Biology subjects

Huffmyer, A. S.

Publications and source records attributed to Huffmyer, A. S..

12 recordsLinked to original sources

bioRxiv2026

Contrasting defensive strategies underlie differential susceptibility of corals to crown-of-thorns sea star (CoTS; Acanthaster cf. solaris) predation

Crown-of-thorns sea star (CoTS), Acanthaster cf. solaris, outbreaks are a major cause of hard coral cover decline across the west Pacific, threatening coral reefs. Coral taxa vary in susceptibility to CoTS predation from preferred (Acropora spp.) to non-preferred (Porites spp.), yet the mechanisms underlying these differences are poorly understood. We investigated coral defenses during an ongoing CoTS outbreak in Moorea, French Polynesia by examining gene expression (including putative toxin genes) in healthy and actively predated colonies of a preferred (Acropora hyacinthus) and a non-preferred (Porites sp.) coral prey species. During predation, A. hyacinthus exhibited molecular signatures of cellular stress responses involving oxidative stress signalling, inflammation, and tissue proteolysis. In contrast, Porites sp. showed enrichment of genes involved in mitochondrial metabolic adjustment and aerobic metabolism, suggesting metabolic compensation to maintain cellular function. Furthermore, A. hyacinthus demonstrated a reactive defense behaviour by differentially expressing toxins (e.g., kunitz-type neurotoxins) while Porites sp. employed constitutive expression of all putative toxins regardless of active predation, suggesting a proactive defense strategy. Together, these findings suggest that preferred and non-preferred coral prey exhibit fundamentally different molecular and defensive strategies during CoTS predation, shedding light on the evolutionary arms race between corals and their predators.

molecular biology↗

bioRxiv2025

Parental immune priming reshapes offspring growth, metabolism, and thermal tolerance in the Pacific Oyster

Pacific Oysters (Magallana/Crassostrea gigas) are marine bivalves that are widely cultivated but increasingly experience summer mortality due to interacting stressors. Two major concerns are (1) the rising severity and frequency of marine heat waves and (2) disease outbreaks (e.g., OsHV-1). It is critical to understand how these interacting stressors influence oyster resilience and how stress memory is passed down from parent to offspring. Specifically, it is not known how parental immune stress impacts offspring tolerance to other stressors, including heat stress. Therefore, we tested the effects of parental immune challenge on offspring performance under elevated temperature. Broodstock were exposed to a Poly(I:C) immune challenge, then their offspring were reared to the seed stage and assessed for survival, growth, and metabolic responses under thermal stress in the lab. We found that parental immune priming elicited metabolic flexibility in offspring, which may underlie altered stress tolerance. Offspring of immune-challenged parents were 6.5% larger by 236 days post-fertilization at the end of the study. Under elevated temperatures, offspring from treated parents had 35% lower mortality than controls at 40{degrees}C, but this was reversed at 42{degrees}C with 17% higher mortality compared to controls, suggesting thermal limits to priming benefits. Metabolic assays further revealed that at moderately elevated temperature (36{degrees}C), primed offspring had 43% higher metabolic activity, whereas at higher temperature (40{degrees}C), they exhibited 30% lower metabolic activity than controls. Offspring of immune primed parents differentially expressed heat shock (HSP70, HSP90) and immune genes (viperin) under acute stress, suggesting molecular mechanisms underlying immune priming effects. This pattern indicates that parental immune challenge may influence offspring metabolic flexibility, potentially enhancing thermal tolerance through an increased capacity for metabolic depression at extreme temperatures. Together, the results of this study highlight cross-generational links between immune priming and thermal tolerance.

physiology↗

bioRxiv2025

Seasonal plasticity of symbiotic strategies clarifies coral holobiont resistance and resilience

As coral reefs face unprecedented declines driven by thermal stress and the breakdown of coral symbiosis (i.e., coral bleaching), restoration efforts increasingly rely on coral health and resilience rankings. However, seasonal plasticity in symbiosis and holobiont metabolism, along with the presence of cryptic species, can complicate data interpretation. Therefore, quantifying seasonal plasticity in coral physiology and incorporating genetic identification are essential for accurately interpreting and drawing conclusions from trait-based and fitness-based analyses. To test the effect of seasonal and site variation on physiological plasticity we sampled three ecologically dominant genera, Acropora, Pocillopora, and Porites across three lagoon sites (n=15 tagged colonies genus-1 site-1) on the north shore of Moorea French Polynesia in January, March, September, and December of 2020. We identified coral host and intracellular symbiotic Symbiodiniaceae to the highest taxonomic resolution possible and quantified 13 physiological variables within the holobiont. Genetic analyses identified A. pulchra along with cryptic lineages in Pocillopora (P. meandrina, P. tuahiniensis) and Porites (P. evermanni, P. lobata/lutea). A. pulchra was dominated by Durusdinium trenchii and also contained Symbiodinium microadriaticum. Symbiont communities differed between cryptic congeners, with P. meandrina hosting Cladocopium latusorum and P. tuahiniensis hosting Cladocopium pacificum, whereas P. evermanni and P. lobata/lutea both hosted Cladocopium (C15), but each with unique C15 profiles. Weedy taxa such as Acropora and Pocillopora displayed a cycle of symbiont boom and bust in response to seasonally variable light and temperature, likely contributing to the high stress sensitivity of these taxa. In contrast, despite seasonal environmental variability, Porites displayed greater symbiont stability, with temperature--rather than light--serving as the stronger explanatory variable of seasonal variation in host physiology. Increased host biomass under cooler conditions, which provides energy reserves, may serve as an important stabilizing factor in massive Porites well-documented stress resilience. Collectively, our data provide essential evidence of the need for integrative analyses considering baseline physiological states across seasons along with host and symbiont genetics, particularly in light of the plethora of climate change related stress test assays taking place throughout the year across coral taxa with cryptic lineages.

physiology↗

bioRxiv2025

From Blue to Pink: Resazurin as a High-Throughput Proxy for Metabolic Rate in Oysters

Metabolic rate assays are critical tools for assessing organismal stress and resilience, yet their widespread application in aquaculture and ecological monitoring is limited. Improving these assays is essential for hatchery managers, farmers, and scientists seeking to identify resilient stocks and monitor stress in shellfish populations. Resazurin, a redox-sensitive dye commonly used in cell viability assays, offers a promising, high-throughput assay for metabolic rate assessment, but its application at the whole-organism level remains under explored. This study evaluates the efficacy of a resazurin-based metabolic assay in oysters (Crassostrea gigas and Crassostrea virginica) through four experimental approaches: (1) adaptation of the resazurin assay to measure oyster metabolism, (2) examination of temperature effects on oyster metabolism, (3) characterization of acute thermal stress responses, (4) examination of genetic variability in metabolism, and (5) correlations between metabolism and predicted performance in a selective breeding case study. Our findings confirm that resazurin fluorescence is correlated with oxygen consumption, validating its use as a measure of metabolism. Thermal performance assays reveal expected metabolic responses to temperature, including identification of optima and tipping points where metabolic stimulation shifts to depression under temperature stress. Acute thermal stress experiments demonstrate that oysters exhibiting greater metabolic depression are more likely to survive, supporting metabolism as a predictor of mortality. Further, genetic variation in stress responses is detected as family-level variation in metabolism. Metabolism of 50 families (C. virginica) selectively bred for performance in varying environments was measured and significantly correlated with predicted performance. By establishing resazurin as an additional reliable and scalable method for metabolic assessment, this study lays the groundwork for its broader adoption in aquaculture and conservation. Implementing this approach may provide a tool to enhance stock selection, improve hatchery management practices, and support adaptive strategies in the face of climate variability and increased environmental stress in coastal oceans.

physiology↗

bioRxiv2025

Non-coding RNA Repertoire in Reef-Building Corals

Non-coding RNAs (ncRNAs) play critical regulatory roles in gene expression regulation that influences diverse biological processes in response to environmental change. Yet their characterization in non-model organisms, particularly sessile, benthic ecosystem engineers such as reef-building corals that are sensitive to climate change, remains limited. This study provides the first comprehensive analysis of the ncRNA repertoire of species from three ecologically important coral genera from Moorea, French Polynesia: Acropora pulchra, Pocillopora tuahiniensis, and Porites evermanni. These species demonstrate differing symbiotic partners, life history strategies, and physiological traits, offering a broad framework for documenting ncRNA variation in corals. We identified homologs for ncRNA biogenesis and functional machinery, characterized long ncRNAs (lncRNAs), microRNAs (miRNAs), and piwiRNAs (piRNAs), and assessed their genomic context and potential targets. Our findings reveal the presence of conserved ncRNA machinery across these coral species, indicating their capability to generate and utilize ncRNAs for the regulation of gene expression. We identified only a single miRNA conserved with corals and Eumetazoans (miR-100), four miRNAs shared across all three species, previously identified in other cnidarian taxa (miR-100, miR-2023, miR-2025, miR-2036), as well as several species-specific miRNAs. Predicted gene targets of the characterized miRNAs included immune response regulation in A. pulchra and P. tuahiniensis and signal transduction pathways in P. evermanni and P. tuahiniensis. Proximity analysis indicated >71-99% of piRNAs overlapped with genes, with genomic maintenance and stability identified as the primary functional enrichment of those genes. Our characterization of lncRNAs found little sequence overlap across each species (<2%), although lncRNAs in all three species were often in proximity to immune-related genes. This study lays the groundwork for the repertoire and regulatory roles of ncRNAs in reef-building corals, thereby expanding our understanding of epigenetic regulation in environmentally sensitive marine invertebrates and its potential implications in acclimatization and adaptation to environmental change.

molecular biology↗

bioRxiv2025

Coral venom and toxins as protection against crown-of-thorns sea star attack

Crown-of-thorns sea star (CoTS) outbreaks are one of the leading causes of hard coral cover decline across the Indo-Pacific, posing a major threat to the health and resilience of coral reefs. However, the drivers underlying feeding on preferred (e.g., Acropora spp.) versus non-preferred (e.g., Porites spp.) are poorly understood. We hypothesised that coral venom may influence CoTS food preferences. We investigated whether coral venom toxin and peptide families may drive CoTS prey preferences by comparing the genomes and transcriptomes of preferred (five Acropora species) and non-preferred (five Porites species and Echinopora lamellosa) prey species of CoTS. We constructed databases of known cnidarian venom toxins, and along with the full UniProtKB/Swiss-Prot Tox-Prot database, used these to identify toxin peptides and investigate function and phylogeny. The most abundant toxins across all coral species included kunitz-type neurotoxins, neurotoxic turripeptides, snake venom lectins, toxic proteases and actinoporins. There were proteins present only in certain Porites species but completely absent from all Acropora species (e.g., tereporin/conoporin, snake venom peptides) and vice versa (e.g., sarafotoxin). Further, Porites species contained a homolog to conkunitzin, a toxin known to disintegrate the tube feet of CoTS, suggesting a potential mechanism for their lower susceptibility to predation. We also observed a greater diversity of jellyfish-like proteins in CoTS-exposed Porites species compared to naive Porites species, suggesting these proteins deter CoTS. These findings have direct applications to assessing reef corals susceptibility to future CoTS outbreaks and active reef management.

bioinformatics↗

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↗

bioRxiv2024

Coral larvae employ nitrogen sequestration mechanisms to stabilize carbon provisioning from algal symbionts under increased temperature

Rising sea surface temperatures are increasingly causing breakdown in the nutritional relationship between corals and algal endosymbionts (Symbiodiniaceae), threatening the basis of coral reef ecosystems and highlighting the critical role of coral reproduction in reef maintenance. The effects of thermal stress on metabolic exchange (i.e., transfer of fixed carbon photosynthates from symbiont to host) during sensitive early life stages, however, remains understudied. We exposed symbiotic Montipora capitata coral larvae in Hawaii to high temperature (+2.5{degrees}C for 3 days), assessed rates of photosynthesis and respiration, and used stable isotope tracing (4mM 13C sodium bicarbonate; 4.5 h) to quantify metabolite exchange. While larvae did not show any signs of bleaching and did not experience declines in survival and settlement, metabolic depression was significant under high temperature, indicated by a 19% reduction in respiration rates, but with no change in photosynthesis. Larvae exposed to high temperature showed evidence for maintained translocation of a major photosynthate, glucose, from the symbiont, but there was reduced metabolism of glucose through central carbon metabolism (i.e., glycolysis). The larval host invested in nitrogen cycling by increasing ammonium assimilation, urea metabolism, and sequestration of nitrogen into dipeptides, a mechanism that may support the maintenance of glucose translocation under thermal stress. Host nitrogen assimilation via dipeptide synthesis appears to be used for nitrogen limitation to the Symbiodiniaceae, with the outcome of reduced symbiont population growth and retention of fixed carbon, effectively simulating photosynthate translocation to the host. Collectively, our findings indicate that although these larvae are susceptible to metabolic stress under high temperature, they can combat bleaching by diverting energy to nitrogen assimilation to maintain symbiont population density, photosynthesis, and carbon translocation.

cell biology↗

bioRxiv2024

DNA methylation modulates transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)

Ocean acidification significantly affects marine calcifiers like oysters, warranting the study of molecular mechanisms like DNA methylation that contribute to adaptive plasticity in response to environmental change. However, a consensus has not been reached on the extent to which methylation modules gene expression, and in turn plasticity, in marine invertebrates. In this study, we investigated the impact of pCO2 on gene expression and DNA methylation in the eastern oyster, Crassostrea virginica. After a 30-day exposure to control (572 ppm) or elevated pCO2 (2,827 ppm), whole genome bisulfite sequencing (WGBS) and RNA-Seq data were generated from adult female gonad tissue and male sperm samples. Although differentially methylated loci (DML) were identified in females (89) and males (2,916), there were no differentially expressed genes, and only one differentially expressed transcript in females. However, gene body methylation impacted other forms of gene activity in sperm, such as the maximum number of transcripts expressed per gene and changes in the predominant transcript expressed. Elevated pCO2 exposure increased gene expression variability (transcriptional noise) in males but decreased noise in females, suggesting a sex-specific role of methylation in gene expression regulation. Functional annotation of genes with changes in transcript-level expression or containing DML revealed several enriched biological processes potentially involved in elevated pCO2 response, including apoptotic pathways and signal transduction, as well as reproductive functions. Taken together, these results suggest that DNA methylation may regulate gene expression variability to maintain homeostasis in elevated pCO2 conditions and could play a key role in environmental resilience in marine invertebrates.

physiology↗

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

Marine heatwaves depress metabolic activity and impair cellular acid-base homeostasis in reef-building corals regardless of bleaching susceptibility

Ocean warming is causing global coral bleaching events to increase in frequency, resulting in widespread coral mortality and disrupting the function of coral reef ecosystems. However, even during mass bleaching events, many corals resist bleaching despite exposure to abnormally high temperatures. While the physiological effects of bleaching have been well documented, the consequences of heat stress for bleaching resistant individuals are not well understood. In addition, much remains to be learned about how heat stress affects cellular level processes that may be overlooked at the organismal level, yet are crucial for coral performance in the short term and ecological success over the long term. Here we compared the physiological and cellular responses of bleaching resistant and bleaching susceptible corals throughout the 2019 marine heatwave in Hawai i, a repeat bleaching event that occurred four years after the previous regional event. Relative bleaching susceptibility within species was consistent between the two bleaching events, yet corals of both resistant and susceptible phenotypes exhibited pronounced metabolic depression during the heatwave. At the cellular level, bleaching susceptible corals had lower intracellular pH than bleaching resistant corals at the peak of bleaching for both symbiont-hosting and symbiont-free cells, indicating greater disruption of acid-base homeostasis in bleaching susceptible individuals. Notably, cells from both phenotypes were unable to compensate for experimentally induced cellular acidosis, indicating that acid-base regulation was significantly impaired at the cellular level even in bleaching resistant corals and in cells containing symbionts. Thermal disturbances may thus have substantial ecological consequences, as even small reallocations in energy budgets to maintain homeostasis during stress can negatively affect fitness. These results suggest concern is warranted for corals coping with ocean acidification alongside ocean warming, as the feedback between temperature stress and acid-base regulation may further exacerbate the physiological effects of climate change.

ecology↗

bioRxiv2020

Bleaching resistant corals retain heat tolerance following acclimatization to environmentally distinct reefs

Urgent action is needed to prevent the demise of coral reefs as the climate crisis leads to an increasingly warmer and more acidic ocean. Propagating climate change resistant corals to restore degraded reefs is one promising strategy; however, empirical evidence is needed to determine if resistance is retained following transplantation within or beyond a corals natal reef. Here we assessed the performance of bleaching-resistant individuals of two coral species following reciprocal transplantation between environmentally distinct reefs (low vs high diel variability) to determine if stress resistance is retained following transplantation. Critically, transplantation to either environment had no influence on coral bleaching resistance, indicating that this trait was relatively fixed and is thus a useful metric for selecting corals for reef restoration within their native range. In contrast, growth was highly plastic, and native performance was not predictive of performance in the novel environment. Coral metabolism was also plastic, with cross transplants of both species matching the performance of native corals at both reefs within three months. Coral physiology (autotrophy, heterotrophy, and metabolism) and overall fitness (survival, growth, and reproduction) were higher at the reef with higher flow and fluctuations in diel pH and dissolved oxygen, and did not differ between native corals and cross-transplants. Conversely, cross-transplants at the low-variability reef had higher fitness than native corals, thus increasing overall fitness of the recipient population. This experiment was conducted during a non-bleaching year, which suggests that introduction of these bleaching-resistant individuals will provide even greater fitness benefits to recipient populations during bleaching years. In summary, this study demonstrates that propagating and transplanting bleaching-resistant corals can elevate the resistance of coral populations to ocean warming while simultaneously maintaining reef function as the climate crisis worsens.

ecology↗