Cell physiology of coral-Symbiodinium symbiosis
Coral communication with their endosymbiotic algae is crucial for coral survival. I am currently investigating the cellular mechanisms that regulate this symbiosis using a combination of live-cell assays, biochemistry, immunostaining, and whole-organism physiology. 
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.
 
Relevant Publications:
  
Barott et al. Identification of a molecular sensor of pH in coral. Proceedings of the Royal Society B 2017

Barott et al. Coral host cells acidify symbiotic algal microenvironment to promote photosynthesis. PNAS 2015.
  
Barott et al. Differential localization of ion transporters suggests distinct cellular mechanisms for calcification and photosynthesis between two coral species. American Journal of Physiology 2015. 
 
Characterizing pathways involved in coral calcification and photosynthesis 
We have a lot to learn about even the most fundamental pathways involved in regulating coral physiology. For example, we still do not know what proteins supply the coral symbionts with the compounds they need for photosynthesis, how this process is regulated, or how these interactions vary between coral species and symbiont clades.
Image: Fluorecence image showing the localization of a potential bicarbonate transporting protein (red) in the tissue of the coral Acropora yongei. Coral and Symbiodinium nuclei are stained with a dye that labels DNA (blue). 
Relevant Publications:
  
Barott et al. Differential localization of ion transporters suggests distinct cellular mechanisms for calcification and photosynthesis between two coral species. American Journal of Physiology 2015.  
  
Barott et al. Coral host cells acidify symbiotic algal microenvironment to promote photosynthesis. PNAS 2015.  
"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
Image: Coral reef ecosystem.
Microbial ecology
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. I am 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.
Relevant Publications:
  
Kelly, Williams, Barott, et al. (2014) Local genomic adaptation of coral and algal-associated microbiomes to gradients of natural variability and anthropogenic stressors. PNAS 111(28): 10227-10232. 
   
Janouškovec, et al. (2013) Environmental distribution of coral-associated relatives of apicomplexan parasites. ISME Journal, 7: 444-447.
   
Barott et al.. (2011) Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis. Environmental Microbiology 13(5): 1192-1204.
   
Kelly, Barott, et al. (2012) Black reefs: iron-induced phase shifts on coral reefs. ISME Journal 6: 638-649.
  
Janouškovec et al. (2012) Global analysis of plastid diversity reveals new apicomplexan-related lineages associated with coral reefs. Current Biology 22(13): R518-519.
  
Vega Thurber, Barott, et al. (2008) Metagenomic analysis indicates that stressors induce production of Herpes-like viruses in the coral Porites compressa. PNAS 105(47): 18413-18418.
    
Image: Various coral and algae species competing for space on the reef benthos.
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. 
Relevant Publications:
  
Barott and Rohwer. (2012) Unseen players shape benthic competition on coral reefs. Trends in Microbiology 20(12): 621-628. 
  
Barott et al. (2012) Natural history of coral-algae competition across a gradient of human activity in the Line Islands. Mar Ecol Prog Ser 460: 1-12. 
  
Barott et al. (2012) Microbial to reef scale interactions between the reef-building coral Montastraea annularis and benthic algae. Proceedings of the Royal Society B. 279(1733): 1655-1664.
  
Barott K, et al. (2009) Hyperspectral and physiological analyses of coral-algal interactions. PLoS ONE 4(11): e8043.