14:I[71133,["4507","static/chunks/e2799680-446c489506865058.js","7665","static/chunks/7665-81c5407bc4489ff9.js","8500","static/chunks/8500-e4dd1cb1bb626827.js","9753","static/chunks/9753-028c0a26aa71f2d4.js","8437","static/chunks/8437-a09d0b83fcec76af.js","4557","static/chunks/4557-64c5efa221bc528f.js","947","static/chunks/947-410627998426400f.js","5357","static/chunks/5357-6142894e88cb7da2.js","1498","static/chunks/app/dataset/%5Bid%5D/data/view/%5Bfileid%5D/page-177ea8adea7aed86.js"],"default"] 15:Tb62,

To sample each coral, 6-8 polyps were excised from outplanted corals using bone cutters and temporarily stored in individual Whirl-Paks on ice until reaching shore. Upon shore, samples were transferred from Whirl Parks using flame-sterilized tweezers placed in a 1.5mL microcentrifuge tube containing 1mL of DNA/RNA shield (Zymo Research, R1100-250, Irvine, CA, USA). Samples were transferred to a -80℃ freezer for long-term storage. In preparation for DNA extractions, the samples were removed from the -80℃ freezer and thawed on ice. With flame-sterilized tweezers, half of the biomass was transferred to a Disruptor Tube (Omega Bio-Tek, Norcross, GA, USA), the other half was kept as a bioarchive and returned to -80℃. DNA from each sample was isolated utilizing the E.Z.N.A.® Soil DNA Kit (Omega Bio-Tek, Norcross, GA, USA) with slight modifications to the manufacturer’s protocol to increase yield. DNA isolates were stored at -80℃. DNA quantity and quality was assessed utilizing a NanoDrop spectrophotometer (Thermo Fisher Scientific™, Waltham, MA, USA). Samples were submitted to MR DNA for 16S rRNA PCR amplification and sequencing (www.mrdnalab.com, Shallowater, TX, USA). Amplification of the 16S rRNA gene was conducted using the 515F-806R primer set, which targets the V4 region of the 16S rRNA, with barcodes on the forward primer (Apprill et al., 2015). The 16S rRNA gene V4 variable region was amplified via a 30-cycle PCR using the HotStarTaq Plus Master Mix Kit (Qiagen, Germantown, MD) under the following conditions: 95°C for 5 minutes, followed by 30 cycles of 95°C for 30 seconds, 53°C for 40 seconds and 72°C for 1 minute, after which a final elongation step at 72°C for 10 minutes was performed. After amplification, PCR products were checked in 2% agarose gel to determine the success of amplification and the relative intensity of bands. Samples were multiplexed using unique dual indices and were pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples were purified using calibrated Ampure XP beads (Beckman Coutler, CA, USA). Then the pooled and purified PCR product was used to prepare an Illumina DNA library. A PCR negative control was included in library preparation but did not produce a viable library. Paired-end sequencing was performed at MR DNA on an Illumina MiSeq following the manufacturer's guidelines.

Sampling locations:

- Mote's in situ nursery. Approximate central coordinate 24.56257, -81.40009.
- Site in Looe Key National Marine Sanctuary: U-10, U-11, and U-12. Approximate central coordinate 24.54093, -81.43539.
- Site in Looe Key National Marine Sanctuary: Unnamed site west of U-11. Approximate central coordinate 24.54069, -81.43652.

Samples collected under permit number FKNMS-2020-188

16:T733,This section documents curation actions performed prior to publication review with the submitter, and additional information relevant to understanding and reusing this dataset. It distinguishes changes made to the submitted (meta)data from unresolved issues and/or enhancements that improve future reuse and interoperability. CURATION ACTIONS PERFORMED ON DATA - Created summary table of NCBI files - Imported all tables, treating "", nd and NA as missing values. - Merged all tables, removing duplicate columns. Joins based on the sample/BioSample identifiers: BioSample↔biosample_accession, SampleName↔sample_name, LibraryName↔sample_id - Renamed the two conflicting genotype columns to outplant_els_genotype and NCBI_genotype - Removed emptyRemoved empty, constant-valued (with value "new"), and redundant file-pointer columns and redundant file-pointer columns - Added plain-language equivalents of the ENVO environment ontology codes. - Split latitude & longitude values into a separate column, made west values negative - Replaced special characters, spaces and periods from parameter names with underscores - Standardized dates: zero-padded days, expanded 2-digit years, converted to ISO format yyyy-mm-dd CURATION ACTIONS PERFORMED ON METADATA - BCO-DMO's standard metadata entry and text formatting steps were performed. See: https://www.bco-dmo.org/how-to/standard-curation-edits - NCBI BioProject PRJNA1023616 was recorded as a related resource. ISSUES POTENTIALLY IMPACTING REUSE - The submitted text used 'Aquarickettsia rohweri'. Proposed to change this to 'Candidatus Aquarickettsia rohweri' to match NCBI Taxonomy (taxid 2602574), under which the dataset's sequence accessions are registered. - Parameter descriptions were not supplied. Inferred descriptions for all parameters where possible 17:Td1b,A pervasive association exists between the bacterium Aquarickettsia rohweri and Caribbean Acropora, as A. rohweri dominates microbiomes of field-collected samples of this coral species. In particular, this bacterial species is highly abundant in genotypes of Acropora cervicornis susceptible to white band disease with reduced abundance in disease-resistant genotypes. A. rohweri, a member of the order Rickettsiales, is hypothesized to be an obligate symbiont dependent on the coral holobiont for nutrition and energy. Many other closely-related parasites within Rickettsiales are transmitted vertically, and A. rohweri is unlikely to persist in a free-living stage due to its limited metabolic capabilities. This bacterial parasite was therefore expected to be transmitted vertically between host generations. However, phylogenomic analyses of Acropora spp. and A. rohweri did not reveal the co-evolutionary characteristics expected of a vertically transmitted symbiont. These characteristics could be obscured, however, by horizontal transmission between hosts. The identification of A. rohweri in evolutionarily distant aquatic hosts ranging from ctenophores to sponges also strongly supports horizontal transmission of this species. To better understand the transmission dynamics of Aquarickettsia, populations of this bacteria were quantified in early life stages of A. cervicornis (gametes, planula larvae, early sexual recruits, and year-old juveniles) produced and raised in the land-based nursery at Mote Marine Laboratory in the Florida Keys. These corals were produced via controlled two-parent crosses involving six different genotypes across three annual spawning events. We found that Aquarickettsia was absent from captive-raised individuals though present in parental genotypes maintained in Mote Marine Laboratory’s in situ coral nursery. In March 2021, offspring were transferred to the same in situ nursery or outplanted to reef plots either near to or far from (> 50 m) adult A. cervicornis to determine if proximity to other colonies affected parasite acquisition. Corals were sampled one week, one month, and two months post-transplantation to assess timing of Aquarickettsia infection and to examine shifts in the coral microbiome overall due to transplantation. We determined that proximity to wild or outplanted A. cervicornis influenced Aquarickettsia acquisition in outplanted conspecifics that lacked Aquarickettsia prior to outplanting. Only corals that were in close proximity to adult A. cervicornis acquired Aquarickettsia, and acquisition took between 1 and 6 months. Importantly, corals outplanted far from previously-extant outplants did not acquire Aquarickettsia by a full year after transplantation to the reef. This suggests that horizontal transmission is important in the acquisition of this putative parasite, and the parasite is likely transmitted by other A. cervicornis or reef organisms primarily associated with outplanted A. cervicornis (e.g. corallivorous snails, ciliates, bearded fireworms). We also observed that not all conspecifics from the same families acquired the parasite, even within the same site. This suggests that Aquarickettsia acquisition may require prolonged contact with a vector, or that there is an element of chance in exposure to and subsequent infection with Aquarickettsia.18:T1060,NSF Award Abstract: Historically one of the most abundant reef-building corals in Florida and the wider Caribbean, the staghorn coral, Acropora cervicornis, is now listed as critically endangered primarily because of previous and reoccurring disease events. Understanding the holistic mechanisms of disease susceptibility in this coral is a top concern of practitioners engaged in conservation and restoration. The investigators recently discovered a group of parasitic bacteria common within the microbial community of A. cervicornis that can reduce the growth and health of corals when reefs are exposed to nutrient polluted waters. Determining how interactions among the coral host, this parasitic microbe, and the environment are linked to disease susceptibility provides critical insight and greater success of future restoration efforts. Yet the complexity of animal microbiomes and the contextual nature of disease make it difficult to identify the specific cause of many disease outbreaks. In this project, the investigators conduct experiments to explore the interactions among different genetic strains of coral and these bacteria in various nutrient scenarios to better understand how this bacterium affects the susceptibility of staghorn coral to diseases. This project also characterizes the genomics, host range, and local and global distribution of this bacterial coral parasite to determine how its evolutionary history and physiology drive disease susceptibility in this important coral species. The project trains two postdocs, one technician, and seven students (one graduate, six undergraduates) in integrative sciences that span marine science, physiology, genetics, microbiology, omics, and statistical modeling. A research-based after school program in Florida is expanded to include microbiology and create a new program module called Microbial warriors, with a focus on women in science. The investigators produce documentary style films and outreach materials to broadly communicate the project science and conservation efforts to local and national communities via presentations at Mote Marine Lab and the Oregon Museum of Science and Industry. This project is co-funded by the Biological Oceanography Program in the Division of Ocean Sciences and the Symbiosis, Defense, and Self-recognition Program in the Division of Integrative Organismal Systems. The investigators recently identified a marine Rickettsiales bacterium that, in corals, can be stimulated to grow in the presence of elevated nitrogen and phosphorous species. Based on genomic reconstruction and phylogeography, this bacteria is classified as a novel bacterial genus, Candidatus Aquarickettsia, and showed that it is broadly associated with scleractinian corals worldwide. Importantly, using a model system, the endangered Acropora cervicornis coral, the team has also shown that the growth of this bacterium in vivo is associated with reduced host growth and increased disease susceptibility. This project aims to more completely evaluate the mechanisms behind and impacts of these inducible infections on coral physiology and host-bacterial symbiosis. The investigators conduct nutrient dosing experiments on different coral genotypes with various Rickettsiales abundances. Using a range of omics and microscopy techniques, the team quantifies the resulting effects on holobiont phenotypes. The investigators are also comparing the genomes of these bacteria in the different Acroporid hosts and other coral genera to evaluate facets of the bacterium's evolutionary history, as well as to identify possible mechanisms of its proliferation, virulence, and host specificity. This interdisciplinary project mechanistically links nutrients to temporal changes in host, algal symbiont, and bacterial parasite physiology and also explain why there is natural variation in these responses by exploring how host and parasite genotypes and growth dynamics combined with environmental contextuality alter holobiont phenotypes. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.6:["$","$L14",null,{"dataset":{"_id":"924594","description":"","problem":"","acquisition":"$15","processing":"

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single or paired end sequencing reads

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