Major Hurricane Maria, on 20 September 2017, wrecked havoc on the island of Puerto Rico. This powerful atmospheric event provided an opportunity to examine the effects of extreme physical forces on the coral reefs of Puerto Rico. Although much is known about the effects of Hurricanes on shallow-water reefs, there is little information on their effects on reefs found in deeper waters. Our research team concentrated efforts on the mesophotic reefs (MCEs), which rival shallow water coral reefs in diversity and beauty. MCEs are benthic communities made mostly of corals, sponges and macroalgae. They are found between 30 and 150 m depth, depending on how clear the water is, and could potentially serve as refugia for the declining shallow water coral reefs because they are further removed from anthropogenic and natural stressors. Oceanographic instruments that measured temperature, water pressure, flow rate and direction were deployed prior to Hurricane Maria providing a unique opportunity to measure the physical environment of the mesophotic reefs before, during and after the passage of a major hurricane. Hurricane Maria hit southwestern coast of Puerto Rico with reduced intensity compared to the east coast, softening somewhat the forecasted effects. Lower sea temperatures were observed 11 hours after the eye passage, immediately following the wake impact. The shape and orientation of the Puerto Rican shelf relative to the storm stabilized and strengthen sea stratification, reducing water mixing and maintaining elevated sea surface temperatures during the storm. These physical observations show our limited knowledge of how hurricanes affect island coasts. At the same time, we could document the hurricane effects on the presumably sheltered, mesophotic reefs by comparing before-and-after photographic data from pre-established monitoring locations. All in situ field work was accomplished through rebreather Trimix diving technology, which allows divers to work at these depths safely and efficiently. Our technical divers reported throughout the duration of the project that the extent of macro-disruption was minimal (e.g., displaced corals and sponges, colony breakage, or physical damage, scouring of algae). These observations were made in two mesophotic reefs at both 50 m and 70 m depth and two shallow water reefs at 20 m depth, all located in southwestern Puerto Rico. The visual impact of Hurricane Maria at these depths was much less than originally expected mostly due to the reduction of hurricane intensity in the southwestern coast of Puerto Rico. Alarmingly though, a 28% loss of total species diversity was observed in the mesophotic reefs of southwestern Puerto Rico between 2009-2010 and 2018-2019 indicating that mesophotic coral ecosystems are not stable over time, as originally thought. These findings have negative implications for the refugia hypothesis of mesophotic reefs and the assertion that these reefs are sheltered from stressors that affect shallow water reefs. Another major objective of the study was to estimate the genetic connectivity patterns of one of the most important coral species of the mesophotic reefs, Agaricia lamarcki and its symbiotic community in order assess the ecosystem stability hypothesis of mesophotic coral ecosystems. This objective was based on the expectation that Hurricane Maria will heavily impact the structure of these deeper reefs. Hurricane Maria did not cause obvious reef structural damage in our transects and nearby areas as visually surveyed by the divers. In the absence of visible reef damage and dislodged coral colonies we are establishing a baseline of connectivity measurements among corals and their symbiotic microbial communities. This baseline can be used as reference against future disturbance events at the mesophotic reefs. Our analysis is based on genomic variation of 36 colonies of A. lamarcki. A high-quality draft genome of A. lamarcki, is currently being assembled, and will guide the identification of genomic variation. In addition, genetic data from the bacterial communities and the symbiotic algae from each of the 36 colonies was used to test if these coral symbiotic communities show changes depending on depth. We observed significant changes in the microbial communities associated with A. lamarcki across a depth gradient, particularly at depths greater than 50 m. Depth is an important factor determining the species composition of coral symbiotic communities. Our interdisciplinary approach used physical, ecological and genetic data to assess effects of Major Hurricane Maria on mesophotic reefs of (southwest) Puerto Rico. We are describing the physical environment of mesophotic reefs during a major hurricane and are providing detailed ecological data from before and after the passage of the Hurricane. Hurricane Maria did not result in catastrophic changes at the mesophotic reefs studied, yet significant measurable changes can be detected in the community compared to pre-impact data indicating the vulnerability of these reefs. Our data is not compatible with the refugia hypothesis based on community stability and distance from coastal stressors, rather we suggest that mesophotic reefs are susceptible to major climatic events such as Major Hurricane Maria. Last Modified: 03/07/2021 Submitted by: Nikolaos Schizas