The Eco-Evo Lab Blog

How much time do you devote to thinking about the microbial organisms that share our environment with us. Perhaps you think of them before washing your hands or when someone sneezes next to you in the bus. Perhaps you think about them all the time. Perhaps you are not willing to confess here, just how much you think about bacteria, fungi and protozoans swimming in the water, covering all surfaces, floating in the air.

Honestly, I would love to be able to see them. I realize that scale is an issue and I would need to be around 10um tall to be able to appreciate the marvels of the microbial world. Thus, I fully prepared for the advent of technology that will make us tiny. Here is my top 5 of sights to see if I ever get to be around 10 um tall.

5. Colony on agar:

Early microbiologists relied on colony morphology to identify, describe and study microorganisms. They would report the size, color (pigmentation), shape, margin, texture and abundance. Importantly, each colony is made out of thousands of cells arranged along a density gradient from a dense center of the colony to a sparse periphery. If you were walking on top of the agar towards the colony, you would first see few cells, arranged seemingly at random – not unlike walking towards a patch of forest and finding trees are sparse at the edge. Then, cells will become more densely packed, probably one on top of the other, to the point where the colony is elevated over the substrate and cells are packed in dense layers. Interestingly, cells arrangements would differ across bacterial species as they differ across types of forests. But bear in mind that each colony grows from a single cell and all of its constituents are clones of one another. You have just walked through a forest of clones. See some spectacular pictures of bacterial cell arrangements here and, less spectacular but more informative, see here for electron microscopy of different sections of colonies of B. subtilis and B. cereus.

4. Bacterioplankton

Bacteria floating in lakes, rivers and oceans are critical for chemical transformations providing resources for phytoplankton and zooplankton alike. Bacteria are capable of fixing nitrogen, providing critical nutrients for photosynthetic processes, thus fueling primary productivity. But bacteria are also important in recycling organic matter and in providing resource for bacterivorous species of ciliates, flagellates, and other eukaryotic microorganisms. This is an incomplete list of the role bacteria play in aquatic systems (they can also transform sulfur, iron, manganese and mercury, among many more). I can imagine immersing myself in this environment, to see them clump around copepod fecal pellets, colonize the surface of diatoms or turning into a nanoflagellate’s lunch. It has to be a fantastic view, tiny bacterial cells moving across an aquatic landscape of colorful eukaryotic plankton. It sounds terrifying to be chased by a ciliate, unable to swim due to drag. Perhaps I’ll bring a little propeller with me.

3. Marine biofilm

Submerged surfaces in aquatic environments are readily colonized by microorganisms. In particular, bacteria attach to the surface and begin the formation of a three dimensional structure composed of exopolysaccharide (EPS) and protein secretions. This newly formed habitat can then house other kinds of bacteria, in addition to algae and diatoms becoming a complex tiny jungle, a mature biofilm. I imagine climbing through the bridges of EPS as one climbs across the roots of a mangrove forest. I wonder if we can see slow migrations of cells across the different layers, sudden changes in the chemical environment driven by quorum sensing or the death of an old biofilm, when all inhabitants leave and the structures degrade like an old, abandoned city.

2. Gut bacterial community

The entrails of our bodies remain a source of inquiry for scientists and non-scientists alike. I vividly remember cartoons and drawings of voyages (accidental or on purpose) across the gut. Now we know that a large portion of the function of our stomach and intestines is facilitated by millions of bacterial cells that reside right there, inside of us (see here for the Human Microbiome Project). I can imagine being able to walk down the small intestine, trying not to step on large colonies of bacteria lining the floor, walls and roof around me. It would be interesting to see whether they are clumped, well distributed or completely randomized in their distribution across the surface. I would not want to be there when the food bolus coming in – a mix between the scene from Indiana Jones running away from a big rock sphere and a laparoscopic video of your small intestine.

1. Hydrothermal vents.

I would like to see this full ecosystem thriving away from the sunlight. As columns of thick smoke seep into the cold waters, bacteria chemosynthesis provides resources for worms, crustaceans and snails in an oasis of productivity amongst a desert of darkness and emptiness. I would like to see yeti crabs waving their hairy claws full of bacteria, or vestimentiferan tube worms waving in the current like weird bald palm trees. I would like to see the bacteria on their tissues and the mats of bacteria covering the seeps. I would even settle for visiting while fully human sized, the deep see seems as a crazy place as the microbial world.

What microbial habitats would you like to see if you were 10 um tall?

Note 1: I have to confess I am aquatic in my heart which is reflected in the lack of terrestrial habitats.

Note 2: Michael Crichton is way ahead of me, and if this is all sounding interesting to you, you should probably read Micro too.

Note 3: But I did write a song about it.

Notice: before you go wondering around as a 10um sized creature, remember that drag, gravity and viscosity will work differently on a tiny organism. Practice swimming in honey.

Can a coral reef die?

An inaccurate (and possibly tongue in cheek) article went viral and triggered many crying-emojis on the internet over the past few days. Its bold claim? “The Great Barrier Reef is dead, RIP.” The reality is a little less bleak and more nuanced, but when is a reef, or any other ecosystem made up of thousands upon thousands of different species, “dead”? And can it come back?

Bleached corals dot the back reef in Okinawa, which, like much of the globe, experienced severe bleaching this year (photo by the author).

First, just some brief fact checking: the Great Barrier Reef is not dead. This claim arises, however, from an alarming fact: last Austral summer (so winter 2015-16 for us Northern Hemisphere folks), a record number of corals on the GBR, particularly in the north, bleached and died. This happened because the El Niño conditions at the time were among the strongest ever, making the ocean much, much warmer than usual. Corals can live in a wide variety of environments, but this sort of sudden change (which will likely become more common as the planet warms) upsets the balance between corals and the tiny algae that live in their tissues and provide the corals with food. The corals expel the algae, and then they starve to death.

This is also not the first time this has happened. The 1998/1999 El Niño was of similar strength, and sparked a similarly devastating global bleaching event. But while many reefs lost most of their corals during that El Niño, some recovered their hard corals and some did not. Some grew back as soft coral communities rather than reefs, while others were reborn as unsightly algae beds. Now that this El Niño has ended, the same will likely be true for the Great Barrier Reef. Ten years from now, corals will have grown back in places, and others will be unrecognizable, possibly barren, possibly replaced by ecosystems that are unlike anything we’ve seen before. Scientists will work hard to try to understand why some reefs are resilient and others aren’t, and these ecosystems will continue to die and regrow and change as the planet heats up.

We are entering (or, more accurately, have already entered) an era of great change for this planet. The ecosystems of 2116 will undoubtedly differ greatly from those today – but we may have the power to guide these changes. By limiting carbon emissions as much as possible, investing in scientific research, and using this knowledge to manage natural resources in new and creative ways, we can avoid the worst of all possible outcomes, and hopefully preserve much of the earth’s biodiversity. I believe this article achieved its goal of starting conversation about the perils faced by reefs among people who never would have thought about it otherwise. While some are worried that the article prompted fatalism among those who took it literally – were these people really about to save coral reefs anyway?

A reef can die, but it can also be reborn. We may not have been able to stop this bleaching event, but the actions we take over the next few decades will determine the fate of these ecosystems, and all ecosystems, as our planet continues to warm.

Recently, I was hiking on a trail near Los Angeles, enjoying the weekend and my days off from grad school. It was great to hear the crunch of leaves under my feet, feel the sun on my skin, and breathe in the substantially cleaner air of Topanga State Park. As a busy grad student, such moments of relief from stress and anxiety are often fleeting and hard to come by. At the end of the trail, I looked out over the beaches below and the ocean extending out from there, trying to take in the scenery, sounds, and wildlife—those birds chirping as they settle in for the night, the wind creating lines and waves on the ocean’s surface. Then, like the sound of a siren as it approaches from afar, the moment of silence was interrupted when the scientist portion of my brain slowly crept in to fill the void.

What sort of things are those birds trying to communicate? Are they trying to gather their young or warn friends about predators? They’re pretty close to me, how have all the human visitors to the park affected their behavior? Their survival? Their fitness?

Is there any kelp along the shore? Are those waves helping disperse kelp spores to supplement the population? Or are they building and building to break the kelp at the stipe and send the entire individual down to San Diego? How would that affect all the fish that use that kelp for habitat? Poor poor Dory, lost from her family…silly Disney, blue tangs don’t live in temperate waters!

Once my mind starts, it jumps from question to question with such rapid fire speed that I often forget what question started this whole death spiral…which makes me disgruntled. So now I’m disgruntled and surrounded by nature and I can’t just sit there in silence and appreciate it. This, to me, is part of the curse of being a scientist—there is no aspect of life where science can’t interject questions and hypotheses. However, this curse is also a blessing at times.

We go through life analyzing everything through scientific lens and constantly asking questions, but that’s just the best part—we’re always asking questions, thinking about the way that things work, allowing the gears in our curious minds to turn. It is this constant state of thinking and wondering and questioning that makes being a scientist a constant adventure, and emboldens us to keep doing what we’re doing. While having a critical mind may initially seem like a curse for simply observing the world, it is also the blessing that has led to so many great scientific discoveries by people who let their mind wander and acted on a wacky suggestion from the scientific voice in their heads.

Sunrise from our bungalow

Our study species, P. rus

Tucking our reciprocal transplant blocks in for the night

Zoë collecting P. rus in the back reef. Colonies are less common in the back reef than in the fringing reef, making for a more difficult day in the field.

Before leaving our blocks behind. We later used this picture to help find them!

Our nightly visitor who, despite looking through several reference books, we were unable to ID. Any ideas?

Zoë performing DNA extractions. To maintain the integrity of the DNA, we had to go straight to the lab from the boat to start extractions.

Me with our reciprocal transplant cinder blocks

Last month Zoë and I were lucky enough to return to Mo’orea, French Polynesia as a follow-up to Casey and Zoë’s trip last year. Last year’s exploratory trip sparked a larger and improved version of the project: investigating the microbial communities of 3 different color morphs of the coral Porites rus from two different locations on the reef (the fringing reef and the back reef). We spent two weeks collecting countless samples, completing 180 DNA extractions, and setting up a reciprocal transplant experiment. The time spent on extractions in the overly air conditioned lab made our fieldwork and free time even more rewarding. Anticipating a potential blog post, I decided to keep track of some of our notable events from the trip!

On May 18th, we arrived in the beautiful and pleasantly humid Tahiti as the sun was rising after an 8-hour flight. It took me at least an hour to truly understand that I would be in paradise for the next 2 weeks. Our first day was a tired blur of unpacking, assisting fellow CSUN graduate students, and taking far too many pictures of the same stunning scenery.

Our accommodations, a water-front bungalow, far surpassed my expectations.  With a quaint outdoor kitchen, a 5-step walk into the Pacific Ocean, and a stunning view of Cook’s Bay, Zoë and I often asked, “How could you ever be unhappy here?” The birds would wake me up early, but it gave me time to enjoy my coffee while watching the sunrise. Who wouldn’t want to wake up like that? At sunset, we would sit at the kitchen table eagerly watching the water for sharks and rays. One night I saw a blacktip reef shark and a nurse shark, along with several large rays during our stay. At night we often walked in the shallow water in front of our bungalow with our headlamps on observing the various fishes and crabs, that is until we saw a not-so welcomed visitor. This eel-like fish (seen in the slideshow) would swim stealthily along the shoreline every night, and its eerie, glowing, eyes were enough to keep us out of the water at night. 

Although our quiet bungalow was the perfect place to relax with a glass of wine after a long day, there were some interesting moments. One night I was washing the dishes from our surprisingly delicious lasagna, when a black, hairy object fell out of the window right in front of me, running away in a panicked scuttle just as I did. At first I thought it was a bat, but we quickly realized that there was a rat nest above the kitchen sink, the rat running across the beam above tipped us off. It must have been the night of falling objects, as my mosquito net also fell on me right after I tucked myself into it, and this was promptly followed by the startling bang of a coconut falling on our metal roof, just in time to wake us as we were finally drifting to sleep.

The best memories from our trip were certainly made in the field. We were in the water almost every day, and despite the hard work that we were doing, I made it a priority to take in my surroundings. Life’s beauty can often pass you by if you don’t focus on the small things, such as curious gobies in the sand or the playful sounds of nearby spinner dolphins. For all of the great experiences we had in the field, we also had several stress inducing ones. For example, I never realized how much corals could stress me out until I was in charge of directing Zoë around bommies (stand-alone coral structures) as she drove the boat.

For our reciprocal transplant experiment, we used Z-Spar to adhere coral nubbins to cinder blocks, which would either stay at their home reef (fringing or back) or be transplanted to the other reef. These were very long days, as they required both collecting and adhering the corals to the blocks. In the excitement of completing all of the gluing, we tucked our coral nubbins in between two bommies for the night and went for a relaxing swim, took some pictures, and drove back to the station…thinking we could easily find our blocks in the large expanse of the back reef. Hah. We searched for 2 days, and a total of 6 hours via snorkel and the boat, and even looked at the pictures we had taken both underwater and above (seen in the slideshow) for clues as to where we left them. We almost gave up, until, thanks to a diligent search pattern, Zoë spotted the blocks on our way back to the station. We jumped up and down, danced, and could not stop shaking our heads in disbelief. And of course, we promptly took GPS coordinates of the blocks so that this never happens again. Neither of us will ever forget a GPS, that’s for sure. This was, hands down, our happiest moment of the trip. We completed the transplant that afternoon, and could now relax for the remainder of our trip.

We took full advantage of our free time by kayaking, tagging along on collection trips with other students, and enjoying paradise. We swam with countless rays and blacktip sharks. We moved our hands through the water, and watched the surface light up with bioluminescence.  We watched a spotted eagle ray, one of the most stunning and graceful animals on earth in my opinion, off of the station dock. We went out for crepes with our friends at the station. We stargazed in silence, in disbelief that the Milky Way could be so bright. And, of course, we went to happy hour to celebrate our accomplishments. No wonder it was so hard to say goodbye.