Cell physiology of coral-Symbiodinium symbiosis
Coral communication with their endosymbiotic algae is crucial for coral survival. We are currently investigating the cellular mechanisms that regulate this symbiosis from both the host and the symbiont perspective, using a combination of live-cell assays, biochemistry, immunostaining, and whole-organism physiology. While corals need their symbionts to survive, many coral symbionts can also survive on their own in the water column. We are exploring how algal physiology changes when making the transition to or from the symbiotic state, and how that process might be influenced by climate change stressors like temperature and ocean acidification. Furthermore, not all symbiont species are equally beneficial to their hosts, we are investigating how different symbiont species influence their host's responses to environmental stress.
Image: Confocal microscopy image of a single live coral cell containing three ​​​Symbiodinium (red indicates chlorophyll fluorescence). Shown in green is the symbiosome, the intracelluar compartment housing each algal cell, which is loaded with a pH-sensitive fluorescent dye (Lysosensor Green). The green staining indicates that this compartment is acidic. Photo by K. Barott.
 
Characterizing coral responses to climate change
We are interested in understanding the mechanisms that determine coral responses to climate change, and in particular how ocean acidification and temperature stress interact. We have been monitoring the bleaching and recovery of paired coral colonies in Hawaii since the 2015 bleaching event, and are exploring how exposure to different pH dynamics throughout a coral's lifetime may influence coral responses to acute pH and temperature stress.
Image: A pair of rice coral colonies (​​Montipora capitata) during a coral bleaching event in Hawaii in 2019. The white coral on the left has bleached and lost its symbionts, while the brown coral on the right has not. Photo by T. Innis.
Roles of pH regulation in cnidarian symbiosis
​The survival of Anthozoans, including reef-building corals and sea anemone, is threatened by the increasing acidity of our planet’s oceans (ocean acidification). If not regulated, this environmental change will alter the pH within an animal’s cells and cause enormous physiological distress. We investigate “molecular sentinels,” which are proteins that can both sense and compensate for chemical disequilibrium within cells. Using a combination of biochemistry, cell biology and organismal physiology, we have identified an enzyme, called soluble adenylyl cyclase, that acts as a pH sentinel within these species. Currently, we are using the sea anemone Exaiptasia pallida (Aiptasia) as a model for understanding the dynamics of this molecular pathway and its sensitivity to ocean acidification. 
Image: A symbiotic sea anemone (​​Aiptasia pallida). Photo by G. Ortiz.
Image: Aiptasia larva after taking up a few algal symbionts (green). Coral nuclei are shown in blue, and red staining indicates the presence of soluble adenylyl cylcas, a pH sensing enzyme. Photo by D. Novikov. 
Role of pH regulatory pathways in early life stages of corals and sea anemones
We are currently exploring the role of pH regulatory proteins in different coral life stages, from sperm function to larval development and the establishment of symbiosis. All animals must maintain their internal environment within a narrow pH range, and by better understanding how corals perform this function we can better predict how they will respond to climate change.
Image: Coral reef ecosystem. Photo by K. Barott 
Microbial ecology of corals
Corals and other benthic reef macroorganisms are host to a diverse ecosystem of microorganisms, from their endosymbiotic dinoflagellates to their associated bacteria, archaea, viruses, and fungi. We are interested in understanding how different factors such as stress, host species, and competition influence the the dynamics of these communities, and the role these communities play in host physiology.
Image: Various coral and algae species competing for space on the reef benthos. Photo by K. Barott.
Benthic competition
Carving out space is key for surviving on a coral reef. I am interested in understanding how corals fight for and maintain space on the reef, the role of microbes in promoting or hindering coral success, and how competitive outcomes are affected by human influence. Coral reefs are becoming increasingly dominated by seaweeds, making it important to understand how these competitors affect coral health and distribution. 
"There is pleasure in the pathless woods, there is rapture in the lonely shore, there is society where none intrudes, by the deep sea, and music in its roar; I love not Man the less, but Nature more."  ~ Lord Byron