Biology subjects

Baker, A. C.

Publications and source records attributed to Baker, A. C..

12 recordsLinked to original sources

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↗

bioRxiv2025

Markers of resilience to stony coral tissue loss disease and probiotic potential in the microbiome of the threatened coral, Orbicella faveolata

Stony coral tissue loss disease (SCTLD) is widespread within the Caribbean and affects at least 22 species of reef-building coral. Bacteria have been implicated in the etiology of SCTLD, but the community of bacteria and archaea may also contribute to SCTLD resistance. To identify potential mechanisms through which microbes contribute to SCTLD resistance, we sequenced metagenomes from 41 colonies of the threatened coral, Orbicella faveolata, in the lower Florida Keys. All colonies were fate-tracked for three to five years and disease lesions were treated with amoxicillin. By 2024, 20% were never diseased, 10% had lesions before sampling but recovered, 22% were apparently healthy but were eventually susceptible to infection, and 49% had regular repeated infections. Within the coral microbiome, diseased and yet-to-be diseased colonies exhibited higher variability in functional genes. In contrast, corals that remained unaffected or recovered had less variable microbiomes with greater abundances of vitamin and antibiotic biosynthesis, secretion system, and quorum sensing genes that may support host health and resilience to pathogens. Though on some colonies antibiotic treatments were applied repeatedly, there was no effect on the diversity of beta-lactamases, antibiotic resistance genes that may confer amoxicillin resistance. Additional potentially probiotic gene clusters for the production of antimicrobial and bioactive compounds were present in many colonies regardless of fate. Taken together, we find significant probiotic potential in the coral microbiome to armor host O. faveolata corals against SCTLD infection, which may underpin intraspecific variation in stony coral tissue loss disease resilience and susceptibility.

microbiology↗

bioRxiv2025

Temporal transcriptional rhythms govern coral-symbiont function and microbiome dynamics

Diel rhythms align physiological processes with light/dark cycles, driving predictable oscillations in gene expression and protein activity through tightly controlled transcriptional-translational feedback loops. Transcriptomic analyses in the stony coral Pseudodiploria strigosa revealed tightly regulated transcriptional control: dawn triggers a molecular reset marked by RNA metabolism and protein turnover; midday emphasizes anabolic and phosphate-regulated pathways; dusk reflects transitional lipid and amino acid metabolism; and midnight reveals stress-responses, mRNA catabolism, and mitochondrial organization. The photosymbiont Breviolum sp. exhibits subtler but distinct diel regulation, with photoprotective activation at dawn, metabolite transport and nitrogen cycling through midday and dusk, and cell cycle and ion homeostasis at night. Microbial communities show time-dependent restructuring of co-occurrence networks. Carbohydrate-catabolizing taxa associated with Symbiodiniaceae during daylight, while nighttime assemblages feature methylotrophs likely facilitating dimethylsulfoniopropionate (DMSP) metabolism. Together, these findings present the first system-level molecular framework of diel regulation across the coral-photosymbiont-microbe holobiont, revealing strong time-specific transcriptional control as a key driver of coordinated function and homeostasis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=190 SRC="FIGDIR/small/668741v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@1cb5740org.highwire.dtl.DTLVardef@cd58ceorg.highwire.dtl.DTLVardef@1815777org.highwire.dtl.DTLVardef@9550a8_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Local alkalinity enhancement using artificial substrates increases survivorship of early-stage coral recruits

Efforts to restore coral reefs using sexually derived coral recruits are often hindered by their low survivorship and growth, hence scalable interventions to improve these parameters are urgently needed. Here, we developed novel settlement substrates that modify the local chemical and hydrodynamic environments to provide local alkalinity enhancement (AE) within the laminar boundary layer to aid in coral restoration. Cement tiles with four different chemistries and two different surface topographies were tested in a novel flume system to quantify their ability to change local pH under reef-like conditions and their effect on larval settlement, survivorship, and growth of the endangered Caribbean coral, Orbicella faveolata. Chemistry had a minimal effect on the initial settlement of coral larvae, and textured tiles were preferred over smooth tiles. However, substrates that created a more alkaline local environment increased post-settlement survivorship. The increased survivorship of O. faveolata recruits on AE tiles was not due to increased growth on AE tiles, although trends in growth were dependent on chemistry and topography of tiles. Our results indicate that mixing sodium bicarbonate or sodium carbonate into cement used to fabricate artificial reef structures could be an effective means to enhance the development of coral cover. Significance StatementReef-building coral populations in South Florida and the Caribbean are nearing crisis, with low survivorship rates of new recruits being identified as a critical bottleneck limiting their recovery. Since ocean acidification is known to stress corals and hinder their growth, we hypothesized that enhancing substrate alkalinity could help mitigate ocean acidification effects by boosting coral growth and increasing survivorship during their critical early stages. This hypothesis was experimentally tested by adding sodium bicarbonate or sodium carbonate to settlement substrates and studying coral settlement preference, and coral spat growth and survival. Our results showed significantly higher survivorship on alkalinity enhanced substrates, indicating that this could be a promising restoration intervention.

ecology↗

bioRxiv2023

Sediment source and dose influence the larval performance of the threatened coral Orbicella faveolata

The effects of turbidity and sedimentation stress on early life stages of corals are poorly understood, particularly in Atlantic species. Dredging operations, beach nourishment, and other coastal construction activities can increase sedimentation and turbidity in nearby coral reef habitats and have the potential to negatively affect coral larval development and metamorphosis, reducing sexual reproduction success. In this study, we investigated the performance of larvae of the threatened Caribbean coral species Orbicella faveolata exposed to sediments collected from a reef site in southeast Florida recently impacted by dredging (Port Miami), and compared it to the performance of larvae exposed to sediments collected from the offshore, natal reef of the parent colonies. In a laboratory experiment, we tested whether low and high doses of each of these sediment types affected the survival, settlement, and respiration of coral larvae compared to a no-sediment control treatment. In addition, we analyzed the sediments used in the experiments with 16S rRNA gene amplicon sequencing to assess differences in the microbial communities present in the Port versus Reef sediments, and their potential impact on coral performance. Overall, O. faveolata larvae exposed to high doses of either sediment type (Port or Reef) exhibited reduced survival and settlement rates, but only the Port sediments resulted in adverse effects in the low-dose treatment. Sediments collected near the Port also contained different microbiomes than Reef sediments, and higher relative abundances of the bacteria Desulfobacterales, which has been associated with coral disease. We hypothesize that differences in microbiomes between the two sediments may be a contributing factor in explaining the observed differences in larval performance. Together, these results suggest that the settlement success and survival of O. faveolata larvae are more readily compromised by encountering port inlet sediments compared to reef sediments, with potentially important consequences for the recruitment success of this species in affected areas.

ecology↗

bioRxiv2023

Marine heatwaves threaten cryptic coral diversity and erode associations amongst coevolving partners

Climate change-amplified heatwaves are known to drive extensive mortality in marine foundation species. However, a paucity of longitudinal genomic datasets has impeded understanding of how these rapid selection events alter species genetic structure. Impacts of these events may be exacerbated in species with obligate symbioses, where the genetics of multiple co-evolving species may be affected. Here, we tracked the symbiotic associations and fate of reef-building corals for six years through a prolonged heatwave. Coral genetics strongly predicted survival of the common coral Porites through the event, with strong differential survival (15 to 64%) apparent across morphologically identical -but genetically distinct- lineages. The event also disrupted strong associations between coral lineages and their symbiotic partners, homogenizing symbiotic assemblages across lineages and reducing the specificity of coral-algal symbioses. These results highlight that marine heatwaves threaten cryptic genetic diversity of foundation species and have the potential to decouple tight relationships between co-evolving host-symbiont pairs.

ecology↗

bioRxiv2022

A meta-analysis of the stony coral tissue loss disease microbiome finds key bacteria in lesions and unaffected tissue of diseased colonies

Stony coral tissue loss disease (SCTLD) has been causing significant whole colony mortality on reefs in Florida and the Caribbean. The cause of SCTLD remains unknown, with limited concurrence of SCTLD-associated bacteria among studies. We conducted a meta-analysis of SSU 16S ribosomal RNA gene datasets generated by 16 field and laboratory SCTLD studies to find consistent bacteria associated with SCTLD across disease zones (vulnerable, endemic, and epidemic), coral species, coral compartments (mucus, tissue, and skeleton), and disease states (apparently healthy colony tissue [AH], and unaffected [DU] and lesion [DL] tissue from diseased colonies). We also evaluated bacteria in seawater and sediment, which may be sources of SCTLD transmission. Although AH colonies in endemic and epidemic zones harbor bacteria associated with SCTLD lesions, and aquaria and field samples had distinct microbial compositions, there were still clear differences in the microbial composition among AH, DU, and DL in the combined dataset. Alpha diversity between AH and DL was not different; however, DU showed increased alpha diversity compared to AH, indicating that, prior to lesion formation, corals may undergo a disturbance to the microbiome. This disturbance may be driven by Flavobacteriales, which were especially enriched in DU. While Rhodobacterales and Peptostreptococcales-Tissierellales were prominent in structuring microbial interactions in DL. Peptostreptococcales-Tissierellales specifically may contribute to lesion progression through an alpha-toxin. We provide a consensus of SCTLD-associated bacteria both prior to and during lesion progression and identify how these taxa vary across studies, coral species, coral compartments, seawater, and sediment.

microbiology↗

bioRxiv2022

Microbiome signatures in Acropora cervicornis are associated with genotypic resistance to elevated nutrients and heat stress

The staghorn coral, Acropora cervicornis, was once abundant in the Caribbean, but now is listed as critically endangered. To recover A. cervicornis populations, restoration efforts have focused on preserving genetic diversity and increasing coral cover. However, identifying stress-resistant corals can help to increase restoration success, by allocating genotypes to reefs where they are more likely to survive. We assessed the performance (growth, survivorship, and photochemical efficiency) and characterized the microbiome (prokaryotes) of six A. cervicornis genotypes that were maintained at control temperatures (~26 {degrees}C) and either ambient nutrients or elevated nutrients (elevated NH4, and elevated NH4 + PO4) for > 2 months. We then compared how these parameters changed when the corals were exposed to heat-stress (3-weeks at ~31.5 {degrees}C). We found that exposure to elevated nutrients reduced A. cervicornis performance under control temperatures and heat stress. However, there was a wide range of variation among genotypes, with three genotypes maintaining relatively higher survivorship and growth rates when exposed to nutrients alone, and nutrients followed by heat stress. Heat stress alone changed the microbial composition among genotypes more than elevated nutrients alone, but heat stress also interacted with nutrient pre-exposure to affect microbial communities. The relative abundance of Midichloriaceae and Spirochaetaceae varied by coral genotype and a high abundance of these bacterial taxa was a positive predictor of coral survivorship rate, suggesting a microbial signature that could aid in identifying resistant A. cervicornis genotypes. Our findings suggest there is significant variation among genotypes in the response of A. cervicornis to elevated nutrients and temperatures. Resistant genotypes may be identifiable via their microbiomes and prioritized for outplanting at sites characterized by high levels of nutrient pollution. Large-scale microbiome screening may help expedite targeted outplanting and could be tested and extended to facilitate the identification of genotypes with other resistance characteristics.

ecology↗

bioRxiv2021

Effect of species, size, and chimerism on the susceptibility of Caribbean brain coral recruits to stony coral tissue loss disease (SCTLD)

Stony coral tissue loss disease (SCTLD) has devastated coral populations along Floridas Coral Reef and beyond. Although widespread infection and mortality of adult colonies have been documented, no studies have yet investigated the susceptibility of recruits to this disease. Here, we exposed eight-month-old Diploria labyrinthiformis recruits and four-month-old Colpophyllia natans recruits to two sequential doses of SCTLD in the laboratory to track infection and assess potential resilience. Both species began to develop lesions as early as 48 h after exposure began. During the first dose, 59.0% of C. natans recruits lost all tissue (died) within two to eight days of developing lesions, whereas D. labyrinthiformis recruits experienced significantly slower rates of tissue loss and minimal eventual mortality. In C. natans, larger recruits and those fused into groups of multiple genets (chimeras) exhibited the highest survivorship. In contrast, smaller and/or single (ungrouped) recruits had the lowest survivorship (9.9 - 26.5%). After 20 days, a second SCTLD dose was delivered to further test resistance in remaining recruits, and all recruits of both species succumbed within 6 days. Although no recruits showed absolute resistance to SCTLD following repeated exposures, our results provide evidence that interactions between species, size, and chimerism can impact relative resistance. This study represents the first report of SCTLD in Caribbean coral recruits and carries implications for natural species recovery and reef restoration efforts. Additional research on the susceptibility of coral juveniles to SCTLD is urgently needed, to include different species, locations, parents, and algal symbionts, with the goal of assessing relative susceptibility and identifying potential sources of resilience for this critical life history stage.

ecology↗

bioRxiv2021

Variation in susceptibility among three Caribbean coral species and their algal symbionts indicates the threatened staghorn coral, Acropora cervicornis, is particularly susceptible to elevated nutrients and heat stress

Coral cover is declining worldwide due to multiple interacting threats. We compared the effects of elevated nutrients and temperature on three Caribbean corals: Acropora cervicornis, Orbicella faveolata, and Siderastrea siderea. Colonies hosting different algal types were exposed to either ambient nutrients (A), elevated NH4 (N), or elevated NH4 + PO4 (N+P) at control temperatures (26 {degrees}C) for > 2 months, followed by a 3-week thermal challenge (31.5 {degrees}C). A. cervicornis hosted Symbiodinium (S. fitti) and was highly susceptible to the combination of elevated nutrients and temperature. During heat stress, A. cervicornis pre-exposed to elevated nutrients experienced 84%-100% mortality and photochemical efficiency (Fv/Fm) declines of 41-50%. In comparison, no mortality and lower Fv/Fm declines (11-20%) occurred in A. cervicornis that were heat-stressed but not pre-exposed to nutrients. O. faveolata and S. siderea response to heat stress was determined by their algal symbiont community and was not affected by nutrients. O. faveolata predominantly hosted Durusdinium trenchii or Breviolum, but only corals hosting Breviolum were susceptible to heat, experiencing 100% mortality, regardless of nutrient treatment. S. siderea colonies predominantly hosted Cladocopium C1 (C. goreaui), Cladocopium C3, D. trenchii, or variable proportions of Cladocopium C1 and D. trenchii. This species was resilient to elevated nutrients and temperature, with no significant mortality in any of the treatments. However, during heat stress, S. siderea hosting Cladocopium C3 suffered higher reductions in Fv/Fm (41-56%) compared to S. siderea hosting Cladocopium C1 and D. trenchii (17-26% and 10-16%, respectively). These differences in holobiont susceptibility to elevated nutrients and heat may help explain historical declines in A. cervicornis starting decades earlier than other Caribbean corals. Our results suggest that tackling only warming temperatures may be insufficient to ensure the continued persistence of Caribbean corals, especially A. cervicornis. Reducing nutrient inputs to reefs may also be necessary for these iconic coral species to survive.

physiology↗

bioRxiv2020

Neighboring colonies influence uptake of thermotolerant endosymbionts in threatened Caribbean coral recruits

Intervention strategies to enhance coral resilience include manipulating the association between corals and their algal endosymbionts. While hosting thermotolerant Durusdinium trenchii can increase bleaching thresholds in adults, its effects remain largely unknown during the early life stages of Caribbean corals. Here, we tested if Orbicella faveolata recruits could establish symbiosis with D. trenchii supplied by nearby "donor" colonies and examined the resulting ecological trade-offs to evaluate early Symbiodiniaceae manipulation as a scalable tool for reef restoration. We exposed aposymbiotic recruits to 29{degrees}C or 31{degrees}C and to fragments of either Montastraea cavernosa (containing Cladocopium) or Siderastrea siderea (containing D. trenchii). After 60 days, recruits reared with D. trenchii donors hosted nearly three times more D. trenchii than those with Cladocopium donors, suggesting that recruits can acquire Symbiodiniaceae from nearby corals of different species. Temperature did not affect D. trenchii uptake. Next, donor colonies were removed and surviving recruits were maintained for three months at ambient temperatures, after which a subset was exposed to a 60-day heat stress trial. Recruits previously reared at 31{degrees}C survived twice as long at 34{degrees}C as those reared at 29{degrees}C, suggesting that pre-exposure to heat can prime recruits to withstand future thermal stress. In addition, recruits hosting primarily D. trenchii survived twice as long at 34{degrees}C as those hosting little or no D. trenchii. However, the proportion of D. trenchii hosted was negatively correlated with polyp size and symbiont density, indicating a trade-off between growth (of both host and symbiont) and heat tolerance. These findings suggest that, while donor colonies may be effective sources for seeding coral recruits with thermotolerant symbionts, practitioners will need to balance the likely benefits and costs of these approaches when designing restoration strategies.

ecology↗

bioRxiv2020

Host genotype and stable differences in algal symbiont communities explain patterns of thermal stress response of Montipora capitata following thermal pre-exposure and across multiple bleaching events

As sea surface temperatures increase worldwide due to climate change, coral bleaching events are becoming more frequent and severe, resulting in reef degradation. Leveraging the inherent ability of reef-building corals to acclimatize to thermal stress via pre-exposure to protective temperature treatments may become an important tool in improving the resilience of coral reefs to rapid environmental change. We investigated whether historical bleaching phenotype, coral host genotype, and exposure to protective temperature treatments would affect the response of the Hawaiian coral Montipora capitata to natural thermal stress. Fragments were collected from colonies that demonstrated different bleaching responses during the 2014-2015 event in K[a]neohe Bay (Oahu, Hawaii) and exposed to four different artificial temperature pre-treatments (and a control at ambient temperature). After recovery, fragments experienced a natural thermal stress event either in laboratory conditions or their native reef environment. Response to thermal stress was quantified by measuring changes in the algal symbionts photochemical efficiency, community composition, and relative density. Historical bleaching phenotype was reflected in stable differences in symbiont community composition, with historically bleached corals containing only Cladocopium symbionts and historically non-bleached corals having mixed symbiont communities dominated by Durusdinium. Mixed-community corals lost more Cladocopium than Cladocopium-only corals during the natural thermal stress event, and preferentially recovered with Durusdinium. Laboratory pre-treatments exposed corals to more thermal stress than anticipated, causing photochemical damage that varied significantly by genotype. While none of the treatments had a protective effect, temperature variation during treatments had a significant detrimental effect on photochemical efficiency during the thermal stress event. These results show that acclimatization potential is affected by fine-scale differences in temperature regime, host genotype, and relatively stable differences in symbiont community composition that underpin historical bleaching phenotypes in M. capitata.

ecology↗