1. Bonacolta, A.M., M.T. Connelly, S.M. Rosales, J. del Campo, and N. Traylor-Knowles. The starlet sea anemone, Nematosella vectensis, possesses body-region specific bacterial associations with spirochetes dominating the capitulum. FEMS Microbiology Letters, 368(3):fnab002, https://doi.org/10.1093/femsle/fnab002 2021

    Abstract:

    Sampling of different body regions can reveal highly specialized bacterial associations within the holobiont and facilitate identification of core microbial symbionts that would otherwise be overlooked by bulk sampling methods. Here, we characterized compartment-specific associations present within the model cnidarian Nematostella vectensis by dividing its morphology into three distinct microhabitats. This sampling design allowed us to uncover a capitulum-specific dominance of spirochetes within N. vectensis. Bacteria from the family Spirochaetaceae made up 66% of the community in the capitulum, while only representing 1.2% and 0.1% of the communities in the mesenteries and physa, respectively. A phylogenetic analysis of the predominant spirochete sequence recovered from N. vectensis showed a close relation to spirochetes previously recovered from wild N. vectensis. These sequences clustered closer to the recently described genus Oceanispirochaeta, rather than Spirochaeta perfilievii, supporting them as members of this clade. This suggests a prevalent and yet uncharacterized association between N. vectensis and spirochetes from the order Spirochaetales.

  2. Clark, A.S., S.D. Williams, K. Maxwell, S.M. Rosales, L.K. Huebner, J.H. Landsberg, J.H. Hunt, and E.M. Muller Characterization of the microbiome of corals with stony coral tissue loss disease along Florida’s reef coast. Microorganisms, 9(11):2181, https://doi.org/10.3390/microorganisms9112181 2021

    Abstract:

    Stony coral tissue loss disease (SCTLD) is an emergent and often lethal coral disease that was first reported near Miami, FL (USA) in 2014. Our objective was to determine if coral colonies showing signs of SCTLD possess a specific microbial signature across five susceptible species sampled in Florida’s Coral Reef. Three sample types were collected: lesion tissue, apparently unaffected tissue of diseased colonies, and tissue of apparently healthy colonies. Using 16S rRNA high-throughput gene sequencing, our results show that, for every species, the microbial community composition of lesion tissue was significantly different from healthy colony tissue and from the unaffected tissue of diseased colonies. The lesion tissue of all but one species (Siderastrea siderea) had higher relative abundances of the order Rhodobacterales compared with other types of tissue samples, which may partly explain why S. siderea lesions often differed in appearance compared to other species. The order Clostridiales was also present at relatively high abundances in the lesion tissue of three species compared to healthy and unaffected tissues. Stress often leads to the dysbiosis of coral microbiomes and increases the abundance of opportunistic pathogens. The present study suggests that Rhodobacterales and Clostridiales likely play an important role in SCTLD. 

  3. Palacio-Castro, A.M., C.E. Dennison, S.M. Rosales, and A.C. Baker. Variation in susceptibility among three Caribbean coral species and their algal symbionts indicate the threatened staghorn coral, Acropora cervicornis, is particularly susceptible to elevated nutrients and heat stress. Coral Reefs, 40(5):1601-1613, https://doi.org/10.1007/s00338-021-02159-x 2021

    Abstract:

    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 symbionts were exposed to either ambient nutrients (A), elevated NH4(N), or elevated NH4 + PO4(N+P) at control temperatures (26°C) for > 2 months, followed by a 3-week thermal challenge (31.5°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. sidereal  hosting Cladocopium C3 suffered higher reductions in Fv/Fm (41–56%) compared to S. siderea hostingCladocopium 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. 

  4. Messyasz, A., S.M. Rosales, R.S. Mueller, T. Sawyer, A.M.S. Correa, A.R. Thurber, and R. Vega. Coral bleaching phenotypes associated with differential abundances of nucleocytoplasmic large DNA viruses. Frontiers in Marine Science, 7:555474, https://doi.org/10.3389/fmars.2020.555474 2020

    Abstract:

    Eukaryotic viruses and bacteriophage have been implicated in disease and bleaching in corals, but the compositional and functional diversity of these viruses in healthy and compromised hosts remains underexplored. To investigate whether viral assemblages differ in concert with coral bleaching, we collected bleached and non-bleached conspecific pairs of corals during a minor bleaching event in 2016 from reefs on the island of Mo’orea, French Polynesia. Using electron microscopy (EM), we identified several viral particle types, all reminiscent of medium to large-sized nucleocytoplasmic large DNA viruses (NCLDV). We also found that viral metagenomes from bleached corals have significantly more eukaryotic virus sequences, whereas bacteriophage sequences are significantly more abundant in viral metagenomes from non-bleached colonies. In this study, we also initiated the assembly of the first eukaryotic dsDNA coral virus genome. Based on our EM imagery and our taxonomic annotations of viral metagenome sequences, we hypothesize that this genome represents a novel, phylogenetically distinct member of the NCLDVs, with its closest sequenced relative being a distant marine flagellate-associated virus. We also showed that this NCLDV is abundant in bleached corals, but it is also present in apparently healthy corals, suggesting it plays a role in the onset and/or severity of coral bleaching.

  5. Rosales S.M., A.S. Clark, L.K. Huebner, R.R. Ruzicka, and E.M. Muller. Rhodobacterales and hizobiales are associated with stony coral tissue loss disease and its suspected sources of transmission. Frontiers in Microbiology, 11:681, https://doi.org/10.3389/fmicb.2020.00681 2020

    Abstract:

    In 2014, Stony Coral Tissue Loss Disease (SCTLD) was first detected off the coast of Miami, FL, United States, and continues to persist and spread along the Florida Reef Tract (FRT) and into the Caribbean. SCTLD can have up to a 61% prevalence in reefs and has affected at least 23 species of scleractinian corals. This has contributed to the regional near-extinction of at least one coral species, Dendrogyra cylindrus. Initial studies of SCTLD indicate microbial community shifts and cessation of lesion progression in response to antibiotics on some colonies. However, the etiology and abiotic sources of SCTLD transmission are unknown. To characterize SCTLD microbial signatures, we collected tissue samples from four affected coral species: Stephanocoenia intersepta, Diploria labyrinthiformis, Dichocoenia stokesii, and Meandrina meandrites. Tissue samples were from apparently healthy (AH) corals, and unaffected tissue (DU) and lesion tissue (DL) on diseased corals. Samples were collected in June 2018 from three zones: (1) vulnerable (ahead of the SCTLD disease boundary in the Lower Florida Keys), (2) endemic (post-outbreak in the Upper Florida Keys), and (3) epidemic (SCTLD was active and prevalent in the Middle Florida Keys). From each zone, sediment and water samples were also collected to identify whether they may serve as potential sources of transmission for SCTLD-associated microbes. We used 16S rRNA gene amplicon high-throughput sequencing methods to characterize the microbiomes of the coral, water, and sediment samples. We identified a relatively higher abundance of the bacteria orders Rhodobacterales and Rhizobiales in DL tissue compared to AH and DU tissue. Also, our results showed relatively higher abundances of Rhodobacterales in water from the endemic and epidemic zones compared to the vulnerable zone. Rhodobacterales and Rhizobiales identified at higher relative abundances in DL samples were also detected in sediment samples, but not in water samples. Our data indicate that Rhodobacterales and Rhizobiales may play a role in SCTLD and that sediment may be a source of transmission for Rhodobacterales and Rhizobiales associated with SCTLD lesions.

  6. Young, B.D., X.M. Serrano, S.M. Rosales, M.W. Miller, D. Williams, and N. Traylor-Knowles. Innate immune gene expression in Acropora palmata is consistent despite variance in yearly disease events. PLoS ONE, 15(10):e0228514, https://doi.org/10.1371/journal.pone.0228514 2020

    Abstract:

    Coral disease outbreaks are expected to increase in prevalence, frequency and severity due to climate change and other anthropogenic stressors. This is especially worrying for the Caribbean branching coral Acropora palmata which has already seen an 80% decrease in cover primarily due to disease. Despite the importance of this keystone species, there has yet to be a characterization of its transcriptomic response to disease exposure. In this study we provide the first transcriptomic analysis of 12 A. palmata genotypes and their symbiont Symbiodiniaceae exposed to disease in 2016 and 2017. Year was the primary driver of gene expression variance for A. palmata and the Symbiodiniaceae. We hypothesize that lower expression of ribosomal genes in the coral, and higher expression of transmembrane ion transport genes in the Symbiodiniaceae indicate that a compensation or dysbiosis may be occurring between host and symbiont. Disease response was the second driver of gene expression variance for A. palmata and included a core set of 422 genes that were significantly differentially expressed. Of these, 2 genes (a predicted cyclin-dependent kinase 11b and aspartate 1-decarboxylase) showed negative Log2 fold changes in corals showing transmission of disease, and positive Log2 fold changes in corals showing no transmission of disease, indicating that these may be important in disease resistance. Co-expression analysis identified two modules positively correlated to disease exposure, one enriched for lipid biosynthesis genes, and the other enriched in innate immune genes. The hub gene in the immune module was identified as D-amino acid oxidase, a gene implicated in phagocytosis and microbiome homeostasis. The role of D-amino acid oxidase in coral immunity has not been characterized but could be an important enzyme for responding to disease. Our results indicate that A. palmata mounts a core immune response to disease exposure despite differences in the disease type and virulence between 2016 and 2017. These identified genes may be important for future biomarker development in this Caribbean keystone species.

  7. Klinges, J.G., S.M. Rosales, R. McMinds, E.C. Shaver, A.A. Shantz, E.C. Peters, M. Eitel, G. Worheide, K.H. Sharp, D.E. Burkepile, B.R. Silliman, and R.L. Vega Thurber. Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov. The ISME Journal, 13(12):2938-2953, https://doi.org/10.1038/s41396-019-0482-0 2019

    Abstract:

    Bacterial symbionts are integral to the health and homeostasis of invertebrate hosts. Notably, members of the Rickettsiales genus Wolbachia influence several aspects of the fitness and evolution of their terrestrial hosts, but few analogous partnerships have been found in marine systems. We report here the genome, phylogenetics, and biogeography of a ubiquitous and novel Rickettsiales species that primarily associates with marine organisms. We previously showed that this bacterium was found in scleractinian corals, responds to nutrient exposure, and is associated with reduced host growth and increased mortality. This bacterium, like other Rickettsiales, has a reduced genome indicative of a parasitic lifestyle. Phylogenetic analysis places this Rickettsiales within a new genus we define as “Candidatus Aquarickettsia.” Using data from the Earth Microbiome Project and SRA databases, we also demonstrate that members of “Ca. Aquarickettsia” are found globally in dozens of invertebrate lineages. The coral-associated “Candidatus A. rohweri” is the first complete genome in this new clade. “Ca. A. rohweri” lacks genes to synthesize most sugars and amino acids but possesses several genes linked to pathogenicity including Tlc, an antiporter that exchanges host ATP for ADP, and a complete Type IV secretion system. Despite its inability to metabolize nitrogen, “Ca. A. rohweri” possesses the NtrY-NtrX two-component system involved in sensing and responding to extracellular nitrogen. Given these data, along with visualization of the parasite in host tissues, we hypothesize that “Ca. A. rohweri” reduces coral health by consuming host nutrients and energy, thus weakening and eventually killing host cells. Last, we hypothesize that nutrient enrichment, which is increasingly common on coral reefs, encourages unrestricted growth of “Ca. A. rohweri” in its host by providing abundant N-rich metabolites to be scavenged.

  8. Rosales, S.M., C. Sinigalliano, M. Gidley, P.R. Jones, and L.J. Gramer. Oceanographic habitat and the coral microbiomes of urban-impacted reefs. PeerJ, 7:e7552, doi:10.7717/peerj.7552 2019

    Abstract:

    Coral reefs are in decline worldwide. In response to this habitat loss, there are efforts to grow, outplant, and restore corals in many regions. The physical oceanographic habitat of corals—such as sea temperature, waves, ocean currents, and available light—is spatially heterogeneous. We therefore hypothesize that outplant location may affect microbiomes, and ultimately, coral health and restoration success. We evaluated the influence of the physical oceanographic habitat on microbes in wild Porites astreoides and Siderastrea siderea. Tissue samples were collected at four Florida reefs in March, June, and September of 2015. We estimated oceanographic conditions from moored instruments, diver observations, remote sensing data, and numerical models. We analyzed microbiomes using amplicon 16S rRNA high-throughput sequencing data. We found microbial alpha-diversity negatively correlated with in situ sea temperature (which represented both the annual cycle and upwelling), as well as modeled alongshore currents, in situ sea-level, and modeled tide. Microbial beta-diversity correlated positively with significant wave height and alongshore currents from models, remotely-sensed relative turbidity, and in situ temperature. We found that archaea from the order Marine Group II decrease with increases in significant wave height, suggesting that this taxon may be influenced by waves. Also, during times of high wave activity, the relative abundance of bacteria from the order Flavobacteriales increases, which may be due to resuspension and cross-shelf transport of sediments. We also found that bacteria from the order SAR86 increase in relative abundance with increased temperature, which suggests that this taxon may play a role in the coral microbiome during periods of higher temperature. Overall, we find that physical oceanographic variability correlates with the structure of these coral microbiomes in ways that could be significant to coral health.

  9. Rosales, S.M., M.W. Miller, D.E. Williams, N. Traylor-Knowles, B. Young, and X.M. Serrano. Microbiome differences in disease-resistant vs. susceptible Acropora corals subjected to disease challenge assays. Scientific Reports, 9:18279, https://doi.org/10.1038/s41598-019-54855-y 2019

    Abstract:

    In recent decades coral gardening has become increasingly popular to restore degraded reef ecosystems. However, the growth and survivorship of nursery-reared outplanted corals are highly variable. Scientists are trying to identify genotypes that show signs of disease resistance and leverage these genotypes in restoring more resilient populations. In a previous study, a field disease grafting assay was conducted on nursery-reared Acropora cervicornis and Acropora palmata to quantify relative disease susceptibility. In this study, we further evaluate this field assay by investigating putative disease-causing agents and the microbiome of corals with disease-resistant phenotypes. We conducted 16S rRNA gene high-throughput sequencing on A. cervicornis and A. palmata that were grafted (inoculated) with a diseased A. cervicornis fragment. We found that independent of health state, A. cervicornis and A. palmata had distinct alpha and beta diversity patterns from one another and distinct dominant bacteria. In addition, despite different microbiome patterns between both inoculated coral species, the genus Sphingomonadaceae was significantly found in both diseased coral species. Additionally, a core bacteria member from the order Myxococcales was found at relatively higher abundances in corals with lower rates of disease development following grafting. In all, we identified Sphingomonadaceae as a putative coral pathogen and a bacterium from the order Myxococcales associated with corals that showed disease resistant phenotypes.

  10. Sinigalliano, C.D., I.C. Enochs, S.J. Stamates, P.R. Jones, C.M. Featherstone, M.L. Gidley, S.M. Rosales, L.J. Gramer, C. Staley, and T.P. Carsey. Water quality and coral reef monitoring along the southeast Florida coast. NOAA Technical Report, OAR-AOML-47, doi:10.25923/aanj-0912 2019

    Abstract:

    This 3-year project was designed to assist in providing data for use in the development of nutrient numeric criteria, as required by the Florida Department of Environmental Protection. Researchers with AOML's Ocean Chemistry and Ecosystems Division conducted field work during the first 2 years of the project, followed by the development of various deliverables, including this final report, which describes in detail four separate efforts: (1) water quality cruises; (2) ocean current measurements; and (3) coral assessments; and (4) microbiological assessments.