Methods

We deployed ARMS at 6 reefs per reef system in Raja Ampat and Cenderawasih Bay (3 in protected reserves, 3 in areas of anthropogenic stress), and at each reef we will deploy 3 replicates consisting of 3 ARMS each and one temperature logger at 10m depth (6 reefs, 3 replicates of 3, or 54 ARMS, total).

Morphological and genetic analysis will be conducted in the laboratory. Genetic analysis will consist of amplification and DNA sequencing of mitochondrial cytochrome oxidase 1 (mtDNA CO1) and/or other suitable nuclear genes. Individual samples are identified through a combination of morphological and genetic analysis via DNA Barcoding. Next, the plates are scraped clean into a DNA extraction buffer, and the resulting DNA slurry is subjected to a metagenomic analysis that allows for identification of any remaining encrusting macrofauna as well as the microbial community.

  1. DNA extraction
  2. Polymerase chain reaction (PCR)
  3. PCR Product “Clean-up”: SAP/EXO
  4. DNA Sequencing
  5. Electrophoresis

Collaborators

  • Smithsonian
  • UNIPA
  • UB
  • IBRC

Fundings:

  • USAID