Biology subjects

Kenkel, C. D.

Publications and source records attributed to Kenkel, C. D..

At least 19 recordsLinked to original sources

bioRxiv2026

Integrating single-cell and bulk transcriptomes identifies neuronal heat-stress-associated candidate genes in a reef-building coral

Cell-type-specific molecular responses are obscured in bulk RNA sequencing, whereas generating matched single-cell datasets across environmental conditions remains costly and technically challenging, particularly in non-model organisms. Here, we present a workflow that integrates existing bulk and single-cell RNA-seq resources to prioritize cell-type-associated environmental-response genes. We demonstrate the workflow by examining heat-stress-associated neuronal genes in the reef-building coral Stylophora pistillata. Neuronal genes were first identified based on cell type-specific expression in single-cell transcriptomic data and then intersected with differentially expressed genes from bulk RNA-seq datasets under heat-stress. In parallel, we applied a deconvolution approach to infer cell type-specific expression changes directly from bulk data, independently capturing neuronal transcriptional responses. This integrated pipeline reduced thousands of heat-responsive genes previously identified in bulk RNA-seq studies to nine heat-associated, neuron-enriched candidates. Eight of the nine candidates showed their highest mean expression in the same neuronal subcluster. Targeted sequence-based characterization supported the identification of a TRPA-family ion channel, two calmodulin/centrin-family Ca2+-binding proteins, and a Class A/rhodopsin-like GPCR of unresolved ligand specificity. Two additional candidates were predicted secreted proteins belonging to conserved coral protein families, while the molecular functions of the remaining candidates remained unresolved. Their coordinated regulation suggests heat-associated remodeling of neuronal sensory and intracellular signaling processes. Our workflow provides a scalable framework for extracting cell type-associated molecular responses from existing transcriptomic resources and prioritizing candidates for further investigation. More broadly, it offers a generalizable strategy for investigating cell type-specific gene expression responses across organisms, cell types, and environmental conditions without requiring new single-cell datasets.

molecular biology↗

bioRxiv2026

Limited neutral and adaptive genomic divergence suggests Acropora cervicornis can be managed as a single conservation unit across its range

Genomic signatures can provide key insight into the evolutionary history and remaining adaptive potential of threatened populations. As demographic decline erodes both diversity and the processes maintaining it, understanding how remaining variation is distributed becomes increasingly important for conserving species like the staghorn coral, Acropora cervicornis, a foundational but critically endangered Caribbean reef-builder. We analyzed 46 high-coverage A. cervicornis genomes from 10 locations across the tropical western Atlantic to evaluate neutral and adaptive structure, genomic diversity, demographic history, inbreeding, and connectivity, and generated a regional haplotype reference panel for future genomic monitoring. Genome-wide analyses recovered recurring regional substructure, but differentiation was modest and partly explained by isolation-by-distance and spatial variation in effective migration. Subpopulations had similar levels of genomic diversity, shared demographic history, and limited evidence of local adaptation. These patterns support interpreting sampled Caribbean populations as a single evolutionarily significant unit (ESU) containing multiple regional management units (MUs), rather than as deeply divergent evolutionary lineages. Despite substantial retained variation and low current inbreeding, estimated contemporary effective population size was small, suggesting an increased vulnerability to the effects of drift as demographic collapse continues, especially if structure is reinforced by isolated management. Together, our findings emphasize the urgent need for interventions that preserve and enhance genomic diversity, including risk-managed assisted gene flow. Supported by the haplotype reference panel developed here, these strategies will require coordinated efforts across regional entities to conserve and restore A. cervicornis as a jointly managed, single ESU.

genomics↗

bioRxiv2026

Genomic variation associated with endosymbiont shuffling and areal growth in the endangered elkhorn coral, Acropora palmata

Biodiversity losses continue to outpace traditional management, underscoring the need to understand adaptive capacity and the potential for interventions to increase fitness under climate change. We undertook a genome-wide association study on 156 Acropora palmata genets to investigate the genomic basis of areal growth, endosymbiont association, and thermal tolerance. Seven peaks on chromosomes 1, 3 and 14 were associated with endosymbiont shuffling and two peaks on chromosome 4 were associated with areal growth. As variants were located in non-coding regions we incorporated additional data from an independent field-transplant experiment to investigate their relationship with patterns of gene expression. Intersection of these datasets implicated melanocortin-like receptor activity and Ran GTPase activating protein 1 in endosymbiont composition and surface area growth, respectively. Results indicate that growth and endosymbiont associations may represent more viable intervention targets than temperature tolerance and highlight the need to better understand the role of non-coding variation in basic biology and development of restoration interventions.

genomics↗

bioRxiv2026

High relatedness in sexually produced restoration cohorts of the endangered elkhorn coral, Acropora palmata

Climate change is driving the decline of coral populations around the world such that many are unlikely to recover without human intervention. Assisted sexual reproduction is one intervention proposed to enhance genetic diversity and support population recovery, yet its genetic outcomes remain poorly quantified. We evaluated genome-wide relatedness and genetic diversity in 168 restoration genets of the endangered Caribbean coral Acropora palmata, including 153 sexually produced offspring derived from multi-parent batch and biparental crosses. We detected high relatedness within multi-parent batch cross cohorts, with many genets comprising only one or a few full-sibling groups, indicating highly unequal parental contributions. Nucleotide diversity was lower in one batch cross cohort relative to founder populations, but the absolute difference was small and runs of homozygosity were relatively short indicating that inbreeding depression is not yet a concern. These patterns suggest that common larval propagation approaches can successfully generate large numbers of new genets but underscore the need to manage inbreeding risk, especially in small breeding stocks such as the Caribbean Acropora spp. Specifically, our results highlight the need for comprehensive genetic management to integrate assisted sexual reproduction into coral restoration, including parentage tracking, broodstock rotation, and relatedness-informed outplanting designs.

genomics↗

bioRxiv2026

Reproductive Trade-offs in Caribbean Corals: Plasticity Accelerates While Fragmentation Delays Reproductive Capacity

In modular organisms, where growth and fragmentation blur the boundaries between individuals, the interplay between asexual and sexual reproduction creates complex fitness trade-offs. Life-history theory predicts that resources allocated to one fitness component necessarily reduce investment in others, yet detecting these trade-offs in wild populations of clonal organisms remains challenging. Phenotypic plasticity can enhance survival, yet its influence on reproductive capacity and life history trade-offs remains poorly understood. Using a fully crossed reciprocal transplant design, we tracked 263 colonies of the branching coral Acropora cervicornis across nine reef sites over 42 months, investigating relationships between fragmentation, morphological plasticity, and the capacity for sexual reproduction. Breakage patterns reflected both environmental and genetic factors. Primary branch breaks created a "double negative" effect--simultaneously more than doubling mortality risk and delaying attainment of a validated reproductive size class by [~]40%. Conversely, higher morphological plasticity in surface area-to-volume ratio accelerated sexual maturation up to 6-fold, counteracting the negative effects of fragmentation. In parallel, a simple demographic model parameterized with published fecundity data estimated that primary breakage reduces expected cumulative reproductive output by [~]58%, a result robust across a wide range of parameter assumptions. These results demonstrate a fundamental reproductive trade-off in which asexual reproduction through fragmentation undermines sexual reproductive potential by reducing colony size. Moreover, our findings reveal that fragmentation susceptibility is broadly heritable and subject to selection, and identify a compensatory mechanism through which plasticity enhances fitness beyond immediate survival.

evolutionary biology↗

bioRxiv2026

Environmentally-determined symbiont communities highlight flexibility of Aiptasia-algal symbiosis

The mechanisms driving host-symbiont associations across space and time in contemporary mutualisms can give insight into the capacity for symbiotic organisms to respond to environmental change. High specificity between partners can increase cooperation and facilitate efficient holobiont selection, whereas low specificity could reduce host benefit, but facilitate adaptive associations across heterogeneous environments. The present study explores specificity in natural populations of a cnidarian-algal model, Exaiptasia diaphana, across a latitudinal gradient to understand the genetic and environmental effects driving host-symbiont associations, and their relation to heritable and/or environmental symbiont acquisition. We found that symbiotic associations were extremely flexible in E. diaphana, regardless of transmission mode. E. diaphana were capable of associating with diverse symbiont communities across genetically identical hosts seeded with vertically transmitted symbionts, as well as across highly connected host populations which acquire symbionts horizontally. Host population connectivity was complex and unrelated to geographic distance, whereas symbiont community composition tracked the thermal gradient, potentially due to context dependent biotic interactions. These results indicate that in a flexible symbiosis, symbiont communities are environmentally-determined, suggesting the future of this symbiosis will likely depend on climate adaptation of symbionts.

ecology↗

bioRxiv2025

Morphological plasticity in a reef-building coral is context-dependent and trades off with resistance to thermal stress

In sessile, long-lived organisms, such as reef-building corals, phenotypic plasticity may play a key role in mitigating the impacts of climate change. Plasticity is often context-dependent and has costs and limits, ultimately resulting in adaptive, neutral, or maladaptive effects. However, our understanding of the mechanisms that maintain variation in, and therefore drive the evolution of, plasticity is still limited. We use a field-based transplant experiment to show context-dependent tradeoffs to morphological plasticity in Acropora cervicornis under real-world conditions driven by climate change. We find that while morphological plasticity is neutral under some conditions, it trades off with thermal tolerance during moderate temperature stress during a marine heatwave. Additionally, we find that plasticity changes over time, underlining the importance of its temporal dynamics in long-lived organisms. Our results demonstrate a key role for environmental change in the eco-evolutionary dynamics of plasticity by demonstrating context-dependent costs under real-world thermal stress.

evolutionary biology↗

bioRxiv2024

Resilience in a time of stress: revealing the molecular underpinnings of coral survival following thermal bleaching events

Coral bleaching events from thermal stress are increasing globally in duration, frequency, and intensity. Bleaching occurs when a corals algal symbionts are expelled, resulting in a loss of color. Some coral colonies survive bleaching, reacquire their symbionts and recover. In this study, we experimentally bleached Montipora capitata colonies to examine molecular and physiological signatures of intrinsic differences between corals that recover (resilient) compared to those that die (susceptible). All colonies were collected from the same bay and monitored for eight months post-bleaching to identify specific colonies exhibiting long-term resilience and survival. Using an integrated systems-biology approach that included quantitative mass spectrometry-based proteomics, 16S rRNA of the microbiome, total lipids, symbiont density and diversity, we explored molecular-level mechanisms of tolerance in pre- and post-bleached colonies and found biomarkers of resilience that can confidently identify resilient and susceptible corals before thermal-induced bleaching events. Prior to thermal stress, resilient corals were characterized by a more diverse microbiome and increased abundances of proteins involved in multiple carbon and nitrogen acquisition strategies, symbiont retention and acquisition, and pathogen resistance. Susceptible corals had early signs of symbiont rejection and had resorted to utilizing urea uptake pathways for carbon and nitrogen. Further, molecular signatures identified prior to bleaching were amplified after bleaching, suggesting these pathways may be deterministic in a colonys fate. Our results have important implications for the future of reefs, revealing molecular factors necessary for survival through thermally-induced bleaching events and providing diagnostic biomarkers for coral reef management. Significance statementCorals are being negatively impacted by the increase in the number and duration of thermal-induced bleaching events. There are, however, some individuals within a single species that will bleach and, after time, reacquire symbionts and physiologically recover while neighboring colonies will die. Here, we used a multidisciplinary approach to understand the biochemical details of the physiological changes of resilient and susceptible Montipora capitata to thermal-induced bleaching. Resilient corals were characterized by their use of multiple carbon and nitrogen acquisition strategies, metabolically active symbiont relationships, abundant antiviral proteins, and a diverse microbiome. We reveal a multi-factor molecular-level approach for confidently identifying resilient and susceptible coral colonies so that environmental managers can rapidly select quality candidates for propagation while in the field.

ecology↗

bioRxiv2023

Bio-optical signatures of insitu photosymbionts predict bleaching severity prior to thermal stress in the Caribbean coral species Acropora palmata

The identification of bleaching tolerant traits among individual corals is a major focus for many restoration and conservation initiatives but often relies on large scale or high-throughput experimental manipulations which may not be accessible to many front-line restoration practitioners. Here we evaluate a machine learning technique to generate a predictive model which estimates bleaching severity using non-destructive chlorophyll-a fluorescence photophysiological metrics measured with a low-cost and open access bio-optical tool. First, a four-week long thermal bleaching experiment was performed on 156 genotypes of Acropora palmata at a land-based restoration facility. Resulting bleaching responses (percent change in Fv/Fm or Absorbance) significantly differed across the four distinct phenotypes generated via a photophysiology-based dendrogram, indicating strong concordance between fluorescence-based photophysiological metrics and future bleaching severity. Next, these correlations were used to train and then test a Random Forest algorithm-based model using a bootstrap resampling technique. Correlation between predicted and actual bleaching responses in test corals was significant (p < 0.0001) and increased with the number of corals used in model training (Peak average R2 values of 0.42 and 0.33 for Fv/Fm and absorbance, respectively). Strong concordance between photophysiology-based phenotypes and future bleaching severity may provide a highly scalable means for assessing reef corals.

physiology↗

bioRxiv2023

Performance of Orbicella faveolata larval cohorts does not align with previously observed thermal tolerance of adult source populations

Orbicella faveolata, commonly known as the mountainous star coral, is a dominant reef-building species in the Caribbean, but populations have suffered sharp declines since the 1980s due to repeated bleaching and disease-driven mortality. Prior research has shown that inshore adult O. faveolata populations in the Florida Keys are able to maintain high coral cover and recover from bleaching faster than their offshore counterparts. However, whether this origin-specific variation in thermal resistance is heritable remains unclear. To address this knowledge gap, we produced purebred and hybrid larval crosses from O. faveolata gametes collected at two distinct reefs in the Upper Florida Keys, a nearshore site (Cheeca Rocks, CR) and an offshore site (Horseshoe Reef, HR), in two different years (2019, 2021). We then subjected these aposymbiotic larvae to severe (36 {degrees}C) and moderate (32 {degrees}C) heat challenges to quantify their thermal tolerance. Contrary to our expectation based on patterns of adult thermal tolerance, HR purebred larvae survived better and exhibited gene expression profiles that were less driven by stress response under elevated temperature compared to purebred CR and hybrid larvae. One potential explanation could be compromised reproductive output of CR adult colonies due to repeated summer bleaching events in 2018 and 2019, as gametes originating from CR in 2019 contained less storage lipids than those from HR. These findings provide an important counter-example to the current selective breeding paradigm, that more tolerant parents will yield more tolerant offspring, and highlight the importance of adopting a holistic approach when evaluating larval quality for conservation and restoration purposes.

physiology↗

bioRxiv2023

Microhabitat acclimatization shifts physiological baselines and thermal tolerance of the symbiotic anemone, Anthopleura elegantissima

Contemporary organisms in extreme environments can give insight into how species will respond to environmental change. The intertidal forms an environmental gradient where stress increases with tidal height. Here, we explore the contribution of fixed genotypic and plastic environmental effects on thermal tolerance of the intertidal anemone Anthopleura elegantissima and its algal symbionts using a laboratory-based tank experiment. High intertidal anemones had lower baseline symbiont-to-host cell ratios under control conditions, but their symbionts had higher baseline maximum quantum yield compared to low intertidal anemone symbionts, despite identical symbiont communities. High intertidal anemones maintained greater maximum quantum yield and symbiont-to-host cell ratios under heat stress compared to low intertidal anemones, suggesting that high intertidal holobionts have greater thermal tolerance. However, thermal tolerance of clonal anemones acclimatized to different zones was not explained by tidal height alone, indicating emersion duration is not the sole environmental driver of physiological variation. Fixed genotypic effects also influenced physiological baselines, but did not modulate thermal tolerance, demonstrating thermal tolerance is largely driven by environmental history. These results indicate that this symbiosis is highly plastic and may be able to rapidly acclimatize to climate change, defying the convention that symbiotic organisms are more susceptible to environmental stress.

ecology↗

bioRxiv2023

Abundance of Oligoflexales bacteria is associated with algal symbiont density independent of thermal stress in Aiptasia anemones

Many multicellular organisms, such as humans, plants, and invertebrates, depend on symbioses with microbes for metabolic cooperation and exchange. Reef-building corals, an ecologically important order of invertebrates, are particularly vulnerable to environmental stress in part because of their nutritive symbiosis with dinoflagellate algae, and yet also benefit from these and other microbial associations. While coral microbiomes remain difficult to study because of their complexity, the anemone Aiptasia is emerging as a simplified model. Research has demonstrated co-occurrences between microbiome composition and the abundance and type of algal symbionts in cnidarians. However, whether these patterns are the result of general stress-induced shifts or depletions of algal-associated bacteria remains unclear. Our study aimed to distinguish the effect of changes in symbiont density and thermal stress on the microbiome of symbiotic Aiptasia strain CC7 by comparing them with aposymbiotic anemones, depleted of their native symbiont, Symbiodinium linucheae. Our analysis indicated that overall, thermal stress had the greatest impact on disrupting the microbiome. We found that three bacterial classes made up most of the relative abundance (60-85 %) in all samples, but the rare microbiome fluctuated between symbiotic states and following thermal stress. We also observed that S. linucheae density correlated with abundance of Oligoflexales, suggesting these bacteria may be primary symbionts of the dinoflagellate algae. The findings of this study help expand knowledge on prospective multipartite symbioses in the cnidarian holobiont and how they respond to environmental disturbance.

ecology↗

bioRxiv2022

Long term maintenance of heterologous symbiont association in Acropora palmata on natural reefs

The sensitivity of reef-building coral to elevated temperature is a function of their symbiosis with dinoflagellate algae in the family Symbiodiniaceae. Changes in the composition of the endosymbiont community in response to thermal stress can increase coral thermal tolerance. Consequently, this mechanism is being investigated as a human-assisted intervention for rapid acclimation of coral in the face of climate change. Successful establishment of novel symbioses that increase coral thermal tolerance have been demonstrated in laboratory conditions; however, it is unclear how long these heterologous relationships persist in nature. Here, we show that Acropora palmata can form a novel symbiosis with Durusdinium spp. when reared in land-based aquaria. We tested the stability of this heterologous relationship by outplanting clonal replicates (ramets) of five A. palmata host genotypes to natural reefs in the lower Florida Keys. Amplicon sequencing analysis of ITS2-type profiles revealed that the majority of surviving ramets remained dominated by Durusdinium spp. two years after transplantation. However, 15% of ramets, including representatives of all genotypes, did exhibit some degree of symbiont shuffling or switching at six of eight sites, including complete takeover by site-specific strains of the native symbiont, Symbiodinium fitti. The predominant long-term stability of the novel symbiosis supports the potential effectiveness of symbiont modification as a management tool. However, the finding that 6-7 year-old coral can alter symbiont community composition in the absence of bleaching indicates that Symbiodiniaceae communities are indeed capable of greater flexibility under ambient conditions.

microbiology↗

bioRxiv2022

Reduced representation sequencing accurately quantifies relative abundance and reveals population-level variation in Pseudo-nitzschia spp.

Certain species within the genus Pseudo-nitzschia are able to produce the neurotoxin domoic acid (DA), which can cause illness in humans, mass-mortality of marine animals, and closure of commercial and recreational shellfisheries during toxic events. Understanding and forecasting blooms of these harmful species is a primary management goal. However, accurately predicting the onset and severity of bloom events remains difficult, in part because the underlying drivers of bloom formation have not been fully resolved. Furthermore, Pseudo-nitzschia species often co-occur, and recent work suggests that the genetic composition of a Pseudo-nitzschia bloom may be a better predictor of toxicity than prevailing environmental conditions. We developed a novel next-generation sequencing assay using restriction site-associated DNA (2b-RAD) genotyping and applied it to mock Pseudo-nitzschia communities generated by mixing cultures of different species in known abundances. On average, 94% of the variance in observed species abundance was explained by the expected abundance. In addition, the false positive rate was low (0.45% on average) and unrelated to read depth, and false negatives were never observed. Application of this method to environmental DNA samples collected during natural Pseudo-nitzschia spp. bloom events in Southern California revealed that increases in DA were associated with increases in the relative abundance of P. australis. Although the absolute correlation across time-points was weak, an independent species fingerprinting assay (Automated Ribosomal Intergenic Spacer Analysis) supported this and identified other potentially toxic species. Finally, we assessed population-level genomic variation by mining SNPs from the environmental 2bRAD dataset. Consistent shifts in allele frequencies in P. pungens and P. subpacifica were detected between high and low DA years, suggesting that different intraspecific variants may be associated with prevailing environmental conditions or the presence of DA. Taken together, this method presents a potentially cost-effective and high-throughput approach for studies aiming to evaluate both population and species dynamics in mixed samples. HighlightsO_LI2bRAD method facilitates species- and population-level analysis of the same sample C_LIO_LIMethod accurately quantifies species relative abundance with low false positives C_LIO_LIConsistent shifts in allele frequencies were detected between high and low DA years C_LIO_LICertain Pseudo-nitzschia spp. populations may be more associated with DA presence C_LI

genomics↗

bioRxiv2022

Divergent transcriptional response to thermal stress among life stages could constrain coral adaptation to climate change

The ability for adaptation to keep pace with environmental change largely depends on how efficiently selection can act on heritable genetic variation. Complex life cycles may either promote or constrain adaptation depending on the integration or independence of fitness-related traits over development. Reef-building corals exhibit complex life cycles and are sensitive to increasing temperatures, highlighting the need to understand the heritable potential of the thermal stress response and how it is regulated over development. Here we used tag-based RNA-seq to profile global gene expression in inshore and offshore P. astreoides adults and their offspring recruits in response to a 16-day heat stress, and larvae from separate families in response to a 4-day heat stress, to test whether gene expression patterns differentiating adult populations, and potentially underlying differences in thermal tolerance, persist in thermally naive life stages. Host developmental stage had a major effect on both host and symbiont expression, despite symbionts being directly inherited from parent colonies, and modulated the response to thermal stress, suggesting the holobiont response to selection varies across life stages. Populations also exhibited origin-specific treatment responses, but the magnitude of the response differed among populations and life stages. Inshore parents and their juvenile offspring exhibited a more robust response to heat stress compared to offshore-origin corals, indicating expression plasticity may be heritable. However, larval populations exhibited the opposite response, possibly due to stage-specific differences or exposure duration. Overall, this study shows that putatively adaptive regulatory variation can be heritable, but the identity of thermally responsive genes are stage-specific, which will have major implications for predicting the evolutionary response of corals in a changing environment.

molecular biology↗

bioRxiv2022

Cross-generational heritability analysis of physiological traits in Porites astreoides across an inshore-offshore gradient in the Lower Florida Keys

Estimating the heritable genetic variation in fitness-related traits is key to projecting the adaptive evolution of organisms in response to a changing environment. While heritability studies on reef-building corals to date support adaptive capacity, little is known about the dynamics of trait heritability across life stages in which distinct selective pressures can have long-lasting effects both within and across generations. In this study, we obtained heritability estimates for energetic and thermal stress response traits in larval, recruit, and adult Porites astreoides from two populations in the Lower Florida Keys. To induce bleaching phenotypes among individual families, larvae were exposed to a 4-day thermal stress at 32 {degrees}C, whereas adults and recruits received the same treatment for 22 days. Origin-dependent tolerance was observed in two life stages where offshore recruits lost more symbiont cells under heat than inshore recruits compared to their respective controls and heat-treated offshore adults suffered a greater loss in total protein content. Surprisingly, larvae appeared to be largely insensitive to heat regardless of origin. Broad sense heritability (H2) estimates varied greatly among traits and life stages, which may reflect changes in the relative importance of genetic and environmental variation throughout development. Notably, more than 80% of the variation in larval chlorophyll a concentration was attributed to genetic factors. The overall moderate to high H2 estimates measured here suggest these corals have considerable potential to adapt to environmental change.

ecology↗

bioRxiv2022

Evidence for adaptive morphological plasticity in the Caribbean coral, Acropora cervicornis.

Genotype-by-environment interactions (GxE) indicate that variation in organismal traits cannot be explained by fixed effects of genetics or site-specific plastic responses alone. For tropical coral reefs experiencing dramatic environmental change, identifying the contributions of genotype, environment, and GxE on coral performance will be vital for both predicting persistence and developing restoration strategies. We quantified the impacts of G, E, and GxE on the morphology and survival of the endangered coral, A. cervicornis, through an in situ transplant experiment exposing common garden (nursery) raised clones of ten genotypes to nine reef sites in the Florida Keys. By fate-tracking outplants over one year with colony-level 3D photogrammetry, we uncovered significant GxE on coral size and survivorship indicating that no universal winner exists in terms of colony performance. Moreover, the presence of GxE also implies the existence of intraspecific variation in phenotypic plasticity. Rather than differences in mean trait values, we find that individual-level morphological plasticity is adaptive in that the most plastic individuals also exhibited the fastest growth and highest survival. This indicates that adaptive morphological plasticity may continue to evolve, influencing the success of A. cervicornis and resulting reef communities in a changing climate. As focal reefs are active restoration sites, the knowledge that variation in phenotype is an important predictor of performance can be directly applied to restoration planning. Taken together, these results establish A. cervicornis as a system for studying the eco-evolutionary dynamics of phenotypic plasticity that also can inform genetic- and environment-based strategies for coral restoration.

ecology↗

bioRxiv2021

Host-specific epibiomes of distinct Acropora cervicornis genotypes persist after field transplantation

Microbiome studies across taxa have established the influence of host genotype on microbial recruitment and maintenance. However, research exploring host-specific epibionts in scleractinian corals is scant and the influence of intraspecific differences across environments remains unclear. Here, we studied the epibiome of ten Acropora cervicornis genotypes to investigate the relative roles of host genotype and environment in structuring the epibiome. Coral mucus was sampled in a common garden nursery from replicate ramets of distinct genotypes (T0). Coral fragment replicates (n=3) of each genotype were then transplanted to nine different field sites in the Lower Florida Keys and mucus was again sampled one year later from surviving ramets (T12). 16S rRNA amplicon sequencing was used to assess microbial composition, richness, and beta-diversity. The most abundant and consistent amplicon sequencing variants (ASVs) in all samples belonged to Fokiniaceae (MD3-55 genus) and Cyanobacteria (Synechococccus). The abundances of these bacterial taxa varied consistently between genotypes whereas neither the composition nor taxonomic abundance were significantly different among field sites. Interestingly, several high MD3-55 hosting genotypes showed rapid diversification and an increase in MD3-55 following transplantation. Overall, our results indicate healthy A. cervicornis genotypes retain distinct epibiome signatures through time, suggesting a strong host component. Lastly, our results show that differences in MD3-55 abundances can be consistently detected in the epibiome of distinct host-genotypes of A. cervicornis. As this organism (sensu Aquarickettsia rohweri) has been implicated as a marker of disease resistance, this finding reinforces the potential use of microbial indicators in reef restoration efforts via non-invasive surface/mucus sampling.

ecology↗