation pathways is lacking and although some benthic foraminifera are known to maintain intracellular pools of nitrate and/or to denitrify, the potential use of nitrate-derived nitrogen for anabolic processes has not been systematically studied. In the present study, NanoSIMS isotopic imaging correlated with transmission electron microscopy was used to trace the incorporation of isotopically labeled inorganic nitrogen (ammonium or nitrate) and sulfate into the biomass of twelve benthic foraminiferal species from different marine environments. On timescales of twenty hours, no detectable 15N-enrichments from nitrate assimilation were observed in species known to perform denitrification, indicating that, while denitrifying foraminifera store intra-cellular nitrate, they do not use nitrate-derived nitrogen to build their biomass. Assimilation of both ammonium and sulfate, with corresponding 15N and 34S-enrichments, were observed in all species investigated (with some individual exceptions for sulfate). Assimilation of ammonium and sulfate thus can be considered widespread among benthic foraminifera. These metabolic capacities may help to underpin the ability of benthic foraminifera to colonize highly diverse marine habitats.

Secondary Ion Mass Spectrometry (SIMS) extracts chemical, elemental, or isotopic information about a localized area of a solid target by performing mass spectrometry on secondary ions sputtered from its surface by the impact of a beam of charged particles. This primary beam sputters ionized atoms and small molecules (as well as many neutral particles) from the upper few nanometers of the sample surface. The physical basis of SIMS has been applied to a large range of applications utilizing instruments optimized with different types of mass analyzer, either dynamic SIMS with a double focusing mass spectrometer or static SIMS with a Time of Flight (TOF) analyzer. Here, we present a short review of the principles and major applications of three different SIMS instruments located in Switzerland.

The human gut hosts trillions of microorganisms that exert a profound influence on human biology. Gut bacteria communicate with their host by secreting small molecules that can signal to distant organs in the body. Bile acids are one class of these signaling molecules, synthesized by the host and chemically transformed by the gut microbiota. Among bile acid metabolizers, bile acid 7-dehydroxylating bacteria are commensals of particular importance as they carry out the 7-dehydroxylation of liver-derived primary bile acids to 7-dehydroxylated bile acids. The latter represents a major fraction of the secondary bile acid pool. The microbiology of this group of gut microorganisms is understudied and warrants more attention. Here, we detail the bile acid transformations carried out by the 7-dehydroxylating bacterium Clostridium scindens in vitro and in vivo. In vitro, C. scindens exhibits not only 7α-dehydroxylating capabilities but also, the ability to oxidize other hydroxyl groups and reduce ketone groups in primary and secondary bile acids. This study revealed 12-oxolithocholic acid as a major transient product in the 7α-dehydroxylation of cholic acid. Furthermore, the in vivo study included complementing a gnotobiotic mouse line (devoid of the ability to 7-dehydroxylate bile acids) with C. scindens and investigating its colonization dynamics and bile acid transformations. Using NanoSIMS (Nanoscale Secondary Ion Mass Spectrometry), we demonstrate that the large intestine constitutes a niche for C. scindens, where it efficiently 7-dehydroxylates cholic acid to deoxycholic acid. Overall, this work reveals a novel transient species during 7-dehydroxylation as well as provides direct evidence for the colonization and growth of 7-dehydroxylating bacteria in the large intestine.

Aiptasia is an emerging model organism to study cnidarian symbioses due to its taxonomic relatedness to other anthozoans such as stony corals and similarities of its microalgal and bacterial partners, complementing the existing Hydra (Hydrozoa) and Nematostella (Anthozoa) model systems. Despite the availability of studies characterizing the microbiomes of several natural Aiptasia populations and laboratory strains, knowledge on basic information, such as surface topography, bacterial carrying capacity, or the prospect of microbiome manipulation is lacking. Here we address these knowledge gaps. Our results show that the surface topographies of the model hydrozoan Hydra and anthozoans differ substantially, whereas the ultrastructural surface architecture of Aiptasia and stony corals is highly similar. Further, we determined a bacterial carrying capacity of ∼104 and ∼105 bacteria (i.e., colony forming units, CFUs) per polyp for aposymbiotic and symbiotic Aiptasia anemones, respectively, suggesting that the symbiotic status changes bacterial association/density. Microbiome transplants from Acropora humilis and Porites sp. to gnotobiotic Aiptasia showed that only a few foreign bacterial taxa were effective colonizers. Our results shed light on the putative difficulties of transplanting microbiomes between cnidarians in a manner that consistently changes microbial host association at large. At the same time, our study provides an avenue to identify bacterial taxa that exhibit broad ability to colonize different hosts as a starting point for cross-species microbiome manipulation. Our work is relevant in the context of microbial therapy (probiotics) and microbiome manipulation in corals and answers to the need of having cnidarian model systems to test the function of bacteria and their effect on holobiont biology. Taken together, we provide important foundation data to extend Aiptasia as a coral model for bacterial functional studies.

Five years in the making, a massive oil spill of 1 million barrels is imminent in the Red Sea off the coast of Yemen. Emergent action must be taken by the United Nations and its International Maritime Organization (IMO) to remove the oil, despite regional political tensions, as a spill will have disastrous environmental and humanitarian consequences, especially if it occurs during winter. With millions of barrels of oil passing through the Red Sea each day, a regional strategy must be drafted for leak prevention and containment that is specific to the Red Sea’s unique ecosystems, unusual water currents, and political landscape.

Nitrogen availability often limits biological productivity in marine systems, where inorganic nitrogen, such as ammonium is assimilated into the food web by bacteria and photoautotrophic eukaryotes. Recently, ammonium assimilation was observed in kleptoplast-containing protists of the phylum foraminifera, possibly via the glutamine synthetase/glutamate synthase (GS/GOGAT) assimilation pathway imported with the kleptoplasts. However, it is not known if the ubiquitous and diverse heterotrophic protists have an innate ability for ammonium assimilation. Using stable isotope incubations (15N-ammonium and 13C-bicarbonate) and combining transmission electron microscopy (TEM) with quantitative nanoscale secondary ion mass spectrometry (NanoSIMS) imaging, we investigated the uptake and assimilation of dissolved inorganic ammonium by two heterotrophic foraminifera; a non-kleptoplastic benthic species, Ammonia sp., and a planktonic species, Globigerina bulloides. These species are heterotrophic and not capable of photosynthesis. Accordingly, they did not assimilate 13C-bicarbonate. However, both species assimilated dissolved 15N-ammonium and incorporated it into organelles of direct importance for ontogenetic growth and development of the cell. These observations demonstrate that at least some heterotrophic protists have an innate cellular mechanism for inorganic ammonium assimilation, highlighting a newly discovered pathway for dissolved inorganic nitrogen (DIN) assimilation within the marine microbial loop.

Coral reefs are under threat and innovative management strategies are urgently required. However, discoveries from innovative fields of coral reef research are rarely transposed in practical conservation actions. This is mainly due to the difficulties in knowledge exchange between scientists and conservation stakeholders. The ManaCo consortium (http://manaco.ird.nc/) is an international network federating conservation stakeholders and researchers in a common effort to preserve the coral reefs. The focus is on using modern tools to build a bridge between indigenous knowledge and scientific innovation. ManaCo aims to orientate research toward relevant conservation needs and to facilitate the transposition of research into concrete management strategies. This will allow to coordinate a collaborative response against coral reef decline. We invite anyone sharing the same interests in joining us.

Glucose utilization increases in tumors, a metabolic process that is observed clinically by 18F-fluorodeoxyglucose positron emission tomography (18F-FDG-PET). However, is increased glucose uptake important for tumor cells, and which transporters are implicated in vivo? In a genetically-engineered mouse model of lung adenocarcinoma, we show that the deletion of only one highly expressed glucose transporter, Glut1 or Glut3, in cancer cells does not impair tumor growth, whereas their combined loss diminishes tumor development. 18F-FDG-PET analyses of tumors demonstrate that Glut1 and Glut3 loss decreases glucose uptake, which is mainly dependent on Glut1. Using 13C-glucose tracing with correlated nanoscale secondary ion mass spectrometry (NanoSIMS) and electron microscopy, we also report the presence of lamellar body-like organelles in tumor cells accumulating glucose-derived biomass, depending partially on Glut1. Our results demonstrate the requirement for two glucose transporters in lung adenocarcinoma, the dual blockade of which could reach therapeutic responses not achieved by individual targeting.

Rapid ocean warming due to climate change poses a serious risk to the survival of coral reefs. It is estimated that 70–90 percent of all reefs will be severely degraded by mid-century even if the 1.5°C goal of the Paris Climate Agreement is achieved. However, one coral reef ecosystem seems to be more resilient to rising sea temperatures than most others. The Red Sea’s reef ecosystem is one of the longest continuous living reefs in the world, and its northernmost portion extends into the Gulf of Aqaba. The scleractinian corals in the Gulf have an unusually high tolerance for the rapidly warming seawater in the region. They withstand water temperature anomalies that cause severe bleaching or mortality in most hard corals elsewhere. This uniquely resilient reef employs biological mechanisms which are likely to be important for coral survival as the planet’s oceans warm. The Gulf of Aqaba could potentially be one of the planet’s largest marine refuges from climate change. However, this unique portion of the Red Sea’s reef will only survive and flourish if serious regional environmental challenges are addressed. Localized anthropogenic stressors compound the effects of warming seawater to damage corals and should be mitigated immediately. Reefs in the rest of the Red Sea are already experiencing temperatures above their thermal tolerance and have had significant bleaching, though they too would benefit from fewer local anthropogenic stressors. The countries bordering the entire Red Sea will need to cooperate to enable effective scientific research and conservation. The newly established Transnational Red Sea Center, based at the Ecole Polytechnique Fédérale de Lausanne (EPFL), can serve as the regionally inclusive, neutral organization to foster crucial regional scientific collaboration.

Textural and chemical differences in coeval rhyolitic effusive and explosive eruptions are commonly observed, and numerical models predict different timescales for the eruption of crystal-rich mushes versus crystal-poor magmas. We compare quartz zonation and diffusion timescales of crystal-rich rhyolitic ignimbrites and crystal-poor rhyolitic lava flows from the Jurassic Chon Aike Province exposed in Patagonia (Argentina). The timescales are assessed by using diffusion modeling based on nanoscale secondary ion mass spectrometry (NanoSIMS) analysis of titanium (Ti) concentration profiles in quartz crystals oriented by image analysis using micro-tomography. Quantitative Ti-data were acquired by SIMS to estimate crystallization temperatures. The textural and geochemical analysis revealed clear differences between crystal-poor rhyolitic lava flows and crystal-rich rhyolitic ignimbrites. Quartz crystals from rhyolitic lava flows display simple oscillatory cathodoluminescence (CL) zoning interpreted to be magmatic and diffusion chronometry suggest a short timescale for quartz crystallization from 5.6 ± 2.2 to 41.6 ± 9.8 years. Resorption textures are rare, and hence crystals in rhyolitic lava flows recorded a simple, rapid extraction, transport and eruption history for these crystal-poor melts. Rhyolitic ignimbrites, in contrast, reveal complex zoning patterns, reflecting several episodes of partial resorption and growth throughout their crystallization history. The complex quartz zoning textures together with longer diffusion times (

The nutritional symbiosis between coral hosts and photosynthetic dinoflagellates is fundamental to the functioning of coral reefs. Rising seawater temperatures destabilize this relationship, resulting in drastic declines in world-wide coral cover. Thermal history is thought to play an important role in shaping a coral's response to subsequent thermal stress. Here, we exposed Pocillopora damicornis to two thermal acclimation regimes (ambient vs. warm) and compared the effect that acclimation had on the coral holobiont's response to a subsequent seven day heat stress event. We conducted daily physiological measurements at the holobiont level (gross photosynthesis, respiration, host protein content, symbiont density and chlorophyll content) throughout the heating event, as well as cellular-level imaging of 13C-bicarbonate and 15N-nitrate assimilation (using NanoSIMS) at the end of the heat stress event. Thermal acclimation history had a negligible effect on the measurements conducted at the holobiont level during the heat stress event. No differences were observed in the O2-budget between ambient and warm-acclimated corals and only small fluctuations in host protein, symbiont density and chlorophyll content were detected. In contrast, this lack of differential response, was not mirrored at the cellular level. Warm-acclimated corals had substantially higher 13C enrichment in the host gastrodermis and lipid bodies, but significantly lower 15N-nitrate assimilation in the symbionts and the host tissue layers, relative to the ambient-acclimated corals. We discuss potential reasons for the disconnect that occurred between symbiont bicarbonate and nitrate assimilation (in the absence of photosynthetic breakdown) in the warm-acclimated corals. We suggest this represents either a shift in nitrogen utilization, or supply limitation by the host. Our findings raise several interesting hypotheses regarding the role that nitrogen metabolism plays in thermal stress, which will warrant further investigation if we are to understand the acclimatization capacity of the coral holobiont.

Coral reefs are currently experiencing substantial ecological impoverishment as a result of anthropogenic stressors, and the majority of reefs are facing immediate risk. Increasing ocean surface temperatures induce frequent coral mass bleaching events—the breakdown of the nutritional photo-symbiosis with intracellular algae (genus: Symbiodinium). Here, we report that Stylophora pistillata from a highly diverse reef in the Gulf of Aqaba showed no signs of bleaching despite spending 1.5 months at 1–2°C above their long-term summer maximum (amounting to 11 degree heating weeks) and a seawater pH of 7.8. Instead, their symbiotic dinoflagellates exhibited improved photochemistry, higher pigmentation and a doubling in net oxygen production, leading to a 51% increase in primary productivity. Nanoscale secondary ion mass spectrometry imaging revealed subtle cellular-level shifts in carbon and nitrogen metabolism under elevated temperatures, but overall host and symbiont biomass proxies were not significantly affected. Now living well below their thermal threshold in the Gulf of Aqaba, these corals have been evolutionarily selected for heat tolerance during their migration through the warm Southern Red Sea after the last ice age. This may allow them to withstand future warming for a longer period of time, provided that successful environmental conservation measures are enacted across national boundaries in the region.

High input of organic carbon and/or slowly renewing bottom waters frequently create periods with low dissolved oxygen concentrations on continental shelves and in coastal areas; such events can have strong impacts on benthic ecosystems. Among the meiofauna living in these environments, benthic foraminifera are often the most tolerant to low oxygen levels. Indeed, some species are able to survive complete anoxia for weeks to months. One known mechanism for this, observed in several species, is denitrification. For other species, a state of highly reduced metabolism, essentially a state of dormancy, has been proposed but never demonstrated. Here, we combined a 4 weeks feeding experiment, using 13C-enriched diatom biofilm, with correlated TEM and NanoSIMS imaging, plus bulk analysis of concentration and stable carbon isotopic composition of total organic matter and individual fatty acids, to study metabolic differences in the intertidal species Ammonia tepida exposed to oxic and anoxic conditions. Strongly contrasting cellular-level dynamics of ingestion and transfer of the ingested biofilm components were observed between the two conditions. Under oxic conditions, within a few days, intact diatoms were ingested, degraded, and their components assimilated, in part for biosynthesis of different cellular components: 13C-labeled lipid droplets formed after a few days and were subsequently lost (partially) through respiration. In contrast, in anoxia, fewer diatoms were initially ingested and these were not assimilated or metabolized further, but remained visible within the foraminiferal cytoplasm even after 4 weeks. Under oxic conditions, compound specific 13C analyses showed substantial de novo synthesis by the foraminifera of specific polyunsaturated fatty acids (PUFAs), such as 20:4(n-6). Very limited PUFA synthesis was observed under anoxia. Together, our results show that anoxia induced a greatly reduced rate of heterotrophic metabolism in Ammonia tepida on a time scale of less than 24 hours, these observations are consistent with a state of dormancy.

Understanding the evolution of scleractinian corals on geological timescales is key to predict how modern reef ecosystems will react to changing environmental conditions in the future. Important to such efforts has been the development of several skeleton-based criteria to distinguish between the two major ecological groups of scleractinians: zooxanthellates, which live in symbiosis with dinoflagellate algae, and azooxanthellates, which lack endosymbiotic dinoflagellates. Existing criteria are based on overall skeletal morphology and bio/geo-chemical indicators-none of them being particularly robust. Here we explore another skeletal feature, namely fine-scale growth banding, which differs between these two groups of corals. Using various ultra-structural imaging techniques (e.g., TEM, SEM, and NanoSIMS) we have characterized skeletal growth increments, composed of doublets of optically light and dark bands, in a broad selection of extant symbiotic and asymbiotic corals. Skeletons of zooxanthellate corals are characterized by regular growth banding, whereas in skeletons of azooxanthellate corals the growth banding is irregular. Importantly, the regularity of growth bands can be easily quantified with a coefficient of variation obtained by measuring bandwidths on SEM images of polished and etched skeletal surfaces of septa and/or walls. We find that this coefficient of variation (lower values indicate higher regularity) ranges from ~40 to ~90% in azooxanthellate corals and from ~5 to ~15% in symbiotic species. With more than 90% (28 out of 31) of the studied corals conforming to this microstructural criterion, it represents an easy and robust method to discriminate between zooxanthellate and azooxanthellate corals. This microstructural criterion has been applied to the exceptionally preserved skeleton of the Triassic (Norian, ca. 215 Ma) scleractinian Volzeia sp., which contains the first example of regular, fine-scale banding of thickening deposits in a fossil coral of this age. The regularity of its growth banding strongly suggests that the coral was symbiotic with zooxanthellates.

ABSTRACT Reef-building corals form essential, mutualistic endosymbiotic associations with photosynthetic Symbiodinium dinoflagellates, providing their animal host partner with photosynthetically derived nutrients that allow the coral to thrive in oligotrophic waters. However, little is known about the dynamics of these nutritional interactions at the (sub)cellular level. Here, we visualize with submicrometer spatial resolution the carbon and nitrogen fluxes in the intact coral-dinoflagellate association from the reef coral Pocillopora damicornis by combining nanoscale secondary ion mass spectrometry (NanoSIMS) and transmission electron microscopy with pulse-chase isotopic labeling using [13C]bicarbonate and [15N]nitrate. This allows us to observe that (i) through light-driven photosynthesis, dinoflagellates rapidly assimilate inorganic bicarbonate and nitrate, temporarily storing carbon within lipid droplets and starch granules for remobilization in nighttime, along with carbon and nitrogen incorporation into other subcellular compartments for dinoflagellate growth and maintenance, (ii) carbon-containing photosynthates are translocated to all four coral tissue layers, where they accumulate after only 15 min in coral lipid droplets from the oral gastroderm and within 6 h in glycogen granules from the oral epiderm, and (iii) the translocation of nitrogen-containing photosynthates is delayed by 3 h. IMPORTANCE Our results provide detailed in situ subcellular visualization of the fate of photosynthesis-derived carbon and nitrogen in the coral-dinoflagellate endosymbiosis. We directly demonstrate that lipid droplets and glycogen granules in the coral tissue are sinks for translocated carbon photosynthates by dinoflagellates and confirm their key role in the trophic interactions within the coral-dinoflagellate association.