Biology subjects

Mass, T.

Publications and source records attributed to Mass, T..

13 recordsLinked to original sources

bioRxiv2026

Cell-resolved transcriptional responses during heat-induced coral bleaching and recovery

Coral reefs depend on an intracellular symbiosis between cnidarian hosts and photosynthetic dinoflagellates that is disrupted by ocean warming, causing coral bleaching. Yet how these responses are distributed across coral cell types during stress and recovery remains unclear. Here, we generate a temporal single-cell transcriptomic atlas of the reef-building coral Stylophora pistillata, profiling 20,000 cells during seven days at 32 {degrees}C and after 45 days of recovery. Heat stress reduced symbiont abundance and photosynthetic efficiency, followed by partial restoration. Early oxidative-stress, detoxification, and proteostasis programmes gave way to mitochondrial, cytoskeletal, and vesicular remodelling. These shared responses accompanied cell type-specific changes: epidermal cells activated tissue-renewal programmes, calicoblasts repressed calcification genes, and alga-hosting cells progressively lost transport, lipid-biosynthesis, and nutrient-exchange functions. Targeted profiling of sorted alga-positive cells revealed rare transcriptional states, including a population consistent with symbiont engulfment. Our results reveal how bleaching and recovery are coordinated across coral tissues and symbiotic cell states.

genomics↗

bioRxiv2026

Novel insights into conserved biomineralization mechanisms revealed from a cold-water scleractinian coral skeletal proteome

Stony corals exhibit striking morphological plasticity across diverse environments and trophic strategies, raising fundamental questions about the conservation of their biomineralization machinery. Here, we characterize the skeletal organic matrix proteome of the cold-water, asymbiotic coral Desmophyllum pertusum and compare it with skeletal proteomes from a facultatively photosymbiotic temperate coral and an obligately photosymbiotic subtropical coral. Despite pronounced differences in habitat, symbiotic status, and skeletal micro-density, we observe convergence on a conserved "biomineralization toolkit". Comparative proteomics, genomics, and structural predictions reveal that this toolkit integrates diverse acidic matrix proteins, carbonic anhydrases, adhesion and structural proteins, and signaling components with multiple cellular export pathways. Together, these findings redefine coral biomineralization as a dynamic, coordinated network of cellular pathways rather than a static assemblage of matrix components. The symbiont-free model D. pertusum provides a mechanistic framework for dissecting coral calcification across environments and for assessing the resilience of this conserved machinery.

biochemistry↗

bioRxiv2026

Asymmetric depth acclimation and plasticity limit the refugial potential of mesophotic Porites astreoides

Mesophotic coral ecosystems have been proposed as climate refugia for shallow reefs, yet the capacity of mesophotic corals to persist across depth gradients remains unresolved. We conducted a 7-month reciprocal transplantation of the Caribbean coral Porites astreoides between shallow (10 m) and mesophotic (40 m) reefs to assess physiological, skeletal, and transcriptomic plasticity. Shallow colonies exhibited higher metabolic activity and skeletal extension, whereas mesophotic colonies showed reduced protein content, slower extension, and elevated expression of skeletal organic matrix genes. Transplant responses were asymmetric: shallow-to-deep corals acclimated through coordinated physiological and transcriptional adjustments, while deep-to-shallow transplants experienced elevated mortality and limited plasticity. SNP-based analyses suggest incomplete isolation across depth, while reciprocal transplant responses reflect greater phenotypic plasticity in shallow corals and indications of depth-specific specialization in mesophotic corals. Our findings indicate that shallow populations harbor greater acclimatory capacity, whereas mesophotic corals show constrained upward resilience, challenging the generality of deep reefs as refugia under rapid environmental change.

ecology↗

bioRxiv2025

Exposure to a gradient of warming and acidification highlights physiological, molecular, and skeletal tolerance thresholds in Pocillopora acuta recruits

Ocean warming and acidification are among the biggest threats to the persistence of coral reefs. Organismal stress tolerance thresholds are life stage specific, can vary across levels of biological organization, and also depend on natural environmental variability. Here, we exposed the early life stages of Pocillopora acuta in K[a]ne ohe Bay, Hawai i, USA, a common reef-building coral throughout the Pacific, to projected ocean warming and acidification scenarios. We measured ecological, physiological, biomineralization, and molecular responses across the critical transition from larvae to newly settled recruits following 6 days of exposure to diel fluctuations in temperature and pH in Control (26.8-27.9{degrees}C, 7.82-7.96 pHTotal), Mid (28.4-29.5{degrees}C, 7.65-7.79 pHTotal) and High conditions (30.2-31.5{degrees}C, 7.44-7.59 pHTotal). We found that P. acuta early life stages are capable of survival, settlement, and calcification under all scenarios. The High conditions, however, caused a significant reduction in survival and settlement capacity, with changes in the skeletal fiber deposition patterns. In contrast to a limited impact on the expression of biomineralization genes, the dominant transcriptomic response to the High conditions relative to the two other treatments included depressed metabolism, reduced ATP production and increased activity of DNA damage-repair processes. Collectively, our findings indicate that corals living in environments with large diurnal fluctuations in seawater temperature and pH, such as K[a]ne ohe Bay, can tolerate exposure to moderate projected increased temperature and reduced pH. However, under more severe environmental conditions significant negative effects on coral cellular metabolism and overall organismal survival jeopardize species fitness and recruitment.

molecular biology↗

bioRxiv2023

New record of Dendronephthya hemprichi (Family: Nephtheidae) fromMediterranean, Israel- an evidence for tropicalization?

Bioinvasions have the potential to provoke cascade effects that can disrupt natural ecosystems, and cause ecological regime shifts. The Mediterranean Sea is particularly prone to bioinvasions as the changing water conditions, evoked by climate change, are creating advantageous conditions for Lessepsian migrants from the Red Sea. Recently, in May 2023, a new alien species was documented in the Mediterranean Sea - a soft coral of the genus Dendronephthya. This discovery was made by divers conducting Long Term Ecological Research surveys, along the coast of Israel, at a depth of 42 m. Genetic and morphological testing were utilized to confirm the species identity as Dendronepthya hemprichi, an Indo-Pacific coral, common in the Red Sea. According to life history traits of this species such as accelerated attachment to available surfaces and fast growth, we expect it to rapidly expand its distribution and abundance across the Mediterranean. HighlightsO_LIPotential Tropicalization of the Mediterranean Sea C_LIO_LIIncreasing water temperatures are an important vector for marine bioinvasion C_LIO_LIA second soft coral species, associated with Lessepsian migration, was identified in the Mediterranean C_LIO_LIThe importance of a long-term ecological monitoring program for identifying ecosystem changes C_LI

ecology↗

bioRxiv2023

Multi-omic analysis of coral development elucidates the metabolic transitions from parental provisioning to endosymbiotic nutritional exchange

Climate change accelerates coral reef decline and jeopardizes recruitment essential for ecosystem recovery. Adult corals rely on a vital nutritional exchange with their symbiotic algae (Symbiodiniaceae), but the dynamics and sensitivity of this reliance from fertilization to recruitment are understudied. We investigated the physiological, metabolomic, and transcriptomic changes across 13 developmental stages of Montipora capitata, a coral in Hawai i that inherits symbionts from parent to egg. We found that embryonic development depends on maternally provisioned mRNAs and lipids, with a rapid shift to symbiont-derived nutrition in swimming larvae. Symbiont density and photosynthesis peak once swimming to fuel pelagic larval dispersal. In contrast, respiratory demand increases significantly during metamorphosis, settlement, and calcification, reflecting this energy-intensive morphological reorganization. Symbiont ontogenetic proliferation is driven by symbiont ammonium assimilation with little evidence of nitrogen metabolism in the coral host. As development progresses, the host enhances nitrogen sequestration, regulating symbiont populations, and ensuring the transfer of fixed carbon to support metamorphosis, with both metabolomic and transcriptomic indicators of increased carbohydrate availability. Although algal symbiont communities remained stable, bacterial communities shifted with ontogeny, associated with holobiont metabolic reorganization. Our study reveals extensive metabolic changes during development, increasingly reliant on symbiont nutrition. Metamorphosis and settlement emerge as the most critical periods of energetic vulnerability to projected climate scenarios that destabilize symbiosis. This highly detailed elucidation of symbiotic nutritional exchange relative to sensitive early life stages provides essential knowledge for understanding and forecasting nutritional symbiosis integration, and specifically, coral survival and recruitment in a future of climate change.

physiology↗

bioRxiv2021

Energetics but not development is impacted in coral embryos exposed to ocean acidification

In light of the chronic stress and mass mortality reef-building corals face under climate change, it is critical to understand the processes essential to reef persistence and replenishment, including coral reproduction and development. Here we quantify gene expression and size sensitivity to ocean acidification across a set of developmental stages in the rice coral, Montipora capitata. Embryos and swimming larvae were exposed to pH treatments 7.8 (Ambient), 7.6 (Low) and 7.3 (Xlow) from fertilization to 9 days post-fertilization. Embryo and larval volume, and stage-specific gene expression were compared between treatments to determine the effects of acidified seawater on early development. While there was no measurable size differentiation between fertilized eggs and prawn chips exposed to pH 7.8, 7.6, and 7.3, early gastrula and planula raised in reduced pH treatments were significantly smaller than those raised in ambient seawater, suggesting an energetic cost to developing under low pH. However, no differentially expressed genes emerged until 9 days post-fertilization. Notably, gene expression patterns of larvae developing at pH 7.8 and pH 7.3 were more similar than those developing at pH 7.6. Larvae from pH 7.6 showed upregulation of genes involved in cell division, regulation of transcription, lipid metabolism, and oxidative stress in comparison to the other two treatments. While low pH appears to increase energetic demands and trigger oxidative stress, the developmental process is robust to this at a molecular level, with swimming larval stage reached in all pH treatments. Summary statementThis developmental time series tracks the physiological and transcriptomic outcomes of early coral development under ambient pH (pH 7.8), and two low pH conditions (pH 7.6 and 7.3).

physiology↗

bioRxiv2021

The calcifying interface in a stony coral's primary polyp: An interplay between seawater and an extracellular calcifying space

Stony coral exoskeletons build the foundation to the most biologically diverse yet fragile marine ecosystems on earth, coral reefs. Understanding corals biomineralization mechanisms is therefore crucial for coral reef management and for using coral skeletons in geochemical studies. In this study, we combine in-vivo and cryo-electron microscopy with single-cell RNA-seq data to gain novel insights into the calcifying micro-environment that facilitates biomineralization in primary polyps of the stony coral Stylophora pistillata. We show an intimate involvement of seawater in this micro-environment. We further document increased tissue permeability and a highly dispersed cell packing in the tissue secreting the coral skeleton (i.e. calicoblastic). We also observe an extensive filopodial network containing carbon-rich vesicles extruding from some of the calicoblastic cells. Single-cell RNA-Seq data interrogation shows that calicoblastic cells express genes involved in filopodia and vesicle structure and function. These observations provide a new conceptual framework for resolving stony corals biomineralization processes.

developmental biology↗

bioRxiv2021

Combined responses of primary coral polyps and their algal endosymbionts to decreasing seawater pH

With coral reefs declining globally, resilience of these ecosystems hinges on successful coral recruitment. However, knowledge of the acclimatory and/or adaptive potential in response to environmental challenges such as ocean acidification (OA) in earliest life stages is limited. Our combination of physiological measurements, microscopy, computed tomography techniques and gene expression analysis allowed us to thoroughly elucidate the mechanisms underlying the response of early life stages of corals, together with their algal partners, to the projected decline in oceanic pH. We observed extensive physiological, morphological and transcriptional changes in surviving recruits, and the transition to a less-skeleton/more-tissue phenotype. We found that decreased pH conditions stimulate photosynthesis and endosymbiont growth, and gene expression potentially linked to photosynthates translocation. Our unique holistic study discloses the previously unseen intricate net of interacting mechanisms that regulate the performance of these organisms in response to OA.

developmental biology↗

bioRxiv2021

Developmental series of gene expression clarifies maternal mRNA provisioning and maternal-to-zygotic transition in the reef-building coral Montipora capitata

BackgroundMaternal mRNA provisioning of oocytes regulates early embryogenesis. Maternal transcripts are degraded as zygotic genome activation (ZGA) intensifies, a phenomenon known as the maternal-to-zygotic transition (MZT). Here, we examine gene expression over nine developmental stages in the Pacific rice coral, Montipora capitata, from eggs and embryos at 1, 4, 9, 14, 22, and 36 hours-post-fertilization (hpf), as well as swimming larvae (9d), and adult colonies. ResultsWeighted Gene Coexpression Network Analysis revealed four expression peaks, identifying the maternal complement, two waves of the MZT, and adult expression. Gene ontology enrichment revealed maternal mRNAs are dominated by cell division, methylation, biosynthesis, metabolism, and protein/RNA processing and transport functions. The first MZT wave occurs from [~]4-14 hpf and is enriched in terms related to biosynthesis, methylation, cell division, and transcription. In contrast, functional enrichment in the second MZT wave, or ZGA, from 22 hpf-9dpf, includes ion/peptide transport and cell signaling. Finally, adult expression is enriched for functions related to signaling, metabolism, and ion/peptide transport. Our proposed MZT timing is further supported by expression of enzymes involved in zygotic transcriptional repression (Kaiso) and activation (Sox2), which peak at 14 hpf and 22 hpf, respectively. Further, DNA methylation writing (DNMT3a) and removing enzymes (TET1) peak and remain stable past [~]4 hpf, indicating that methylome programming occurs before 4 hpf. ConclusionsOur high-resolution insight into the coral maternal mRNA and MZT provides essential information regarding setting the stage for, and the sensitivity of, developmental success and parental carryover effects under increasing environmental stress.

developmental biology↗

bioRxiv2021

Physiological and transcriptomic variability indicative of differences in key functions within a single coral colony

Polyps in different locations on individual stony coral colonies experience variation in numerous environmental conditions including flow and light, potentially leading to transcriptional and physiological differences across the colony. Here, we describe high-resolution physiological measurements and differential gene expression from multiple locations within a single colony of Stylophora pistillata, aiming to relate these to environmental gradients across the coral colony. We observed broad transcriptional responses in both the host and photosymbiont in response to height above the substrate, cardinal direction, and, most strongly, location along the branch axis. Specifically, several key physiological processes in the host appear more active toward branch tips including several metabolic pathways, toxin production for prey capture or defense, and biomolecular mechanisms of biomineralization. Further, the increase in gene expression related to these processes toward branch tips is conserved between S. pistillata and Acropora spp. The photosymbiont appears to respond transcriptionally to relative light intensity along the branch and due to cardinal direction. These differential responses were observed across the colony despite its genetic homogeneity and likely inter-polyp communication. While not a classical division of labor, each part of the colony appears to have distinct functional roles related to polyps differential exposure to environmental conditions.

genomics↗

bioRxiv2020

Optimization of skeletal protein preparation for LC-MS/MS sequencing yields additional coral skeletal proteins in Stylophora pistillata

Stony corals generate their calcium carbonate exoskeleton in a highly controlled biomineralization process mediated by a variety of macromolecules including proteins. Fully identifying and classifying these proteins is crucial to understanding their role in exoskeleton formation, yet no optimal method to purify and characterize the full suite of extracted coral skeletal proteins has been established and hence their complete composition remains obscure. Here, we tested four skeletal protein purification protocols using acetone precipitation and ultrafiltration dialysis filters to present a comprehensive scleractinian coral skeletal proteome. We identified a total of 60 proteins in the coral skeleton, 44 of which were not present in previously published stony coral skeletal proteomes. Extracted protein purification protocols carried out in this study revealed that no one method captures all proteins and each protocol revealed a unique set of method-exclusive proteins. To better understand the general mechanism of skeletal protein transportation, we further examined the proteins gene ontology, transmembrane domains, and signal peptides. We found that transmembrane domain proteins and signal peptide secretion pathways, by themselves, could not explain the transportation of proteins to the skeleton. We therefore propose that some proteins are transported to the skeleton via non-traditional secretion pathways.

biochemistry↗

bioRxiv2020

A tentacle for every occasion: comparing the hunting tentacles and sweeper tentacles, used for territorial competition, in the coral Galaxea fascicularis

Coral reefs are among the most diverse, complex and densely populated marine ecosystems. To survive, morphologically simple and sessile cnidarians have developed mechanisms to catch prey, deter predators and compete with adjacent corals for space, yet the mechanisms underlying these functions are largely unknown. Here, we characterize the histology, toxic activity and gene expression patterns in two different types of tentacles from the scleractinian coral Galaxea fascilcularis - catch tentacles (CTs), used to catch prey and deter predators, and sweeper tentacles (STs), specialized tentacles used for territorial aggression. STs exhibit more mucocytes and higher expression of mucin genes than CTs, and lack the ectodermal cilia used to deliver food to the mouth and remove debris. STs and CTs also express different sensory g-protein coupled receptors, suggesting they may employ different sensory pathways. Each tentacle type has a different complement of stinging cells (nematocytes), and the expression in the two tentacles of genes encoding structural nematocyte proteins suggests the stinging cells develop within the tentacles. CTs have higher neurotoxic and hemolytic activities, consistent with a role in prey capture, whereas the STs have higher phospholipase A2 activity, which we speculate may have a role in inducing tissue damage during territorial aggression. The toxin genes expressed in each tentacle are also different. These results show that the same organism utilizes two distinct tentacle types, each equipped with a different venom apparatus and toxin composition, for prey capture and defense and for territorial aggression.

ecology↗