Studying best friends: Corals, zooxanthallae and biochemical questions

Posted on January 28, 2013 by


Author: Maggie Sogin

When you introduce yourself to other people as a marine biologist their brains are programmed to assume that (1) you study dolphins and (2) you get to spend all of your time outside SCUBA diving in warm tropical waters.

reef "escapes"

reef “escapes”

First off, I have never wanted to study marine mammals, not even when I was a little girl dreaming of swimming with them.  Second, much to my own doing, the majority of my working hours are spent inside a laboratory or in an office trying to obtain, understand, and interpret data that may explain patterns we observe in the oceans.  The problem is that being a marine biologist (and that includes coral biologists such as myself) goes hand-in-hand with being an ecologist, or a geologist, or a chemist, or a statistician, or a writer, and maybe even a crazy conglomerate all of these fields and more.   Ultimately, the bigger questions we want to answer are far more complex then just being able to get into the water and admire the colorful creatures living on reefs. Of course this is true with all disciples in biology. Collaboration, and importantly creativity (which is often underplayed in its importance to science), is the key to unraveling the truths of the world.

Over the past few days, I have been thinking a lot about how creativity has played into my own scientific development.  Originally for this post I was going to write an in depth description of my day-to-day activities in the lab, but really those activities are now pretty mundane and stale (I could probably run my extractions in my sleep now).  But thanks to a seminar discussion slated for this afternoon on “how creativity and innovation influences the scientific process”, I’ve been forced to consider how new ideas have developed through time (especially my own). If this subject interests you, and you wish to learn more on understanding creativity and its role in the sciences, check out Loehle, C.  1990.  A guide to increased creativity in research: inspiration or perspiration?  BioScience 40:123-129.


How my friends started to call me a chemist…

I entered my Ph.D. program with Dr. Ruth Gates at HIMB originally thinking that I wanted study horizontal gene transfer between an algal symbiont, called Symbiodinium (Also known as Zooxanthellae), and it’s coral host.

As a side note Zooxanthallae are dinoflagellate algae that reside within the coral’s tissues and produce carbon products (like sugars) through photosynthesis (a coral’s best friend).  The algae pass these products to the coral host, where they are used to meet the coral’s nutritional needs and thus allow corals to thrive in otherwise nutrient poor waters.  Importantly, symbiotic algae have facilitated the success of carbonate reefs at tropical latitudes throughout the majority of the geological history of reefs.


Even if you haven’t really read anything about horizontal gene transfer studies, you should know that they are incredibly difficult to prove even when both your host and their partner(s) have published genomes! Researchers are looking for gene sequences that originated in a symbiotic partner and were passed to the host partner or visa versa.

The best example of this is based on the Endosymbiotic Theory, which argues that eukaryotic cells and certain organelles (mitochondria, chloroplasts, and plastids) originated from a symbiotic relationship between bacterial cells. Eventually, over evolutionary time, genes from the symbiotic partners were incorporated into the host genome, which allows the host to produce these important organelles independently (when this was first proposed in the 1900s, people thought that the researcher (Konstantin Mereschkowski ) was nuts and it wasn’t until the 1960s when Lynn Margulis uncovered the theory again that it was finally accepted in biology).

When I entered UH in 2009, we still didn’t have a coral genome (thankfully, now we do), and there still isn’t a complete dinoflagellate genome (which is the group Zooxanthallae fall under)! This is partly attributed to the shear size of the group’s genome (can be up to 80x that of the half the human genome).  Clearly, in 2009 (and for that matter today!) it would have been extremely difficult for me to begin to address horizontal gene transfer in coral-zooxanthellae symbioses.

So, with the pointed help of my advisor, I began to try to think about the questions underlying my original interests. What was it that originally sparked my desire to understand gene transfer? What was the driving question? These are still the questions we, as scientists, mull over every day. We think about them in the shower, on our drive to work, in our dreams (and nightmares!) and while we are doing sports or errands.  As a scientist, it is so hard to let go of the questions.  And the best scientist’s brains are full of them, stocked pilled for another day when they can figure out the tools that will answer them. I filed my horizontal gene transfer question away, and began to think about what really had driven me to Ruth’s lab.

I am fascinated with the functional diversity of corals and when I do my research, I like to ask big questions. For instance, when you look at a reef, why do some corals bleach but other remain healthy?


Is it related to the diversity of the symbionts present in the coral tissue?


Are there tight controls in the nutritional regulation between the partners?


Which partner is in control?


Is this propagated through time to allow some corals to survival environmental stressors?


Will there be corals in the future with the unwavering impacts of global climate change?

These are the kinds of questions that not only fascinate me but lots of other researchers in my field. But if you go through the literature it feels like the answers are just out of reach.  We are almost there, but we can’t quite grasp the meaning of the results or the implications of the data in order to understand what is actually occurring on reefs. We want to have bigger, better tools that can start to address these questions, and the only way out of a spiraling pit of questions is to grasp onto distant ideas proposed in other (model) systems.

Which brings me back around to the start of my post. I am a marine biologist that dabbles in chemistry, statistics and biology. With the careful guidance of my advisor (who is a biologist), I took a road less traveled in my field and started to develop a new metabolite profiling technique, which I hope will be applied to all of the questions I have laid out above.  My research has taken a play from the plant and human biology literature, and I am using metabolomics methods to understand the biology of corals.  In venturing out on the edge of science, you often feel alone and you are forced to find new resources to help guide you through your degree. You are required to be creative to find new solutions to your problems or apply old solutions to your new system.  It is exciting and can be rewarding, but it is also a struggle and can be extremely challenging and mentally damaging.  I don’t think that this is the best way to do a PhD, it would be better to start with a less risky project, something that will give you an answer one way or another, but I suppose that those questions don’t really interest me.  And I guess deep down, I prefer to shoot for the moon, than stay on planet Earth (metaphorically).  The real test is if my results get published – stay tuned for a post on that topic later this spring.

Check out the Gates lab website to find out more about all the questions that interest us!