Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Related Publications
• Parameters
• Instruments
• Project Information
• Funding

These data can be found by accessing the NCBI Sequence Read Archive BioProject ID: PRJNA498285 (http://www.ncbi.nlm.nih.gov/bioproject/498285, last accessed 2018-11-14).

Metagenetic amplicon sequence FASTA file for multiple coral species from Heron Island, Great Barrier Reef, Australia (23.4423° S, 151.9148° E), Hawaii (21.4433° N, 157.7490° W), and Curacao (12.1696° N, 68.9900° W).

Samples of corals were collected on shallow reefs in Australia, Hawaii and Curacao and preserved in DNA /RNA preservation buffer, Genomic DNA and RNA were extracted and sequenced.  Sequences were assembled and annotated as required for each dataset.

fastq base calling and quality control

Description from NSF award abstract:
Coral reefs provide crucial services for people and are becoming increasingly threatened by climate change. But many important questions about coral reefs remain unanswered, such as how their incredibly high biodiversity has developed and is maintained. It is well known that reef-forming corals consist of many different groups of bacteria and algae that live in the tissues of corals, but the function of most of these microbes remain unknown. One of the reported microbial functions is the process called nitrogen fixation. Nitrogen fixation is better known as a very important process on land. For example, alfalfa in agricultural fields has microbes associated with its roots that can capture nitrogen from the air and replace nitrogen lost from soils in water. The nitrogen cycle in the oceans is less well known, especially in tropical waters where nitrogen levels are low, although nitrogen in coral reef systems is known to derive mainly from nitrogen fixation. Recently nitrogen-fixing bacteria have been discovered in the tissues of corals, which begs the overarching question of this project: how important is the contribution of this fixed nitrogen to corals and to the surrounding environment? This research will integrate with an educational program that fosters critical thinking and cooperative learning among participants by involving undergraduate students who will work closely with the scientists. Students from underrepresented backgrounds will be recruited; the undergraduates will become part of an existing undergraduate research opportunities program where they receive mentoring, financial support, and intensive writing support while conducting original research projects of their own. Also a new program will be developed with the university's veterans office to attract and transition veterans into science fields across campus. Finally, outreach activities will be organized at local public high schools, and some public environmental education lectures about the ecology and biology of coral reefs are planned.

Significant gaps in understanding exist about the role of prokaryotes in the physiology, biochemistry and ecology of reef-forming corals. This project will assess how different prokaryotic communities affect the biogeochemistry of nitrogen, specifically nitrogen fixation, within the coral holobiont and how nitrogen fixation contributes to the dissolved organic nitrogen (DON) content of excreted mucus. The introduction of "new nitrogen" though nitrogen fixation and release of DON could have significant impacts on the biogeochemistry of nitrogen in the adjacent benthic communities surrounding corals. High throughput sequencing tools will be used to quantify the taxonomic and functional diversity of these symbioses in corals from the Pacific and Caribbean, as well as the taxonomic diversity of nifH genes in the tissues of corals. Rates of nitrogen fixation on several coral species from Australia, Hawaii and Curacao will be measured, along with the translocation of fixed nitrogen to all compartments of the coral holobiont, and the contribution of "new nitrogen" to the DON of mucus released to the environment determined. The results will increase our understanding of the taxonomic and functional biodiversity of symbiotic prokaryotes in corals. This project will also help guide future studies on the biogeochemical cycling of coral-derived nitrogen on coral reefs.