• Nicole Pittoors

A Dissertation's Worth of Samples in 11 Days

Updated: Aug 31



In August of 2021, our lab and the Meyer Lab from the Smithsonian Institution joined forces to collect 36 Autonomous Reef Monitoring Structures (ARMS) from mesophotic reefs within Flower Garden Banks National Marine Sanctuary. This was a part of the Connectivity of Coral Ecosystems (CYCLE) project that aims to understand the environmental factors that drive biodiversity hotspots and how populations of benthic species are connected across the banks.


ARMS are traditionally used to study shallow-water reefs and are recovered via SCUBA diving. The ARMS for this project were deployed in the mesophotic zone between 50 and 80 meters (165-260 feet), which requires very skilled divers and many tanks and decompression stops. Therefore, the most efficient tool for recovering these ARMS and also collecting coral tissue samples was Oceaneering's ROV Global Explorer. Once the ARMS are recovered and brought on deck, we keep them chilled while our team begins processing.


Above Video: Ambient light levels of a mesophotic coral reef within FGBNMS. Everything appears blue due to blue wavelengths being the last wavelengths that are transmitted at great depths.



ARMS Recovery

A selfie of the ROV Global Explorer among numerous Stichopathes corals.


A milk crate lined with fine mesh is latched to the u-bolts of an ARMS, creating a seal and preventing motile and sessile organisms residing on the ARMS from escaping.


The ROV places the ARMS with their recovery crates into an elevator. A crane hook from the ship is lowered down to the elevator, where the ROV then attaches the hook to the elevator to be brought back up to the ship deck.


ARMS are placed in industrial fishing coolers (large blue boxes), where chilled water is circulated by a keg chilling system (yes, the ones used for beer). The tubing lines circulating cold water are insulated with pool noodles. Because the surface temperature on deck is about 30C, this ensures that ARMS are kept at their normal bottom temperature of 19-20C, ensuring the preservation of organisms' DNA.



ARMS Processing


ARMS are disassembled in a holding container. After plates are removed and placed in another bin for further processing, the remaining water is passed through a sieve to collect motile organisms and sediments.


Pictured is an example of one of the ARMS plates hosting a variety of sponges, bryozoans, spirorbid worms, and tunicates.


Plates are then photographed. Photographs of plates will later aid in the identification of sessile species and will also be processed through machine learning software that sorts settle species into functional taxonomic groups and quantifies percent cover.


Sieved motile organisms are sorted, identified, photographed, and preserved. Once back on land, we extract DNA from their tissues and assign DNA "barcodes" to their taxonomic identifications. Identifying such a wide range of benthic species takes a team of taxonomy experts, such as the zoologists and curators at the National Museum of Natural History, who have been assisting with species identification. We have even found a few possible new species!


A small subset of motile organisms that were collected and photographed on our ARMS.


Sessile species on the plate are identified and photographed. Then a small piece of tissue is extracted and preserved for DNA barcoding.

All sessile organisms on the plates are scraped off using a paint scraper.

Scraped organisms are then blended into a critter smoothie for one minute, creating a homogenized mixture of their tissues.

ARMS scrapings are preserved and then frozen until it's time to extract DNA.


DNA is extracted from the blended scrapings and then sent out to be sequenced.


In the end, all organisms residing on the ARMS are represented in this tiny pellet of DNA (circled in blue in the image on the right). With the DNA, we use metabarcoding to identify species: